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Ecology
Where does lifes diversity come from? Where do new species come from? Why do some species go
extinct?
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These are just a few of the questions that can be answered by an understanding of evolution, genetics,
and biodiversity. These disciplines explain the mechanisms that shape how organisms interact with their environment and, in
turn, how the environment shapes organisms over many generations.
Genetics
To study ecology without an understanding of evolutionary theory is to watch a sporting event without first learning the rules;
players run, points are scored, whistles shrill, but the guiding principles underlying these events remain a mystery. With an
understanding of the rules, however, even the smallest intricacies of the game can be appreciated, even loved. So it is with
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Evolution Is Change in the Inherited Traits of a Population through Successive

Generations
By: Andrew A. Forbes (Dept. of Biology, University of Iowa) & Billy A. Krimmel (Dept. of Entomology, University of California at
Davis) 2010 Nature Education
Citation: Forbes, A. A. & Krimmel, B. A. (2010) Evolution Is Change in the Inherited Traits of a Population through
Successive Generations. Nature Education Knowledge 1(10):6
Evolution describes changes in inherited traits of populations through successive generations.

To fully understand the science of ecology, one must first be able to grasp evolutionary
concepts.
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The geneticist Theodosius Dobzhansky (1964) famously wrote "nothing in biology makes sense except in the light of evolution," and the field of ecology
is no exception to this broadly-embraced principle. To study ecology without an understanding of evolutionary theory is to watch a sporting event without
first learning the rules players run, points are scored, whistles shrill, but the guiding principles underlying these events remain a mystery. With an
understanding of the rules, however, even the smallest intricacies of the game can be appreciated, even loved. So it is with ecology: Evolution provides
a canon by which we may better understand the interactions of organisms with their environments. In this section, we define evolution as it is
understood to modern biology and as it applies to ecology.
Evolution is defined as the change in the inherited traits of a population of organisms through successive generations. When living organisms
reproduce, they pass on to their progeny a collection of traits. These traits may be tangible and obvious, such as the patterns in a butterfly's wing or the
number of scales on a crocodile, but they also include characteristics as relatively anonymous as the sequence of nucleotide bases that make up an
organism's DNA. In fact, when we talk about evolutionary inheritance, the latter is what we are actually referring to: the transfer of genetic sequences
from one generation to the next. When particular genetic sequences change in a population (e.g., via mutation) and these changes are inherited across
successive generations, this is the stuff of evolution.
What Evolution Is Not

The term "evolution" is commonly misused, often accidentally but sometimes with purpose, so it is also necessary to clarify what evolution is not.
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Most importantly, evolution does not progress toward an ultimate or proximate goal (Gould 1989). Evolution is not "going somewhere"; it just describes
changes in inherited traits over time. Occasionally, and perhaps inevitably, this change results in increases in biological complexity, but to interpret this
as "progress" is to misunderstand the mechanism. For instance, that single-celled organisms eventually gave rise to multicellular organisms might
appear to exemplify directed movement towards so-called "higher" life-forms. But as Gould (1996) and others point out, there is a left-hand wall to
complexity; by definition, the simplest possible organism can only become more complex or stay the same. In this sense, evolution is a "drunkards
walk" (Figure 1), wherein certain lineages inevitably attain unexplored novelty in form and function. By the same token, terms like "reverse evolution"
and "devolution" are nonsensical; similar traits and gene sequences may recur at different moments in biological history, but this is still just evolution:
change over time.
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Figure 1: The "drunkard's walk" as an explanatory metaphor for patterns of increasing complexity in evolution
A drunken man leaving a bar at the end of the night starts with the (locked) door to his back and is equally likely to stagger to the left
or to the right. Because he cannot move back through the door, it is inevitable that he will eventually fall into the gutter despite not
having made a conscious decision to move in that direction. Evolutionary change likewise does not progress towards a goal or final
destination.
2010 Nature Education All rights reserved.
A second important point is that evolution and natural selection are not equivalent terms. Natural selection is one force that can drive and influence
evolutionary change, but other mechanisms can be equally important. Trait changes among the members of a population are not always a result of
selective processes. For instance, the appearance and accumulation of a deleterious trait (e.g., a genetic disease) in a population should not be
ascribed to direct selection for the trait in question. Similarly, alleles that have no effect on traits under selection may undergo mutations that do not
influence the fitness of the organism carrying them. Proponents of the neutral theory of molecular evolution argue that many, if not most, of the genetic
differences between species are selectively neutral. What follows is an overview of the variety of forces, including natural selection, that can drive or
otherwise influence evolutionary change.
Microevolution and Macroevolution

One can distinguish between two general classes of evolutionary change: microevolution (change below the level of the species) and macroevolution
(change above the level of the species).
Population ecologists, conservation biologists, and behavioral ecologists are most directly concerned with microevolutionary processes. These include
shifts in the values and frequencies of particular traits among members of populations, often due to ecological processes such as the movement of
organisms and changing environmental conditions as well as interactions with members of different species (e.g. predator-prey interactions, hostparasite interactions, competition) or the same species (e.g. sexual selection, competition). These processes can, but do not necessarily, lead to the
formation of new species over time but instead result in fluctuating frequencies of traits within populations tracking ever-changing selective pressures
(Thompson 1998). Since some microevolutionary processes may occur over just a few generations, they can often be observed in nature or in the
laboratory.
An appropriate illustration of microevolution in action is the well-documented tendency for insects to rapidly develop resistance to pesticides (Gassmann
et al. 2009). For example, during summer in Southern France, pesticides are applied to control Culex mosquitoes from the Mediterranean coast to about
20 km inland. Certain mosquito genes confer resistance to the pesticides but are costly in the absence of pesticides (Figure 2); frequencies of the
pesticide-resistance gene increase during summers in areas where spraying is common, but do not increase in areas where spraying is not practiced.
(Lenormand et al. 1999).
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Figure 2: Frequencies of the pesticide-resistance allele Ace.1 in summer (top) and winter (bottom) populations of Culex
mosquitoes in costal France
Pesticides are applied between 0 km and 20 km from the coast during summer months. Coastal frequencies of Ace.1 increase
during the summer but then decrease again in the winter.
Usually macroevolutionary changes cannot typically be observed directly because of the large time scales generally involved, though many instances of
macroevolutionary change have been observed in the laboratory (Rice & Hostert 1993). Instead, studies of macroevolution tend to rely on inferences
from fossil evidence, phylogenetic reconstruction, and extrapolation from microevolutionary patterns. Often the focus of macroevolutionary studies is on
speciation: the process by which groups of previously-interbreeding organisms become unable (or unwilling) to successfully mate with each other and
produce fertile offspring.
Ecologists may be interested in macroevolution as a means to make inferences regarding present-day ecological questions. Scientists interested in
modeling the effects of present-day climate change, for instance, can couple prehistoric climatological data with fossil-derived patterns of speciation and
extinction to understand how contemporary animal and plant species are faring today and how they will fare in the future. For example, many marine
invertebrates (e.g. corals, snails, clams) construct their shells using calcium carbonate harvested from ocean water. As anthropogenic CO2 accumulates
in the atmosphere, a significant fraction of it dissolves into the ocean, releasing free hydrogen ions in the process and thus decreasing oceanic pH.
Among other things, this ocean acidification reduces the amount of carbonate available to shell-making marine invertebrates that rely on it for their
calcium-carbonate shells, making it difficult for them to make and maintain their shells.
By combining oceanic pH data from hundreds of millions of years ago with fossil records of foramifera (shell-making marine invertebrates), Zachos et al.
(2005) show the effects that ocean acidification have had on the diversification and extinction of past marine invertebrate fauna. From these data, one
can model current patterns of ocean acidification and begin to predict its effects on present-day and future marine animals (e.g. Orr et al. 2005).
Conclusion
Evolution describes changes to the inherited traits of organisms across generations. Evolutionary change is not directed towards a goal, nor is it solely
dependent on natural selection to shape its path. Ecology, as with any biological discipline, is rooted in evolutionary concepts and best understood in its
terms.
References and Recommended Reading

Dobzhansky, T. Biology, Molecular and Organic. American Zoologist 4, 443452 (1964).
Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907913 (2000).
Gassmann A .J. et al. Evolutionary analysis of herbivorous insects in natural and agricultural environments. Pest Management Science 65, 117481
(2009).
Gould, S. J. Wonderful Life: The Burgess Shale and the Nature of History. New York, NY: W. W. Norton and Company, 1989.
Gould, S. J. Full House: The Spread of Excellence from Plato to Darwin. New York, NY: Harmony Books, 1996.
Lenormand, T. et al. Tracking the evolution of insecticide resistance in the mosquito Culez pipiens. Nature 400, 861864 (1999).
Page 4 of 4
Orr, J. C. et al. Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681686 (2005).
Rice, W. R. & Hostert, E. E. Laboratory experiments on speciation: what have we learned in 40 years? Evolution 47, 16371653 (1993).
Thompson, J. N. Rapid evolution as an ecological process. Trends in Ecology and Evolution 13, 329332 (1998).
Zachos, J. C. et al. Rapid acidification of the ocean during the Paleocene-Eocene thermal maximum. Science 308, 16111615 (2005).
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By: Christine A. Andrews (Biological Sciences Collegiate Division, University of Chicago) 2010 Nature Education
Citation: Andrews, C. (2010) The Hardy-Weinberg Principle. Nature Education Knowledge 1(8):65
The Hardy-Weinberg theorem characterizes the distributions of genotype frequencies in

populations that are not evolving, and is thus the fundamental null model for population
genetics.

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Basic Mendelian Genetics

Under the now-discredited theory of blending inheritance, the hereditary material was conceived as a fluid that combines the traits from two individuals
into phenotypically intermediate offspring. Given observed patterns of resemblance between parents and offspring, blending inheritance may seem
intuitively reasonable, as it did to many of Charles Darwins contemporaries. This mode of inheritance, however, posed problems for Darwins theory of
natural selection (1859), which depends on the existence of heritable trait variation in populations of organisms. Blending inheritance would quickly
erode such variation, since all traits would be combined from one generation to the next until all individuals shared the same blended phenotype. In his
famous experiments on pea plants, Gregor Mendel rejected this hereditary mechanism in favor of particulate inheritance by demonstrating that
alternative versions of genes (alleles) account for variations in inherited characters, though he didnt actually know about genes as such. Although
Mendel published his results in 1866, his work remained obscure until its rediscovery in 1900 (reviewed in Monaghan & Corcos 1984), which helped
give rise to the modern field of genetics.
Mendels Law of Segregation, in modern terms, states that a diploid individual carries two individual copies of each autosomal gene (i.e., one copy on
each member of a pair of homologous chromosomes). Each gamete produced by a diploid individual receives only one copy of each gene, which is
chosen at random from the two copies found in that individual. Under Mendels Law of Segregation, each of the two copies in an individual has an equal
chance of being included in a gamete, such that we expect 50% of an individuals gametes to contain one copy, and 50% to contain the other copy
(Figure 1).
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Figure 1: Mendel's Law of Segregation
An individuals genotype is the combination of alleles found in that individual at a given genetic locus. If there are two alleles in a population at locus A
(A and a), then the possible genotypes in that population are AA, Aa, and aa. Individuals with genotypes AA and aa are homozygotes (i.e., they have
two copies of the same allele). Individuals with genotype Aa are heterozygotes (i.e., they have two different alleles at the A locus). If the heterozygote is
phenotypically identical to one of the homozygotes, the allele found in that homozygote is said to be dominant, and the allele found in the other
homozygote is recessive.
Even after many geneticists had accepted Mendels laws, confusion lingered regarding the maintenance of genetic variation in natural populations.
Some opponents of the Mendelian view contended that dominant traits should increase and recessive traits should decrease in frequency, which is not
what is observed in real populations. Hardy (1908; Figure 2) refuted such arguments in a paper that, along with an independently published paper by
Weinberg (1908; Figure 3) laid the foundation for the field of population genetics (Crow 1999; Edwards 2008).
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Figure 2: G. H. Hardy
The Hardy-Weinberg Equilibrium

The Hardy-Weinberg Theorem deals with Mendelian genetics in the context of populations of diploid, sexually
reproducing individuals. Given a set of assumptions (discussed below), this theorem states that:
1. allele frequencies in a population will not change from generation to generation.
2. if the allele frequencies in a population with two alleles at a locus are p and q, then the expected genotype
frequencies are p2, 2pq, and q2. This frequency distribution will not change from generation to generation
once a population is in Hardy-Weinberg equilibrium. For example, if the frequency of allele A in the
population is p and the frequency of allele a in the population is q, then the frequency of genotype AA = p2,
the frequency of genotype Aa = 2pq, and the frequency of genotype aa = q2. If there are only two alleles at a
locus, then p + q , by mathematical necessity, equals one. The Hardy-Weinberg genotype frequencies, p2 +
2pq + q2, represent the binomial expansion of (p + q)2, and also sum to one (as must the frequencies of all
genotypes in any population, whether it is in Hardy-Weinberg equilibrium). It is possible to apply the HardyWeinberg Theorem to loci with more than two alleles, in which case the expected genotype frequencies are
given by the multinomial expansion for all k alleles segregating in the population: (p1 + p2 + p3 + . . . + pk)2.
The conclusions of the Hardy-Weinberg Theorem apply only when the population conforms to the following
assumptions:
Figure 3: Wilhelm
Weinberg
1. Natural selection is not acting on the locus in question (i.e., there are no consistent differences in
probabilities of survival or reproduction among genotypes).
2. Neither mutation (the origin of new alleles) nor migration (the movement of individuals and their genes into or out of the population) is
introducing new alleles into the population.
3. Population size is infinite, which means that genetic drift is not causing random changes in allele frequencies due to sampling error from
one generation to the next. Of course, all natural populations are finite and thus subject to drift, but we expect the effects of drift to be more
pronounced in small than in large populations.
4. Individuals in the population mate randomly with respect to the locus in question. Although nonrandom mating does not change allele
frequencies from one generation to the next if the other assumptions hold, it can generate deviations from expected genotype frequencies,
and it can set the stage for natural selection to cause evolutionary change.
If the genotype frequencies in a population deviate from Hardy-Weinberg expectations, it takes only one generation of random mating to bring them into
the equilibrium proportions, provided that the above assumptions hold, that allele frequencies are equal in males and females (or else that individuals
are hermaphrodites), and that the locus is autosomal. If allele frequencies differ between the sexes, it takes two generations of random mating to attain
Hardy-Weinberg equilibrium. Sex-linked loci require multiple generations to attain equilibrium because one sex has two copies of the gene and the other
sex has only one.
Given these conditions, it is easy to derive the expected Hardy-Weinberg genotype frequencies if we think about random mating in terms of the
probability of producing each genotype via random union of gametes into zygotes (Table 1). If each allele occurs at the same frequencies in sperm and
eggs, and gametes unite at random to produce zygotes, then the probability that any two alleles will combine to form a particular genotype equals the
product of the allele frequencies. Since there are two ways of generating the heterozygous genotype (A egg and a sperm, or a egg and A sperm), we
sum the probabilities of those two types of union to arrive at the expected Hardy-Weinberg frequency of the heterozygous genotype (2pq).
Table 1: A Punnett square depicting the probabilities of generating all possible

genotypes at a diallelic Mendelian locus in a population that conforms to HardyWeinberg assumptions.
It is important to recognize that the Hardy-Weinberg equilibrium is a neutral equilibrium, which means that a population perturbed from its HardyWeinberg genotype frequencies will indeed reach equilibrium after a single generation of random mating (if it conforms to the other assumptions of the
theorem), but it will be a new equilibrium if allele frequencies have changed. This property distinguishes a neutral equilibrium from a stable equilibrium,
in which a perturbed system returns to the same equilibrium state. It makes sense that the Hardy-Weinberg equilibrium is not stable, since a change
from the equilibrium genotype frequencies will generally be associated with a change in allele frequencies (p and q), which will in turn lead to new
values of p2, 2pq and q2. Thereafter, a population that meets Hardy-Weinberg assumptions will remain at the new equilibrium until perturbed again.
Given a population in which we know the number of individuals with each genotype, we can test for statistical deviation from Hardy-Weinberg
equilibrium using a simple chi-square goodness-of-fit test or a more powerful exact test. The latter class of methods has proved particularly useful for
large-scale genomic studies, in which scientists evaluate thousands of loci segregating for multiple alleles (Wiggington et al. 2005). Observed genotype
proportions in natural populations typically conform to Hardy-Weinberg expectations, as we might expect given that a population perturbed from
equilibrium can achieve new equilibrium frequencies after only one generation of random mating.
Although statistical deviation from Hardy-Weinberg expectations generally indicates violation of the assumptions of the theorem, the converse is not
necessarily true. Some forms of natural selection (e.g., balancing selection, which maintains multiple alleles in a population) can generate genotypic
frequency distributions that conform to Hardy-Weinberg expectations. It may also be true that migration or mutation is occurring, but at such low rates as
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to be undetectable using available statistical methods. And, of course, all real populations are finite and thus susceptible to at least some evolution via
genetic drift.
Evolutionary Implications of the Hardy-Weinberg Theorem

The Hardy-Weinberg Theorem demonstrates that Mendelian loci segregating for multiple alleles in diploid populations will retain predictable levels of
genetic variation in the absence of forces that change allele frequencies. A common way of visualizing these expectations is to plot p2, 2pq and q2 as a
function of allele frequencies (Figure 4). This graphical presentation emphasizes two important consequences of the Hardy-Weinberg principle:
1. Population heterozygosity (the frequency of heterozygotes) is highest when p = q = 0.5.
2. Rare alleles are found primarily in heterozygotes, as they must be, given that q2 is much smaller than 2pq when q is near zero, and p2 is
much smaller than 2pq when p is near zero.
The second point takes on particular significance if we consider the potential for natural selection to influence the frequencies of new mutations. If a
population conforms to all other Hardy-Weinberg assumptions, selection will eventually fix an advantageous allele in the population such that all
individuals are homozygous for that allele. The initial increase in frequency of a rare, advantageous, dominant allele is more rapid than that of a rare,
advantageous, recessive allele. This is because, as we have seen, rare alleles are found mostly in heterozygotes, such that a new recessive mutation
cant be seen by natural selection until it reaches a high enough frequency (perhaps by drift in a real, finite population) to start appearing in
homozygotes. A new dominant mutation, however, is immediately visible to natural selection because its effect on fitness is seen in heterozygotes.
Thus, although Hardy (1908) demonstrated that dominance alone does not change allele frequencies at a locus, the dominance relationships among
alleles can have substantial influence on evolutionary trajectories.
Figure 4: A plot of Hardy-Weinberg equilibrium genotype frequencies (p to the 2, 2pq, q to the 2) as a

function of allele frequencies (p and q).
Selection, mutation, migration, and genetic drift are the mechanisms that effect changes in allele frequencies, and when one or more of these forces are
acting, the population violates Hardy-Weinberg assumptions, and evolution occurs. The Hardy-Weinberg Theorem thus constitutes a null model for the
discipline of population genetics, and is fundamental to the study of evolution.

Crow, J. F. Eighty years ago: the beginnings of population genetics. Genetics 119, 473-476 (1988).
Crow, J. F. Hardy, Weinberg and language impediments. Genetics 152, 821-825 (1999).
Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London, UK: John
Murray, 1859. (link)
Edwards, A. W. F. & Hardy, G. H. 1908 and Hardy-Weinberg Equilibrium. Genetics 179, 1143-1150 (2008).
Futuyma, D. J. Evolutionary Biology, 3rd ed. Sunderland, MA: Sinauer & Associates, 1998.
Gillespie, J. H. Population Genetics: A Concise Guide, 2nd ed. Baltimore, MD: Johns Hopkins University Press, 2004.
Hardy, G. H. Mendelian proportions in a mixed population. Science 28, 49-50 (1908).
Mendel, G. Versuche ber Plflanzen-hybriden. Verhandlungen des naturforschenden Ver-eines in Brnn, Bd. IV fr das Jahr 1865, Abhand-lungen
(1886): 3-47. (link)
Monaghan, F. & Corcos, A. On the origins of the Mendelian laws. Journal of Heredity 75, 67-69 (1984).
Weinberg, W. ber den Nachweis der Vererbung beim Menschen. Jahreshefte des Vereins Varterlndische Naturkdunde in Wrttemberg 64, 369-382
(1908).
Wigginton, J. E., Cutler, D. J. et al. A note on exact tests of Hardy-Weinberg equilibrium. The American Journal of Human Genetics 76, 887-893 (2005).
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Using Molecular Techniques to Answer Ecological Questions

By: Kirsten. J. Monsen-Collar (Biology and Molecular Biology Department, Montclair State University) & Paola Dolcemascolo (Earth and
Environmental Studies Department, Montclair State University) 2010 Nature Education
Citation: Monsen-Collar, K. J. & Dolcemascolo, P. (2010) Using Molecular Techniques to Answer Ecological
Questions. Nature Education Knowledge 1(11):1
This article explores the tools used in molecular ecology and how these tools enhance
traditional ecological studies. Also, it examines a number of seminal studies that have used
molecular ecology tools and discusses the limitations of molecular ecology.

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The Beginnings of Molecular Ecology

As far back as the late 1800s, researchers realized that answers to some ecological questions could be obtained by examining the molecular
composition of organisms. One of the earliest attempts at using molecules to address an ecological question was by Church in the late 1860s. Church
studied relationships among birds and found that the pigment turacin was present only in birds of the Musophagidae family (Figure 1). He and others
went on to determine that evolutionary relationships could be inferred according to whether species shared particular molecules. Early studies were
limited to organic molecules obtained through diet and so may at times have confused relationships among organisms. However, the idea that the study
of molecules could be a useful technique for understanding animals, their relationships, and their evolution had been firmly planted within the mind of
the scientific community. And it is from this idea that the discipline of molecular ecology eventually emerged.
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Figure 1: Musophaga rossae, one of the bird species with turacin in its feathers
What exactly is molecular ecology? As we will see, it is an interdisciplinary approach to some of the most fundamental questions in organismal biology.
Some scientists today do not consider it to be its own discipline but rather an "approach" taken in certain cases to answer certain questions. Most
scientists, however, agree that it is distinct from other studies of organismal biology. Molecular ecology is defined as "the application of molecular
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techniques to answer ecological questions" (Beebee & Rowe 2004). In this article we explore the tools used in molecular ecology and how these tools
enhance traditional ecological studies. We examine a number of seminal studies that have used molecular ecology tools. We also discuss the limitations
of molecular ecology.
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Molecular ecology's development as a field of study can be seen to run

parallel to advances in what would become the tool of the trade: the
molecular marker. Molecular markers are sections of an organismal genome.
These sections of DNA can be more readily obtained through a procedure
known as the polymerase chain reaction (PCR) (Figure 2). There are many
different types of DNA markers used in molecular ecology, including:
microsatellites (highly repetitive sequences of DNA that mutate rapidly and
are often used to identify individuals), minisatellites (similar to microsatellites
but with longer repetitive sequences), restriction fragment length
polymorphisms (RFLPs, specific sites of DNA that can be cut by enzymes
yielding different-sized fragments of DNA in different species, populations,
and rarely individuals), and DNA sequence data (the bases of DNA are
determined and similarities and differences are compared to identify species,
populations, and individuals) (Figure 3). These markers are by no means a
comprehensive list, and the marker (or markers) one chooses to use depends
greatly on the type of question being addressed in the study.
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One of the reasons why molecular ecology has advanced rapidly as a field of
Figure 2: Principle of polymerase chain reaction (PRC) to
study is the advent of PCR. PCR makes it possible to amplify billions of
amplify target DNA sequence
copies of a specific piece of DNA from the genome with very few starting
copies. In other words, it is possible to take a small sample of tissue to obtain
enough DNA for study. This contrasts with earlier approaches that often
required large amounts of DNA or protein, which often meant killing the organism of study. Obviously, killing one's study organism can be counterproductive, particularly if the intent of the study is to advance conservation efforts or protect endangered species. The fact that only a small starting
amount of DNA is needed now for molecular ecology studies has opened the door for non-invasive sampling methods. It is now possible to isolate DNA
from hair, urine, shed skin, and feces, thus preventing harm to endangered and non-endangered species. PCR also amplifies old and/or degraded DNA,
such as that found in fossils (Figure 2).
The development of molecular markers has led to an explosion of studies that
have used them to answer questions ranging from relatedness among
species, to the evolutionary history of populations, the amount of genetic
variation within a species, patterns of behavior, how patterns of gene
expression can vary among closely related populations, and many other
aspects of organismal variation. For example, in one of the earliest molecular
Figure 3: Example of DNA sequence data
ecological studies, O'Brien and his colleagues (1983) found that the genetic
diversity among cheetahs in South Africa was extremely low (Figure 4). In
fact, O'Brien et al. (1985) transplanted skin grafts between different cheetahs
and found that the cheetahs were so genetically similar, their immune
systems did not reject the tissue grafts. This and other early studies triggered the debate, which continues today, over the importance of genetic
diversity to the persistence of a population and how genetic diversity is related to environmental change. If every organism in a population has the same
genetic make up, it is likely each will respond the same way to any environmental change. If this environmental change hinders an organism's ability to
survive or reproduce, it is probable that all genetically similar individuals in the population will be affected in the same way, thus increasing the chance of
extinction. However, this is not always the case since some genetically similar populations appear to thrive. As such, the importance of genetic diversity
for population survival continues to be a subject of debate.
Figure 4: Acinonyx jubatus, the cheetah, has been shown to have low genetic diversity.
Moving Beyond Traditional Ecological Approaches

Molecular techniques can be useful to, and sometimes necessary for, the field of ecology. Traditional approaches to ecology have limitations that can
sometimes be addressed with molecular techniques. For one, traditional ecological approaches have relatively narrow timeframes of observation.
Unless a long history of data has been directly collected on a particular organism through the years, traditional ecological approaches are limited to the
period over which a study is conducted. Extrapolations can be made, but support for these extrapolations can be tenuous. On the other hand, historical
events leave distinct signatures in the molecules of organisms that can be accurately interpreted.
8/9/2011
Page 3 of 4
The divergence time between species, for example, can be readily calculated provided the divergence
can be associated with significant historical and environmental events. For instance, if one can associate
the divergence between two species with a known geologic event, one can calibrate a molecular clock. In
turn, a molecular clock can be used to determine the time since other species diverged from each other
based on the amount of genetic differences observed at a specific molecular marker. Beerli et al. (1996)
were able to calibrate a protein clock for populations of the Rana esculenta frog group separated by
saltwater barriers in the Aegean Sea using known geological dates of island isolation. Since frogs can't
survive in salt water, they were most likely separated when these salt water barriers appeared. As a
result, the researchers were able to date the separation of frogs on these islands. They then measured
how many genetic differences exist between these groups and used these data to estimate how many
genetic changes occurred over time.
A second important limitation of traditional ecological approaches is dependence on direct observation.
One of the most commonly used methods of tracking animal movements and immigration into new
populations is telemetry (Figure 5). Simply understanding an animal's physical movement from one place
to another, however, often gives an incomplete picture of that animal's behavior and how it relates to its
environment. One fundamental limitation of telemetry is that it cannot detect whether a dispersing animal
successfully mates in its new territory or upon joining a new population. Reproductive success is an
indication of fitness and, therefore, of the long-term survival of a population a fundamental issue in
ecology. But a DNA-based approach can provide much more insight into the mating behaviors of
dispersing animals. By looking at molecular markers in a particular group of animals, researchers can
establish the familial relationships among the members of that group; therefore, they can get an accurate
picture of who is mating with whom. Recent immigrants will have slight differences in their molecular
markers and they can be identified. If those immigrants are mating successfully in their new group, those
differences will be passed onto their offspring and will appear more frequently. If immigrants do not mate,
those differences will disappear.
Figure 5: Ursus americanus, the

black bear, being fitted with a radio
telemetry collar
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Finally, since traditional ecological approaches are based on direct observations of organisms, they frequently do not detect underlying variation in
organisms that does not influence physical appearances. It is possible for organisms to appear the same physically while exhibiting as much genetic
divergence as found between distinct species. Cryptic variation can sometimes only be detected by comparing DNA.
These examples are intended to illustrate how molecular techniques can supplement and enhance information gained through traditional
methodologies. We can get an even better idea of how molecular techniques have refined traditional ecology by looking at some of the fundamental
questions answered by molecular ecology.
Answering Ecological Questions with Molecular Techniques

Some of the earliest molecular ecology studies involved examining the mating systems of birds. It was long thought that birds were monogamous. DNA
samples of parents and their offspring challenged this idea. Indeed, it was found that extra-pair copulations were very frequent among bird species
thought to be monogamous. As a result of the extensive use of DNA sampling of parents and their offspring, it is now understood that only a very small
number of bird species adhere to a strictly monogamous mating system. Mating behaviors have also been described using molecular techniques in
many other organisms including (among others) pipefish, frogs, beetles, and turtles.
Our understanding of habitat use has changed as the result of molecular techniques. Habitat use can be relatively simple to assess when animals can
be tracked and directly observed using their habitat. But what happens when specific patterns of habitat use cannot be directly observed? There have
been a number of studies on genetic structuring of populations that appeared to be uniformly distributed across a particular landscape. These studies
found that populations were highly structured, indicating that organisms preferred to settle and mate in certain habitats over others. These findings
contradicted observed distribution patterns at the landscape level because observational approaches were unable to track mating patterns.
Early studies involving use of molecular techniques also found evidence of
extreme variation among apparently physically-identical individuals within a
species. Indeed, several studies among salamanders of the genus Plethodon
demonstrated extreme genetic divergence among animals that appeared
identical. These early studies also demonstrated a mixture of different
Plethodontid genomes within individuals, providing evidence of hybridization
between different species, information that was not yet available by traditional
ecological methods. Identifying cryptic species has become extremely
important in the field of conservation genetics, especially with regard to the
protection of endangered species. For example, the spotted frog Rana
pretiosa, which occurs in the Pacific Northwest of the United States, displays
Figure 6: Rana luteiventris (a) and Rana pretiosa (b), an
almost no physical variation among populations (Figure 6). However, genetic
example of cryptic variation
analysis has revealed that populations in Oregon are as genetically distinct
from other populations in the Pacific Northwest as separate species. The
discovery of genetic divergence within the species led to the classification of
two separate species, both of which are now protected. The existence of cryptic species is not surprising given that these organisms, and many others,
often rely on non-visual cues, such as chemicals and/or sound, to identify a mate. Molecular ecology has allowed researchers to explore why there are
genetic differences in the absence of morphological differences. Not only does molecular ecology allow the detection of genetic differences, but it also
allows for the interpretation of how the differences came to be since certain phenomena (e.g., natural selection, mate choice, differential habitat use)
may leave different genetic signatures.
Molecular approaches have also played a significant role in endangered species conservation besides addressing the question of cryptic variation. For
example, molecular studies have have been used to identify migration corridors between populations that can prevent isolation of endangered
populations. Molecular approaches have also been used to identify ideal populations for transfer to extinct or declining populations, methods for
maximizing genetic variation in captive-bred animals, and species identification of contraband goods. Identifying species has been especially important
for prosecuting poachers for harvesting endangered species when the only remains of the harvested animal is a piece of meat, bone, or fur. In fact,
molecular techniques have been developed that can identify species based on the DNA from tissue even if the tissue has been cooked and mixed with
other ingredients.
Limitations of Molecular Ecology

Molecular ecology has important limitations to consider. First, marker development can be time-consuming and expensive. Second, while it can be
beneficial that molecular ecology is not dependent on direct observation of behaviors, this benefit can often be a limitation. Since the behavior is not
directly observed, scientists must deduce the behavior that led to a specific molecular pattern, and there can often be multiple explanations for the same
observed pattern. Third, it is not practical to look at the entire genome of all organisms, so one must look at a small subset of markers. Different markers
may show discordant patterns or may not be representative of the entire genome. Finally, there are some questions that molecular ecology simply
cannot answer and must be addressed with direct observation. For example, some behaviors important to the natural history of an organism, such as
parental care and courtship behavior, can only be documented through direct observation.
8/9/2011
Page 4 of 4

Beebee T. & Rowe, G. An Introduction to Molecular Ecology, 2nd ed. New York, NY: Oxford University Press, 2008.
Beerli P., Hotz, H., et al. Geologically dated sea barriers calibrate an average protein clock in water frogs of the Aegean region. Evolution 50, 1676
1687 (1996).
Green D. M., Kaiser, H., et al. Cryptic species of spotted frogs, Rana pretiosa complex, in western North America. Copeia 1997, 18 (1997).
Highton R. Speciation in Eastern North American Salamanders of the Genus Plethodon. Annual Review of Ecology and Systematics 26, 579600
(1995).
Highton R. Frequency of hybrids between introduced and native populations of the salamander Plethodon jordani in their first generation of sympatry.
Herpetologica 54, 143153 (1998).
Highton R. & Webster, T. P. Geographic protein divergence and variation in populations of the salamander Plethodon cinereus. Evolution 30, 3345
(1976).
Moore M. K., Berniss, J. A., et al. Use of restriction fragment length polymorphisms to identify sea turtle eggs and cooked meats to species.
Conservation Genetics 4, 95103 (2003).
O'Brien, S. J., Wildt, D. E., et al. The cheetah is depauperate in genetic variation. Science 221, 459462 (1983).
O'Brien, S.J., Roelke, M. E., et al. Genetic basis for species vulnerability in the cheetah. Science 227, 14281434 (1985).
Valenzuela N. Multiple paternity in side-neck turtles Podocnemis expansa: evidence from microsatellite DNA data. Molecular Ecology 9, 99105 (2001).
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By: Joel L. Carlin (Department of Biology, Gustavus Adolphus) 2011 Nature Education
Citation: Carlin, J. L. (2011) Mutations Are the Raw Materials of Evolution. Nature Education Knowledge 2(1):10

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mutation is a change in the sequence of an organism's DNA. What causes a mutation? Mutations can be caused by high-energy sources such as
radiation or by chemicals in the environment. They can also appear spontaneously during the replication of DNA.
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Mutations generally fall into two types: point mutations and chromosomal aberrations. In point mutations, one base pair is changed. The human
genome, for example, contains over 3.1 billion bases of DNA, and each base must be faithfully replicated for cell division to occur. Mistakes, although
surprisingly rare, do happen. About one in every 1010 (10,000,000,000) base pair is changed. The most common type of mistake is a point substitution.
More uncommon is the failure to copy one of the bases (deletion), the making of two copies for a single base (point duplication) or the addition of a new
base or even several bases (insertion). Chromosomal aberrations are larger-scale mutations that can occur during meiosis in unequal crossing over
events, slippage during DNA recombination or due to the activities of transposable events. Genes and even whole chromosomes can be substituted,
duplicated, or deleted due to these errors (Figure 1).
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Figure 1: Mutations in DNA sequence from seven related species of tropical fishes (data are from intron 6 of LDHA gene sequenced by the author from epinepheline serranids)
At top are the original sequences, at bottom are the sequences adjusted to vertically align similar DNA bases. Point
substitutions are in red, and the yellow box with dashes indicates a deletion of 12 bases.
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Mutations can have a range of effects. They can often be harmful. Others have little or no detrimental effect. And sometimes, although very rarely, the
change in DNA sequence may even turn out to be beneficial to the organism.
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A mutation that occurs in body cells that are not passed along to subsequent generations is a somatic mutation. A mutation that occurs in a gamete or in
a cell that gives rise to gametes are special because they impact the next generation and may not affect the adult at all. Such changes are called germline mutations because they occur in a cell used in reproduction (germ cell), giving the change a chance to become more numerous over time. If the
mutation has a deleterious affect on the phenotype of the offspring, the mutation is referred to as a genetic disorder. Alternately, if the mutation has a
positive affect on the fitness of the offspring, it is called an adaptation. Thus, all mutations that affect the fitness of future generations are agents of
evolution.
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Mutations are essential to evolution. Every genetic feature in every organism was, initially, the result of a mutation. The new genetic variant (allele)
spreads via reproduction, and differential reproduction is a defining aspect of evolution. It is easy to understand how a mutation that allows an organism
to feed, grow or reproduce more effectively could cause the mutant allele to become more abundant over time. Soon the population may be quite
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ecologically and/or physiologically different from the original population that lacked the adaptation. Even deleterious mutations can cause evolutionary
change, especially in small populations, by removing individuals that might be carrying adaptive alleles at other genes.
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Most mutations occur at single points in a gene, changing perhaps a single

protein, and thus could appear unimportant. For instance, genes control the
structure and effectiveness of digestive enzymes in your (and all other
vertebrate) salivary glands. At first glance, mutations to salivary enzymes
might appear to have little potential for impacting survival. Yet it is precisely
the accumulation of slight mutations to saliva that is responsible for snake
venom and therefore much of snake evolution. Natural selection in some
ancestral snakes has favored enzymes with increasingly more aggressive
properties, but the mutations themselves have been random, creating
different venoms in different groups of snakes. Snake venoms are actually a
cocktail of different proteins with different effects, so genetically related
species have a different mixture from other venomous snake families. The
ancestors of sea snakes, coral snakes, and cobras (family Elapidae) evolved
venom that attacks the nervous system while the venom of vipers (family
Viperidae; including rattlesnakes and the bushmaster) acts upon the
cardiovascular system. Both families have many different species that
inherited a slight advantage in venom power from their ancestors, and as
mutations accumulate the diversity of venoms and diversity of species
increased over time.
Although the history of many species have been affected by the gradual
accumulation of tiny point mutations, sometimes evolution works much more
quickly. Several types of organisms have an ancestor that failed to undergo
meiosis correctly prior to sexual reproduction, resulting in a total duplication of
every chromosome pair. Such a process created an "instant speciation" event
in the gray treefrog of North America (Figure 2).
Figure 2: The history of the gray treefrog, Hyla versicolor, is an

example of mutation and its potential effects. When an
ancestral Hyla chrysocelis gray treefrog failed to sort its 24
chromosomes during meiosis, the result was H. versicolor.
This treefrog is identical in size, shape and color to H.
chrysocelis but has 48 chromosomes and a mating call that is
different from the original H. chrysocelis.
2011 Center for Invasive Species and Ecosystem Health
Courtesy of David Cappaert, Michigan State University. All
The consequence of doubling the genome size in plants is often abnormally

rights reserved.
large seeds or fruits, a trait that can be of distinct advantage if you are a
flowering plant! Most cereals that humans eat have enormous seeds
compared to other grasses, and this is often due to the genomic duplications that occurred in the ancestors of modern rice and wheat and, because the
mistake occurred in reproductive organs, was successfully passed on to future generations. Humans themselves have mimicked this process by
interbreeding individual plants with the largest fruits and seeds in the process of artificial selection, creating many of our modern agricultural crop
strains. The idea of evolution by natural selection, first described by Charles Darwin and Alfred Russell Wallace, requires differential survival due to
some individuals having greater evolutionary fitness. Whether that fitness is affected by genetic disorders, venomous saliva or enlarged offspring,
heritable variation can only arise by mutation. Evolution is simply not possible without random genetic change for its raw material.

Allendorf, F. W. & Luikart, G. Conservation and the Genetics of Populations. Malden, MA: Blackwell Publications, 2007.
Freeland, J. Molecular Ecology. Chichester, UK: John Wiley & Sons, 2005.
King, R. C. et al. A Dictionary of Genetics, 7th ed. Oxford, UK: Oxford University Press 2007.
Nei, M. & Kumar, S. Molecular Evolution and PhylogeneticS. Oxford, UK: Oxford University Press, 2000.
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By: Richard P. Shefferson (Odum School of Ecology, University of Georgia) 2010 Nature Education
Citation: Shefferson, R. P. (2010) Why Are Life Histories So Variable? Nature Education Knowledge 1(12):1
The life spans of plants, animals, and microbes range from minutes to millennia. Some
reproduce only once and others many times. Why are life histories so diverse?

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Imagine an organism capable of producing infinite numbers of offspring and living forever. This hypothetical organism is referred to as a Darwinian
demon, and one has never evolved into being (Law 1979). Instead, evolution has resulted in a diversity of life histories including all combinations of
reproduction, life span, and life stages. Why has this diversity evolved?
Life Histories as Evolutionary Responses

A life history is a unique combination of developmental stages and demographic events comprising what an organism
goes through from birth to death. At their most basic, life histories may be modeled as series of major life stages, each
with its own probabilities of mortality and transition, and rates of fertility (Figure 1). Among the first to consider the
evolution of specific life history strategies was Lamont Cole. Cole suggested that, all else being equal, the advantage of
living and reproducing more than one year was not much more than if an annual life history were maintained (Cole
Figure 1
1954). The fact that nature includes a diversity of long- and short-lived organisms reproducing once to many times
contradicts Cole's hypothesis and led it to be termed Cole's paradox (Charnov & Schaffer 1973). Cole's model is now
seen as too simplistic because mortality, reproduction, and other aspects of life histories vary within populations due
both to factors inherent in the organism, referred to as intrinsic factors, and to environmental factors, referred to as extrinsic factors. Life histories are
evolved responses to these sets of factors.
Intrinsic factors include relationships among genes, as well as among physiological, behavioral, and demographic traits. Such relationships are
commonly referred to as trade-offs or costs because of the commonness of negative relationships among traits, particularly under the physical limits
imposed by finite stores of resources. Trade-offs imply that the evolution of a trait both involves impacts on other traits and is constrained by these
relationships. For example, higher allocation of resources to growth as an adult may come at a cost to current reproduction, which may also require
significant inputs of resources. However, this same allocation to growth may decrease adult mortality, increasing the chance that an adult will reproduce
in the future.
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Trade-offs are complicated by associations among the genes responsible for them, as well as by patterns in resource
allocation (de Jong 1993). For example, two traits X and Y may occur in the same combinations more often than
expected by chance due to past evolution or the same or nearby genes controlling their expression, resulting in linkage
between the traits. Here, natural selection favoring a particular value for trait X will also inevitably cause Y to be
positively but indirectly selected. Such patterns can also arise if individuals in a population vary systematically in their
allocation patterns to each trait, causing correlations among life history trait values (Figure 2). Finally, some trade-offs
can favor the evolution of complex life histories. For example, the trade-off between parental care of self v. care of
offspring is thought to have favored the evolution of larval stages in many kinds of organisms, including amphibians and
insects. Because the diet of a larva is typically different from that of an adult of the same species, the production of
larvae reduces the possibility of food competition between parent and offspring.
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Figure 2
Life histories evolve in response to the environment (i.e., extrinsic factors) as well as to internal constraints. The environment is continually changing,
giving natural selection a "moving target". The Red Queen hypothesis states that the tendency for natural selection to change over time, due to
continual change in the environment, creates a situation in which no organism is perfectly adapted and all species continually evolve (van Valen 1973).
The hypothesis' name is a reference to the character in Lewis Carroll's book, Through the Looking-Glass, who tells Alice that it takes all her energy to
run just to stay in the same place.
The degree and pattern of environmental variation can favor specific life history strategies. Environmental variability can be temporal or spatial and
deterministic, stochastic, or predictable. Deterministic environmental variability is a shift in an environmental factor away from the previous mean and is
not thought to commonly result in the evolution of specific life histories. For example, current climate change is a deterministic change toward a warmer
climate, and its main impact on species is likely to be to cause changes in geographic distribution. Stochastic environmental variability is random
variation in an environmental factor and does not involve long-term changes in the mean value of the factor. Predictable environmental variability is
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typically cyclical, as are diurnal or seasonal patterns in sunlight or temperature. Strong levels of environmental variation can create stressful conditions
for the organisms that experience them. Many of the adaptations that allow organisms to deal with or escape these kinds of variability have created the
diversity of life histories currently observed in nature.
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Random Variation
Stochastic environmental variability favors changes in life span and
reproductive strategy. This kind of variability most often causes evolutionary
response via natural selection on juveniles. Juveniles have a stronger
relationship to fitness than mature individuals, due to the generally negative
relationship between age and fitness impact (Hamilton 1966). Increased
mortality and variability in mortality in the juvenile period both favor the
evolution of delayed reproduction, provided that delaying reproduction
increases the chance of producing viable offspring. The chance of producing
viable offspring may increase if the individual gains a greater ability to
produce greater numbers of offspring or to produce offspring of greater
quality (Figure 3). Such an increase in juvenile mortality may also favor a
longer reproductive life span. In contrast, decreased juvenile mortality favors
the evolution of earlier maturity. When extreme, stochastic environmental
variation can involve catastrophes. Although catastrophes may wipe
populations out of existence, they also introduce strong selection for life
stages capable of tolerating harsh environmental conditions.
Stochastic environmental variation may favor the evolution of bet-hedging
traits. These traits involve an apparent drop in fitness in the short-term in
order to maximize fitness in the long-term. Fitness is a geometric property,
meaning that it is multiplicative rather than additive across generations. Its
geometric nature means that mean fitness is more strongly influenced by
harsh periods than favorable periods, and so increased variability in fitness
causes mean fitness to drop across generations. Bet-hedging traits
counteract the influence of harsh periods on fitness by stabilizing the variation
in fitness over time. By stabilizing fitness over the long-term, bet-hedging
traits may be favored over other traits that appear to convey greater fitness in
the short-term. Vegetative dormancy in herbaceous plants may be one such
trait because although it involves the foregoing of reproduction and sprouting
in a particular year, it may also prevent mortality from increasing to
substantial levels and make future reproduction more likely (Shefferson 2009;
Figure 4).
Figure 3: Greater numbers v. greater quality of offspring

High mortality in the juvenile state typically favors the evolution of
delayed reproduction, and greater resource allocation to
reproduction once maturity occurs. Greater resource allocation to
reproduction may be expressed in the form of increased numbers
of offspring, or as increased quality of offspring born in each
reproductive event. Most orchids are very long-lived plants with
extremely poor germination and juvenile survival. These plants
produce fruits with thousands of dust seeds, each with a tiny
chance of growth into an adult. The production of high numbers of
dust seeds may be an adaptation to deal with high juvenile
mortality.
2010 Nature Education Courtesy of Richard Shefferson. All
rights reserved.
Predictable Environmental Variation

Predictable environmental variation involves temporal cycles between different environmental conditions. Such cycles
are routine and repeated, and do not change dramatically in any random or deterministic ways. This kind of variation
favors the evolution of timed and often cyclical life history strategies. Examples include seasonal or diurnal resting
stages, such as hibernation in mammals, winter-dormant seeds, and programmed senescence in annual plants (Roach
1993). The overall impact of predictable variation on life histories is the evolution of additional life stages and potentially
complex life cycles.
Cyclical variation in the environment causes natural selection to favor different strategies at different times. Phenotypic
Figure 4
plasticity, in which one genotype produces different phenotypes under different environmental conditions, is a common
result (Schlichting 1986). Phenotypic plasticity can include gradual change in a trait or dramatic and discrete change
from time to time. As an example of dramatic change, plants often flower according to a mechanism of discrete
phenotypic plasticity, in which they sense seasonal changes in red:far-red light ratios, and use them to sprout at the proper time of the year. As an
example of gradual change, within a growing season, plant growth will change to compensate for expected patterns in precipitation and temperature, as
well as available nutrients.
Historical Contingency
Evolutionary history can impact the evolution of life history strategies by making some strategies more or less likely to
evolve. Life histories exhibit some degree of phylogenetic signal, meaning that closely related species share similar
evolutionary responses due to stronger biological similarities than among more distantly related species. Phylogenetic
signal is typically due to the evolution of specific traits and genetic systems controlling them, including those that are
phenotypically plastic, which are then passed down to all species derived from that particular ancestor species (Figure
5). Some such traits become fixed in a group of related species, while others still evolve, though not necessarily at the
same rate among all such groups. These evolutionary events create constraints on evolution, such that extreme
deviations from what previously evolved are unlikely.
Figure 5

Charnov, E. L. & Schaffer, W. M. Life-history consequences of natural selection: Cole's result revisited. American Naturalist 107, 791793 (1973).
Cole, L. C. The population consequences of life history phenomena. Quarterly Review of Biology 29, 103137 (1954).
De Jong, G. Covariances between traits deriving from successive allocations of a resource. Functional Ecology 7, 7583 (1993).
Hamilton, W. D. The moulding of senescence by natural selection. Journal of Theoretical Biology 12, 1245 (1966).
Law, R. Optimal life histories under age-specific predation. The American Naturalist 114, 399417 (1979).
Roach, D. A. Evolutionary senescence in plants. Genetica 91, 5364 (1993).
Page 3 of 3
Roff, D. A. Life History Evolution. Sunderland, MA: Sinauer Associates, Inc., 2002.
Schlichting, C. D. The evolution of phenotypic plasticity in plants. Annual Review of Ecology and Systematics 17, 667693 (1986).
Shefferson, R. P. The evolutionary ecology of vegetative dormancy in mature herbaceous perennial plants. Journal of Ecology 97, 10001009 (2009).
Stearns, S. C. The Evolution of Life Histories. Oxford, UK: Oxford University Press, 1992.
Van Valen, L. A new evolutionary law. Evolutionary Theory 1, 130 (1973).
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By: Jeffrey Touchman (School of Life Sciences, Arizona State University) 2010 Nature Education
Citation: Touchman, J. (2010) Comparative Genomics. Nature Education Knowledge 1(8):13
Comparison of whole genome sequences provides a highly detailed view of how organisms
are related to each other at the genetic level. How are genomes compared and what can these
findings tell us about how the overall structure of genes and genomes have evolved?

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Comparative genomics is a field of biological research in which the genome sequences of different species human, mouse, and a wide variety of
other organisms from bacteria to chimpanzees are compared. By comparing the sequences of genomes of different organisms, researchers can
understand what, at the molecular level, distinguishes different life forms from each other. Comparative genomics also provides a powerful tool for
studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give
each organism its unique characteristics.
What Is a Genome Made Of?

