Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia

Abstract

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.

Dispersal and habitat dynamics shape the genetic structure of the Northern chamois in the Alps

“…A similar pattern has been shown for red deer (Cervus elaphus; Doan et al, 2022) and the Valais shrew (Sorex antinorii; Yannic et al, 2012). Here, the contact zone of the two chamois lineages lies around the Rhone valley in Switzerland and corresponds to the contact zone found in some alpine plant species that also underwent a range expansion after the last glaciation (Jay et al, 2012), although this appears to be located further west than that of red deer (Doan et al, 2022). However, in contrast to the red deer range expansion following the last glaciation, which was dominated by the northeastward expansion of populations from south-western refugia (Doan et al, 2022), the recolonization by chamois was likely dominated by the eastern lineage, which expanded west over large parts of the Alps.…”

“…These two lineages probably represent two sources of recolonization of the Alps after the last glaciation, originating from populations isolated from each other during that time. A similar pattern has been shown for red deer (Cervus elaphus; Doan et al, 2022) and the Valais shrew (Sorex antinorii; Yannic et al, 2012). Here, the contact zone of the two chamois lineages lies around the Rhone valley in Switzerland and corresponds to the contact zone found in some alpine plant species that also underwent a range expansion after the last glaciation (Jay et al, 2012), although this appears to be located further west than that of red deer (Doan et al, 2022).…”

Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes

“…Deer haplogroups introduced to selected regions are marked with an asterisk*. The distribution ranges were compiled from several sources 2 , 104 – 119 . Figure was created in CorelDRAW Graphics Suite 11 ( https://www.coreldraw.com/en/ ) based on OpenStreetMap (URL https://www.openstreetmap.org/copyright ; ODbL licence 1.0 https://opendatacommons.org/licenses/odbl/1-0/ by OSMF).…”

Human Impact on Antler Conformation in Western Red Deer (Cervus elaphus elaphus Linnaeus, 1758)

“…A genetic signal congruent with these mtDNA results has recently also been identified in the nuclear genome, haplogroup A being most widely distributed from Iberia throughout continental Europe, the British Isles, and Scandinavia. In central/eastern Europe it co-occurs with haplogroup C of southeastern Europe, occurring in the Balkans and the Carpathians respectively [2].…”

“…Although red deer has often been translocated by humans, it seems that its present-day phylogeographic pattern in Europe reflects predominantly natural processes, in response to environmental changes and natural replacement between mtDNA lineages [2]. A major body of data on extant antlers has been used here to contextualize the morphometric characteristics of the stray find from Sweden.…”