Yamna the likely source of modern horse domesticates; the closest lineage, from East Bell Beakers

Open access Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series, by Fages et al. Cell (2019).

Interesting excerpts (emphasis mine):

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,

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Mitogenomes suggest rapid expansion of domesticated horse before 3500 BC

Open access Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives, by Yoon et al. PLOS One (2018).

Abstract (emphasis mine)

The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed

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Origin of horse domestication likely on the North Caspian steppes

Open access Late Quaternary horses in Eurasia in the face of climate and vegetation change, by Leonardi et al. Science Advances (2008) 4(7):eaar5589.

Interesting excerpts (emphasis mine):

Here, we compiled an extensive continental-scale database, consisting of 3070 radiocarbon dates associated to horse paleontological and archeological finds across the whole of Eurasia, that has been analyzed in association with coarse-scale paleoclimatic reconstructions. We further collected the number of identified specimens (NISP) frequency data for horses versus other ungulates in 1120 archeological layers in Europe (…) This ma.ssive amount of data allowed us to track,with unprecedented details, how the geographic

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Decline of genetic diversity in ancient domestic stallions in Europe

Open access research article Decline of genetic diversity in ancient domestic stallions in Europe, by Wutke et al., Science (2018), 4(4):eaap9691.

Abstract (emphasis mine):

Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and

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Ancient DNA upends the horse family tree

New paper, behind paywall, Ancient genomes revisit the ancestry of domestic and Przewalski’s horses, by Gaunitz et al., Science (2018)

Abstract:

The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5,500 ya, but the exact nature of early horse domestication remains controversial. We generated 42 ancient horse genomes, including 20 from Botai. Compared to 46 published ancient and modern horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4,000 ya to present only

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