Lynx canadensis and Lynx rufus samples for selection genome-wide genomic scan
Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In this study, we performed genome-wide scans for recent selective sweeps in the four extant species of the Lynx genus—Lynx canadensis (Canada lynx), Lynx rufus (bobcat), Lynx lynx (Eurasian lynx), and Lynx pardinus (Iberian lynx)—using a composite likelihood ratio test based on genotype frequency spectrum. Analyzing whole-genome sequences from 80 individuals, we identified species-specific selective sweeps and conducted functional enrichment analyses to explore biological processes under selection. Results revealed distinct adaptive mechanisms shaped by ecological specialization and demographic histories of different species. In Canada lynx, enriched functions include olfactory signaling and pigmentation-related processes; the Eurasian lynx showed signals related to cardiac and neural development; the Iberian lynx exhibited enrichment in immune-related pathways, potentially reflecting pathogen-mediated selection under strong genetic drift; and the bobcat displayed functional signals in reproductive and metabolic regulation. Our study revealed the species-specific nature of recent signatures of ecological differentiation in the genomes of closely related species of the genus Lynx, with minimal overlap, illustrating their diverse evolutionary trajectories and shedding light into the mechanism of adaptation among highly specialized carnivores.