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Evolutionary Genetics
Evolutionary Genetics
I.
Speciation
A. Definition: Mayr’s ‘biological species concept’ – “a
group of actually or potentially interbreeding organisms that is
reproductively isolated from other such groups”.
Evolutionary Genetics
I.
Speciation
A. Definition: Mayr’s ‘biological species concept’ – “a
group of actually or potentially interbreeding organisms that is
reproductively isolated from other such groups”.
- only appropriate for sexually reproducing species
- Reproductive isolation will inevitably lead to greater
genetic divergence (even just by chance), and an increased
likelihood of genetic uniqueness/incompatibility.
Evolutionary Genetics
I. Speciation
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
Drosophila speciation on the Hawaiian Islands.
Recent divergences involve a specie colonizing a new
island (Hawai’i); older divergence occurred in the past,
when older islands first crested above the ocean and
Obbard D J et al. Mol Biol Evol 2012;29:3459-3473
were made available for colonization.
© The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular
Biology and Evolution.
Vicariance – the splitting of a range by a new
geographic feature, such as a river or land mass
(next).
Almost all most recent
divergence events date to 3 my,
and separate species on either
side of the isthmus; suggesting
that the formation of the isthmus
was a cause of speciation in all
these species pairs.
Snapping ‘Pistol’ Shrimp
Mayr – Peripatric Speciation
Small population in
new environment;
the effect of drift and
selection will cause
rapid change, resulting
in a speciation event.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
2. Temporal Isolation
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
2. Temporal Isolation
3. Behavior Isolation - don't recognize one another as mates
Western Meadowlark
Eastern Meadowlark
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
2. Temporal Isolation
3. Behavior Isolation - don't recognize one another as mates
4. Mechanical isolation - genitalia don't fit; limit pollinators
You’re
cute…
You’re
crazy…
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
2. Temporal Isolation
3. Behavior Isolation - don't recognize one another as mates
4. Mechanical isolation - genitalia don't fit; limit pollinators
5. Gametic Isolation - gametes transferred but sperm can't fertilize egg;
this is a common isolation mechanism in species that spawn at the same time
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
B. Post-Zygotic Isolation
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
B. Post-Zygotic Isolation
1. Genomic Incompatibility - zygote dies
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
B. Post-Zygotic Isolation
1. Genomic Incompatibility - zygote dies
2. Hybrid Inviability - F1 has lower survival
Crazy hybrids
A ‘zedonk’
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
B. Post-Zygotic Isolation
1. Genomic Incompatibility - zygote dies
2. Hybrid Inviability - F1 has lower survival
3. Hybrid Sterility - F1 has reduced reproductive success
Horse: 64 chromosomes
Donkey: 62 chromosomes
Mule: 63 non-homologous
chromosomes
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
B. Post-Zygotic Isolation
1. Genomic Incompatibility - zygote dies
2. Hybrid Inviability - F1 has lower survival
3. Hybrid Sterility - F1 has reduced reproductive success
4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes
AABB
x
aabb
F1: AaBb = ok
F2:
A-B- = ok
A-bb = no
aaB- = no
aabb = ok
Evolutionary Genetics
II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers
1. Geographic Isolation (large scale or habitat)
2. Temporal Isolation
3. Behavior Isolation - don't recognize one another as mates
4. Mechanical isolation - genitalia don't fit; limit pollinators
5. Gametic Isolation - gametes transferred but sperm can't fertilize egg; this is a
common isolation mechanism in species that spawn at the same time
B. Post-Zygotic Isolation
1. Genomic Incompatibility - zygote dies
2. Hybrid Inviability - F1 has lower survival
3. Hybrid Sterility - F1 has reduced reproductive success
4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes
All of these – except geographic isolation - are fundamentally genetic in nature because
physiology (gametic), morphology (mechanical), and behavior (temporal and behavioral)
have a genetic component. Obviously, the post-zygotic barriers are entirely genetic.
Speciation is the process of creating a genetically distinct population, which maintains its
distinction in the face of possible hybridization.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
- Evolution and speciation are not the same:
Evolution is a change in the genetic structure of a population
Speciation is the establishment of reproductive isolation
between populations.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
- Evolution and speciation are not the same:
Evolution is a change in the genetic structure of a population
Speciation is the establishment of reproductive isolation
between populations.
- Two populations can evolve over time, but maintain gene flow and not
speciate.
