Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae).

We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.

Phylogeny, diversity and biogeography of Neotropical sipo snakes (Serpentes: Colubrinae: Chironius).

Neotropical sipo snakes (Chironius) are large diurnal snakes with a long tail and big eyes that differ from other Neotropical snakes in having 10 or 12 dorsal scale rows at midbody. The 22 currently recognized species occur from Central America south to Uruguay and northeastern Argentina. Based on the largest geographical sampling to date including ∼90% of all species, we analyzed one nuclear and three mitochondrial genes using phylogenetic methods to (1) test the monophyly of Chironius and some of its widely distributed species; (2) identify lineages that could represent undescribed species; and (3) reconstruct ancestral distributions. Our best hypothesis placed C. grandisquamis (Chocoan Rainforest) + C. challenger (Pantepui) as sister to all other species. Based on phylogeny and geographic distribution, we identified 14 subclades as putative species within Chironius fuscus, C. multiventris (including C. foveatus and C. laurenti), C. monticola, and C. exoletus. Under current taxonomy, these species show nearly twice as much genetic diversity as other species of Chironius for ND4. Biogeographical analyses using BioGeoBEARS suggest that current distribution patterns of Chironius species across South America resulted from multiple range expansions. The MRCA of the clade C. challenger + C. grandisquamis was most likely distributed over the Pantepui region, the Andes, and the Chocoan Rainforest, whereas the remaining lineages probably evolved from an Amazonian ancestor.

Phylogeny and biogeography of the most diverse clade of South American gymnophthalmid lizards (Squamata, Gymnophthalmidae, Cercosaurinae).

Nearly 50% of the diversity of the speciose Neotropical lizard clade Gymnophthalmidae is nested within the subclade Cercosaurinae. The taxonomy of Cercosaurinae lizards has been historically confusing because many diagnostic characters of those clades traditionally ranked as genera do not represent true diagnostic apomorphies. Even though molecular phylogenies of several 'genera' have been presented in the last few years, some of them remain poorly sampled (e.g., Anadia, Echinosaura, Potamites, Riama). In this paper we present a more comprehensive phylogeny of Cercosaurinae lizards with emphasis on Andean taxa from Ecuador and Peru, as well as a time-calibrated phylogeny with reconstruction of ancestral areas. Our analysis includes 52% of all recognized species of Cercosaurinae (67 species) and 1914 characters including three mitochondrial and one nuclear gene. We find that Anadia, Echinosaura, Euspondylus, Potamites, Proctoporus, and Riama are not monophyletic: the Tepuian Anadia mcdiarmidi is not sister to Andean species of Anadia; Echinosaura sulcarostrum is not included in the same clade formed by other species of Echinosaura and their more recent common ancestor; Teuchocercus is nested within Echinosaura; species of Euspondylus included in this study are nested within Proctoporus; Riama laudahnae is included in Proctoporus; and Potamites is paraphyletic and split in two separate clades, one of which we name Gelanesaurus, also a new genus-group name. Within Potamites, P. ecpleopus is paraphyletic, and P. strangulatus strangulatus and P. strangulatus trachodus are recognized as two distinct species. We also identify three unnamed clades (i.e., not nested within any of the recognized 'genera') from Andean populations in Ecuador and Peru. The estimated age of the clade Cercosaurinae (∼60Ma) corresponds to the early stages of the northern Andes. Even though the distribution of the most recent common ancestor of Cercosaurinae remains equivocal, our analysis shows that these lizards colonized and radiated along the northern Andes before reaching the central Andes in Peru. Finally, we present phylogenetic definitions for some of the recovered clades to promote a clear and precise classification of Cercosaurinae lizards.

A new species of spiny-tailed iguanid lizard (Iguania: Stenocercus) from northwestern Peru.

We describe a new species of Stenocercus from the interandean valley of Río Chotano on the Amazonian slope of the northern portion of the Cordillera Occidental of Peru (Cajamarca Region), at elevations of between 1997 and 2318 m. Stenocercus arndti sp. nov. differs from other Stenocercus, except from S. bolivarensis, S. carrioni, S. chlorostictus, S. crassicaudatus, S. empetrus, S. eunetopsis, S. simonsii, and S. torquatus, in having granular scales on the posterior surface of the thighs, two caudal whorls per autotomic segment, mucronate caudal scales, and distinct longitudinal row of enlarged vertebral scales. However, Stenocercus arndti sp. nov. is easily distinguished from these species in having a bold black transversal band at midbody that extends ventrolaterally in adult males.

Two new sympatric species of Stenocercus (Squamata: Iguania) from the inter-Andean valley of the Mantaro River, Peru.

We describe two new sympatric species of Stenocercus from the seasonally dry forest of the inter-Andean valley of the Mantaro River (Huancavelica department) in the Central Andes of central-southern Peru, at elevations of 1,693 to 2,920 m asl. Stenocercus diploauris sp. nov. is similar to S. formosus and S. ochoai, but differs in having a longitudinal neck fold and C-shaped nuchal mite pocket around the oblique fold and posteriorly limited by the antehumeral fold. Stenocercus nigrobarbatus sp. nov. is similar to S. frittsi and S. variabilis, however it can be distinguished by having a postfemoral mite pocket with one or more vertical folds or ridges and by the presence, in adult males, of a continuous black patch covering the infralabials, throat, chest, ventral surfaces of forelimbs, belly (as a midventral line), ventral surfaces of hind limbs, and pelvic region.

Tachiramantis lassoalcalai (Barrio-Amorós, Rojas-Runjaic amp; Barros, 2010) (Anura, Craugastoridae): a new combination revealed by molecular evidence, with a description of its advertisement call.