Although living creatures look and behave in a myriad of ways, all of their genomes consist of DNA, the chemical chain that harbors the genes that code
for thousands of different kinds of proteins. Within DNA are the instructions sufficient to make an organism and the means by which organisms pass
information along to their offspring. Remarkably, this information is coded by only four nucleotides: adenosine (A), cytosine (C), guanine (G), and
thymine (T). Understanding the order of these nucleotides in linear DNA molecules has been an active pursuit since the discovery of DNAs doublehelical structure (Watson et al. 1953). As such, DNA sequencing has emerged as a fundamental approach to molecular biology research. The power of
DNA sequencing as a research tool has spurred the dramatic advancement of DNA sequencing technology, which is allowing ever more genomes to be
sequenced and making comparative genomics an accessible focal point for the study of any form of life.
What Genomes Have Been Sequenced?
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In addition to sequencing the three billion letters in the human genetic instruction book (Lander et al. 2001), researchers involved in the International
Human Genome Project (HGP) sequenced the genomes of a number of important model organisms. These include chimpanzee (Lander et al. 2005),
mouse (Waterston et al. 2002), rat (Gibbs et al. 2004), two puffer fish (Jaillon et al. 2004; Aparicio et al. 2002), fruit fly (Adams et al. 2000), two sea
squirts (Dehal et al. 2002; Small et al. 2007), two roundworms (Stain et al. 2003; Stein et al. 1998), baker's yeast (Goffeau et al. 1996), and the
bacterium Escherichia coli (Blattner et al. 1997). Since the completion of the HGP, sequence drafts of the chicken (Blattner et al. 2004), cow (Elsik et al.
2009), dog (Lindblad-Toh et al. 2005), honey bee (Lindblad-Toh et al. 2006), sea urchin (Sodergren et al. 2006) and rhesus macaque monkey (Gibbs et
al. 2007) (to name just a few) have also been established.
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Together with over 1,000 prokaryote genomes, a total of over 1,300 species have been completely sequenced and published (ca. 2010; see here) and
this number continues to grow at a prodigious rate, providing a rich source of genomic data for comparison.
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A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into
comparative genomic analysis. Data for several fully-sequenced model organisms is shown in Table 1. The comparisons highlight some striking
findings. For example, while the tiny flowering plant Arabidopsis thaliana has a smaller genome than that of the fruit fly Drosophila melanogaster (157
million base pairs v. 165 million base pairs, respectively) it possesses nearly twice as many genes (25,000 v. 13,000). In fact A. thaliana has
approximately the same number of genes as humans (~25,000). Thus, a very early lesson learned in the "genomic era" is that genome size does not
correlate with evolutionary status, nor is the number of genes proportionate to genome size.
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Table 1: Comparative genome sizes of humans and other model organisms
Finer-resolution comparisons are possible by direct DNA sequence comparisons between

species. Figure 1 depicts a chromosome-level comparison of the human and mouse genomes
that shows the level of synteny between these two mammals. Synteny is a situation in which
genes are arranged in similar blocks in different species. The nature and extent of conservation
of synteny differs substantially among chromosomes. For example, the X chromosomes are
represented as single, reciprocal syntenic blocks. Human chromosome 20 corresponds entirely
to a portion of mouse chromosome 2, with nearly perfect conservation of order along almost
the entire length, disrupted only by a small central segment. Human chromosome 17
corresponds entirely to a portion of mouse chromosome 11. Other chromosomes, however,
show evidence of more extensive interchromosomal rearrangement. Results such as these
provide an extraordinary glimpse into the chromosomal changes that have shaped the mouse
and human genomes since their divergence from a common ancestor 7580 million years ago.
Comparison of discrete segments of genomes is also possible by aligning homologous DNA
from different species. An example of such an alignment is shown in Figure 2, where a human
gene (pyruvate kinase: PKLR) and the corresponding PKLR homologs from macaque, dog,
mouse, chicken, and zebrafish are aligned. Regions of high DNA sequence similarity with
human across a 12-kilobase region of the PKLR gene are plotted for each organism. Notice the
high degree of sequence similarity between human and macaque (two primates) in both PKLR
exons (blue) as well as introns (red) and untranslated regions (light blue) of the gene. In
contrast, the chicken and zebrafish alignments with human only show similarity to sequences in
the coding exons; the rest of the sequence has diverged to a point where it can no longer be
reliably aligned with the human DNA sequence. Using such computer-based analysis to zero in
on the genomic features that have been preserved in multiple organisms over millions of years,
researchers are able to locate the signals that represent the location of genes, as well as
sequences that may regulate gene expression. Indeed, much of the functional parts of the
human genome have been discovered or verified by this type of sequence comparison (Lander
et al. 2001) and it is now a standard component of the analysis of every new genome
sequence.
Figure 1: Conserved segments in the human

and mouse genome
Human chromosomes, with segments containing
at least two genes whose order is conserved in
the mouse genome as color blocks. Each color
corresponds to a particular mouse chromosome.
Centromeres, subcentromeric heterochromatin of
chromosomes 1, 9 and 16, and the repetitive
short arms of 13, 14, 15, 21 and 22 are in black.
(International Human Genome Sequencing
Consortium; Lander, E. S. et al. 2001)
Figure 2: Human PKLR gene region compared to the macaque, dog, mouse, chicken, and zebrafish
genomes
Numbers on the vertical axis represent the proportion of identical nucleotides in a 100-bp window for a point on
the plot. Numbers on the horizontal axis indicate the nucleotide position from the beginning of the 12-kilobase
human genomic sequence. Peaks shaded in blue correspond to the PKLR coding regions. Peaks shaded in
light blue correspond to PKLR mRNA untranslated regions. Peaks shaded in red correspond to conserved noncoding regions (CNSs), defined as areas where the average identity is > 75%. Alignment was generated using
the sequence comparison tool VISTA (http://pipeline.lbl.gov).
8/9/2011
We have learned from homologous sequence

alignment that the information that can be gained by
comparing two genomes together is largely
dependent upon the phylogenetic distance between
them. Phylogenetic distance is a measure of the
degree of separation between two organisms or their
genomes on an evolutionary scale, usually expressed
as the number of accumulated sequence changes,
number of years, or number of generations. The
distances are often placed on phylogenetic trees,
which show the deduced relationships among the
organisms (Figure 3). The more distantly related two
organisms are, the less sequence similarity or shared
genomic features will be detected between them.
Thus, only general insights about classes of shared
genes can be gathered by genomic comparisons at
very long phylogenetic distances (e.g., over one
billion years since their separation). Over such very
large distances, the order of genes and the signatures
of sequences that regulate their transcription are
rarely conserved.
Page 3 of 4
Figure 3: Comparisons of genomes at different phylogenetic distances serve to

address specific questions.
At closer phylogenetic distances (50200 million years of divergence), both functional and non-functional DNA is found within the conserved segments.
In these cases, the functional sequences will show signatures of selection by virtue of their sequences having changed less, or more slowly than, nonfunctional DNA. Moreover, beyond the ability to discriminate functional from non-functional DNA, comparative genomics is also contributing to the
identification of general classes of important DNA elements, such as coding exons of genes, non-coding RNAs, and some gene regulatory sites.
In contrast, very similar genomes separated by about 5 million years of evolution (such as human and chimpanzee) are particularly useful for finding the
sequence differences that may account for subtle differences in biological form. These are sequence changes under directional selection, a process
whereby natural selection favors a single phenotype and continuously shifts the allele frequency in one direction. Comparative genomics is thus a
powerful and promising approach to biological discovery that becomes more and more informative as genomic sequence data accumulate.
What Are the Benefits of Comparative Genomics?

Dramatic results have emerged from the rapidly developing field of comparative genomics. Comparison of the fruit fly genome with the human genome
reveals that about sixty percent of genes are conserved (Adams et al. 2000). That is, the two organisms appear to share a core set of genes.
Researchers have also found that two-thirds of human genes known to be involved in cancer have counterparts in the fruit fly.
In addition to its implications for human health, comparative genomics may benefit the broader animal world and ecological studies as well. As
sequencing technology grows easier and less expensive, it will find wide applications in agriculture, biotechnology, and zoology as a tool to tease apart
the often-subtle differences among animal and plant species. Such efforts might also lead to the rearrangement of our understanding of some branches
of the evolutionary "tree of life," as well as point to new strategies for conserving rare and endangered species.

Adams, M. D., Celniker, S. E. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
Aparicio, S., Chapman, J. et al, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310 (2002).
Blattner, F. R., Plunkett, G. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997).
Blattner, F. R., Plunkett, G. et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature 432, 695-716 (2004).
Deha, P., Satou, Y. et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298, 2157-2167 (2002).
Elsik, C. G., Tellam, R. L. et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528 (2009).
Gibbs, R. A,. Rogers, J. et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234 (2007).
Gibbs, R. A., Weinstock, G. M. et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521 (2004).
Goffeau, A., Barrell, B. G. et al. Life with 6000 genes. Science 274, 546, 563-547 (1996).
Jaillon, O., Aury, J. M. et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946957 (2004).
Lander, E. S., Linton, L. M. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
Lander, E. S., Linton, L. M. et al. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).
Lindblad-Toh, K., Wade, C. M. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819
(2005).
Lindblad-Toh, K., Wade, C. M. et al. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443, 931-949 (2006).
Small, K. S., Brudno, M. et al. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 8, R41
(2007).
Sodergren, E., Weinstock, G. M. et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314, 941-952 (2006).
Stein, L. D., Bao, Z. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1, E45 (2003).
Stein, L. D., Bao Z. et al. Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium.
Science 282, 2012-2018 (1998).
Waterston, R.H., Lindblad-Toh, K., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562 (2002).
Watson, J.D., Crick, F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737-738 (1953).
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Case Study: The Glorious, Golden, and Gigantic Quaking Aspen

By: Michael Grant (Department of Ecology and Evolutionary Biology, University of Colorado at Boulder) & Jeffry Mitton (Department of
Ecology and Evolutionary Biology, University of Colorado at Boulder) 2010 Nature Education
Citation: Grant, M. & Mitton, J. (2010) Case Study: The Glorious, Golden, and Gigantic Quaking Aspen. Nature
Education Knowledge 1(8):40
Most massive living organism? Huge geographic range? Great beauty? A Phoenix species?
What in the world?

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Populus tremuloides, the quaking aspen of the North American continent, stands as one of the most easily recognized, most beautiful and most admired
of all tree species. In order to help appreciate this magnificent species, we here highlight some of its key biological attributes.
Perhaps most impressively, along with its very similar sister species of European and Asian distribution the Eurasian aspen (Populus tremula)
these two species occupy the broadest range of any tree species in the world. Why is that so?
Quaking aspen can be found from Alaska to Mexico and from Vancouver to Maine (Jones et al. 1985; Mitton & Grant 1996). In the north-central part of
the continent, quaking aspen occurs at almost any elevation, while in the southern part of the US and in Mexico, it tends to be found only at higher
elevations. A similar distribution pattern exists for Populus tremula in Europe and Asia. Admirers frequently note the striking white bark of quaking
aspen. This bark lives and carries out photosynthesis, attributes that make it unique among North American trees and likely contribute to its impressive
geographic range (Figure 1).
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Figure 1: Living bark

The white bark is living tissue, unique among North American trees.
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Aspen drops its leaves in winter but, of course, remains alive and thus requires metabolic energy. The soft tan to greenish hues often visible in aspen
bark mark an important photosynthetic capability provided by the differing levels of chloroplasts. Stem photosynthesis contributes significantly to aspens
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over-wintering survival capabilities (Bervieller et al. 2007; Foote et al. 1978; Knowlton et al. 1976). The disadvantages of this type of bark include low fire
resistance, ease with which people carve their initials in it and attractiveness as a food source for elk, numerous insects and fungi.
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Aspen form individual patches comprised of numerous stems, termed ramets, each with its own trunk, branches, leaves and a shared root system
(Figure 2). All of these structures arose from a single aspen seed, often in the very distant past; while these patches remain connected via root systems,
they comprise a single clone. If the root system between patches is severed, the patches form physiologically separate entitites but are generally still
considered part of the same clone given that they are composed of genetically identical patches and parts, having been produced vegetatively. The
boundaries of different clones stand out most clearly in the early spring when flowering and leafing-out occur (in that order). Aspen occur as males and
females separately (dioecious), unlike the majority of tree species, which support both male and female reproductive parts on each individual
(monoecious or hermaphroditic).
Figure 2: Aspen asexual and sexual reproduction
In early spring, an aspen clone will produce small, inconspicuous strings of reproductive parts called catkins, which are either male and produce pollen
or female and produce eggs. Huge numbers of viable, tiny seeds mature and float off from the female on a tangle of cotton-like seed hairs that catch air
currents, sometimes traveling great distances. Immediately after shedding their pollen and seeds, the clones then produce leaves that usually appear at
the same time in all stems of a given clone. This time of the spring is when the boundaries of aspen clones stand out most visibly and reliably.
However, most aspen watchers tend to focus on the brilliant colors of aspen in the late fall prior to dropping their leaves (Figure 3). The dramatic visual
show in the Rocky Mountains attracts many "leaf peepers" who find the brilliant gold, yellow, rose and even red leaf colors especially striking set against
the dark green of their evergreen neighbors. But these color patches do not mark clonal boundaries as reliably as does leafing in the early spring
because the chemical processes that produce the colors tend to be very sensitive to local micro-climate conditions such as aspect (whether north or
south facing), soil moisture, etc. (personal observations). A single clone may exhibit multiple colors simultaneously. In aspen, all the pigments that give
rise to these glorious colors can be found in the leaf from spring all the way through fall (see here). As summer begins to end and overnight
temperatures drop, the aspen begin to first break down the green chlorophyll molecules that dominate the spring through summer color. The other
pigment molecules there all summer then become more and more visible. This process reveals the golds, yellows and reds allowing aspen to
really show their stuff until their leaves drop (Vogel 1993).
Figure 3: September colors

Numerous aspen clones are embedded in a lodgepole pine forest in Colorado.
For many years, most western forest ecologists thought aspen reproduction from seeds was so rare as to warrant a publication of a single found
seedling (Ellison 1943). However, it turns out that successful establishment of aspen via seeds occurs more frequently than previously thought (Mock et
al. 2008). The ability of aspen to produce whole stands of "trees" vegetatively provides yet another key element in explaining the species ability to
occupy huge geographic ranges.
There are several benefits of asexual expansion spreading via roots which then send up shoots. As is true of other species of vegetatively-spreading
plants (DeByle 1964; de Kroon & van Groenendael 1997; Jnsdttir & Watson, 1997), one part of a clone might be near an important water source and
thus "share" that water with parts of the clone (i.e., the other ramets in the clone) while those in a drier area may have greater access to a vital soil
nutrient (e.g., phosphorous) that can also be distributed around the clone (Hansen & Dickson, 1979; Peltzer 2002; Pitelka & Ashmun 1985).
Quaking aspen also tends to be a disturbed habitat species, meaning it often lives where avalanches, mudslides and fires occur frequently. So both the
regenerative capability and the clonal reproductive capability allow aspen to initially establish or to re-establish into an area after disturbances occur,
especially spectacular ones like the 1988 fires in Yellowstone National Park (Romme et al. 1997). Careful observers of steep mountainous slopes along
the Rocky Mountain Cordillera will regularly see avalanche and mudslide tracks populated by young, light-green aspen clones re-colonizing those
spaces with shoot densities up to 30,000 per acre (Jones et al. 1985). Similar patterns often follow forest fires. Rarely will a fire burn hot enough to kill
the entire root system from which these stems arise, so an individual clone may occupy a given space and be completely wiped out on the surface but
re-grow from the root system many times.
Indeed, one remarkable clone in the Fishlake National Forest named Pando (Latin
for "I spread"; Grant 1993) represents the astonishing capabilities of an individual
clone to spread itself over a huge area (Barnes 1966, 1975; Grant et al. 1992).
Pando covers about 107 acres and contains about 47,000 individual ramets, each
complete with stem, branches and leaves (Barnes 1975; Grant et al. 1992; DeWoody
et al. 2008). To date, this clone remains the most massive living organism ever
reported with an estimated weight of at least 6,600 tons, exceeding that of the
famous giant sequoia, General Sherman (Figure 4).
Given its size, it may also be very old, perhaps 80,000 years, but good dating of the
time the original, tiny seed germinated and established this clone lies beyond current
scientific capabilities. Plausible estimates have been offered ranging from several
thousands to a million years in age, although recent molecular work argues that
these may be overestimates (Barnes 1975; Mock et al. 2008). Whatever its age,
Pando certainly represents one of the most remarkable individuals among all living
organisms.
In order to have this single genotype occupy this space for those huge spans of time,
the external environment must have had just the right balance of disturbance and
stability. If an aspen stand does not experience periodic disturbances such as fire or
avalanche, more shade-tolerant conifers tend to establish and shade out the highlight-requiring aspen stems. If the disturbances are too frequent, then the clone could
not establish and spread to this extent.
Clone structure varies with geography but also varies due to the strong influences of
rainfall and relative humidity. The largest clones generally occur in semi-arid
environments such as the mountains of the western and southwestern US. Clones
tend to be smaller in areas where the climate supports seed germination and
establishment somewhat more readily (e.g., the eastern parts of North America and
the upper Midwest).
Figure 4: Part of Pando

There are approximately 47,000 of these ramets (i.e.
"trees") in this single clone.
The last particular attribute of quaking aspen we here highlight as important in

contributing to its ability to occupy huge ranges derives from the comparatively high
level of genetic variability among clones (Cheliak & Dancik 1982; Kanaga et al. 2008;
Madritch et al. 2009; Mock et al. 2008). These interclonal levels of variability provide the raw material for evolutionary change across generational times.
The large number of seeds produced from genetically variable sources generates an enormous array of potentially successful genotypes for
establishment in newly opened areas and probably takes place at higher rates than previously thought by forest ecologists. These insights derive from
the application of modern molecular techniques to quaking aspen in the field.
With only a bit of whimsy, we have saved one of the most obvious attributes for last: Why do quaking aspen leaves quake and tremble? The leaves of
this species quake, shake and tremble in the presence of even the slightest breeze due to the physical structure of the leaf stem (petiole) which traces a
flat, oblong, elliptical pattern when viewed in cross section (i.e., perpendicular to the stem itself) so it has strength in one dimension (the long part of the
ellipsis) and minimal strength in the second dimension (the narrow part of the ellipsis), so even a gentle wind causes shaking, quaking and trembling.
We understand this phenomenon very well mechanically, yet a deeper question can be posed: Why does the petiole develop this way? Plant
physiologists have pointed out several consequences of the trembling leaf behavior to include minimizing the risk of too much sunlight on the
photosynthetic apparatus (photoinhibition), reducing the risk of overheating in intense, high elevation sunlight and improving photosynthetic rates by
keeping a fresh supply of carbon dioxide near the leaf surface where the plant takes up that compound. Taking a different approach, one of our students
did a small scale independent study several years ago where she identified matched pairs of aspen leaves and stabilized one with tubing to reduce its
ability to tremble, then measured the amount of leaf damage due to insects near the end of the summer, comparing the leaves which could tremble with
ones that could not. She found the insect damage to the fixed leaves was, on average, about 27% higher in the stabilized members of the pairs.
This tree species seems to almost have it all: powerful, opportunistic, sexual reproduction, long-distance seed dispersal, effective vegetative spread,
clonal reproduction, regeneration from roots, high levels of genetic variability, living bark and a potentially enormous life span.
We anticipate that this glorious, golden, and gigantic species will provide great pleasure for future admirers of its beauty as well as revealing a rich trove
of scientific insights as we learn from its enormously successful colonization of a huge geographic range.

Barnes, B. V. The clonal growth habit of American aspens. Ecology 47, 439-447 (1966).
Barnes, B. V. Phenotypic variation of trembling aspen of western North America. Forest Science 21, 319-328 (1976).
Berveiller, D. & Damesin, D. Interspecific variability of stem photosynthesis among tree species. Tree Physiology 27, 53-61 (2007).
Cheliak, W. M., Dancik, B. P. Genic diversity of natural populations of a clone forming tree. Populus tremuloides. Canadian Journal of Genetics and
Cytology 24, 611-616 (1982).
DeByle N. V. Detection of functional intraclonal aspen root connections by tracers and excavation. Forest Science 10, 386-396 (1964)
de Kroon H. & van Groenendael, J. The Ecology and Evolution of Clonal Plants. Leiden, The Netherlands: Backhuys Publishers, 1997.
DeWoody, J., Rowe, C. A. et al. "Pando" lives: molecular genetic evidence of a giant aspen clone in central Utah. Western North American Naturalist
68, 493-497 (2008).
Ellison, L. A natural seedling of western aspen. Journal of Forestry 41, 767-768 (1943).
Foote, K. C. & Schaedle, M. Diurnal and seasonal patterns of photosynthesis and respiration by stems of Populus tremuloides Michx. Plant Physiology
58, 651-655 (1976).
Foote, K. C. & Schaedle, M. The contribution of aspen Bark photosynthesis to the energy balance of the stem. Forest Science 24, 569-573 (1978).
Grant, Michael C. "The Trembling Giant." Discover Magazine (October 1993).
Grant, M. C., Mitton, J. B., et al. Even larger organisms. Nature 360, 216 (1992).
Hansen, E. A. & Dickson, R. E. Water and mineral nutrient transfer between root systems of juvenile Populus. Forest Science 25: 247-252 (1979).
Jnsdttir, I. S. & Watson, M. A. Extensive physiological integration: an adaptive trait in resource-poor environments?. In The Ecology and Evolution of
Clonal Plants, eds. de Kroon, H. & van Groenendael, J. (Leiden: Backhuys Publishers, 1997) 109-136.
Kanaga, M. K., Ryel, R. J. et al. Quantitative-genetic variation in morphological and physiological traits within a quaking aspen (Populus tremuloides)
population. Canadian J. of Forest Research 38, 1690-1694 (2008).
Madritch, M. D., Greene, S. L. et al. Genetic mosaics of ecosystem functioning across aspen-dominated landscapes. Oecologia 160, 119-127 (2009).
Mitton, J. B. & Grant, M. C. Genetic variation and the natural history of quaking aspen. BioScience 46, 25-31 (1996).
Mock, K. E., Rowe, C. A. et al. Clonal dynamics in western North American aspen (Populus tremuloides). Molecular Ecology 17, 4827-4844 (2008).
Peltzer, D. A. Does clonal integration improve competitive ability? A test using aspen (Populus tremuloides (Salicacae) invasion into a prarie. American
Journal of Botany 89, 494-499 (2002).
Pitelka L. F. & Ashmun, J. Physiology and integration of ramets in clonal plants. In Population biology and evolution of clonal organisms, eds. Jackson,
J. B. C., Buss, L. W., & Cook, R. E. (New Haven, Connecticut: Yale University Press, 1985): 399-437.
Romme, W. H., Turner, M. G. et al. A rare episode of sexual reproduction in aspen (Populus tremuloides) following the 1988 Yellowstone fires. Natural
Areas Journal, 17, 17-25 (1997).
Vogel, Steven. When leaves save the tree. Natural History 102, 48-63 (1993).
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By: Quentin Wheeler (School of Life Sciences, Arizona State University) & Antonio G. Valdecasas (Museo Nacional de Ciencias Naturales,
CSIC) 2010 Nature Education
Citation: Wheeler, Q. & Valdecasas, A. G. (2010) Cybertaxonomy and Ecology. Nature Education Knowledge 1
(11):6
What is cybertaxonomy and how will it advance the field of ecology?

