Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site.

ABSTRACT: It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state-maximum parsimony-is prone to misinference. Estimates of counts of sites that have a certain number of copies of the derived allele in a sample (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species using information from two outgroups while assuming simple models of nucleotide substitution. Here, we extend this approach to allow multiple outgroups (implemented for three outgroups), potentially any phylogenetic tree topology, and more complex models of nucleotide substitution. We find

SUBMITTER: Keightley PD 

PROVIDER: S-EPMC6028244 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature