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 3047 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.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.