Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids

Pleistocene caballine horses exhibited considerable genetic diversity and maintained broad population connectivity across their range. The extinct Dalian horse (Equus dalianensis) from northeastern China likely contributed to this network. Here, we sequenced 20 complete mitochondrial and two nuclear genomes, establishing the Dalian horse as a distinct genetic clade within Northeast Eurasian caballines and extending its known geographic distribution. Ancestry component analyses revealed a distinctive component of Eastern Beringian (E-EBer), i.e. American ancestry in Dalian horses, absent from other Northeast Asian equids. The proportion of this ancestry fluctuated between approximately 50ka and approximately 32ka, consistent with contact with E-EBer populations followed by dilution through later admixture. Combined with published evidence of very low (<0.7%) and uneven E-EBer ancestry in Late Pleistocene Northeast Siberian (NEsib) horses, our data document spatiotemporal overlap and gene flow between Dalian and NEsib horses, supporting the hypothesis that Dalian horses served as intermediaries in the transmission of American ancestry to Eurasia. When integrated with stable isotope evidence, these genomic results suggested that Dalian horse's specialized dietary niche constrained its ability to adapt to rapid Late Pleistocene environmental change, ultimately contributing to its extinction. These findings highlight the Dalian horse's role in Late Pleistocene connectivity and extinction dynamics in northern Asia.