Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history

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.This work was supported by: Portuguese national funds through the FCT (Fundação para a Ciência e a Tecnologia), FEDER funds (Fundo Europeu de Desenvolvimento Regional) through Programa Operacional Potencial Humano-Quadro de Referência Estratégico Nacional (POPH-QREN) from the European Social Fund and Portuguese Ministério da Educação e Ciência and the project ‘Genomics applied to genetic resources’, North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte); the EU grant ‘Harmonised approaches in monitoring wildlife population health, and ecology and abundance’ (APHAEA, 219235_FP7_ERA-NET_EMIDA) and CDTI. This is also a contribution to grant AGL20111-30041 from MINECO, Spain. MB is currently an employee and CEO of SABIOtec commercial company. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of grants to the authors (SFRH/BD/73732/2010 PhD grant to JQ, SFRH/BD/5880/2008 PhD grant to JPVS and SFRH/BSAB/1278/2012 sabbatical grant to PCA) and/or research materials.Peer reviewe