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Introduction
A revolution in taxonomic practice is underway that will make taxonomy an even more reliable source of information for ecologists. How taxonomic
information is created, tested, accessed, thought about, and used, is changing dramatically with the emergence of cybertaxonomy.
What is Cybertaxonomy?
Cybertaxonomy is a contraction of "cyber-enabled taxonomy." It shares the traditional goals of taxonomy: to explore, discover, characterize, name, and
classify species; to study their phylogenetic relationships; and to map their geographic distributions and ecological associations. Through
cyberinfrastructure and the adoption of digital technologies, cybertaxomy is able to produce results faster and better than ever before (Wheeler 2008,
2010).
Cybertaxonomy should not be confused with the practice of creating databases of taxonomic information. Databases are an integral part of the process,
but cybertaxonomy refers to a wide range of hardware, software, instrumentation, communication tools, and work practices that collectively allow
taxonomists to do their work more efficiently while maintaining the highest levels of excellence. Consequently, users will find taxonomic information
more reliable, comprehensive, and easily accessible.
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Cybertaxonomy, like traditional taxonomy, is integrative. That is, taxonomists pull together, synthesize, and analyze all available evidence that is
informative at the taxonomic level(s) being studied. Typical data sources include morphological, molecular, fossil, and ontogenetic as well as
ethological, physiological, biochemical, and other sources of data, as appropriate. Cybertaxonomy can be visualized as a GIS-like environment with
multiple data layers: morphological, distributional, molecular, image, and sound recordings (to name just a few). In addition, there are layers with
algorithms and applications to process data in regard to phylogenetic, temporal, spatial, or ecological relations. Users may activate any combination of
"layers" to retrieve desired information in a multi-layered "mesh". The possibilities are numerous and diverse: dichotomous or interactive diagnostic
keys, checklists of species in particular areas plotted over seasonal occurrences, distribution maps (point data or predicted ranges based on climate and
environment), three-dimensional visualizations of phenotypic variation, etc. Just as individual taxonomists have traditionally synthesized all available
knowledge into periodically published monographs, international teams of experts collaborating in cyberspace will be able to assemble and maintain,
with up-to-the-minute accuracy, all data and information pertaining to the species of a taxon. Even these taxon knowledge bases will be combinable by
ecologists seeking to compare and contrast species that co-occur (or might co-occur, given future climate change, for example) in a particular
ecosystem.
State of Cybertaxonomy
When fully implemented, cybertaxonomy will impact nearly every aspect of the creation and use of taxonomic information. Taxonomists require research
resources on a scale unlike that of any other life science discipline: primary literature dating back to 1753, thousands of specimens from the full
geographic ranges of scores of related species, type specimens to assure nomenclatural stability, and specimens and data from dozens of museums or
herbaria in many countries. Cybertaxonomy holds the promise of unprecedented access to such resources, including digital image archives, openaccess databases, remotely operable instrumentation, and electronic publishing tools.
Traditional printed sources of taxonomic information are almost always out of date, often by the time of release. Since publication, there may be any
number of new species, name changes, distribution records, or natural history observations added, all of which are of great value to the ecologist.
Cybertaxonomy will open access to full and current information drawn from a taxon knowledge base that is constantly updated by the taxonomic
community.
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Cybertaxonomy will increase the arsenal of species identification tools available to the field ecologist, including browser-based field guides, interactive
diagnostic keys, automated identifications from photographs, direct access to a specialist, or the collecting of tissue samples for molecular identifications
the latter uniquely useful for associating very dissimilar life stages such as those observed between larval and adult insects.
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As taxonomists make more species known, it will become possible to improve and better test assumptions and models on species diversity,
distributions, co-occurrences, and co-varying factors; detect climate change; track species losses or gains; deepen our understanding of interactions
among species in ecosystems; improve strategies and priorities for conservation; and predict the expansion or contraction of ranges. Among the uses
for taxonomic information in ecology are:
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Species identifications
Cybertaxonomy will provide a wide range of tools to assist in the immediate and accurate identification of species, the training of field ecologists to
identify target taxa, and video-mediated consultation.
Checklists
Cybertaxonomy will make checklists available for particular localities and ecosystems that are complete and up to the minute.
Names
Scientific names are the unique identifiers used to store and retrieve what we know in databases and publications. Cybertaxonomy will allow
taxonomists to improve the reliability, stability, and informativeness of names and to retrieve all relevant data and citations recorded under older names.
Phylogenetic Classification
By viewing species within their phylogenetic context, ecologists can make predictions about their contributions to ecological functions. Closely related
species frequently have similar food sources, reproductive strategies, physiologies, and behaviors.
Geographic Distributions
Cybertaxonomy is mobilizing the information content of the natural history collections of the world, whose estimated three billion specimens provide a
wealth of information about the distributions of species, including irreplaceable historical records.
Virtual Ecological Assemblages

For taxonomic research, specimens are curated according to their phylogenetic relationships. With the tools of cybertaxonomy, the ecologist can
virtually reassemble all the specimens, regardless of taxon, collected in any one place at the same time or over a sequence of times.
Conservation-relevant Information
Cybertaxonomy will facilitate access to information about the status, abundance, and rarity of species, the species-richness of particular localities, and
other data relevant to conservation evaluation and reserve designs.
Morphologically Structured Information

As image archives grow, incorporating both digitized publications and images of specimens, it will be possible to harvest and analyze such visual
information to understand phenotypic variation in relation to environmental conditions, population structure, morphoclines, and other factors.
Online Access to Museum Specimens

Telemicroscopy has been used by pathologists and histologists for decades and will soon be able to network global collections such that actual
specimens in addition to stored images may be accessed, manipulated, compared, measured, and studied in real time.
Conclusions
Cybertaxonomy is not only changing the way that taxonomists work but also the ways in which ecologists can access and make use of taxonomic data,
information, and knowledge. As new ways to harvest, structure, and analyze taxonomic and related natural history information emerge, ecologists will
be able to understand complex ecosystems in greater detail, detect and monitor environmental change more precisely, and more effectively achieve
goals for sustainable ecological services.

Gaston, K. J. & O'Neill, M. A. Automated species identification: why not? Philosphical Transactions of the Royal Society B 359, 655667 (2004).
Polaszek, A. A universal register for animal names. Nature 437, 477 (2005).
Wheeler, Q. D., ed. The New Taxonomy. The Systematics Association Special Volumes Series 76. Boca Raton, FL: CRC Press, 2008.
Wheeler, Q. D. What would NASA do? Mission-critical infrastructure for species exploration. Systematics and Biodiversity 8, 1115 (2010).
Wilson, E. O. The encyclopedia of life. Trends in Ecology and Evolution 18, 7780 (2003).
Winterton, S. L. Revision of the stiletto fly genus Neodialineura Mann (Diptera: Threvidae): an empirical example of cybertaxonomy. Zootaxa 2157, 133
(2009).
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Molecular Genetic Techniques and Markers for Ecological Research

By: Gerard J. Allan (Environmental Genetics & Genomics Facility, Dept. of Biology, Northern Arizona University) & Tamara L.
Max (Environmental Genetics & Genomics Facility, Dept. of Biology, Northern Arizona University) 2010 Nature Education
Citation: Allan, G. J. & Max, T. L. (2010) Molecular Genetic Techniques and Markers for Ecological
Research. Nature Education Knowledge 1(11):2
The recent union of molecular genetic methods and ecology is a great advance in evolutionary
biology research. Molecular ecologists employ an array of molecular tools to study the genetic
biodiversity of Earth.

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Introduction
Ecology is inextricably intertwined with the evolutionary history of organisms. Through the process of descent with modification, organisms are
continually passing genetic information from one generation to the next, information that is then recorded in the DNA of their descendents. Molecular
biology's ability to access this record to better understand the origins of species and the ecological bases of their existence has become a cornerstone
of modern ecological research.
In this article we briefly review the molecular tools and methods available to modern ecologists seeking a deeper understanding of the genetic bases of
species formation, diversification, and evolutionary adaptation as they interact with ever-changing, complex environments.
PCR: An Ecologist's Best Friend
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Most molecular-based studies begin with the extraction of DNA from a particular organism, followed by the amplification (i.e., generation of many
copies) of particular segments of DNA using the polymerase chain reaction (PCR) (Figure 1). The utility of PCR lies in the fact that only minute
quantities of DNA are needed (e.g., nanogram amounts). This is particularly useful when researchers are unable to obtain large amounts of tissue (e.g.,
as in the case of rare plant or animal species) or when numerous samples are needed, as in the case of population genetic studies. For example, an
ecologist might ask: How genetically diverse are populations comprising a single species across a broad environmental gradient? The answer begins by
obtaining DNA from different individuals from multiple populations and subjecting it to a PCR-based survey of genetic diversity. Such a survey can lead
to inferences about the historical processes that led to differences in the genetic makeup of populations spanning a broad range of geographic and
environmental conditions. Alternatively, one might want to know about the evolutionary history and relationships among members of a group of species.
Consider, for instance, Darwin's finches. (Figure 2). Once again, PCR is used to amplify particular coding or non-coding regions of DNA from different
species, with the ultimate goal of reconstructing the phylogenetic history of each species within the complex. Once determined, the phylogenetic tree
resulting from this study can provide information on how diverse the species complex is and which species are most closely related to one another
(Figure 3). In turn, this can provide insight into the ecological (e.g., niche space use) and behavioral factors (e.g., foraging) that have contributed to the
diversity of a species complex.
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Figure 1: Polymerase chain reaction (PCR)

The PCR method begins with total genomic DNA extracted from an organism. The DNA is combined with sitespecific primers, taq polymerase, and other reagents (e.g., MgCl2, buffer, dNTPs) and subjected to repeated cycles,
each of which consists of a denaturation phase, annealing phase and extension phase. Denaturation separates
double stranded DNA, allowing primers to anneal to specific sites, followed by incorporation of deoxynucleotide
triphosphates (dNTPs; A, C, G, T), thereby extending the target site in the 5'-3' direction (on both separated strands).
The first cycle is completed when one round of denaturation, annealing and extension is finished, resulting in two
new copies of the target site. Subsequent cycles (typically 30-35) repeat the 3-phase process, resulting in many
million-fold copies of amplified DNA.
Markers and Methods

There are many different types of DNA markers used in molecular ecology, including: microsatellites (MSATs, highly repetitive sequences of DNA that
mutate rapidly and are often used to identify individuals), minisatellites (similar to microsatellites but with longer repetitive sequences), restriction
fragment length polymorphisms (RFLPs, specific sites of DNA that can be cut by enzymes yielding different-sized fragments of DNA in different species,
populations, and rarely individuals), and DNA sequence data (the bases of DNA are determined and similarities and differences are compared to
identify species, populations, and individuals). Markers generated by these methods are also visualized in different ways. Traditionally, MSATs and
RFLPs were visualized as discrete bands revealed by agarose gel electrophoresis. The nucleotides comprising DNA sequences, however, require finer
levels of resolution, often achieved using polyacrylamide gels and autoradiography. Today, these marker types are typically visualized using
chemifluorescence and genetic analyzers, which detect the fluorescent emission of labeled primers (as in the case of MSATs) or the fluorescentlylabeled nucleotides of DNA sequences. These markers and visualization methods are by no means a comprehensive list, and the technique one
chooses depends greatly on the type of question being addressed in the study. By understanding the different kinds of information provided by different
marker methods, one can come to an informed decision on which is best for a particular study. Below, we describe three molecular methods commonly
used in molecular ecological studies.
Figure 2: Darwin's finches

Public Domain The Complete Works of Charles Darwin Online.
There are three different classes of markers that can be easily distinguished based on the type of information they provide. Anonymous markers include
those generated by a method called amplified fragment length polymorphisms (AFLPs) (Figure 4). This technique uses restriction enzymes combined
with PCR to generate many thousands of unique fragments that can be used to genetically fingerprint individuals within or among species within the
same genus. The utility of the AFLP method lies in that it does not require prior knowledge of an organism's genome. In other words, the regions of the
genome that are targeted by this method are unknown to the investigator (hence, "anonymous"). Nevertheless, this method often provides a rich source
of information about basic levels of genetic diversity and differentiation. AFLP markers are thus often used as a first step when investigating population
or species differences. The downside to the use of AFLPs, however, is that they are somewhat limited in the type of information they can provide. For
example, because theses markers are of unknown origin and nucleotide composition (i.e., they simply constitute fragments of varying length within the
genome), they are of limited use in reconstructing the evolutionary history of a group of organisms. Furthermore, AFLP markers are commonly referred
to as dominant markers and are scored as being either "present" or "absent," which means that it is generally not possible to determine if a band on a
gel represents a homozygous (AA) or heterozygous (Aa) genotype . This is because AFLP fragments represent unique restriction sites that are either
present or absent in each individual and thus only one allele (if present) is amplfied, thereby limiting the amount of information that can be obtained.
Another similar method called random amplified polymorphic DNA (RAPD) also generates dominant markers, which are typically viewed using agarose
gel electrophoresis. This method, however, has largely been replaced by the AFLP method, which typically uses chemifluorescence and a genetic
analyzer for visualization.
Figure 3: Evolutionary tree

Another class of markers, known as sequence-tagged site (STS) markers,

provides an alternative approach to characterizing genetic diversity within and
among species. A sequence-tagged site is a short (200-500 bp) sequence of
nucleotides that has a unique location within a genome and is targeted using
PCR with primers designed by an investigator. One type of STS marker is
represented by microsatellites (MSATs), also known as simple sequence
repeats (SSRs) or variable number tandem repeats (VNTRs). Unlike AFLPs,
these markers do require some knowledge of specific regions containing
tandemly repeated nucleotide motifs, such as "ATC" or "GAG," which typically
appear in non-coding regions of DNA. In combination with primers specifically
designed to target these sites and amplification via PCR, the STS method
provides a much finer level of discrimination among individuals. As
codominant markers they are able to reveal whether an individual is
heterozygous at a particular locus (e.g., Aa v. AA) because both alleles (A
and a) are amplified during the PCR process. Given that their exact
nucleotide composition (e.g., whether each repeat is always "ATC") is not
always known, these markers share the same limitation as AFLPs for
phylogenetic reconstruction because the homology of the markers is not
known. One way to extend the utility of STS markers whose exact nucleotide
composition is unknown is to sequence fragments derived from polymorphic
loci. One marker method known as sequence characterized amplified regions
(SCARs) uses fragments that have been cloned and sequenced to determine
their exact nucleotide composition. Once sequenced, primers can be
designed around the SCAR, and then re-amplified to look for fragment length
polymorphisms on an agarose gel. Interestingly, this method is often used in
combination with anonymous, dominant markers such as AFLPs and RAPDs,
thereby also extending their utility.
Figure 4: Amplified fragment length polymorphisms
An alternative, non-PCR-based marker method that is sometimes used by
(AFLPs)
molecular ecologists is allozyme analysis. These markers are derived from
loci encoding enzymes used in important metabolic processes (e.g.,
glycolysis). Although they are not as rapidly evolving as STS markers, they
often yield moderate to high levels of genetic variation, depending on the
organism. In either case, information from STS or allozyme markers can be used to determine if heterozygosity within populations is correlated with
some ecological variable. For example, one could examine levels of heterozygosity relative to growth rate and performance in plants or adaptive
response to environmental change in animals.
A third class of markers often used by molecular ecologists are those derived from direct DNA sequencing of targeted regions within the genome. These
are often called Sanger sequencing (Figure 5). As with STS markers, DNA sequencing requires precise knowledge of specific genes, or gene regions,
that are of interest to the investigator. Combined with PCR and well-designed primers, this method provides the finest and most fundamental level of
genetic detail currently available to molecular ecologists. This is because the exact nucleotide sequence can be obtained for cross-comparison analysis
of a wide range of taxonomic levels, from phyla to species, and, depending on levels of variation, even among individuals within a population. Thus,
DNA sequencing is ideal for determining the evolutionary history of a group of organisms and for inferring evolutionary processes and patterns such as
the genetic basis of adaptive trait loci (e.g., genes involved in responses to day length in plants), the historical patterns of migration and expansion of
animal species (e.g, from the Pleistocene to present day), and the evolution of specific traits involved in taxonomic diversification (e.g., the origin of a
notochord leading to vertebrates) to name only a few. One particularly useful genome that has been used extensively by molecular ecologists
studying animal phylogenetics is the organellar genome of mitochondrial DNA (mtDNA). One region of mtDNA that has proven especially informative at
low taxonomic levels (i.e., species level) is the cytochrome oxidase I (COI) region, also known as the "bar-coding" region because of its ability to use
universal primers and genetically barcode groups of diverse species. Another genome frequently used by plant molecular ecologists is the chloroplast
genome, which has been used extensively to track historical patterns of plant migration and reconstruct plant phylogenies.
Figure 5: Sanger sequencing method

DNA sequencing has also enabled the development of another highly polymorphic, codominant marker type called single nucleotide polymorphisms
(SNPs). When multiple sequences of a particular region are generated for multiple members within a species, single base differences among individuals
are often detected. Depending on the level of DNA sequencing (e.g., individual regions v. whole genomes), SNPs can provide broad genome coverage,
show high levels of variability, and can be used for phylogenetic reconstruction because the homology of these markers is known.
Another different but related approach to targeting individual gene regions is whole genome sequencing. One recently developed method that rapidly
generates short sequenced segments that can be analyzed and compiled into whole genomes is called Next Generation Sequencing. Although typically
limited to organisms with small genomes (e.g., bacteria or viruses), Next Generation Sequencing is becoming an important tool for molecular ecologists
interested in probing entire genomes for clues to ecologically-based questions.
Given the strengths and weaknesses of different molecular genetic techniques, one might wonder how best to design an experiment for answering a
particular ecological question. This subject requires careful consideration of both marker method and marker information content.
Experimental Design: From Random Molecules to Appropriate Methods

A key question to ask when employing genetic techniques is: Which one is best suited for my particular question? The answer to this question will be
determined by several factors, all of which must be evaluated both individually and together in order to arrive at a cohesive plan for launching a
successful molecular ecology study. Figure 6 shows a flow diagram for initial consideration of which method (or methods) best apply to your particular
question. Although there are many different ways to approach this question, one simple strategy is to begin with the taxonomic level of investigation.
Figure 6: Decision tree

Are you interested in population-level differences within species? Are anonymous markers the only ones available for your organism of interest? If so,
then AFLPs might be the marker of choice.
Do you need to know details such as observed or expected heterozygosity? Or, are you trying to correlate neutral marker variation (i.e., ones that are
not under selection) with some environmental variable? In this case, AFLPs might be useful, but STS or allozyme markers might be a better way to go.
Are you interested in reconstructing the evolutionary history of a group of organisms? If so, at what level of inquiry is your question aimed: among
species within genera, among genera, or at higher taxonomic levels (e.g., families, even phyla)? Depending on the region you intend to target (e.g,
coding v. non-coding DNA, nuclear v. organellar mtDNA), homologous markers derived from DNA sequencing will likely provide the greatest dividends.
Do your interests revolve around genome evolution? For example, you might be interested in understanding how the genomes of pathogenic v. nonpathogenic bacteria differ and whether there are ecological or environmental correlates to the virulence of pathogen-related genes.
In this case, whole genome sequencing (not just individual gene regions), which is now feasible and can be easily used to analyze small genomes,
would provide a rich source of information for the question of interest.
Although there are multiple ways to assess which marker is best for which question, thinking carefully about what levels of genetic variation you need
and at which taxonomic level is paramount to choose the best approach. Understanding this very simple strategy and applying it thoughtfully can
ultimately determine the degree to which your question is both answerable and publishable within the field of molecular ecology.
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By: John N. Griffin (Department of Zoology, University of Florida) & Brian R. Silliman (Department of Zoology, University of
Florida) 2011 Nature Education
Citation: Griffin, J. N. & Silliman, B. R. (2011) Resource Partitioning and Why it Matters. Nature Education
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Similar species commonly use limiting resources in different ways. Such resource partitioning helps to explain how seemingly similar species can
coexist in the same ecological community without one pushing the others to extinction through competition. Understanding resource partitioning among
species may help us to predict how ongoing species declines will impact the functioning of ecosystems.
The Diversity of Life

One of the most striking features of life on Earth is its amazing diversity. There are so many species, in fact, that even after centuries of exploring
different ecosystems, describing species, and cataloguing them, the total number of species on planet Earth is still unknown. Estimates range from 530
million, but we have only named and described a mere 2 million (the most obvious ones!). Individual ecological communities can hold almost
unbelievable numbers of species. For example, it is not uncommon to find 100 species of coral on a reef in Fiji or Hawaii or 150 species of fish feeding
on or sheltering among the same corals. Biodiversity is not something that is just observable in tropical paradises a close look at birds in a local park
or the fish caught in a local pond will reveal numerous species.
How is this tremendous diversity of life maintained (i.e., why do so many species coexist), and what are the effects of the rapid loss of species we are
currently experiencing on the functioning of ecosystems? An understanding of resource partitioning may be key to answering both of these questions.
Similar Species Compete for Limiting Resources

There are only a limited number of ways of "making a living" within ecological communities. For example, on a coral reef, there are hard-skeleton corals
that gain food from capturing planktonic animals in their tentacles and, in exchange for providing a suitable habitat and nutrients, gain extra sources of
energy from sugar-synthesizing symbiotic algae. Within groups of species that make a living in a similar way, species compete for the same resources.
These resources, which include nutrients and habitat, are the raw materials needed by organisms to grow, live, and reproduce. However, resources are
not unlimited, and individuals from different species commonly compete for resources (interspecific competition).
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Complete Competitors Cannot Coexist

Classic experiments and mathematical models show that two species cannot coexist on the same limiting resource if they use it in the same way: The
superior competitor will always win out. If ecologically similar species (like corals on a reef or plants in a field) compete with one another for limiting
resources, what stops the best competitor from out-competing all the others? The answer may lie in species "doing their own thing" specializing in
their use of resources and thereby limiting their competition with others.
Dividing the Resource Pie

Species can divide up a limiting resource, such as food, water, or habitat (in other words the resource "pie"), by using different slices or even using the
same "slice" but in different places (i.e., they are dining in different restaurants, to take the analogy one step further) or at different times ("do you have a
table free at eight o'clock?").
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How Do Potential Competitors Partition Resources in Nature?

Careful and detailed study has revealed some of the many ways in which potential competitors show differences in patterns of resource use.
Perhaps the most obvious way that species can partition resources is in terms of what they consume. This is often underpinned by differences in their
morphological adaptations that allow differential resource use. For example, a detailed study of bumblebees in the mountains of Colorado (Figure 1)
neatly shows how different species can be best adapted to specific forms of a resource (Pyke 1982). Bumblebee species all compete for nectar from
flowers, but crucially these flowers vary in the length of their corolla. Matching this variation, different bumblebees in this area appear to be adapted to
specific species of plant that have different corolla lengths in their flowers. Careful observations of bumblebee visits to different flowers revealed clear
resource partitioning different species preferred different length corollas in accordance with their proboscis length (i.e., long proboscis, long corolla;
short proboscis, short corolla).
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Ecologists have found it relatively easy to document the various differences in the ways that ecologically similar animal species use their environment
and resources. In many cases nothing more than a pair of binoculars and careful observation is required. Studying resource partitioning in plants can be
much more challenging, and the relative lack of such examples has led many ecologists to wonder whether plants really do show resource partitioning;
after all, they all require a limited suite of resources (light, water, and nutrients). However, ecologists do not give up easily, and recent work has shown
that coexisting plant species often differ in the forms of nitrogen (e.g., ammonium versus nitrate or organic v. inorganic) they prefer (Kahmen et al.
2006). Differences in rooting depth and light-use optima have also been documented. Nevertheless, how common or important resource partitioning is
in plants remains uncertain and is an active area of current research.
Figure 1: Resource partitioning among bumble bees (Bombus spp.)

Species have proboscises of different lengths, enabling them to specialize in the exploitation of plants with different length corollas.
Species with similar length proboscises occur at different altitudes (Pyke 1982).
2011 Nature Education Adapted from Begon et al. (1990). All rights reserved.
Same Slice, Different Restaurant

When species use a resource similarly in one respect (i.e., they show "overlap" in their use of a resource along one axis), they commonly show
differences in some other respect (along another axis). For example, the bumblebee study mentioned above was conducted over sites varying in
altitude. Pyke (1982), the author of this work, found that although several bumblebee species had similarly long proboscises and so could forage on
similar species of plant, they were differentially specialized to altitude, so that sites at different altitudes were dominated by a different pair of long- and
short-length proboscis species. Another striking example comes from tree-dwelling Anolis lizards on the Caribbean island of Bimini (Schoener 1974;
Figure 2). In this case, species either foraged in the same places (as determined by the thickness of branches they perched on) or ate similar sized
prey, but in no cases did two species do both of these. In contrast, individuals of the same species commonly showed a high degree of overlap along
both of these resource axes (Figure 2).
Figure 2: Similarity in structural habitat and prey size in pairs of individual Anolis lizards from the Caribbean island of
Bimini
Pairs of classes that do not belong to the same species (interspecific) do not show high overlap along both axes (i.e., there are no
interspecific pairs in the dashed box).
2011 Nature Education Adapted from Schoener (1974). All rights reserved.
Is Resource Partitioning a Solution for Coexistence?

