Mechanisms of Evolution

Chapter 22: Descent with

Modification

Evolution
= change over time
= descent with modification (=Darwins definition)
= the changes in a populations genetic composition over time

Important People to Know:

Aristotle: proposed that all living things could be arranged in a system of
plants (herbs, tree, shrub) and animals (water, land, air)and each group of
organisms was permanent and perfect
Carolus Linnaeus: father of taxonomy (=the science of classification)
who developed a binomial system for naming organisms according to their
genus and species
James Hutton: father of modern geology who proposed that immense
changes in Earths geology are the cumulative result of slow but continuous
processes
Georges Curier: developed paleontology, the study of fossils. Fossils
are remnants or traces of past organisms, usually found in sedimentary rocks
formed through the compression of layers of sand and mud into
superimposed layers called strata. He advocated catastrophism, the idea
that the extinctions and differences in the fossils found in different strata are
the result of local sudden catastrophic events and not indicative of evolution.
Charles Lyell: developed a theory of uniformitarianism, stating that the
rates of geological processes have remained the same through Earths history
and continue in the present
Jean Baptist Lamarck: Lamarcks hypothesis explained the mechanism of
evolution with 2 principles: the use and disuse of body parts leading to their
development or deterioration, and the inheritance of acquired characteristics.
- Although present genetic knowledge rejects his mechanism, Lamarck
proposed several key evolutionary ideas: that evolution is the best
explanation for the fossil record and that adaptation to the environment is
the main result of evolution.
Thomas Malthus: organisms can overproduce and outgrow the food
supply

Alfred Russel Wallace

Darwin took 2 ideas from the observations of Hutton and Lyell: Earth must be
very old, and very slow processes can produce substantial change, perhaps even
in living species

Darwins Research

Darwin sailed on the HMS Beagle and went on a voyage collecting thousands
of specimens of South America, observing the various adaptations of

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organisms living in very diverse habitats, and making special note of the
geographic distribution of the distinctly South American species
Adaptations are characteristics that help organisms survive and reproduce
in specific environments
Darwin proposed that adaptations arise through natural selection, a
process in which individuals with beneficial inherited traits produce more than
offspring without those traits.

The Origin of Species

Darwin published his book On the Origin of Species by Means of Natural

Selection
His book developed 2 main points:
1) Descent with modification as the basis of lifes unity and

diversity
-

All organisms are related through descent from some unknown

ancestor and develop increasing modifications as they adapt to
various habitats
The history of life is like a tree, with a common ancestor at the fork of
each new branch, and present day species at the tips of the latest
branches
-Darwin figured out the idea of this branching idea of life from
looking at the taxonomy developed by Linnaeus provided a
hierarchical organization

2) Natural selection as the mechanism that matches organisms

with their environment

-

Using the example of artificial selection in the breeding of

domesticated plants and animals, Darwin found evidence that
selection in a population can lead to substantial evolutionary change
Darwin studied Malthus and found support for the capacity of
organisms to overproduce
Natural selection results in the evolution of populations, not
individuals.
Natural selection affects only those traits that are heritable acquired
traits cannot evolve.
Natural selection depends on the specific environment factors
present in a region at a given time. If the environment changes,
different adaptations will be favored.

Scientific Support for Evolution

Direct Observations of Evolutionary Change

J. Endler observed variations in the color patterns of male guppies that

correlate with the intensity of predation- the more predators, the less
brightly colored fish.

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He transported guppies from pools with active predators to pools with less
active predators and observed an increase in the number of size and
colored spots (in 15 generations)
This is an example of evolution in a natural setting over a relatively
short period of time
The evolution of drug resistance in HIV demonstrates 2 facets of natural
selection:
1. It is an editing, not a creative, mechanism that selects for variations
already present in a population.
2. It is regional and temporal, selecting for traits that are beneficial in the
local environment at that current time.

The Fossil Record

The fossil record documents that present and past organisms differ, and that
many species have become extinct.
Fossils also trace the evolution of new groups, as in the origin of whales from
land mammals.
The major branches of evolutionary descent established with evidence from
anatomy and molecular data have been tested and supported by the
sequence of fossil forms found in the fossil record.

Homology

Homology is similarity resulting from common ancestry.

