Evolutionary Genetics

EVOLUTIONARY GENETICS
Biological evolution
A heritable change in one or more characteristics of a
population or species across many generations
It can be viewed on a small scale (single gene)
Or large scale (formation of a new species)
Microevolution
Changes in the gene pool with regard to particular alleles
over measurable periods of time
Macroevolution
Relatively large changes in form and function that are
sufficient to produce new species and higher taxa
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Molecular evolution refers to the molecular changes
in genetic material that underlie the phenotypic
changes associated with evolution
Evolutionary developmental biology focuses on the

role of developmental genes in the evolution of new
species
Genes affecting embryonic development can have
dramatic impacts on the phenotypes of the organism
Greatly increases our understanding of the widely varied
and yet interrelated species on our planet
NAME: Charles Darwin
OCCUPATION: Biologist
BIRTH DATE: February 12, 1809
DEATH DATE: April 19, 1882
EDUCATION: University of
Edinburgh, Cambridge
PLACE OF BIRTH: Shrewsbury,
England
PLACE OF DEATH: Downe,
England
Full Name: Charles Robert
Darwin
ORIGIN OF SPECIES
Charles Darwin (1809-1882) was the first to theorize
that existing species evolved from preexisting ones
His broad background in science enabled him to see

connections among different disciplines
Three important influences helped Darwin develop

his Theory of Evolution
1. Theories of geology
The Earth is very old
Slow geological processes can change the earths characteristics
2. Darwins own experimental observations

He made a voyage aboard the HMS Beagle (1832-1836)
He carefully examined many different species
He noted similarities, but also differences that enabled various species
to adapt to different environmental conditions
3. Thomas Malthus Essay on the Principle of

Population
In this essay, published in 1798, Malthus asserted that resources
cannot keep up with the reproductive potential of humans
He argued that famine, war, and disease will limit population growth,
especially among the poor
With these three ideas in mind, Darwin had largely formulated
his theory of evolution by the mid-1840s
In 1856, he began to write a long book to explain his ideas
Alfred Wallace, a naturalist working in the East Indies,

independently proposed the same ideas concerning evolution
In 1858, two papers, one by Darwin and one by Wallace, were
published in the Proceedings of the Linnaean Society of London
In 1859, Darwin published his book, On the Origin of Species

by Means of Natural Selection
In it, Darwin expounded his ideas in greater detail and with
experimental support
The book received high praise from some scientists and
scorn from others
The debate concerning evolution was ON
Darwins work represents one of the most important

contributions to our understanding of biology
Darwin called his theory of evolution the theory of descent

with modification through variation and natural selection
As its name suggests, it is based on two important principles
1. Genetic variation
2. Natural selection
A modern interpretation of evolution can view these

principles with regard to speciation and microevolution
1. Genetic variation at the species level
Genetic variation is a consistent feature of most natural
populations
Darwin assumed that some phenotypic variation is passed
from parent to offspring
However, he did not know the genetic basis for inheritance of traits
At the gene (microevolutionary) level

Genetic variation can involve
Allelic differences in genes
Changes in chromosome structure
Alterations in chromosome number
All of these influence the phenotype of the individual
2. Natural selection at the species level
Most species produce many more offspring than survive
and reproduce
This creates a struggle for existence that results in the
survival of the fittest
The ultimate result of natural selection is to make a species better
adapted to its environment and/or more efficient at reproduction
At the gene (microevolutionary) level

Some alleles may encode proteins that provide the
individual with a selective advantage
Over time, natural selection may change the allele
frequencies of genes
Thus, leading to the fixation of beneficial alleles and the elimination
of detrimental alleles
A Biological Species
Darwin was interested in the origin of species
Before we can consider how biologists study the
evolution of new species, we need to understand
how species are defined and identified
A species refers to a group of organisms that

