Summary 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.

The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, 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 ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.

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Based on geological and archaeological proxies from NW Russia and NE Estonia and on GIS-based modelling, shore displacement during the Stone Age in the Narva-Luga Klint Bay area in the eastern Gulf of Finland was reconstructed. The reconstructed shore displacement curve displays three regressive phases in the Baltic Sea history, interrupted by the rapid Ancylus Lake and Litorina Sea transgressions c. 10.9-10.2 cal. ka BP and c. 8.5-7.3 cal. ka BP, respectively. During the Ancylus transgression the lake level rose 9 m at an average rate of about 13 mm per year, while during the Litorina transgression the sea level rose 8 m at an average rate of about 7 mm per year. The results show that the highest shoreline of Ancylus Lake at an altitude of 8-17 m a.s.l. was formed c. 10.2 cal. ka BP and that of the Litorina Sea at an altitude of 6-14 m a.s.l., c. 7.3 cal. ka BP. The oldest traces of human activity dated to 8.5-7.9 cal. ka BP are associated with the palaeo-Narva River in the period of low water level in the Baltic basin at the beginning of the Litorina Sea transgression. The coastal settlement associated with the Litorina Sea lagoon, presently represented by 33 Stone Age sites, developed in the area c. 7.1 cal. ka BP and existed there for more than 2000 years. Transformation from the coastal settlement back to the river settlement indicates a change from a fishing-and-hunting economy to farming and animal husbandry c. 4.4 cal. ka BP, coinciding with the time of the overgrowing of the lagoon in the Narva-Luga Klint Bay area.