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贝氏新扁叶甲（Neochlamisus bebbianae）枫树共生种群与柳树共生种群的遗传分化及生态物种形成的贡献。针对15组种群两两比较实验，本研究鉴定出“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（AFLP）位点中，有15%的位点在多组种群比较中被判定为异常位点，且低连锁不平衡（linkage disequilibrium）结果表明，这些异常位点源自基因组的多个区域。若某异常位点在“不同宿主”种群比较中反复被检测为异常，但从未在“同宿主”比较中出现，则将其进一步归类为“宿主特异性异常位点”；反之，若异常位点呈现相反的分布模式，则归类为“宿主非依赖性异常位点”。宿主特异性异常位点占总位点数的5%，且出现频率高于宿主非依赖性异常位点，这表明宿主适应性在种群基因组分化中发挥着重要作用。种群系统树的分析结果进一步证明，即便存在基因流，宿主相关的选择仍可推动种群分化。当数据集包含宿主特异性异常位点时，系统树的拓扑结构由宿主关联类型决定；但若基于中性位点构建系统树，则会将同域种群聚为一类，无法体现宿主关联的影响。最后，在全部9组不同宿主种群比较中，有3个宿主特异性异常位点均呈现出高度分化。鉴于宿主适应性可推动这类叶甲的生殖隔离，这些位点可作为未来开展生态物种形成分子研究的极具潜力的候选基因区域。