Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species

Abstract

The major climatic oscillations that characterized the Quaternary had a great influence on the evolution and distribution of several species. During cold periods, the distribution of temperate‐adapted species became fragmented with many surviving in southern refugia (Iberian, Italian, and Balkan Peninsulas). Red deer was one of the species that contracted its original range to southern refugia. Currently, two main lineages have been described for the species: western and eastern. We have analyzed fossils pre‐dating the last glacial maximum (LGM) from Liñares cave (NW Spain) that belongs to the peripheral range of the western clade, and fossils from the Danish Holocene belonging to the central part of the same clade. Phylogenetic analyses place our samples in the western clade. However, some specimens from Liñares represent an early split in the tree along with other pre‐LGM western samples from previous studies. Despite low bootstrap values in the Bayesian phylogenies, haplotype networks connect these foreign haplotypes to the eastern clade. We suggest a mixed phylogeographical model to explain this pattern with range expansions from the east during the expansion phase after the cold periods in marine isotope stage 3. We find slight isolation by distance in post‐LGM populations that could be a consequence of the recolonization from southern refugia after the LGM.

Multiplex PCRs for the specific identification of marsupial and deer species from faecal samples as a basis for non-invasive epidemiological studies of parasites

“…MN746795) was identical to those representing Sri Lankan subclade B (GenBank: MF176994, MF177001 and MF177018; [30]); the cytb gene sequence derived from a red deer from Yan Yean, Victoria (accession no. MN746793) was identical to that of the Western and Central European red deer clade (GenBank: KX496937 and MF872247; [38,39]); cytb gene sequence derived from a fallow deer from Cardinia, Victoria (accession no. MN746794) was identical to that from GenBank (JN632629; [27]).…”

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

“…Due to its physiographic complexity, multiple glacial refugia for various animal and plant species have been described in Iberia, supporting the ‘refugia within refugia’ model [27,32]. In particular, the demographic and evolutionary history of the red deer in Iberia and its relation with western European populations has been studied substantially over the last years, although the majority of wide-ranging phylogeographical studies are based in a limited number of populations and/or molecular markers [15,18–20,25,33–37]. Recent studies focused on Iberia using ancient [37] and contemporary [36] Iberian red deer samples have revealed a complex phylogeographical history.…”

“…In particular, the demographic and evolutionary history of the red deer in Iberia and its relation with western European populations has been studied substantially over the last years, although the majority of wide-ranging phylogeographical studies are based in a limited number of populations and/or molecular markers [15,18–20,25,33–37]. Recent studies focused on Iberia using ancient [37] and contemporary [36] Iberian red deer samples have revealed a complex phylogeographical history. The analysis of ancient red deer specimens detected Western and Eastern European D-loop haplotypes in northwestern Spain during pre-LGM times [37].…”

“…Recent studies focused on Iberia using ancient [37] and contemporary [36] Iberian red deer samples have revealed a complex phylogeographical history. The analysis of ancient red deer specimens detected Western and Eastern European D-loop haplotypes in northwestern Spain during pre-LGM times [37]. Moreover, analysis of contemporary samples by Carranza et al [33] revealed two mtDNA D-loop sub-lineages within the Western European lineage, and the authors argued that one of them contributed to the northern postglacial re-colonization of western Europe even though nuclear data were not adequate in this respect.…”

Population dynamics and range shifts of moose (Alces alces) during the Late Quaternary

“…Most of the focus has been on Europe, northern Asia and North America (e.g. Brace et al., 2012; Cooper et al., 2015; Rey‐Iglesia et al, 2017; Stuart & Lister, 2012; Valdiosera et al., 2007), while relatively little work has been conducted on mammalian species that survived the Pleistocene extinction event elsewhere in Asia (e.g. Barnes, Matheus, Shapiro, Jensen, & Cooper, 2002; Campos et al., 2010; Meiri et al., 2013; Turvey, Tong, Stuart, & Lister, 2013).…”