- Two populations can become geographically isolated and be ‘good
species’, while being genetically similar.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
- Evolution and speciation are not the same:
Evolution is a change in the genetic structure of a population
Speciation is the establishment of reproductive isolation
between populations.
- Two populations can evolve over time, but maintain gene flow and not
speciate.
- Two populations can become geographically isolated and be ‘good
species’, while being genetically similar.
- Small genetic differences can create genomic incompatibility, change in
genitalia, or behavioral differences that cause speciation. So, while increasing
genetic divergence increases the probability of speciation, small changes can
cause reproductive isolation, too.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- rate of mutation, introducing new variation
(AIDS virus – error-prone reverse transcriptases
introduce many mutations each generation, changing the surface proteins and
making it very hard for our immune systems to eliminate all of them.)
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- rate of mutation, introducing new variation
- size of the population
(freq of new allele = 1/2N; so a mutation in a small
population will be at a higher frequency that it would be in a large population)
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- rate of mutation, introducing new variation
- size of the population
- effect of this variation
(deleterious and adaptive mutations will change
frequency rapidly in response to selection; neutral variation will change by drift,
alone.)
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- rate of mutation, introducing new variation
- size of the population
- effect of this variation
- rate of reproduction of the population
Populations with high reproductive rates should change
faster that populations with low reproduction rates.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
As a result of the sequencing boom that began in the 1960’s, biologists
realized that there was an extraordinary amount of genetic variation in most
populations – variation at the molecular level in DNA sequence.
- On average, About 20-30% of all loci are polymorphic
(have at least 2 alleles with frequencies over 1%).
- D. melanogaster has 10,000 loci, so 3000 are polymorphic.
- At these polymorphic loci, Heterozygosity = 0.33
Variation in the alcohol dehydrogenase gene, fixed in different populations
of Drosophila melanogaster
This is the only
variation that
changes an
amino acid; all
others are
‘silent’
The frequency of different disease-causing mutations in the CFTR gene.
Each different mutation is a different allele; most of them are very rare
(<1.0%), and all of them are deleterious so selection keeps them rare.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
As a result of the sequencing boom that began in the 1960’s, biologists
realized that there was an extraordinary amount of genetic variation in most
populations – variation at the molecular level in DNA sequence.
- On average, About 20-30% of all loci are polymorphic
(have at least 2 alleles with frequencies over 1%).
- D. melanogaster has 10,000 loci, so 3000 are polymorphic.
- At these polymorphic loci, Heterozygosity = 0.33
Selection can’t maintain all this heterozygosity (like with sickle cell); we would
each be homozygous for at least one deleterious recessive and have reduced
fitness. Something ELSE must be maintaining this variation….. Motoo Kimura
suggested that most variation was neutral, maintained by drift.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
- Predictions of the Neutral Model:
Rates of substitution should be higher in non-functional
(neutral) regions of proteins, in introns, and in the third position of
codons, because changes here are neutral. - CONFIRMED
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
- Predictions of the Neutral Model:
Rates of substitution should be higher in non-functional (neutral) regions of
proteins, in introns, and in the third position of codons, because changes here are
neutral. – CONFIRMED
The rate of molecular evolution (substitutions) should be
independent of the rate of morphological change; a species that
changes slowly morphologically can still be changing as rapidly,
genetically, as a species that changes fast morphologically. CONFIRMED
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
- Predictions of the Neutral Model:
Rates of substitution should be higher in non-functional (neutral) regions of
proteins, in introns, and in the third position of codons, because changes here are
neutral. – CONFIRMED
The rate of molecular evolution (substitutions) should be independent of the
rate of morphological change; a species that changes slowly morphologically can still be
changing as rapidly, genetically, as a species that changes fast morphologically. –
CONFIRMED
The rate of substitution of one allele in a population by another
allele should occur at a constant rate – a molecular ‘clock’ CONFIRMED.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
- depends on:
- patterns:
- Predictions of the Neutral Model:
- Problem:
In the neutral model, mutations should accumulate at a constant
rate…but constant in relative time – relative to the generation time of the
organism. Species with short generation times should accumulate changes more
rapidly than species that have longer generation times. This is true for non-coding
DNA, as expected for neutral DNA.
But it is NOT true for proteins and protein coding sequences, where AA
substitution rates are constant in absolutely time across species – suggesting that
some selection is acting. Ohta’s “nearly neutral” model
The Nearly Neutral Model (Ohta)
Sub. Rate
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
OBS.
EXP.
Short
GEN TIME
Long
The Nearly Neutral Model (Ohta)
SO.
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
- So, something must be 'slowing down' this rate of substitution in
species with short gen. times. What's slowing it down is their large
populations size, such that the effects of drift, alone, are reduced.
Sub. Rate
LARGE
POP. SIZE
OBS.
EXP.
Short
GEN TIME
Long
The Nearly Neutral Model (Ohta)
SO.
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
- So, something must be 'slowing down' this rate of substitution in
species with short gen. times. What's slowing it down is their large
populations size, such that the effects of drift, alone, are reduced.
- Likewise, species with long generation times have small
populations, and substitution by drift and fixation is more rapid than
expected based on generation time, alone.
Sub. Rate
SMALL POP.
SIZE
OBS.
EXP.
Short
GEN TIME
Long
The Nearly Neutral Model (Ohta)
SO.
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
- So, something must be 'slowing down' this rate of substitution in
species with short gen. times. What's slowing it down is their large
populations size, such that the effects of drift, alone, are reduced.
- Likewise, species with long generation times have small
populations, and substitution by drift and fixation is more rapid than
expected based on generation time, alone.
SMALL POP.
SIZE
Sub. Rate
SO.
- The constant
rate of AA
substitution
across species
is due to the
balance between
generation time
and population
size.
OBS.
EXP.
Short
GEN TIME
Long
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
C. Using Molecular Clocks
- the more differences there are, the more time must have elapsed since
a common ancestor for these differences to accumulate.
- If we know the rate of change for a given set of genes or proteins, then
we can estimate the absolute time since divergence.
Sequences of cytochrome c from NCBI
>Arabidopsis
MASFDEAPPGNPKAGEKIFRTKCAQCHTVEKGAGHKQGPNLNGLFGRQSGTTPGYSYSAA
NKSMAVNWEEKTLYDYLLNPKKYIPGTKMVFPGLKKPQDRADLIAYLKEGTA
>Euglena
GDAERGKKLFESRAGQCHSSQKGVNSTGPALYGVYGRTSGTVPGYAYSNANKNAAIVWED
ESLNKFLENPKKYVPGTKMAFAGIKAKKDRLDIIAYMKTLKD
>Hippo
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQSPGFSYTDANKNKGITWG
EETLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKQATNE
>Mosquito
MGVPAGDVEKGKKLFVQRCAQCHTVEAGGKHKVGPNLHGLFGRKTGQAAGFSYTDANKAK
GITWNEDTLFEYLENPKKYIPGTKMVFAGLKKPQERGDLIAYLKSATK
>Rice
MASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTA
NKNMAVIWEENTLYDYLLNPKKYIPGTKMVFPGLKKPQERADLISYLKEATS
Euglena
0.02
Eu glen a
Mosquito
Mosquit o
Hippo
Hippo
Rice
Ri ce
Arabidopsis
Arabidopsis
Unresolved molecular phylogenies of gibbons
and siamangs (Family: Hylobatidae) based on
mitochondrial, Y-linked, and X-linked loci
indicate a rapid Miocene radiation or sudden
vicariance event
Molecular Phylogenetics and Evolution, Volume
58, Issue 3, March 2011, Pages 447-455
H. Israfil, S.M. Zehr, A.R. Mootnick, M. Ruvolo,
M.E. Steiper
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
C. Using Molecular Clocks
D. Concordant Phylogenies
D. Concordant Phylogenies
IF species are descended from common ancestors (like people
in a family), and
IF we know the rate of genetic change (mutation),
THEN we should be able to compare genetic similarity and
predict when common ancestors lived.
AND, if the fossil record is also a product of evolution, THEN the
species though to be ancestral to modern groups should exist at
this predicted age, too.
In other words, we should be able to compare DNA and protein
sequences in living species and predict where, in the
sedimentary strata of the Earth’s crust, a third different species
should be.
D. Concordant Phylogenies
Clustering analysis based on amino acid
similarity across seven proteins from 17
mammalian species.
D. Concordant Phylogenies
Now, we date the oldest mammalian fossil,
which our evolution hypothesis dictates
should be ancestral to all mammals, both the
placentals (species 1-16) and the marsupial
kangaroo. …. This dates to 120 million years
16
D. Concordant Phylogenies
And, through our protein analysis, we already
know how many genetic differences
(nitrogenous base substitutions) would be
required to account for the differences we see
in these proteins - 98.
16
D. Concordant Phylogenies
So now we can plot genetic change against time, hypothesizing
that this link between placentals and marsupials is ancestral to
the other placental mammals our analysis.
