Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae).

The genus Pipa is a species-poor clade of Neotropical frogs and one of the most bizarre-looking due to many highly derived anatomical traits related to their fully aquatic lifestyle. With their African relatives, they form the Pipidae family, which has attracted much attention, especially regarding its anatomy, reproductive biology, paleontology and biogeography. However, the actual diversity and phylogenetic relationships within Pipa remain poorly understood, and thus so do their historical biogeography and the evolution of striking features, such as the absence of teeth and endotrophy in some species. Using short mtDNA sequences across the distribution of the genus, we identified 15 main lineages (Operational Taxonomic Units - OTUs). This more than doubles the number of the currently seven valid nominal species. Several closely related OTUs do not share nuDNA alleles, confirming species divergence. Time-calibrated phylogenies obtained from mitogenomes and from 10 nuclear loci provide highly similar topologies but strikingly distinct node ages for Pipa. High dN/dS ratios and the variation of substitution rates across the trees suggest a strong effect of saturation on fast evolving positions of mtDNA, producing a substantially shorter stem branch of Pipa. Focusing on the nuDNA topology, we inferred an early Neogene Amazonian origin of the diversification of Pipa, with an initial split between the Guiana-Brazilian Shields and Western Amazonia, a pattern observed in many other co-distributed groups. All the western species are edentate, suggesting a single loss in the genus. Each of these groups diversified further out of Amazonia, toward the Atlantic Forest and toward trans-Andean forests, respectively. These events are concomitant with paleogeographic changes and match patterns observed in other co-distributed taxonomic groups. The two Amazonian lineages have probably independently acquired endotrophic larval development.

Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi.

BACKGROUND: Pandi's mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information. METHODS: We conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA. RESULTS: We report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two main activity peaks, in which niche time-partitioning was observed. Across the surveyed area, we found a healthy, stable, highly dense population of B. pandi (>1,300 individuals), with seasonal variability between development stages. DISCUSSION: Given the high habitat specificity of B. pandi, the species is highly vulnerable to local changes. Thus, we recommend that B. pandi be retained as Endangered (EN) on the IUCN Red List, based on the IUCN Criterion B, given its restricted extent of occurrence (ca. 2,500 km2) and the ongoing threats from agriculture, cattle ranching, logging, and urban development, which continue to reduce its suitable habitat.

A new Terrarana frog of genus Pristimantis from an unexplored cloud forest from the eastern Andes, Colombia.

A new species of Pristimantis (Craugastoridae, subgenus Pristimantis) is described from a relict and unexplored cloud forest in the western slope from Cordillera Oriental of the Colombian Andes. The specific name was chosen by consensus expert scientists and local people. Pristimantis chamezensis sp. nov. is easily distinguished from congeneric species by having a gray iris with black reticulations in life, subconical tubercles on the upper eyelid, the chin edged with irregular, dark-brown blotches, and conical heel tubercles. The phylogenetic analyses suggest that the origin and radiation of its clade may have occurred in the highlands. With the description of P. chamezensis sp. nov., we identify 14 species distributed throughout the eastern slope of the Andes that are associated with the Orinoco Basin.

Thermal tolerance and the importance of microhabitats for Andean frogs in the context of land use and climate change.

Global warming is having impacts across the Tree of Life. Understanding species' physiological sensitivity to temperature change and how they relate to local temperature variation in their habitats is crucial to determining vulnerability to global warming. We ask how species' vulnerability varies across habitats and elevations, and how climatically buffered microhabitats can contribute to reduce their vulnerability. We measured thermal sensitivity (critical thermal maximum-CTmax ) of 14 species of Pristimantis frogs inhabiting young and old secondary, and primary forests in the Colombian Andes. Exposure to temperature stress was measured by recording temperature in the understorey and across five microhabitats. We determined frogs' current vulnerability across habitats, elevations and microhabitats accounting for phylogeny and then ask how vulnerability varies under four warming scenarios: +1.5, +2, +3 and +5°C. We found that CTmax was constant across species regardless of habitat and elevation. However, species in young secondary forests are expected to become more vulnerable because of increased exposure to higher temperatures. Microhabitat variation could enable species to persist within their thermal temperature range as long as regional temperatures do not surpass +2°C. The effectiveness of microhabitat buffering decreases with a 2-3°C increase, and is almost null under a 5°C temperature increase. Microhabitats will provide thermal protection to Andean frog communities from climate change by enabling tracking of suitable climates through short distance movement. Conservation strategies, such as managing landscapes by preserving primary forests and allowing regrowth and reconnection of secondary forest would offer thermally buffered microhabitats and aid in the survival of this group.

Para determinar la vulnerabilidad de las especies al calentamiento global es indispensable considerar la tolerancia fisiológica de las especies al cambio de temperatura y las condiciones ambientales a las que están expuestas. En este estudio exploramos la vulnerabilidad de especies a través de diferentes hábitats y altitudes y examinamos si ciertos microhábitats contribuyen a reducir la vulnerabilidad al calentamiento global. Medimos la tolerancia térmica (CTmax ) de catorce especies de ranas Pristimantis en bosques secundarios jóvenes y viejos, y bosques primarios en los Andes tropicales. Registramos la temperatura a la que estas especies están expuestas en el sotobosque así como dentro de cinco microhábitats. Usando CTmax y las temperaturas a las que están expuestas, determinamos la vulnerabilidad de las especies en diferentes hábitats, elevaciones y microhábitats. También preguntamos cómo cambiará esta vulnerabilidad si la temperatura incrementa: 1.5°C, 2°C, 3°C y 5°C. CTmax fue constante en todos los hábitats y elevaciones. Las especies de bosques secundarios jóvenes son más vulnerables pues están expuestas a temperaturas más altas. Al utilizar microhábitats, las especies estarán protegidas si el aumento de temperatura no supera los + 2°C. Todos los microhábitats seguirán proporcionando refugio térmico si la temperatura aumenta 1.5°C, pero esta protección térmica disminuirá si la temperatura aumenta 2-3°C y será casi nula con un aumento de temperatura de 5°C. Los microhábitats proporcionarán protección térmica a la comunidad de ranas de los Andes contra el cambio climático. Estrategias de conservación, como la regeneración natural y la reconexión de bosques secundarios y la preservación de bosques primarios, ayudaría a la supervivencia de las ranas al tener microhábitats que ofrecen refugio térmico.

Description of a new diminutive Hyloxalus (Anura: Dendrobatidae: Hyloxalinae) from the Magdalena Valley of Colombia.

Using different sources of evidence (i.e., integrative taxonomy), we describe a new species of Hyloxalus, Hyloxalus arliensis sp. nov. The new species occurs in the middle Magdalena River valley on slopes between the Cordillera Central and Cordillera Oriental of the Andes of Colombia. Previously, the new species was referred to as Hyloxalus "Ibagué" but was not formally described. Phylogenetic re-analyses of 2440 base pairs (bp) of mitochondrial DNA (mtDNA), revealed the species to be a sister taxon of H. lehmanni, within a monophyletic clade also comprising H. delatorreae lineage 1, H. pulchellus and H. vertebralis. The adult males of H. arliensis sp. nov. have a pale arm gland, which differentiates it from all other species of the genus, except for H. saltarius. The new species also differs from other species of Hyloxalus by its smaller size, disc on Finger III not expanded, toes unwebbed, dorsolateral stripe absent, oblique lateral stripe present, white spots on ventrolateral flanks in life and cloacal tubercles absent. The advertisement call consists of long trains of a single note repeated at a rate of 89-132 notes/min with a dominant frequency ranging from 4808-6387 Hz. The new species is a tiny frog that inhabits the sheltered areas around streams in sub-Andean forests. Aspects of its natural history are described.

