Supplementary material from: Deep divergences among inconspicuously colored clades of Epipedobates poison frogs

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 inconspi..., 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 an..., , # Supplementary material from: Deep Divergences Among Inconspicuously Colored Clades of Epipedobates Poison Frogs

[https://doi.org/10.5061/dryad.4xgxd25h3](https://doi.org/10.5061/dryad.4xgxd25h3)

We examined genetic and phenotypic data from 116 *Epipedobates* frogs. The frogs were collected from 29 locations spanning southwest Colombia to southwest Ecuador, covering the entire range of *E. boulengeri* and including type localities of several species. Mean pairwise p-distances and haplotype networking were calculated, and species limits were estimated using ASAP and GMYC methods. Phylogenetic relationships were determined using Maximum Likelihood and Bayesian Inference methods. The study was carried out under permits from Colombian and Ecuadorian authorities and voucher specimens were deposited in Museo de Zoología de Pontificia Universidad Católica del Ecuador and Museo ANDES at Universidad de los Andes, Bogotá, Colombia, with specific codes for specimens at the Museo de Historia Nat...