Rxivist logo

Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture

By √Čadaoin Harney, Nick Patterson, David Reich, John Wakeley

Posted 10 Apr 2020
bioRxiv DOI: 10.1101/2020.04.09.032664

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 Statement The authors have declared no competing interest.

Download data

  • Downloaded 1,703 times
  • Download rankings, all-time:
    • Site-wide: 11,969
    • In genomics: 1,202
  • Year to date:
    • Site-wide: 16,546
  • Since beginning of last month:
    • Site-wide: 31,711

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide