Exploring the genomic architecture of habitat-driven divergence and of ecologically-relevant traits aids understanding of how genomic divergence originates. In this study, we examined genome-wide patterns of genomic divergence driven by small-scale heterogeneity in snowmelt timing. In addition, we explored genetically based variation in ecologically relevant traits. We sampled 180 individuals of Salix herbacea at early- and late- snowmelt microhabitats in three independent mountain localities and genotyped 99,497 GBS-derived SNP markers. Nine ecologically-relevant traits were phenotyped during three years in these individuals.
Results/Conclusions
We identified ten narrow regions as genomic islands for microhabitat-driven divergence, suggesting that genomic divergence can arise at very local geographic scales. These divergence peaks were recovered across mountain localities and therefore are unlikely a consequence of drift. Regions with divergence peaks were embedded in regions with high linkage disequilibrium and negative Tajima’s D. This pattern is indicative of novel variants being fixed in different microhabitats. The main divergence peaks in chromosomes XV and XIX overlapped with major sex determining regions, likely because the latter are more prone to show differentiation at early steps of ecological divergence due to suppressed recombination. Ecological selection on unmeasured traits may be shaping small-scale genomic divergence. The ecologically-relevant traits we surveyed here did not show consistent variation between microhabitats. Nonetheless, variation in these traits was associated with 10 well-known candidate genes for phenological and tolerance traits. Fast-evolving microhabitat-driven genomic divergence, as well as genetic variation for ecologically-relevant traits at a larger scale, likely increases chances for population persistence in heterogeneous and variable environments.