Ecological theory shows that interspecific competition will be less likely to result in competitive exclusion if it is weaker than intraspecific competition
(Chesson 2000). Resource partitioning can result in exactly this! By consuming slightly different forms of a limiting resource or using the same limiting
resource at a different place or time, individuals of different species compete less with one another (interspecific competition) than individuals of the
same species (intraspecific competition). Species, therefore, limit their own population growth more than they limit that of potential competitors, and
resource partitioning acts to promote the long-term coexistence of competing species. Other theories have been put forward that attempt to explain the
coexistence of large numbers of species in local communities, and assessing their importance relative to resource partitioning is likely to be an active
Page 3 of 4
area of research for years to come. There is no doubt, however, that mechanisms reducing interspecific relative to intraspecific competition act to
promote coexistence, and resource partitioning can achieve this.
Competition Can Drive the Evolution of Differences

So far we have discussed the phenomenon of resource partitioning and its role in reducing interspecific competition and therefore promoting
coexistence. Where does resource partitioning come from in the first place (i.e., what causes species to be able to partition resources)?
Competition can limit the growth, and ultimately the reproductive success, of individuals. It can consequently serve as a selection pressure driving
differential reproductive success and the evolution of traits that enable organisms to use resources differently compared to their competitors. This
process has been clearly demonstrated in the evolutionary events that have followed the colonization of volcanic islands. For example, a single species
of seed-eating finch originally colonized the Galapagos Islands and was faced with a diverse range of seed types and sizes. However, the beak of the
founding species only allowed it to eat a small subset of the available seed types and sizes. The advantages gained by individuals that were able to
exploit slightly different seed types drove evolution of many new species, each with different shaped beaks enabling them to specialize in a particular
size of seed (Grant 1986).
There is convincing evidence that competition (and not another selection pressure such as predation) drove and maintains differences in beak
sizes between these species. When species occur on their own on an island (i.e., there is no interspecific competition), they have similarly sized beaks
and presumably exploit similarly sized seeds. When several species occur on the same island however, they show clear differences in beak shapes,
showing that it is interspecific competition that maintains differences between species and resultant resource partitioning (Figure 3).
An interesting new twist has been added to this story of the evolution of resource partitioning. Around 25 years ago the island of Daphne Major,
originally host to just a single species of Darwin's finch (Geospiza fortis) was invaded by another, larger beaked species (G. magnirostris). Amazingly,
researchers have documented a rapid evolutionary shift in the sizes of beaks in G. fortis. In response to severe competition for larger seeds it has
evolved to take full advantage of small seeds. This study is particularly important because the researchers were able to document the process of
character displacement, and by monitoring the levels of resources, show that competition was the most likely possible cause (Grant & Grant 2006).
Figure 3: A classic example of character displacement

When multiple species of Darwin's finches co-occur on an island, they show differences in bill depth (and eat different sized seeds)
compared to when they are alone on an island.
2011 Nature Education Adapted from Morin (1999). All rights reserved.
Resource Partitioning, Species Extinction, and the Functioning of Ecosystems

Humans are causing widespread extinctions of species on local and even global scales. Recently, ecologists have realized that resource partitioning
may have important implications for our understanding of the effects of losing species on the functioning of entire ecosystems.
Groups of ecologically similar species may all contribute toward the same, aggregate ecological processes; for example, grasses in a meadow all
contribute towards overall primary production and predatory spiders in the same meadow may all contribute towards the control of plant herbivores.
Maintenance of such ecological processes is important for the overall functioning of ecosystems, including ecosystem services that humans benefit
from.
Resource partitioning can help scientists understand how aggregate ecological processes will be impacted by species extinction. If species show a high
degree of resource partitioning, when a species is lost so too is the capacity of the ecological group to exploit the particular slice of the resource pie that
the deleted species was adapted to exploit. For example, extinction of a species of grass that was uniquely specialized to use ammonium as a source of
nitrogen would leave ammonium in the soil unused. Because this slice (ammonium) of the resource pie will not be exploited, the overall rate of new
growth of meadow grass (primary production), as well as associated processes like uptake of carbon dioxide and production of oxygen, will be reduced.
A vast number of recent experiments show that species extinction, on average, reduces levels of ecosystem processes (Cardinale et al. 2006).
Resource partitioning is thought to play an important role in causing this effect, although ecologists are only just beginning to directly test this (Griffin et
al. 2008, Finke & Snyder 2008). There is an important application of this ongoing work by considering the degree of resource partitioning among
species scientists may be able to predict those ecosystems that are most vulnerable to the loss of species.
Page 4 of 4
Summary
The long-term coexistence of ecologically similar species, and thus the astounding diversity of life on Earth, has long fascinated ecologists. Resource
partitioning may hold the answer to the coexistence of species that make a living in similar ways (i.e., species are able to "stay out of the way of each
other" and reduce interspecific competition by using resources differently). Indeed, the benefit of tapping into resources that another competing species
cannot use as effectively can be so great that following the addition of a competitor, new traits can literally evolve right in front of the eyes of scientists!
The astounding diversity of species on Earth is at least partly attributable to the various ways in which potentially competing species have evolved
specialized traits and intricately partitioned resource exploitation. Ecologists are beginning to realize that the very resource partitioning that helps
maintain species diversity may also leave the overall functioning of ecosystems highly sensitive to species extinction.

Chesson, P. Mechanisms of maintenance of species diversity. Annual Review of Ecology, Evolution and Systematics 31, 343366 (2000).
Finke, D. L. & Snyder, W. E. Niche partitioning increases resource exploitation by diverse communities. Science 321: 14881490 (2008).
Grant, P. R. Ecology and Evolution of Darwin's Finches. Princeton, NJ: Princeton University Press, 1986.
Grant, P. R. & Grant, B. Evolution of character displacement in Darwin's finches. Science 313, 224226 (2006).
Griffin, J. N. et al. Predator diversity and ecosystem functioning: density modifies the effect of resource partitioning. Ecology 89, 298305 (2008)
Kahmen A. et al. Niche complementarity for nitrogen use An explanation for the biodiversity and ecosystem functioning relationship in grasslands?
Ecology 87, 12441255. (2006)
Pyke, G. H. Local geographic distributions of bumblebees near Crested Butte, Colorado: competition and community structure. Ecology 63, 555573
(1982).
Schoener, T.W. Resource partitioning in ecological communities. Science 185, 2739 1974.
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By: Zachary Aidala (Graduate Center, CUNY) & Mark E. Hauber (Dept. of Psycology at Hunter College, CUNY) 2010 Nature Education
Citation: Aidala, Z. & Hauber, M. E. (2010) Avian Egg Coloration and Visual Ecology. Nature Education
Knowledge 1(9):4
Birds and humans perceive colors differently, so scientists rely on instruments and genetics to
accurately describe the diversity of avian color signals.

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Evolutionary processes have generated diverse color patterns of avian feathers, skin patches, and egg shells, which perform countless functions,
including mimicry, crypsis, prey detection, predator avoidance, and signaling individual identity or mate quality (Hill & McGraw 2006). If color patterns
function to communicate information, then do we need to understand the sensory and perceptual systems responsible for detecting these complex
patterns? Recent technological and theoretical efforts have revolutionized the study of avian vision so that we now can use genetic sequencing of the
opsin genes involved in avian color vision to reconstruct light-receptor sensitivity parameters, and this information can be used in perceptual models of
birds' vision. Combined, these two approaches allow for a better understanding of the role that visual ecology plays in the evolution of avian
communication and recognition systems, especially in the study of egg mimicry, ultraviolet (UV) light sensitivity, and their role in shaping the sensory
ecology and behavioral patterns of diverse bird species (Hubbard et al. 2010).
The Evolution of Egg Color Patterns

Why do bird eggs range in color from uniformly white to brightly colored and/or densely speckled (maculated; see Banner photo)? Based on a
comparison of eggshell patterns between different avian families, one of the most prevalent ecological factors responsible for the diversity of egg
coloration is the interaction between brood parasites and their hosts (Kilner 2006). Obligate brood parasitic birds lay their eggs in nests of other species,
thereby imposing a cost on hosts to raise genetically unrelated young (Davies 2000). Egg coloration and maculation play important roles in whether
hosts accept or reject the fitness costs imposed by parasitism. For example, the blackcap (Sylvia atricapilla) is a host of the parasitic common cuckoo
(Cuculus canorus) in Europe and typically rejects all non-mimetic (dissimilar) eggs (Honza et al. 2004). By experimentally parasitizing blackcap nests
with host-like mimetic eggs (using eggs of other blackcaps), egg rejection drops to 36% (Polacikova et al. 2007). Accurate rejection of foreign eggs even
at seemingly low rates can still be an adaptive behavior because the host reduces its chances of spending time and energy raising overly needy and
genetically unrelated offspring.
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These and other cuckoo hosts appear to have evolved a simple rule of thumb to direct their behavior: "eject the egg unlike your own". But how does a
bird know what its own eggs look like? Researchers have tackled this question by experimentally manipulating the appearance of the bird's own egg by
dying one, more, or all eggs in the same brood (Figure 1). Such studies reveal that great reed warbler (A. arundinaceus) hosts rely on both color
differences between eggs and learned memories of their own eggs to recognize and reject cuckoo eggs (Moskt et al. 2010).
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Figure 1: Dyeing birds' own eggs (here in the nest of the song thrush Turdus philomelos) allows for an
experimental manipulation of (a) color and/or (b) maculation, without the confounds of changing size, shape, or
eggshell thickness, to assess the role of visual ecology in discriminating own and foreign eggs.
The photo on the left shows an experimentally darkened song thrush egg among unmarked eggs. The photo on the right
shows two song thrush eggs whose spots have been experimentally expanded next to an unmarked egg.
2010 Nature Education Courtesy of M. Hauber. All rights reserved.
Truly astounding, though, is that selection for visual cues of recognition has resulted in the evolution of extreme level of egg color mimicry of specific
hosts by different parasitic cuckoos (Figure 2). Through the process of coevolutionary arms race, egg mimicry also has likely influenced the perceptual
sensitivities of hosts and their abilities to correctly identify and reject foreign eggs from the nest. The perceptual acuity necessary to make a correct
rejection invites direct investigation; researchers can experimentally parasitize the nests of hosts with eggs of varying degrees of similarity, in order to
determine the thresholds in color and maculation at which hosts make decisions to reject dissimilar, and likely foreign, eggs from their nest.
Figure 2: Nests with both host and parasitic common cuckoo eggs, illustrating near-perfect mimicry to the human
eye. Black arrows identify cuckoo egg.
2010 Nature Education Courtesy of M. Honza, T. Grim, & C. Moskat. All rights reserved.
Avian Color Perception

Before an experimenter can set out to manipulate egg colors, especially the ones hypothesized to be important for foreign egg rejection, it must be first
established which colors that host species can see. The cone photoreceptors of the vertebrate retina (Figure 3) are responsible for color vision. The
genes for opsins encode specific photopigments expressed in these cones, generating different combinations of proteins with maximal sensitivities to a
particular wavelength of light (max). The cone cells of all color-sensitive vertebrates express opsins. The number of different opsins that an individual
possesses is related to the number of colors to which it is sensitive.
Page 3 of 6
Figure 3: Schematic diagram of the mammalian retina.

Public Domain WikiMedia Commons.
Avian retinas differ from those of mammals in many ways, notably in the number of cone types that they possess. Unlike mammals, which typically have
only two or three different cone types (Figure 4), bird species possess 4 distinct single cone types in their retinas, making them tetrachromatic (Figure 5;
Hunt et al. 2009). Tetrachromats are theoretically able to see twice as many colors as trichromats (e.g., humans). For example, two eggs might appear
indistinguishable to us, but a bird might see them displaying two distinct colors. This has direct implications for scientific investigations of avian
perception how can we manipulate egg colors when birds themselves may be more sensitive than we are to subtle differences in color?
Figure 4: Differences in wavelengths of maximum absorbance of the three cone opsins (S, M, and L) and
rhodopsin (R) in the human retina.
Public Domain WikiMedia Commons.
Some avian lineages, including many passerines, are able to see light in the ultraviolet (UV) range, which humans cannot see (Hart 2001). The hosts of
brood-parasitic cuckoos in Europe and brown-headed cowbirds (Molothrus ater) in North America are passerines, implying that they might be able to
perceive cryptic (to human) UV differences between their own and parasitic eggs to discriminate and reject parasitic eggs. One of the types of opsins
(SWS1) is sensitive to the shortest wavelengths of light, and is found in all vertebrate classes (Hazel et al. 2006). In humans and many bird species, the
SWS1 opsin is expressed in cones that respond maximally to violet light (such species are termed violet-sensitive, VS). In some passerine species,
however, the SWS1 opsin gene codes for a photoreceptor with a max that crosses into the UV portion of the light spectrum (Figure 6). Species with this
type of SWS1 cone are UV-sensitive (UVS; Hart 2001; deen & Hstad 2003; Hunt et al. 2009).
Page 4 of 6
Figure 5: Differences in wavelength of maximum absorbance between species possessing the UVS v. the VS
SWS1 opsin photoreceptor
A UV-sensitive SWS1 is apparently ancestral among vertebrates, but was subsequently lost in primates and birds (Yokoyama 2000; Jacobs & Rowe
2004; this is a great review for those interested in the evolution of color vision in vertebrates). Among birds, however, UVS has re-evolved independently
at least 4 times via a shift in SWS1 sensitivity (Hunt et al. 2009). UV-sensitivity in turn can serve a number of adaptive behavioral and ecological
functions, including sexual displays, predator/prey detection, intraspecific communication to avoid detection by VS predators (Hstad et al. 2005), and
defense mechanisms against egg mimicry in brood parasitism (Honza et al. 2007; Underwood & Sealy 2008). These two latter studies demonstrate that
the UV-reflectance of eggs differs between host and parasite, suggesting that hosts can use UV-only visible patterns to discriminate between their own
and foreign eggs. Whether UV-sensitivity evolved as a response to brood parasitism or was already available for hosts to utilize at the onset of their
evolutionary history with brood parasitism, remains still unknown (Underwood & Sealy 2008).
Regarding other ecological contexts, eggs of cavity-nesting species tend to have higher UV-reflectance than eggs of open cup nesters (Aviles et al.
2006), providing further evidence that UV light can both be seen and be informative for parental birds' behavioral decisions. Accordingly, cavity-nesting
spotless starlings (Sturnus unicolor) are more likely to accept experimental eggs placed just outside the nest cup within the cavity (by pulling them them
into the nest) with high UV-reflectance than eggs with low UV-reflectance.
But how can we know whether the SWS1 opsin of a particular bird species will be maximally sensitive to UV or violet wavelengths of light? Much of our
knowledge of the avian sensory world now derives from physiological and molecular techniques which describe the sensitivities of opsins present in the
eye. The traditional method of microspectrophotometry allowed researchers to determine the max of any photoreceptor by transmitting light through it
and measuring which wavelengths are absorbed (Govardovskii et al. 2000). More recently, DNA sequencing of the SWS1 opsin gene has allowed
researchers to assign VS/UVS states in a more cost-effective and non-lethal manner, relevant for large scale comparative studies (deen & Hstad
2003), including work with bird species of conservation concern for which invasive studies cannot be done (Igic et al. 2010).
The molecular machinery of the SWS1 photoreceptor requires only one amino acid substitution in a select few sites of the protein's amino-acid chain to
change a VS species or individual to a UVS species or individual (Yokoyama et al. 2000). Genetic sequencing of the SWS1 opsin gene is now regarded
as an accurate, reliable and economical alternative to microspectrophotometry (but see Smith et al. 2002).
Perceptual Modeling of the Avian Visual System

Integrative research spanning the fields of molecular genetics, physical light reflectance measurements, and behavioral experiments, has allowed
researchers to quantify color patterns as birds would see and use them (Vorobyev & Osorio 1998; Endler & Mielke 2005). To interpret physiological and
genetic data, however, requires perceptual models which are mathematical representations of what a bird can see, based on a number of different
parameters, including the amount of light that reaches the retina and the relative abundance and type of photoreceptors present in that particular
species' eyes. Using physiological data generated from genetic sequencing of the opsin genes (deen & Hstad 2003), researchers can now produce
reasonably accurate models of avian visual perception and its behavioral implications in egg rejection decisions (Cassey et al. 2008). Typically, the light
reflectance of surfaces of interest, such as eggshells, is measured with a spectrophotometer and the resulting relative light reflectance data are then
filtered through the perceptual model's equations to assess whether a species in question can see differences between particular light reflectance
patterns, or colors.
Color Vision Links Sensory Ecology with Behavioral Decisions

Perceptual modeling has been adapted to study a wide range of phenomena; these include the perceived variability in eggshell colorations across many
bird species (e.g. Cassey et al. 2009; Cassey et al. 2010), the adaptive use of human-made refuse as nesting material (Igic et al. 2009), as well as
sexual dimorphism (Igic et al. 2010). Future studies of perceptual modeling should focus on the differences in egg colors between brood parasites and
their hosts, and whether or not hosts are visually equipped to perceive these differences. Overall, molecular techniques and sensory modeling now
allow researchers to begin to study the mechanisms underlying avian color vision, and do not require severely invasive methods. These integrative
approaches make it possible for future researchers to accurately describe and manipulate salient color information in studies of mimicry, crypsis, mate
quality, and other behavioral functions critical for survival and reproduction across diverse species of birds and other visually oriented animal lineages.

Aviles, J. M., Soler, J. J. & Prez-Contreras, T. Dark nests and egg colour in birds: a possible functional role of ultraviolet reflectance in egg
detectability. Proceedings of the Royal Society of London B 273, 28212829 (2006).
Cassey, P., Honza, M., Grim, T. & Hauber, M. E. The modeling of avian visual perception predicts behavioural rejection responses to foreign egg
colours. Biology Letters 4, 515517 (2008).
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Cassey, P. et al. Are avian eggshell colours effective intraspecific communication signals in the Muscicapoidea? A perceptual modelling approach. Ibis
151, 689698 (2009).
Cassey, P. et al. Variability in avian eggshell colour: a comparative study of museum eggshells. PLoS ONE 5, e1 2054 (2010).
Davies, N. B. Cuckoos, Cowbirds, and Other Cheats. London: Poyser, 2000.
Endler, J. A. & Mielke, P. W. Comparing entire colour patterns as birds see them. Biological Journal of the Linnaean Society 86, 405-431 (2005).
Govardovskii, V. I., Fyhrquist, N., Reuter, T., Kuzmin, D. G. & Donner, K. In search of the visual pigment template. Visual Neuroscience 17, 509528
(2000).
Hart, N. S. The visual ecology of avian photoreceptors. Progress in Retinal and Eye Research 20, 675703 (2001).
Hstad, O., Victorsson, J. & deen, A. Differences in color vision make passerines less conspicuous in the eyes of their predators. Proceedings of the
National Academy of Sciences USA 102, 63916394 (2005).
Hill, G. E. & McGraw, K. J. Bird Coloration. Mechanisms and Measurements, vol. 1. Cambridge, MA: Harvard University Press, 2006.
Honza, M. et al. Are blackcaps current winners in the evolutionary struggle against the common cuckoo? Journal of Ethology 22, 175180 (2004).
Honza, M., Polacikov, L. & Prochazka, P. Ultraviolet and green parts of the colour spectrum affect egg rejection in the song thrush (Turdus
philomelos). Biological Journal of the Linnean Society 92, 269276 (2007).
Hubbard, J. K., Uy, J. A. C., Hauber, M. E., Hoekstra, H. E. & Safran, R. J. Vertebrate pigmentation: from underlying genes to adaptive function. Trends
in Genetics 26, 231239 (2010).
Hunt, D. M., Carvalho, L. S., Cowing, J. A. & Davies, W. L. Evolution and spectral tuning of visual pigments in birds and mammals. Philosophical
Transactions of the Royal Society of London B 364, 29412955 (2009).
Igic, B., Cassey, P., Samas, P., Grim, T. & Hauber, M. E. Cigarette butts form a perceptually cryptic component of song thrush (Turdus philomelos)
nests. Notornis 56, 134138 (2009).
Igic, B. et al. Size dimorphism and avian-perceived sexual dichromatism in a New Zealand endemic bird, the whitehead Mohoua albicilla. Journal of
Morphology 271, 697704 (2010).
Jacobs, G. H. & Rowe, M. P. Evolution of vertebrate colour vision. Clinical and Experimental Optometry 87, 206216 (2004).
Kilner, R. M. The evolution of egg colour and patterning in birds. Biological Reviews 81, 383406 (2006).
Moskt, C., Bn, M., Szkely, T., Komdeur, J., Lucassen, R. W. G., van Boheemen, L. A. & Hauber, M. E. Discordancy or template-based recognition?
Dissecting the cognitive basis of foreign eggs in hosts of avian brood parasites. Journal of Experimental Biology 213, 19761983 (2010).
deen, A. & Hstad, O. Complex distribution of avian color vision systems revealed by sequencing the SWS1 opsin from total DNA. Molecular Biology
and Evolution 20, 855861 (2003).
Polacikova, L., Honza, M., Prochazka, P., Topercer, J. & Stokke, B.G. Colour characteristics of the blunt egg pole: cues for recognition of parasitic eggs
as revealed by reflectance spectrophotometry. Animal Behaviour 74, 419427 (2007).
Smith, E. L., Greenwood, V. J. & Bennet, A. T. D. Ultraviolet colour perception in European starlings and Japanese quail. Journal of Experimental
Biology 205, 32993306 (2002).
Underwood, T. J. & Sealy, S. G. UV reflectance of eggs of brown-headed cowbirds (Molothrus ater) and accepter and rejecter hosts. Journal of
Ornithology 149, 313321 (2008).
Van Hazel, I., Santini, F., Mller, J. & Chang, B. S. W. Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics. BMC
Evolutionary Biology 6, 97 (2006).
Vorobyev, M. & Osorio, D. Receptor noise as a determinant of colour thresholds. Proceedings of the Royal Society of London B 265, 351358 (1998).
Yokoyama, S. Molecular evolution of vertebrate visual pigments. Progress in Retinal and Eye Research 19, 385420 (2000).
Yokoyama, S., Radlwimmer, F. B. & Blow, N. S. Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. Proceedings
of the National Academy of Sciences USA 97, 73667371 (2000).
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By: Rebecca Croston (Biology Program at the Graduate Center, CUNY) & Mark E. Hauber (Dept. of Psychology at Hunter College,
CUNY) 2010 Nature Education
Citation: Croston, R. & Hauber, M. E. (2010) The Ecology of Avian Brood Parasitism. Nature Education
Knowledge 1(9):3
Brood parasitic birds lay their eggs in the nests of others, sparing themselves the expense of
rearing their own young. The resulting coevolutionary arms race includes sophisticated
defenses by hosts and escalating tools of exploitation by parasites.

