The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 14C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100–24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000–26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Częstochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 14C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.

Aim Migrants of the Atlantic sturgeon, Acipenser oxyrinchus, from North America are thought to have founded the Baltic sturgeon population during the Little Ice Age around 1200 years ago, replacing the European sturgeon, Acipenser sturio. To test this hypothesis and to further elucidate the colonization of the Baltic Sea by A. oxyrinchus, we carried out DNA analyses of ancient and contemporary populations of both species. Location We analysed DNA from 188 specimens of sturgeons collected from archaeological sites and museums in Poland and of 225 contemporary specimens from North American and European populations. Methods Several mitochondrial DNA fragments were sequenced and eight microsatellite loci were genotyped for species identification, polymorphism and population structure analyses. Approximate Bayesian computation was used to estimate when the Baltic Sea was colonized. Results Of 125 ancient sturgeon specimens from the Baltic Sea, only four were classified as A. sturio, the remainder being A. oxyrinchus oxyrinchus. The ancient A. o. oxyrinchus population over two different time periods was highly polymorphic and genetically distant from contemporary populations of this taxon. The time of entry into the Baltic Sea was estimated to be 4000–5000 years ago. We also detected introgression of A. sturio into the A. o. oxyrinchus gene pool, caused by a prior hybridization event. Main conclusions For the past 2000 years at least, A. o. oxyrinchus has been the dominant sturgeon in the Baltic Sea, indicating a much earlier origin than previously suggested. The most similar extant sturgeon populations to the extinct Baltic stock are those from the St John and St Lawrence rivers in Canada. These populations should be considered the best source of breeding material for the ongoing sturgeon restitution programmes in Poland and Germany.

Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.

The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.

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21Climate changes that occurred during the Late Pleistocene have profound effects on the distribution of 22 many plant and animal species and influenced the formation of contemporary faunas and floras of 23 Europe. The course and mechanisms of responses of species to the past climate changes are now 24 being intensively studied by the use of direct radiocarbon dating and genetic analyses of fossil 25 remains. Here, we review the advances in understanding these processes by the example of four 26 mammal species: woolly mammoth (Mammuthus primigenius), cave bear (Ursus spelaeus s. l.), saiga 27 antelope (Saiga tatarica) and collared lemmings (Dicrostonyx ssp.). The cases discussed here as well 28 as others show that the migrations, range shifts and local extinctions were the main responses to 29 climate changes and that the dynamics of these climate driven processes were much more profound 30 2 than it was previously thought. Each species reacted by its individual manner, which depended on its 31 biology and adaptation abilities to the changing environment and climate conditions. The most severe 32 changes in European ecosystems that affected the largest number of species took place around 33-33 31 ka BP, during the Last Glacial Maximum 22-19 ka BP and the Late Glacial warming 15-13 ka BP. 34 35 37 38 84 2008; Palkopoulou et al., 2013). The divergence of lineages I and II was previously estimated to ca. 1 85 Ma ago (Debruyne et al., 2008; Gilbert and Drautz, 2008), however, most recent estimations suggest 86 much younger date about 300 ka BP (Palkopoulou et al., 2013). Coalescent simulations suggested 87 that actual split of three mammoth populations took place around 200 ka BP and was followed by a 88 demographic expansion that started around 121 ka BP (Palkopoulou et al., 2013). This expansion 89 coincides broadly with the end of Eemian Interstadial, which suggests that mammoths survived this 90 4 warm period confined to refugial areas and expanded as climate got cooler at the beginning of 91 Weichselian glaciation (Palkopoulou et al., 2013). Surprisingly, this was not supported by the analyses 92 of the whole paleogenomes, which indicated a much earlier expansion ca. 280 ka years ago and the 93 maximum effective population size during Eemian (Palkopoulou et al., 2015).94 95 96 Fig. 1. Woolly mammoth (Mammuthus primigenius). A -Bayesian phylogeny of Holarctic woolly 97 mammoths based on mtDNA cytochrome b sequences. The tree is a chronogram where branch 98 lengths denote time elapsed since divergence and the position of tips corresponds to calibrated 99 radiocarbon age of samples; B -distribution of paleontological sites with woolly mammoth 100 remains radiocarbon-dated to the indicated periods. Colours indicate mitochondrial DNA lineages 101 (modified after Palkopoulou et al., 2013). 103Despite, the ambiguities in the early history of mammoth populations, ancient DNA revealed also two 104 more recent population turnovers. In the Eemian Interglacial and Early Weichselian, woolly mammoths 105 that belonged to clad...

Cat remains from Poland dated to 4,200 to 2,300 y BCE are currently the earliest evidence for the migration of the Near Eastern cat (NE cat), the ancestor of domestic cats, into Central Europe. This early immigration preceded the known establishment of housecat populations in the region by around 3,000 y. One hypothesis assumed that NE cats followed the migration of early farmers as synanthropes. In this study, we analyze the stable isotopes in six samples of Late Neolithic NE cat bones and further 34 of the associated fauna, including the European wildcat. We approximate the diet and trophic ecology of Late Neolithic felids in a broad context of contemporary wild and domestic animals and humans. In addition, we compared the ecology of Late Neolithic NE cats with the earliest domestic cats known from the territory of Poland, dating to the Roman Period. Our results reveal that human agricultural activity during the Late Neolithic had already impacted the isotopic signature of rodents in the ecosystem. These synanthropic pests constituted a significant proportion of the NE cat’s diet. Our interpretation is that Late Neolithic NE cats were opportunistic synanthropes, most probably free-living individuals (i.e., not directly relying on a human food supply). We explore niche partitioning between studied NE cats and the contemporary native European wildcats. We find only minor differences between the isotopic ecology of both these taxa. We conclude that, after the appearance of the NE cat, both felid taxa shared the ecological niches.