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.

First record of Tmesiphantes Simon, 1892 (Araneae, Theraphosidae) in Peru: a new species and its phylogenetic placement.

The tarantula genus Tmesiphantes Simon, 1892 includes 20 valid species distributed in Argentina and Brazil. These spiders are distinguished from other Theraphosinae genera by the presence of an incrassate femur III, more evident in males, urticating hair types III and IV on the abdominal dorsum, few cuspules on the labium (0 to 30), maxillae with a maximum of 200 cuspules and sternum rounded. From recent examination of material from Peru, we discovered specimens that share all the morphological characters of Tmesiphantes, but did not fit with any known species. In the present study T. intiyaykuy sp. nov. is diagnosed, described, and illustrated. This new species resembles T. caymmii in the circular patch with stiff setae on midventral abdomen but can be distinguished by the shape of the palpal bulb and spermathecae. Also, we performed a phylogenetic analysis using morphological characters to infer the taxonomic placement of the new species. The analysis included 26 terminal species and 36 characters. Representatives of Tmesiphantes formed a monophyletic group and T. intiyaykuy sp. nov. is close related with T. caymmii. A dichotomous identification key and a geographic distribution map were constructed for recognized species of Tmesiphantes.

Phylogenetic relationships of the Boana pulchella Group (Anura: Hylidae).

In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test of its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included>300 specimens of 37 of the 38 species currently included in the group, plus 36 outgroups, exemplars of the diversity of Boana and the other genera of the hylid tribe Cophomantini. The dataset included eight mitochondrial genes (12S, 16S, CytB, COI, ND1, tRNAIle, tRNALeu, and tRNAVal) and five nuclear genes (RHO, TYR, RAG-1, CXCR4, SIAH1). The phylogenetic analyses recover the monophyly of the B. pulchella Group with lower support than previous studies, as a result of the inclusion of the B. claresignata Group, which is recovered as its sister taxon. Within the B. pulchella Group, the inclusion of almost all species of the group had little impact on previous notions of its phylogeny, except for the rejection of the hypothesized B. polytaenia Clade (B. goiana and B. phaeopleura are nested in the clade here called the B. prasina Clade), which is redefined. Phylogenetic support is strong for five major clades, which collectively include all but three of the species sampled: the B. balzani Clade (B. aguilari, B. balzani, B. gladiator, B. melanopleura, B. palaestes), the redefined B. polytaenia Clade (B. botumirim, B. buriti, B. cipoensis, B. jaguariaivensis, B. leptolineata, B. polytaenia, B. stenocephala, and two undescribed species), the B. prasina Clade (B. bischoffi, B. caingua, B. cordobae, B. goiana, B. guentheri, B. marginata, B. phaeopleura, B. prasina, B. pulchella, and one undescribed species), the B. riojana Clade (B. callipleura, B. marianitae, B. riojana), and the B. semiguttata Clade (B. caipora, B. curupi, B. joaquini, B. poaju, B. semiguttata, B. stellae, and two undescribed species). The monophyly of the B. prasina + B. riojana Clades, and that of the B. polytaenia + B. semiguttata Clades are well-supported. The relationships among these two clades, the B. balzani Clade, B. ericae + B. freicanecae, and B. cambui (representing the deepest phylogenetic splits within the B. pulchella Group) are recovered with weak support. We discuss the phenotypic evidence supporting the monophyly of the B. pulchella Group, and the taxonomy of several species, identifying three new synonyms of Boana polytaenia, one new synonym of Boana goiana, and one new synonym of B. riojana.

Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification.

We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23-49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10-15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.

Earless toads sense low frequencies but miss the high notes.

Sensory losses or reductions are frequently attributed to relaxed selection. However, anuran species have lost tympanic middle ears many times, despite anurans' use of acoustic communication and the benefit of middle ears for hearing airborne sound. Here we determine whether pre-existing alternative sensory pathways enable anurans lacking tympanic middle ears (termed earless anurans) to hear airborne sound as well as eared species or to better sense vibrations in the environment. We used auditory brainstem recordings to compare hearing and vibrational sensitivity among 10 species (six eared, four earless) within the Neotropical true toad family (Bufonidae). We found that species lacking middle ears are less sensitive to high-frequency sounds, however, low-frequency hearing and vibrational sensitivity are equivalent between eared and earless species. Furthermore, extratympanic hearing sensitivity varies among earless species, highlighting potential species differences in extratympanic hearing mechanisms. We argue that ancestral bufonids may have sufficient extratympanic hearing and vibrational sensitivity such that earless lineages tolerated the loss of high frequency hearing sensitivity by adopting species-specific behavioural strategies to detect conspecifics, predators and prey.

Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).

The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in the grasslands of the high Andes, with at least five dispersals contributing to montane forest species.

An Endemic and Endangered New Species of the Lizard Liolaemus montanus Group from Southwestern Peru (Iguania: Liolaemidae), with a Key for the Species of the L. reichei Clade.

The southwestern Andes of Peru harbor a hidden taxonomic diversity of reptiles. We describe a new species of Liolaemus Wiegmann (Iguania: Liolaemidae) from xerophytic environments of the southwestern slopes of the Andes of Peru, 2,400-2,900 m asl. The new species, previously considered to be a population of L. insolitus Cei, exhibits unique diagnostic characters of morphology, scalation and color pattern, and molecular evidence that suggest that it belongs in the Liolaemus montanus species group and the L. reichei clade. Moreover, the species is endemic to the eastern slopes of La Caldera batholith in the Department of Arequipa, southern Peru. We also provide information on the conservation status of the species and suggest it be included in the IUCN red list of the threatened species as endangered (EN). A key for the species of the L. reichei clade is provided.

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.

A new species of Bothrops (Serpentes: Viperidae: Crotalinae) from Pampas del Heath, southeastern Peru, with comments on the systematics of the Bothrops neuwiedi species group.

We describe a new species of pitviper of the genus Bothrops from the Peruvian Pampas del Heath, in the Bahuaja-Sonene National Park. Pampas del Heath is an area of seasonally flooded savannas and a northwestern extension of the Gran Chaco Boliviano-Paraguayo. The new species is easily distinguished from its congeners by the exclusive combination of dorsal color pattern of body consisting of small C-shaped blotches, postocular stripe originating posteriorly to the eye, covering posterior supralabials, dorsum of the head with paired markings arranged symmetrically, venter cream heavily speckled with brown, prelacunal scale discrete in contact with second supralabial, three to five prefoveals, subfoveal single usually present, postfoveals absent to two, canthals two, seven intersupraoculars, one or two suboculars, two or three postoculars, seven or eight supralabials, nine to eleven infralabials, 26-27 interrictals, 23-25 middorsal scales, 172 ventrals in the female and 169-173 in males, 45 subcaudals in the female and 50 in males. We performed separate and combined phylogenetic analyses based on morphology and five mitochondrial genes and recovered the new species as a member of the Bothrops neuwiedi species group. All lineages of this clade inhabit the South American dry diagonal. This novel species of pitviper increases the known diversity of the genus Bothrops and adds to the number of described taxa from the unique and scarcely known ecosystem of Pampas del Heath.

A Pan-Amazonian species delimitation: high species diversity within the genus Amazophrynella (Anura: Bufonidae).

Amphibians are probably the most vulnerable group to climate change and climate-change associate diseases. This ongoing biodiversity crisis makes it thus imperative to improve the taxonomy of anurans in biodiverse but understudied areas such as Amazonia. In this study, we applied robust integrative taxonomic methods combining genetic (mitochondrial 16S, 12S and COI genes), morphological and environmental data to delimit species of the genus Amazophrynella (Anura: Bufonidae) sampled from throughout their pan-Amazonian distribution. Our study confirms the hypothesis that the species diversity of the genus is grossly underestimated. Our analyses suggest the existence of eighteen linages of which seven are nominal species, three Deep Conspecific Lineages, one Unconfirmed Candidate Species, three Uncategorized Lineages, and four Confirmed Candidate Species and described herein. We also propose a phylogenetic hypothesis for the genus and discuss its implications for historical biogeography of this Amazonian group.

