2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2017

Eleftheria Palkopoulou, Swapan Mallick, Pontus Skoglund, Jacob Enk, Nadin Rohland, Heng Li, Ayca Omrak, Sergey Vartanyan, Hendrik Poinar, Anders Gotherstrom, David Reich, Love Dalen. Complete genomes reveal signatures of demographic and genetic declines in thewoolly mammoth. Current biology : CB, 25(10):1395-1400. 2015.

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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. However, whether
such genetic factors have had an impact on species prior to their extinction is
unclear; 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 approximately 4,300 years before present,
representing one of the last surviving individuals on Wrangel Island. The second 
mammoth, sequenced at 11.2-fold coverage, was obtained from an approximately
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 comprises 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.