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. Sex and Evolution 9.
Forensic Applications 10. Human Evolutionary
Genetics 11. Conservation Genetics
Background
Applications
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Individuality and Parentage

• Sexual reproduction genetic variation large
• amount of genotypic variation
• - every individual in a population
  genetically
• unique

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Individuality and Parentage

• Ramets and Genets (sexual and asexual)
• Genetic parentage

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Facultative Sexual/Asexual

• Vegetative reproduction (proliferation of
• somatic
  tissue)
• - attached replicates (runners, rhizomes)
• - detached replicates (bulbs, fragments)

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Facultative Sexual/Asexual

• Genet genetic individual originating from a
• single sexually produced zygote
• Ramet a clonally produced individual

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Genet - Ramet
Ramet
Genet
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Genetic Consequences

• Sexual high genotypic diversity
• Asexual low genotypic diversity
• Mixtures intermediate diversity
• Genetic markers ? used to infer mode of
• reproduction

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Detecting Asexual Reproduction

• Population sample
• (a) deviation from HWE
• (b) association among loci
• (c) genotypic diversity (MLG)
• (d) combined analysis
• 2. Compare offspring and mother genotypes

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Detecting Asexual Reproduction

• Examples
• 1. Seaweed (Enteromorpha linza)
• 2. Dwarf Birch (Betula glandulosa)
• 3. Moss (Polytrichum juniperinum)
• 4. Water Flea (Daphnia pulex)

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4. Water Flea Daphnia pulex
Facultative Parthenogenesis
(FP - Sexual)
meiosis
Sexual Phase
Parthenogenetic Phase
Clone
Recombination
Genet
Ramets
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Obligate Parthenogenesis
?
(OP asexual)
Parthenogenetic Phase
Parthenogenesis
Clone
Clone
Ephippia eggs No mating required
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Mode of Reproduction
Sexual
Asexual
- Few MLG - Fixed Heterozygotes
22 MLG
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Detecting Asexual
1. Number of MLG (Clones) 2. GDR genotypic
diversity ratio 3. log p from a X2 for
HWE p 0.05 1.3 p 0.0001 4.0
FP- sexual
OP- asexual
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Daphnia pulex Ponds in Southern Ontario
Obligate parthenogens (OP asexual)
Facultative parthenogens (FP sexual)
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Clonal Discovery
within
Number of MLG (Clones)
Sexual high genotypic diversity
Asexual low genotypic diversity
Number of Loci
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Distribution of Clones (MLG)
Most clones found at one site (69 )
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Other Asexual Invertebrates
Sea stars fission sexual recruitment Corals
fission, fragmentation - asexual
planula larvae - sex Sea anemones
fission, planula larvae, clones
distributed 100s of km -variation in
sex/asex among species
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Asexual Vertebrates
Whiptail lizard
Parthenogenetic clones derived from hybrids
between sexual species (often polyploid)
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Asexual Vertebrates
Parthenogenesis Gynogenesis
Hybridogenesis
AB -------gt AB AB --------gt AB
C AB x CC ----gtAC x BB----gt AB
Poeciliopsis
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Age of Clones

• clonal genotypes ecologically successful
• expect clonal genotypes to be short lived
• - lack of recombination (evolutionary
  potential)
• - accumulation of deleterious mutations
  (Mullers
• 
  Ratchet)
• Asexual taxa ? recent origin
• Exceptions? ? Bdelloid rotifers
• 360 spp.
  No males

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Mullers Ratchet Stochastic loss of least loaded
clone Mutation genetic load always increasing
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Meselson Effect

• Diploid asexuals
• - no recombination
• - alleles at each locus should diverge
  over
• 
  time

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• Method
• Sequence alleles of a gene in asexual and sexual
  species
• Count frequency of synonymous substitutions

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Sexual
Asexual
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Clonal Microorganisms

• Protozoa, Bacteria, Fungi
• agents of human disease
• asexual strains with particular medical
• characteristics
• sex and recombination new strains
• (resistance and virulence)

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Individuality and Parentage

• Ramets and Genets (sexual and asexual)
• Genetic parentage

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Genetic Parentage

• Clonal reproduction ? no recombination
• inheritance of one MLG
• Sexual reproduction ? recombination
• Genetic parentage
• combining genetic markers with rules of
  mendelian
• inheritance (segregation independent
  assortment)

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Genetic Parentage

• Question addressed
• Are the adults associated with particular
• young the true biological parents?
• Answers
• - No then genetic exclusion achieved
• - one parent known problem becomes
• determining paternity or maternity
• - both parents sometimes can be specified

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Genetic Parentage - Situations

• 1. Maternity and paternity uncertain
• 2. Maternity certain paternity among candidate
  males
• - mating systems monogamy
• polyandry
• polygyny
• polygynandry
• 3. Hermaphroditic selfing
• outcrossing
• 4. Selfing vs. parthenogenesis

