Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Antoine Fages; Kristian Hanghøj; Naveed Khan; Charleen Gaunitz; Andaine Seguin-Orlando; Michela Leonardi; Christian McCrory Constantz; Cristina Gamba; Khaled A.S. Al-Rasheid; Silvia Albizuri; Ahmed H. Alfarhan; Morten Allentoft; Saleh Alquraishi; David Anthony; Nurbol Baimukhanov; James H. Barrett; Jamsranjav Bayarsaikhan; Norbert Benecke; Eloísa Bernáldez-Sánchez; Luis Berrocal-Rangel; Fereidoun Biglari; Sanne Boessenkool; Bazartseren Boldgiv; Gottfried Brem; Dorcas Brown; Joachim Burger; Eric Crubézy; Linas Daugnora; Hossein Davoudi; Peter de Barros Damgaard; María de los Ángeles de Chorro y de Villa-Ceballos; Sabine Deschler-Erb; Cleia Detry; Nadine Dill; Maria do Mar Oom; Anna Dohr; Sturla Ellingvåg; Diimaajav Erdenebaatar; Homa Fathi; Sabine Felkel; Carlos Fernández-Rodríguez; Esteban García-Viñas; Mietje Germonpré; José D. Granado; Jón H. Hallsson; Helmut Hemmer; Michael Hofreiter; Aleksei Kasparov; Mutalib Khasanov; Roya Khazaeli; Pavel Kosintsev; Kristian Kristiansen; Tabaldiev Kubatbek; Lukas Kuderna; Pavel Kuznetsov; Haeedeh Laleh; Jennifer A. Leonard; Johanna Lhuillier; Corina Liesau von Lettow-Vorbeck; Andrey Logvin; Lembi Lõugas; Arne Ludwig; Cristina Luis; Ana Margarida Arruda; Tomas Marques-Bonet; Raquel Matoso Silva; Victor Merz; Enkhbayar Mijiddorj; Bryan K. Miller; Oleg Monchalov; Fatemeh A. Mohaseb; Arturo Morales; Ariadna Nieto-Espinet; Heidi Nistelberger; Vedat Onar; Albína H. Pálsdóttir; Vladimir Pitulko; Konstantin Pitskhelauri; Mélanie Pruvost; Petra Rajic Sikanjic; Anita Rapan Papeša; Natalia Roslyakova; Alireza Sardari; Eberhard Sauer; Renate Schafberg; Amelie Scheu; Jörg Schibler; Angela Schlumbaum; Nathalie Serrand; Aitor Serres-Armero; Beth Shapiro; Shiva Sheikhi Seno; Irina Shevnina; Sonia Shidrang; John Southon; Bastiaan Star; Naomi Sykes; Kamal Taheri; William Taylor; Wolf Rüdiger Teegen; Tajana Trbojević Vukičević; Simon Trixl; Dashzeveg Tumen; Sainbileg Undrakhbold; Emma Usmanova; Ali Vahdati; Silvia Valenzuela-Lamas; Catarina Viegas; Barbara Wallner; Jaco Weinstock; Victor Zaibert; Benoit Clavel; Sébastien Lepetz; Marjan Mashkour; Agnar Helgason; Kári Stefánsson; Eric Barrey; Eske Willerslev; Alan K. Outram; Pablo Librado; Ludovic Orlando

doi:10.1016/j.cell.2019.03.049

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Antoine Fages, Kristian Hanghøj, Naveed Khan, Charleen Gaunitz, Andaine Seguin-Orlando, Michela Leonardi, Christian McCrory Constantz, Cristina Gamba, Khaled A.S. Al-Rasheid, Silvia Albizuri, Ahmed H. Alfarhan, Morten Allentoft, Saleh Alquraishi, David Anthony, Nurbol Baimukhanov, James H. Barrett, Jamsranjav Bayarsaikhan, Norbert Benecke, Eloísa Bernáldez-Sánchez, Luis Berrocal-RangelFereidoun Biglari, Sanne Boessenkool, Bazartseren Boldgiv, Gottfried Brem, Dorcas Brown, Joachim Burger, Eric Crubézy, Linas Daugnora, Hossein Davoudi, Peter de Barros Damgaard, María de los Ángeles de Chorro y de Villa-Ceballos, Sabine Deschler-Erb, Cleia Detry, Nadine Dill, Maria do Mar Oom, Anna Dohr, Sturla Ellingvåg, Diimaajav Erdenebaatar, Homa Fathi, Sabine Felkel, Carlos Fernández-Rodríguez, Esteban García-Viñas, Mietje Germonpré, José D. Granado, Jón H. Hallsson, Helmut Hemmer, Michael Hofreiter, Aleksei Kasparov, Mutalib Khasanov, Roya Khazaeli, Pavel Kosintsev, Kristian Kristiansen, Tabaldiev Kubatbek, Lukas Kuderna, Pavel Kuznetsov, Haeedeh Laleh, Jennifer A. Leonard, Johanna Lhuillier, Corina Liesau von Lettow-Vorbeck, Andrey Logvin, Lembi Lõugas, Arne Ludwig, Cristina Luis, Ana Margarida Arruda, Tomas Marques-Bonet, Raquel Matoso Silva, Victor Merz, Enkhbayar Mijiddorj, Bryan K. Miller, Oleg Monchalov, Fatemeh A. Mohaseb, Arturo Morales, Ariadna Nieto-Espinet, Heidi Nistelberger, Vedat Onar, Albína H. Pálsdóttir, Vladimir Pitulko, Konstantin Pitskhelauri, Mélanie Pruvost, Petra Rajic Sikanjic, Anita Rapan Papeša, Natalia Roslyakova, Alireza Sardari, Eberhard Sauer, Renate Schafberg, Amelie Scheu, Jörg Schibler, Angela Schlumbaum, Nathalie Serrand, Aitor Serres-Armero, Beth Shapiro, Shiva Sheikhi Seno, Irina Shevnina, Sonia Shidrang, John Southon, Bastiaan Star, Naomi Sykes, Kamal Taheri, William Taylor, Wolf Rüdiger Teegen, Tajana Trbojević Vukičević, Simon Trixl, Dashzeveg Tumen, Sainbileg Undrakhbold, Emma Usmanova, Ali Vahdati, Silvia Valenzuela-Lamas, Catarina Viegas, Barbara Wallner, Jaco Weinstock, Victor Zaibert, Benoit Clavel, Sébastien Lepetz, Marjan Mashkour, Agnar Helgason, Kári Stefánsson, Eric Barrey, Eske Willerslev, Alan K. Outram, Pablo Librado, Ludovic Orlando^*

^*Corresponding author for this work

65 Citations (Scopus)

Abstract

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management. Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.

Original language	English
Journal	Cell
Volume	177
Issue number	6
Pages (from-to)	1419-1435.e31
ISSN	0092-8674
DOIs	https://doi.org/10.1016/j.cell.2019.03.049
Publication status	Published - 30 May 2019

Keywords

ancient DNA
animal breeding
diversity
domestication
equestrian civilizations
extinct lineages
horses
management
mules
selection

Access to Document

10.1016/j.cell.2019.03.049

Cite this

Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin-Orlando, A., Leonardi, M., McCrory Constantz, C., Gamba, C., Al-Rasheid, K. A. S., Albizuri, S., Alfarhan, A. H., Allentoft, M., Alquraishi, S., Anthony, D., Baimukhanov, N., Barrett, J. H., Bayarsaikhan, J., Benecke, N., Bernáldez-Sánchez, E., ... Orlando, L. (2019). Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell, 177(6), 1419-1435.e31. https://doi.org/10.1016/j.cell.2019.03.049

Fages, A, Hanghøj, K, Khan, N, Gaunitz, C, Seguin-Orlando, A, Leonardi, M, McCrory Constantz, C, Gamba, C, Al-Rasheid, KAS, Albizuri, S, Alfarhan, AH, Allentoft, M, Alquraishi, S, Anthony, D, Baimukhanov, N, Barrett, JH, Bayarsaikhan, J, Benecke, N, Bernáldez-Sánchez, E, Berrocal-Rangel, L, Biglari, F, Boessenkool, S, Boldgiv, B, Brem, G, Brown, D, Burger, J, Crubézy, E, Daugnora, L, Davoudi, H, de Barros Damgaard, P, de los Ángeles de Chorro y de Villa-Ceballos, M, Deschler-Erb, S, Detry, C, Dill, N, do Mar Oom, M, Dohr, A, Ellingvåg, S, Erdenebaatar, D, Fathi, H, Felkel, S, Fernández-Rodríguez, C, García-Viñas, E, Germonpré, M, Granado, JD, Hallsson, JH, Hemmer, H, Hofreiter, M, Kasparov, A, Khasanov, M, Khazaeli, R, Kosintsev, P, Kristiansen, K, Kubatbek, T, Kuderna, L, Kuznetsov, P, Laleh, H, Leonard, JA, Lhuillier, J, Liesau von Lettow-Vorbeck, C, Logvin, A, Lõugas, L, Ludwig, A, Luis, C, Arruda, AM, Marques-Bonet, T, Matoso Silva, R, Merz, V, Mijiddorj, E, Miller, BK, Monchalov, O, Mohaseb, FA, Morales, A, Nieto-Espinet, A, Nistelberger, H, Onar, V, Pálsdóttir, AH, Pitulko, V, Pitskhelauri, K, Pruvost, M, Rajic Sikanjic, P, Rapan Papeša, A, Roslyakova, N, Sardari, A, Sauer, E, Schafberg, R, Scheu, A, Schibler, J, Schlumbaum, A, Serrand, N, Serres-Armero, A, Shapiro, B, Sheikhi Seno, S, Shevnina, I, Shidrang, S, Southon, J, Star, B, Sykes, N, Taheri, K, Taylor, W, Teegen, WR, Trbojević Vukičević, T, Trixl, S, Tumen, D, Undrakhbold, S, Usmanova, E, Vahdati, A, Valenzuela-Lamas, S, Viegas, C, Wallner, B, Weinstock, J, Zaibert, V, Clavel, B, Lepetz, S, Mashkour, M, Helgason, A, Stefánsson, K, Barrey, E, Willerslev, E, Outram, AK, Librado, P & Orlando, L 2019, 'Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series', Cell, vol. 177, no. 6, pp. 1419-1435.e31. https://doi.org/10.1016/j.cell.2019.03.049

@article{f0f663c84f9d45c3a7b0e5db66dc6241,

title = "Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series",

abstract = "Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management. Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.",

keywords = "ancient DNA, animal breeding, diversity, domestication, equestrian civilizations, extinct lineages, horses, management, mules, selection",

author = "Antoine Fages and Kristian Hangh{\o}j and Naveed Khan and Charleen Gaunitz and Andaine Seguin-Orlando and Michela Leonardi and {McCrory Constantz}, Christian and Cristina Gamba and Al-Rasheid, {Khaled A.S.} and Silvia Albizuri and Alfarhan, {Ahmed H.} and Morten Allentoft and Saleh Alquraishi and David Anthony and Nurbol Baimukhanov and Barrett, {James H.} and Jamsranjav Bayarsaikhan and Norbert Benecke and Elo{\'i}sa Bern{\'a}ldez-S{\'a}nchez and Luis Berrocal-Rangel and Fereidoun Biglari and Sanne Boessenkool and Bazartseren Boldgiv and Gottfried Brem and Dorcas Brown and Joachim Burger and Eric Crub{\'e}zy and Linas Daugnora and Hossein Davoudi and {de Barros Damgaard}, Peter and {de los {\'A}ngeles de Chorro y de Villa-Ceballos}, Mar{\'i}a and Sabine Deschler-Erb and Cleia Detry and Nadine Dill and {do Mar Oom}, Maria and Anna Dohr and Sturla Ellingv{\aa}g and Diimaajav Erdenebaatar and Homa Fathi and Sabine Felkel and Carlos Fern{\'a}ndez-Rodr{\'i}guez and Esteban Garc{\'i}a-Vi{\~n}as and Mietje Germonpr{\'e} and Granado, {Jos{\'e} D.} and Hallsson, {J{\'o}n H.} and Helmut Hemmer and Michael Hofreiter and Aleksei Kasparov and Mutalib Khasanov and Roya Khazaeli and Pavel Kosintsev and Kristian Kristiansen and Tabaldiev Kubatbek and Lukas Kuderna and Pavel Kuznetsov and Haeedeh Laleh and Leonard, {Jennifer A.} and Johanna Lhuillier and {Liesau von Lettow-Vorbeck}, Corina and Andrey Logvin and Lembi L{\~o}ugas and Arne Ludwig and Cristina Luis and Arruda, {Ana Margarida} and Tomas Marques-Bonet and {Matoso Silva}, Raquel and Victor Merz and Enkhbayar Mijiddorj and Miller, {Bryan K.} and Oleg Monchalov and Mohaseb, {Fatemeh A.} and Arturo Morales and Ariadna Nieto-Espinet and Heidi Nistelberger and Vedat Onar and P{\'a}lsd{\'o}ttir, {Alb{\'i}na H.} and Vladimir Pitulko and Konstantin Pitskhelauri and M{\'e}lanie Pruvost and {Rajic Sikanjic}, Petra and {Rapan Pape{\v s}a}, Anita and Natalia Roslyakova and Alireza Sardari and Eberhard Sauer and Renate Schafberg and Amelie Scheu and J{\"o}rg Schibler and Angela Schlumbaum and Nathalie Serrand and Aitor Serres-Armero and Beth Shapiro and {Sheikhi Seno}, Shiva and Irina Shevnina and Sonia Shidrang and John Southon and Bastiaan Star and Naomi Sykes and Kamal Taheri and William Taylor and Teegen, {Wolf R{\"u}diger} and {Trbojevi{\'c} Vuki{\v c}evi{\'c}}, Tajana and Simon Trixl and Dashzeveg Tumen and Sainbileg Undrakhbold and Emma Usmanova and Ali Vahdati and Silvia Valenzuela-Lamas and Catarina Viegas and Barbara Wallner and Jaco Weinstock and Victor Zaibert and Benoit Clavel and S{\'e}bastien Lepetz and Marjan Mashkour and Agnar Helgason and K{\'a}ri Stef{\'a}nsson and Eric Barrey and Eske Willerslev and Outram, {Alan K.} and Pablo Librado and Ludovic Orlando",

year = "2019",

month = may,

day = "30",

doi = "10.1016/j.cell.2019.03.049",

language = "English",

volume = "177",

pages = "1419--1435.e31",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "6",

}

TY - JOUR

T1 - Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

AU - Fages, Antoine

AU - Hanghøj, Kristian

AU - Khan, Naveed

AU - Gaunitz, Charleen

AU - Seguin-Orlando, Andaine

AU - Leonardi, Michela

AU - McCrory Constantz, Christian

AU - Gamba, Cristina

AU - Al-Rasheid, Khaled A.S.

AU - Albizuri, Silvia

AU - Alfarhan, Ahmed H.

AU - Allentoft, Morten

AU - Alquraishi, Saleh

AU - Anthony, David

AU - Baimukhanov, Nurbol

AU - Barrett, James H.

AU - Bayarsaikhan, Jamsranjav

AU - Benecke, Norbert

AU - Bernáldez-Sánchez, Eloísa

AU - Berrocal-Rangel, Luis

AU - Biglari, Fereidoun

AU - Boessenkool, Sanne

AU - Boldgiv, Bazartseren

AU - Brem, Gottfried

AU - Brown, Dorcas

AU - Burger, Joachim

AU - Crubézy, Eric

AU - Daugnora, Linas

AU - Davoudi, Hossein

AU - de Barros Damgaard, Peter

AU - de los Ángeles de Chorro y de Villa-Ceballos, María

AU - Deschler-Erb, Sabine

AU - Detry, Cleia

AU - Dill, Nadine

AU - do Mar Oom, Maria

AU - Dohr, Anna

AU - Ellingvåg, Sturla

AU - Erdenebaatar, Diimaajav

AU - Fathi, Homa

AU - Felkel, Sabine

AU - Fernández-Rodríguez, Carlos

AU - García-Viñas, Esteban

AU - Germonpré, Mietje

AU - Granado, José D.

AU - Hallsson, Jón H.

AU - Hemmer, Helmut

AU - Hofreiter, Michael

AU - Kasparov, Aleksei

AU - Khasanov, Mutalib

AU - Khazaeli, Roya

AU - Kosintsev, Pavel

AU - Kristiansen, Kristian

AU - Kubatbek, Tabaldiev

AU - Kuderna, Lukas

AU - Kuznetsov, Pavel

AU - Laleh, Haeedeh

AU - Leonard, Jennifer A.

AU - Lhuillier, Johanna

AU - Liesau von Lettow-Vorbeck, Corina

AU - Logvin, Andrey

AU - Lõugas, Lembi

AU - Ludwig, Arne

AU - Luis, Cristina

AU - Arruda, Ana Margarida

AU - Marques-Bonet, Tomas

AU - Matoso Silva, Raquel

AU - Merz, Victor

AU - Mijiddorj, Enkhbayar

AU - Miller, Bryan K.

AU - Monchalov, Oleg

AU - Mohaseb, Fatemeh A.

AU - Morales, Arturo

AU - Nieto-Espinet, Ariadna

AU - Nistelberger, Heidi

AU - Onar, Vedat

AU - Pálsdóttir, Albína H.

AU - Pitulko, Vladimir

AU - Pitskhelauri, Konstantin

AU - Pruvost, Mélanie

AU - Rajic Sikanjic, Petra

AU - Rapan Papeša, Anita

AU - Roslyakova, Natalia

AU - Sardari, Alireza

AU - Sauer, Eberhard

AU - Schafberg, Renate

AU - Scheu, Amelie

AU - Schibler, Jörg

AU - Schlumbaum, Angela

AU - Serrand, Nathalie

AU - Serres-Armero, Aitor

AU - Shapiro, Beth

AU - Sheikhi Seno, Shiva

AU - Shevnina, Irina

AU - Shidrang, Sonia

AU - Southon, John

AU - Star, Bastiaan

AU - Sykes, Naomi

AU - Taheri, Kamal

AU - Taylor, William

AU - Teegen, Wolf Rüdiger

AU - Trbojević Vukičević, Tajana

AU - Trixl, Simon

AU - Tumen, Dashzeveg

AU - Undrakhbold, Sainbileg

AU - Usmanova, Emma

AU - Vahdati, Ali

AU - Valenzuela-Lamas, Silvia

AU - Viegas, Catarina

AU - Wallner, Barbara

AU - Weinstock, Jaco

AU - Zaibert, Victor

AU - Clavel, Benoit

AU - Lepetz, Sébastien

AU - Mashkour, Marjan

AU - Helgason, Agnar

AU - Stefánsson, Kári

AU - Barrey, Eric

AU - Willerslev, Eske

AU - Outram, Alan K.

AU - Librado, Pablo

AU - Orlando, Ludovic

PY - 2019/5/30

Y1 - 2019/5/30

N2 - Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management. Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.

AB - Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management. Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.

KW - ancient DNA

KW - animal breeding

KW - diversity

KW - domestication

KW - equestrian civilizations

KW - extinct lineages

KW - horses

KW - management

KW - mules

KW - selection

UR - http://www.scopus.com/inward/record.url?scp=85065780395&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2019.03.049

DO - 10.1016/j.cell.2019.03.049

M3 - Journal article

C2 - 31056281

AN - SCOPUS:85065780395

SN - 0092-8674

VL - 177

SP - 1419-1435.e31

JO - Cell

JF - Cell

IS - 6

ER -

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this