RT Journal Article
SR Electronic
T1 Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.09.032664
DO 10.1101/2020.04.09.032664
A1 Éadaoin Harney
A1 Nick Patterson
A1 David Reich
A1 John Wakeley
YR 2020
UL http://biorxiv.org/content/early/2020/04/10/2020.04.09.032664.abstract
AB qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and non-human) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.Competing Interest StatementThe authors have declared no competing interest.