Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae).

Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of Bothrops lojanus, which may lead to the paraphyly of either Bothrops or Bothrocophias. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.

Four new species of polychromatic spiny-tailed iguanian lizards, genus Stenocercus (Iguania: Tropiduridae), from Peru.

The tropical Andes Mountains exhibit high levels of endemism and spatial turnover in the distribution of species. The lizard genus Stenocercus Dumril Bibron, 1837, contains 76 species and most of them occur in the tropical Andes, reaching elevations up to 4,000 m. We describe four new species of Stenocercus based on the examination of newly collected material from the Amazonian slopes of the Peruvian Andes. Stenocercus asenlignus sp. nov. inhabits the premontane forest of northern and central Peru, departments of Amazonas, San Martn and Hunuco, at elevations between 1,500 and 2,036 m, in the basins of the Mayo, Huayabamba, and Huallaga rivers. Stenocercus leybachi sp. nov. inhabits the premontane forest of the upper Huallaga River, Hunuco department in central Peru, at elevations between 824 and 1,270 m. Stenocercus qalaywasi sp. nov. was collected in a small village at the headwaters of the Mantaro River, Junn department in central Peru, at an elevation of 2,587 m. Finally, S. nigrocaudatus sp. nov. inhabits the montane forest from extreme northern Peru, Cajamarca department, at elevations of 1,700 and 1,892 m. These species are characterized by having granular scales on the posterior surface of the thighs, relatively short tail, caudals spinose, two caudal whorls per autotomic segment, and the ability to change coloration from green to brown or gray; they differ from other species of Stenocercus in scutellation features and color pattern.

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.

Applied science facilitates the large-scale expansion of protected areas in an Amazonian hot spot.

Meeting international commitments to protect 17% of terrestrial ecosystems worldwide will require >3 million square kilometers of new protected areas and strategies to create those areas in a way that respects local communities and land use. In 2000-2016, biological and social scientists worked to increase the protected proportion of Peru's largest department via 14 interdisciplinary inventories covering >9 million hectares of this megadiverse corner of the Amazon basin. In each landscape, the strategy was the same: convene diverse partners, identify biological and sociocultural assets, document residents' use of natural resources, and tailor the findings to the needs of decision-makers. Nine of the 14 landscapes have since been protected (5.7 million hectares of new protected areas), contributing to a quadrupling of conservation coverage in Loreto (from 6 to 23%). We outline the methods and enabling conditions most crucial for successfully applying similar campaigns elsewhere on Earth.

Ampliación de la distribución geográfica y estado de conservación de Ctenoblepharys adspersa (Tschudi, 1845)

Ampliamos la distribución geográfica de Ctenoblepharys adspersa (Liolaemidae), una especie de saurio endémico y amenazado del desierto peruano. Nuestro nuevo registro extiende la distribucion de esta especie en 60 km (línea recta) de la localidad más oriental previamente conocida, la Reserva Nacional de Paracas. Registramos dos tipos de hábitat nuevos para C. adspersa al interior de las estribaciones andinas e identificamos las plantas nativas asociadas a sus hábitats. Además, revisamos el estado de conservación de esta especie y los desafíos que implican su conservación, resaltando que la mayoría de las poblaciones son vulnerables a los impactos en su hábitat producto del desarrollo de infraestructura urbana y/o agrícola.

We extend the geographical distribution of Ctenoblepharys adspersa (Liolaemidae) an endemic and threatened lizard species from the Peruvian desert. Our new record extends the known species distribution ca. 60 km (straight line) east-southeastern from the eastemost record at Paracas National Reserve. We recorded two new type of habitat for C. adspersa that reach to the Pacific foothills and identified the native plants associated to its habitats. Moreover, we review the conservation status and the challenges that facing it, highlighted that most of its populations are vulnerable to the impacts on their habitat caused by the development of urban and agricultural infrastructure.

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.

A new species of pitviper of the genus Bothrops (Serpentes: Viperidae: Crotalinae) from the Central Andes of South America.

