Abstract
Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixture tract lengths in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of decomposition of an individual’s admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. We perform extensive simulations to quantify the error in the estimation of ancestral admixture proportions under various conditions. To illustrate the utility of the method, we apply it to real genetic data.
Highlights
Ancestry inference is one of the most commonly used tools in human genetics
Ancestry inference is an important problem in genetics and is used commercially by a number of companies affecting millions of consumers of genetic ancestry tests
We show that it is possible, to estimate the ancestry fractions of an individual, and, with some uncertainty, to estimate the ancestry fractions of an individual’s recent ancestors
Summary
Ancestry inference is one of the most commonly used tools in human genetics. It arguably provides the most popular information from commercial genotyping companies such as Ancestry. com and 23andMe to millions of customers. A primary objective for participants to join is to learn more about their genetic ancestry Consumers consider such information relevant for their identity and for understanding their family history, and results are often compared to knowledge handed down orally. In some cases, such as for adopted children, ancestry tests can be important. Many subsequent methods are based on the same model including FRAPPE [5] and ADMIXTURE [6] Notice that this model implicitly assumes that the admixture proportions for each parent of an individual are the same. This assumption is arguably unrealistic for many human populations. The commonly used methods for admixture inference do not allow estimation of ancestry components separately for two parents
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