A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status.

We describe and name a new species of poison-dart frog from the Amazonian slopes of the Andes in Manu Province, Madre de Dios Department, Peru; specifically within the Amarakaeri Communal Reserve and the buffer zone of Manu National Park. Ameerega shihuemoy sp. nov. is supported by a unique combination of characters: black dorsum with cream to light orange dorsolateral lines, blue belly reticulated with black, and the lack of axillary, thigh and calf flash marks. Within Ameerega, it shares the general appearance of A. altamazonica, A. boliviana, A. hahneli, A. ignipedis, A. petersi, A. picta, A. pongoensis, A. pulchripecta, A. simulans, A. smaragdina, and A. yungicola; each possessing a granular black to brown dorsum, a light labial bar, a conspicuous dorsolateral line running from the snout to the groin, and a metallic blue belly and underside of arms and hind limbs. From most of these species it can be distinguished by lacking flash marks on the axillae, thighs, and calves (absent in only A. boliviana and A. smaragdina, most A. petersi, and some A. pongoensis), by having bright cream to orange dorsolateral stripes (white, intense yellow, or green in all other species, with the exception of A. picta), and by its blue belly reticulated with black (bluish white and black in A. boliviana, green and blue with black marbling in A. petersi, and green and blue lacking black marbling in A. smaragdina). Its mating call also shows clear differences to morphologically similar species, with a lower note repetition rate, longer space between calls, and higher fundamental and dominant frequencies. Phylogenetic analyses based on the 16S mitochondrial rRNA fragment also support the distinctiveness of the new species and suggest that A. shihuemoy is most closely related to Ameerega macero, A. altamazonica, A. rubriventris, and two undescribed species (Ameerega sp. from Porto Walter, Acre, Brazil, and Ameerega sp. from Ivochote, Cusco, Peru). Genetically, the new species is most similar to the sympatric A. macero, from which it clearly differs in characteristics of its advertisement call and coloration. The new species is found near rocky streams during the dry season and near temporary water bodies during the rainy season. Tadpoles are found in lentic water along streams, or in shallow, slow-moving streams. Given its small geographic range, we recommend that A. shihuemoy should be considered 'Near threatened' (NT) according to IUCN Red List criteria.

Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru.

A new species of the genus Amazophrynella (Anura, Bufonidae) is described from the departments of Madre de Dios, Cusco and Junin in Peru. An integrative taxonomy approach is used. A morphological diagnosis, morphometrics comparisons, description of the advertisement call, and the phylogenetic relationships of the new species are provided. Amazophrynella javierbustamantei sp. n. differs from other species of Amazophrynella by: intermediate body-size (snout-vent length 14.9 mm in males, n = 26 and 19.6 mm in females, n = 20), tuberculate skin texture of body, greatest hand length of the Amazophrynella spp. (3.6 mm in males, n = 26 and 4.6 mm in females, n = 20), venter coloration yellowish, tiny rounded black points covering the venter, and thirteen molecular autapomorphies in the 16S RNA gene. Its distribution varies from 215 to 708 m a.s.l. This discovery highlights the importance of the remnant forest in preserving the biodiversity in Peru, and increase in seven the species formally described in the genus Amazophrynella.

ResumenDescribimos una nueva especie del género Amazophrynella (Anura, Bufonidae) del Perú de los Departamentos de Madre de Dios, Cusco y Junin de Peru. Utilizamos un método de taxonomía integrativa. Obtuvimos la diagnosis morfológica, comparaciones morfométricas, descripción del canto de reproducción y las relaciones filogenéticas de la nueva especie. Amazophrynella javierbustamanteisp. n. difiere de las otras Amazophrynella spp. por poseer tamaño medio (Hocico-cloaca en machos 16.9 mm, n = 26 y en hembras 19.6 mm, n = 20); textura de la piel tuberculada; tamaños de las manos mayores (3.6 mm en machos, n = 26 y 4.6 mm en hembras, n = 20); coloración ventral amarillento-pálida, pequeños puntos redondos de color negro en el vientre y por trece autopomorfias moleculares en el gen 16S RNA. Su distribución varía desde 215 m hasta 708 m a.s.n.m. Este descubrimiento resalta la importancia de los remanentes de la selva Peruana en términos de conservación, e incrementa en siete las especies formalmente descritas en del género Amazophrynella.

