Testing for ancient admixture between closely related populations
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Cites background from "Testing for ancient admixture betwe..."
...In application to dogs, we show that the boxer and basenji breeds have a considerable component of ancestry from grey wolves subsequent to domestication....
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1,877 citations
Cites background from "Testing for ancient admixture betwe..."
...…history of populations can be made using the magnitudes of allele frequency correlation statistics, an idea that is exploited to great advantage by Durand et al. (2011); however, for this approach to work, it is essential to analyze sites with rigorously documented ascertainment, as are…...
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...These have been introduced in some form in earlier articles (Reich et al. 2009; Green et al. 2010; Durand et al. 2011; Moorjani et al. 2011) but not coherently together and with the key material placed in supplementary sections, making it difficult for readers to understand the methods and their…...
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...Further theory and applications of D-statistics can be found in Reich et al. (2010) and Durand et al. (2011)....
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...Durand et al. (2011) showed that replacing population allele frequencies (w9, y9, etc.) by the sample allele frequencies yields unbiased estimates of Numi, Deni....
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References
3,575 citations
"Testing for ancient admixture betwe..." refers background or methods or result in this paper
...Green et al. (2010) defined a new statistic, called the D statistic, to test for admixture between three closely related populations....
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...As a consequence, detectable ancient admixture is more likely to be found in extant populations when introgression with archaic populations occurred during a range expansion, as is thought to be the case for modern humans and Neandertals (Currat et al. 2008; Green et al. 2010)....
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...…this statistic, CABBA(i) and CBABA(i) are indicator variables; they can be 0 or 1 depending on whether an ABBA or a BABA pattern is seen at base i. Green et al. (2010) denoted this statistic by D, and we have DðP1; P2; P3;OÞ5 Pn i5 1 CABBAðiÞ CBABAðiÞPn i5 1 CABBAðiÞ þ CBABAðiÞ : ð1Þ We further…...
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...Green et al. (2010) developed a formal test for admixture based on the direct comparison of DNA sequences from Neandertals and modern human populations....
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...However, we note that the main conclusion regarding the test for admixture of Green et al. (2010) held when applied to genotype data....
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3,038 citations
"Testing for ancient admixture betwe..." refers background in this paper
...Under the null hypothesis, the two nonconcordant gene trees should occur with equal frequencies (Tajima 1983; Hudson 1983), and D should equal zero....
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2,748 citations
"Testing for ancient admixture betwe..." refers background in this paper
...Introgression is often asymmetrical between hybridizing species (Barton and Hewitt 1985; Orive and Barton 2002)....
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...Admixture occurs during secondary contact between previously isolated populations, and it can play an important role in the speciation process (Barton and Hewitt 1985; Barton 2001)....
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1,457 citations
"Testing for ancient admixture betwe..." refers methods in this paper
...By computing the variance of the D statistic over the sequences M times leaving each block of the sequence in turn, and then multiplying by M and taking the square root, we can obtain an approximately normally distributed standard error using the theory of the jackknife (Reich et al. 2009)....
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