Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

杂交带（hybrid zone）是研究物种形成过程、鉴定发生分化的基因组区域，以及解析其中涉及的生态（外在）与非生态（内在）因子的重要研究工具。本研究以北美大黄凤蝶（Papilio glaucus）与加拿大凤蝶（Papilio canadensis）之间的杂交带为研究对象，解析了其分化的基因组与地理分布格局。本研究通过对28417个ddRAD单核苷酸多态性（SNP）位点进行基因组扫描，鉴定了潜在受选择的基因组区域，并结合已报道的生态适应候选基因，分析了这些区域的分布特征。研究结果显示，分化广泛存在于整个基因组中，涉及多个生态适应候选基因，尤其是与季节适应及宿主植物解毒相关的基因。Z染色体与4条常染色体呈现出不成比例的分化程度，提示这些染色体上的基因可能在生殖隔离中发挥作用。对显著分化的基因组SNP以及物种诊断性遗传标记进行渐变群（cline）分析后发现，其地理重合度达81%、一致性达80%，且与气候介导的发育阈值（生长季长度）的地理分布显著相关。约1.3%的分化选择异常位点并未与生态适应候选基因相关联，这或许反映出这两个物种间存在此前未被发现的内在生殖隔离屏障。上述结果表明，外在（气候介导）与内在（未知机制）的渐变群可能已发生耦合，并共同作用以强化生殖隔离。这种同时从基因组与地理分布格局维度评估分化的研究策略，可为解析生殖隔离的遗传架构与内外源选择之间的相互作用提供新的认知。