Genotyping of Capreolus pygargus Fossil DNA from Denisova Cave Reveals Phylogenetic Relationships between Ancient and Modern Populations

Abstract

BackgroundThe extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.Methodology/Principal FindingsWe analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.Conclusion/SignificanceAnalysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.

Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer

“…It arose 23 kyr ago at the latest, and the haplotypes were possessed by most of the introgressed individuals (nearly 75%) and were found in every admixed population. The haplotypes are closely related to those found in Siberian roe deer from western and central Siberia but have not been detected within its natural distribution range in previous species-wide studies (Vorobieva et al 2011;Zvychaynaya et al 2011a), suggesting ancient origin of present introgression. The same unique C. pygargus haplotypes found in Poland were also predominant in the Moscow area (Zvychaynaya et al 2011b), which supports the proposed gene surfing on the eastward expansion wave of European roe deer after hybridization event(s) with Siberian roe deer in Central Europe.…”

“…The haplotypes are closely related to those found in Siberian roe deer from western and central Siberia but have not been detected within its natural distribution range in previous species‐wide studies (Vorobieva et al . ; Zvychaynaya et al . ), suggesting ancient origin of present introgression.…”

“…The presence of two haplotypes (H59 and H60) belonging to a group currently found only in the Altai Mountains (Vorobieva et al . ) is most likely the result of introductions of Siberian roe deer in nineteenth and twentieth centuries in Poland, Slovakia or Ukraine (Danilkin & Hewison ), as the haplotypes' occurrence was limited to the southeastern Poland.…”

Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus)

“…The presence of an animal lacking Bs raised the question of whether this could be a misidentified C. capreolus individual. The analysis of the mitochondrial DNA control region allowed us to unambiguously describe the species as C. pygargus (the haplotype Ns99 is identical to the ancient haplotype DC6 ([28], GenBank: GU811828). This finding indicates that the amount of B chromosomes in the Siberian roe deer is highly variable between individuals (0 to 14) and that the presence of B chromosomes is not essential for animal physiology and cannot be used as a species discriminating character.…”

“…Recently, we have studied the standard karyotype of the Siberian roe deer by comparative chromosome painting and found it to be highly conserved and similar to that of the cervid ancestor [25]. Although some authors proposed the classification of several subspecies of C. pygargus [26,27], our studies of the mitochondrial DNA control region in the populations of extant and ancient roe deer failed to reveal any subspecies structure [28]. …”