Applying ancestry tracts to human genetics: disentangling admixture history and characterizing gene conversion
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Local ancestry is central to a variety of inference problems in population and medical genetics. Here I propose new methods for studying admixture demography and inferring non-crossover gene-conversion from admixture tracts. First, I present PAPI (Parental Admixture Proportion Inference), a Bayesian tool for inferring admixture proportions and admixture times from the un-genotyped parents of an admixed sample. PAPI's components are a binomial model of ancestry and a hidden Markov model (HMM) that relies on a pooled-Markovian approximation to pedigree crossover dynamics, recapitulates admixture tract length distributions well, and serves as an important re-parameterization of transition probabilities. I show that PAPI outperforms existing tools and is highly accurate in simulated data as well as in ASW (African Ancestry in Southwest USA) trios. I apply PAPI to the PAGE dataset of African Americans and discover strong patterns of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (
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Booth, James
Clark, Andrew