A Whole-Genome and Ancient DNA Perspective on the Drivers of Genetic Diversity and Structure in Palearctic True Lemmings

True lemmings (genus Lemmus) underwent substantial range shifts during the Late Pleistocene and the Pleistocene-Holocene transition, but the impact of these events on present-day diversity remains poorly understood. Here, we used whole-genome sequencing data from modern and ancient samples across the Palearctic range to address this knowledge gap. Reconstruction of autosomal phylogeny revealed that Palearctic true lemmings exhibit relatively shallow genetic structure, contrasting with the deep divergence inferred from mitochondrial genomes. Genetic variation largely follows an isolation-by-distance pattern, and no elevated nuclear divergence was detected between the major mitochondrial lineages. Window-based phylogenetic analyses identified several peripheral populations with high concordance factors, including Norway and Amur lemmings. The high degree of phylogenetic concordance along the genome in these populations is likely a consequence of postglacial bottlenecks and isolation, as indicated by reduced heterozygosity and the presence of runs of homozygosity in them. Overall, our results indicate that the modern genomic structure of Palearctic lemmings was shaped primarily by range fragmentation and population isolation following the broad distribution of the genus during the Last Glacial Maximum. Thus, the current genetic structure appears to represent only a fraction of the Late Pleistocene true lemming diversity. This is illustrated by a genetically distinct ancient specimen ([~]40 ka BP) from the Indigirka River basin that does not cluster with any modern lineage. From a taxonomic perspective, these findings do not support strong species-level differentiation among the major Palearctic lineages and highlight the discrepancy between mitochondrial and nuclear patterns of diversity within the genus.