Sergey Vartanyan

Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.

Temporal genetic change in the last remaining population of woolly mammoth

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.

The population size and breeding range of the Scaly-sided Merganser Mergus squamatus

Based on surveys during 2000–2012 and best available knowledge, we estimate the global population size of the Endangered Scaly-sided Merganser Mergus squamatus to be c.1,940 pairs (or c.4,660 birds prior to reproduction). In Russia, surveys identified the breeding range in the Sikhote-Alin mountain range and the area adjoining the lower Amur River. Particular effort was made to define the edge of the range. Breeding densities in the Sikhote-Alin were applied to un-surveyed rivers within the range to estimate overall numbers. The breeding range comprises c.7,800 km of 120 rivers: 6,800 km in Russia, 600 in China and 400 in DPR Korea. In Russia it comprises 88 rivers of both the western and eastern slopes of the Sikhote-Alin Range, and two small isolated areas, one in central Khabarovsk and the other in the Jewish Autonomous Oblast. All known and potential breeding areas were surveyed in China, where the breeding range comprises the western slope of the Changbai Mountains, and one isolated river system in the Lesser Xingan Mountains. Scaly-sided Mergansers are also assumed to breed on the eastern slope of the Changbai Mountains in DPR Korea. No recent surveys have been made there but numbers were estimated by applying densities from China to rivers with apparently suitable habitat. Detailed examination of past records suggests that an earlier claim of breeding Scaly-sided Mergansers on the Dep River was erroneous and we conclude that the breeding range never extended as far west as has been portrayed in most literature. The lack of comparable surveys previously precludes an assessment of change in population range or size, though it seems inevitable that habitat loss in China is likely to have resulted in some loss of range and numbers, particularly in Heilongjiang Province, in recent decades.

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.

According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the populations genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high‐quality mitogenomes from 21 radiocarbon‐dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.