Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

The rich fossil record of equids has made them a model for evolutionary processes1. 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)2, 3. Our data represent the oldest full genome sequ...

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Main Authors:	Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P., Fumagalli, M., Vilstrup, J., Raghavan, M., Korneliussen, T., Malaspinas, A., Vogt, J., Szklarczyk, D., Kelstrup, C., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J., Weinstock, J., Gregersen, K., Roed, K., Eisenmann, V., Rubin, C., Miller, D., Antczak, D., Bertelsen, M., Brunak, S., Al-Rasheid, K., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, Thomas, Kjær, K., Sicheritz-Ponten, T., Jensen, L., Olsen, J., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, Jun, Willerslev, E.
Format:	Journal Article
Published:	Nature Publishing Group 2013
Subjects:	Evolutionary Genetics
Online Access:	http://www.nature.com/nature/journal/v499/n7456/full/nature12323.html http://hdl.handle.net/20.500.11937/21771

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author	Orlando, L. Ginolhac, A. Zhang, G. Froese, D. Albrechtsen, A. Stiller, M. Schubert, M. Cappellini, E. Petersen, B. Moltke, I. Johnson, P. Fumagalli, M. Vilstrup, J. Raghavan, M. Korneliussen, T. Malaspinas, A. Vogt, J. Szklarczyk, D. Kelstrup, C. Vinther, J. Dolocan, A. Stenderup, J. Velazquez, A. Cahill, J. Rasmussen, M. Wang, X. Min, J. Zazula, G. Seguin-Orlando, A. Mortensen, C. Magnussen, K. Thompson, J. Weinstock, J. Gregersen, K. Roed, K. Eisenmann, V. Rubin, C. Miller, D. Antczak, D. Bertelsen, M. Brunak, S. Al-Rasheid, K. Ryder, O. Andersson, L. Mundy, J. Krogh, A. Gilbert, Thomas Kjær, K. Sicheritz-Ponten, T. Jensen, L. Olsen, J. Hofreiter, M. Nielsen, R. Shapiro, B. Wang, Jun Willerslev, E.
author_facet	Orlando, L. Ginolhac, A. Zhang, G. Froese, D. Albrechtsen, A. Stiller, M. Schubert, M. Cappellini, E. Petersen, B. Moltke, I. Johnson, P. Fumagalli, M. Vilstrup, J. Raghavan, M. Korneliussen, T. Malaspinas, A. Vogt, J. Szklarczyk, D. Kelstrup, C. Vinther, J. Dolocan, A. Stenderup, J. Velazquez, A. Cahill, J. Rasmussen, M. Wang, X. Min, J. Zazula, G. Seguin-Orlando, A. Mortensen, C. Magnussen, K. Thompson, J. Weinstock, J. Gregersen, K. Roed, K. Eisenmann, V. Rubin, C. Miller, D. Antczak, D. Bertelsen, M. Brunak, S. Al-Rasheid, K. Ryder, O. Andersson, L. Mundy, J. Krogh, A. Gilbert, Thomas Kjær, K. Sicheritz-Ponten, T. Jensen, L. Olsen, J. Hofreiter, M. Nielsen, R. Shapiro, B. Wang, Jun Willerslev, E.
author_sort	Orlando, L.
building	Curtin Institutional Repository
collection	Online Access
description	The rich fossil record of equids has made them a model for evolutionary processes1. 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)2, 3. 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 Equus4, 5. 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 population6. 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.
first_indexed	2025-11-14T07:40:44Z
format	Journal Article
id	curtin-20.500.11937-21771
institution	Curtin University Malaysia
institution_category	Local University
last_indexed	2025-11-14T07:40:44Z
publishDate	2013
publisher	Nature Publishing Group
recordtype	eprints
repository_type	Digital Repository
spelling	curtin-20.500.11937-217712017-02-28T01:36:29Z Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse Orlando, L. Ginolhac, A. Zhang, G. Froese, D. Albrechtsen, A. Stiller, M. Schubert, M. Cappellini, E. Petersen, B. Moltke, I. Johnson, P. Fumagalli, M. Vilstrup, J. Raghavan, M. Korneliussen, T. Malaspinas, A. Vogt, J. Szklarczyk, D. Kelstrup, C. Vinther, J. Dolocan, A. Stenderup, J. Velazquez, A. Cahill, J. Rasmussen, M. Wang, X. Min, J. Zazula, G. Seguin-Orlando, A. Mortensen, C. Magnussen, K. Thompson, J. Weinstock, J. Gregersen, K. Roed, K. Eisenmann, V. Rubin, C. Miller, D. Antczak, D. Bertelsen, M. Brunak, S. Al-Rasheid, K. Ryder, O. Andersson, L. Mundy, J. Krogh, A. Gilbert, Thomas Kjær, K. Sicheritz-Ponten, T. Jensen, L. Olsen, J. Hofreiter, M. Nielsen, R. Shapiro, B. Wang, Jun Willerslev, E. Evolutionary Genetics The rich fossil record of equids has made them a model for evolutionary processes1. 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)2, 3. 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 Equus4, 5. 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 population6. 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. 2013 Journal Article http://hdl.handle.net/20.500.11937/21771 http://www.nature.com/nature/journal/v499/n7456/full/nature12323.html Nature Publishing Group restricted
spellingShingle	Evolutionary Genetics Orlando, L. Ginolhac, A. Zhang, G. Froese, D. Albrechtsen, A. Stiller, M. Schubert, M. Cappellini, E. Petersen, B. Moltke, I. Johnson, P. Fumagalli, M. Vilstrup, J. Raghavan, M. Korneliussen, T. Malaspinas, A. Vogt, J. Szklarczyk, D. Kelstrup, C. Vinther, J. Dolocan, A. Stenderup, J. Velazquez, A. Cahill, J. Rasmussen, M. Wang, X. Min, J. Zazula, G. Seguin-Orlando, A. Mortensen, C. Magnussen, K. Thompson, J. Weinstock, J. Gregersen, K. Roed, K. Eisenmann, V. Rubin, C. Miller, D. Antczak, D. Bertelsen, M. Brunak, S. Al-Rasheid, K. Ryder, O. Andersson, L. Mundy, J. Krogh, A. Gilbert, Thomas Kjær, K. Sicheritz-Ponten, T. Jensen, L. Olsen, J. Hofreiter, M. Nielsen, R. Shapiro, B. Wang, Jun Willerslev, E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
title	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_short	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
topic	Evolutionary Genetics
url	http://www.nature.com/nature/journal/v499/n7456/full/nature12323.html http://hdl.handle.net/20.500.11937/21771

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

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