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

Authors Antoine Fages, Kristian Hanghøj, Naveed Khan, Alan K. Outram, Pablo Librado, Ludovic Orlando

In Brief

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.


  • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago
  • Iberian and Siberian horses contributed limited ancestry to modern domesticates
  • Modern breeding practices were accompanied by a significant drop in genetic diversity

Fages et al., 2019, Cell 177, 1–17 May 30, 2019 ª 2019 The Author(s). Published by Elsevier Inc.



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 (R1-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.

Part 4 of 4

Rejecting Iberian Contribution to Modern Domesticates

The genome sequences of four 4,800- to 3,900-year-old IBE specimens characterized here allowed us to clarify ongoing debates about the possible contribution of Iberia to horse domestication (Benecke, 2006; Uerpmann, 1990; Warmuth et al., 2011). Calculating the so-called fG ratio (Martin et al., 2015) provided a minimal boundary for the IBE contribution to DOM2 members (Cahill et al., 2013) (Figure 7A). The maximum of such estimate was found in the Hungarian Dunaujvaros_ Duk2_4077 specimen (11.7%–12.2%), consistent with its TreeMix clustering with IBE when allowing for one migration edge (Figure S7B). This specimen was previously suggested to share ancestry with a yet-unidentified population (Gaunitz et al., 2018). Calculation of f4-statistics indicates that this population is not related to E. lenensis but to IBE (Figure 7B; STAR Methods). Therefore, IBE or horses closely related to IBE, contributed ancestry to animals found at an Early Bronze Age trade center in Hungary from the late 3rd mill. BCE. This could indicate that there was long-distance exchange of horses during the Bell Beaker phenomenon (Olalde et al., 2018). The fG minimal boundary for the IBE contribution into an Iron Age Spanish horse (ElsVilars_UE4618_2672) was still important (9.6%–10.1%), suggesting that an IBE genetic influence persisted in Iberia until at least the 7th century BCE in a domestic context. However, fG estimates were more limited for almost all ancient and modern horses investigated (median = 4.9%–5.4%; Figure 7A). Analytical predictions and population modeling with momi2 further confirmed that IBE contributed only minimal ancestry (1.4%– 3.8%) to modern DOM2 horses and well prior to their domestication (34–44 kya).

Figure 7
Figure 7. Influence of Native Iberian Horses within DOM2 Domesticates (A) Estimates of native IBE ancestry in DOM2 horses, based on the fraction of polymorphisms shared between IBE and DOM2 horses relative to Botai and Borly4 horses, and the level of polymorphisms shared between two IBE horses relative to Botai and Borly4 horses. The ratio of these values approximates a minimal boundary for the fraction of genomic ancestry present in DOM2 genomes pertaining to IBE or a closely related lineage. Consistent estimates are retrieved when replacing Botai with Borly4 horses, an 5,000 years-old group directly descending from Botai. (B) Admixture tests. The f4-statistics in the form of (outgroup, [IBE,(DOM2,Botai-Borly4)]) and (outgroup,[E. lensensis,(DOM2,Botai-Borly4)]) are provided. Negative values indicate excess of shared derived polymorphisms between IBE (or E. lenensis) and DOM2. More negative values indicate a more likely contribution of IBE (than E. lenensis) into DOM2. Testing all DOM2 individual genomes provided negative values, except two samples (Saadjave_Saa1_1117 and Friesian_0296A_0), which are not represented and for which other unidentified ancestry components could be present.


Recent advances in ancient DNA research have opened access to the complete genome sequence of past individuals. These have so far mostly improved our understanding of the evolutionary history of our own lineage, based on hundreds of individual whole genomes and genome-scale data from thousands of individuals (Marciniak and Perry, 2017). Our study represents the first effort to apply the available technology at similar scales to a non-human organism. With 129 ancient genomes and genome-scale data from 149 additional ancient animals, our dataset unveils the past complexity of horse evolution, including the recent impact of humans by means of diversity management, selection and hybridization.

We genetically identified two mules within the La Te` ne Iron Age site of Saint-Just (France). Mules represented invaluable animals to past societies, being more sure-footed, more resistant to diseases, and harder working than horses. They are, however, difficult to identify morphologically from fragmentary material.

Our work gives definitive proof that mules have been bred since at least 2,200 years ago, despite considerable cost implications of producing sterile stock (Laurence, 1999). We found that Y chromosome diversity in horses declined steadily within the last 2,000 years, with male reproductive success becoming skewed following the (Gallo-) Roman period. This indicates that breeders increasingly chose specific stallions for breeding from the Middle Ages onward, consistent with the dominance of an 700 to 1,000-year-old Arabian haplogroup in most modern studs (Felkel et al., 2018; Wallner et al., 2017).

Together with the increasing affinity to Sassanid Persian horses detected in the genomes of European and Asian horses after the C7th–C9th, this suggests that the Byzantine-Sassanid wars and the early Islamic conquests significantly impacted breeding and exchange. The legacy of these historical events has persisted until now as the majority of the modern breeds investigated here clustered within a phylogenetic group related to Sassanid Persian horses. During the same time period, the horse phenotype was also significantly reshaped, especially for locomotion, speed capacity, and morpho-anatomy. Whether this partly or fully reflects the direct influence of Arabian lines requires further tests.

Most strikingly, we found that while past horse breeders maintained diverse genetic resources for millennia after they first domesticated the horse, this diversity dropped by 16% within the last 200 years. This illustrates the massive impact of modern breeding and demonstrates that the history of domestic animals cannot be fully understood without harnessing ancient DNA data. Importantly, recent breeding strategies have also limited the efficacy of negative selection and led to the accumulation of deleterious variants within the genome of horses. This illustrates the genomic cost of modern breeding. Future work should focus on testing how much recent progress in veterinary medicine and the improving animal welfare have contributed to limit the fitness impact of deleterious variants.

