Transcript Powerpoint

Gene flow
Natural populations of a species
typically are not completely isolated,
but instead exchange genes with one
another to a greater or lesser extent
Gene flow, if unopposed by other
factors, homogenizes a population
Models of Gene flow
Island models
Stepping stone models
Isolation by distance models
Gene flow
 Homogenizes the populations within a
species (unopposed by other forces)
 Rate of gene flow = m
 A1 varies among populations (pi) resident
 the average allele frequency in source
population is p (i.e. immigrant coming from)
 within population i (pi), a proportion of m of
the gene copies enter from other
populations, and the frequency is p
Gene flow
m
= migrant
Source
p
pi
resident
Gene flow
 A proportion (1-m) of the gene copies are
non-immigrants and among these the
frequency is pi
 After 1 generation the populations new
allele freq (p’) is:
pi’ = pi(1-m) + pm
or
pi’ = pi-pim + pm
So........Δp = m(p – pi)
Gene flow
m
= 0.001
p=0.3
p=0.1
resident
Source
1 in a 1000 is a migrant
Gene flow
Δpi = m(p-pi) = 0.001(0.3-0.1) =.0002
pi’ = pi(1-m) + pm = 0.1(1-0.001)+0.3*0.001
=0.1002
Equilibrium Frequency
 Equilibrium frequency is found by setting p’ = 0
(or Δp = 0), which is where p’ is not changing
between generations and is, thus, in equilibrium
So... Δp = 0 = m(p-p) thus p = p
Therefore, each population will ultimately
attain the same allele frequencies showing
that gene flow homogenizes populations
Gene flow and drift
 In the absence of gene flow populations tend to
diverge due to drift
 Fst = fraction of autozygotes in a sub-population
at time t
 Another way to look at this is that Fst is a
measure of the observed variation in allele
frequency among populations
Fst = 1- (1-½N)t
see page 315, box 11.D
Gene flow and Drift
Fst must reach an equilibrium
between drift and gene flow
Thus Fst = 1 / (4Nm + 1)
Gene flow
 We can rearrange Fst = 1 / (4Nm + 1) so
that we can estimate the average # of
immigrants into a population per
generation
Nm = 1 / (Fst – 1)
 Notice! This tells us that the higher the
rate of gene flow, the more similar the
allele frequencies between populations
 Conversely, observing a strong
divergence indicates that the balance
between gene flow and drift is tipped
toward drift
Estimating Fst
Direct estimates of gene flow
Mark-recapture studies...
Indirect estimates of gene flow
Alleles used to calculate Fst are neutral
Allele frequencies must have reached
equilibrium between gene flow and drift
Gene Flow Example!
 Water snakes of Lake Erie
 Nerodia sipedon
 Live on mainland and on several islands
 Color pattern variable
 Strongly banded to unbanded
 Banding controlled by a single locus with two
alleles
 Banded is dominant over unbanded
 On mainland most snakes are banded
 On island many are unbanded
Gene Flow...
 Water snakes of Lake Erie
 Banding pattern due to natural selection
 On islands snakes bask on rocks
 On mainland stay closer to vegetation
 Why is the unbanded allele not fixed on
islands?
 Banded snakes migrate from mainland
each generation
 Bring banded alleles to island gene pool
 Migration works in opposition to natural
selection
Conservation Genetics
 Westermeier’s hypothesis
 Destruction of prairie did two things
 Reduced population size
 Fragmented remaining population
 Remaining prairie chickens were trapped in
two islands in seas of farmland
 Genetic drift caused decline in heterozygosity
 Inbreeding depression occurred
Conservation Genetics
 Accumulation of deleterious recessives
leads to reduction in population size
 Effectiveness of genetic drift is increased
 Speed and proportion of deleterious
mutations going to fixation increases
 Population size decreases more
 Mutational Meltdown (synergistic
interaction between mutation, pop. Size
and drift)
Conservation Genetics
Prairie chickens caught in mutational
meltdown
Reproductive success decreased
Hatching success low
Birds had fallen into extinction
vortex
Birds needed gene flow
Conservation Genetics
 In 1992 conservationists trapped birds
from Minnesota, Kansas, and Nebraska
and moved them to Jasper County, Illinois
 Hatching rate increased and population
began to grow
 Migration, genetic drift, and nonrandom
mating all contributed to fate of Illinois
greater prairie chickens
Conclusions about Gene Flow
1. Certain taxa display substantial gene
flow over long distances
2. But on average the level of gene flow is
greatly restricted over short distances


Implies local populations can diverge
substantially due to drift
Thus, species can adapt to local
conditions!!!!
Neutrality
A new mutation takes 4Ne to be fixed
What happens if you have a large Ne?
