Diversity Dynamics in Nymphalidae Butterflies: Effect of Phylogenetic Uncertainty on Diversification Rate Shift Estimates, 2014

This data set is a part of the project "From host plants to host ants: Evolution of phyto-predation in butterflies, 2014". The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. In this project phylogenetic uncertainty was investigated, and if different results can be produced by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, the results indicate that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, accelerated diversification was found for Ithomiini butterflies. Binary speciation and extinction model (BiSSE) were used and showed that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. The results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. Data are freely available for downloading (follow the link under related materials).

本数据集隶属于2014年立项的“从宿主植物到宿主蚂蚁：蝴蝶植食捕食（phyto-predation）的演化”项目。物种丰富的蛱蝶科（Nymphalidae）已被广泛用于探究植物与昆虫间的演化互作关系。昆虫-宿主植物动态理论预测，关键创新事件将推动类群分化速率加快。在演化生物学领域，使用MEDUSA软件（基于逐步AIC准则构建演化多样性模型）对最大可信树（maximum credibility tree）开展分析，是估算分化速率转变的主流方法之一。本项目旨在探究系统发育不确定性（phylogenetic uncertainty）对分析结果的影响，并验证：若将该分析方法扩展应用于贝叶斯推演后验分布中随机抽取的树样本，能否得到差异化的分析结论。借助MultiMEDUSA方法完成分析后，结果显示系统发育不确定性会对分化速率估算产生显著影响：针对同一演化支（clade），不同的系统发育树得到的分化速率区间跨度极大，从极高值近乎降至零；部分演化支中还同时观测到分化速率显著升高与降低的情况。在最大分支可信树（maximum clade credibility tree）上发现的18处显著速率转变中，仅有4处在多数抽样树中保持一致。其中，透翅蝶族（Ithomiini）蝴蝶被检测到存在分化速率加速的现象。研究采用二元物种形成与灭绝模型（Binary Speciation and Extinction model, BiSSE），结果表明：透翅蝶族的宿主植物转移至茄科（Solanaceae），与其净分化速率提升显著相关，这与弥散共成种假说（diffuse cospeciation hypothesis）的推测相符。本研究结果证实，在估算净分化速率转变时，纳入系统发育不确定性的考量至关重要——若仅使用最大分支可信树与后验分布中的其他系统发育树开展分析，可得到差异悬殊的结论。数据集可免费下载，相关材料下方附下载链接。