maintains a distinctive set of attributes in nature
A single species may exist in two or more distinct
populations that are evolving slowly into different species
If the time of separation is short, the populations may be
very similar
A Biological Species can be
defined in many ways
If the populations are separated for a long time,
significant changes may have occurred
They may show unequivocal differences
These allow them to maintain distinct features
When differences between populations are
significant, but not enough to warrant classification
as different species they are classified as subspecies
Bacterial species can be subdivided into ecotypes,
each adapted to its local environment
A Biological Species can be
defined in many ways
Can be difficult to always identify distinct species
Different characteristics may be used to distinguish
species
physical or morphological traits
ability to interbreed
molecular features
evolutionary relationships
ecological factors
The characteristics used may depend on the species in

question
Morphological Traits to define
species
Organisms are classified as the same species if their
anatomical traits appear to be very similar
Microorganisms can be classified by morphological
traits at the cellular level
Many problems with this system

Hard to decide which specific traits to use
Quantitative traits like size and weight can vary within a
species
Level of difference of appearance can vary widely
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Mark Smith/Photo Researchers Pascal Goetgheluck/ardea.com
(a) Frogs of the same species
North
America
Ron Austing/Photo Researchers
Eastern
The frogs at the top look meadowlark
completely different, but are (Sturnella magna)
members of the same
species
The birds look nearly identical,
but are different species
Rod Planck/Photo Researchers
Western meadowlark
Western meadowlark Eastern meadowlark
(Sturnella neglecta) Zone of overlap
(b) Birds of different species
Reproductive Isolation
Dobzhansky proposed in the late 1920s that species are
reproductively isolated from other species
Thus, they cannot successfully interbreed with other species
Ernst Mayr expanded on the ideas of Dobzhansky and

proposed the biological species concept
A species is a group of individuals whose members can
interbreed to produce viable, fertile offspring
The members of one species, cannot successfully
interbreed with members of other species
There are several different ways to achieve
reproductive isolation
Prezygotic barriers block fertilization from

occurring by:
Impeding different species from attempting
to mate
Preventing the successful completion of
mating
Hindering fertilization if mating is successful
2011 Pearson Education, Inc.

Prezygotic barriers
Habitat Temporal Behavioral Mechanical Gametic

Isolation Isolation Isolation Isolation Isolation
Individuals
of MATING
different ATTEMPT FERTILIZATION
species
(a) (c) (e) (f) (g)
(d)
(b)
Postzygotic barriers prevent the hybrid zygote
from developing into a viable, fertile adult:
Reduced hybrid viability

Reduced hybrid fertility
Hybrid breakdown
2011 Pearson Education, Inc.

Postzygotic barriers
Reduced Hybrid Reduced Hybrid Hybrid
Viability Fertility Breakdown
VIABLE,
FERTILE
FERTILIZATION OFFSPRING
(h) (i) (l)
(j)
(k)
Mule :
offspring of a donkey and a horse
There are several problems using
reproductive isolation to define species
Nonoverlapping geography may prevent
members of same species from mating
Species may be capable of mating in the wild,
but may maintain distinct characteristics
Does not apply to asexual species such as
bacteria
Cannot be applied to extinct species
Because of the above, used primarily to

distinguish closely related species of animals
and plants that reproduce sexually
Molecular Features
Evolutionary biologists will compare:
DNA sequences within genes
gene order along chromosomes
chromosome structure
chromosome number
Can look at sequence differences in bacteria

Hard to use morphology or sexual isolation
Can be difficult to decide what the cutoff is
when sequences are nearly identical
Ecological Factors
Variety of ecological factors can be used
Where different species of related birds forage
Some in bushes
Other in tall trees
What resources different bacterial species use
types of sugar
types of vitamins
Growth conditions
temperature
pH
Same species may show great variations
Evolutionary Relationships
In 1961 George Simpson proposed the
evolutionary lineage concept
A species is derived from a single lineage that is
distinct and has its own evolutionary tendencies
and historical fate
In 1976 Leigh Van Valen proposed the

ecological species concept
Each species occupies an ecological niche
The unique set of habitat resources the species requires
Evolutionary Relationships
In 1998 Kevin de Queiroz proposed the general
lineage concept
Each species is a population of an independently

