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满足大型宏观进化研究所需的数据整合需求。本研究以真骨鱼类（teleost fishes）成对鳍丢失频率这一经典科学问题为案例，旨在开发自动化方法，以助力大规模性状数据与大规模物种水平系统发育树的整合工作。与此前已报道的附肢进化模式类似，鱼类进化过程中，胸鳍（pectoral fin）与腹鳍（pelvic fin）的退化及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，用于鉴定12582个物种的胸鳍与腹鳍存在/缺失状态。为此，我们整合了两类数据：一是来自Phenoscape知识库（Phenoscape Knowledgebase）的真骨鱼类胸鳍与腹鳍表型数据合成形态超级矩阵（包含3047个分类群的2个存在/缺失性状）；二是来自生命之树开放项目（Open Tree of Life project）的真骨鱼类物种水平系统发育树（涵盖38419个物种）。本文详述的整合方法采用了一种全新的联合策略，即结合基于本体论推理（ontological inference）的数据与系统发育传播（phylogenetic propagation）数据，以降低整体的数据缺失率。通过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，缺失率进一步降至34.8%。借助这些方法，我们将性状数据覆盖范围拓展至额外11293个物种，最终使拥有性状数据的物种总数达到12582个。胸鳍至少在19个演化支中独立丢失，腹鳍则至少在48个演化支中独立丢失。尽管物种水平的系统发育分辨率不足限制了本研究的解读，但研究结果显示，在鳍丢失之后，胸鳍与腹鳍分别独立重现了至少3次、至多14次。针对胸鳍推定重现事件的专项调查显示，所有此类事件均发生在鳗鲡目（Anguilliformes）一个演化支内，且胸鳍在丢失后至少重现了2次。总体而言，本研究明确了若干真骨鱼类演化支，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，将有助于我们理解胸鳍性状逆转的模式与频率。