PRJNA487082
Untangling relationships among terraranan frogs: a phylogenomic approach based on 2,665 loci
Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,000 described species, encompassing ~15% of all named frog species. The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among three recent phylogenomic studies utilizing 95, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. The preferred data matrix consisted of 2,665 nuclear loci from ultra-conserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses both recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + “Strabomantidae”))). Our placement of Brachycephalidae agrees with two previous phylogenomic studies but conflicts with another. Our results place Strabomantis (of the Strabomantidae) with (or within) Craugastor (Craugastoridae) rather than with other strabomantid genera, rendering Strabomantidae paraphyletic with respect to Craugastoridae. We recommend placing Strabomantidae in the synonymy of the older Craugastoridae. Furthermore, our results suggest that Pristimantinae is paraphyletic with respect to Holoadeninae, and should be subsumed into the older Holoadeninae. We also found that using matrices of UCE loci with less missing data (and concomitantly fewer loci) generally decreased support for most nodes on the tree. Overall, our results strongly resolve controversial relationships within one of the largest clades of frogs, with a dataset ~7 times larger than previous studies focused on this clade.