Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements.

The Amazonian poison frog genus Ameerega is one of the largest yet most understudied of the brightly colored genera in the anuran family Dendrobatidae, with 30 described species ranging throughout tropical South America. Phylogenetic analyses of Ameerega are highly discordant, lacking consistency due to variation in data types and methods, and often with limited coverage of species diversity in the genus. Here, we present a comprehensive phylogenomic reconstruction of Ameerega, utilizing state-of-the-art sequence capture techniques and phylogenetic methods. We sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. We generated topologies using maximum likelihood and coalescent methods and compared the use of maximum likelihood and Bayesian methods for estimating divergence times. Our phylogenetic inference diverged strongly from those of previous studies, and we recommend steps to bring Ameerega taxonomy in line with the new phylogeny. We place several species in a phylogeny for the first time, as well as provide evidence for six potential candidate species. We estimate that Ameerega experienced a rapid radiation approximately 7-11 million years ago and that the ancestor of all Ameerega was likely an aposematic, montane species. This study underscores the utility of phylogenomic data in improving our understanding of the phylogeny of understudied clades and making novel inferences about their evolution.

The tadpole of Ameerega boehmei in southeastern Bolivia.

To date, half (16 of 32) of the species of Ameerega have had their tadpoles described: A. altamazonica, A. bassleri, A. bilinguis, A. braccata, A. cainarachi, A. flavopicta, A. hahneli, A. macero, A. parvula, A. petersi, A. picta, A. rubriventris, A shihuemoy. A. silverstonei, A. smaragdina, and A. trivittata (Lescure, 1976; Silverstone, 1976; Duellman, 1978; Myers Daly, 1979; Rodriguez Myers, 1993; Haddad Martins, 1994; Lötters et al., 1997; Duellman, 2005; Costa et al., 2006; Twomey Brown, 2008; Brown Twomey, 2009; Poelman et al., 2010; Schulze et al., 2015). Ameerega boehmei is a putative member of a clade containing Ameerega braccata, A. flavopicta, A. berohoka, A. munduruku, all of which inhabit various parts of the 'dry diagonal' between the Amazon and Atlantic rainforests (Prado Gibbs, 1993). Adult frogs in this group are morphologically similar, generally dark-bodied with yellow dorsolateral stripes, orange flash marks and some also possessing bright-yellow dorsal spots. Despite considerable research on their breeding behavior, acoustics and systematics (Lötters et al., 2009; Forti et al., 2013), the tadpole of Ameerega boehmei, the southern-most and western-most distributed species in this tentative group, has not been described.