The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

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This study investigated the levels of genetic diversity and variation exhibited by red and sika deer in Ireland, along with the extent and regional location of hybridisation between these two species. Bi-parental (microsatellites) and maternally-inherited (mitochondrial DNA) genetic markers were utilised that allowed comparisons between 85 red deer from six localities and 47 sika deer from 3 localities in Ireland. Population genetic structure was assessed using Bayesian analysis, indicating the existence of two genetic clusters in sika deer and three clusters in red deer. Levels of genetic diversity were low in both red and sika deer. These genetic data presented herein indicate a recent introduction of sika deer and subsequent translocations in agreement with historical data. The origins of the current red deer populations found in Ireland, based on genetic data presented in this study, still remain obscure. All hybrid deer (red/sika) found in this study were found in Wicklow, Galway and Mayo where the 'red-like' deer exhibited sika deer alleles/haplotypes, and vice versa in the case of Wicklow. Molecular methods proved invaluable in the identification of the hybrid deer because identification of hybrids based on phenotypic external appearances (pelage and body proportions) can be misleading. Areas where red and sika deer are sympatric need to be assessed for the level and extent of hybridisation occurring and thus need to be managed in order to protect the genetic integrity of 'pure' red deer populations.

1. Throughout Europe, the range of many deer species is expanding. We provide current distribution maps for red deer Cervus elaphus, sika Cervus nippon, fallow deer Dama dama and muntjac deer Muntiacus sp. in Ireland, and estimates of range expansion rates for red deer, sika and fallow deer. 2.There was a considerable expansion in the ranges of red deer, sika and fallow deer between 1978 and 2008. The compound annual rate of expansion was 7% for red deer, 5% for sika and 3% for fallow deer. The total range increase was 565% for red deer, 353% for sika and 174% for fallow deer. The potential implications of these expansions are discussed. 3. There are unknown numbers of red-sika hybrid deer in some parts of Ireland. Range expansion is likely to lead to further hybridizations with implications for the genetic integrity of deer stocks. 4. Sightings of free-roaming muntjac deer were first recorded in 2007. The distribution of confirmed sightings of single and multiple animals in the eastern region of Ireland suggests multiple releases. 5. Deer are already impacting on both the economic and biodiversity values of habitats in Ireland, where, at present, no sustainable deer management policy exists.