title: Detecting hybridization using ancient DNA.
abstract: It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.
authors.affiliation: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.|UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
authors.forename: Nathan K
authors.initials: NK
authors.lastname: Schaefer
authors.affiliation: UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.|Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
authors.forename: Beth
authors.initials: B
authors.lastname: Shapiro
authors.affiliation: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.|UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
mesh_terms: D000818:Animals; D005075:Biological Evolution; D000072441:DNA, Ancient; D005580:Fossils; D051456:Gene Flow; D023281:Genomics / Q000379:methods*; D015186:Hominidae / Q000235:genetics; D063426:Human Migration; D006801:Humans; D006824:Hybridization, Genetic; D008957:Models, Genetic; D015233:Models, Statistical; D059125:Neanderthals / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D000072441:DNA, Ancient
keywords: D-statistics; admixture; ancient DNA; f-statistics; hybridization; palaeogenomics
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