Biology 4250 Evolutionary Genetics

1
Biology 4250 Evolutionary Genetics

• Winter 2007
• Dr. David Innes
• Dr. Dawn Marshall
• Lab Monday 3pm
• Readings for Monday Lab.
• http//www.mun.ca/biology/dinnes/B4250/Biol4250.ht
  ml
• Lab 2 exercise

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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, Population Structure 6. Phylogenetic
Methods Species Level Phylogenies --------
Midterm break --------------------- 7.
Phylogeography 8. Speciation, Hybridization and
Introgression 9. Human Evolutionary Genetics 10.
Conservation Genetics
Background
Applications
3
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

4
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)

5
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)

6
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

7
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

8
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
12
Different

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

Fst
Same
Number of migrants per generation (Nm)
13
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

15
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)

16
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
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. 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

35
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

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Vagility, Philopatry and Dispersal Scale

• - Spatial scale of gene flow influenced by
  mobility
• But
• - population structure not tightly linked
  to vagility
• Why not?
• - physical or ecological barriers
• behaviour social interactions, habitat choice,
  philopatry
• - gender-biased dispersal and gene flow
• - natural selection on genetic markers
• - historical demographic events

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Physical Dispersal Barriers

• Waterstriders
• within streams Fst 0.01
• between streams Fst 0.46

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Philopatry to Natal Site
Wide ranging but return specific localities to
breed (natal sites) gene flow restricted Turtles
, Salmon Birds some species exhibit nest-site
philopatry allozyme Fst 0.02
suggesting high interpopulation gene
flow However, mtDNA revealed a wide variety of
population genetic structures - minimal
differentiation
- historical subdivisions
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Gender-Biased Dispersal
Faithfulness to natal site or social group gender
biased Mammals male-biased dispersal Birds
female-biased dispersal Gender-biased dispersal
differences in genetic structure among -
biparental transmission loci (most nuclear)
- uniparental transmission (mtDNA, Y, W)
(Exceptions)
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Non-neutrality of Genetic Markers
Neutral markers (not under selection)
Therefore, all markers should provide the same
information on genetic structure Variation in
Fst estimates among loci could indicate

selection Loci with Low Fst
- neutral high gene flow
- limited gene flow selection
High Fst - neutral low gene
flow - high
dispersal selection
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Non-neutrality of Genetic Markers
Allozyme loci enzyme protein phenotype
potential for selection Advice
from Avise use a large number of independent
genetic markers small selective effects may
average out and the dominant pattern
reflects gene flow
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Historical Demographic Events
Population genetic models assume equilibrium

(drift/gene flow) Many populations not likely in
equilibrium Bottlenecks (founder events) can
reduce Ne Historical demographic events
non-equilibrium conditions must affect genetic
structure Difficult to test particular
explanations Alternative explanations often
compatible with data
44
Historical Demographic Events
Boileau et al. (1992) - arctic pond
invertebrates genetic structure - no
association between dispersal potential and
degree of genetic differentiation -
de-glaciation history populations lt 3000 years
old therefore populations not in
equilibrium - simulations founder
event ? genetic differentiation rapid
increase in population size genetic
structure resistant to decay by gene flow

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Population Genetic Structure Summary
Criticism Whitlock and McCauley (1998)
Fst 1/(4Nm 1) Fst a good
measure of genetic structure but not useful to
translate into an estimate of contemporary gene
flow Bossart and Prowell (1998) (several
problems) - multiple explanations for patterns
- confounding contemporary patterns with
historical associations
46
Spiders
Silene acaulis
Fst
Pardosa hyperborea 0.019
Pardosa moesta 0.068
Pardosa groenlandica 0.184
Araneus diadematus 0.074
Fst 0.241
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Geographic Population Structure

• General relationships with ecological and
  life-history factors
• Example Degree of genetic differentiation in
  plants
• associated with
• Breeding system (selfing
  outcrossing)
• Reproductive mode (sexual
  asexual)
• Pollination mechanism (animal
  wind)
• Floral morphology (monoecious
  dioecious)
• Life form (annual perennial)
• Successional stage (early late)

48
Geographic Population Structure

• General relationships with ecological and
  life-history factors
• Animals meta-review
• - more mobile organisms show less genetic
  structure
• than relatively sedentary organisms
• coefficient
  of
• gene
  differentiation
• birds 0.076
• insects 0.097
• reptiles 0.258
• amphibians 0.315

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Gastropods
Sea stars
Genetic differentiation
Overall Rank correlation -0.72
Rank dispersal ability
Bohonak, 1999
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Autogamous mating systems

• Plants
• Avena barbata
• -introduced into California
• self-pollinating
• intense selection limited recombination
• two co-adapted multi-locus genotypes
• xeric, mesic soils
• microgeographic differentiation

51
Autogamous mating systems

• Animals
• Hermaphoditic snail Rumina decollata
• two strains
• dark covered, mesic habitats
• light open, xeric habitats
• Strong multilocus associations
• Introduced into E. NA single genotype
• distributed across a variety of habitats

52
Distribution of Dark and light snails
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Gametic and Zygotic dispersal

• Pollen and Seeds - outcrossing plants
• - pollen mobile male gametes (wind, insect,
  mammals)
• - egg - sedentary
• - seeds (zygotes) dispersed animals,
  gravity, wind
• Gametic and Zygotic dispersal mechanisms can
  influence gene flow and genetic structure

54
Gametic and Zygotic dispersal

• Approach
• 1. Rank order species predict magnitude of
• gene flow based on pollen and seed
  dispersal
• 2. Empirical estimates of gene flow
• Tropical trees (outcrossing, animal pollination
  and seed dispersal)
• - significant association (50 of
  variation)
• Temperate zone trees (broad distributions, wind
  pollinated)
• - moderate to high gene flow
• - lower gene flow for species with
  isolated populations

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Gametic and Zygotic dispersal

• Plant population genetic structure
• Reviews of 300 450 published allozyme data
  sets
• What life-history and ecological traits
  associated with degree of genetic
  differentiation?
• - 16 of heterogeneity in genetic structure
  explained
• - Most important predictor of genetic
  structure
• selfing annual

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Pollen vs Seed Dispersal
Fragmented landscapes reduced gene flow Pollen
thought to be main vector for gene flow Showed
that seed dispersal 6X as effective as pollen
dispersal for gene flow Fraxinus excelsior common
ash
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Potential seed dispersal events (pair-wise
distances between 88 trees and 60 seedlings)
Observed seed dispersal 5 microsatellite loci
used to identify parent tree 68 88 seed
dispersal from outside remnant Pollen gene flow
13 18