Pristimantis lassoalcalai Barrio-Amorós, Rojas-Runjaic Barros, 2010 is a poorly known terrarana, endemic to the eastern slope of Sierra de Perijá in Venezuela. Although a close relationship of this species with Tachiramantis has been suspected based on its overall morphological similarity, this relationship had not been tested so far. On the basis of molecular data (two fragments of the 12S and 16S mtDNA genes) obtained from the type series, we reconstruct its evolutionary relationships and establish its phylogenetic position as a member of Tachiramantis. Based on this phylogenetic hypothesis, we transfer Pristimantis lassoalcalai to Tachiramantis as Tachiramantis lassoalcalai comb. nov. In addition, we describe its advertisement call. This is the fourth known species of the genus and the second to which its vocalization is described.

A new species of iguanid lizard, genus Stenocercus (Squamata, Iguania), from the Central Andes in Peru.

We describe a new species of Stenocercus from the montane forest of the right margin of the Marañón river in the northern portion of the Central Andes in northern Peru (Amazonas and La Libertad departments), at elevations ranging from 2300 to 3035 m. Stenocercus omari sp. nov. differs from other Stenocercus species, with the exception of S. amydrorhytus, S. chrysopygus, S. cupreus, S. johaberfellneri, S. latebrosus, S. melanopygus, S. modestus, S. ornatissimus, S. orientalis, and S. stigmosus, by having granular scales on the posterior surfaces of thighs, a conspicuous antehumeral fold and by lacking a vertebral crest. However, Stenocercus omari sp. nov. is easily distinguished from the aforementioned species, except S. orientalis, by the presence of prominently keeled dorsal head scales. The new species differs from S. orientalis by lacking a prominent oblique neck fold and by having a distinct deep postfemoral mite pocket.

A revision and key for the tribe Diaphorolepidini (Serpentes: Dipsadidae) and checklist for the genus Synophis.

The genus Synophis contains a number of enigmatic species, distributed primarily in the Andean highlands of northern South America. Their extreme crypsis and rarity has precluded detailed study of most species. A recent flurry of collection activity resulted in the accession of many new specimens, and the description of 4 new species in 2015, doubling the number of described taxa. However, lingering questions remain regarding the assignment of many new and historical specimens, the morphological limits and geographical ranges of the species, and their phylogenetic relationships. We analyze new and existing morphological and molecular data to produce a new molecular phylogeny and revised morphological descriptions. We validate the previously unavailable tribe name Diaphorolepidini Jenner, Pyron, Arteaga, Echevarría, & Torres-Carvajal tribe nov., describe a 9th species Synophis niceforomariae Pyron, Arteaga, Echevarría, & Torres-Carvajal sp. nov., and offer new Standard Names in English and Spanish for the group: Andean Shadow Snakes and Culebras Andinas de la Sombra, respectively. A variety of features such as vertebrae and hemipenes show an interesting range of variation in the group, which should be evaluated in future studies, to refine species limits and diagnoses further. Cryptic and undiscovered diversity undoubtedly remains, and we hope this summary provides a robust basis for future work.

Description and phylogeny of three new species of Synophis (Colubridae, Dipsadinae) from the tropical Andes in Ecuador and Peru.

The discovery of three new species of Synophis snakes from the eastern slopes of the tropical Andes in Ecuador and Peru is reported. All previous records of Synophis bicolor from eastern Ecuador correspond to Synophis bogerti sp. n., which occurs between 1000-1750 m along a large part of the Amazonian slopes of the Ecuadorian Andes. In contrast, Synophis zamora sp. n. is restricted to southeastern Ecuador, including Cordillera del Cóndor, between 1543-1843 m. Synophis insulomontanus sp. n. is from the eastern slopes of the Andes in central and northern Peru, between 1122-1798 m, and represents the first record of Synophis from this country. All three new species share in common a large lateral spine at the base of the hemipenial body. A molecular phylogenetic tree based on three mitochondrial genes is presented, including samples of Diaphorolepis wagneri. Our tree strongly supports Synophis and Diaphorolepis as sister taxa, as well as monophyly of the three new species described here and Synophis calamitus. Inclusion of Synophis and Diaphorolepis within Dipsadinae as sister to a clade containing Imantodes, Dipsas, Ninia, Hypsiglena and Pseudoleptodeira is also supported.

ResumenSe reporta el descubrimiento de tres especies nuevas de serpientes Synophis de las estribaciones orientales de los Andes tropicales en Ecuador y Perú. Todos los registros previos de Synophis bogerti del oriente ecuatoriano corresponden a Synophis bogertisp. n., la cual ocurre entre 1000­1750 m a lo largo de gran parte de las estribaciones amazónicas de los Andes ecuatorianos. En contraste, Synophis zamorasp. n. se restringe al suroriente de Ecuador, incluyendo la Cordillera del Cóndor, entre 1543­1843 m. Synophis insulomontanussp. n. es de las estribaciones orientales de los Andes del centro y norte del Perú, entre 1122­1798 m, y representa el primer registro de Synophis para este país. Todas las tres especies nuevas comparten en común una espina lateral larga en la base del cuerpo del hemipene. Un árbol molecular filogenético, basado en tres genes mitocondriales es presentado, incluyendo muestras de Diaphorolepis wagneri. Nuestro árbol apoya fuertemente a Synophis y Diaphorolepis como taxa hermanos, así como la monofilia de las tres especies descritas y de Synophis calamitus. La inclusión de Synophis y Diaphorolepis dentro de Dipsadinae, como hermanas a un clado que contiene a Imantodes, Dipsas, Ninia, Hypsiglena y Pseudoleptodeira también es apoyada.