In addition to the two extant lineages of horses, we report two other lineages at the far eastern and western range of Eurasia, in Iberia (IBE) and Siberia (E. lenensis). Their genomes suggest the presence of other yet unidentified ghost populations. The IBE and E. lenensis lineages are now extinct but lived at the time horses were first domesticated. None of them, however, contributed significant ancestry to modern domesticates. Interestingly, Upper Paleolithic cave paintings in Europe have often been proposed to depict Przewalski’s horses due to striking morphological resemblance (Leroi-Gourhan, 1958). Our sample set included one horse from the Goyet cave, Belgium dated to 35,870 years ago. Although characterized at limited coverage (0.49-fold), D-statistics revealed closer genetic affinity to IBE and DOM2 than to the ancestors of Przewalski’s horses (15.5 < Z scores < 2.4). European cave painting is, therefore, unlikely to depict Przewalski’s horses. It may instead represent the ancestors of the Tarpan, assuming that this taxonomically contentious lineage neither represents domestic horses turned feral nor domestic-wild hybrids but truly wild horses that went extinct in the late C19th (Groves, 1994).

Iberia was suggested as a possible domestication center for horses on the basis of both archaeological arguments (Benecke, 2006) and geographic patterns of genetic variation in modern breeds (Uerpmann, 1990; Warmuth et al., 2011). Previous ancient DNA data were limited to short mtDNA sequences of pre-Bronze Age to medieval specimens (Lira et al., 2010), and remained indecisive regarding the contribution of Iberia to horse domestication. Our work shows that IBE horses have not genetically contributed to the vast majority of DOM2 domesticates investigated here, ancient or modern alike, excepting one horse in Bronze Age Hungary, possibly following the Bell-Beaker phenomenon, and an additional one in Iron Age Iberia. Population modeling also confirmed limited contribution within modern domesticates, largely pre-dating domestication. Therefore, IBE cannot represent a main domestication source. Given that other candidates in the Eneolithic Botai culture from Central Asia do not represent DOM2 ancestors (Gaunitz et al., 2018), the origins of the modern domestic horse remain open.

Future work must focus on mapping genomic affinities in the 3rd and 4th mill. BCE, especially at other candidate regions for early domestication in the Pontic-Caspian (Anthony, 2007) and Anatolia (Arbuckle, 2012; Benecke, 2006). Finer mapping of the Persian-related influence at around the time of the Islamic conquest and the diversity hotspots in place prior to modern stud breeding will also improve our understanding of the source(s) and dynamics underlying the makeup of modern diversity.


Detailed methods are provided in the online version of this paper and include the following:

    • Belgium (Goyet A1)
    • China
    • Croatia (Bapska, Nustar, Otok)
    • Estonia (Otepa¨ a¨ hill-fort, Ridala, Saadja¨ rve)
    • France (Beauvais: Maladrerie Saint-Lazare and rue de L’Isle-Adam, Boinville-en-Woe¨ vre, Boves ‘‘Chemin de Glisy,’’ Capesterre, Chartres ‘‘Boulevard de la Courtille,’’ Evreux ‘‘Clos-au-Duc 3 rue de la Libe´ ration – 2007,’’ Longueil-Annel, Maˆ con ‘‘Rue Rambuteau,’’ Metz ‘‘Place de la Re´ publique,’’ Saint-Claude, Saint- Laurent Blangy ‘‘Actiparc 2002,’’ Vermand 2005 and Saint-Just-en-Chausse´ e)
    • Georgia (Dariali)
    • Germany (private collections, Schloßvippach)
    • Iceland (Berufjo¨ rður and Granastaðir)
    • Iran (Belgheis, Kulian Cave, Sagzabad, Shahr-i-Qumis, Tepe Hasanlu, Tepe Mehr Ali)
    • Kazakhstan (Belkaragay, Halvai)
    • Kyrgyzstan (Boz-Adyr)
    • Lithuania (Marvel _e cemetery)
    • Moldova (Miciurin)
    • Mongolia (Gol Mod II, Khatuu 2, Olon-Kurin-Gol (Olon Guuriin Gol), Uushgiin Uvur, Talvan Tolgoi, Khotont)
    • Poland (Bruszcewo)
    • Portugal (Santare´ m)
    • Russia (Altata, Arzhan II, Balagansk, Bateni – Karasuk, Derkul, Kokorevo, Krasnaya Gorka, Lebyanzhinka IV, Merzly Yar, Oktyabrsky, Potapovka I, Sayangorsk, Sintashta)
    • Slovakia (Sebastovce)
    • Spain (Camino de las Yeseras, Cantorella, Capote, El Acequio´ n, Els Vilars)
    • Sweden (Uppsala)
    • Switzerland (Augusta Raurica, Stein am Charregass, Solothurn Vigier)
    • Turkey (Yenikapi)
    • United Kingdom (Brough of Deerness, Quoygrew, Whitehall Roman Villa and Witter Place)
    • Uzbekistan (Yerqorqan/Erkurgan)
    • Museum
    • Comparative dataset
    • DNA extraction and genome sequencing
    • Radiocarbon dating
    • Read alignment, rescaling and trimming
    • Uniparental markers
    • Autosomal and sex chromosomes
    • Selection targets
    • TreeMix population tree
    • Struct-f4
    • Modeling IBE contribution to DOM2
    • Species and sex identification



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