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Brood Parasitism as a Reproductive Strategy

Avian brood parasitism, or the laying of one's eggs in the nest of another individual, is a reproductive strategy whereby parasites foist the cost of rearing
their offspring onto another individual, the host (Davies 2000). Brood parasitism may be facultative at the species or individual levels, with some eggs
incubated by the mother and others laid in foreign nests, or obligate. Brood parasitism may also be intraspecific, with eggs laid in other nests of the
parasite's own species, or interspecific, with all eggs laid in the nests of other species. Cowbirds and cuckoos are the most commonly studied avian
brood parasites (Davies 2000), although obligate interspecific brood parasitism has evolved at least 7 separate times among various avian clades,
including cowbirds (Icteridae), honeyguides (Indicatoridae), Old World cuckoos (Cuculinae), twice in the New World cuckoos (Neomorphinae),
indigobirds and their allies (Ploceidae), and the Black-headed duck (Anatidae).
For the parasite, benefits include increased fecundity due to greater allocation of resources toward mating and producing more eggs rather than
defending nests, incubating eggs, and feeding young. For hosts of brood parasitic birds, the costs of parasitism range from diminished nestling growth
rate, due to competition with larger and more competitive parasitic offspring (cowbirds, whydahs), to total loss of breeding by the abandonment of
parasitized broods (cowbirds, cuckoos), the eviction of all host eggs by the early-hatching parasites (cuckoos), or the killing of host hatchlings by
parasitic hatchlings (cuckoos, honeyguides) (Kilner 2005; Servedio & Hauber 2006). These costs exert reciprocal natural selection on parasites and
hosts, such that in many cases host-parasite interactions result in escalating coevolution between intimately tied and interdependent species (Langmore
et al. 2003). In turn, many hosts are able to discriminate against and reject foreign eggs or chicks based on visual, acoustic, or multimodal sensory cues
(Cassey et al, 2008). The eggs of many brood parasites, for example, mimic those of their hosts (to deceive hosts to accept), have harder shells (to
impede rejection by puncture), and require slightly shorter incubation times (causing a size advantage for parasitic nestlings) (Davies 2000) (Figure 1).
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Figure 1: Common Cuckoos (Cuculus canorus) parasitizing Common Redstarts (Phoenicurus phoenicurus) in Europe lay
eggs whose colors mimic closely host egg colors (the parasite egg is the slightly larger egg). In contrast (inset), Brownheaded Cowbirds (Molothrus ater) in North America lay speckled eggs which do not resemble the pure white eggs of one
of their many hosts, the Eastern Phoebe (Sayornis phoebe).
2010 Nature Education Courtesy of T. Grim & M. Hauber. All rights reserved.
Evolution and Maintenance

There are two major hypotheses that have been implemented in attempting to explain the evolution and maintenance of the complex and often
paradoxical reproductive strategies that fall under brood parasitism (Rothstein & Robinson, 1998). The evolutionary lag hypothesis posits that rejection
is almost always more adaptive than acceptance, so that 1. hosts accept parasitism only because they have not yet evolved mechanisms for defense
against parasites and/or 2. parasites fail with certain hosts because they have not yet evolved mechanisms for overcoming existing host defenses.
Historically recent contact, due to natural or anthropogenic change (e.g., deforestation, forest fragmentation), the acceptance of foreign eggs even when
these do not resemble host eggs (nonmimetic), and a high cost of parasitism without apparent defenses to prevent and recognize parasitism, all
suggest that evolutionary lag is the mechanism for host acceptance of parasitic eggs, but as it is difficult to test this hypothesis directly, it is often the
default or fall-back explanation (Peer & Sealy 2004).
In contrast, the evolutionary equilibrium hypothesis posits that hosts accept parasitism only because the cost associated with the rejection of parasitic
eggs is greater than the cost of rearing cowbird offspring (Klippenstine & Sealy 2008). Rejection costs may be incurred via misrecognition of parasitic
eggs, so that hosts mistakenly eject their own eggs, or via rejection costs, when hosts accidentally damage their own eggs while attempting to remove
parasitic eggs. Host-egg mimicry and increased eggshell thickness by parasitic eggs have both evolved repeatedly in diverse lineages of obligate
parasites, rendering the recognition and removal of parasitic eggs more costly, and thereby increasing selective pressure to accept parasitism or delay
the evolution of costly and error-prone discrimination mechanisms to reject parasites.
The Coevolutionary "Arms-Race"

Egg Mimicry
Most host defenses against costly parasitism occur at the egg stage with the recognition and removal of parasitic eggs. This ability may have evolved
from behaviors such as nest sanitation (removal of fecal sacs and broken shells), and morphological traits such as large bills, which serve as
preadaptations for removal of parasitic eggs (Peer & Sealy 2004). Egg recognition thereby exerts selective pressure on the parasites to lay eggs that
mimic in appearance those of their host, and reciprocal pressure on hosts to fine-tune their discriminative abilities. This "arms race" is at the heart of
brood parasitism as a coevolutionary phenomenon. The degree of egg mimicry and concurrent host specialization varies dramatically among parasitic
clades. A recent study by Klippenstine and Sealy (2008) has shown that grassland cowbird hosts possess the ability to discriminate between and reject
foreign eggs when the eggs differ dramatically (in color and maculation) from their own eggs, but these same species do not eject real or model cowbird
eggs. This suggests that a more generalized form of egg mimicry than that employed by cuckoos, and that Brown-headed cowbird (Molothrus ater) eggs
loosely mimic a wide range of potential grassland hosts. In contrast, individual females of many old world cuckoos, lay eggs that are specific to
particular hosts that is, they mimic eggs of a specific subset of their host species. Generalist cowbirds, by contrast, do not lay highly mimetic eggs,
and parasitize a wide range of hosts rather than specializing on a particular species of host or host-egg race. Recognition and removal of parasitic eggs
is based largely on differences between own and foreign eggs in background color, with size, shape, and maculation acting in various combinations to
elicit egg rejection. A major caveat in studies of degree of egg color matching to date has been that eggs are assessed according to the human visual
system. As many birds possess a fourth, UV-sensitive photoreceptor type relevant in behavioral decision-making, biologically realistic sensory models
should be used in future studies to determine the parameters eliciting egg rejection (Cassey et al. 2008; Honza et al. 2007).
Nestling Mimicry
If constraints surrounding egg recognition and removal make rejection at the egg stage too costly, the recognition and rejection of nestlings may provide
an effective alternative defense strategy for host species, ultimately resulting in plumage, mouth, and begging call mimicry (Langmore et al. 2003;
Anderson et al. 2009). For post-hatching discrimination to evolve, parasitism rates must be sufficiently high to outweigh the cost of recognition errors,
and hosts must have sufficiently high fecundity to bear the cost of mistakenly rejecting their own chicks (Langmore et al. 2003). Host rejection of
parasitic nestlings has been demonstrated in Superb Fairy-wrens (Malurus cyaneus), and may have selected for the evolution of nestling begging call
mimicry in Horsfield's Bronze-Cuckoos (Chalcites basalis) (Langmore et al, 2003). Nestling discrimination by hosts is, however, relatively rare, despite
hosts having various behavioral and cognitive traits that would enable such behavior. This is likely because nestling discrimination can only evolve when
egg discrimination has failed (Grim 2006).
Hosts may discriminate nestlings using cues such as size, color, vocalization, and overall clutch size. Mouth coloration and gape patterns of parasitic
nestlings can stimulate higher rates of provisioning by host parents by serving as a supernormal stimulus and enabling parasites to outcompete host
Page 3 of 4
young (Kilner et al. 1999). In parasitic indigobirds, nestling flange markings may resemble those of healthy hosts in order to stimulate greater
provisioning (Hauber & Kilner 2007) and to avoid discrimination through reduced feeding by host parents (Schuetz 2005).
Identity Crisis?
If parasitic nestlings are not exposed to conspecifics during development, then how are they able to identify members of their own species with which to
mate? Rather than relying solely on cues learned from parents and nestmates, brood parasites must employ some other mechanism for species
recognition in order to avoid mistakenly courting heterospecifics. Brown-headed Cowbirds seem to rely on a combination of self-referent phenotype
matching and a "password" like vocal trigger that unlocks learning of species-specific cues at their first encounter with a conspecific (Hauber et al. 2000,
2001). Such a combination of developmental paths and recognition mechanism may apply to brood parasites more generally, and could represent a
difficult-to-evolve behavioral algorithm, as was seen recently in an experimental study where male facultative interspecific brood parasitic ducks
mistakenly courted females of the host species instead of their own (Sorenson et al. 2010).
Conservation Impacts of Brood Parasitism

As a widespread generalist brood parasite, the native Brown-headed Cowbird poses a conservation threat to several of its North American passerine
hosts. Selective pressure resulting from cowbird parasitism is likely higher now than in the past, owing to increased suitable habitat provided by
deforestation, leaving more and novel hosts vulnerable to parasitism by increasing numbers of cowbirds (Davis & Sealy 2000). For brown-headed
cowbird host populations already in decline, such as the endangered Kirtland's Warblers (Dendroica kirtlandii), Black-capped Vireos (Vireo atricapilla),
Least Bell's Vireos (Vireo bellii pusillus), and Southwestern Willow Flycatchers (Empidonax traillii extimus), the effects of this can be devastating, and
human control of cowbird population size may be necessary to prevent local extinctions (Smith et al. 2000). This is a particular consideration for
conservation biologists working with hosts of generalist brood parasites, because even when a species declines in number it may continue to be
parasitized at high rates, since as generalist parasites, the cowbird population will not be impacted reciprocally with that of individual host species.
These applied aspects of host-parasite interactions confirm that scientifically informed conservation management is critical for the efficient and
productive planning and implementation of long term goals (Hauber 2009; Parker et al. 2010).

Anderson, M. G., Ross, H. A., et al. Begging call matching between a specialist brood parasite and its host: A comparative approach to detect coevolution. Biological Journal of the Linnean Society 98, 208216 (2009).
Cassey, P., Honza, M., et al.The modeling of avian visual perception predicts behavioural rejection responses to foreign egg colours. Biology Letters 4,
515517 (2008).
Davies, N. B. Cuckoos, Cowbirds and other Cheats. London, UK: T. & A. D. Poyser, 2000.
Davis, S. K. & Sealy, S. G. Cowbird parasitism and nest predation in fragmented grasslands of southwestern Manitoba. In Ecology and Management of
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The Geography and Ecology of Diversification in Neotropical Freshwaters

By: James S. Albert (University of Louisiana at Lafayette) & William G. R. Crampton (University of Central Florida) 2010 Nature Education
Citation: Albert, J. S. & Crampton, W. G. (2010) The Geography and Ecology of Diversification in Neotropical
Freshwaters. Nature Education Knowledge 1(10):13
This article addresses central themes in the study of tropical biodiversity, exploring the roles
that speciation, extinction, and dispersal play in the formation of regional assemblages.

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The unparalleled diversity of tropical ecosystems has drawn the attention of naturalists since the earliest voyages of discovery in the eighteenth and
nineteenth centuries. The fundamental question then, as now, is: Why so many species? One influential perspective seeks to explain species richness
at the community level in terms of mechanisms for ecological coexistence (Gause 1934, Hutchinson 1957). The central idea is that each species
occupies a unique ecological niche, a distinct functional role within the ecosystem (Darwin 1859). Under this view species richness arises from the
actions of natural selection to reduce competition or increase adaptive specialization.
Another view stresses the importance of historical or phylogenetic aspects of species diversification (Whittaker 1972). For example, the "species-pool"
hypothesis describes local diversity by reference to the size (species richness) of the regional or global pool of species from which the local assemblage
may be recruited (Taylor et al. 1990). From a macroevolutionary perspective, net rates of diversification within a geographic region arise from differential
rates of speciation, extinction, and immigration (Rosensweig 1995, Stanley 1998, Jablonski 2000). Although the mechanisms of these processes remain
incompletely understood for most biotas, we have known for at least a century and a half that evolutionary diversification takes place both in space and
time. Biodiversity, biogeography, and paleontology are therefore all intimately related subjects.
Exceptional Amazonia
Amazonia exhibits all the principle features associated with aquatic species richness globally (Albert & Reis 2011). It is the greatest interconnected
fluvial system on the planet, extending over more than seven million km2. The Amazon River alone carries about a sixth of the all world's flowing
freshwater. Its tropical location, straddling the equator, means it receives high levels of solar radiation and precipitation, and the region is largely
covered by humid lowland rainforests. From a purely ecological perspective, therefore, Amazonia as it exists today appears to be an excellent
environment for diversification in fishes.
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Yet the species-rich Amazonian ichthyofauna is ancient and did not arise under the geological conditions of the modern Amazon Basin (Lundberg et al.
2010). Direct fossil evidence shows that many phenotypes and lineages date to the early Neogene or Paleogene (16 to 65 million years ago; Ma),
before the Amazon assumed its modern courses. For example, the Amazon River only adopted its current east-flowing course after about 11 Ma; prior
to this it flowed west and north into the Caribbean (Figueiredo et al. 2009).
Furthermore, data from species-level phylogenetic and biogeographic studies tell us that Amazonian ichthyofaunas accumulated incrementally over a
period of tens of millions of years, principally by means of allopatric speciation, and in an arena extending over most of the area of tropical South
America (Albert & Reis 2011). In other words, unlike some of the well-known insular faunas (Galapagos finches, Hawaiian drosophilid flies, African rift
lake cichlids), the species-rich Amazonian ichthyofauna is not the result of recent adaptive radiations.
Vicariance and Geodispersal

The geological history of landscapes is tightly linked with the evolution of their resident biotas. For freshwater organisms, landscapes are divided
naturally into discrete drainage basins by watersheds, episodically isolated and reunited by erosional hydrodynamics. In regions like the Amazon Basin
with an exceptionally low (flat) topographic relief, the many waterways have had a highly reticulated history over geological time.
Stream capture is an important geographic factor affecting the evolution and distribution of freshwater organisms. Stream capture occurs when an
upstream portion of one river drainage is diverted to the downstream portion of an adjacent basin. This can happen because of geophysical uplift (or
subsidence), natural damming as a result of a landslide, or by headward or lateral erosion of the watershed between adjacent basins.
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Figure 1: Effects of stream capture on species-richness of adjacent drainage basins based on dispersal,
vicariance, and extinction
Stream capture event at t2 simultaneously separates and permits dispersal of populations between adjacent basins.
In this hypothetical example the newly diverged species at t3 may subsequently disperse throughout the Eastern
basin (E). Stream capture also changes the total area of each basin, and by means of the species-area relationship,
the rates of speciation and extinction. The area of the Western basin (W) decreases in area, and may therefore
maintain fewer species over evolutionary time.
From a biogeographic perspective, stream capture almost always involves

both vicariance and geodispersal (Figure 1). Vicariance is the emergence of
geographic barriers to dispersal and gene flow, which spatially isolates
populations and may lead to the formation of new species (i.e., allopatric
speciation; Figure 2). This contrasts with parapatric and sympatric models in
which selection and ecology are necessarily involved in the formation of new
species lineages. Geodispersal is the erosion of such barriers (e.g., the
formation of portals, corridors or bridges between formerly isolated regions).
A well-known instance of geodispersal was the Plio-Pleistocene rise of the
Panamanian isthmus around 3 Ma that connected Central and South America
and led to the Great American Biotic Interchange.
Geodispersal of a geographic area is different from the physical movements
of organisms (dispersal), although the erosion of geographic barriers can and
does facilitate organismal dispersal. Geodispersal, like vicariance, is an Earth
history process while dispersal is a biotic process. As Earth history events,
both vicariance and geodispersal may be spatially and temporally extensive,
affecting most or all of the evolving lineages in a regional biota.
Figure 2: Modes of speciation differ based on the relative roles

of space (geography) and ecology (selection) in the formation
of barriers to gene flow
NA indicates that speciation is unlikely in sympatry when selection
is very weak.
In tropical South America groups of closely related fish species usually exhibit
non-overlapping geographic ranges, a pattern suggesting divergence in
allopatry (Albert & Reis 2010). Allopatric speciation occurs when two or more
populations of a species become genetically isolated following the formation
of barriers to dispersal and gene flow. However, species-level phylogenies and distributions cannot be used to unambiguously prove a particular
geographic mode of speciation (e.g., sympatric v. allopatric) because geographical ranges may change following speciation.
Permeability of Geographical Barriers

The emergence of large tectonic structures, like ocean basins and mountain chains, usually forms impermeable barriers to dispersal and gene flow.
Many groups of plants and animals, including freshwater fishes, were permanently isolated on either side of the newly-formed Atlantic Ocean during the
final separation of Africa from South America in the Upper Cretaceous (around 110 Ma). Similarly, the early Neogene (around 12 Ma) rise of the Eastern
Cordillera of the northern Andes permanently separated lowland northern South America into taxonomically distinct cis- and trans-Andean biotas (Albert
et al. 2006). Impermeable barriers such as these are often spatially expansive, affecting broad geographic areas and multiple phylogenetically
independent clades. Impermeable barriers are therefore excellent systems to study the role of vicariance in the formation of regional biotas.
Yet tectonic activity is highly punctuated in time and space. Most mountain building in the Andes occurred in relatively discrete pulses lasting just 510
million years each, interrupted by much longer periods of tectonic quiescence. By contrast, most of lowland tropical South America has changed
gradually through the perennial action of erosion. Stream capture results in subtle and complex patterns in the geographic separation and merging of
river basins and freshwater biotas. As noted above, a single stream capture event has both vicariant and geodispersal effects, simultaneously isolating
a headwater tributary from one basin and connecting it to that of an adjacent basin.
In tropical South America, with its flat topography and low-altitude watersheds, many basins boundaries have been semipermeable over geological time
scales (Lovejoy et al. 2010a). Semipermeable watersheds are environmental filters in the sense that they allow differential dispersal among adjacent
basins. Fish species with high vagility between basins are those able to inhabit small streams and seasonal wetlands of the intervening areas and to
tolerate suboptimal environmental conditions (e.g., dysoxia, variable temperatures). Species that are ecologically restricted to large lowland rivers and
floodplains have far less vagility across watersheds.
Stream capture also differentially affects taxa depending on their demographic susceptibilities to extinction. Populations isolated on either side of a
newly-formed watershed are likely to have reduced population sizes, which may accelerate genetic divergence and speciation or lead to local extinction.
Taxa with high riverine vagility may use the new connections to expand their ranges and avoid extinction. Such newly arrived exotics may also
adversely affect members of the resident fauna. Although the responses of individual taxa are varied, the response of a fauna as a whole to stream
capture is likely to be increased rates of both speciation and extinction; in other words, increased rates of net diversification.
Phylogenetic and biogeographic patterns in the electric fish Gymnotus (Gymnotidae) illustrate how stream capture across low-elevation watersheds on
the relatively flat South American platform contribute to elevated species richness of regional assemblages (Figure 3). The Neogene rise of the northern
Andes resulted in relatively impermeable barriers to fish dispersal, isolating cis- and trans-Andean lineages in both the G. carapo and G. tigre groups.
By contrast, most watersheds in lowland Amazonia are relatively more permeable, several of which are indicated by dashed gray bars in Figure 3. Due
to post-speciation dispersal, the Gymnotus species of the Amazon basin do not form a monophyletic group but rather represent an assemblage of
species with origins in several basins (Albert et al. 2004).
Figure 3: Effects of vicariance and geodispersal on the formation of regional assemblages

(A) Schematic phylogenies of two clades of the electric fish Gymnotus (Gymnotidae). Some species of the G. carapo
group (in red) are omitted for clarity. Thick horizontal bars represent geographic barriers. Note polyphyletic origin of
the Amazonian assemblage. (B) Paleogeographic vicariance and coupled geodispersal events used to constrain
divergence times. Dates represent minimum lineage divergence time estimates in millions of years ago (Ma).
Semipermeable watersheds are "leaky" and do not provide reliable minimum divergence times (i.e., dates for
semipermeable barriers represent date ranges that extend to 0 Ma). Data from Lovejoy et al. (2010a, 2010b).
Phylogenetic Niche Conservatism

The empirically observed predominance of allopatric (versus sympatric) speciation highlights the important role of geography in the formation of species
richness. However, it does not mean that diversification occurs in an ecological vacuum. Species differ substantially in how they respond to the
formation and erosion of geographic barriers and exhibit different patterns of dispersal and demographic cohesion. Even under a purely allopatric model
of speciation, the autecological requirements of a species help define the nature and permeability of barriers to gene flow and dispersal. Furthermore,
the idiosyncratic ecological requirements of individual species may affect the ways in which populations disperse as geographic barriers form and
become eroded. The very existence and strength (i.e., permeability) of geographic barriers to dispersal and gene flow emerge directly from the
ecological and habitat requirements peculiar to a species.
Vicariant speciation is in this view a consequence of phylogenetic niche conservatism: a failure to adapt to the conditions of an intervening habitat.
Niche conservatism is the tendency of species to retain ancestral ecological characteristics. The conditions for ecological speciation are more restrictive
than for allopatric speciation (Figure 2). Because adaptive (parapatric or sympatric) speciation is so much less common than non-adaptive allopatric
speciation, species tend to retain their ancestral ecological characteristics.
Formation of Regional Assemblages

Niche conservatism is also important in constraining the assembly of species into local and regional biotas (Cornell & Lawton 1992). Species become
part of a local assemblage as immigrants from an adjacent area or as colonists from different habitats in the same area (Ricklefs 2008, Winemiller et al.
2008). Because of niche conservatism, immigration from ecologically similar areas is more likely than adaptive evolution (Wiens 2004). Immigration is
easier if a species is already adapted to local habitat conditions. In this case, a species need only overcome the ecological or physical barriers to
dispersal. If a species is already present in a region but in a different habitat, dispersal requires the evolution of new ecological or physiological traits.
Hence local communities are more often assembled by recruitment of species from a wide landscape. This seems to the rule among Neotropical fishes,
in which the great majority of species originated in allopatry without ecological divergence (Albert et al. 2011). For example, cases in which one sister
species occupies deep river channels while the other occupies seasonally-anoxic floodplain systems are not known among electric knifefishes
(Crampton 2011). In contrast, there are many cases of species in floodplains and rivers that have sister species occupying the same habitat in an area
of geographical allopatry (e.g., the deep river specialist Compsaraia samueli from the Amazon and C. compsus from the Orinoco). To summarize, while
adaptive transitions between very distinct ecosystems are rare, immigration by pre-adapted species is likely the dominant way in which local
communities fill with species or replace species that become extinct.
Conclusion
Phylogenetic and biogeographic patterns in Neotropical freshwater fishes suggest that most speciation has occurred along geographic, not ecological
lines. In most groups of Neotropical fishes, diversification occurred incrementally over large spatial and temporal scales, with speciation occurring over
much of the continental platform and requiring tens of millions of years. Vicariance and geodispersal are complimentary biogeographic processes that
have profoundly influenced the formation of new species and the taxonomic composition of regional biotas. Together these processes interact in a
complex duet of Earth history events and biological diversification. These results from Neotropical freshwater fishes support an emerging paradigm shift
within the field of ecology: Geography and phylogenetic history play an immensely important role in the formation of local species assemblages.

Albert, J. S., & Reis, R. E. Historical Biogeography of Neotropical Freshwater Fishes. Berkeley, CA: University of California Press, 2011 (in press).
Albert, J. S., Crampton, W. G. R., et al. Phylogenetic systematics and historical biogeography of the Neotropical electric fish Gymnotus (Teleostei:
Gymnotiformes). Systematic and Biodiversity 2, 375417 (2004).
Albert, J. S., Lovejoy, N. R., et al. Miocene tectonism and the separation of cis- and trans-Andean river basins: Evidence from Neotropical fishes.
Journal of South American Earth Sciences. 21, 14-27 (2006).
Cornell, H. V., & Lawton, J. H. Species interactions, local and regional processes, and limits to the richness of ecological communities. Journal of
Animal Ecology 61, 112 (1992).
Crampton, W. G. R. An ecological perspective on diversity and distributions. In Historical biogeography of Neotropical Freshwater Fishes, eds. Albert, J.
S & Reis, R. E. (Berkeley, CA: University of California Press, 2011 [in press]).
Darwin, C. R. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle For Life. London, UK:
John Murray, 1859.
Figueiredo, J., Hoorn, C., et al. Late Miocene onset of the Amazon River and the Amazon deep-sea fan: Evidence from the Foz do Amazonas Basin.
Geology 37, 619622 (2009).
Gause, G. F. The Struggle For Existence. Baltimore, MD: Williams and Wilkins, 1934.
Hutchinson, G. E. Concluding remarks. Cold Spring Harbor Symposium Quantitative Biology 22, 415427 (1957).
Jablonski, D. Micro- and macroevolution: scale and hierarchy in evolutionary biology and paleobiology. Paleobiology 26, 1552 (2000).
Lovejoy, N. R., Willis, S. C., et al. Molecular signatures of Neogene biogeographic events in the Amazon fish fauna. In Amazonia, Landscape and
Species Evolution: A Look into the Past, eds. Hoorn, C. M. & Wesselingh, F. P. (London, UK: Blackwell Publishing, 2010a): 405417.
Lovejoy, N. R., Lester, K., et al. Phylogeny, biogeography, and electric signal evolution of Neotropical electric fishes of the genus Gymnotus
(Osteichthyes: Gymnotidae). Molecular Phylogenetics and Evolution 54, 278290 (2010b).
Lundberg, J. G., Sabaj Prez, M. H., et al. The Amazonian Neogene fish fauna. In Amazonia, Landscape and Species Evolution: A Look into the Past
eds. Hoorn, C. M. & Wesselingh, F. P. (London, UK: Blackwell Publishing, 2010): 281301.
Ricklefs, R. E. Disintegration of the ecological community. American Naturalist 172, 741750 (2008).
Rosensweig, M. L. Species Diversity in Space and Time. Cambridge, MA: Cambridge University Press, 1995.
Stanley, S. M. Macroevolution. Pattern and Process. Baltimore, MD: The Johns Hopkins University Press,1998.
Taylor, D. R., Aarssen, L. W., et al. On the relationship between r/K selection and environmental carrying capacity: a new habitat templet for plant life
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Whittaker, R. H. Evolution and measurement of species diversity. Taxon 21, 213251 (1972).
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Orinoco and Amazon basins. Journal of Biogeography 35, 15511563 (2008).
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By: Jonathan M. Levine (Department of Ecology, Evolution, and Marine Biology, University of California) & Janneke
HilleRisLambers (University of Washington, Department of Biology) 2010 Nature Education
Citation: Levine, J. M. & HilleRisLambers, J. (2010) The Maintenance of Species Diversity. Nature Education
Knowledge 1(10):67
Earth is home to an astonishing diversity of species that provide food, medicine and other
infrastructure necessary for the existence of humankind. Given intense competition between
species for limited resources, how is this diversity maintained? Ecologists have shown that
differences in how species interact with their environment counter the inevitable loss of
biodiversity that occurs when better competitors overrun their inferior counterparts.
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The ecosystems of the world contain a remarkable diversity of species. An area of tropical rainforest the size of fifteen city blocks may contain over a
thousand different tree species (Figure 1a, Kraft et al. 2008). As ecologists have found in a Panamanian rainforest, close examination of just one of
these tree species can yield as many as 945 different species of beetles alone (Figure 1b, Erwin et al. 1980). This astonishing diversity also extends to
aquatic environments. Africas Lake Malawi is home to over 500 species of fish belonging to a single genus (Figure 1c; Kornfield & Smith 2000). In fact,
the number of species on Earth is so overwhelming that the 1.7 to 2 million species currently described by biologists (Millenium Ecosystem Assessment
2005) is likely to be only a small fraction of the true total.
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Figure 1: The diversity of species

(A) Tropical rainforests can contain 1,000 tree species in the area of fifteen city blocks. (B) 945 beetles were found on just one species of tropical tree.
(C) Lake Malawi in Africa is home to over 500 fish species from the same genus. (1B courtesy of Duane McKenna)
This astonishing biodiversity is valued for many reasons. The crops and livestock we rely on for food are derived from wild species long ago
domesticated, and future improvements to agricultural productivity and sustainability depend, to a large extent, on genes derived from wild rather than
domesticated populations. From a human health perspective, a significant fraction of medicines prescribed today contain chemical compounds that
were originally isolated from wild organisms, including aspirin (from willow trees), the cancer drug taxol (from yew trees), and penicillin (from a fungus).
In addition, diverse habitats are increasingly understood to be more stable in their provisioning of ecosystem services including clean water and the
pollination of agricultural crops (Millenium Ecosystem Assessment 2005).
Humankind derives tremendous benefits from the wide diversity of species on Earth, but this diversity also poses a fundamental ecological puzzle.
Speciation, the evolutionary process by which new species are formed, is clearly responsible for the ultimate generation of species diversity over
geologic time. But once generated, how is this diversity maintained? What prevents the single best competitor from displacing all other species? How
different species coexist (co-occur in the same location for many generations) is a long-standing and not fully resolved question for ecologists (Gause
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1934, Hutchinson 1961).