evolving lineage
Each species has evolved from a specific series of
ancestors
As a consequence, each forms a group of organisms with
a particular set of characteristics
Multiple criteria are used to determine if a given
population is part of an independent evolutionary lineage.
Morphology, reproductive isolation, DNA sequence and ecology
Patterns of Speciation
Speciation is the formation of new species via
evolution
By examining fossil records, evolutionary biologists
have found two different patterns of speciation
Anagenesis
From the Greek, ana, meaning up and genesis meaning origin
A single species is transformed into a different species over the
course of many generations
Cladogenesis
From the Greek, clados, meaning branch
A single species is divided into two or more species
This is the most common form of speciation
New species better Each new species develops
adapted to survive in characteristics that prevent it
original or new from interbreeding with the
environment original one
(a) Anagenesis (b) Cladogenesis

- prevailing mechanism of speciation
Cladogenesis Can be Allopatric,
Parapatric, or Sympatric
As mentioned earlier, divergent evolution is
the most common form of speciation
Depending on the geographic locations of the
evolving populations, speciation is
characterized as
Allopatric
Parapatric
Sympatric same country
(a) Allopatric speciation. (b) Sympatric speciation.
A population forms a A subset of a population
new species while forms a new species
geographically isolated without geographic
from its parent population. separation.
Allopatric :
two large populations are separated by
geographic barriers
a small founding population separates from
the main population
Parapatric : two populations occupy overlapping

ranges, so a limited amount of interbreeding occurs
Sympatric : within a population occupying a single

habitat in a continuous range, a small group evolves
into a reproductively isolated species
(rare)
Allopatric speciation
From the Greek, allos, other and patria, homeland
The most prevalent way for a species to diverge
It occurs when members of a species become
geographically separated from other members
This is accomplished by two different mechanisms
1. Geological processes
These geographically subdivide two large populations
Figure 26.3 shows two closely related species of antelope squirrels
that occupy opposite rims of the grand canyon
2. Founder effect
Thought to be more rapid and frequent than the above
A small group migrates to a new location that is geographically
separated from the main population
In a relatively short period of time, the founding population may
evolve into a new species
Speciation by Founder Effect can be relatively rapid
Genetic drift may lead to rapid fixation of certain alleles and

elimination of others
When a small group migrates to a new environment, the
adaptive landscape is likely to be changed
Allele combinations that were highly adaptive in the original
environment may be much less so in the new environment
Natural selection may then lead to a shift toward a new
adaptive peak
Parapatric speciation
From the Greek, para, beside
It occurs when members of a species are not completely
geographically isolated
This is accomplished by two different mechanisms
1. Partial separation by geological processes
A mountain range may divide a species into two populations
But breaks in the range allow (infrequent) interbreeding
2. Sedentary species
Certain organisms are so sedentary that 100 to 1,000 meters
may be sufficient to limit interbreeding between groups
Plants, terrestrial snails, grasshoppers and lizards may
speciate in this manner
Prior to parapatric speciation, the zones where two
populations can interbreed are known as hybrid zones
For speciation to occur, the amount of gene flow within
the hybrid zones must become very limited
In other words, there must be selection against the offspring
produced in the hybrid zones
One way that this can happen is
Each of the two parapatric populations may accumulate different
chromosomal rearrangements
Such as inversions and balanced translocations
Hybrids will thus have one normal chromosome and one
abnormal chromosome
Crossing-over during meiosis can lead to the production of grossly
abnormal chromosomes
Therefore, the hybrid will be substantially less fertile
Sympatric speciation
From the Greek, sym, together
It occurs when members of a species initially occupy the
same habitat within the same range
In plants a common way for sympatric speciation to occur
is the formation of polyploids
Polyploidy is so frequent in plants that is a major form of speciation
By comparison, polyploidy is far less common in animals
The formation of a polyploid can abruptly lead to

reproductive isolation
Lets consider the probable formation of a natural species
of common hemp nettle known as Galeopsis tetrahit
Sympatric speciation
Galeopsis tetrahit is thought to be the allotetraploid derived

by combining the genomes of G. pubescens and G.
speciosa (Figure 26.4a)
While all three species are physically similar and occupy

similar niches, they cannot interbreed because crosses
between them would produce monoploids which would
likely be sterile (Figure 26.4b)
Figure 26.4
Diploid
Allotetraploid
species
Galeopsis tetrahit G. pubescens G. speciosa
Monoploid for one set and

diploid for the other
(a) Chromosomal composition of 3 Galeopsis species
Fertile Infertile Infertile

