Inference of recent admixture using genotype data

Abstract The inference of biogeographic ancestry (BGA) has become a focus of forensic genetics. Misinference of BGA can have profound unwanted consequences for investigations and society. We show that recent admixture can lead to misclassification and erroneous inference of ancestry proportions, using state of the art analysis tools with (i) simulations, (ii) 1000 genomes project data, and (iii) two individuals analyzed using the ForenSeq DNA Signature Prep Kit. Subsequently, we extend existing tools for estimation of individual ancestry (IA) by allowing for different IA in both parents, leading to estimates of parental individual ancestry (PIA), and a statistical test for recent admixture. Estimation of PIA outperforms IA in most scenarios of recent admixture. Furthermore, additional information about parental ancestry can be acquired with PIA that may guide casework. Highlights We improve statistical methods as used in STRUCTURE and ADMIXTURE for Biogeographical Ancestry (BGA) inference to account for recent admixture, i.e. different admixture of both parents. The resulting recent admixture model has a higher accuracy in estimating individual admixture in most cases. We give a likelihood ratio test for recent admixture, which is both highly specific and sensitive for recent admixture. We find evidence of recent admixture in the 1000 genomes dataset. The self-report on recent admixture of two self-sequenced samples was only confirmed in one case.