Summary The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [1]. However, whether such genetic factors have had an impact on species prior to their extinction is unclear [2, 3]; examining this would require a detailed reconstruction of a species’ demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage, and dates to ~4,300 years before present, constituting one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from a ~44,800 year old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that is comprised of runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.
THE cause of extinction of the woolly mammoth, Mammuthus primigenius (Blumenbach), is still debated. A major environmental change at the Pleistocene-Holocene boundary, hunting by early man, or both together are among the main explanations that have been suggested. But hardly anyone has doubted that mammoths had become extinct everywhere by around 9,500 years before present (BP). We report here new discoveries on Wrangel Island in the Arctic Ocean that force this view to be revised. Along with normal-sized mammoth fossils dating to the end of the Pleistocene, numerous teeth of dwarf mammoth dated 7,000-4,000 yr BP have been found there. The island is thought to have become separated from the mainland by 12,000 yr BP. Survival of a mammoth population may be explained by local topography and climatic features, which permitted relictual preservation of communities of steppe plants. We interpret the dwarfing of the Wrangel mammoths as a result of the insularity effect, combined with a response to the general trend towards unfavourable environment in the Holocene.
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.
We present and discuss a full list of radiocarbon dates for woolly mammoth and other species of the Mammoth fauna available from Wrangel Island, northeast Siberia, Russia. Most of the radiocarbon dates are published here for the first time. Of the124 radiocarbon dates on mammoth bone, 106 fall between 3700 and 9000 yr ago. We believe these dates bracket the period of mammoth isolation on Wrangel Island and their ultimate extinction, which we attribute to natural causes. The absence of dates between 9–12 ka probably indicates a period when mammoths were absent from Wrangel Island. Long bone dimensions of Holocene mammoths from Wrangel Island indicate that these animals were comparable in size to those on the mainland; although they were not large animals, neither can they be classified as dwarfs. Occurrence of mammoth Holocene refugia on the mainland is suggested. Based on other species of the Mammoth fauna that have also been radiocarbon on Wrangel Island, including horse, bison, musk ox and woolly rhinoceros, it appears that the mammoth was the only species of that fauna that inhabited Wrangel Island in the mid-Holocene.
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