- The forelimbs of all mammals are homologous structures, containing
the same skeletal elements regardless of function or eternal shape.
Comparative anatomy and embryology illustrate that evolution is a
remodeling process in which ancestral structures become modified for new
functions
- Vestigial organs are rudimentary structures, of little or no value to the
organism, that are historical remnants of ancestral structures.
Homologies can be seen on a molecular level.
- DNA, RNA, and an essentially universal genetic code, which have been
passed along through all branches of evolution, are important evidence
that all forms of life descended from the earliest organisms and are thus
related
Homology is evident on different hierarchical levels, reflecting evolutionary
history in a nested pattern of descent.
- An evolutionary tree diagrams ancestral relationships.
- Each branch point represents the common ancestor of all the species
beyond that point.
- Evolutionary trees are hypotheses based on available data that represent
patterns of evolutionary descent.
Distantly related organisms may appear similar as a result of convergent
evolution, the independent evolution of similar characteristics.
- These analogous structures arise as a result of evolutionary adaption to
similar environments.

Biogeography
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The geographic distribution of species, or biogeography, has been

influenced by continental drift, the slow movements of Earths continents.
The single land mass called Pangaea formed 250 million years ago and
began to break apart 200 million years ago.
- The gradual separation of continents helps to explain and predict where
fossils of different groups and their descendants are found
Islands often have endemic species, found nowhere else and usually closely
related to species on the nearest island or mainland.
Widely separated areas having similar environments are not likely to be
populated by closely related species.
- Rather, each area is more likely to have species that are taxonomically
related to those of their region, regardless of environment.

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Chapter 23: Evolution of Populations

Individuals are selected for or against by natural selection, but populations

actually evolve.
Microevolution is changes in allele frequencies of a population over
generations

Mutation and sexual reproduction produce the

genetic variation making evolution possible
Genetic Variation

Variation in an individual genotype leads to variation in an individual

phenotype
Not all phenotypic variation is heritable. Environment can affect phenotype.
For example, you can dye your hair or build muscles.
Natural selection can only act on variation with a genetic component
Discreet characteristics can be classified on an either-or basis and are
very distinct phenotypes. They are usually determined by a single gene locus.
Quantitative characteristics vary along a continuum within a population.
They are usually affected by 2 or more gene loci.
- These characteristics represent most of the heritable variation within a
population
Measures of genetic variation look at both gene variability and nucleotide
variety.
- The average heterozygosity of a population is the average percent of
loci that are heterozygous.
- Nucleotide variability measures the average percent of differences in
nucleotide sites between individuals of a population.

Geographical Variation

Most species exhibit geographic variation: regional genetic differences

between populations
A cline is a graded change or variation in a character along a geographic
area.
- Clines may parallel an environment gradient.
- For example: the number of plants changes as you go up a mountain

Mutation

Mutations are any change in the DNA sequence.

Only mutations in gametes are passed on to offspring
- Most mutations occur in somatic cells and cannot be passed on to the
next generation.
Point mutations that occur in noncoding DNA or do not change the amino acid
sequence of a protein are often harmless.
- Mutations that do alter the phenotype are usually harmful.
- Rarely, however, a mutant allele may enhance an individuals
reproductive success.

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Chromosomal mutations are more often deleterious.

Duplication of small DNA segments, introduced by transposons or errors
in cell division, may provide an expanded genome with extra loci that
could eventually take on new functions by mutation.
Mutation rates are low in animals and plants and on average occur in 1 in
100,000 genes per generation.
Mutation rates are higher in viruses and prokaryotes due to their short
generation spans.

Sexual Reproduction

Sexual reproduction can shuffle existing alleles into new combinations in

each individual.
This allows organisms to survive in a changing environment
In sexual reproduction, the 3 processes of crossing over, independent
assortment, and random fertilization all create unique genetic combinations
in offspring and increase variation.

The Hardy Weinberg equation can be used to test

whether a population is evolving
Populations and Gene Pools

A population is a localized group of individuals capable of interbreeding and

producing fertile offspring.
The gene pool is the term for all the alleles at all the loci present in a
population.
A locus is fixed if all individuals in a population are homozygous for the same
allele
More often, 2 or more alleles are present in the gene pool in some relative
frequency.
- In a case with 2 alleles at a particular gene locus, the letters p and q
represent the frequencies of the 2 alleles within a population, and p + q =
1

The Hardy-Weinberg Equation

The Hardy-Weinberg equation predicts allele frequencies in an

unchanging environment
Hardy-Weinberg equilibrium is a non-evolving gene pool there are no
population changes
Allele frequency determines the proportion of gametes that will contain
that allele

H-W equation: p2 + 2pq + q2 = 1

Allele frequencies:
- p is the frequency of the dominant allele
- q is the frequency of the recessive allele
Genotype frequencies:
- p2 = homozygous dominant frequency

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- 2pq = heterozygous dominant frequency

- q2 = homozygous recessive frequency
Phenotype frequencies:
- p2 + 2pq = dominant phenotype frequency
- q2 = recessive phenotype frequency
Number of individuals:
- Multiply the frequency by the total population