G. tetrahit x G. tetrahit G. tetrahit x G. pubescens G. tetrahit x G. speciosa
(b) Outcome of intraspecies and interspecies crosses

Speciation Can Be Fast or Slow
The rates of evolutionary change are not constant
Darwin himself suggested that evolution can occur at fast
and slow paces
There are two different ways to consider the tempo
of evolution
Gradualism
Each new species evolves continuously over long spans of time
Punctuated Equilibrium
Species exist relatively unchanged for many generations
These long periods of equilibrium with the environment are
punctuated by short periods where evolution occurs at a rapid rate
Morphology of
a species
gradually
changes due
to the
accumulation
of small
genetic
changes
(a) Gradualism
Figure 26.5
Equilibrium Equilibrium Equilibrium

Morphology
of a species
rapidly
changes,
then
Rapid evolutionary
Rapid evolutionary change remains in
change
equilibrium
for many
generations
(b) Punctuated equilibrium

Figure 26.5
Evolution Can Be Fast or Slow
Rapid evolutionary change can be explained by
genetic phenomena
A small number of changes in a few genes may
have dramatic effects
May alter the phenotype enough to make a new species
Changes in chromosome structure or number may
abruptly create new phenotypic traits
These changes can be rapid on an

evolutionary time scale
Evolution Can Be Fast or Slow
Species may be subjected to sudden environmental
changes
A group may migrate to a new environment
Could change selective advantage of some alleles
The environment can change
Climate change
local or global
Introduction of new predator
Phylogenetic Trees
Phylogeny is the sequence of events involved

in the evolutionary development of a species
or group of species
A phylogenetic tree is a diagram that
describes the phylogeny of a species
Systematists are the biologists interested in

gathering and assembling this information
Phylogenetic Trees
Willi Hennig proposed that evolutionary relationships
should be inferred from new features shared by
descendants of a common ancestor.
Phylogenetic trees are based on homology
Similarities that occur because species are
derived from a common ancestor
Wing of bat, arm of human, leg of cat are homologous
Wing of bat and wing of insect are not
They arose independently of each other
Homology is studied at the level of morphology or
genes
Morphological features have been used to construct
evolutionary trees
Physiology
Biochemistry
Even behavior
Increasingly, molecular data concerning properties of the

genetic material is being used
Nucleotide and amino acid sequence data are very well-

suited to the construction of evolutionary trees
Differences in nucleotide sequences are quantitative
Can be mathematically analyzed
Can be objectively compared
Comparisons can be made between dissimilar organisms
Can compare bacteria and humans at DNA level
Phylogenetic Trees Depict the Evolutionary
Relationships Among Different Species
The nodes or branch points of the tree illustrate

when a species diverges into two or more species,
known as cladogenesis, with their vertical position
related to time.
The tips of the branches represent species that

became extinct or modern species (at the top of the
tree)
A monophyletic group or clade is a group of species

consisting of all descendants of the groups most
common ancestor
Phylogenetic Terms:
Cladogram : A diagram, which depicts a

hypothetical branching sequence of lineages
leading to the taxa under consideration. The
points of branching within a cladogram are
called nodes. All taxa occur at the endpoints
of the cladogram.
Clade : from the Greek word klados,
meaning branch or twig.
Nodes : the points of branching within a
cladogram
OTU : operational taxonomical unit (a branch
end) 47
Cladogram:
48
Phylogenetic Tree
49
Phylogenetic Tree
50
Species E, F, G, I, H, and J, at the tips of branches, are modern species.
E F Species A, B, D, and C at tips G I H J

