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.

尽管学界对协同演化（coevolution）在物种多样化中的作用抱有浓厚兴趣，但能够证明协同演化推动物种形成（speciation）的实例却始终难以寻觅。本研究基于既往研究成果——这些研究已证实南山交嘴雀与扭叶松（Pinus contorta）之间存在协同演化关系，且北美红交嘴雀（Loxia curvirostra）复合群中，南山交嘴雀与其他生态型（ecotypes）之间存在高水平生殖隔离（reproductive isolation）。我们采用测序分型（Genotyping by Sequencing）技术生成群体基因组数据，并运用系统发育与群体遗传学分析方法，对9种生态型内部及彼此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（固定指数Fst=0.011~0.035），但我们发现多数生态型内部存在遗传一致性，且生态型间存在相对遗传分化（以Fst衡量）。正如对游牧性兼机会主义繁殖者的预期一致，我们未检测到距离隔离（isolation-by-distance）现象。唯一的定居型生态型——南山交嘴雀——在遗传上最为独特，其分化主要源于少数位点的升高分化，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演化相关的机制（例如，基于资源的强密度依赖性限制了基因流），已在存在基因流的情况下与基因组分化相关联。我们的研究进一步刻画了一个显著的案例：协同演化在短短6000年内便推动了物种形成。