Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth

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. Howev...

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Vydané v:	Current biology Ročník 25; číslo 10; s. 1395
Hlavní autori:	Palkopoulou, Eleftheria, Mallick, Swapan, Skoglund, Pontus, Enk, Jacob, Rohland, Nadin, Li, Heng, Omrak, Ayça, Vartanyan, Sergey, Poinar, Hendrik, Götherström, Anders, Reich, David, Dalén, Love
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	England 18.05.2015
Predmet:	Animals Extinction, Biological Female Genetic Variation Genetics, Population Genome Heterozygote Mammoths - genetics Population Density Sequence Analysis, DNA Siberia Siberia
ISSN:	1879-0445, 1879-0445
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Abstract	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 ∼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 ∼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.
AbstractList	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 ∼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 ∼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.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 ∼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 ∼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. 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 ∼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 ∼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.
Author	Palkopoulou, Eleftheria Götherström, Anders Vartanyan, Sergey Omrak, Ayça Poinar, Hendrik Skoglund, Pontus Rohland, Nadin Li, Heng Mallick, Swapan Enk, Jacob Dalén, Love Reich, David
Author_xml	– sequence: 1 givenname: Eleftheria surname: Palkopoulou fullname: Palkopoulou, Eleftheria email: elle.palkopoulou@gmail.com organization: Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden. Electronic address: elle.palkopoulou@gmail.com – sequence: 2 givenname: Swapan surname: Mallick fullname: Mallick, Swapan organization: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA – sequence: 3 givenname: Pontus surname: Skoglund fullname: Skoglund, Pontus organization: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden – sequence: 4 givenname: Jacob surname: Enk fullname: Enk, Jacob organization: McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, 5692 Plymouth Road, Ann Arbor, MI 48105, USA – sequence: 5 givenname: Nadin surname: Rohland fullname: Rohland, Nadin organization: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA – sequence: 6 givenname: Heng surname: Li fullname: Li, Heng organization: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA – sequence: 7 givenname: Ayça surname: Omrak fullname: Omrak, Ayça organization: Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden – sequence: 8 givenname: Sergey surname: Vartanyan fullname: Vartanyan, Sergey organization: N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia – sequence: 9 givenname: Hendrik surname: Poinar fullname: Poinar, Hendrik organization: McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada – sequence: 10 givenname: Anders surname: Götherström fullname: Götherström, Anders organization: Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden – sequence: 11 givenname: David surname: Reich fullname: Reich, David organization: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA – sequence: 12 givenname: Love surname: Dalén fullname: Dalén, Love email: love.dalen@nrm.se organization: Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden. Electronic address: love.dalen@nrm.se
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Snippet	The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a...
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SubjectTerms	Animals Extinction, Biological Female Genetic Variation Genetics, Population Genome Heterozygote Mammoths - genetics Population Density Sequence Analysis, DNA Siberia
Title	Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth
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