Estimating genetic diversity (  within populations  =  a function of the number of polymorphic sites in a population (S) “Watterson’s theta” Allele 1: ACTGGCTGAACTT Allele 2: ACTGGTTGAACTT Allele 3: GCTGGTTGAACCT * * * S=3 n = number of alleles

A second estimate of 4N  Allele 1: ACTGGCTGAACTT Allele 2: ACTGGTTGAACTT Allele 3: GCTGGTTGAACCT k = number of differences between pairs of alleles i and j n = number of alleles

Testing neutrality Tajima’s D statistic proportional to: Under neutrality, Tajima’s D ≈ 0

Under directional selection, Tajima’s D < 0 Testing neutrality

1. Gene trees don’t always match the species tree 2. Gene divergence often precedes population divergence Gene tree Species tree T/4N e 2N e Two rules of gene trees near the species boundary

30 gene trees from Australian finches Jennings & Edwards (2005) Evolution 59, P. acuticaudaP. heckiP. cincta

Gene flow erodes population monophyly Migration event reconstructed by parsimony

Counting the number of interpopulation coalescent events

s as an index of divergence time

s as an index of gene flow

Gene flow erodes population monophyly

Genetic differentiation between populations or b, between populations; w, within populations

Identifying outlier loci using Fst

Identifying loci under pollution-driven selection using Fst and outlier loci

Distribution of F st among loci in humans

Gene tree monophyly as an indicator of natural selection European corn borer

Faster approach to concordance for mtDNA versus nuclear DNA

Different behavior of nuclear and organelle genes ParameterNuclearorganelle: uniparental, haploid (e.g., mtDNA, cpDNA or Y chromosome) Comments Effective population sizeNeNe N eo = 1/4N e When sex ratios are 1:1 Chance of fixation in a local populationlowerhigher" " " Founder effectmildstrong Depth of gene tree (in generations)deepshallowT = 4N e Genetic diversitymoderatehighdiversity = 4N e µ Time to reciprocal monophyly of lineages in sister populations longshortT = 4N e, N eo F st -- geographic variationlowhighmigration rates of sexes equal Concordance between gene and species trees lowerhigherdepends on length of phase of incomplete isolation of populations;

Examples of discordance between gene and species trees

Examples of large mtDNA breaks within species

Snow geese: widespread distribution of two divergent mtDNA clades Snow goose

Structured populations of hyperthermophilic Archaea

past present Genetic diversity (  ) or population size Signatures of stable and expanding populations Long internal branches Short external branches Short internal branches Long external branches Stable population Expanding population

Holarctic songbirds Star phylogenies in holarctic species