Data from: Genome divergence and diversification within a geographic mosaic of coevolution

Despite substantial interest in coevolution's role in diversification, examples of coevolution contributing to speciation have been elusive. Here we build upon past studies that have shown both coevolution between South Hills crossbills and lodgepole pine (Pinus contorta), and high levels of reproductive isolation between South Hills crossbills and other ecotypes in the North American red crossbill (Loxia curvirostra) complex. We used genotyping by sequencing to generate population genomic data and applied phylogenetic and population genetic analyses to characterize the genetic structure within and among nine of the ecotypes. Although genome-wide divergence was slight between ecotypes (Fst = 0.011-0.035), we found evidence of relative genetic differentiation (as measured by Fst) between and genetic cohesiveness within many of them. As expected for nomadic and opportunistic breeders, we detected no evidence of isolation-by-distance. The one sedentary ecotype, the South Hills crossbill, was genetically most distinct because of elevated divergence at a small number of loci rather than pronounced overall genome-wide divergence. These findings suggest that mechanisms related to recent local coevolution between South Hills crossbills and lodgepole pine (e.g., strong resource-based density dependence limiting gene flow) have been associated with genome divergence in the face of gene flow. Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6,000 years.尽管学界对协同进化在物种分化中的作用抱有浓厚兴趣，但能证实协同进化推动物种形成的实例却始终难以寻觅。本研究基于既往研究成果——这些研究均证实，南山交嘴雀（South Hills crossbills）与扭叶松（Pinus contorta）之间存在协同进化关系，且南山交嘴雀与北美红交嘴雀（Loxia curvirostra）类群内的其他生态型之间存在高度生殖隔离。我们通过测序分型（genotyping by sequencing）技术获取种群基因组数据，并运用系统发育与种群遗传学分析方法，对9个生态型内部及相互间的遗传结构进行了表征。尽管各生态型间的全基因组分化程度较低（遗传分化系数Fst值为0.011~0.035），但我们仍发现，多数生态型内部存在遗传一致性，而生态型间则呈现出以Fst值衡量的相对遗传分化。正如针对游牧性兼机会主义繁殖物种的预期那般，我们未检测到距离隔离效应的存在。唯一的定居型生态型——南山交嘴雀，其遗传特征最为独特，这源于少数位点上的分化程度升高，而非全基因组范围内的显著整体分化。上述研究结果表明，与南山交嘴雀和扭叶松近期的局部协同进化相关的机制（例如，基于资源的强密度制约限制了基因流），已与存在基因流情况下的基因组分化产生关联。我们的研究进一步刻画了一个极具代表性的案例：协同进化在短短约6000年的时间尺度内便推动了物种形成。