We document major declines of many species of salamanders at several sites in Central America and Mexico, with emphasis on the San Marcos region of Guatemala, one of the best studied and most diverse salamander communities in the Neotropics. Profound declines of several formerly abundant species, including 2 apparent extinctions, are revealed. Terrestrial microhabitat specialists at mid- to high elevations have declined more than microhabitat generalists. These terrestrial microhabitat specialists have largely disappeared from multiple sites in western Guatemala, including in well-protected areas, suggesting that the phenomenon cannot be explained solely by localized habitat destruction. Major declines in southern Mexican plethodontid salamanders occurred in the late 1970s to early 1980s, concurrent with or preceding many reported frog declines. The species in decline comprise several major evolutionary lineages of tropical salamanders, underscoring that significant portions of the phylogenetic diversity of Neotropical salamanders are at risk. Our results highlight the urgent need to document and understand Neotropical salamander declines as part of the larger effort to conserve global amphibian diversity.

We present a molecular phylogenetic analysis of the hylid tribe Hylini, with the goals of testing the monophyly of the genera Duellmanohyla, Isthmohyla, and Ptychohyla and providing a discussion on the monophyly of Bromeliohyla, Charadrahyla, Ecnomiohyla, Exerodonta, Megastomatohyla, and Sarcohyla. Our results indicate the paraphyly of Ptychohyla, with Bromeliohyla and Duellmanohyla nested within it, and, as in previous analyses, the paraphyly of Duellmanohyla (due to Ptychohyla legleri and P. salvadorensis being nested within it). To resolve this situation, we restrict the contents of Ptychohyla, redelimit those of Duellmanohyla and Bromeliohyla, and erect two new genera, one to include the former Ptychohyla panchoi and P. spinipollex, and the other for the former Ptychohyla acrochorda, P. sanctaecrucis, P. zoque, and tentatively, P. erythromma. Exerodonta as currently defined is not monophyletic, inasmuch as Exerodonta juanitae is nested within Charadrahyla. Consequently, we transfer this species and, tentatively, E. pinorum to Charadrahyla. Also, we discuss some possible taxonomic problems within Exerodonta. Our results indicate that Isthmohyla is polyphyletic, the bromeliad-dwelling Isthmohyla melacaena being the sister taxon of our only exemplar of Bromeliohyla, B. bromeliacia. For this reason, we transfer I. melacaena to Bromeliohyla, rendering Isthmohyla monophyletic. The former Isthmohyla pictipes Group is shown to be paraphyletic due to having the non-monophyletic I. pseudopuma Group within it. Accordingly, we recognize a redelimited I. pseudopuma Group (contents: I. infucata and I. pseudopuma), an I. zeteki Group (contents: I. picadoi and I. zeteki), and a newly defined I. tica Group (contents: I. angustilineata, I. calypsa, I. debilis, I. graceae, I. lancasteri, I. pictipes, I. tica, I. rivularis, and, tentatively, I. insolita and I. xanthosticta). The three groups of Isthmohyla are supported by molecular evidence with jackknife support values > 90%, and two of them by putative morphological synapomorphies. We discuss the recognition of Dryophytes, Hyliola, Rheohyla, and Sarcohyla and whether it is useful to recognize Anotheca, Diaglena, and Triprion as three distinct, monotypic genera. Finally, we discuss a recent taxonomic proposal involving changes in rank and from ranked to unranked names in hylids that overall we consider to have been poorly justified and only superficially discussed.

BackgroundThe 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.ResultsDeep 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.ConclusionsSpecies 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.

Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.

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.