Ne = 2000  fixation in 8000 gens.
Ne = 1000  fixation in 4000 gens.
Ne = 500  fixation in 2000 gens.
Neutrality
In larger populations (larger Ne)
fixation may take a very long long
time!
Other mutations arise in the interim
Additional mutations arise!
 For example, if the mutation rate is 10-9
(=substitutions per site per gamete per
generation)
 Given a gene is 1000 nucleotides long...
 What is our mutation rate over this
gene/gamete/generation?
  10-6 if we have Ne = 1000 (with 2N gene
copies)
 10-6(mutations/gene) X 2000(=2N) X 4000(generations)=
8 mutations per gene over 4000 generations!!!
Additional mutations arise!
 Given an estimated 8 mutations in a gene
over 4000 generations
 And the probability that a new mutation
will be fixed 1/2Ne
 There will be a STEADY substitution of
alleles
 Therefore: in such large effective
populations, we generally expect at least
moderate levels of polymorphism
(multiple alleles per loci) given our
calculations above!
What have we assumed during
these calculations?
In calculating the preceding stats for
mutation and allele generation we
assumed NO selection for or against
particular alleles
We therefore assumed they were
selectively NEUTRAL....
The Assumption of Neutrality
Mayr:
“It is unlikely that two genes would have
identical selective values under all
conditions that they must exist in a
population Thus, cases of neutral
polymorphisms do not exist, it then
appears that random fixation is of
negligible evolutionary importance”
The Assumtion of Neutrality
 Lewontin and Hubby (1966)
 “Natural selection could not maintain so much
genetic variation.” Suggested that much of the
variation is selectively neutral.
 M. Kimura (1968)
 Demonstrated similar rates of evolution
between lineages. Concluded that such a
constancy could not be maintained by natural
selection, must instead be by mutation and
genetic drift.
The Neutral Theory of
Molecular Evolution
 Contends that:
 a small minority of mutations in DNA
sequences are advantageous and are fixed by
Natural Selection and although some are
disadvantageous and are eliminated by
“purifying” Selection...
 the great majority of mutations that are fixed
are effectively neutral with respect to fitness,
and are fixed by genetic drift
The Neutral Theory of
Molecular Evolution
 Most genetic variation is selectively neutral and
lacks adaptive significance
 BUT, this is not to say that phenotypic change
evolves by genetic drift!..... Instead, phenotypic
characters evolve by natural selection
 The neutral theory acknowledges that many
mutations are deleterious and are eliminated by
natural selection
 It holds that MOST of the variation we see at the
molecular level is neutral and has no adaptive
role (i.e. No effect on fitness)
The Neutral Theory of
Molecular Evolution
 Neutral Mutation Rate u0 = f0ut
 Certain alleles are effectively neutral
 No benefit or hindrance to fitness or so
small it is not a problem (eg. s=0.001)
 In other words, the mutant allele is so
similar to other alleles in fitness that
changes in its frequency are governed by
drift alone, not by natural selection!
The Neutral Theory of
Molecular Evolution
 Small population (500) and s=0.001
 simulations show that most variation is
due to drift...
 But, in a large population (5000), natural
selection will be more important since the
power of drift decreases (given the large
pop. size)
 Thus, an allele may be effectively neutral
in one population but not in another,
simply due to the Ne
The Neutral Theory of
Molecular Evolution
 Examples (Genetic constraints, codons)
 The amino acid Leucine is encoded by 6
possible codons:
CUU
Here we can envision that changing the
DNA sequence to any one of the 6 possible
Leucine codons would be unlikely to have
any effects on fitness or even phenotype!
CUC
CUA
CUG
UUA
UUG
Types of DNA Substitution
Synonymous VS. Nonsynonymous
DNA1
DNA2
= AAA GCT CAT
= AAG GCT GAT
Protein1 = Lys
Protein2 = Lys
Ala
Ala
Synonymous
mutation
His
Asp
GTA GAA
GTA GAA
Val
Val
Glu
Glu
Nonsynonymous
mutation
Substitutions in DNA
Mutations occur at the 3rd position
most frequently and 2nd most
infrequently
Neutral mutation rate would be
greatest in DNA seq. that is not
transcribed and has known function
(e.g. Pseudogenes, introns, spacers,
etc.)
Substitutions in DNA
The number of new mutations is
u0 * 2Ne
We know that a mutation will become
fixed at a frequency of p, which
equals 1/2Ne since 2Ne gene copies
might mutate
Substitutions in DNA
 The number of neutral mutations that will
someday become fixed is
2Neu0 * 1/2Ne
 This can be reduced to u0 (which is the
neutral mutation rate)
 This rate of mutation is theoretically
constant and equals the neutral mutation
rate!!!!!
