Fig 1. Distinct evolutionary patterns of TAS2Rs in amphibian genomes compared to other vertebrates.

(A) Evolution of TAS2R gene content across the 645 vertebrate species examined. Bars adjacent to the phylogeny represent TAS2R counts observed in extant species, and are colored by taxonomic lineage. Tree branches are colored according to DupliPHY ancestral state reconstructions, and were plotted following Revell, 2013 [117]. Note that the color bar is on a logarithmic scale to facilitate visualization. The evolutionary regime shifts from the best-fitting models of continuous traits are labeled as dots on tree branches. The red dots represent the five well-supported shifts considered, and the gray dot represents the sixth shift, which had ambiguous support (see Results section and S3 Fig for details). (B) Boxplots of TAS2Rs content in vertebrate genomes grouped by taxonomic group. (C) CAFE4 birth (λ) and death (μ) rate estimates for the TAS2R family in four vertebrate lineages. (D) Radial phylogenetic tree showing 9,306 TAS2Rs from 681 unique species. The tree also includes 214 published TAS2R sequences which were used to scaffold the alignment, in addition to six zebrafish ORA sequences as outgroups. Branches were colored according to major taxonomic groups, as indicated on the right. Approximate Bayes (aBayes) probabilities are noted as circles on the deep nodes, with red showing confidence greater than 0.95, orange showing confidence 0.90 to 0.95, and yellow showing confidence below 0.90. The tree data with NCBI accessions is shown in S3 Data.