Comparisons Between Large‐Scale Genomic Variants and SNPs in Driving Population Divergence and Local Adaptation

ABSTRACT Genomic variations, such as indels (2–49 bp) and structural variants (SVs, ≥50 bp), are larger‐scale mutations than single nucleotide polymorphisms (SNPs) and can substantially impact evolutionary processes, including speciation, adaptation, and phenotypes. Despite their functional importance, integrative population genetic analyses that jointly consider genome‐wide SNPs, indels, and SVs remain under‐explored. The ground tit ( Pseudopodoces humilis ), an endemic species to the Qinghai–Tibet Plateau (QTP), exhibits divergence across distinct glacial refugia, accompanied by habitat and morphological divergence, making it an excellent example for investigating how different types of genomic variants contribute to population divergence and local adaptation. Here, by retrieving 81 whole‐genome sequence data, over 13 million SNPs, 2 million indels, and 22,101 SVs were identified. Variants were unevenly distributed across the genome, characterized by distinct hotspot regions. Indels and SVs revealed four genetic clusters consistent with previous SNP‐based results, thereby validating the reliability of our variant datasets. F ST and genotype‐environment association (GEA) analyses independently revealed numerous candidate indels and SVs; each showed minimal overlap with previously identified SNPs, and were enriched in similar functional pathways such as signal transduction, skeletal muscle development, water transport, DNA repair, reproduction, nervous system development, and immunity. Collectively, our results demonstrated that indels and SVs could capture additional signatures besides SNPs. Furthermore, similar but distinct gene functions among different types of genomic variants collectively and complementarily drive genomic divergence across environmental gradients in such a high‐elevation endemic species, underscoring its evolutionary relevance in local adaptation.