Measures_of_Genetic_Differentiation.ppt

Measures of Genetic Differentiation Stacie Hooper, Sree Kanthaswamy, Mary Brooke McEachern, and Wes Savage Questions we are addressing How reproductively isolated are a group of populations? Which populations are more related? Outline Week 1: Measurements of Differentiation Wright’s F-statistics Various analogs of F-statistics AMOVA (Φ) Week 2: Testing Significance Fisher’s exact test Bootstrap and Jacknife Baysian Methods Software programs: Genepop, Arlequin, FSTAT Population Substructure Many species naturally subdivide themselves into herds, flocks, colonies, schools etc. Patchy environments can also cause subdivision Subdivision decreases heterozygosity and generates genetic differentiation via: Natural selection Genetic drift Step 1: Calculate mean heterozygosities at each population level Heterozygosity = mean percentage of heterozygous individuals per locus Assuming H-W, heterozygosity (H) = 2pq where p and q represent mean allele frequencies HS = sum of all subpopulation heterozygosities divided by the total number of subpopulations Wright’s Fixation Index Equals the reduction in heterozygosity expected with random mating at one level of population hierarchy relative to another more inclusive level. FST = (HT – HS)/ HT Hierarchical structure of a desert plant (from Wright 1943) Example calculation- desert plant FST = (0.2371 – 0.1424)/ 0.2371 = 0.3993 Overall reduction in average H is close to 40% of the total heterozygosity Subpopulations in this species are highly differentiated Interpreting FST Can range from 0 (no genetic differentiation) to 1 (fixation of alternative alleles). Wright’s Guidelines: 0 - 0.05, little differentiation 0.05 – 0.15, moderate 0.15 – 0.25, great 0.25, very great FST for various organisms RST, GST, and θ? RST: explicitly accounts for mutation rates at microsatellite loci (Slatkin 1995) RST =(ST – SW)/ST RST is the fraction of the total variance of allele size that is between populati