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The mystery of species coexistence is rooted in the competitive exclusion principle, which states that two species competing for the same resource
cannot coexist (Gause 1934, Hutchinson 1961). The species that is better at gaining the limiting resource will eventually eliminate the inferior
competitor. This intuitive idea has been central to the field of ecology at least since Darwins exposition of his theory of evolution, but mathematical
theory and laboratory experiments with single-celled organisms in the early part of the twentieth century reinforced this foundation (Gause 1934).
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The simple prediction of the competitive exclusion principle is schematically portrayed in Figure 2a. If a superior and an inferior competitor are placed
into a habitat at initially equal abundance, the former will inevitably eliminate the latter. Envision, for example, two rodent species, one that has a much
greater ability than the other to consume seeds, the food resource limiting their growth. Eventually, the better seed competitor will win (the blue species
in Figure 2a). The take home message is that differences in the competitive ability of different species cause their abundances to diverge over time,
resulting in one species becoming more common while the other becomes less common (Gause 1934, Chesson 2000). If the differences in the
competitive ability of species are large, the poorer competitor will be rapidly excluded. If these differences are small, exclusion will be slow.
Figure 2: Competitive exclusion and coexistence

(A) Differences between species in their competitive ability drive the superior to dominance and the inferior to exclusion. Both rodent species depicted
in consume the same size seeds, though the blue species consumes more of them. (B) Niche differences between species hinder competitive
exclusion, helping maintain species diversity. The two rodent species depicted in consume different size seeds, an important niche difference, allowing
their coexistence.
The central prediction of the competitive exclusion principle, the elimination of all but the best competitor, lies in sharp contrast with what we see in
nature; the coexistence of numerous species (Figure 1). This contrast poses an enigma. Ecologists resolve this enigma by reasoning that other species
properties must prevent the elimination of the inferior competitors. These are what ecologists call niche differences, species differences that maintain
diversity by preventing competitive exclusion (Figure 2b; Chesson 2000, Adler et al. 2007).
The niche is an abstract and often debated concept, but simply put, it defines how a species interacts with its environment (Chase & Liebold 2003). For
example, the niches of the two rodent species in Figure 2b include their diet; the quantity and size of seeds consumed. A niche difference between
species arises, for example, when one rodent (the blue) tends to consume larger seeds than the other (the orange) (Figure 2b). But how do such niche
differences maintain species diversity?
Envision a scenario in which the rodent eating large seeds (the blue) becomes so common that its competitor becomes rare. This shift in rodent
abundance will cause a deficit of large seeds and an abundance of small seeds in the habitat. Such a shift will benefit the small seed consuming
species (in orange), at the expense of its competitor (in blue). Conversely, if the small seed consuming species becomes common, large seeds would
be in abundance, allowing the large seed competitor to recover. Thus, the defining feature of a niche difference is that it causes each species to limit
individuals of its own species more than it limits individuals of its competitor (Chesson 2000, Adler et al. 2007). Niche differences thereby disfavor
species that become common and advantage those that are rare, which hinders competitive exclusion and maintains biodiversity (Figure 2b).
With competitive ability differences driving assemblages of species toward dominance by a single competitor, and niche differences opposing
competitive exclusion by favoring species that drop to low abundance (Figure 2b), the outcome of competition (exclusion or coexistence) depends on
the balance between the two types of species differences (Chesson 2000, Adler et al. 2007). If the stabilizing effects of niche differences are stronger
than the differences in competitive ability, species will coexist and diversity will be maintained. By contrast, if differences in competitive ability are great,
competitive exclusion will occur even with modest niche differences. In our example, this would occur if the rodents differed only slightly in the sizes of
seeds consumed, but one species ate far more seeds than the other.
An analogy to the more familiar case of competing businesses reinforces the way ecologists think about species coexistence. Two airlines sharing the
same routes are not likely to both stay in business (i.e., coexist) if passengers consistently value one airline over the other (a competitive ability
difference). Nevertheless, the less competitive airline can still persist by offering different routes than its superior counterpart, thereby capitalizing on a
different customer base (a niche difference). Of course, for coexistence, the offered routes must be sufficiently different, which in ecological language
would be expressed as the need for the niche difference to outweigh the difference in competitive ability.
The niche differences studied by ecologists today can be more complex than the example in Figure 2b, but they all share the defining features of our
hypothetical example. Figure 3 presents two results from the recent ecological literature. Scientists have shown that coexisting plant species in the
arctic use different forms of nitrogen (Figure 3a; McKane et al. 2002). Such differences can stabilize plant coexistence by disfavoring species that
become so abundant that their preferred form of nitrogen becomes less available.
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Figure 3: Niche differences ecologists have used innovative field observations and manipulations to quantify niche differences between
species
(A) Ecologists studying arctic tundra have used chemical tracers to show that different plant species consume different forms of nitrogen (glycine versus
ammonium versus nitrate) (McKane et al. 2002). This forms a niche difference because it causes Carex to compete more with other Carex individuals
than it does with Vaccinium. (B) Cherry species limit individuals of their own species more than those of other species via fungal disease. This disease
preferentially kills cherry seedlings when near infected parent trees and infected seedlings of their own species (Packer & Clay 2000). Away from trees
of their own species (where cherries are at much lower abundance), seedling survival is higher. As shown in the photograph, fungal disease causes
seedlings to wilt before dying (Figure 3A redrawn from Nature 415, 68-71; 3B, Nature 404, 278-281). (3B courtesy of Keith Clay)
Other niche differences involve consumers and disease. For example, when species are attacked by a specialist pathogen, a disease that harms only
them, individuals are only contagious to others of the same species. This causes individuals of the diseased species to limit other individuals of their
own species more than they limit their competitors. As is true for resource-based niche differences (Figures 2b and 3a), disease niches can thereby
cause species to gain advantages when rare (when disease prevalence is low), and disadvantages when common (when disease prevalence is high).
For example, seedlings of Pin Cherry, a North American tree, are more likely to escape fungal disease when rare, and not surrounded by other infected
Pin Cherry individuals (Figure 3b; Packer & Clay 2000).
Other important niche differences arise when species grow best different habitats, such as shallow or deep soils for plants, or in different types of years
(wet years versus dry years) (Chesson 2000). As long as these and other niche differences sufficiently benefit species that fall to low abundance in their
habitat, diversity is maintained.
Although ecologists have a firm handle on the need for niche differences to maintain species diversity, many unresolved questions remain. For example,
are there really hundreds of niche differences between species explaining the wide diversity found in tropical forests? Identifying the niche differences
operating in specific habitats, and hyper diverse ecological systems (Figure 1) in particular, has proven challenging (Adler et al. 2007, Levine &
HilleRisLambers 2009). This is because niche differences can arise through a wide variety of ecological interactions (Figure 3), and may operate over
long time scales that are difficult to study. As a consequence, ecologists have yet to determine which niche differences are most important for the
maintenance of diversity, and whether the identity of those niches changes with the habitat or organisms studied.
Ecologists also know little about how strongly niche differences stabilize coexistence in natural communities (Levine & HilleRisLambers 2009). Although
the competitive exclusion principle states that two species competing for the same resource cannot coexist indefinitely (hence the importance of niches),
evenly matched competitors can co-occur for long periods of time without any niche differences. This is the foundation of the recently proposed neutral
theory (Hubbell 2001), which suggests that a competitive stalemate might be the best explanation for the diversity of species seen in nature. While
ecologists generally agree that species are unlikely to be perfectly matched competitors, the influence of competitive ability differences and niche
differences on coexistence remains difficult to quantify in natural habitats (Levine & HilleRisLambers 2009).
How species diversity is maintained may seem an abstract question, of interest only to ecologists. However, the dramatic impacts of humans on the
environment, which include increasing global temperatures, the removal of top predators, or the addition of nitrogen (from the use of fertilizers) to
habitats, can strongly alter the relative competitive ability and niche differences between co-occurring species. For example, nitrogen deposition can
favor weedy species over slow growing competitors by minimizing the importance of competitive ability for nitrogen. The introduction of non-native
species into new habitats may allow them to "escape" their natural enemies and become overwhelmingly abundant at the cost of native diversity. A
better understanding of the mechanisms that contribute to species diversity will allow ecologists and conservation biologists to better predict and
manage future biodiversity.

Adler, P. B., Hille Ris Lambers, J., & Levine, J. M. A niche for neutrality. Ecology Letters 10, 95104 (2007).
Chase, J. M. & Leibold, M. A. Ecological Niches: linking classical and contemporary approaches. London, UK: The University of Chicago Press, 2003.
8/9/2011
Page 4 of 4
Chesson, P. Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics 31, 343366 (2000).
Erwin, T. L. & Scott, J. C. Seasonal and Size Patterns, Trophic Structure, and Richness of Coleoptera in the Tropical Arboreal Ecosystem: The Fauna of
the Tree Luehea seemannii Triana and Planch in the Canal Zone of Panama. The Coleopterists Bulletin 34, 305322 (1980).
Gause, G. F. The struggle for existence. New York, NY: Hafner Publishing Company, 1934.
Hubbell, S. P. The unified neutral theory of biodiversity and biogeography. Princeton, NJ: Princeton University Press, 2001.
Hutchinson, G. E. The paradox of the plankton. The American Naturalist 95, 137145 (1961).
Kornfield I. & Smith, P. F. African cichlid fishes: model systems for evolutionary biology. Annual Review of Ecology and Systematics 31, 163196
(2000).
Kraft, N. J. B., Valencia, R., & Ackerly, D. D. Functional traits and niche-based tree community assembly in an Amazonian forest. Science 322, 580582
(2008).
Levine, J. M. & HilleRisLambers, J. The importance of niches for the maintenance of species diversity. Nature 461, 254257 (2009).
McKane, R. B. et al. Resource-based niches provide a basis for plant species diversity and dominance in arctic tundra. Nature 415, 6871 (2002).
Millennium Ecosystem Assessment (2005).
Packer, A. & Clay, K. Soil pathogens and spatial patterns of seedling mortality in a temperature tree. Nature 404, 278281 (2000).
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By: Christine A. Andrews (Biological Sciences Collegiate Division, University of Chicago) 2010 Nature Education
Citation: Andrews, C. A. (2010) Natural Selection, Genetic Drift, and Gene Flow Do Not Act in Isolation in Natural
Populations. Nature Education Knowledge 1(10):5
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In natural populations, the mechanisms of evolution do not act in isolation. This is crucially
important to conservation geneticists, who grapple with the implications of these evolutionary
processes as they design reserves and model the population dynamics of threatened species
in fragmented habitats.

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Natural selection, genetic drift, and gene flow are the mechanisms that cause changes in allele frequencies over time. When one or more of these
forces are acting in a population, the population violates the Hardy-Weinberg assumptions, and evolution occurs. The Hardy-Weinberg Theorem thus
provides a null model for the study of evolution, and the focus of population genetics is to understand the consequences of violating these assumptions.
Natural selection occurs when individuals with certain genotypes are more likely than individuals with other genotypes to survive and reproduce, and
thus to pass on their alleles to the next generation. As Charles Darwin (1859) argued in On the Origin of Species, if the following conditions are met,
natural selection must occur:
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1. There is variation among individuals within a population in some trait.

2. This variation is heritable (i.e., there is a genetic basis to the variation, such that offspring tend to resemble their parents in this trait).
3. Variation in this trait is associated with variation in fitness (the average net reproduction of individuals with a given genotype relative to that
of individuals with other genotypes).
Directional selection leads to increase over time in the frequency of a favored allele. Consider three genotypes (AA, Aa and aa) that vary in fitness such
that AA individuals produce, on average, more offspring than individuals of the other genotypes. In this case, assuming that the selective regime
remains constant and that the action of selection is the only violation of Hardy-Weinberg assumptions, the A allele would become more common each
generation and would eventually become fixed in the population. The rate at which an advantageous allele approaches fixation depends in part on the
dominance relationships among alleles at the locus in question (Figure 1). The initial increase in frequency of a rare, advantageous, dominant allele is
more rapid than that of a rare, advantageous, recessive allele because rare alleles are found mostly in heterozygotes. A new recessive mutation
therefore can't be "seen" by natural selection until it reaches a high enough frequency (perhaps via the random effects of genetic drift see below) to
start appearing in homozygotes. A new dominant mutation, however, is immediately visible to natural selection because its effect on fitness is seen in
heterozygotes. Once an advantageous allele has reached a high frequency, deleterious alleles are necessarily rare and thus mostly present in
heterozygotes, such that the final approach to fixation is more rapid for an advantageous recessive than for an advantageous dominant allele. As a
consequence, natural selection is not as effective as one might naively expect it to be at eliminating deleterious recessive alleles from populations.
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Figure 1: Allele-frequency change under directional selection favoring (a) a dominant advantageous allele and (b)
a recessive advantageous allele
Balancing selection, in contrast to directional selection, maintains genetic polymorphism in populations. For example, if heterozygotes at a locus have
higher fitness than homozygotes (a scenario known as heterozygote advantage or overdominance), natural selection will maintain multiple alleles at
stable equilibrium frequencies. A stable polymorphism can also persist in a population if the fitness associated with a genotype decreases as that
genotype increases in frequency (i.e., if there is negative frequency-dependent selection). It is important to note that heterozygote disadvantage
(underdominance) and positive frequency-dependent selection can also act at a locus, but neither maintains multiple alleles in a population, and thus
neither is a form of balancing selection.
Genetic drift results from the sampling error inherent in the transmission of gametes by individuals in a finite population. The gamete pool of a
population in generation t is the total pool of eggs and sperm produced by the individuals in that generation. If the gamete pool were infinite in size, and
if there were no selection or mutation acting at a locus with two alleles (A and a), we would expect the proportion of gametes containing the A allele to
exactly equal the frequency of A, and the proportion of gametes containing a to equal the frequency of a. Compare this situation to tossing a fair coin. If
you were to toss a coin an infinite number of times, the proportion of heads would be 0.50, and the proportion of tails would be 0.50. If you toss a coin
only 10 times, however, you shouldn't be too surprised to get 7 heads and 3 tails. This deviation from the expected head and tail frequencies is due to
sampling error. The more times you toss the coin, the closer these frequencies should come to 0.50 because sampling error decreases as sample size
increases.
In a finite population, the adults in generation t will pass on a finite number of gametes to produce the offspring in generation t + 1. The allele
frequencies in this gamete pool will generally deviate from the population frequencies in generation t because of sampling error (again, assuming there
is no selection at the locus). Allele frequencies will thus change over time in this population due to chance events that is, the population will undergo
genetic drift. The smaller the population size (N), the more important the effect of genetic drift. In practice, when modeling the effects of drift, we must
consider effective population size (Ne), which is essentially the number of breeding individuals, and may differ from the census size, N, under various
scenarios, including unequal sex ratio, certain mating structures, and temporal fluctuations in population size.
At a locus with multiple neutral alleles (alleles that are identical in their effects on fitness), genetic drift leads to fixation of one of the alleles in a
population and thus to the loss of other alleles, such that heterozygosity in the population decays to zero. At any given time, the probability that one of
these neutral alleles will eventually be fixed equals that allele's frequency in the population. We can think about this issue in terms of multiple replicate
populations, each of which represents a deme (subpopulation) within a metapopulation (collection of demes). Given 10 finite demes of equal Ne, each
with a starting frequency of the A allele of 0.5, we would expect eventual fixation of A in 5 demes, and eventual loss of A in 5 demes. Our observations
are likely to deviate from those expectations to some extent because we are considering a finite number of demes (Figure 2). Genetic drift thus removes
genetic variation within demes but leads to differentiation among demes, completely through random changes in allele frequencies.
Figure 2: Simulations of allele-frequency change in 10 replicate populations (N = 20)
Since the initial frequency of the A allele = 0.5, we expect A to be fixed in 5 populations and lost in 5 populations, but our
observations deviate from expectations because of the finite number of populations. In this run of simulations, we see 7
instances of fixation (p = 1), 2 instances of loss (p = 0), and one instance in which there are still two alleles after 100
generations. In this last population, A would eventually reach fixation or loss.
Gene flow is the movement of genes into or out of a population. Such movement may be due to migration of individual organisms that reproduce in their
new populations, or to the movement of gametes (e.g., as a consequence of pollen transfer among plants). In the absence of natural selection and
genetic drift, gene flow leads to genetic homogeneity among demes within a metapopulation, such that, for a given locus, allele frequencies will reach
equilibrium values equal to the average frequencies across the metapopulation. In contrast, restricted gene flow promotes population divergence via
selection and drift, which, if persistent, can lead to speciation.
Natural selection, genetic drift and gene flow do not act in isolation, so we must consider how the interplay among these mechanisms influences
evolutionary trajectories in natural populations. This issue is crucially important to conservation geneticists, who grapple with the implications of these
evolutionary processes as they design reserves and model the population dynamics of threatened species in fragmented habitats. All real populations
are finite, and thus subject to the effects of genetic drift. In an infinite population, we expect directional selection to eventually fix an advantageous allele,
but this will not necessarily happen in a finite population, because the effects of drift can overcome the effects of selection if selection is weak and/or the
population is small. Loss of genetic variation due to drift is of particular concern in small, threatened populations, in which fixation of deleterious alleles
can reduce population viability and raise the risk of extinction. Even if conservation efforts boost population growth, low heterozygosity is likely to
persist, since bottlenecks (periods of reduced population size) have a more pronounced influence on Ne than periods of larger population size.
We have already seen that genetic drift leads to differentiation among demes within a metapopulation. If we assume a simple model in which individuals
have equal probabilities of dispersing among all demes (each of effective size Ne) within a metapopulation, then the migration rate (m) is the fraction of
gene copies within a deme introduced via immigration per generation. According to a commonly used approximation, the introduction of only one
migrant per generation (Nem = 1) constitutes sufficient gene flow to counteract the diversifying effects of genetic drift in a metapopulation.
Natural selection can produce genetic variation among demes within a metapopulation if different selective pressures prevail in different demes. If Ne is
large enough to discount the effects of genetic drift, then we expect directional selection to fix the favored allele within a given focal deme. However, the
continual introduction, via gene flow, of alleles that are advantageous in other demes but deleterious in the focal deme, can counteract the effects of
selection. In this scenario, the deleterious allele will remain at an intermediate equilibrium frequency that reflects the balance between gene flow and
natural selection.
Conclusion
The common conception of evolution focuses on change due to natural selection. Natural selection is certainly an important mechanism of allelefrequency change, and it is the only mechanism that generates adaptation of organisms to their environments. Other mechanisms, however, can also
change allele frequencies, often in ways that oppose the influence of selection. A nuanced understanding of evolution demands that we consider such
mechanisms as genetic drift and gene flow, and that we recognize the error in assuming that selection will always drive populations toward the most
well adapted state.

Carroll, S. P. & Fox, C. W., eds. Conservation Biology: Evolution in Action. New York, NY: Oxford University Press, 2008.
Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London, England:
John Murray, 1859.
Futuyma, D. J. Evolutionary Biology, 3rd ed. Sunderland, MA: Sinauer Associates, 1998.
Gillespie, J. H. Population Genetics: A Concise Guide, 2nd ed. Baltimore, MD: The Johns Hopkins University Press, 2004.
Haldane, J. B. S. A mathematical theory of natural and artificial selection, Part I. Transactions of the Cambridge Philosophical Society 23, 1941 (1924).
Hedrick, P. W. Genetics of Populations, 3rd ed. Sudbury, MA: Sinauer & Associates, 2005.
Wright, S. Evolution: Selected Papers. Chicago, IL: University of Chicago Press, 1986.
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By: W. Stanley Harpole (Department of Ecology, Evolution, and Organismal Biology, Iowa State University) 2010 Nature Education
Citation: Harpole, W. (2010) Neutral Theory of Species Diversity. Nature Education Knowledge 1(8):31
No need for niches? Neutral theory explains biodiversity when species are identical.
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Niche differences, or the unique ways that each species

makes its living in nature, are the classical explanation
that ecologists have used since Darwin to explain the
amazing diversity of life on Earth. More precisely, a
species niche encompasses all of the factors it requires for
growth and reproduction and how a species impacts its
environment. For example, plants require water and
nutrients at some minimum amounts, and by growing,
plants decrease the availability of those resources, which
negatively affects the growth of competitors. Because
many factors limit organisms, and because no organism is
best adapted for all conditions, species have tradeoffs,
which allow them to perform better in some environments,
but necessarily worse in others. Niche differences are a
mechanism that can maintain biodiversity by allowing
species to coexist. But what might ecological communities
look like if there were no niche differences between
species?
Building on foundational ideas described in island
Figure 1: Neutral and niche
biogeography and the neutral theory of molecular
(A) Very similar herbivores might be considered to be equivalent and essentially
evolution, the neutral theory of species diversity makes the
neutral. (B) Herbivores that eat different plants, or even the same plants but at
provocative assumption that all individuals are ecologically
different times or at different heights, would have different or overlapping niches. In
identical, and that niche differences are not needed to
contrast, neutral theory suggests that even species that look very different from each
explain biodiversity patterns. Individuals of certain species
other might be considered to be ecologically equivalent. (C-E) Species have greatest
may all share characteristics that make them look or
fitness at some point along an environmental gradient or niche axis. Neutral species
function different from other species, but those differences
have completely overlapping niches; they share the same niche and their fitness
do not influence diversity. An individual in a community
changes identically along an environmental gradient or niche axis. Greater niche
interacts with and experiences its neighbors as though they
differences correspond to less niche overlap between species; species differ in their
were exactly the same, regardless of species. This
fitness at different points along an environmental gradient or niche axis.
assumption of equivalence is the essential feature of
neutrality, which differs from typical niche-based
assumptions that an individuals fitness depends on who its
neighbors are: are they stronger or weaker competitors or do they belong to different species with different niche requirements (Figure 1)? Neutral
theory predicts that species have perfectly overlapping niches at the other extreme would be species with unique, non-overlapping niches. Real
communities, of course, likely represent neither of these extremes but are somewhere in the middle (Figure 1). What neutral theory forces us to ask is
how ecologically different are species, and how important are those differences for determining biodiversity?
How Neutral Theory Works

Under the neutral theory, highly diverse communities of equivalent species arise because chance extinctions are balanced by speciation. Specifically,
the assumption of fitness equivalence combined with stochastic or random processes that include death, immigration from a regional pool of species,
and speciation can lead to species-rich communities (Figure 2). As an example, imagine a field, which will be the local community, made up of many
species of plants. Plants in the surroundings will represent the regional species pool. The field is thus part of a larger collection of plant communities
called a meta-community. Individuals in the local community die at random and create openings for seeds to grow. Individuals from the metacommunity, and from the local community, randomly disperse their seeds into the field (Figure 2). If there are more individuals of some species than
others they will contribute more seeds than will rare species, but each individual seed has an equal chance of establishing. Individuals are in that sense
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competing for open sites. If dispersal from the meta-community is strong, the local community will look like a small version of the region; if dispersal
from outside is weak, random deaths and extinctions combined with random mutations and speciation will cause the local community to drift and differ
more and more from other communities over time, but in an unpredictable way. This random change in species abundance over time is termed
ecological drift. There can be a limit to the number of individuals in the local community this is known as a zero sum assumption: if the community is
full, a new individual can only establish if another one dies and makes space (Figure 2).
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Figure 2: Modeling a neutral process

A local community (a) represents a subset of all of the species found in the region or meta-community. Some
individuals die at random in a local community (16 identical individuals from 6 species, in this example), which
creates open sites (b). Open sites are then filled by random dispersal from both the meta-community and from
the local community (c), including the addition of a new species from the meta-community. Random mutation
(not shown) can also lead to the formation of new species. The sequence repeats leading to ecological drift
where species abundances change randomly over time.
What Neutral Theory Is; What It Isnt

