Supplementary material from: Deep divergences among inconspicuous clades of Epipedobates poison frogs
Creators: name: López-Hervas, Karem
name: Santos, Juan C.
name: Ron, Santiago R.
name: Betancourth-Cundar, Mileidy
name: Cannatella, David C.
name: Tarvin, Rebecca
Publisher: name: Zenodo
Year: 2023
Subjects: aposematism
cryptic species
genetic divergence
Polytypic species
Species delimitation
Phylogenetics

description: Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ~11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador.
description: Funding provided by: Society of Systematic BiologistsCrossref Funder Registry ID: https://ror.org/0575b2v60Award Number: 
Funding provided by: North Carolina Herpetological Society*Crossref Funder Registry ID: Award Number: 
Funding provided by: Society for the Study of Reptiles and Amphibians*Crossref Funder Registry ID: Award Number: 
Funding provided by: Chicago Herpetological SocietyCrossref Funder Registry ID: http://dx.doi.org/10.13039/100013511Award Number: 
Funding provided by: Texas Herpetological Society*Crossref Funder Registry ID: Award Number: 
Funding provided by: The University of Texas at AustinCrossref Funder Registry ID: https://ror.org/00hj54h04Award Number: 
Funding provided by: National Science FoundationCrossref Funder Registry ID: https://ror.org/021nxhr62Award Number: 
Funding provided by: National Science FoundationCrossref Funder Registry ID: https://ror.org/021nxhr62Award Number: 
Funding provided by: National Geographic SocietyCrossref Funder Registry ID: https://ror.org/04bqh5m06Award Number: #9468-14
Funding provided by: National Science FoundationCrossref Funder Registry ID: https://ror.org/021nxhr62Award Number: 1556967
Funding provided by: Secretaría Nacional de Educación Superior, Ciencia, Tecnología e Innovación del Ecuador *Crossref Funder Registry ID: Award Number: 
Funding provided by: Pontificia Universidad Católica del EcuadorCrossref Funder Registry ID: https://ror.org/02qztda51Award Number:
description: Please see López-Hervas et al. (2024) for the full methods. In this study, we evaluate and clarify the phylogeny of the dendrobatid poison frog genus Epipedobates. Although Epipedobates is considered one of the youngest clades in the Dendrobatidae family, we find tremendous phenotypic variation within and among species, making them an interesting group for taxonomists and evolutionary biologists. We aimed to comprehensively assess the phylogenetic relationships among species within this clade, which until now has remained incomplete despite several in-depth studies. Briefly, we sequenced mtDNA and nDNA and estimated phylogenetic trees using Bayesian and Maximum Likelihood approaches (see Data S1, Fig. S1, Fig. S2, Table S2). We estimated and reviewed haplotypes based on each sequenced gene (Table S3). We then used alignments of mtDNA to estimate putative species limits in 1) Assemble Species by Automatic Partitioning (ASAP) and 2) Generalized Mixed Yule Coalescent (GYMC) (see Data S2 and Fig. S3). We reviewed published specimen data to estimate species ranges and differences in body sizes among putative species (see Data S3). Finally, we reviewed images of all examined specimens (Fig. S4-S27) as well as accompanying metadata (Table S1) to qualitatively compare color among species.