Estimating genetic diversity ( within populations = a function of the number of polymorphic sites in a population (S) Wattersons 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 Tajimas D statistic proportional to: Under neutrality, Tajimas D 0 Under directional selection, Tajimas D < 0 Testing neutrality 1. Gene trees dont 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 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