Supplementary material 8 from Fur colour in the Arctic fox: genetic architecture and consequences for fitness

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox <i>Vulpes lagopus</i> fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

全基因组关联研究为探究野生种群适应性性状的遗传基础提供了良好契机。然而，既往研究往往难以鉴定出具有主效效应的基因。本研究利用了某野生非模式物种的高密度单核苷酸多态性（single nucleotide polymorphism, SNP）数据与个体适合度数据。通过全基因组分析策略，我们鉴定出MC1R基因是决定北极狐（*Vulpes lagopus*）毛色的唯一因果基因。进一步，我们通过关联生态与进化过程的适合度指标，证实了毛色基因型的适应性意义。我们发现，在毛色位点呈杂合状态的蓝狐，其适合度往往高于纯合白色狐。基因型对适合度的影响不受冬季时长的调控，但会随猎物可获得性发生变化，在啮齿动物种群数量增长的年份中该效应最为显著。MC1R基因所在的基因组区域基因密度较高，我们还探讨了通过连锁与多效性产生间接选择的潜在可能性。本研究表明，全基因组分析可成功应用于野生物种，并鉴定出适应性性状背后的主效基因。此外，我们还展示了该方法可用于识别当前在理解生态与进化之间相互作用时存在的知识空白。