Whole-genome resequencing reveals population genetic structure and selective sweeps in Bombus waltoni

BACKGROUND: Bombus waltoni is a typical alpine bumblebee species and an important indicator species of the Qinghai-Tibetan Plateau. However, whole-genome studies of bumblebees from this region remain limited. In this study, we investigated the genetic diversity, population structure, and adaptive genomic variation of B. waltoni, providing essential genomic resources for understanding its population genetic structure and signatures of local adaptation. RESULTS: Based on whole-genome SNP data, genetic diversity was relatively similar across B. waltoni populations, with expected heterozygosity (He) ranging from 0.2265 to 0.2601, unbiased expected heterozygosity (uHe) from 0.2517 to 0.2729, and nucleotide diversity (π) from 0.00104504 to 0.00113178. Genetic diversity was significantly associated with elevation after correction for multiple testing. Population structure analyses consistently resolved the 18 populations into two major genetic clusters corresponding to northeastern and southwestern regions, a pattern supported by ADMIXTURE, PCA, and phylogenetic analyses. Although overall genetic differentiation was low, a significant pattern of isolation by distance was detected. Multiple gene flow analyses suggested that population differentiation was inconsistent with complete isolation. Selective sweep analyses identified distinct sets of candidate genes and functional enrichment patterns between the two clusters. CONCLUSION: Significant but low genetic differentiation was detected among B. waltoni populations within the northeastern Qinghai-Tibetan Plateau, and populations showed relatively similar levels of genetic diversity. Gene flow signals suggested that population differentiation was inconsistent with complete isolation, while multiple genomic regions under selection suggest potential adaptive responses to elevation- and latitude-associated environmental heterogeneity. These results provide genomic evidence for population differentiation and local adaptation in a high-altitude pollinator, offering a scientific basis for region-specific conservation and management.