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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.


Horses provided humans with the first opportunity to spread genes, diseases, and culture well above their own speed (Allentoft et al., 2015; Haak et al., 2015; Rasmussen et al., 2014). Horses remained paramount to transportation even after the advent of steam locomotion and until the widespread use of motor vehicles (Kelekna, 2009). Horses also revolutionized warfare, pulling chariots at full speed in the Bronze Age, providing the foundation for mounted battle in the early Iron Age, and facilitating the spread of cavalry during Antiquity (Drews, 2004). Today, horses remain essential to the economy of developing countries and to the leisure and racing industries of developed countries (Faostat, 2009). The earliest archaeological evidence of horse milking, harnessing, and corralling is found in the 5,500-year-old Botai culture of Central Asian steppes (Gaunitz et al., 2018; Outram et al., 2009; see Kosintsev and Kuznetsov, 2013 for discussion). Botai-like horses are, however, not the direct ancestors of modern domesticates but of Przewalski’s horses (Gaunitz et al., 2018). The genetic origin of modern domesticates thus remains contentious, with suggested candidates in the Pontic-Caspian steppes (Anthony, 2007), Anatolia (Arbuckle, 2012; Benecke, 2006), and Iberia (Uerpmann, 1990; Warmuth et al., 2011). Irrespective of the origins of domestication, the horse genome is known to have been reshaped significantly within the last 2,300 years (Librado et al., 2017; Wallner et al., 2017; Wutke et al., 2018). However, when and in which context(s) such changes occurred remains largely unknown.


Genome Dataset

To clarify the origins of domestic horses and reveal their subsequent transformation by past equestrian civilizations, we generated DNA data from 278 equine subfossils with ages mostly spanning the last six millennia (n = 265, 95%) (Figures 1A and 1B; Table S1; STAR Methods). Endogenous DNA content was compatible with economical sequencing of 87 new horse genomes to an average depth-of-coverage of 1.0- to 9.3-fold (median = 3.3-fold; Table S2). This more than doubles the number of ancient horse genomes hitherto characterized. With a total of 129 ancient genomes, 30 modern genomes, and new genomescale data from 132 ancient individuals (0.01- to 0.9-fold, median = 0.08-fold), our dataset represents the largest genomescale time series published for a non-human organism (Tables S2, S3, and S4; STAR Methods).

Most specimens were genetically confirmed as horses (175 males, 70 females; Table S1; STAR Methods). Six belonged to other equine species, including three hemiones from Chalcolithic, Bronze, and Iron Age sites of Iran and three Roman and Byzantine donkeys (Figure 1A). A total of 27 specimens were genetically assigned to mules (the offspring of a donkey jack and a horse mare), which are difficult to identify in fragmentary fossil records using morphology alone (Schubert et al., 2017). The oldest mules identified are from the La Te` ne Iron Age site of Saint-Just (France), but they were also found in Roman and medieval Europe as well as Byzantine Turkey.

Figure 1. Equine Archaeological Remains (A) Location of archaeological sites. Pie charts are proportional to the total number of specimens providing DNA data compatible with the determination of sex, species and hybrid status. The names and temporal ranges (years ago) of the sites where hybrids and non-caballine species could be genetically identified are indicated. (B) Temporal distribution of ancient specimens. Eight individuals showing uncertain age determination are not included. See also Tables S1, S2, S3, and S4.
Figure 1. Equine Archaeological Remains (A) Location of archaeological sites. Pie charts are proportional to the total number of specimens providing DNA data compatible with the determination of sex, species and hybrid status. The names and temporal ranges (years ago) of the sites where hybrids and non-caballine species could be genetically identified are indicated. (B) Temporal distribution of ancient specimens. Eight individuals showing uncertain age determination are not included. See also Tables S1, S2, S3, and S4.

Changes in Horse Management through Time and Their Impact on Diversity

Previous work comparing the sequence variation present in modern horse genomes and the genomes of 11 ancient horses belonging to the Scythian Pazyryk culture suggested important changes in the management of available genetic resources within the last 2,300 years (Librado et al., 2017). Our thorough temporal genome sampling allowed us to delineate more precisely when these changes happened. We ensured accurate diversity estimates in ancient horses by only considering genomes sequenced at minimum 1-fold depth-of-coverage and implementing the three following approaches. First, enzymatic treatment against the most prevalent post-mortem DNA damage helped avoid inflating past diversity estimates (STAR Methods). Second, only sites least affected by damage, such as non- CpG dinucleotides and transversion sites, were considered. Third, we checked that diversity measurements were robust both to residual error rates and sequencing depth (Figure S1; STAR Methods).

All modern breeds investigated here showed an 16.4% median drop in individual heterozygosity levels relative to horses that lived prior to 200 years ago (Wilcoxon test, p value = 2.0 3 1013) (Figures 2C and S2; STAR Methods). This contrasts with steady heterozygosity levels during the previous four millennia, reflecting that earlier equestrian civilizations managed and maintained higher levels of genetic diversity. A similar trend was found in autosomal p diversity, which severely declined during the most recent time interval with sufficient data to enable calculations (i.e., the last 400 years). Autosomal p profiles also supported a demographic expansion from La Te` ne to Roman Europe, possibly pertaining to the growing demand for horses during Roman times (Figure 2A; STAR Methods). The recent decays of autosomal p diversity and heterozygosity suggest a severe reduction in horse breeding stock within the last few centuries, parallel to the significant changes in agricultural practices underpinning modern studs. This reduction in effective size is expected to have increased mutational loads genome-wide by reducing the efficacy of purifying selection (Cruz et al., 2008; Schubert et al., 2014a). To test this, we calculated conservative estimates for the mutational loads at homozygous sites within protein-coding genes and accounting for possible inbreeding differences (Librado et al., 2017) (calculations at heterozygous sites were proven impracticable, in agreement with Pedersen et al. [2017]) (Figures S3A and S3B). As expected, mutational load estimates correlated with reduced selection, as measured from differential diversity patterns at non-synonymous and synonymous sites, and from sites classified as deleterious and non-deleterious on the basis of their evolutionary conservation across multiple vertebrate species (STAR Methods). We found mutational loads increasing during the last 200 years, parallel to changes in breed reproductive management (4.6% median load increment; Wilcoxon test, p value = 8.3 3 10 12) (Figure 2D). Our data therefore support the contention that reproductive strategies implemented in the last few centuries reduced the chance to eliminate deleterious variants from domestic horse stock.

Figure 2
Figure 2. Genetic Diversity Patterns (A) Nucleotide diversity (p) estimates and Y-to-autosomal p ratio per equestrian culture. The dashed red line indicates Y-to-autosomal p ratios of 0.25, corresponding to the expected ratio under even male reproductive success. (B) Autosomal and Y chromosome p estimates through time. See also Figure S2E for more details. (C) Individual error-corrected heterozygosity estimates. Only transversions were considered to minimize the impact of post-mortem DNA damage. See also Figures S1 and S2. (D) Conservative individual mutational loads from homozygous sites. Violin plots contrast the heterozygosity levels and genetic loads present in ancient (pink) and modern (blue) genomes belonging to the DOM2 lineage. See also Figure S3 and Table S5.

This article originally appeared on The Cell and is being published here as an abstract in 4 parts, published weekly. You can find other interesting information and articles in our section on Health & Education.

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