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

• 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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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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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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Potential Gene Flow

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

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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, scnDNA genetic break
Atlantic Gulf
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Oyster
Interpretation 1. mtDNA indicate population
subdivision (limited gene flow) and allozyme loci
under balancing selection? or 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

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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 flightless Aquaris remigis
• Among populations within streams Fst 0.01
• Populations 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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Among-Locus Variation in Fst Fish, Allozymes and
theLewontin-Krakauer Test RevisitedCharles F.
Baer (1999)

• Variance among allozyme loci in 102 published
  data sets from fishes.
• Populations with low gene flow should exhibit
  greater variation among loci in Fst than
  populations with high gene flow, because gene
  flow acts to homogenize allele frequencies among
  subpopulations.
• In these data, among-locus variation in Fst is
  not greater for populations with expected low
  levels of gene flow than for populations with
  expected high levels of gene flow.
• There is thus no evidence that locus-specific
  forces are of general importance in shaping the
  distribution of allele frequencies at enzyme loci
  among populations of fishes.

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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
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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
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Different
Small differences in calculated Fst can result
in large variation in estimated Nm
Fst
Same
Number of migrants per generation (Nm)
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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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Fish
Gastropods
Sea stars
Genetic differentiation
Fish
Fish
Fish
Overall Rank correlation -0.72
Corals
Fish
Fish
Rank dispersal ability (low high)
Bohonak, 1999
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Silene acaulis
Fst 0.241
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Spiders
Fst
Pardosa hyperborea 0.019
Pardosa moesta 0.068
Pardosa groenlandica 0.184
Araneus diadematus 0.074
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Deglaciation History
14000 bp
12000 bp
11000 bp
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Plant 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)

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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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Autogamous mating systems

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

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Autogamous mating systems

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

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Distribution of Dark and light snails in France
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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

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Genetic StructureSummary

• Genetic structure allozyme genetic variation
• - gene flow
  (selection)
• - no phylogenetic
  information
• Phylogeography mtDNA (non-recombining,
• phylogenetic
  geographical
• relationships)

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Phylogeography