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Aim: Brown bear populations in Scandinavia show a strong mitochondrial DNA (mtDNA) phylogeographic structure and low diversity relative to other parts of Europe. Identifying the timing and origins of this mtDNA structure is important for conservation programs aimed at restoring populations to a natural state. Therefore, it is essential to identify whether contemporary genetic structure is linked to post-glacial recolonisation from divergent source populations or an artefact of demographic impacts during recent population bottlenecks. We employed ancient DNA techniques to investigate the timing and potential causes of these patterns. Location: Scandinavia and Europe. Methods: Ancient mtDNA sequences from 20 post-glacial Scandinavian bears were used to investigate phylogeographic structure and genetic diversity over the last 6000 years. MtDNA from 19 Holocene Norwegian bears was compared with 499 sequences from proximate extant populations in Sweden, Finland, Estonia and western Russia. A single mtDNA sequence from a Holocene Denmark sample was compared with 149 ancient and modern bears from Western Europe. Results: All nineteen Holocene Norwegian samples are identical to or closely related to the most common mtDNA haplotype found in northern Europe today. MtDNA diversity was low and not significantly different from extant populations in northern Europe. In Denmark, we identified a single mtDNA haplotype that is previously unrecorded from Scandinavia. Main conclusions: The current discrete phylogeographic structure and lack of mtDNA diversity in Scandinavia is attributed to serial founder effects during post-glacial recolonisation from divergent source populations rather than an artefact of recent anthropogenic impacts. In contrast to previous interpretations, the recolonisation of southern Scandinavia may not have been limited to bears from a single glacial refugium. Results highlight the importance of conserving the long-term evolutionary separation between northern and southern populations and identify southern Scandinavia as an important reservoir of mtDNA diversity that is under threat in other parts of Europe. © 2012 Blackwell Publishing Ltd.

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain