Dataset Information

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.

SUBMITTER: Fages A

PROVIDER: S-EPMC6547883 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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

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

Cell 20190502 6

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 ...[more]

PMID: 31056281

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Project description:BackgroundDNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets.ResultsIn this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.ConclusionsOur study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.

Dataset Information

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

Publications

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

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