Testing for ancient admixture between closely related populations
Open accessAbstract
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.
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Domestic helmeted guinea fowl from Sudan had significantly positive D values (Z > 3), suggesting gene flow between domestic helmeted guinea fowl from Sudan and wild helmeted guinea fowl from Kenya/Sudan.
“D statistics (Durand et al. 2011) were calculated and showed that the domestic HGF from Sudan had significantly positive D values (Z > 3), suggesting gene flow between domestic HGF from Sudan and wild HGF from Kenya/Sudan (supplementary fig. S5, Supplementary Material online).”
From Genomic Analyses Unveil Helmeted Guinea Fowl (<i>Numida meleagris</i>) Domestication in West Africa (2021) · cites this paper as Durand et al. 2011
ARG-based estimates of genome-wide percent admixture are similar to, but lower than, D statistic-based estimates in all non-African genomes.
“ARG-based estimates are similar to, but lower than, D statistic–based estimates in all non-African genomes, which we expected because of our aggressive filtering strategy for eliminating ILS”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [19]
The Application to Neandertal section discusses D statistics and reports that their values were lower for SNP data than for sequencing data. It does not compare ARG-based and D-statistic-based admixture estimates across non-African genomes. A search for ARG-based estimates and aggressive filtering of incomplete lineage sorting found no passage addressing that comparison. (LLM, conf=0.76)
Experimental — accuracy not yet measuredSeveral methods (IBS tract, ∂a∂i, D statistics) were used to fully elucidate patterns of gene flow between polar and brown bear populations since their divergence.
“To fully elucidate patterns of gene flow between polar and brown bear populations since their divergence, we used several methods: (i) the IBS tract method; (ii) ∂a∂i; and (iii) D statistics, also known as the ABBA-BABA test (Durand et al., 2011; Green et al., 2010) (Extended Experimental Procedures Section Gene Flow and Introgression).”
From Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears (2014) · cites this paper as Durand et al., 2011
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- Authors
- Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M.
- Affiliations
- University of California, Berkeley (US)
- Broad Institute (US)
- Corresponding author
- Durand, Eric Y.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-02-15
- Volume
- 28
- Issue
- 8
- Pages
- 2239-2252
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3144383
- OpenAlex
- W2052395225
- Cited by
- 1,375
- References
- 34
- Citations by year
- 2026: 123 · 2025: 130 · 2024: 120 · 2023: 115 · 2022: 137 · 2021: 149 · 2020: 113 · 2019: 102 · 2018: 96 · 2017: 75 · 2016: 76 · 2015: 48 · 2014: 39 · 2013: 28 · 2012: 15
- FWCI
- 17.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM040282, R01‑GM40282)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- archaic admixture, D-statistic, interbreeding, sequencing errors, false positive rate, population subdivision
- MeSH terms
- Algorithms, Animals, Computer Simulation, Genetics, Population, Humans, Genetic Variation, Models, Statistical, Genome, Evolution, Molecular, Gene Flow
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