Geographical barriers, asymmetric hybridization, and postglacial demography drive the evolutionary history of three threatened European sousliks

Abstract

Abstract Speciation, hybridization, and historical demography jointly shape evolutionary trajectories, yet their combined effects remain poorly resolved in many threatened mammals. We used single-nucleotide polymorphisms obtained by genome-wide double-digest restriction site-associated DNA sequencing to assess evolutionary relationships, hybridization patterns, and demographic histories in three threatened European sousliks: Spermophilus citellus, Spermophilus suslicus, and Spermophilus odessanus. Population genomic analyses showed that all three species are genetically well differentiated, with the Dnieper River forming a major barrier to gene flow and with a narrow contact zone occurring only between S. citellus and S. odessanus in Moldova and western Ukraine. Genome polarization identified admixed individuals between S. citellus and S. odessanus, all carrying S. odessanus mitochondrial haplotypes. D-Statistics supported introgression between these species, and TreeMix inferred historical gene flow from S. citellus into S. odessanus. Spermophilus suslicus showed no evidence of admixture, consistent with its allopatric distribution and fixed karyotypic differences. Demographic reconstructions indicated that all three species experienced a pronounced bottleneck around the Last Glacial Maximum, followed by postglacial range expansion. Subsequently, S. suslicus maintained relatively stable population sizes, whereas S. citellus and S. odessanus underwent gradual long-term declines. Our findings provide a genomic foundation for European sousliks and demonstrate that effective conservation should recognize the distinct evolutionary histories of each species.