The Neotropical bolitoglossine salamanders represent an impressive adaptive radiation, comprising roughly 40% of global salamander species diversity. Despite decades of morphological studies and molecular work, a robust multilocus phylogenetic hypothesis based on DNA sequence data is lacking for the group. We estimated species trees based on multilocus nuclear and mitochondrial data for all major lineages within the bolitoglossines, and used our new phylogenetic hypothesis to test traditional biogeographical scenarios and hypotheses of morphological evolution in the group. In contrast to previous phylogenies, our results place all Central American endemic genera in a single clade and suggest that Central America played a critical role in the early biogeographical history of the group. The large, predominantly Mexican genus Pseudoeurycea is paraphyletic, and analyses of the nuclear data place two lineages of Pseudoeurycea as the sister group of Bolitoglossa. Our phylogeny reveals extensive homoplasy in morphological characters, which may be the result of truncation or alteration of a shared developmental trajectory. We used our phylogenetic results to revise the taxonomy of the genus Pseudoeurycea.

We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species, T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. Adult Thorius pinicola sp. nov., T. longicaudus sp. nov., and T. tlaxiacus sp. nov. are larger than T. minutissimus and possess elliptical rather than oval nostrils; T. pinicola and T. longicaudus also have longer tails. All three new species occur west of the range of T. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other named Thorius in Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribe T. minutissimus and a related species, T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiated Thorius that cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature. Thorius may be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.

The cloud forests of Mesoamerica are notable for their high endemism, and plethodontid salamanders provide a striking example of divergence and microendemism across cloud forest blocks at a regional level. Salamanders that make use of arboreal bromeliad microhabitats in the cloud forest appear to be especially prone to divergence driven by natural habitat fragmentation, and are expected to show high endemism at small spatial scales. We use a multilocus dataset to investigate the biogeographic history and relationships among species of a small genus of salamander, Cryptotriton, restricted to the cloud forests of Nuclear Central America. We use a morphological data set along with a coalescent species delimitation method to reveal the presence of at least one undescribed species from an isolated cloud forest in eastern Guatemala. Biogeographic analyses show that Cryptotriton has a different biogeographic history than another clade of cloud forest-restricted salamanders in the same region, perhaps indicating that each genus restricted the spatial expansion and diversification of the other through preemptive occupancy. Our results suggest that isolation across relatively short geographic distances has led to range fragmentation and deep divergence between species. Exploration of remaining patches of cloud forest likely will continue to reveal undetected diversity.

Abstract Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton) using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. Results Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. Conclusions Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B. nympha, in contrast to the other widespread species in the subgenus, may be due to historical forest contraction and more recent range expansion in the region. Phylogeographic data provide substantial insight into the evolutionary history of these morphologically similar species of salamanders, and contribute to our understanding of factors that have generated the high biodiversity of Mesoamerica.

Chiropterotriton is a relatively small genus that comprises 15 species with great morphological and ecological diversity. In previous studies, molecular data provided evidence for a considerable number of species that remain undescribed. In this study, we describe one new species, Chiropterotriton chico sp. nov. based on molecular and morphological characters. We present mtDNA phylogenetic analyses using Bayesian inference and maximum likelihood that include all described and several undescribed species. Morphometric data from eight recognized species provide evidence for the distinctiveness of the new taxon. Description of this new species adds to the already high salamander diversity of the state of Hidalgo, which is an important area for the diversification of the genus.

We describe a new species of Bolitoglossa (Nanotriton) from the Sierra de Juárez and Sierra Mixe of Oaxaca, Mexico. Bolitoglossa chinantecasp. n. is distinguished from the three other species in the subgenus Nanotriton by its more robust body, by having substantial numbers of maxillary teeth and differences in relative head width, foot width, and limb length. The new species occurs in sympatry with Bolitoglossa (Nanotriton) rufescens at the type locality. The description of another species of salamander from the Sierra de Juárez is noteworthy, given the already high plethodontid salamander species richness of the region.

The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico's amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has 18 described species including terrestrial, arboreal and cave-dwelling species. In previous molecular studies, the presence of multiple undescribed species was evident. We present a phylogenetic hypothesis based on mitochondrial data, which includes all described species and six undescribed taxa. Based on the morphological analyses and, when available, combined with molecular data, we describe five new species of the genus; Chiropterotriton casasi sp. nov., C. ceronorum sp. nov., C. melipona sp. nov., C. perotensis sp. nov. and C. totonacus sp. nov. In addition, we redescribe two others: Chiropterotriton chiropterus and C. orculus, and provide a comparable account of one additional sympatric congener. This increases the number of species in the genus to 23, which represent a considerable component of Mexican plethodontid richness.

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history-and predict the future impacts-of this devastating pathogen.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.