Single Nucleotide Polymorphisms, Structural Variants, and Short Tandem Repeats Capture Distinct Signals of Adaptive Divergence in the Atlantic Puffin

The Arctic has been the scene for (re)colonization, diversification, and adaptation of boreal and Arctic fauna. As anthropogenic warming of the Arctic environment increases the extinction risk for peripheral populations, understanding patterns of local adaptation is imperative. The Atlantic puffin (Fratercula arctica) comprises multiple genetically and morphologically distinct populations with an Arctic-boreal distribution. Yet, patterns of adaptation between these populations remain poorly understood. Here, we investigate potential adaptive divergence between High Arctic (F. a. naumanni) and boreal (F. a. arctica) puffin subspecies using whole-genome sequence data. We analyze different types of intraspecific DNA variation, including single nucleotide polymorphisms (SNPs), structural variants (SVs) and short tandem repeats (STRs). Patterns of elevated levels of genetic divergence vary across these types, with STRs uncovering the largest unique proportion (47.2%) of genomic outlier loci. Notably, 94.5% of all outlier genes are exclusive to one type of variation and several such genes are linked to phenotypic differences observed between these subspecies, including body size, skeletal development, adipose tissue accumulation and the sensory system. Our observations indicate that F. a. naumanni harbors unique genetic diversity within puffins suggesting adaptation to its Arctic environment. Importantly, we show that SNPs, SVs, and STRs capture distinct signals of adaptive divergence, underscoring the importance of integrating multiple genomic markers to fully understand the complexity of local adaptation. These results offer a broader perspective on genomic patterns of adaptive divergence in Arctic fauna and can inform conservation strategies aimed at preserving genetic diversity in the Atlantic puffin.