Exploring the phylogeography and population dynamics of the giant deer (Megaloceros giganteus) using Late Quaternary mitogenomes

Increased incidences of cervical ribs in deer indicate extinction risk

Mammals as a rule have seven cervical vertebrae, a number which remains remarkably conserved. Occasional deviations of this number are usually due to the presence of cervical ribs on the seventh vertebra, indicating a homeotic transformation from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. These transformations are often associated with major congenital abnormalities or pediatric cancers (pleiotropic effects) that are, at least in humans, strongly selected against. Based on data from Late Pleistocene mammoths (Mammuthus primigenius) and woolly rhinoceroses (Coelodonta antiquitatis) from the North Sea, we hypothesized that high incidences of cervical ribs in declining populations are due to inbreeding and/or adverse conditions impacting early pregnancies. In this study, we investigated the incidence of cervical ribs in an extinct Late Pleistocene megaherbivore, giant deer (Megaloceros giganteus) from Ireland and in the extant highly inbred Père David deer (Elaphurus davidianus) and in twenty other extant species. We show that the incidence of cervical ribs is exceptionally high in both the Irish giant deer and the Père David deer and much higher than in extant outbred deer. Our data support the hypothesis that inbreeding and genetic drift increase the frequencies of maladaptive alleles in populations at risk of extinction. The high incidence of cervical ribs indicates a vulnerable condition, which may have contributed to the extinction of megaherbivore species in the Late Pleistocene. We argue that cervical rib frequency may be a good proxy for extinction risk in inbred populations.

Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia

The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.

Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

The Exceptional Presence of Megaloceros giganteus in North-Eastern Iberia and Its Palaeoecological Implications: The Case of Teixoneres Cave (Moià, Barcelona, Spain)

In this article we announce the discovery of the first remains of Megaloceros giganteus found in Catalonia (north-eastern Iberia) from the Late Pleistocene: a fragment of maxillary. Dated between 35,000 and 37,000 cal BP, it is also among the youngest occurrence of this taxon in the Iberian Peninsula, while its last known occurrence is dated to the Neolithic period. Through a comparison with the giant deer of the northern Pyrenees, we analyzed the herbivore guilds in which this taxon was associated to understand the context in which it was able to enter the Iberian Peninsula. By comparing its diet with those of specimens from Northern Europe, we detail the ecological adaptations of this taxon in this new environment. We suggest that Megaloceros accompanied the migrations of cold-adapted species by taking advantage of the opening of corridors on both sides of the Pyrenees during the coldest periods of the Late Pleistocene. The diet of the Iberian individuals, which is oriented towards abrasive plants, suggests an adaptation to a different ecological niche than that found in Northern European individuals. The northern Iberian Peninsula may have been an extreme in the geographical expansion of M. giganteus. More specimens will be needed in the future to establish the variability of the southern Megaloceros populations.

Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China

Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.

Taxonomy, Systematics and Evolution of Giant Deer Megaloceros Giganteus (Blumenbach, 1799) (Cervidae, Mammalia) from the Pleistocene of Eurasia

The article presents a preliminary morphological description of the holotype of Megaloceros giganteus (Blumenbach, 1799) that serves for the description of the species. The article proposes a taxonomical and morphological revision of the nominotypical subspecies M. giganteus giganteus and morphological comparison with other subspecies of M. giganteus. The cluster analysis of diagnostic craniodental and antler characters revealed the systematic position and phylogenetic relationships of M. giganteus with other cervid groups. The genus Praedama is regarded as a closely related phylogenetic branch that linked to the direct cursorial forerunner of Megaloceros that evolved in the middle latitudes of Western Siberia and northern Kazakhstan. The genus Dama has a distant relationship with Megaloceros and represents an earlier phylogenetic branch that evolved in the Ponto-Mediterranean area. The article discusses the secondary adaptations of M. giganteus forms to forest and woodland habitats in Europe and general paleobiogeographic features of the Megaloceros lineage.