A new species of Caecilia (Gymnophiona, Caeciliidae) from the Magdalena valley region of Colombia.

A new species of the genus Caecilia (Caeciliidae) from the western foothills of the Serranía de los Yariguíes in Colombia is described. Caecilia pulchraserrana sp. nov. is similar to C. degenerata and C. corpulenta but differs from these species in having fewer primary annular grooves and a shorter body length. With this new species, the currently recognized species in the genus are increased to 35. Mitochondrial DNA sequences, including newly sequenced terminals representing two additional, previously unanalyzed species, corroborate the phylogenetic position of the new species within Caecilia and the monophyly of the genus. This analysis also included newly sequenced terminals of Epicrionops aff. parkeri (Rhinatrematidae) and trans-Andean Microcaecilia nicefori (Siphonopidae). Evidence was found for the non-monophyly of the family Siphonopidae and the siphonopid genera Microcaecilia and Siphonops. The implications of these results for caecilian systematics are discussed and the status of the trans-Andean populations of Caecilia degenerata is commented upon.

The advertisement call of Allobates niputidea (Anura: Aromobatidae).

In anurans, acoustic signal traits are useful for understanding patterns of evolutionary processes, behavioral interactions, and providing diagnostic characters for inferring phylogenetic relationships and delimiting species (Cocroft Ryan 1995). The advertisement call, which is the vocalization emitted to attract females or segregate conspecific males, is the most conspicuous and studied acoustic signal (Toledo et. al. 2014). However, it remains unknown for many anuran species (Köhler et al. 2017; Guerra et al. 2018).

A morphological database for Colombian anuran species from conservation-priority ecosystems.

Species traits provide a strong link between an organism's fitness and processes at community and ecosystem levels. However, such data remain scarce for amphibians in the Neotropics. Colombia is the country with the highest number of threatened amphibians and the second greatest number of amphibian species worldwide. We present a data set containing eight morphological traits for 4,623 museum specimens of the seven largest collections in the country corresponding to 293 species of 14 families. The number of measured specimens per species ranged from 1 to 118 individuals with a median of 8 individuals per species. Overall, this database gathered morphological information for 37.6% of Colombian anuran diversity. Species measured were mainly distributed in the high Andean forest, the páramo, and wetland ecosystems, and was part of a national initiative led by the Instituto Alexander von Humboldt. The morphological traits were selected on the basis of their role in species' responses to environmental variability and their contributions to ecosystem processes. These traits were related to habitat use, (forearm length, tibia length, femur length, foot length, and foot webbing), predation and food chains (head width and mouth width), and nutrient recycling (snout-vent length). We expect this data set will be used in studies on functional diversity in amphibians and the development of conservation planning for these taxa. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin Cochran, 1963 (Anura: Brachycephaloidea).

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered Niceforonia nana nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus Hypodactylus in the synonymy of Niceforonia to resolve the paraphyly and place Niceforonia in the subfamily Hypodactylinae. Based on our revised concept of the genus Niceforonia we conducted preliminary morphological comparisons using specimens and literature descriptions. Finally, Nicefornia nana is quite divergent from other species of Niceforonia (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted.

First record of Saprolegnia sp. in an amphibian population in Colombia / Primer registro de Saprolegnia sp. en una población de anfibios en Colombia / Primeiro registro de Saprolegnia sp. numa população de anfíbios na Colômbia