Present of branches in past are
extinct species.
B D C
E I H
Millions of years ago (mya)
5
A
B C
Clade: The species
Time
in green are all derived

from a common
ancestor, species C.
A B
10 Cladogenesis:
Species A diverged
into species A and B.
A
Branch points indicate when
a species diverged into 2 or
more different species.
Figure 26.6 - An example of a phylogenetic tree

52
Vertical / Horizontal Gene Transfer and
Evolution of Species
Vertical evolution
involved genetic
changes in a
series of
ancestors that
form a lineage
Species can also accumulate genetic changes by
another process called horizontal gene transfer
This involves the exchange of genetic material among
different species
Horizontal gene transfer was widespread
during early stages of evolution
Remains prevalent in prokaryotes
Far less common among eukaryotic species
multicellularity and sexual reproduction may be barriers
Horizontal transfer has changed our

understanding of evolution
All life may have arisen from a community of
lineages that transferred information and evolved
as a whole
In contrast to idea of single universal ancestor
Molecular Evolution
Homologous Genes are Derived from a
Common Ancestral Gene
Two genes are said to be homologous if they
are derived from the same ancestral gene
Orthologous genes or orthologs are homologous
genes found in different species
Paralogous genes or paralogs are homologous
genes found within a single species
A gene family consists of two or more copies of
homologous genes within the genome of a single
organism
The sequences are homologous between humans
and horses because of their evolutionary relationship
Human and horse a-globin genes are orthologs
Human and horse b-globin genes are orthologs
Human a-globin and b-globin genes are paralogs
Note that the sequences of the orthologs are more

similar to each other than the paralogs
This suggests that the gene duplications that created the
a- and b-globin genes occurred long before the
evolutionary divergence of the mammalian species
Thus, there was a greater amount of time for the a- and b-globin
genes to accumulate changes
This idea is schematically shown in Figure 26.13
a b a b
Human Horse
Accumulation of
additional mutations
a b a b
Human Horse
Divergence into different
species to create orthologs
a b
Accumulation of
different mutations
a b
Thought to have occurred Gene duplication

400 million years ago, 200 to create paralogs
million years before
speciation of mammals
Ancestral globin gene

Figure 26.13 Evolution of paralogous and orthologous genes
Neutral Changes and Variation
During the last few decades, a great debate has
occurred among geneticists
The debate centers on the reason for genetic variation in
natural populations
Is it due primarily to mutations that are favored by natural selection
or to random genetic events?
A nonneutral mutation is one that affects the

phenotype and can be acted on by natural selection
According to Darwin, natural selection is the dominant
force in changing the genetic composition of populations
It thereby leads to variation
Neutral Variation
differences in DNA sequence that do not confer a selective

advantage or disadvantage; recessive alleles in diploid
eukaryotes (for example eye colors)
Neutral mutations
are changes in DNA sequence that are neither beneficial
nor destructive to the ability of an organism to survive and
reproduce.
In population genetics, neutral mutations are mutations in
which natural selection does not affect the spread of the
mutation in a species.
Motoo Kimura proposed the neutral theory of
evolution
Most genetic variation observed in natural populations is
due to the accumulation of neutral mutations
Neutral mutations do not affect the phenotype of the
organism
Neutral alleles are thus not acted on by natural selection
They, therefore, spread throughout a population according to their
frequency of appearance and to genetic drift
This theory has been called the survival of the

luckiest and also non-Darwinian evolution
In order to contrast it with Darwins survival of the fittest
Kimura agreed that natural selection is responsible
for adaptive changes in a species during evolution
However, his main argument is that most modern variation
in gene sequences is explained by neutral variation
Not adaptive variation, as Darwin proposed
Kimura, and his colleague Tomoko Ohta, suggested

five principles that govern the evolution of genes at
the molecular level
1. For each protein, the rate of evolution, in terms of amino
acid substitutions, is approximately constant with regard to
neutral substitutions
Evidence: As an example, the amount of genetic variation between
the coding sequence of the human a- and b-globin genes is about the
same as the difference between the horse a- and b-globin genes
2. During evolution, proteins (or parts thereof) that are

