Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
peer reviewed The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full ge...
Published in: | Nature |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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Nature Publishing Group
2013
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Subjects: | |
Online Access: | https://orbilu.uni.lu/handle/10993/24785 https://doi.org/10.1038/nature12323 |
id |
ftunivluxembourg:oai:orbilu.uni.lu:10993/24785 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
University of Luxembourg: ORBilu - Open Repository and Bibliography |
op_collection_id |
ftunivluxembourg |
language |
English |
topic |
Animals Conservation of Natural Resources DNA/analysis/genetics Endangered Species Equidae/classification/genetics Evolution Molecular Fossils Genetic Variation/genetics Genome/genetics History Ancient Horses/classification/genetics Phylogeny Proteins/analysis/chemistry/genetics Yukon Territory Life sciences Biochemistry biophysics & molecular biology Sciences du vivant Biochimie biophysique & biologie moléculaire |
spellingShingle |
Animals Conservation of Natural Resources DNA/analysis/genetics Endangered Species Equidae/classification/genetics Evolution Molecular Fossils Genetic Variation/genetics Genome/genetics History Ancient Horses/classification/genetics Phylogeny Proteins/analysis/chemistry/genetics Yukon Territory Life sciences Biochemistry biophysics & molecular biology Sciences du vivant Biochimie biophysique & biologie moléculaire Orlando, Ludovic Ginolhac, Aurélien Zhang, Guojie Froese, Duane Albrechtsen, Anders Stiller, Mathias Schubert, Mikkel Cappellini, Enrico Petersen, Bent Moltke, Ida Johnson, Philip L. F. Fumagalli, Matteo Vilstrup, Julia T. Raghavan, Maanasa Korneliussen, Thorfinn Malaspinas, Anna-Sapfo Vogt, Josef Szklarczyk, Damian Kelstrup, Christian D. Vinther, Jakob Dolocan, Andrei Stenderup, Jesper Velazquez, Amhed M. V. Cahill, James Rasmussen, Morten Wang, Xiaoli Min, Jiumeng Zazula, Grant D. Seguin-Orlando, Andaine Mortensen, Cecilie Magnussen, Kim Thompson, John F. Weinstock, Jacobo Gregersen, Kristian Roed, Knut H. Eisenmann, Vera Rubin, Carl J. Miller, Donald C. Antczak, Douglas F. Bertelsen, Mads F. Brunak, Soren Al-Rasheid, Khaled A. S. Ryder, Oliver Andersson, Leif Mundy, John Krogh, Anders Gilbert, M. Thomas P. Kjaer, Kurt Sicheritz-Ponten, Thomas Jensen, Lars Juhl Olsen, Jesper V. Hofreiter, Michael Nielsen, Rasmus Shapiro, Beth Wang, Jun Willerslev, Eske Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
topic_facet |
Animals Conservation of Natural Resources DNA/analysis/genetics Endangered Species Equidae/classification/genetics Evolution Molecular Fossils Genetic Variation/genetics Genome/genetics History Ancient Horses/classification/genetics Phylogeny Proteins/analysis/chemistry/genetics Yukon Territory Life sciences Biochemistry biophysics & molecular biology Sciences du vivant Biochimie biophysique & biologie moléculaire |
description |
peer reviewed The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication. |
format |
Article in Journal/Newspaper |
author |
Orlando, Ludovic Ginolhac, Aurélien Zhang, Guojie Froese, Duane Albrechtsen, Anders Stiller, Mathias Schubert, Mikkel Cappellini, Enrico Petersen, Bent Moltke, Ida Johnson, Philip L. F. Fumagalli, Matteo Vilstrup, Julia T. Raghavan, Maanasa Korneliussen, Thorfinn Malaspinas, Anna-Sapfo Vogt, Josef Szklarczyk, Damian Kelstrup, Christian D. Vinther, Jakob Dolocan, Andrei Stenderup, Jesper Velazquez, Amhed M. V. Cahill, James Rasmussen, Morten Wang, Xiaoli Min, Jiumeng Zazula, Grant D. Seguin-Orlando, Andaine Mortensen, Cecilie Magnussen, Kim Thompson, John F. Weinstock, Jacobo Gregersen, Kristian Roed, Knut H. Eisenmann, Vera Rubin, Carl J. Miller, Donald C. Antczak, Douglas F. Bertelsen, Mads F. Brunak, Soren Al-Rasheid, Khaled A. S. Ryder, Oliver Andersson, Leif Mundy, John Krogh, Anders Gilbert, M. Thomas P. Kjaer, Kurt Sicheritz-Ponten, Thomas Jensen, Lars Juhl Olsen, Jesper V. Hofreiter, Michael Nielsen, Rasmus Shapiro, Beth Wang, Jun Willerslev, Eske |
author_facet |
