Sébastien Calvignac

Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times.

The genetic diversity of present‐day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35 000 years. However, the post‐last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.

Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts)

Molecular tools have become prominent in ecology and evolution. A target of choice for molecular ecologists and evolutionists is mitochondrial DNA (mtDNA), whose many advantages have also convinced broad-scale, pragmatic programmes such as barcode initiatives. Of course, mtDNA is also of interest to human geneticists investigating mitochondrial diseases. Studies using mtDNA are however put at great risk by the inadvertent co-amplification or preferred amplification of nuclear pseudogenes (numts). A posteriori analysis of putative mtDNA sequences can help in removing numts but faces severe limitations (e.g. recently translocated numts will most of the time go unnoticed). Counter-measures taken a priori, i.e. explicitly designed for avoiding numt co-amplification or preferred amplification, are appealing but have never been properly assessed. Here we investigate the efficiency of four such measures (mtDNA enrichment, cDNA amplification, long-range amplification and pre-PCR dilution) on a common set of numt cases, showing that mtDNA enrichment is the worst performer while the use of pre-PCR dilution is a simple, yet robust method to prevent the pollution of putative mtDNA datasets with numts. Therefore, straightforward recommendations can be made that, if followed, will considerably increase the confidence in the mitochondrial origin of any mtDNA-like sequence.

Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny

Despite numerous studies, questions remain about the evolutionary history of Ursidae and additional independent genetic markers were needed to elucidate these ambiguities. For this purpose, we sequenced ten nuclear genes for all the eight extant bear species. By combining these new sequences with those of four other recently published nuclear markers, we provide new insights into the phylogenetic relationships of the Ursidae family members. The hypothesis that the giant panda was the first species to diverge among ursids is definitively confirmed and the precise branching order within the Ursus genus is clarified for the first time. Moreover, our analyses indicate that the American and the Asiatic black bears do not cluster as sister taxa, as had been previously hypothesised. Sun and sloth bears clearly appear as the most basal ursine species but uncertainties about their exact relationships remain. Since our larger dataset did not enable us to clarify this last question, identifying rare genomic changes in bear genomes could be a promising solution for further studies.

African Great Apes Are Naturally Infected with Polyomaviruses Closely Related to Merkel Cell Polyomavirus

ABSTRACT The oncogenic Merkel cell polyomavirus (MCPyV) infects humans worldwide, but little is known about the occurrence of viruses related to MCPyV in the closest phylogenetic relatives of humans, great apes. We analyzed samples from 30 wild chimpanzees and one captive gorilla and identified two new groups of polyomaviruses (PyVs). These new viruses are by far the closest relatives to MCPyV described to date, providing the first evidence of the natural occurrence of PyVs related to MCPyV in wild great apes. Similar to MCPyV, the prevalence of these viruses is relatively high (>30%). This, together with the fact that humans in West and Central Africa frequently hunt and butcher primates, may point toward further MCPyV-like strains spreading to, or already existing in, our species.

Ancient DNA Identification of Early 20th Century Simian T-Cell Leukemia Virus Type 1

The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to better characterize simian and human T-tropic retrovirus genetic diversity and analyze their origin and evolution, in greater detail.

Does the 43 bp sequence from an 800 000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths

Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al. (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.