functionally less important will accumulate amino acid
substitutions more rapidly than important proteins or regions
Evidence: Histone genes tolerate very few mutations and have
evolved extremely slowly
By comparison, fibrinopeptides, which bind fibrinogen to form a
blood clot, evolve very rapidly
Another example, concerns the amino acid sequences of enzymes
Amino acid substitutions are very rare within the active site
But are more frequent in other parts of the protein
3. Amino acid substitutions that do not disrupt the existing
structure and function of a protein occur more frequently in
evolution than disruptive amino acid changes
Evidence: In a genes coding sequence, mutations in the wobble base
are more common than those in the first or second base of a codon
Furthermore, conservative substitutions (i.e., a nonpolar amino acid
for another nonpolar amino acid) are fairly common
By comparison, nonconservative substitutions are less frequent
Nonsense and frameshift mutations are very rare
Also, intron sequences evolve more rapidly than exon sequences
4. Gene duplication often precedes the emergence of a gene

having a new function
Evidence: Gene duplications have created gene families in which
each family member can evolve somewhat different functional roles
E.g., Globin gene family (Chapter 8) and Hox genes (Chapter 23)
5. Selective elimination of definitely deleterious mutations
and random fixation of selectively neutral or very slightly
deleterious alleles occur far more frequently in evolution than
selection of advantageous mutants
Evidence: The nonconservative mutations (see principle 3) usually
have a negative impact on the phenotype of the organism
They are eliminated from the population by natural selection
On rare occasions, however, an amino acid substitution due to a
mutation may have a beneficial effect on the phenotype
E.g., A nonconservative mutation in the b-globin gene produces HbS
This gives an individual resistance to malaria in the heterozygous
condition
DNA sequence data from thousands of
species has provided strong support for
Kimuras five principles
However, the argument is by no means resolved
Some geneticists, called selectionists, oppose
the neutralist theory
Debate largely cooled by the concept of nearly
neutral mutations
These have a minimal impact on phenotype
slightly beneficial or detrimental
Their prevalence is dependent on natural selection
or genetic drift, depending on the population size
Molecular clocks
Evolutionary time can be measured with a molecular
clock based on the idea that a relatively constant
rate of neutral mutations results in a number of
mutations proportional to the time elapsed since their
last common ancestor
Figure 26.14a shows a theoretical clock

Graphs amino acid replacements in superoxide dismutase
vs. time since the species shared a common ancestor
There is a general trend for species that diverged at an
earlier time to show more differences
However, evolutionary biologists have found that molecular
clocks are often not linear
Figure 26.14
A theoretical
30
molecular clock
Ceratitis vs all other species

One Chymomyza species vs all Drosophila species 20
Drosophila vs Drosophila or
Drosophila vs Scaptodrosophila
10
0
0 20 40 60 80 100 120
Millions of years ago
Molecular clocks
Several factors contribute to the nonlinearity of
molecular clocks:
Differences in population sizes which affect
genetic drift and natural selection
Differences in mutation rates
Differences in generation time of different species
Differences in the relative number of sites in a
gene susceptible to neutral mutations
Analysis of Ancient DNA
It is occasionally possible to obtain DNA sequence
information from species that have lived in the past
Can use tissue samples from museum specimens
In 1984, researchers first succeeded in determining
DNA sequences from extinct species
The organism was the quagga (Equus quagga)
A zebralike species that became extinct in 1883
This pioneering study opened up the field of ancient
DNA analysis, also known as molecular paleontology
Analysis of Ancient DNA
There is some debate concerning how long DNA can
remain significantly intact after an organism has died
Over time, DNA is subject to hydrolysis and loss of purines
Nevertheless, DNA is stable under certain conditions
E.g., Under cold temperature and low oxygen, DNA may be stable
as long as 50,000 to 100,000 years
In most studies involving prehistoric specimens, the

amount of DNA extracted is small
The DNA has to be amplified using PCR
Since these early studies, sequences of ancient
DNA have been derived from a variety of species
Figure 26.17 shows some extinct organisms from

which DNA sequences have been determined
Many samples were tens of thousands of years old

