Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes

Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the presence and absence of pectoral and pelvic fins of 12,582 species. To do this, we integrated a synthetic morphological supermatrix of phenotypic data for the pectoral and pelvic fins for teleost fishes from the Phenoscape Knowledgebase (two presence/absence characters for 3,047 taxa) with a species-level tree for teleost fishes from the Open Tree of Life project (38,419 species). The integration method detailed herein harnessed a new combined approach by utilizing data based on ontological inference, as well as phylogenetic propagation, to reduce overall data loss. Using inference enabled by ontology-based annotations, missing data were reduced from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data propagation. These methods allowed us to extend the data to an additional 11,293 species for a total of 12,582 species with trait data. The pectoral fin appears to have been independently lost in a minimum of 19 lineages and the pelvic fin in 48. Though interpretation is limited by lack of phylogenetic resolution at the species level, it appears that following loss, both pectoral and pelvic fins were regained several (3) to many (14) times respectively. Focused investigation into putative regains of the pectoral fin, all within one clade (Anguilliformes), showed that the pectoral fin was regained at least twice following loss. Overall, this study points to specific teleost clades where strategic phylogenetic resolution and genetic investigation will be necessary to understand the pattern and frequency of pectoral fin reversals.当前可用的整合工具难以实现大规模宏观进化研究 (large-scale macroevolutionary studies) 所需的数据合成工作。我们以硬骨鱼 (teleost fishes) 成对鳍丢失频率这一经典科学问题作为案例研究，旨在开发自动化方法，以助力实现大范围性状数据与大规模物种水平系统发育树 (species-level phylogeny) 的整合。与此前报道的四肢演化模式类似，鱼类的演化历程中，胸鳍与腹鳍的退化和丢失被认为曾独立发生过多次。我们开发了一套生物信息学流程 (bioinformatics pipeline)，用于识别12582个物种的胸鳍与腹鳍的存在与缺失状态。为此，我们将来自表型组学知识库 (Phenoscape Knowledgebase) 的硬骨鱼胸鳍、腹鳍表型数据的综合形态超矩阵（涵盖3047个类群的2个存在/缺失性状），与开放生命之树项目 (Open Tree of Life project) 中的硬骨鱼物种水平系统发育树（包含38419个物种）进行了整合。本文详述的整合方法采用了一种新型联合方案，即同时利用基于本体论的推断 (ontological inference) 以及系统发育传播 (phylogenetic propagation) 策略，以降低整体的数据缺失率。借助基于本体注释的推断，缺失数据占比从98.0%降至85.9%，再通过系统发育数据传播进一步降至34.8%。这些方法使我们得以将性状数据拓展至额外的11293个物种，最终使带有性状数据的物种总数达到12582个。研究发现，胸鳍至少在19个演化支中独立丢失，腹鳍则在48个演化支中独立丢失。尽管物种水平的系统发育分辨率有限，制约了相关解读，但可以明确的是，在丢失之后，胸鳍与腹鳍分别重新演化出现至少3次至多达14次。针对仅在鳗鲡目 (Anguilliformes) 这一个演化支内出现的疑似胸鳍重新获得事件的深入研究显示，胸鳍在丢失后至少重新演化出现了2次。总体而言，本研究指明了部分具有研究价值的硬骨鱼演化支，未来需针对这些类群开展针对性的系统发育分辨率提升与遗传学研究，方能阐明胸鳍演化逆转的模式与频率。