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Review for Exam 2 October 26, 2015 Elephant Seals Practice extreme polygyny: one male has a harem with many females Examined reproductive success of males using paternity analysis on Falkland Islands Results: 7 harems with 334 females 32 mating males detected What is Ne? What if sneaky males were unsuccessful? Assumptions? Fabiani et al. 2004: Behavioural Ecology 6: 961 Example: Effect of Varying Population Size Through Time: Golden Lion Tamarins (Leontopithecus rosalia) Native to coastal Brazilian Rainforests Estimated Population Censuses: http://nationalzoo.si.edu 1940: 10,000 1970: 200 2000: 2,000 What is current effective population size? http://en.wikipedia.org Ne t 1 N i Population Assignment: Likelihood "Assignment Tests" based on allele frequencies in source populations and genetic composition of individuals Likelihood-Based Approaches Calculate likelihood that individual genotype originated in particular population Assume Hardy-Weinberg and linkage equilibria Genotype frequencies corrected for presence of sampled individual Usually reported as log10 likelihood for origin in given population relative to other population Implemented in ‘GENECLASS’ program (http://www.montpellier.inra.fr/URLB/geneclass/g eneclass.html) Pk l p 2 i l for homozygote AiAi in population l at locus k Pk l 2 pil p jl for heterozygote AiAj in population l at locus k m P Pk k 1 for m loci Population Assignment Example: Wolf Populations in Northwest Territories Wolf populations sampled on island and mainland populations in Canadian Northwest Territories Immigrants detected on mainland (black circles) from Banks Island (white circles) Carmichael et al. 2001 Mol Ecol 10:2787 Linanthus parryae population structure u Annual plant in Mojave desert is classic example of migration vs drift u u Allele for blue flower color is recessive u u u FST can be calculated for any hierarchy: Use F-statistics to partition variation among regions, subpopulations, and individuals FRT: Variation due to differentiation of regions FSR: Variation due to differentiation among subpopulations within regions Schemske and Bierzychudek 2007 Evolution Linanthus parryae population structure ö 1 30 æ 2 H S = åç1- å pim ÷ 30 i=1 è m=1 ø æ ö 1 3 2 HR = N r ç1- å prm ÷ å å Nr r=1 è m=1 ø r H T =1- å p m 2 m FSR HR HS HR 0.1589 - 0.1424 = 0.1036 0.1589 H HR T HT FSR = FRT FRT = 0.2371- 0.1589 = 0.3299 0.2371 FST HT H S HT FST = 0.2371- 0.1424 = 0.3993 0.2371 Hartl and Clark 2007 LD and Admixture Two randomly-mating populations of rats in the sewers of Paris have lived in different and completely separate subsewers since the 14th century A sewer renovation in 2015 connects the two systems, allowing completely random intermating Prior to admixture, 50 gametes from each population are genotyped for two unlinked SNP loci. What is LD (D, D’, r) between these loci in the first generation following admixture? Locus A A B B Allele A G C T Pop1 5 45 5 45 Pop2 45 5 45 5 Another part of the sewer dating to the same period was connected at some undetermined date. For this population, r=0.04 for these loci. What is D for this population? Assuming similar differentiation at the time of admixture, how many generations have elapsed since the sewers were connected?