 Most molecular polymorphisms are
selectively neutral
Variation Loss VS Gain
 If a locus evolves purely by drift, all
variation will be ultimately lost (F=1,
autozygous)
 What happens if a mutation arises……it
becomes allozygous (F<1)
 Steady State – a balance between the rate
of loss of variation by genetic drift and by
the rate of gain of variation by mutation
Alleles Continually Arise By Mutation!
 We have just demonstrated that new
alleles arise continuously via mutation
 Many are lost by genetic drift, but others
drift higher and get fixed over 4Ne
generations.
 Remember allele freqs. sum to 1 so
previously common alleles have drifted
lower and are ultimately lost
Steady Turnover in Alleles
 Over time we generally see a steady
turnover in alleles
 The level of variation (H) remains about
the same and is Higher in Large
populations, Lower in Small populations
 Thus, there must be a positive correlation
between heterozygosity at a locus and its
rate of evolution…
Variation within & among
Species
Nonsynonymous and Synonymous
changes in protein coding sequence
expect the ratio of Ks:Ka to be 1:1 or
less (due to purifying selection)
(eg. adh loci)
Rates of Molecular Evolution
What do we expect to see….
We would expect that rates of
evolution are greatest at DNA
positions that, when altered, are
least likely to effect function…
Rates of Molecular Evolution
Rates of Molecular Evolution
Neutralist debate
The fight between selection and drift
Population Structure and gene trees
Coalescence Over time
Coalescence
 If you have a population that is divided by
something and there is no gene flow
between populations what will eventually
happen over time?
 Ultimately, all the gene copies in each will
be descendants of one of the copies that
was included in each population at the
time of isolation
 Each population will have a monophyletic
gene tree (or is at least likely to, given
enough time)
Coalescence
Coalescent Theory
Coalescent Theory tells us that under
certain conditions the Gene tree may
not match the Species tree
Coalescent Theory
Coalescent Theory
 Thus, a gene tree is most likely to provide
accurate information about a phylogeny of
a species if populations have been small
or the time between successive speciation
events have been great
 Similarly, Gene tree is LEAST likely to
match the Species tree when populations
have been large or speciation events
occurred rapidly
CHAPTER 12
Natural Selection
and Adaptation
ADAPTATIONS
ADAPTATIONS
ADAPTATIONS
Most adaptations are complex
The appearance of design
ADAPTATIONS
Adaptations have been “designed”
by a completely “mindless” process
Evolutionary theory does not admit
anticipation of future
Teleological (incorrect) view –
processes which invoke goals or end
points
Adaptation by Evolution by
Natural Selection!!!
Evolutionary theory by Natural
Selection must be able to account for
the origin of complex adaptations
that increase ones fitness
But, Natural Selection must also be
able to account for traits that do not
increase fitness (e.g. bee sting,
anaphylactic shock)
Adaptation
Hitchhiking
linkage to another allele that increases
fitness
Stable Equilibrium
natural selection must be acting in such
ways to maintain variation; it does not
necessarily cause fixation of a single
best genotype
Tungara Frog – Conflicting Selection
If males “CHUCK” females will
respond favorably YET….. Exposes
males to greater risk of predation by
bats
Tungara Frog
Conflicting
Selection
Tuni
Tungara
Natural Selection
 Definition of Natural Selection:
 Include a trait must vary among biological
entities, and there must be a consistent
relationship between the trait and one or more
components of reproductive success
 Short version of Natural Selection:
 Any consistent difference in fitness among
phenotypically different biological entities
(inherited)
Adaptation
Process of becoming adapted
Or
To the features of organisms that
enhance reproductive success
relative to other possible features
Recognizing Adaptation?
 Includes a Phylogenetic Component
 Fleas (wingless adaptation)
 Bristle tails (primitively wingless)
 Traits evolve from pre-existing ones so its’
phylogenetic position is important
 Preadaptation
 a feature that fortuitously serves a new
function (the kea in New Zealand)
What is Adaptation?
Our definition
a feature is an adaptation for some
function if it has become prevalent or is
maintained in a population because of
natural selection for that function
Nonadaptive Traits
 Trait might be necessary consequence
(flying fish)
 Evolved by random genetic drift rather
than Natural Selection (grouse chick
patterns – cryptic but drift in patterns
occur among species)
 Hitchhiking (linkage of traits)
 has not become adaptively altered to a
response (big fruits, extinct mammals)
How do we recognize
adaptations?
 Complexity
 Design
 Experimental Evidence
 Comparative Method – uses phylogeny to
compare trait evolution among groups of
species
 Convergent Evolution – trait which is
correlated between lineages (2 different
groups evolved the same or similar
adaptation independently)