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.当前现有整合工具难以支撑大规模宏观进化研究所需的数据合成工作。我们以硬骨鱼（teleost fishes）成对鳍缺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，以推动大规模性状数据与大规模物种水平系统发育树的整合。与此前报道的四肢进化模式类似，学界普遍认为，在鱼类演化历程中，胸鳍与腹鳍的退化及缺失已独立发生过多次。我们开发了一套生物信息学流程，用于识别12582个物种的胸鳍与腹鳍存在/缺失状态。为此，我们整合了两部分数据：一是来自表型组知识库（Phenoscape Knowledgebase）的硬骨鱼胸鳍、腹鳍表型数据的综合形态超级矩阵（涵盖3047个类群的2个存在/缺失性状）；二是来自开放生命之树项目（Open Tree of Life project）的硬骨鱼物种水平系统发育树（包含38419个物种）。本文详述的整合方法采用了一种新型联合策略：同时利用基于本体论注释的推理方法与系统发育传播方法，以降低整体的数据缺失率。借助基于本体注释的推理，数据缺失率从98.0%降至85.9%；再通过系统发育数据传播，进一步将缺失率降至34.8%。这些方法使我们能够将性状数据拓展至额外的11293个物种，最终获得12582个带有完整性状数据的物种。研究结果显示，胸鳍至少在19个演化支中独立发生缺失，腹鳍则在48个演化支中独立缺失。尽管物种水平系统发育分辨率的不足限制了我们的解读，但结果表明，在鳍部缺失之后，胸鳍和腹鳍分别重新演化出现了至少3次和14次。针对仅在鳗形目（Anguilliformes）一个演化支中出现的胸鳍推定重新演化事件，我们开展了针对性研究，结果显示胸鳍在首次缺失后至少重新演化出现了2次。总体而言，本研究指明了若干关键硬骨鱼演化支，若要全面理解胸鳍反转（即鳍部重新出现）的模式与发生频率，需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。