The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Inferring Demographic History from a Spectrum of Shared Haplotype Lengths
Open accessAbstract
There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.
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Cites
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Cited by
Reference-based phasing using the Haplotype Reference Consortium panel
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Tracing the peopling of the world through genomics
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Self-citationGenomic evidence for the Pleistocene and recent population history of Native Americans
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Self-citationEvidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521
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Metadata
- Authors
- Harris, K., & Nielsen, R.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-06-06
- Volume
- 9
- Issue
- 6
- Pages
- e1003521
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W1967144980
- Cited by
- 229
- References
- 13
- FWCI
- 20.43
- Type
- journal article
- Language
- en
- Open access
- gold
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