We describe a new species of montane pitviper of the genus Bothrops from the Cordillera Oriental of the Central Andes, distributed from southern Peru to central Bolivia. The new species can be distinguished from its congeners by the characteristic combination of a dorsal body color pattern consisting of triangular or subtriangular dark brown dorsal blotches, paired dark brown parallel occipital stripes, a conspicuous dark brown postocular stripe, the presence of canthorostrals in some specimens, prelacunal fused or partially fused with second supralabial, one scale usually separating internasals, rostral trapezoidal, two canthals oval to rounded, similar size or slightly larger than internasals, three or four medial intercanthals, eight to twelve intersupraoculars, intercanthals and intersupraoculars keeled and frequently slightly keeled, supraoculars oval, one to three suboculars, two to three postoculars, loreal subtriangular, two to six prefoveals, subfoveals absent, two or none postfoveals, one or two scales between suboculars and fourth supralabial, seven or eight supralabials, nine or eleven infralabials, 23-25 middorsal scales, 189-195 ventrals in females and 182-190 in males, 48-58 subcaudals in females and 54-63 in males, exceptionally undivided. The new species is apparently restricted to areas within Andean montane forests that are less humid and devoid of large trees.

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.

A new species of Phrynopus from the northeastern Andes of Peru, its phylogenetic position, and notes on the relationships of Holoadeninae (Anura: Craugastoridae).

We report the discovery of a geographically disjunct and morphologically distinctive species of direct-developing frog of the genus Phrynopus (Phrynopus mariellaleo sp. nov.) that changes considerably our understanding of the distribution of species in this Andean genus. The type locality lies on a subcordillera (Cerro de Campanario area) of the extreme northeastern portion of the Cordillera Central of Peru, on the headwaters of the Mayo River, Amazonas department, at 2575 m asl (6°6'42.9''S, 77°26'24''W). This area is situated 170 km to the NE from the northernmost record of Phrynopus known so far. Molecular phylogenetic analyses of a supermatrix (13269 aligned positions of gene sequences of four mitochondrial and ten nuclear genes) of 105 terminals (representing 93 named and 9 unnamed species of Holoadeninae) recover this new species as the sister to Phrynopus auriculatus, a species occurring more than 500 km south of the type locality of the new species. Both Phrynopus auriculatus and the new species occur at moderate elevations on the easternmost stretches of the Andean subcordilleras; their sister relationship point to a potentially broader distribution of species of Phrynopus along the poorly sampled intervening areas of the eastern hills of the Andes. The new species has a conspicuous and visibly large tympanic membrane (a trait rare in the clade), outlined by a marked bold black supratympanic fold and a black facial mask, and exhibits conspicuous dorsolateral, scapular, and middorsal Y-shaped folds. Specimens were found on the forest floor-a rocky substrate covered by a thick layer of leaf litter, moss and roots-of a primary humid montane forest (Yungas ecoregion) with scattered patches of bamboo (Chusquea spp.). Our phylogenetic analyses corroborate the monophyly of all Holoadeninae genera, including Euparkerella and Psychrophrynella, genera for which tests of monophyly were pending, and corroborates Hypodactylus nigrovittatus as part of Hypodactylus and sister to a clade that includes H. brunneus, H. elassodiscus and H. peraccai.

Systematics of South American snail-eating snakes (Serpentes, Dipsadini), with the description of five new species from Ecuador and Peru.

A molecular phylogeny of the Neotropical snail-eating snakes (tribe Dipsadini) is presented including 43 (24 for the first time) of the 77 species, sampled for both nuclear and mitochondrial genes. Morphological and phylogenetic support was found for four new species of Dipsas and one of Sibon, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. Sibynomorphus is designated as a junior subjective synonym of Dipsas. Dipsas latifrontalis and D. palmeri are resurrected from the synonymy of D. peruana. Dipsas latifasciata is transferred from the synonymy of D. peruana to the synonymy of D. palmeri. A new name, D. jamespetersi, is erected for the taxon currently known as Sibynomorphus petersi. Re-descriptions of D. latifrontalis and D. peruana are presented, as well as the first photographic voucher of an adult specimen of D. latifrontalis, along with photographs of all known Ecuadorian Dipsadini species. The first country record of D. variegata in Ecuador is provided and D. oligozonata removed from the list of Peruvian herpetofauna. With these changes, the number of Dipsadini reported in Ecuador increases to 22, 18 species of Dipsas and four of Sibon.

Annotated checklist and key to the species of amphibians and reptiles inhabiting the northern Peruvian dry forest along the Andean valley of the Marañón River and its tributaries.

A checklist of the amphibians and reptiles of 35 localities situated in the northern Peruvian dry forest valley of the Marañón River and its tributaries, containing 14 species of amphibians and 54 species of reptiles, is provided from data collected between July 2005 and April 2014 during several herpetological surveys and from the literature. Detailed accounts are given for each collected species containing morphometric and scalation data, information on natural history, comments regarding their distribution, the conservation status and key literature. Eleven new species were discovered and described during the survey period. At least five additional taxa might also represent new species but more field work and data collection are necessary to determine their status. For two snake species we provide the first country record and for 23 further species new departamental records are provided.

