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.