Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles

This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of the genome. Outliers were further classified as "host-specific" if repeatedly observed in "different-host" population comparisons but never in "same-host" comparisons. Outliers exhibiting the opposite pattern were analogously classified as "host-independent." Host-specific outliers represented 5% of all loci and were more frequent than host-independent outliers, thus revealing a large role for host-adaptation in population genomic differentiation. Evidence that host-related selection can promote divergence despite gene flow was provided by population trees. These were structured by host-association when datasets included host-specific outliers, but not when based on neutral loci, which united sympatric populations. Lastly, three host-specific outliers were highly differentiated in all nine different-host comparisons. Because host-adaptation promotes reproductive isolation in these beetles, these loci provide promising candidate gene regions for future molecular studies of ecological speciation.本研究采用比较基因组扫描（comparative genome scan）技术，评估与宿主植物相关的歧化选择对新贝氏隐唇叶甲（Neochlamisus bebbianae）枫栖种群与柳栖种群的遗传分化及生态物种形成的贡献。针对15组两两种群比较，我们鉴定出了异常位点（outlier loci），这类位点的强烈分化被推测由歧化选择所驱动。在447个扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）位点中，有15%的位点在多组种群比较中被鉴定为异常位点；较低的连锁不平衡（linkage disequilibrium）表明，这些异常位点来源于基因组的多个区域。若异常位点在「异宿主」种群比较中反复被检出，却从未在「同宿主」比较中出现，则将其归类为宿主特异性（host-specific）异常位点；呈现相反模式的异常位点则被同理归类为宿主非依赖性（host-independent）异常位点。宿主特异性异常位点占总位点的5%，且其出现频率高于宿主非依赖性异常位点，这表明宿主适应在种群基因组分化中发挥着重要作用。种群系统树的结果为「即便存在基因流，宿主相关选择仍可推动种群分化」这一观点提供了证据：当数据集包含宿主特异性异常位点时，种群系统树会按照宿主关联进行聚类；但当基于中性位点（neutral loci）构建时，系统树则会将同域种群（sympatric populations）聚为一类，不再按宿主关联分组。最后，在全部9组异宿主种群比较中，有3个宿主特异性异常位点均呈现出强烈的分化特征。鉴于宿主适应可推动这类叶甲的生殖隔离（reproductive isolation），这些位点可为未来生态物种形成相关的分子研究提供极具潜力的候选基因区域。