Random death, dispersal and speciation are all important features of the neutral theory of biodiversity, but its one key, essential feature is the
assumption of identical individuals (species may have differences, but those differences do not matter because all individuals have the same fitness and
experience each other identically). The other features are assumptions about the processes that determine community assembly, or how species are
added to and lost from communities, and how communities change over time their dynamics. Another aspect of neutral theory is that it only applies to
groups of similarly functioning species: trees in a forest or corals in a reef, and not to species of different size or trophic position, like microbes and
elephants, or plants and herbivores. Also, there is no single neutral theory model, and different neutral models make different assumptions about these
other processes. For example, one could imagine a neutral community made up of identical individuals of multiple species without immigration.
Neutral models dont need to follow the zero sum assumption: a local community could remain partly empty, or alternatively the numbers of individuals
might be allowed increase in a model continuously. Stochastic processes are important in neutral models for communities to change over time, but
some parameters might be random while others might be non-random: annual plants always die at the end of the year. Niche models, where individuals
of different species do differ from each other and those differences matter for their fitness, can also be stochastic, and some purely deterministic or truly
non-random processes can also be unpredictable (see chaos theory) and only apparently random. Stochasticity or randomness is often just a
simplification we make when we cant predict exactly the outcome of an event: assuming something is random allows us to conveniently describe a
process in terms of probability or chance.
Although dispersal, stochasticity and speciation are not unique to the neutral theory, neutral models are more interesting and useful when we add in
things like dispersal and stochasticity. For this reason, neutral theory is often described as a dispersal-assembly theory or a stochastic theory, even
though neither dispersal nor stochasticity is a feature uniquely or necessarily neutral. Dispersal and reproductive traits are in fact another way that
species can differ in their fitness, and how organisms move through space can be an important component of a species niche. Consider the enormous
variety shown by flowering plants in their fruits (coconuts to dandelion seeds) and the diverse ways plants can disperse by wind, water or animals, as
well as their different mating strategies, germination and pollination mechanisms. Dispersal may often be highly unpredictable, but it is not necessarily
neutral.
Dispersal and speciation processes in neutral models can lead to highly diverse communities. But the coexistence of species in neutral communities is
unstable there are no mechanisms that cause one species to remain dominant or prevent rare species from going extinct. Because neutral processes
are driven by random events, and because all individuals are competitively identical, their abundances either increase or decrease purely by chance. In
a closed system, stable coexistence, or long-term persisting species, can only occur when there are niche differences that cause individuals to compete
most strongly with individuals of their own species compared to those of other species. Niche-based stabilizing mechanisms limit the growth of species
when they become very abundant, while at the same time stabilizing mechanisms allow rare species to increase because they enjoy higher fitness
when surrounded by neighbors of different species with whom they compete less strongly.
Pattern versus Process

Neutral models can predict realistic species diversity patterns from just a few parameters. One parameter is the Fundamental Biodiversity Number,
which is larger with greater numbers of individuals in the meta-community and with greater speciation rates. With the fundamental biodiversity number
and estimates of dispersal, neutral models can predict the number of species and their relative abundance patterns in different systems. For example,
when we plot the rank of a species against its abundance in a community, we usually find just a few super-abundant species (high rank) along with
many very rare species (low rank) (Figure 3). These species abundance distributions are one type of pattern that neutral models have been very good
at predicting. But it turns out that many types of alternative niche models do so just as well, which makes these pattern-matching approaches a fairly
Page 3 of 4
weak test: showing a pattern doesnt necessarily tell you

the process responsible. Where neutral models have
consistently failed is in stronger tests, such as predicting
which species or traits of species should be abundant, or
under what environmental conditions some species
increase while others decrease.
Figure 3: Species abundance patterns

(A) The individuals from the example in Figure 2c are ranked 1 through 7, from most
to least abundant species. (B) An example of a simulated community of 100 species
showing a characteristic pattern of species rank abundance.
The Utility of Neutral Theory

Neutral theory is still a powerful and useful concept for several reasons. Stephen Hubbells 2001 monograph, The Unified Neutral Theory of Biodiversity
and Biogeography, has sparked vigorous debate among ecologists, and has led to more rigorous, and much needed, tests of niche mechanisms and
explanations of biodiversity. Ironically, neutral theory has reinvigorated niche theory. As with all models, the neutral model is a simplification, albeit a
drastic one, of processes we think important in the natural world (e.g., competition, dispersal). Thus, the strength of the neutral model is that it provides
us with a logical place to start: an elegant and simple null model, with clear and testable assumptions and predictions. We can then ask if other
mechanisms, and their added complexity, are necessary to explain what we observe.
Summary
The neutral theory of species diversity starts with the key assumption that all individuals in a community of trophically similar species are ecologically
identical. Neutral models that additionally include random death, speciation, extinction, and dispersal from the meta-community can lead to highly
diverse communities that have similar species abundance patterns to what we observe in real communities. The abundances of species in neutral
models fluctuate randomly over time leading to ecological drift, where diversity is due to unstable coexistence and the balance between extinction and
speciation, in contrast to niche models that assume the importance of species niche differences and stabilizing mechanisms. Neutral theory provides a
null model, or a starting point, from which we can test niche-based hypotheses for how species evolutionary adaptations and niches maintain
biodiversity.

Adler, P. B., HilleRisLambers, J. et al. A niche for neutrality. Ecology Letters 10, 95-104 (2007).
Alonso, D., Etienne, R. S. et al. The merits of neutral theory. Trends in Ecology and Evolution 21, 451-457 (2006).
Bell, G. Neutral macroecology. Science 293, 2413-2418 (2001).
Chase, J. M. & Leibold, M. A. Ecological Niches: Linking Classical and Contemporary Approaches. Chicago, IL: University of Chicago Press, 2003.
Hubbell, S. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press, 2001.
McGill, B. J. A test of the unified neutral theory of biodiversity. Nature 422, 881-885 (2003).
McGill, B. J., Maurer, B. A. et al. Empirical evaluation of neutral theory. Ecology 87, 1411-1423 (2006).
Silvertown, J. Plant coexistence and the niche. Trends in Ecology and Evolution 19, 605-611 (2004).
Tilman, D. Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly.
Proceedings of the National Academy of Sciences, USA. 101, 10854-10861 (2004).
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Population Genomics
By: Patrick Nosil (EBIO, University of Colorado at Boulder) & Alex Buerkle (Department of Botany, University of Wyoming) 2010 Nature
Education
Citation: Nosil, P. & Buerkle, A. (2010) Population Genomics. Nature Education Knowledge 1(11):8
How do evolutionary processes affect the genome? The field of population genomics surveys
patterns in the genome within and among populations to make inferences about evolution and
the genome.

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Variation in Population Divergence Among Genomic Regions

Independent evolution of populations leads to their genetic divergence. Different regions of the genome are expected to exhibit highly variable levels of
genetic divergence (reviewed by Nosil et al. 2009), ranging from genomic regions exhibiting little to no differentiation between populations to regions
where genetic divergence is extremely pronounced (Figure 1). This pattern of variation in population divergence across regions of the genome has been
referred to as heterogeneous genomic divergence (Nosil et al. 2009). Genomic divergence is expected to be highly heterogeneous during the process of
population divergence and species formation, during which genetic differentiation associated with divergent natural selection accumulates in some
regions while the homogenizing effects of gene flow or inadequate time for random differentiation by genetic drift preclude divergence in other regions.
Many factors contribute to heterogeneous genomic divergence, including selection arising from ecological causes or genetic conflict, the stochastic
effects of genetic drift, variable mutation rates, the genetic basis of traits under selection, and genetic linkage among genes on chromosomes. The
patterns of genomic differentiation among populations record and integrate across these different historical evolutionary and genetic processes, thereby
offering biologists opportunities to reconstruct the forces that shaped evolutionary divergence.
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Figure 1: Three arbitrary classes of loci embedded within a continuous distribution of FST values
(A) Selected loci, or those very tightly linked to them, exhibit particularly high FST and thus are recognized as unlikely,
statistical outliers. (B) Neutral loci that are weakly-linked to selected loci exhibit FST values that are somewhat elevated,
but insufficiently so to be designated outlier loci. (C) Neutral unlinked loci exhibit low FST.
2010 Nature Education Modified from Egan et al. (2008) and reprinted with permission of Wiley-Blackwell. All
rights reserved.
We focus here on the contributions of divergent natural selection to population divergence. Such divergent selection will pull apart allele frequencies
between populations at loci under selection and those physically-linked to them, resulting in strong differentiation of regions affected by selection. This
might occur even if the remainder of the genome remains relatively undifferentiated. Thus, loci under divergent selection and those tightly physicallylinked to them should exhibit greater differentiation than weakly-linked or unlinked neutral regions. If only a subset of loci experiences divergent
selection, the selected loci can be recognized as exceptional relative to the remainder of the genome and as outlier loci whose genetic divergence
exceeds neutral expectations (Figure 2).
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Figure 2: Heterogeneous genomic divergence in a genome scan of a pair of Neochlamisus bebbianae leaf beetle
populations
Simulations determine the upper level of genetic divergence expected under neutral divergence due to genetic drift in the
pair of populations, and loci that exceed this neutrality threshold (solid line, in this case 95% quantile) are recognized as
outlier loci that are likely to have evolved under divergent selection.
2010 Nature Education Modified from Egan et al. (2008) and reprinted with permission of Wiley-Blackwell. All
rights reserved.
The field of population genomics examines patterns in the genome, often using genome scans that examine genetic divergence between populations at
numerous loci across the genome. The degree of genetic divergence is often measured using fixation indices such as FST, with larger index values
representing greater differentiation between populations.
A Brief History of Population Genomics

Population genomic analyses require multi-locus data sets from multiple populations and identify non-neutral or outlier loci by contrasting patterns of
population divergence among genetic regions. This approach was first proposed by Lewontin & Krakauer (1973), and numerous variations on this
original method now exist (Beaumont 2005, Foll & Gaggiotti 2008, Gompert et al. [in review]). Perhaps the most commonly employed of these methods,
particularly in non-model organisms, is the FST outlier analysis developed by Beaumont & Nichols (1996). This test contrasts FST for individual loci with
an expected null distribution of FST based on a neutral model. Under this approach, loci with very high levels of differentiation between populations (i.e.,
high FST) are considered candidates for positive or divergent selection whereas loci with exceptionally low FST are regarded as candidates for balancing
selection. However, many FST outlier analyses may be biased by departures from the assumed demographic history (Excoffier et al. 2009). An
alternative approach to obtain a null distribution of population genetic differentiation is to assume that FST for individual loci represent independent draws
from a common, underlying distribution that characterizes the neutral divergence across the genome and can be estimated directly from multi-locus data
(Foll & Gaggiotti 2008; Figure 3). This alternative approach is more robust to different demographic histories. Recent advances in computational
methods and molecular biology (including next-generation sequencing) allow patterns of genomic divergence to be investigated at previously
unattainable scales. We now turn to describing in some more detail three case studies of population genomic analyses.
Figure 3: Statistics of population differentiation can be estimated by Bayesian methods, which provide a
probabilistic framework in which to interpret differentiation of individual loci.
Differentiation among populations of Lycaeides butterflies in North America was estimated (Gompert et al. 2010) and
summarized in a genome-level estimate of ST (a) and its average deviation (b). This analysis illustrated the high variation
among loci across the genome (c, arbitrary set of 200 scored loci), some of which is likely to have been shaped by
divergent natural selection.
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Case Studies
Population Genomic Evidence for Recent and Rapid Evolutionary Adaptation in Humans
As humans expanded into new geographic regions and came to occupy novel environments, our ancestors experienced diverse patterns of natural
selection that were recorded in the genomes of divergent populations. For example, humans moved from low elevations to occupy some of the highest
plateaus and mountain ranges in the world, including the plateaus of Central Asia and the Andes of South America. These populations exhibit heritable
physiological attributes that allow individuals to function at high altitudes (32504500 m) with low oxygen concentrations that are challenging to humans
from lower elevations. Interestingly, humans from the Tibetan plateau exhibit several physiological attributes that differ from those of Andean
highlanders, suggesting that independent evolutionary trajectories led to different adaptations to high altitude. Three studies have used genome scans
to identify genes with exceptional allele frequency shifts between populations that were likely targets of divergent natural selection in Tibetan
highlanders relative to other human populations (reviewed in Storz 2010). Several genes were identified as associated with a history of positive
selection in Tibetan highlanders; the gene EPAS1 was identified as one of the most exceptional genes in each study and was also shown to be
associated with presumably adaptive variation in hemoglobin concentration.
A second example of adaptive divergence among human populations is related to the persistence of lactase production in adults. Lactase production in
the gut functions in the digestion of the milk sugar lactose, and lactase production in adults is prevalent in humans with ancestry in northern and western
Europe and pastoralist populations in several regions of the world. Adult persistence of lactase is much less common in southern Europe and the Middle
East and rare in non-pastoralist populations in Asia and Africa. Genetic studies have associated adult persistence of lactase with different genes in
different populations that exhibit the trait at high frequency, indicating that the trait has arisen independently in multiple populations (Tishkoff et al. 2007).
Remarkably, genomic variation surrounding each of the underlying genes is consistent with strong natural selection within the last several thousand
years increasing the frequency of the derived, adaptive alleles (Tishkoff et al. 2007).
Genomic Islands in Anopheles Mosquitoes

To help understand regions of divergence in the genome, evolutionary biologists have developed the concept of "genomic islands of
divergence" (Turner et al. 2005; Figure 4). A genomic island is any gene region, be it a single nucleotide or an entire chromosome, that exhibits
significantly greater differentiation than expected under neutrality (and thus generally greater divergence than observed in neighboring genomic
regions). The metaphor, therefore, draws a parallel between genetic differentiation observed along a chromosome and the topography of oceanic
islands and the contiguous sea floor to which they are connected. Following this metaphor, sea level represents the threshold above which observed
differentiation is significantly greater than expected by neutral evolution alone. Thus, an island is composed of both directly selected and tightly linked
(potentially neutral) loci.
Figure 4: An empirical example of genomic islands of divergence involving incipient species of Anopheles
gambiae
The bottom two panels depict patterns of differentiation across chromosome two (Turner et al. 2005). Grey areas were
identified as highly differentiated in sliding window analyses, with differentiation further confirmed by sequencing loci
within these regions (red circles). A large island of exceptionally high differentiation is evident on the left arm, near the
centromere. A small island is also evident on the right arm. The top panel depicts a subsequent study (Turner & Hahn
2007) where portions of all annotated genes within the smaller island were sequenced.
2010 Nature Education Modified from the original studies and reprinted with permission of the Public Library of
Science and the Society of Molecular Biology and Evolution. All rights reserved.
Figure 4 depicts an empirical example of a genomic island from population genomic studies of different forms of Anopheles gambiae mosquitoes. These
insects are vectors for malaria, and Turner et al. (2005) surveyed divergence across the genome of the different mosquito forms. They found just a few
regions that were differentiated (i.e., a few isolated genomic islands) between the forms. In a follow-up study, Turner & Hahn (2007) sequenced portions
of all annotated genes within one of the islands. As expected, sequence differentiation peaked within the "island" but the fine-scale data allowed more
detailed characterization of the nature of the island, showing, for example, that differentiation drops off rapidly with distance from the region of maximum
differentiation.
Other Applications of Population Genomics

In addition to genome scans for differentiation, population genomics also includes many other diverse analyses of population genomic variation. These
include research that more directly ties or genetically maps variation in phenotypes (e.g., body size, bill length, feather color, mating behavior) to genetic
variation in various organisms. Similarly, researchers use other signatures of natural selection (e.g., extended haplotype blocks) to detect genomic
regions that are likely to have experienced selection. As technology has allowed the rate of genomic data acquisition to increase enormously, an
increasing range of biological questions can now be addressed at the scale of the genome rather than focusing on very small fractions of genomic
variance.
8/9/2011
Page 4 of 5
Caveats
Genome scans of differentiation, by virtue of detecting divergent selection via looking for the most differentiated regions, are inevitably destined to
underestimate how widespread the effects of selection are in the genome. In other words, genome scans will often fail to identify regions that are
affected by divergent selection but only weakly so. A recent analysis of divergent selection in two host forms of Rhagoletis flies exemplifies this issue
(Michel et al. 2010). This study reported that standard outlier analyses detected evidence for selection on only a few exceptionally differentiated
genomic regions. In contrast, results from an experiment where the fly's genome was directly subjected to divergent selection revealed that selection
was affecting much of the genome, albeit often quite weakly. The prevalence of selection may also be underestimated because most analytical methods
are unlikely to detect soft sweeps involving smaller shifts in the allele frequency spectrum of multiple loci and are dependent on the genetic architecture
of adaptation.
Conclusions and Future Directions

Population genomics holds great promise for understanding the evolutionary processes affecting genomes. However, population genomics is not a
panacea, and analyses must increasingly be conducted with care. For example, the stochastic nature of next-generation sequencing technologies
creates uneven coverage among individuals and genetic regions, which misses data for many individuals and loci, and thus increased uncertainty in the
genotypes of individuals relative to traditional Sanger sequencing. Appropriately modeling and accounting for this uncertainty is important and preferable
to discarding large amounts of sequence data (Gompert et al. 2010). Further advances in molecular and computational biology and increased
computing power itself will allow more powerful and accurate application of population genomics.

Beaumont, M. A. Adaptation and speciation: what can F-st tell us? Trends in Ecology and Evolution 20, 435440 (2005).
Beaumont, M. A. & Nichols, R. A. Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London B
263, 16191626 (1996).
Egan, S. P. et al. Selection and genomic differentiation during ecological speciation: isolating the contributions of host-association via a comparative
genome scan of Neochlamisus bebbianae leaf beetles. Evolution 62, 11621181(2008).
Excoffier, L. et al. Detecting loci under selection in a hierarchically structured population. Heredity 103, 285298 (2009).
Foll, M. & Gaggiotti, O. A genome scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective.
Genetics 180, 977993 (2008).
Gompert, Z. et al. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides
butterflies. Molecular Ecology 19, 24552473 (2010).
Gompert Z. & Buerkle C. A. Analytical tools for next-generation sequence data. In review.
Lewontin, R. C. & Krakauer, J. Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74, 175195
(1973).
Michel, A. P. et al. Widespread genomic divergence during sympatric speciation. Proceedings of the National Academy of Sciences USA 107, 9724
9729 (2010).
Nosil, P. et al. Divergent selection and heterogeneous genomic divergence. Molecular Ecology 18, 375402 (2009).
Storz, J. F. Genes for high altitudes. Science 329, 4041 (2010).
Tishkoff, S. A. et al. Convergent adaptation of human lactase persistence in Africa and in Europe. Nature Genetics 39, 3140 (2007).
Turner, T. L., & Hahn, M. W. Locus- and population specific selection and differentiation between incipient species of Anopholes gambiae. Molecular
Biology and Evolution 24, 21322138 (2007).
Turner, T. L. et al. Genomic islands of speciation in Anopheles gambiae. Public Library of Science Biology 3, 15721578 (2005).
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By: Truman P. Young (Department of Plant Sciences, University of California at Davis) 2010 Nature Education
Citation: Young, T. P. (2010) Semelparity and Iteroparity. Nature Education Knowledge 1(9):2
Why do some organisms die immediately after reproducing (some salmon and bamboos,
many insects, and all grain crops), while others live on to reproduce repeatedly (most plants
and vertebrates)?

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Semelparity
Many plant and animal species have life histories characterized by death after
first reproduction. This is called semelparity, and its alternative (living to
reproduce repeatedly) is called iteroparity. In plants, the terms monocarpy
and polycarpy are sometimes used instead of semelparity and iteroparity.
However, monocarpy can also be used more restrictively to describe plants in
which individual shoots die after reproducing, but not necessarily the entire
plant.
Examples of short-lived semelparous species include annual and biennial
plants (including all grain crops, and many herbaceous vegetables), and
certain invertebrate species, including many spiders (Figure 1). There are
even a few semelparous marsupial mammals in Australia. It is important to
note that while all annual plants are semelparous, not all perennial plants are
iteroparous. There are a wide variety of plant and animal species that live for
many years before a single, massive, fatal reproductive episode (certain
species of salmon, bamboo, and century plants, Figure 2).
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Semelparity has evolved independently many times, apparently as a derived

state from iteroparous ancestors. This dramatic life history difference offers a
model system for theoretical and empirical studies of adaptive evolution.
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Figure 1: Semelparous plants

Like all grain crops, wheat is semelparous plant. Annual plants die
after first reproduction within a year of germination. (Courtesy of
Simon Howell: freedigitalphotos.net)
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Dilemma and Cost of Reproduction

Natural selection maximizes total lifetime reproductive output. So how could evolution ever favor programmed death after first reproduction? A key clue
lies in the observation that semelparous species typically produce more offspring in their single reproductive episode than closely related species do in
any one of theirs. It appears that when an organism does not need to withhold some resources to ensure future survival and reproduction, it can
mobilize virtually all available resources to put into a single, massive reproductive episode. For example, this fecundity advantage is two to fivefold in
plants. So the essential question becomes, "Under what conditions does the increase in fecundity associated with semelparity more than compensate
for the loss of potential subsequent reproductive episodes?"
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Figure 2: Spawning salmon

Salmon at their spawning grounds, far from the ocean. Here, they will reproduce and die. (Courtesy of Friends
of Butte Creek)
Theoretical Approaches
This question has been the subject of a rich theoretical literature. These models fall into three classes, all of which assume a tradeoff between
reproduction and survival:
1. Demographic models predict that when adult survival is low enough (relative to juvenile survival), evolution should abandon withholding
resources for a future reproduction that is unlikely, and instead favor semelparity (Figure3).
2. Bet-hedging models predict that when adult survival is highly variable, evolution should favor iteroparity, because it does not risk putting all
reproductive effort into a single reproductive episode.
3. Models incorporating non-linear patterns of reproductive costs and benefits predict that semelparity should be more likely to evolve when
most of the costs of reproduction (reduction in future survival or reproduction caused by increases in current reproduction) happen even at
low levels of reproductive effort, or conversely, when the benefits of reproduction accrue most rapidly at high levels of reproductive effort.
8/9/2011
Page 3 of 4
Figure 3: Schematic of the demographic model of the evolution of semelparity

Imagine semelparous and iteroparous populations. The semelparous (annual) individuals produce 2.5 times as
many seeds as the iteroparous individuals (a reasonable estimate of relative fecundity, from natural systems).
In the first year, the semelparous individuals out-produce the iteroparous, but the iteroparous have some
probability of living to reproduce again. If the iteroparous population experiences 50% adult mortality each year,
the average individual will produce 200 seeds in its lifetime, fewer than in the semelparous population. If the
iteroparous population experiences 30% adult mortality each year, the average individual will produce 340
seeds in its lifetime, more than in the semelparous population. Therefore, in populations with sufficiently high
mortality, semelparity will be favored over iteroparity. Demographic models of semelparity explore this more
explicitly.
Empirical Evidence
Despite the abundance of theoretical models for the evolution of semelparity, direct empirical tests for each remain limited. For example, many species
of annual plants are desert species or weedy species that are early arrivals after disturbance in many ecosystems. Both of these groups are subject to
high variation in survivorship, in opposition to the predictions of the bet-hedging model.
In a particularly elegant test of the non-linearity model, it was demonstrated that the taller inflorescences of semelparous yucca species produced
disproportionately more seeds than smaller inflorescences, but that this was not true in iteroparous yucca species. Similarly, pollinators preferred taller
inflorescences of semelparous yucca species, but not iteroparous species. Although this observation fits the non-linear theory nicely, it has been pointed
out that many of these species may not be pollinator-limited, and that inflorescence height patterns may be physiological consequences of life history
differences, and not their evolutionary causes.
There have been several more successful tests of the demographic model, and they all show that semelparity is more likely in species (or populations)
where adult survival would be low even if they were not semelparous. These tests come from diverse systems, including spiders, fish, an alpine
mustard, and a giant rosette plant. In addition, both desert annuals and early successional annuals live in habitats where survival beyond the growing
season might be expected to be low.
Synchronous Semelparity
There is an unusual pattern in semelparous plants characterized by single-aged populations that live for many years, then synchronously flower and die.
Certain bamboos species are well known to exhibit this pattern, but other examples include certain palm species, shrubs in the family Acanthaceae, and
even a tropical forest canopy tree. All of these grow in mesic forests that are climatically more moderate than the extreme environments characteristic of
most semelparous species (e.g., deserts, alpine habitats, bogs, disturbed sites). Periodic cicadas in the eastern U.S. also exhibit this pattern. Predator
satiation has been invoked to explain both synchrony and semelparity in these species, but there is no widespread consensus on its causes.
Species "Approaching" Semelparity

Semelparity and iteroparity have been represented here as a simple dichotomy. Nevertheless, the conceptual framework can be applied more generally.
Several examples have been documented where high levels of adult mortality appear to be related to iteroparous life histories characterized by early
reproduction that is more frequent and/or more intense. These include subalpine fir trees, patas monkeys, and several insect species.
Semelparity in Grain Crops

It is probably no coincidence that many herbaceous crops, including virtually all grain crops, are annuals. Their semelparity results in far higher yields
than if they were iteroparous. It is likely that when selecting grain species for cultivation, early farmers deliberately chose those species with the highest
yields, which were annuals, or selected strongly enough for high yields that iteroparous species evolved into semelparous species. The closest relatives
of both rice and maize are iteroparous.
Given our dependence on semelparous species, it is important that we better understand the evolution and physiology of this curious life history.

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