16
D. Concordant Phylogenies
Now we can test a prediction. IF genetic similarity arises from
descent from common ancestors, THEN we can use genetic
similarity to predict when common ancestors should have lived...
16
D. Concordant Phylogenies
This line represents that prediction. Organisms with more similar
protein sequences (requiring fewer changes in DNA to explain
these protein differences) should have more recent ancestors...
16
D. Concordant Phylogenies
And the prediction here becomes even MORE
precise. For example, we can predict that two
species, requiring 50 substitutions to explain the
differences in their proteins, are predicted to have
a common ancestor that lived 58-60 million years
ago...
16
D. Concordant Phylogenies
Let’s test that prediction. Rabbits and the rodent differ in protein
sequence to a degree requiring a minimum of 50 nucleotide
substitutions... Where is the common ancestor in the fossil record?
D. Concordant Phylogenies
Just where genetic analysis of two different EXISTING species
predicts.
16
D. Concordant Phylogenies
OK, but what about all of our 16 "nodes"? Evolution predicts that
they should also exist on or near this line....
16
D. Concordant Phylogenies
And they are. Certainly to a degree that supports our
hypothesis based on evolution. Concordance between
molecular clocks and the geologic record
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
C. Using Molecular Clocks
D. Concordant Phylogenies
E. Rates of Speciation
- Speciation can be an instantaneous genetic event – through polyploidy,
or mutation that affects specific genes important in forming a reproductive
isolating barrier.
Evolutionary Genetics
II. Making Species - Reproductive Isolation
III. Rates of Evolution and Speciation
A. Evolution and Speciation
B. Rates of Evolution
C. Using Molecular Clocks
D. Concordant Phylogenies
E. Rates of Speciation
- Speciation can be an instantaneous genetic event – through polyploidy,
or mutation that affects specific genes important in forming a reproductive
isolating barrier.
- But speciation can also be a continuous process, reflecting the
accumulation of genetic differences. Still, these differences might accumulate at
a steady rate or at episodic rates.
- But speciation can also be a continuous process, reflecting the
accumulation of genetic differences. Still, these differences might accumulate at
a steady rate or at episodic rates.
- 1972 - Eldridge and Gould - Punctuated Equilibrium
VARIATION
1. Consider a large, well-adapted population
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
1. Consider a large, well-adapted population
VARIATION
Effects of Selection and Drift are small - little
change over time
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
VARIATION
2. There are always small sub-populations "budding off" along the
periphery of a species range...
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
2. Most will go extinct, but some may survive...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
2. These surviving populations will initially be small, and in a new
environment...so the effects of Selection and Drift should be
strong...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
3. These populations will change rapidly in response...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
3. These populations will change rapidly in response... and as they
adapt (in response to selection), their populations should increase
in size (because of increasing reproductive success, by definition).
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
3. As population increases in size, effects of drift decline... and as a
population becomes better adapted, the effects of selection
decline... so the rate of evolutionary change declines...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
4. And we have large, well-adapted populations that will remain
static as long as the environment is stable...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
5. Since small, short-lived populations are less likely to leave a
fossil, the fossil record can appear 'discontinuous' or 'imperfect'
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
5. Large pop's may leave a fossil....
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
5. Small, short-lived populations probably won't...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
6. So, the discontinuity in the fossil record is an expected result of
our modern understanding of how evolution and speciation occur...
VARIATION
X
X
X
TIME
- 1972 - Eldridge and Gould - Punctuated Equilibrium
6. both in time (as we see), and in SPACE (as changing
populations are probably NOT in same place as ancestral species).
VARIATION
X
X
X
TIME
Darwin’s Dilemmas:
Evolution of Complex Traits:
1. Structures with mutually dependent parts CAN
evolve through a stepwise process
Darwin’s Dilemmas:
Evolution of Complex Traits:
Ornamentation and attraction
homeothermy
flight
2. Structures may have evolved for other selective
reasons than we observe now.
Darwin’s Dilemmas:
Evolution of Complex Traits:
Source of Heritable Variation:
…. Genetics!
Nice Job !
You, too!
Darwin’s Dilemmas:
Evolution of Complex Traits:
Source of Heritable Variation:
Discontinuity of Fossil Lineages:
VARIATION
Peripatric Speciation and
Punctuated Equilibrium
Genetics has tested and
confirmed Darwin’s ideas and
solved his dilemmas
TIME