Wednesday, March 9, 2016

[Herpetology • 2015] Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin

Fig 1. Phylogeny and distribution of the Pristimantis acuminatus group in the Amazon Basin.
 (A) Optimal maximum likelihood tree (log likelihood = -6762.95) inferred from a partitioned analysis of 1997 aligned sites of the 12S, 16S and COI (by codon position) mtDNA genes, showing the phylogenetic relationships among 33 specimens identified as P. acuminatus sensu lato and P. tantanti from the Amazon basin. Clade A = Pristimantis limoncochensis sp. nov., clade B = P. omeviridis sp. nov., clade C = P. acuminatus sensu stricto, clade D = P. enigmaticus sp. nov., and clade E = P. tantanti. Stars denote clades with Bayesian posterior probability values1; numbers below clades represent non-parametric bootstrap support values.
(B) Areas of distribution for species in the complex. Dotted circles = Localities of collection from specimens used for the phylogenetic analyses; Polygons = occurrence areas drawn as minimum convex polygons for each clade based on specimens reviewed in collections (S2 Table). Colors of clades in the phylogenetic tree correspond to colors of polygons and dotted circles on the map.


Pluralistic approaches to taxonomy facilitate a more complete appraisal of biodiversity, especially the diversification of cryptic species. Although species delimitation has traditionally been based primarily on morphological differences, the integration of new methods allows diverse lines of evidence to solve the problem. Robber frogs (Pristimantis) are exemplary, as many of the species show high morphological variation within populations, but few traits that are diagnostic of species. We used a combination of DNA sequences from three mitochondrial genes, morphometric data, and comparisons of ecological niche models (ENMs) to infer a phylogenetic hypothesis for the Pristimantis acuminatus complex. Molecular phylogenetic analyses revealed a close relationship between three new species — Pristimantis enigmaticus sp. nov., P. limoncochensis sp. nov. and P. omeviridis sp. nov. — originally confused with Pristimantis acuminatus. In combination with morphometric data and geographic distributions, several morphological characters such as degree of tympanum exposure, skin texture, ulnar/tarsal tubercles and sexual secondary characters (vocal slits and nuptial pads in males) were found to be useful for diagnosing species in the complex. Multivariate discriminant analyses provided a successful classification rate for 83–100% of specimens. Discriminant analysis of localities in environmental niche space showed a successful classification rate of 75–98%. Identity tests of ENMs rejected hypotheses of niche equivalency, although not strongly because the high values on niche overlap. Pristimantis acuminatus and P. enigmaticus sp. nov. are distributed along the lowlands of central–southern Ecuador and northern Peru, in contrast with P. limoncochensis sp. nov. and P. omeviridis sp. nov., which are found in northern Ecuador and southern Colombia, up to 1200 m in the upper Amazon Basin. The methods used herein provide an integrated framework for inventorying the greatly underestimated biodiversity in Amazonia.

Fig 9. Living specimens of the Pristimantis acuminatus complex and their relatives in the Amazon Basin.
(A) Pristimantis acuminatus, QCAZ 53263, (B) Pristimantis tantanti, CORBIDI 12987, (C-D) night and daylight color variation in Pristimantis limoncochensis sp. nov., QCAZ 52987, (E) amplectant pair of Pristimantis omeviridis sp. nov., holotype female QCAZ 55392 and paratype male QCAZ 55391, (F) Pristimantis padiali, specimen not collected, (G-H) night and daylight color variation in Pristimantis enigmaticus sp. nov., specimen not collected.

 Photographs of (B) by V. Durán, (E) by Santiago Ron, (F) by Omar Rojas; all other photographs by H. M. Ortega-Andrade.  DOI: 10.1371/journal.pone.0143392

H. Mauricio Ortega-Andrade, Octavio R. Rojas-Soto, Jorge H. Valencia, Alejandro Espinosa de los Monteros, Juan J. Morrone, Santiago R. Ron and David C. Cannatella. 2015. Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin. PLoS ONE. 10(11): e0143392. DOI: 10.1371/journal.pone.0143392