Species limits within the widespread Amazonian treefrog Dendropsophus parviceps with descriptions of two new species (Anura, Hylidae).

The genus Dendropsophus is one of the most speciose among Neotropical anurans and its number of described species is increasing. Herein, molecular, morphological, and bioacoustic evidence are combined to assess species limits within D. parviceps, a widely distributed species in the Amazon Basin. Phylogenetic relationships were assessed using 3040 bp sequences of mitochondrial DNA, genes 12S, ND1, and CO1. The phylogeny shows three well-supported clades. Bioacoustic and morphological divergence is congruent with those clades demonstrating that Dendropsophus parviceps is a species complex. Dendropsophus parvicepssensu stricto occurs in the Amazon basin of Ecuador, northern Peru, southern Colombia and northwestern Brazil. It is sister to two previously undescribed species, D. kubrickisp. n. from central Peru and D. kamagarinisp. n. from southern Peru, northeastern Bolivia, and northwestern Brazil. Genetic distances (uncorrected p, gene 12S) between D. parviceps and the new species is 3 to 4%. Dendropsophus kamagarinisp. n. can be distinguished from D. parviceps by having a prominent conical tubercle on the distal edge of the upper eyelid (tubercle absent in D. parviceps). Dendropsophus kubrickisp. n. differs from D. parviceps by having scattered low tubercles on the upper eyelids (smooth in D. parviceps). Dendropsophus parviceps and both new species differ from all their congeners by their small size (adult maximum SVL = 28.39 mm in females, 22.73 mm in males) and by having a bright orange blotch on the hidden areas of the shanks and under arms. The advertisement call of the two new species has lower dominant frequency relative to D. parviceps. Probable speciation modes are discussed. Available evidence indicates that ecological speciation along an elevation gradient is unlikely in this species complex.

A new species of arboreal microteiid lizard of the genus Euspondylus (Gymnophtalmidae: Cercosaurinae) from the Andean slopes of central Peru with comments on Peruvian Euspondylus.

We describe a new species of arboreal gymnophtalmid lizard from the eastern Andean slopes in central Peru. Euspondylus excelsum sp. nov. is assigned tentatively to this genus for the presence of a transparent and divided lower palpebral disc, a pair of prefrontals, striated, subimbricated and homogeneous dorsal scales, lateral scales reduced in proximity to ventrals, and a discontinuous series of femoral pores in males and females. We include a revision of the type material of E. maculatus and clarify morphological differences with the new species. Finally, we discuss the taxonomic status of Peruvian species of Euspondylus.

Phylogeny and diversity of neotropical monkey lizards (Iguanidae: Polychrus Cuvier, 1817).

Neotropical monkey lizards (Polychrus) are arboreal lizards with compressed bodies, partially fused eyelids and strikingly long, whip-like tails. The eight currently recognized species occur in the lowlands of South and Central America. Based on the largest taxon and character sampling to date, we analyze three mitochondrial and one nuclear gene using Bayesian methods to (1) infer the phylogeny of Polychrus under both concatenated-tree and species-tree methods; (2) identify lineages that could represent putative undescribed species; and (3) estimate divergence times. Our species tree places P. acutirostris as the sister taxon to all other species of Polychrus. While the phylogenetic position of P. gutturosus and P. peruvianus is poorly resolved, P. marmoratus and P. femoralis are strongly supported as sister to P. liogaster and P. jacquelinae, respectively. Recognition of P. auduboni and P. marmoratus sensu stricto as distinct species indicates that the populations of "P. marmoratus" from the Amazon and the Atlantic coast in Brazil represent separate species. Similarly, populations of P. femoralis from the Tumbes region might belong to a cryptic undescribed species. Relative divergence times and published age estimates suggest that the orogeny of the Andes did not play a significant role in the early evolution of Polychrus.

Correction: Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species.

[This corrects the article DOI: 10.1371/journal.pone.0171785.].

Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species.

