Sex chromosomes differ in their inheritance properties from autosomes and hence may encode complementary information about past demographic events. We compiled and analyzed a range-wide resequencing data set of the red deer (Cervus elaphus), one of the few Eurasian herbivores of the Late Pleistocene megafauna still found throughout much of its historic range. Our analyses of 144 whole genomes reveal striking discrepancies between the population clusters suggested by autosomal and X-chromosomal data. We postulate that the genetic legacy of Late Glacial population structure is better captured and preserved by the X chromosome than by autosomes, for two reasons. First, X chromosomes have a lower Ne and hence lose genetic variation faster during isolation in glacial refugia, causing increased population differentiation. Second, following postglacial recolonization and secondary contact, immigrant males pass on their X chromosomes to female offspring only, which effectively halves the migration rate when gene flow is male mediated. Our study illustrates how a comparison between autosomal and sex chromosomal phylogeographic signals unravels past demographic processes that otherwise would remain hidden.

Biodiversity and Climate Research Center Senckenberg Institute Frankfurt am Main 60325 Germany

Biology and Ethology Unit Faculty of Veterinary University of Extremadura Caceres Spain

Center for Ecological Dynamics in a Novel Biosphere Department of Biology Aarhus University Aarhus C 8000 Denmark

Department of Animal and Food Science Universitat Autònoma de Barcelona Barcelona 08193 Spain

Department of Archaeology and Heritage Studies Aarhus University Højbjerg DK 8270 Denmark

Department of Biodiversity Faculty of Mathematics Natural Sciences and Information Technologies University of Primorska Koper 6000 Slovenia

Department of Chemistry and Bioscience Aalborg University Aalborg 9220 Denmark

Department of Ethology Institute of Animal Science Czech University of Life Sciences 10400 Prague 10 Uhrineves Czechia

Department of Evolutionary Biology University of Vienna Vienna Austria

Department of Game Management and Wildlife Biology Faculty of Forestry and Wood Sciences University of Life Sciences 16500 Prague 6 Suchdol Czechia

Department of Genetics Developmental and Molecular Biology School of Biology Aristotle University of Thessaloniki Thessaloniki 54124 Greece

Department of Genetics University of the Free State Bloemfontein South Africa

Department of Mammal Collection Natural History Museum Vienna Vienna Austria

Department of Natural Resources Isfahan University of Technology Isfahan Iran

Department of Preclinical Sciences and Pathology Norwegian University of Life Sciences P O Box 5003 Ås 1432 Norway

Department of Veterinary Medicine University of Sassari Sassari 07100 Italy

Department of Zoology Fisheries Hydrobiology and Apiculture Faculty of AgriSciences Mendel University in Brno Brno 613 00 Czech Republic

Department of Zoology Institute of Ecology and Earth Sciences University of Tartu Tartu 50409 Estonia

Department of Zoology State Museum of Natural History Stuttgart Stuttgart 70191 Germany

Dept of Ecology and Genetics Uppsala University Uppsala SE 75236 Sweden

Domaine National de Chambord Chambord France

Faculty of Environmental Protection Velenje 3320 Slovenia

Faculty of Forestry University of Belgrade Belgrade 11000 Serbia

Institute for Ecology Evolution and Diversity Goethe University Frankfurt am Main Germany

Institute of Ecology and Evolution School of Biological Sciences University of Edinburgh Edinburgh EH93FL UK

Institute of Ecology Ilia State University Tbilisi 0162 Georgia

Institute of Vertebrate Biology Czech Academy of Sciences Brno 603 00 Czech Republic

Instituto de Investigación en Recursos Cinegéticos IREC Ciudad Real Spain

LOEWE Centre for Translational Biodiversity Genomics Senckenberg Nature Research Society Frankfurt am Main Germany

Mammal Research Institute Polish Academy of Sciences Białowieża 17 230 Poland

Marine and Freshwater Research Centre Department of Natural Resources and the Environment Atlantic Technological University Galway Ireland

Max Perutz Labs Vienna BioCentre Vienna 1030 Austria

Office Français de la Biodiversité Direction de la Recherche et de l'Appui Scientifique Service Anthropisation et fonctionnement des écosystèmes terrestres France

Office Français de la Biodiversité Direction de la Recherche et de l'Appui Scientifique Service Conservation et Gestion Durable des Espèces Exploités France

Research Institute for the Environment and Livelihoods Charles Darwin University Casuarina NT Australia

School of Archaeology University College Dublin Dublin 4 Ireland

Scientific Research Center Musee National d'Histoire Naturelle Luxembourg L 2160 Luxembourg

Tbilisi Zoo Tbilisi 0171 Georgia

The Faculty of Veterinary Medicine University of Zagreb Zagreb Croatia

Tierpark Berlin Friedrichsfelde GmbH Berlin 10319 Germany

Wildlife Ecology and Conservation Group Wageningen University Wageningen PB 6708 The Netherlands

Wildlife Research Unit University of Cordoba Cordoba Spain

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Mol Biol Evol. 2025 Apr 1;42(4):msaf087. doi: 10.1093/molbev/msaf087. PubMed

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