Testing for ancient admixture between closely related populations.

By Eric Durand, Nick Patterson, David Reich, M. Slatkin. Molecular biology and evolution, 2011

1,247 citations recorded by the source corpus.

Subfields: Anthropology, Genetics, Geometry and Topology

View Paper: https://www.semanticscholar.org/paper/c93ed90a4b714f3f7fd4d67404ff5268d4c217f8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Anthropology

In Genetics

In Geometry and Topology

Citations in the corpus

Ancient Admixture in Human History (2012, background): “…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…”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, positive): “On the other hand, postspeciation gene flow can be distinguished from ILS, and there are now a number of methods to do so for single-nucleotide polymorphisms (e.g. Durand et al. 2011; Martin et al. 2015; Pease & Hahn 2015) and retroposon presence/absence patterns (Kuritzin et al. 2016).”
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting (2015, methodology): “Based on high CFs of splits in conﬂict with their species tree followed by a series of ABBA-BABA tests [35], [11] concluded that hybridization or gene ﬂow was widespread in the history of these tropical ﬁshes.”
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci (2014, methodology): “An excess of ABBA patterns is indicative of gene flow between two of the taxa, and can be detected using Patterson’s D statistic (Green et al. 2010; Durand et al. 2011; see Methods for details).”
Genome-wide evidence for speciation with gene flow in Heliconius butterflies (2013, methodology): “For three populations and an outgroup, with the relationship {[(P1,P2),P3],O}, we can test for differential admixture between P3 and either of P1 or P2 by examining the numbers of shared derived alleles between P3 and P2 (ABBAs) and between P3 and P1 (BABAs).”
A genomic history of Aboriginal Australia (2016, methodology): “We characterised the number, timing and intensity of archaic gene flow events using three complementary approaches: SFS-based (Figure 4a, Figure 5c, S07), a goodness-of-fit analysis combining D-statistics (S09), and a method that directly infers putatively derived archaic ‘haplotypes’ (S11).”
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses (2013, methodology): “This currently includes measurement of D-statistics (Durand et al. , 2011) and related tests for genomic introgression (Eaton and Ree, 2013).”
Ancient hybridization fuels rapid cichlid fish adaptive radiations (2017, positive): “ABBA and BABA pattern counts were calculated using allele frequencies by weighting each segregating site according to its ﬁt to the ABBA or BABA pattern 46,72,78 .”
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data (2012, background): “In application to dogs, we show that the boxer and basenji breeds have a considerable component of ancestry from grey wolves subsequent to domestication.”
Dsuite - fast D-statistics and related admixture evidence from VCF files (2020, methodology): “The D statistic and the related estimate of admixture fraction f , referred to as the f 4 -ra- tio (Patterson et al., 2012), are simple to calculate and well suited for taking advantage of genomic-scale data sets, while being robust under most demographic scenarios (Durand et al., 2011).”