Discovery of lost diversity of paternal horse lineages using ancient DNA

Sebastian Lippold (), Michael Knapp, Tatyana Kuznetsova, Jennifer A. Leonard, Norbert Benecke, Arne Ludwig, Morten Rasmussen, Alan Cooper, Jaco Weinstock, Eske Willerslev, Beth Shapiro and Michael Hofreiter
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Sebastian Lippold: Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, D-04103
Michael Knapp: Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago
Tatyana Kuznetsova: Faculty of Geology, Moscow State University
Jennifer A. Leonard: Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092
Norbert Benecke: German Archaeological Institute, D-14195
Arne Ludwig: Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, D-10252
Morten Rasmussen: Centre for GeoGenetics, Copenhagen University, 1350
Alan Cooper: Australian Centre for Ancient DNA, University of Adelaide, South Australia 5005
Jaco Weinstock: School of Humanities (Archaeology), University of Southampton SO17 1BJ
Eske Willerslev: Centre for GeoGenetics, Copenhagen University, 1350
Beth Shapiro: The Pennsylvania State University, University Park
Michael Hofreiter: Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, D-04103

Nature Communications, 2011, vol. 2, issue 1, 1-6

Abstract: Abstract Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.

Date: 2011
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DOI: 10.1038/ncomms1447

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