Differential introgression of mutations reveals selection in spruce

Natural selection plays a pivotal role in maintaining genetic boundaries by counteracting the potentially deleterious effects of alleles introduced through hybridization. Here, we investigated this process through a comparative population genomic analysis of three endemic varieties of Picea likiangensis (vars. likiangensis, linzhiensis, and rubescens) across the Qinghai-Tibetan Plateau (QTP) and adjacent regions.

Leveraging genome-wide single nucleotide polymorphism (SNP) data from 193 individuals, we documented pervasive genetic admixture among these taxa, yet observed a pronounced asymmetric pattern of introgression: synonymous polymorphisms (Hs) exhibited significantly higher introgression levels than non-synonymous polymorphisms (Hn). This pattern indicates that purifying selection may actively eliminate maladaptive non-synonymous mutations, whereas neutrally evolving loci continue to undergo gene flow. Moreover, the relative hybrid index (ω_H = Hn/Hs) was lower in populations adjacent to pure rubescens stands, suggesting stronger selection against introgressed alleles in the core range of the recipient taxon rather than a simple effect of geographic distance. In addition, recombination rate was significantly associated with introgression bias, implying that recombination facilitates the removal of maladaptive genomic segments following hybridization.

Our findings underscore the pivotal role of comparative population genomics in elucidating how natural selection shapes introgression and contributes to the maintenance of genetic boundaries during speciation.