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Genetic Parentage - Situations
Intensity of sexual selection
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Mating Systems

• Genetic and evolutionary consequences of
  different mating systems
• Evolution of mating systems

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Parentage

• Behavioural and evolutionary context of
  parentage
• - realized reproductive success
• - genetic mating system vs. social
• mating systems (ie. monogamous)

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Parentage

• Empirical examples
• Humans
• maternity certain paternity less
  certain
• For humans, the optimal evolutionary strategy is
  monogamy when necessary, polygamy when possible

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Are -U Dad ? (273 8323)
Is-He-Dad (474 3323)
299 399 499 599
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Other Primates

• Social structure dominance hierarchies
• Do males of higher social rank exhibit higher
  fitness?

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Examples

• Rhesus Macaques
• Offspring fathered by alpha male 24
• Offspring fathered by lower ranks 76
• Behaviour-based methods of fitness estimation
  inadequate

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Examples

• Orangutan
• Dominant male
• secondary sex characters
• Subordinate males
• suppression of SSC
• Microsats ? subordinate male sired 50
• alternative mating strategy

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Parentage in Birds

• Parental Care significant investment
• Parental fitness
• - mate and produce offspring
• - ensure parental care of own
  offspring
• Males and females pair to mate and rear offspring

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Genetic markers and bird parentage

• Socially monogamous species
• high frequency of EPO
• EPC extra-pair copulation
• EPF extra-pair fertilization
• EPO extra-pair offspring
• Examples
• Range Monogamous to extreme EPO
• (1 34 )
• Superb fairy-wren ? gt 70 EPO

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Fairy Wren

• Least faithful of all birds 5 of males sire
  over 50 of the offspring
• Females identify good males by their ability
  to moult early into their bright-blue,
• breeding plumage
• Females seek extra-pair copulations from these
  high quality males during pre-
• dawn forays away from their own territory.
• What do females gain from copulating with these
  early-moulting males?
• Early-moulting males may exhibit good genes
  and females offspring will inherit
• high viability.
• Preliminary data analysis provides no support
  for this theory
• Offspring sired by good males do not fare
  any better than those sired by males
• that moulted later in the season.

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Evolutionary Significance

• - no correlation between EPF rate and nesting
  density or
• coloniality
• - females actively seek EPC
• Selective advantage
• - generate high genetic diversity among
  offspring
• - increased chance of obtaining good
  genes
• - high genetic compatibility with male
• - fertilization insurance

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Evolutionary Significance

• EPO benefit females and cuckolding males
• Disadvantage for cuckolded males (where males
  helps raise
• offspring that are not his own)
• Selection for cuckoldry avoidance
• Reed Bunting - high rate of extra-pair
  paternity
• - males can assess
  likelihood of paternity and
• can adjust nestling
  provisioning rates

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Evolutionary Significance

• Correlates of High rates of EPF
• - species that have males with bright plumage
• - relatively large testes
• - males provide little or no offspring care
• - high molecular variation (therefore EPO can
  increase
• genetic diversity of offspring)

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Extra-pair paternity sexual dimorphism
Male
Female
Moller and Birkhead (1994)
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Parentage in Fishes

• Often very large clutches
• Diverse reproductive behaviour
• - group spawning
• - cooperative breeding
• - social monogamy

salmon
Eretmodus cyanostictus is a monogamous
mouthbrooding cichlid in which the clutch is
successively incubated first by the female and
then by the male.
African cichlids
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Parentage in Fishes

• Variation in Parental Care
• - nonexistent
• - one gender only (usually male)
• - biparental
• - communal

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Parentage in Fishes

• sexually monomorphic in appearance and socially
• monogamous.
• microsatellite markers in order to test whether
  social
• monogamy predicts genetic monogamy
• 23/26 nests full sibs
• The first genetic documentation of near-monogamy
  and biparental care in a vertebrate with external
  fertilization.

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Parentage in Fishes

• Paternity studies of nest-guarding male
• Compare genotype of suspected father with
  offspring
• Examples
• 1 male gt 1 female (multiple maternity?half
  sibs)
• 1 male 1 female (monogamy rare)
• 3. Some offspring not sired by resident male
  (cuckoldry)

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Stickleback
Jones et al 1998 A microsatellite assessment of
sneaked fertilizations and egg thievery in the
fifteenspine stickleback Microsatellites 6 loci
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Exclusion Probability
Combined exclusion probability 0.9998
Expected proportion of unrelated males excluded
as the father
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Sneaked 5/28 nests Egg Thievery 4/24 nests
Benefits of sneaking ? obvious Benefits of egg
thievery? - prime the nest - predation
dilution
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Sexual Selection

• Evolution of sexual dimorphism
• - Males compete for females (polygyny)
• Females compete for males (polyandry)
• (role-reversal male choice)