Maintaining the Hardy-Weinberg Equation

Hardy-Weinberg equilibrium is maintained only if all of the following 5 conditions
are met:
1) No natural selection (no differential survival and reproductive success)
2) No gene flow (no movement of alleles into or out of populations)
3) No mutations
4) Random mating (nonrandom mating changes genotype frequencies)
5) An extremely large population to offset chance fluctuations (no genetic
drift)
- Genetic drift is any chance fluctuations (=any changes that result from
random chance)

Natural selection, genetic drift, and gene flow can

alter allele frequencies in a population
Natural Selection

Individuals that have traits that are better suited to their environment tend to
be more successful in producing viable, fertile offspring and pass their alleles
to the next generation in disproportionate numbers, resulting in adaptive
evolution

Genetic Drift

Genetic drift describes how allele frequencies fluctuate unpredictably from

one generation to the next
- Tends to reduce genetic variation through losses of alleles
- These changes are often due to some random factor loss of alleles is
not due to selection
Founder effect occurs when a few individuals become isolated from a larger
population
- Allele frequencies in the small founder population can be different from
those in the larger parent population
Bottleneck effect occurs when some disaster or other factor leads to a
sudden reduction in population size
- The resulting gene pool is unlikely to represent the genetic makeup of the
original population
- Genetic drift will remain a factor until the population grows large enough
for chance events to be less significant
Genetic drift:

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1.
2.
3.
4.

Is significant in small populations

Causes allele frequencies to change at random
Can lead to a loss of genetic variation within populations
Can cause harmful alleles to become fixed

Gene Flow

Gene flow is the migration of individuals and movement of alleles among

populations
- Alleles can be transferred through the movement of fertile individuals or
gametes
- Gene flow tends to reduce differences between populations over time

Natural selection is the only mechanism that

consistently causes adaptive evolution
A Closer Look at Natural Selction

Natural selection results in adaptive evolution by acting on an organisms

phenotype
Relative fitness is measured by who is most likely to leave most offspring
- It is measured by the contribution an individual makes to the gene pool of
the next generation relative to the contributions of other individuals
- It depends on the entire genetic and environment context in which it is
expressed
Types of Selection
1. Directional selection occurs when one extreme is selected against
and the other extreme survives
- Most likely to occur during periods of environmental change
2. Disruptive selection occurs when the environment favors individuals
on both extremes of a phenotypic range
3. Stabilizing selection acts against extreme phenotypes and favors
the more intermediate forms, tending to reduce phenotypic variation
As natural selection increases the frequencies of alleles that enhance survival
and reproduction, the match between organisms and their environment
increases.

Sexual Selection

Sexual selection is the selection for traits that enhance an individuals

chances of obtaining mates
Dimorphism is when the male looks different than the female
Intrasexual selection is when individuals of one sex (usually males)
compete for mates of the opposite sex
Intersexual selection is when individuals of one sex (usually females) are
choosy in selecting their mate
- Is also called mate choice
Male showiness due to mate choice can increase a males chances of
attracting a female, while decreasing his chances of survival (example:
peacocks)

Maintaining Genetic Variation

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1. Diploidy: maintains genetic variation in the form of hidden recessive alleles

in heterozygotes by allowing these alleles to persist in the population

2. Balancing selection: occurs when natural selection maintains stable

frequencies of 2 or more phenotypic forms in a population
3. Heterozygous advantage: heterozygotes have a higher fitness than
both homozygotes, and have survival and reproductive advantages
- Example: sickle cell anemia carriers are malaria resistant
4. Frequency dependent selection: when the fitness of a phenotype
declines if it becomes too common in the population
5. Neutral variation: appears to confer no selective advantage or
disadvantage
- Variation in noncoding regions of DNA or alleles that do not affect fitness
may change randomly by genetic drift

Why no perfect organisms?

Natural selection can only act on variations that are available: new alleles
dont arise as theyre needed.
Each species has evolved from a long line of ancestral forms, many of whose
structures have been co-opted for new situations.
Adaptations are often compromises between the need to do several different
things, such as swim and walk.
And finally, chance events affect a populations evolutionary history.

