Phylogeography of red deer (Cervus elaphus) in Europe

Abstract

Aim To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations). Location Europe. Methods In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics. Results Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by FST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene. Main conclusions The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.

Low genetic variation support bottlenecks in Scandinavian red deer

“…During the last glacial maximum (LGM) around 22-18,000 years before present (BP), most of northern Europe was covered by a thick ice sheet (Andersen and Borns 1994;Clark and Mix 2002;Clark et al 2009). Red deer phylogeography suggests two genetically distinct LGM refuges; (1) the Iberian Peninsula and possibly the Italian Peninsula and (2) the Balkans (Skog et al 2009). …”

“…As the ice sheet retreated through several oscillations until around 8,500 BP (Andersen and Borns 1994), on each side of the Alps red deer expanded from (1) the Iberian refuge into western and northern Europe and (2) from the Balkan refuge into eastern Europe (Sommer et al 2008;Skog et al 2009). The glacial reduction of the sea level had created land bridges that in northern Europe connected the continent with the British Isles and the southern part of the Scandinavian Peninsula (Andersen and Borns 1994).…”

“…Archaeological findings indicate wide prehistoric distributions in Britain (9,500-5,000 BP, Lister 1984) and Sweden (9,000-3,800 BP, Ahlèn 1965) while in Norway the vast majority of prehistoric findings (6,700-2,000 BP) have been made along the west coast (Lønnberg 1906;Ahlèn 1965;Rosvold 2006;Hufthammer 2006). Today, the European red deer is divided into two distinct genetic lineages, one western and one eastern (Ludt et al 2004;Sommer et al 2008;Skog et al 2009). Populations located today in past LGM refuges have higher levels of genetic variation than populations within areas of postglacial colonisation (Skog et al 2009).…”

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

“…These sequences are highly similar to other species of Cervidae [2, 12-13, 25-27, 33]. The conserved sequence blocks, and the termination-associated sequences can be used for fine-scale population studies, since they are amongst the most rapidly evolving segments in the animal mtDNA [19,24,28].…”

“…The lack of the ''DHU'' arm in tRNA Ser has been reported in other species of Cervidae [8,21,[25][26][27]35]. The non-coding control region contains conserved sequence blocks, and termination-associated sequences; and can be used for fine-scale population studies, since it is amongst the most rapidly evolving segments in the animal mtDNA [17,19,24,28]. The high-throughput approach for sequencing was useful for obtaining the whole mitochondrial genome of red deer, so this method could be used broadly among animal taxa.…”