For example the sample of a Neanderthal man was
approximately 30,000 years old
The oldest samples are likely to be in the range of 50 to

100,000 years old
Figure 26.17 Extinct species from which DNA sequences have
been obtained
Evolution is Associated with Changes
in Chromosome Structure and Number
Changes in chromosome structure and/or number
may not always be adaptive
They can lead to reproductive isolation and the origin of a
new species
Figure 26.18 provides an example of variation in

chromosome structure in closely-related species
It compares the banding pattern of the three largest
chromosomes in humans and in apes
Chimpanzee
Chimpanzee
Orangutan
Orangutan
Human
Gorilla
Human
Gorilla
.33
.32 .31
Chimpanzee
.23
.22
6 .21
Orangutan
.3
.13
.12 5 .2
Human
.11 .1
Gorilla
.3 .3
5 .2
4 .1
.3
4 .2 2 3 .3
.2
.1 .1
3 3 .3
.2 .3
2 .3 2 .1 .2
6 .1
.2
.1
1 .3
.3 .3 5 .1
.2
.2
.2 6 .1 .3
1 4 .1
.2
.13 5
.12 4 .3 2 3 .3
.11 1 3
.2
.1 2 .2
.1
.3 .33
.3 .2
2 .2
2 .1 .32
2 .1 .23
.22 1 .31
.3 1 .21
.1 .2
1 .2 .1 .1
.1 .21
.3
1 .23
.23
4 .1
.2
.3
3
Inversion
.2 .1
1 .1 2 .2
2 .2 1 3 .3 3
1 .1
.1
1 .3
.2
1 .1 .2 2 .1
.2 4 .3
1 2
.2
.1 1 .1
.1 1 .2
.21 .3 1
.22 .1 .1
1 .23 2 .2 2 .2
.3
.3 .11
.3 2 .1
.2
1 .12
2 .1 3 .13
2 .2 .3
.1 3 .2
3 .3
.2 .31
.1 .32
.2 4 .3
4 .3
.33
.1
.1 .1 1 .3
.2
5 .2
.3
1 .3
.2
.1
.1
2 .3
.2
.11
1 .2 .12
.13 3
.3 2 .31
.2 4
3 .1 .32
.33 .1
.2
Chromosome 1
Chromosome 2
Chromosome 3
2 .2 .1 5 .32
.31
.3
3 3 .3.2 2 .33
.1
1 4 .2
.11 6
.12
.13 5 .31
.32
4 2
.1
.2 .2
6 .3 .33
Figure 26.18
.3 .1
7 .3
.2
3 .1
8
7 .2
4 .3 9
Eyes and the Pax6 gene
How can a complex, new organ arise?
Darwin (in The Origin of Species) pointed out how
the origin of a complex organ such as the eye was
difficult to understand
He suggested that the complex eye must have evolved
from a simpler structure
He even speculated that a very simple eye could consist of
just two cells, a photoreceptor and a pigment cell
The pigment cell blocks one side, allowing sensing of the direction
from which the light comes
Vision is nearly universal among animals
Demonstrates a strong selective advantage
Anatomically, eyes are very divergent
The eyes of flies, squid and humans are quite varied
This led von Salvini-Plawen and Mayr to propose that eyes
arose independently multiple times during evolution
However, at a molecular genetics level, eyes are
very similar
The Pax6 gene was found to influence eye development in
rodents and humans
The Drosophila homologue, eyeless, was then discovered
eyeless can promote the formation of additional eyes
expression of eyeless or mouse Pax6 in Drosophila
switches on a cascade of 2,500 genes
Can form eyes on the leg or other unexpected places
See Figure 26.22
eyeless and Pax6 are master control genes that

cause the formation of a specific organ-the eye
Since the two are homologs, they likely arose from a

single common ancestor
Normal eye
Eye on
the side
Eye where
of a leg
an antenna
is normally
found
Prof. Walter J. Gehring, University of Basel Prof. Walter J. Gehring, University of Basel
(a) Abnormal expression (b) Abnormal expression of