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Chapter 24: The Origin of Species

Speciation, the origin of new species, is at the focal point of evolutionary

theory.
Microevolution explains evolutionary changes and adaptations that evolve
within a population, confined to one gene pool.
Macroevolution involves evolutionary change above the species level and
considers broader changes

The biological species concept emphasizes

reproductive isolation
The Biological Species Concept

A species is defined as a group of populations whose members have the

potential to interbreed in nature and produce viable, fertile offspring, but
dont breed successfully with other populations
- Gene flow between populations holds the phenotype of a population
together
Reproductive isolation is the existence of biological factors (=barriers)
that impede 2 species from producing viable, fertile hybrids.
- Hybrids are the offspring of crosses between different species.
- Reproductive isolation can be classified by whether it occurs before or
after fertilization.
Prezygote barriers block fertilization from occurring by
preventing mating between species or preventing successful
fertilization if gametes meet.
Postzygote barriers prevent a hybrid zygote from developing into
a viable, fertile adult.
The biological species concept doesnt work for species that are asexual, such
as prokaryotes.

Other Definitions of Species

Most species have been identified on the basis physical characteristics, an

approach called the morphological species concept.
The ecological species concept defines species on the basis of the role they
play and resources they use in the specific environments in which they are
found.
In the phylogenetic species concept, a species is an evolutionary lineage
that represents one branch on the tree of life and has distinct morphology or
molecular sequences.

Speciation can take place with or without

geographic separation
Allopatric Speciation

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Allopatric speciation occurs when geographic isolation interrupts gene flow

between 2 subpopulations
Geographic separation alone is not a reproductive barrier in the biological
sense.
Intrinsic reproductive barriers may arise coincidentally as allopatric
populations go down different evolutionary paths due to mutation, genetic
drift, and natural selection

Sympatric Speciation

In sympatric speciation, the reproductive barriers prevent gene flow

between populations that share the same area.
Mistakes during cell division may lead to polyploidy, the presence of extra
sets of chromosomes.
An autopolyploid has more than 2 sets of chromosomes that have all come
from the same species.
- Failures in cell division can produce tetraploids (4n) which can fertilize
themselves or other tetraploids, but cant reproduce with diploids from the
parent population, resulting in reproductive isolation in just one
generation.
Polyploidy species may also arise through allopolyploidy.
- Interspecific hybrids may propagate asexually, but are usually sterile due
to difficulties in the meiotic production of gametes.
- Future mitotic or meiotic mistakes can result in the production of a fertile
polyploid.
Polyploid speciation has been frequent and important in plant evolution.
Sympatric speciation in animals may involve isolation within the geographic
range of the parent population based on different resource usage.
Sexual selection may also lead to sympatric speciation.

Hybrid zones provide opportunities to study

factors that cause reproductive isolation
Patterns within Hybrid Zones

Hybrid zones are areas where diverging allopatric populations come back
into contact and members of the different species interbreed
For example:
- In the hybrid zone found between the yellow-bellied toad and the firebellied toad, the frequencies of alleles specific to one species range from
100% near that species edge of the hybrid zone to 0% at the edge near
the other species.
- What keeps these hybrids from introducing the alleles of each others
species into the parent populations?
- Their poor survival and reproduction mean that these hybrids produce few
viable offspring if they mate with the parent species.

Hybrid Zones over Time

There are 3 possible outcomes for populations in a hybrid zone:

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Reinforcement: natural selection may strengthen prezygotic barriers to

reproduction when hybrids are less fit (=less viable and reproductive) than
individuals of the parent species.
Fusion: weak reproductive barriers may allow sufficient gene flow that
barriers break down even more and the two hybridizing species fuse into a
single species.
Stability: many hybrid zones appear to be stable, with hybrids
continuing to be formed, but with the two parent gene pools remaining
separate.

Time of Evolution
1. Gradualism(Darwinian Evolution): gradual divergence- organisms
change over long periods of time

2. Punctuated equilibrium: long periods of stasis punctuated by episodes

of relatively rapid speciation and change
- In the fossil record, new forms appear rather suddenly, persist unchanged
for a long time, and then disappear.

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Chapter 26: Phylogeny and the Tree

of Life

Phylogeny is the evolutionary history of a species or group.

Systematics is the discipline focused on classifying organisms and determining
evolutionary relationships.

Phylogenies show evolutionary relationships

Binomial Nomenclature

Each species is assigned a 2-part Latinized name a binomial consisting of

the name of the genus and the specific epithet, designating one species in
that genus

Hierarchical Classification

Taxonomy is concerned with naming and classifying species.

In the Linnaean taxonomic system, genera are grouped into families, which
are then grouped into orders, classes, phyla, kingdoms, and then
domains.
A taxon is a taxonomic unit at any level.