Primer registro de Saprolegnia sp. en una población de anfibios en Colombia. Objetivo. La mayoría de investigaciones en relación al declive de anfibios se han enfocado en la detección del hongo patógeno Batrachochytrium dendrobatidis. Este es el principal patógeno detectado en el mundo. Sin embargo, otras investigaciones han demostrado la presencia de Saprolegnia ferax como un vector mortal en anfibios de Norteamérica. Este trabajo establece una posible transmisión entre especies causada por la presencia de la trucha arcoíris, sugiriendo que el declive de anfibios no solo se atribuye a la presencia de un solo patógeno, sino que puede ser causado por otros patógenos y factores. Materiales y métodos. El estudio revela la presencia de Saprolegnia sp. en la rana de los Andes Atelopus mittermeieri mediante la técnica de impronta con tinción de azul de lactofenol, que permitió la observación de las estructuras típicas de este hongo. Resultados. La importancia de este descubrimiento es la presencia de dos hongos patógenos, B. dendrobatidis y Saprolegnia, afectando simultáneamente una población de anfibios. Este hallazgo enfoca la atención en la eventual presencia de otros microorganismos que podrían estar involucrados individualmente o colectivamente en el declive de especies de anfibios. Conclusiones. Este registro sugiere una posible transmisión entre la trucha arcoiris (Oncorhynchus mykiss), una especie introducida en las montañas de Colombia, que comparte los mismos habitats con diferentes especies de anfibios en el Santuario de Flora y Fauna de Guanentá en el alto río Fonce en la parte media de la Cordillera Oriental de Colombia...

Objective: Most research related to the decline of amphibians has been focused on the detection of the pathogenic fungus Batrachochytrium dendrobatidis. This fungus is the main pathogen detected around the world. However, research has shown the presence of another fungus, Saprolegnia ferax, as a cause of mortality in amphibians in North America. Our study suggests a possible interspecific transmission caused by the presence of rainbow trout; thus, amphibian declines may not be attributable only to the presence of a single pathogen, but to other organisms and factors. Materials and methods. Our study revealed the presence of Saprolegnia sp. in the Andean frog Atelopus mittermeieri using the imprinting technique with lactophenol blue staining, which allowed the typical structures of this fungus to be observed. Results. The importance of this discovery is the presence of two pathogenic fungi, B. dendrobatidis and Saprolegnia, which affecting simultaneously a population of amphibians. This finding brings attention to the eventual presence of other microorganisms that might be involved individually or collectively in the decline of amphibian species. Conclusions. This record suggests a possible transmission between rainbow trout (Oncorhynchus mykiss), an introduced species in the highlands of Colombia, which shares the same habitats with different species of amphibians in the Sanctuary of Flora and Fauna Guanentá in the upper river Fonce in the mid Cordillera Oriental of Colombia...

Primeiro registro de Saprolegnia sp. numa população de anfíbios na Colômbia. Objetivo. A maioria das pesquisas sobre o declínio dos anfíbios tem-se centrado na detecção do fungo patogênico Batrachochytrium dendrobatidis. Este é o principal patógeno encontrado no mundo. No entanto, outros estudos têm demonstrado a presença de Saprolegnia ferax, como vetor mortal de anfíbios de América do Norte. Esta pesquisa estabelece uma possível transmissão entre espécies causada pela presença de truta arco-íris, afirmando que o declínio de anfíbios não só é atribuído à presença de um único patógeno, pudendo ser causado por outros patógenos e fatores. Materiais e métodos. A pesquisa indica a presença de Saprolegnia sp. em rãs dos Andes, Atelopus mittermeieri, pela técnica de impressão com lactofenol-azul-de-algodão, onde observou-se as estruturas típicas deste fungo. Resultados. A importância desta descoberta é a presença de dois fungos (B. dendrobatidis e Saprolegnia) que simultaneamente afetam uma população de anfíbios, concentrando a atenção na presença de outros microorganismos que podem estar envolvidos individualmente ou coletivamente no declínio das espécies de anfíbios. Conclusões. A truta arco-íris (Oncorhynchus mykiss), uma espécie introduzida nas montanhas da Colômbia, que compartilha o mesmo nicho ecológico com Atelopus mittermeieri, no Santuário de Flora e Fauna de Guanentá no Alto Rio Fonce no centro da Cordilheira Oriental da Colômbia, tem sido sugerida por esta pesquisa como o agente transmissor dos fungos as diferentes espécies de anfíbios...