of Drosophila eyeless gene mouse Pax6 gene in a
fruit fly leg
Figure 26.22
Other homologs of Pax6 have been found in many
different species
Always directs eye development
All are transcription factors that control many other genes
Current view is that all eyes evolved from a single

common ancestor consisting of one photoreceptor
and one pigment cell
Exactly what Darwin hypothesized
Eyes were transformed by the addition of more cell types
into the many complex forms seen
Photoreceptor Pigment
The ancestral Pax6 cell cell
gene controlled
other genes that Simple eye
produced a
primitive 2-celled
eye.
Ancestral Pax6 gene
During evolution, species

diverged from each other,
but each species retained
a Pax6 homolog.
Drosophila eyeless gene Mammal Pax6 gene
Over time, gene duplications and other

genetic changes produced many more
genes that added to eye complexity.
These additional genes remained under
the control of the Pax6 gene and its
homologs.
Retina Cornea
Ommatidia
Lens
Iris
Optic nerve
Drosophila eye
Mammal eye
Figure 26.23 Eye evolution

Coalescence : the merging of genetic lineages backwards
to a most recent common ancestor. An introduction for
phylogenetics.
Genealogy known as family history, is the study of

families and the tracing of their lineages and history.

Evolutionary Genetics

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Evolutionary Genetics

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EVOLUTIONARY GENETICS

Evolutionary developmental biology focuses on the

His broad background in science enabled him to see

Three important influences helped Darwin develop

2. Darwins own experimental observations

3. Thomas Malthus Essay on the Principle of

Alfred Wallace, a naturalist working in the East Indies,

In 1859, Darwin published his book, On the Origin of Species

Darwins work represents one of the most important

Darwin called his theory of evolution the theory of descent

A modern interpretation of evolution can view these

At the gene (microevolutionary) level

At the gene (microevolutionary) level

A species refers to a group of organisms that

The characteristics used may depend on the species in

Many problems with this system

Mark Smith/Photo Researchers Pascal Goetgheluck/ardea.com

(a) Frogs of the same species

Ron Austing/Photo Researchers

(b) Birds of different species

Ernst Mayr expanded on the ideas of Dobzhansky and

Prezygotic barriers block fertilization from

2011 Pearson Education, Inc.

Habitat Temporal Behavioral Mechanical Gametic

(a) (c) (e) (f) (g)

Reduced hybrid viability

2011 Pearson Education, Inc.

(h) (i) (l)

Because of the above, used primarily to

Can look at sequence differences in bacteria

In 1976 Leigh Van Valen proposed the

Each species is a population of an independently

(a) Anagenesis (b) Cladogenesis

Parapatric : two populations occupy overlapping

Sympatric : within a population occupying a single

Genetic drift may lead to rapid fixation of certain alleles and

The formation of a polyploid can abruptly lead to

Galeopsis tetrahit is thought to be the allotetraploid derived

While all three species are physically similar and occupy

Galeopsis tetrahit G. pubescens G. speciosa

Monoploid for one set and

Fertile Infertile Infertile

(b) Outcome of intraspecies and interspecies crosses

Equilibrium Equilibrium Equilibrium

(b) Punctuated equilibrium

These changes can be rapid on an

Phylogeny is the sequence of events involved

Systematists are the biologists interested in

Increasingly, molecular data concerning properties of the

Nucleotide and amino acid sequence data are very well-

The nodes or branch points of the tree illustrate

The tips of the branches represent species that

A monophyletic group or clade is a group of species

Cladogram : A diagram, which depicts a

E F Species A, B, D, and C at tips G I H J

in green are all derived

Figure 26.6 - An example of a phylogenetic tree

Horizontal transfer has changed our

Note that the sequences of the orthologs are more

This idea is schematically shown in Figure 26.13

Thought to have occurred Gene duplication

Ancestral globin gene

A nonneutral mutation is one that affects the

differences in DNA sequence that do not confer a selective