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The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations., Competing Interests: We have the following interests. MB has a current affiliation with SABIOtec. SABIOtec did not intervene in experimental design, data collection and analysis. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

Background: The goal of this study was describing the temporal evolution of Aujeszky's disease virus (ADV) contact prevalence among Eurasian wild boar (Sus scrofa) populations under different management regimes and contact likelihoods with domestic pigs. Given the recent increase in wild boar abundance throughout Europe, we hypothesized that wild boar contact with ADV would remain stable in time even after significant reduction of ADV prevalence in domestic pigs., Results: Sera from 1659 wild boar were collected from 2000 to 2010 within 6 areas of the Iberian Peninsula and tested for the presence of antibodies against ADV by ELISA. According to sampling date, wild boar were grouped into three time periods. ADV prevalence was compared through period both globally and by geographic area. Overall seroprevalence for the ten-year study period was 49.6 ± 2.4%. The highest seroprevalence was recorded in areas with intense wild boar management. The annual proportion of positive wild boar sampling sites remained stable through the study period, while the percentage of domestic pig AD positive counties decreased from 70% in 2003 to 1.7% in 2010., Conclusions: Results presented herein confirmed our hypothesis that ADV would remain almost stable in wild boar populations. This evidences the increasing risk wild boar pose in the final stages of ADV eradication in pigs and for wildlife conservation.