Linking Classification and Phylogeny

A phylogenetic tree represents hypotheses about evolutionary relationships

among groups, with branching patters that may reflect their Linnaean
classification.
The phylocode system of classification is based totally on evolutionary
relationships, only naming groups that include a common ancestor and all
descendants.
Each dichotomous branch point on a phylogenetic tree represents the
divergence of two taxa from a common ancestry.
- Sister taxa share the most recent common ancestor.
- Trees are rooted with the oldest branch to the left.
- A polytomy is a branch point involving more than 2 descendants,
indicating that these evolutionary relationships are not yet clear.
Phylogenetic trees show patterns of descent but do not usually indicate when
species evolved or the amount of genetic change in each lineage.
- Also, species next to each other on the tree indicate that they shared a
common ancestor, not that one evolved from the other.

Morphological and Molecular Homology

Morphological and Molecular Homologies

Homologies are similarities due to shared ancestry

The more similar morphologies or DNA sequences are, the more likely that
organisms are closely related

Sorting Homology from Analogy

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Analogy is similarity due to convergent evolution, in which unrelated species

develop similar features because natural selection has led to similar
adaptations.
Homoplasies are analogous structures.
In general, when 2 complex structures share many similar features, they
more likely were inherited from a common ancestry
In molecular comparisons, the more nucleotide sequences shared between
comparable genes, the more likely the genes are to be homologous.

Evaluating Molecular Homologies

Molecular comparisons are complicated by insertion or deletion mutations

that change the lengths of homologous regions of DNA.
- Computer programs identify similar sequences and then insert gaps in
order to align homologous DNA segments properly for nucleotide
comparisons.
- The matching bases between organisms that are not closely related may
be molecular homoplasies.
- Mathematical tools have been developed to identify distant homologous
between extremely divergent sequences
Molecular systematics uses DNA and other molecular comparisons to infer
evolutionary relationships

Phylogenetic trees
Cladistics

Classification based on common descent forms the basis of cladistics

A clade consists of an ancestral species and its entire descendant species.
Such a clade is monophyletic. A paraphyletic group excludes some
species that share a common ancestor with other species in the group, and a
polyphyletic group includes several groups with different ancestors.
Shared ancestral characters are found in a particular clade but evolved in
an ancestor that is not part of that clade.
Shared derived characters are evolutionary novelties that are unique to a
particular clade.
To determine the branching sequence of a group of related species, the group
is compared to an outgroup, a species or group of species that diverged
before the group being studied (the ingroup)
A comparison of the number of characters in each taxon of the ingroup
indicates the sequence in which shared derived characters evolved and
determines the branch points used to produce a phylogenetic tree.

Phylogenetic Trees with Proportional Branch Lengths

The branching pattern of most phylogenetic trees is relative rather than

absolute, indicating only the order in which members of each clade last
shared a common ancestor.

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The branch length of some trees can be scaled to reflect rates of evolutionary
change (for instance, number of changes in DNA sequence) or time (using the
dates of branch points as indicated in the fossil record)

Maximum and Maximum Likelihood

Systematists use morphological characters or molecular comparisons to

choose among many possible phylogenetic trees using the principle of
maximum parsimony the smallest number of evolutionary changes is the
simplest explanation and thus the best hypothesis to consider first.
According to the principle of maximum likelihood, a tree can be found that
represents the most likely sequence of events, given a certain set of
assumptions (such as equal rates of DNA changes).
- Computer programs search for the most parsimonious and most likely
trees

Phylogenetic Trees as Hypotheses

The most parsimonious tree based on the fewest number of evolutionary

changes represents the best hypothesis of the relationship among a set of
species.
A hypothesis of phylogenetic relationships becomes more reliable with ore
data that can be compared.
Phylogenetic hypotheses can be used to make and test predictions.
In phylogenetic bracketing, features shared by two closely related
organisms are predicted to be found in their common ancestor and all its
descendants.
- Fossil discoveries support the prediction that the ancestor of birds and
crocodiles, and therefore also dinosaurs, built nests and brooded their
eggs.

From Two Kingdoms to Three Domains

Historically, taxonomists divided the diversity of life into two kingdomsplants and animals
In the five-kingdom system, the prokaryotes were set apart from the
eukaryotes and placed in the kingdom Monera
The kingdom Protista contained mostly unicellular eukaryotes, while
kingdoms Plantae, Fungi, and Animalia consisted of multicellular eukaryotes
The current three-domian system creates a taxon above the kingdom levels
The domains Bacteria and archaea, although both consisting of single-celled
prokaryotes, differ in many characteristics
The domain Eukarya includes all the eukaryotes: plants, fungi, animals, and
many groups of single-celled organisms.

R strategists: reproduce a lot large populations (fish, insects, fruit flies)

K strategists: dont reproduce a lot small populations (cheetahs, humans, birds)
Phylogenic tree
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Divergent evolution/Adaptive radiation: organisms become more different over

time

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