Data from: Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna

Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow–a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialisation to a particular host plant. Genome-wide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genome-wide divergence associated with both geographic distance and ecological divergence. However, a hybridisation assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different-host associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.即便存在基因流（gene flow），对不同环境的适应也可通过自然选择推动种群分化——这一现象通常出现在生态物种形成过程中。为阐明自然选择如何在物种形成过程中推动并维持种群分化，我们对三种近缘的日本植食性瓢虫开展了种群遗传结构、基因流程度及基因组异质性分化的研究，涉及食植瓢虫属（Henosepilachna）的斑鞘食植瓢虫（H. pustulosa）、蓟食植瓢虫（H. niponica）和蓝升麻食植瓢虫（H. yasutomii）。这三个物种分别为泛食性物种、野生蓟（Cirsium spp.）专食性物种以及蓝升麻（Caulophyllum robustum）专食性物种，其分布范围也相应存在差异。这两种专食性物种的分布区域广泛重叠，但仅因各自对特定寄主植物的高度专化性而实现生殖隔离。全基因组扩增片段长度多态性（amplified fragment-length polymorphism, AFLP）标记与线粒体细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI）基因序列分析均检测到显著的全基因组分化，且该分化与地理距离和生态分化均相关。然而，针对AFLP位点与线粒体序列的杂交检测结果显示，这两种同域分布的专食性物种之间存在一定程度的单向基因流。基于所有可变AFLP位点的主坐标分析（Principal coordinates analysis, PCoA）结果表明，无论物种（即寄主范围）如何，相邻采样点的种群之间均存在遗传相似性。但进一步的比较基因组扫描分析鉴定出占总位点约1%的少量位点，为与不同寄主相关的异常分化位点。上述结果表明，这三个物种的起源较为复杂，而当前的基因流可能掩盖了这一复杂起源；同时还表明，即便同域分布的物种种对之间存在一定程度的基因流，仅需少数与不同寄主利用相关的基因组位点，即可维持生态分化。