Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls.

ABSTRACT: Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inf

SUBMITTER: Avadhanam S 

PROVIDER: S-EPMC9388397 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature