One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.
%0 Journal Article
%1 durand2011testing
%A Durand, E Y
%A Patterson, N
%A Reich, D
%A Slatkin, M
%D 2011
%J Mol Biol Evol
%K ABBA-BABA ancient_genomes introgression methods population_genetics
%N 8
%P 2239-2252
%R 10.1093/molbev/msr048
%T Testing for ancient admixture between closely related populations
%U http://www.ncbi.nlm.nih.gov/pubmed/21325092
%V 28
%X One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.
@article{durand2011testing,
abstract = {One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.},
added-at = {2015-02-18T06:39:26.000+0100},
author = {Durand, E Y and Patterson, N and Reich, D and Slatkin, M},
biburl = {https://www.bibsonomy.org/bibtex/24035e044fa240dc2ff98a308d5c0cf74/peter.ralph},
doi = {10.1093/molbev/msr048},
interhash = {8310e6b9364d6f500ec3623eab41d632},
intrahash = {4035e044fa240dc2ff98a308d5c0cf74},
journal = {Mol Biol Evol},
keywords = {ABBA-BABA ancient_genomes introgression methods population_genetics},
month = aug,
number = 8,
pages = {2239-2252},
pmid = {21325092},
timestamp = {2015-02-18T06:39:26.000+0100},
title = {Testing for ancient admixture between closely related populations},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21325092},
volume = 28,
year = 2011
}