Biology 4250 Evolutionary Genetics

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Biology 4250 Evolutionary Genetics

• Dr. David Innes
• Dr. Dawn Marshall
• W 2008

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Outline of
topics 1. Introduction/History of Interest in
Genetic Variation 2. Types of Molecular
Markers 3. Molecular Evolution 4.
Individuality and Relatedness 5. Population
Demography, Structure Phylogeography 6.
Phylogenetic Methods Species Level
Phylogenies 7. Speciation, Hybridization and
Introgression 8. Human Evolutionary
Genetics 9. Conservation Genetics
Background
Applications
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Geographic Population Structure and Gene Flow

• Most species populations show some genetic
  differentiation
• - siblings near each other and parents
• - local mating (not random across geographic
  range)
• - dispersal seldom includes whole geographic
  range
• Imposes structure
  
• Genetic markers used to reveal population genetic
  structure

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Geographic Population Structure

• Population Genetic Structure due to
• - genetic drift
  (population size)
• - selection
• - spatial habitat
  structure
• - isolation by distance
• - social organization
• - other ecological
  evolutionary
• factors (mating
  system)

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Geographic Population Structure

• Goal
• - Describe pattern of variation within
  between
• populations
• - identify and quantify the biological
  processes
• involved
• - migration and gene flow
• - random genetic drift
• - natural selection
• - mutation
• - genetic recombination
  (function of
• 
  mating system)

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Geographic Population Structure

• Measure of Genetic differentiation
• F statistics (developed by Sewall Wright)
• Inbreeding within population decrease in
  heterozygosity
• 
  
• Inbreeding deviation from random mating
• HWE He 2pq, Ho observed
• 
  F 0 no inbreeding
• F (He - Ho)/He
  F 1 inbreeding
• 
  complete

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Population Genetic Structure

• Population subdivision
• - inbreeding-like effect
• - deviation from random mating
• - greater probability of mating
• within a subdivision
• - effect measured as a decrease
• in heterozygosity

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Population Genetic Structure

• Levels of complexity
• - individual organism (I)
• - subpopulations (S)
• - total population (T)
• HI heterozygosity of an individual in a
  subpopulation
• HS expected heterozygosity of an individual in
  an
• equivalent random mating subpopulation
• HT expected heterozygosity of an individual in
  an
• equivalent random mating total population

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Population Genetic Structure

• Inbreeding coefficients
• FIS (HS - HI)/ HS
• FST (HT - HS)/ HT
• FIT (HT - HI)/ HT
• FST genetic differentiation among populations
  (0 1.0)

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Population Genetic Differentiation
Random Genetic Drift
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Genetic Differentiationdue to genetic drift

• Fst 0
  1.0
• N population size
• m proportion of the pop. that are
• 
  migrants

1
4Nm 1
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Different
Island Model For
any population of size N A small number of
migrants can offset differentiation by genetic
drift

• N m Nm Drift
• .1 1 strong
• 1000 .001 1 weak

Fst
Same
Number of migrants per generation (Nm)
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Gene Flow

• -
• Nm Estimated number of migrants per
• 
  generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
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Summary

• FST and Nm useful measures of genetic
  differentiation and gene flow
• Comparison of gene flow among species
• high, moderate, restricted
• Nm 1 sufficient gene flow to prevent
• high genetic differentiation by
  drift
• alone

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Geographic Population Structure

• General relationships with ecological and
  life-history factors
• - limited dispersal, low gene flow ? genetic
  differentiation
• (rank dispersal ability and potential
  for gene flow)
• - relative importance of gamete and zygote
  dispersal (pollen/seed)
• - association between spatial scale of dispersal
  and spatial
• scale of genetic differentiation
• - autogamous species ? high degree of genetic
• differentiation. Selection on multi-locus
  genotypes

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Marine Gametes and Larvae

• Many marine invertebrates and fish
• - free spawning gametes
• - planktonic larvae
• Wide variation in life-history
• - direct development (no planktonic stage)
• - planktonic larvae (several weeks)
• Expect increased larval dispersal results in
  decreased genetic structure

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Marine Invertebrates Life-histor
y variation, dispersal and gene flow
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Mussel life history
Spat
Settlement
Planktonic larvae 30 days
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Koehn et al. (1984)
II
M. edulis
III
I
Fst 0.006 (5 loci)
III
II
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Marine Fish Species
low
high
high
low
Dispersal ability
Genetic differentiation
Rank order
Waples, 1987
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Marine versus FW

• Marine potential for connections over broad
  areas
• high dispersal limited genetic
  differentiation
• Freshwater discontinuous habitat limited gene
  flow
• Evidence for high levels of genetic
  differentiation for FW copepods and fish.
• Pond Daphnia ?

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Daphnia pulex

• Genetic differentiation among ponds

r 0.28 (p lt0.04)
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Genetic structure Cladocera (Pond/Lake)
Limited genetic differentiation not likely due to
high gene flow. Large population size and weak
genetic drift? Selection?
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Exceptions

• Marine species with pelagic larvae that exhibit
  dramatic population differentiation
• Involving mtDNA differentiation across continuous
  populations best examined using phylogeography
  analysis
• Genetic structure mtDNA vs nuclear genes

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Biogeographic boundary (temperate/tropical) Impedi
ments to gene flow or selection?
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Chaotic Patchiness

• Ephemeral genetic structure
• - highly fecund species (marine invertebrates)
• - variation in sources of larval recruitment
• (recruitment history)
• - larval cohorts differ in genetic composition
• - strong (variable) ecological selection
  pressure
• Examples oyster, intertidal copepod, sea
  urchin, limpet

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Potential Gene Flow

• High dispersal potential - may not translate into
  high gene flow
• - physical impediments to larval movement
• - larval migration and settlement behaviours
• Many larvae fall short of their dispersal
  potential

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Potential Gene Flow

• Selection on marker loci
• High genetic differentiation gives the impression
  of low gene flow
• Allozyme loci may not be neutral
• Example Lap in Mytilus edulis
• Clinal decrease of the Lap94 allele correlated
  with decrease in salinity
• Physiological function associated with
  salinity

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selection
Recruits lt 15 mm
Adults gt 15 mm
Lap94
Mytilus Lap
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Potential Gene Flow

• Contrasting patterns of genetic differentiation
• Allozyme loci - no genetic
  differentiation
• Nuclear DNA markers
• mtDNA
• American Oyster (Crassostrea virginica)

Genetic differentiation
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Oyster
Allozyme loci consistent with high gene flow
mtDNA genetic break
Atlantic Gulf
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Oyster
Interpretation 1. Population subdivision and
allozyme loci under balancing selection? 2.
Allozyme loci indicate high gene flow but mtDNA
differentiation due selection Need for caution
when inferring genetic structure and gene flow
assuming selective neutrality for markers
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Direct Estimates of Dispersal

• Genetic differentiation indirect estimate of
  gene flow
• Direct estimates using rare or unique genetic
  markers
• Example Grosberg 1991

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Pgi-4
Pgi-3
Mdh
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Direct Estimates of Dispersal

• Provides some basic information on dispersal but,
• Limitations
• - finding unique alleles
• - assume no fitness differences
• - difficult to monitor over distance and
  time
• 
  (dilution)
• Undetected rare long-distance gene flow can
  have a significant homogenizing effect