ResumoDescrevemos uma nova espécie do gênero Amazophrynella (Anura, Bufonidae) dos departamentos de Madre de Dios, Cusco e Junin do Peru. Utilizamos um método de taxonomia integrativa. Apresentamos a diagnose morfológica, comparações morfométricas, descrevemos o canto de anúncio e geramos uma hipótese filogenética da nova espécie. Amazophrynella javierbustamanteisp. n. difere das outras Amazophrynella spp. por possuir tamanho médio (Comprimento rostro-cloacal 16.9 mm em machos, n = 26 e 19.6 mm em fêmeas, n=20); textura da pele tuberculada; tamanhos das mãos maiores (3.6 mm em machos, n = 26 e 4.6 mm em fêmeas, n = 20); coloração ventral amarelo-clara, coberta por pequenos pontos redondos pretos e por treze autapomorfias moleculares no gene 16S RNA. Sua distribuição varia entre os 215 m até os 708 m a.n.m. Nossa descoberta aumenta a importância dos remanescentes da floresta Peruana em termos de conservação e incrementa em sete as espécies formalmente descritas no gênero Amazophrynella.

A new species of Andean frog of the genus Bryophryne from southern Peru Anura: Craugastoridae) and its phylogenetic position, with notes on the diversity of the genus.

We describe a new species of terrestrial frog of the genus Bryophryne (Anura: Craugastoridae) from the wet puna and elfin forests of the Amazonian versant of the Andes. The new species seems to be restricted to high altitude environments at elevations between 3506-3651 m in the area now protected by Megantoni National Sanctuary and Manu National Park (Distrito de Echarate, Provincia La Convención, Departamento Cusco, Peru). The new species is characterized by lacking vomerine processes of vomers, by having tympanic annulus and tympanic membrane not evident through the skin, smooth dorsal skin with scattered warts, conspicuous dorsolateral, middorsal, and occipital folds, warty flanks, areolate skin on ventral surfaces of the body, and by lacking finger and toe fringes and basal web on feet. In life, specimens have bright and highly variable dorsal coloration that ranges from olive-green to red with variable combinations of red or orange marks (red or orange in the green form and olive-green in the red form). Molecular phylogenetic analyses of mitochondrial and nuclear DNA place the new species within the genus Bryophryne and as sister group of B. cophites. Bryophryne bustamantei, also sequenced for this study, is found as the sister group of the clade formed by B. cophites and the new species. Bryophryne is found as sister group of Psychrophrynella in maximum likelihood analyses and as the sister group of a large clade of holoadenines in parsimony analyses. The genus Bryophryne now contains nine species, all of them distributed along the Cordillera Oriental of the Peruvian Andes, southeast of the Apurimac River valley.

Una nueva especie de Acanthoscurria (Araneae: Theraphosidae: Theraphosinae) sin órgano estridulador, del sur de Perú / A new species of Acanthoscurria (Araneae: Theraphosidae: Theraphosinae) without stridulatory organ, from southern Peru

Se describe Acanthoscurria sacsayhuaman sp. nov. (Araneae: Theraphosidae) en base a un macho proveniente de Cusco, Perú. Esta especie se diferencia del resto de las especies del género por la ausencia de setas estriduladoras en la cara retrolateral del trocánter del pedipalpo. Además, puede separarse por la forma del bulbo del macho y la apófisis tibial del primer par de patas. Se registra por primera vez el género para Perú.

Acanthoscurria sacsayhuaman sp. nov. (Araneae: Theraphosidae) is described based on a male from Cusco, Peru. The new species is characterized by the absence of stridulatory bristles on retrolateral face of palpal trochanter. Moreover, it can be distinguished by morphology of the male palpal bulb and tibial apophysis of the first pair of legs. The genus is recorded for the first time for Peru.