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relationships and species boundaries of two Amazonian species of the Dendropsophus leucophyllatus species group: D. leucophyllatus and D. triangulum. Our results uncovered the existence of five confirmed and four unconfirmed candidate species. Among the confirmed candidate species, three have available names: Dendropsophus leucophyllatus, Dendropsophus triangulum, and Dendropsophus reticulatus, this last being removed from the synonymy of D. triangulum. A neotype of D. leucophyllatus is designated. We describe the remaining two confirmed candidate species, one from Bolivia and another from Peru. All confirmed candidate species are morphologically distinct and have much smaller geographic ranges than those previously reported for D. leucophyllatus and D. triangulum sensu lato. Dendropsophus leucophyllatus sensu stricto occurs in the Guianan region. Dendropsophus reticulatus comb. nov. corresponds to populations in the Amazon basin of Brazil, Ecuador, and Peru previously referred to as D. triangulum. Dendropsophus triangulum sensu stricto is the most widely distributed species; it occurs in Amazonian Ecuador, Peru and Brazil, reaching the state of Pará. We provide accounts for all described species including an assessment of their conservation status.

A large and unusually colored new snake species of the genus Tantilla (Squamata; Colubridae) from the Peruvian Andes.

A new colubrid species of the genus Tantilla from the dry forest of the northern Peruvian Andes is described on the basis of two specimens, which exhibit a conspicuous sexual dimorphism. Tantilla tjiasmantoi sp. nov. represents the third species of the genus in Peru. The new species is easily distinguished from its congeners by the combination of scalation characteristics and the unusual transversely-banded color pattern on the dorsum. A detailed description of the skull morphology of the new species is given based on micro-computed tomography images. The habitat of this new species is gravely threatened due to human interventions. Conservation efforts are urgently needed in the inter-Andean valley of the Maranon River.

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.

Systematics of Ecnomiohyla tuberculosa with the description of a new species and comments on the taxonomy of Trachycephalus typhonius (Anura, Hylidae).

Ecnomiohyla tuberculosa is an Amazonian hylid of uncertain phylogenetic position. Herein DNA sequences of mitochondrial and nuclear genes are used to determine its phylogenetic relationships. New sequences and external morphology of Trachycephalus typhonius are also analyzed to assess the status of Ecuadorian and Peruvian populations. The phylogeny shows unequivocally that Ecnomiohyla tuberculosa is nested within the genus Tepuihyla, tribe Lophiohylini. This position was unexpected because the remaining species of Ecnomiohyla belong to the tribe Hylini. To solve the paraphyly of the genus Ecnomiohyla, Ecnomiohyla tuberculosa is transferred to the genus Tepuihyla. Comparisons of DNA sequences, external morphology, and advertisement calls between populations of Ecnomiohyla tuberculosa from Ecuador and Peru indicate that the Peruvian population represents an undescribed species. The new species is described and a species account is provided for Ecnomiohyla tuberculosa. Trachycephalus typhonius is paraphyletic relative to Trachycephalus cunauaru, Trachycephalus hadroceps, and Trachycephalus resinifictrix. The phylogenetic position of populations from western Ecuador indicates that they represent a species separate from Trachycephalus typhoniussensu stricto. We resurrect the name Hyla quadrangulum (Trachycephalus quadrangulumcomb. n.) for those populations. Amazonian populations of "Trachycephalus typhonius" from Ecuador and Peru are genetically and morphologically distinct from Trachycephalus typhoniussensu stricto and are conspecific with the holotype of Hyla macrotis. Therefore, we also resurrect Hyla macrotis, a decision that results in Trachycephalus macrotiscomb. n.

Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru.

An integrative taxonomic approach based on morphology, molecular analyses, and climatic niche modeling was used to uncover cryptic diversity in the phyllodactylid gecko species Phyllodactylus reissii. At least three distinct species could be identified among the examined specimens from southern Ecuador and northern Peru. Phyllodactylus magister, described by Noble (1924) from arid Andean valleys of the Chinchipe and Marañón rivers in the Peruvian Department of Cajamarca and synonymized with P. reissii by Dixon & Huey (1970) is elevated from synonymy and a detailed redescription is provided. A new species of the genus Phyllodactylus from the Andean dry forest of the southern Marañón valley is identified and described herein. Phyllodactylus pachamama sp. nov. is differentiated from other South American congeners on the basis of mtDNA sequence divergence, morphological characters, and differences in the realized climatic niche. At least in Peru, P. reissii seems to primarily inhabit the northern coastal region west of the Andes, while the inter-Andean area along the Río Marañón and its tributaries seems to be inhabited mostly by other species of the genus, which are endemic to this area. The Andean valleys are underestimated in terms of biodiversity and lack thorough investigation and conservation actions.