Genealogy and subpopulation differentiation under various models of population structure

On the importance of skewed offspring distributions and background selection in virus population genetics

“…This also allows for the inference of population genetic parameters, including selection coefficients and effective population sizes (N e ), even from time-sampled data (that is, data collected at successive time points) (Ewens, 1979;Williamson and Slatkin, 1999;Malaspinas et al, 2012;Foll et al, 2014;Foll et al, 2015;Ferrer-Admetlla et al, 2016;Malaspinas, 2016). These methods are robust to some violations of WF model assumptions, such as constant population size, random mating, and nonoverlapping generations, and have also been extended to accommodate selection, migration, and population structure (Neuhauser and Krone, 1997;Nordborg, 1997;Wilkinson-Herbots, 1998).…”

Coalescence Times andFST Under a Skewed Offspring Distribution Among Individuals in a Population

“…The expression for F ST in Equation 14 has the same form as the one derived by Wilkinson-Herbots (1998) and by Nei (1975) and Takahata (1983) Nei's (1972) genetic distance is more appropriate for estimating divergence time between species, and F ST -like quantities are more suitable for inferring population structure within species (Slatkin 1991). Nei's (1972) genetic distance measure is given by d N ¼ Àlnð f 1 =f 0 Þ in which f 0 and f 1 are the probabilities of identity by descent of two genes sampled from the same or different subpopulations, respectively, and we add the subscript N to remind us that time is discrete.…”

Ancestral Processes in Population Genetics—the Coalescent

“…For more details see also the reviews already mentioned in the introduction (Section 1). The theory of the coalescent has been extended to more complex models, for example for models with z mutation (Donnelly & TavareH , 2000;TavareH , 1984), for z diploid and two-sex population models (MoK hle, 1998c;MoK hle & Sagitov, 1999b), models with z self-fertilization or partial sel"ng (Fu 1997;MoK hle, 1998b;Nordborg & Donnelly, 1997), further for z sub-divided population models and geographically structured models (Bahlo & Gri$ths, 2000a, b;Beerli & Felsenstein, 1999;Herbots, 1994;Notohara, 1990;Wilkinson-Herbots, 1998), for models with z recombination (Gri$ths & Marjoram, 2000;Hey & Wakeley, 1997;) z selection Krone & Neuhauser, 1997a, b) z models with changing population size (Donnelly & TavareH , 2000;Gri$ths & TavareH , 1994MoK hle, 1998a;Tajima, 1989).…”