Genomic evidence for within-species thermal adaptation in collagen genes

Collagen is the most abundant protein in animals. Its thermal stability depends on its specific amino acid composition within the repeated Gly-X aa -Y aa motifs forming the triple helix structure. Proline increases collagen rigidity, while serine enhances its elasticity—properties that contribute to collagen function and that vary with temperature. Although variation in collagen composition has been linked to temperature adaptation across evolutionary distinct taxa, its role within a species remains unclear. Here, we tested whether collagen genes across populations of the freshwater crustacean, Daphnia magna , show a signature of local adaptation to the ambient temperature. Analysing 39 collagen genes from 215 D. magna populations across three phylogeographic lineages spawning four continents, we found that animals from populations in warmer climates have higher proline and lower serine content in collagen—consistent with enhanced protein stability at higher temperatures. This variation was also associated with experimentally measured upper temperature tolerance. Parallel directional patterns of amino acid change appeared across genetically distinct lineages. Collagen genes also showed strong signatures of positive selection, comparable to that of immune-related genes, supporting a scenario of polygenic molecular role in adaptive responses. Our findings provide evidence of intraspecific molecular evolution in collagen amino acid composition driven by environmental temperature. Additionally, our study bridges macroevolutionary patterns with microevolutionary processes, posing the first intraspecific evidence that collagen genes can contribute to responses to environmental gradients at the molecular level, and thus, advancing our understanding of molecular adaptation of constrained structural proteins in an environmental context.