 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

 Island models
 Stepping stone models
 Isolation by distance models

 Homogenizes the populations within a species (unopposed by other forces)
 Rate of gene flow = m
 A
1 varies among populations (p i
) resident
 the average allele frequency in source population is p
(i.e. immigrant coming from)
 within population i (p i
), a proportion of m of the gene copies enter from other populations, and the frequency is p

Source p
m
= migrant p i resident

 A proportion (1-m) of the gene copies are non-immigrants and among these the frequency is p i
 After 1 generation the populations new allele freq ( p’) is: p i
’ = p i
(1-m) + pm or p i
’ = p i
-p i m + pm
So........
Δp = m(p – p i
)

p=0.3
Source
m
= 0.001
p=0.1
resident
1 in a 1000 is a migrant

Δp i
= m(p-p i
) = 0.001(0.3-0.1) =.0002
p i
’ = p i
(1-m) + pm = 0.1(1-0.001)+0.3*0.001
=0.1002

 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

 In the absence of gene flow populations tend to diverge due to drift
 F st
= fraction of autozygotes in a sub-population at time t
 Another way to look at this is that F st is a measure of the observed variation in allele frequency among populations
F st
= 1- (1½N) t see page 315, box 11.D

 F st must reach an equilibrium between drift and gene flow
 Thus F st
= 1 / (4Nm + 1)

 We can rearrange F st
= 1 / (4Nm + 1) so that we can estimate the average # of immigrants into a population per generation
Nm = 1 / (F st
– 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

st
 Direct estimates of gene flow
 Mark-recapture studies...
 Indirect estimates of gene flow
 Alleles used to calculate F st are neutral
 Allele frequencies must have reached equilibrium between gene flow and drift

 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

 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

 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

 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)

 Prairie chickens caught in mutational meltdown
 Reproductive success decreased
 Hatching success low
 Birds had fallen into extinction vortex
 Birds needed gene flow

 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

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!!!!

 A new mutation takes 4N e to be fixed
 What happens if you have a large N e
?
 N e
 N e
 N e
= 2000  fixation in 8000 gens.
= 1000  fixation in 4000 gens.
= 500  fixation in 2000 gens.

 In larger populations (larger N e
) fixation may take a very long long time!
 Other mutations arise in the interim

 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 N e copies)
= 1000 (with 2N gene
 10 -6
(mutations/gene)
X 2000
(=2N)
X 4000
(generations)
=
8 mutations per gene over 4000 generations!!!

 Given an estimated 8 mutations in a gene over 4000 generations
 And the probability that a new mutation will be fixed 1/2N e
 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!

 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....

 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”

 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.

 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

 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)

 Neutral Mutation Rate u
0
= f
0 u t
 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!

 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 N e

 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

DNA1 = AA A GCT C AT GTA GAA
DNA2 = AA G GCT G AT GTA GAA
Protein1 = Lys Ala His Val Glu
Protein2 = Lys Ala Asp Val Glu
Synonymous mutation
Nonsynonymous mutation

 Mutations occur at the 3 rd position most frequently and 2 nd 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.)

 The number of new mutations is u
0
* 2N e
 We know that a mutation will become fixed at a frequency of p, which equals 1/2N e might mutate since 2N e gene copies

 The number of neutral mutations that will someday become fixed is
2N e u
0
* 1/2N e
 This can be reduced to u
0 neutral mutation rate)
(which is the
 This rate of mutation is theoretically constant and equals the neutral mutation rate!!!!!
 Most molecular polymorphisms are selectively neutral

 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 4N e generations.
 Remember allele freqs. sum to 1 so previously common alleles have drifted lower and are ultimately lost

 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…

 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)

 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…

 The fight between selection and drift
 Population Structure and gene trees

 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)

 Coalescent Theory tells us that under certain conditions the Gene tree may not match the Species tree

 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

 Most adaptations are complex
 The appearance of design

 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

 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)

 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

Tuni
Tungara
Tungara Frog
Conflicting
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)

 Process of becoming adapted
Or
 To the features of organisms that enhance reproductive success relative to other possible features

 Includes a Phylogenetic Component
 Fleas (wingless adaptation)
 Bristle tails (primitively wingless)
 Traits evolve from preexisting ones so its’ phylogenetic position is important
 Preadaptation
 a feature that fortuitously serves a new function (the kea in New Zealand)

 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

 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)

 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)