Data from: Multilocus species trees show the recent adaptive radiation of the mimetic Heliconius butterflies

Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 million years, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.新热带区釉蛱蝶族（Heliconiini）蝴蝶间的缪氏拟态（Müllerian mimicry）是自然选择的绝佳范例，与大规模大陆级辐射演化的物种分化紧密相关。驱动拟态环（mimicry rings）演化的部分过程，可能在该类群中产生不一致的系统发育信号（phylogenetic signals），进而给分类学（systematics）研究带来挑战。本研究依托通过桑格测序（Sanger sequencing）与短读长数据（short read data）从头组装（de novo assembly）获得的、覆盖该族92%物种的22个线粒体与核标记（mitochondrial and nuclear markers）数据集，采用超矩阵（supermatrix）与多物种溯祖（multispecies coalescent）两种分析方法重新审视釉蛱蝶族的系统发育关系，解析冲突信号的分布模式，并对比多种方法论的表现以反映数据集内的异质性。尽管存在大量网状信号（reticulate signal）与标记间的强烈冲突，多数分析始终恢复出近乎一致的拓扑结构，不过超矩阵方法未能体现单个基因座演化历史的潜在差异。但超矩阵仍是一种实用的近似分析方法，可轻松纳入多个以短序列为代表的稀有物种。本研究构建的该类群首个全面的时间校准系统发育树（time-calibrated phylogeny），被用于验证两个假说：一是过去2300万年间新热带区（Neotropics）剧烈的环境变化驱动的分化速率（diversification rate）提升，二是由多样性依赖效应（diversity-dependent effects）对分化速率产生的影响。研究发现，在当前物种最丰富的釉蛱蝶属（Heliconius）所在分支上，分化速率有所提升，但这一变化是渐进发生的，无法明确归因于某一特定环境驱动因子。本研究对哲学理念迥异的物种树重建方法进行了全面对比，并为地球上生物多样性最丰富区域的重要昆虫辐射类群的物种分化研究提供了新见解。