Ancient genomes and Indigenous science reveal Pleistocene North American horse migration patterns

A new study combining Indigenous knowledge systems with Western genomics has uncovered how megafauna – namely ancient horses – were impacted during a period of substantial habitat change. During the late Pleistocene, the study reports, horses repeatedly migrated between North America and Eurasia, but after the Last Glacial Maximum, warming caused a land bridge to be submerged, severing this connection, and ultimately contributing to horses’ decline in North America. The findings could inform modern conservation approaches. Large animals, or megafauna, play critical roles in maintaining ecological balance. Their decline can lead to far-reaching disruptions for both natural and human communities. These risks are particularly pronounced in the rapidly warming Arctic. Indigenous scientific systems have long documented how shifts in climate reshape habitats. Complementing this, the fossil record offers a deep-time perspective on how local megafauna responded to past periods of rapid environmental change. Pleistocene-age horses in Beringia – a once-continuous landmass connecting Asia to North America – are a good model of megafauna so impacted. Still, despite dramatic environmental shifts during the Late Pleistocene, the effects on Beringian horse populations and their legacy remain poorly understood.

To trace how horses responded to environmental shifts over the past 50,000 years, Yvette Running Horse Collin and colleagues merged geochemical and genetic analyses of ancient Beringian horse fossils with Indigenous scientific protocols. Running Horse Collins et al. generated genomes from 67 ancient horse fossils found across Beringia, Siberia, and continental North America and analyzed them alongside data from all known horse lineages. They integrated their genomic data with radiocarbon dates and stable isotope measurements from fossil horse collagen. The findings reveal repeated trans-Beringian horse migrations between 50,000 and 13,000 years ago, with genetic exchanges occurring in both directions – from North America to Eurasia and vice versa. Some horse lineages in Eurasia, including fossils from northeastern Siberia and even as far west as Iberia, show traces of North American ancestry, supporting widespread dispersals. According to the authors, this complex genetic legacy mirrors the interconnectivity emphasized in Indigenous knowledge systems, which view life forms as deeply relational, not isolated. Moreover, the study also suggests that habitat changes due to warming and deglaciation at the Pleistocene-Holocene transition – particularly the shift from dry grasslands to wet, boggy tundra – limited horse mobility and food access, contributing to population decline in North America. In contrast, generalist herbivores such as moose and elk flourished.

These patterns underscore a broader ecological principle found in Indigenous science, particularly the Lakota concept of mitakuye oyasin, which emphasizes that a species’ survival depends not only on geography, but also its relationship with other life forms within a shared, interdependent habitat. Changes to this relational habitat can serve as the driving force for movement or migration.

For reporters interested in further insights into how this work was done, author Ludovic Orlando said, “Establishing collaborations with Indigenous scientists grounded in mutual respect and equal partnership is essential for the future of all scientific disciplines. Indigenous communities have cultivated deep and invaluable knowledge systems over countless generations. However, the structure of project-based science – often driven by tight funding cycles and publication deadlines – can pose challenges to meaningful cross-cultural dialogue and may not always align with Indigenous protocols for sharing traditional knowledge. The co-authors of this study have worked under the guidance of an Indigenous Review Board to ensure that every stage of the research – from study design to publication – respects and adheres to Indigenous protocols. We hope our approach can serve as a valuable model for other researchers and help foster broader adoption of ethically grounded, collaborative scientific practices.”