Orlando, Ludovic Ginolhac, Aurélien Zhang, Guojie Froese, Duane Albrechtsen, Anders Stiller, Mathias Schubert, Mikkel Cappellini, Enrico Petersen, Bent Moltke, Ida Johnson, Philip L. F. Fumagalli, Matteo Vilstrup, Julia T. Raghavan, Maanasa Korneliussen, Thorfinn Malaspinas, Anna-Sapfo Vogt, Josef Szklarczyk, Damian Kelstrup, Christian D. Vinther, Jakob Dolocan, Andrei Stenderup, Jesper Velazquez, Amhed M. V. Cahill, James Rasmussen, Morten Wang, Xiaoli Min, Jiumeng Zazula, Grant D. Seguin-Orlando, Andaine Mortensen, Cecilie Magnussen, Kim Thompson, John F. Weinstock, Jacobo Gregersen, Kristian Roed, Knut H. Eisenmann, Vera Rubin, Carl J. Miller, Donald C. Antczak, Douglas F. Bertelsen, Mads F. Brunak, Soren Al-Rasheid, Khaled A. S. Ryder, Oliver Andersson, Leif Mundy, John Krogh, Anders Gilbert, M. Thomas P. Kjaer, Kurt Sicheritz-Ponten, Thomas Jensen, Lars Juhl Olsen, Jesper V. Hofreiter, Michael Nielsen, Rasmus Shapiro, Beth Wang, Jun Willerslev, Eske |
author_sort |
Orlando, Ludovic |
title |
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
title_short |
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
title_full |
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
title_fullStr |
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
title_full_unstemmed |
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. |
title_sort |
recalibrating equus evolution using the genome sequence of an early middle pleistocene horse. |
publisher |
Nature Publishing Group |
publishDate |
2013 |
url |
https://orbilu.uni.lu/handle/10993/24785 https://doi.org/10.1038/nature12323 |
genre |
permafrost Yukon |
genre_facet |
permafrost Yukon |
op_source |
Nature, 499 (7456), 74-8 (2013) |
op_relation |
urn:issn:1476-4687 https://orbilu.uni.lu/handle/10993/24785 info:hdl:10993/24785 doi:10.1038/nature12323 scopus-id:2-s2.0-84879888373 info:pmid:23803765 wos:000321285600036 |
op_rights |
restricted access http://purl.org/coar/access_right/c_16ec info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1038/nature12323 |
container_title |
Nature |
container_volume |
499 |
container_issue |
7456 |
container_start_page |
74 |
op_container_end_page |
78 |
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1796951804218441728 |
spelling |
ftunivluxembourg:oai:orbilu.uni.lu:10993/24785 2024-04-21T08:10:22+00:00 Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Orlando, Ludovic Ginolhac, Aurélien Zhang, Guojie Froese, Duane Albrechtsen, Anders Stiller, Mathias Schubert, Mikkel Cappellini, Enrico Petersen, Bent Moltke, Ida Johnson, Philip L. F. Fumagalli, Matteo Vilstrup, Julia T. Raghavan, Maanasa Korneliussen, Thorfinn Malaspinas, Anna-Sapfo Vogt, Josef Szklarczyk, Damian Kelstrup, Christian D. Vinther, Jakob Dolocan, Andrei Stenderup, Jesper Velazquez, Amhed M. V. Cahill, James Rasmussen, Morten Wang, Xiaoli Min, Jiumeng Zazula, Grant D. Seguin-Orlando, Andaine Mortensen, Cecilie Magnussen, Kim Thompson, John F. Weinstock, Jacobo Gregersen, Kristian Roed, Knut H. Eisenmann, Vera Rubin, Carl J. Miller, Donald C. Antczak, Douglas F. Bertelsen, Mads F. Brunak, Soren Al-Rasheid, Khaled A. S. Ryder, Oliver Andersson, Leif Mundy, John Krogh, Anders Gilbert, M. Thomas P. Kjaer, Kurt Sicheritz-Ponten, Thomas Jensen, Lars Juhl Olsen, Jesper V. Hofreiter, Michael Nielsen, Rasmus Shapiro, Beth Wang, Jun Willerslev, Eske 2013 https://orbilu.uni.lu/handle/10993/24785 https://doi.org/10.1038/nature12323 en eng Nature Publishing Group urn:issn:1476-4687 https://orbilu.uni.lu/handle/10993/24785 info:hdl:10993/24785 doi:10.1038/nature12323 scopus-id:2-s2.0-84879888373 info:pmid:23803765 wos:000321285600036 restricted access http://purl.org/coar/access_right/c_16ec info:eu-repo/semantics/restrictedAccess Nature, 499 (7456), 74-8 (2013) Animals Conservation of Natural Resources DNA/analysis/genetics Endangered Species Equidae/classification/genetics Evolution Molecular Fossils Genetic Variation/genetics Genome/genetics History Ancient Horses/classification/genetics Phylogeny Proteins/analysis/chemistry/genetics Yukon Territory Life sciences Biochemistry biophysics & molecular biology Sciences du vivant Biochimie biophysique & biologie moléculaire journal article http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article peer reviewed 2013 ftunivluxembourg https://doi.org/10.1038/nature12323 2024-03-27T14:11:08Z peer reviewed The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication. Article in Journal/Newspaper permafrost Yukon University of Luxembourg: ORBilu - Open Repository and Bibliography Nature 499 7456 74 78 |