Abstract
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.
Highlights
VOL. 67 law, that is, that the loss of a complex trait is evolutionarily irreversible (Gould 1970; Farris 1977), questions concerning the taxonomic scope, frequency of reversal, and potential genetic bases (Collin and Miglietta 2008) remain unanswered
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
The VTO is built upon the National Center for Biotechnology Information (NCBI) taxonomy, which provides the hierarchical backbone for extant taxa; valid species are drawn from the expert source, the Catalog of Fishes (CoF; Eschmeyer et al 2013)
Summary
VOL. 67 law, that is, that the loss of a complex trait is evolutionarily irreversible (Gould 1970; Farris 1977), questions concerning the taxonomic scope, frequency of reversal, and potential genetic bases (Collin and Miglietta 2008) remain unanswered. Addressing any broad-scale question concerning the evolution of traits requires a comprehensive source of data Such large data sets must be readily extractable and computable, as manual aggregation from a dispersed literature is essentially intractable. While comprehensively synthesizing all available paired fin trait data for teleosts was the first step in investigating patterns in fin evolution, we applied new methods to extend existing data, while minimizing overall data loss. Using questions concerning the frequency of paired fin loss in fishes as an example, we demonstrate the use of new knowledge resources to address basic questions involving large-scale phenotypic evolution. The bioinformatics pipeline developed in the process of this work reflects a set of essential requirements for large-scale macroevolutionary syntheses
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