Genetics 2- Genetic drift extended

Genetics 2- Genetic drift extended

1. Decay of heterozygosity--- Modelling drift by looking forward in time

   • Occurs as a result of drift--- related to f
   • Heterozygosity (H)= 1- F
   • Small pops-- rapid decay-- conservation concern
   • Genetic bottlenecks
     • Occurs after loss of variation--- variation recovers slower than pop size
     • Most species are not driven to extinction before genetic factors impact on them
     • Fragmented Iberian Lynx populations
       • Heavily persecuted
       • Heavily fragmented for long period of time--- would have thought this would led to unique adaptations to own geographic range
       • reduction in genetic diversity due to drift due to small pops as a result of fragmentation
       • Conservation--- genetic restoration through translocation

2. Mutation/drift in the wright-fisher model

   • Drift decreases diversity 1/2N
   • Mutation increases diversity 2NU
   • Mutation and drift reach an equilibrium--- mutation drift equilibrium
   • new way of defining f statistic when drift and mutation are occuring
   • /U= Mutation rate--- probability of a new allele= 2N x /U
     • Mutation rate is also equivalent to the probabliity of a new allele fixating
     • Neutral theory of evolution

3. Molecular evolution

   • p= rate of evolution= rate of fixation of a mutation
   • Population will be polymorphic for a mutation whilst its present--- either drifts away or drifts to high frequency and becomes fixed
   • Count up the mutations between different lineages--- find the divergence time between different lineages

4. The Coalescent theory

   • K sequences in N diploid individuals
   • Assumes
     • Lineages coalesce independently
     • Coalescence is rare-- no more than one coalescent event per generation
     • No drift, flow or selection
   • The probability that k alleles all have different parental alleles is
   • Features of neutral coalescent
     • Lineages will coalesce very rapidly at the start
     • Small sample-- high probability of containing deepest MRCA
     • Adding another sequence will usually add another branch
     • Adding a new branch does not change the length of terminal branches
     • Adding a new branch will increase the length of the tree by a factor of 1/K

5. Uses of Coalescent theory

   • Testing multiregionality of modern human origins
     • 10 human loci sequenced
     • Sequenced geneologies for each loci to determine location of MRCA
     • 9/10 loci placed MRCA in Africa--- consistent with out of Africa model
   • Selection on the dot chromosome of Drosophila melanogaster
     • Phylogeny of the dot chromosome using transposable element insertions
     • Was the selection best explained by an old selective sweep (linkage to positively selected region), recent selective sweep or background selection (linked to deleterious variation within a pop)?
     • Simulations generated phylogenies under background selection and selective sweep models
     • Empirical tree most consistent with the background selection model

6. Gene genealogies

   • Gene genealogies are unobservable-- can only sample alleles present in current population
   • Samples still have genealogies-- even WITHOUT variation
   • A variant present in a single sequence is compatible with any terminal branch
   • Need variation in more than one sequence

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