RESEARCH ARTICLE Ancient DNA reveals prehistoric habitat fragmentation and recent domestic introgression into native wild reindeer Knut H. Røed • Gro Bjørnstad • Øystein Flagstad • Hallvard Haanes • Anne K. Hufthammer • Per Jordhøy • Jørgen Rosvold Received: 13 January 2014 / Accepted: 3 April 2014 Ó Springer Science+Business Media Dordrecht 2014 Abstract Introgression and admixture from domestic or foreign conspecifics into wild populations are of great concern in wildlife conservation. The issue is of particular interest in ungulates where translocations and re-introduc- tions have been common practice. In Europe, the only large remaining wild populations of reindeer (Rangifer tarandus L.) are found in the mountainous habitats of southern Norway. These populations have during the last centuries been exposed to extensive habitat modifications and peri- ods of contact with domestic reindeer. Through analyses of ancient and extant mitochondrial DNA (mtDNA) we doc- ument extensive intra- and inter-population genetic chan- ges during the last millennium. Our data indicate population reduction within a short time interval during the 11th–12th century during a period when mass trapping of reindeer was common. Significant differentiation between the ancient herds suggests an ancient genetic structuring of the reindeer herds in southern Norway, although not as strong as between modern herds. Two different mtDNA lineages characterized the ancient herds. A Bayesian approach to reconstruct the recent evolutionary history suggests that the reindeer herds in southern Norway orig- inate from two populations separated in different refugia during the last glacial period. The presence of two addi- tional extant lineages, characteristic of domestic herds, suggests substantial introgression into the native wild reindeer. The putatively different refugial origins of the lineages represented by the extant herds in Rondane/Dovre, Hardangervidda and those with a mainly domestic origin may well reflect different adaptations to environmental conditions, including degree of human interference. Fur- ther research on this issue would provide important insights for conservation priorities and a sustainable and flexible Electronic supplementary material The online version of this article (doi:10.1007/s10592-014-0606-z) contains supplementary material, which is available to authorized users. K. H. Røed (&) Á G. Bjørnstad Á H. Haanes Department of Basic Sciences & Aquatic Medicine, Norwegian University of Life Sciences, PO Box 8146 Dep., 0033 Oslo, Norway e-mail: knuth.roed@nmbu.no G. Bjørnstad e-mail: gro.bjornstad@iakh.uio.no H. Haanes e-mail: hallvard.haanes@ntnu.no G. Bjørnstad Department of Archaeology, Conservation and History, University of Oslo, PO Box 1008 Blindern, 0315 Oslo, Norway Ø. Flagstad Á P. Jordhøy Norwegian Institute for Nature Research, Tungasletta 2, 7485 Trondheim, Norway e-mail: oystein.flagstad@nina.no P. Jordhøy e-mail: per.jordhoy@nina.no H. Haanes Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway A. K. Hufthammer University Museum, University of Bergen, Box 7800, 5020 Bergen, Norway e-mail: anne.hufthammer@bum.uib.no J. Rosvold NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway e-mail: jorgen.rosvold@ntnu.no 123 Conserv Genet DOI 10.1007/s10592-014-0606-z