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 inference of parental admixture times. In simulations, we find that PAPI’s admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI’s admixture time estimates were strongly correlated with the truth () but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples’ ancestry proportions are highly correlated ( = 0.87) and are closer to each other than expected under random mating (p < 10). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

中文翻译：

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从无阶段的本地祖先调用中同时推断亲本混合比例和混合时间


对当地祖先的群体遗传分析通常假设个体父母双方的祖先混合过程是相同的，但在考虑最近的混合时，这一假设可能是无效的。在这里，我们提出了亲本混合比例推断（PAPI），这是一种贝叶斯工具，用于推断单个混合个体的每个亲本的混合比例和混合时间。 PAPI 分析非定相的本地祖先区域，并具有两个组成部分：利用全基因组祖先分数来推断亲本混合比例的二项式模型和根据区域长度推断混合时间的隐马尔可夫模型 (HMM)。至关重要的是，隐马尔可夫模型通过近似谱系交叉动态来解释未观察到的祖先内重组，从而能够推断亲本混合时间。在模拟中，我们发现 PAPI 的混合比例估计与真实情况平均偏差 0.047，分别比 ANCESTOR 和 PedMix 好 46.0% 和 57.6%。此外，PAPI 的混合时间估计与真相 () 密切相关，但平均向下偏差为 1.01 代，部分原因是当地血统推断的不准确。为了说明其实用性，我们对 PAGE 研究中的非裔美国人基因型 (N = 5,786) 进行了 PAPI 分析，发现了按血统比例进行选型交配的有力证据：夫妇的血统比例高度相关 (= 0.87)，并且彼此更接近与随机交配下的预期不同 (p < 10)。我们预计 PAPI 将有助于研究混合的种群动态，并且也会引起寻求了解其个人谱系的个人的兴趣。