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Sci Adv. 2020 Mar 13;6(11):eaay0456. doi: 10.1126/sciadv.aay0456. eCollection 2020 Mar.

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.

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Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
Department of Physical Geography, Geomorphology and Paleogeography, Chernivtsi 'Yuriy Fed'kovych' National University, Kotsubynskogo 2, 58012 Chernivtsi, Ukraine.
Department of Palaeontology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria.
Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany.
Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia.
State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China.
Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany.
Brown Hyena Research Project, Luderitz, Namibia, Centre of Wildlife Management, University of Pretoria, Pretoria, South Africa.
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, Germany.
Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
Section of Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.


The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

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