Ongoing declines for the world's amphibians in the face of emerging threats.

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

There is no evidence that Podoctidae carry eggs of their own species: Reply to Machado and Wolff (2017).

In our recent publication (Sharma et al., 2017), we tested the hypothesis that eggs attached to the legs of male Podoctidae (Opiliones, Laniatores) constituted a case of paternal care, using molecular sequence data in tandem with multiple sequence alignments to test the prediction that sequences of the eggs and the adults that carried them would indicate conspecific identity. We discovered that the sequences of the eggs belonged to spiders, and thus rejected the paternal care hypothesis for these species. Machado and Wolff (2017) recently critiqued our work, which they regarded as a non-critical interpretation and over-reliance on molecular sequence data, and defended the traditional argument that the eggs attached to podoctids are in fact harvestman eggs. Here we show that additional molecular sequence data also refute the identity of the eggs as conspecific harvestman eggs, using molecular cloning techniques to rule out contamination. We show that individual gene trees consistently and reliably place the egg and adult sequences in disparate parts of the tree topology. Phylogenetic methods consistently place all egg sequences within the order Araneae (spiders). We submit that evidence for the paternal care hypothesis based on behavioral, morphological, and natural history approaches is either absent or insufficient for concluding that the eggs of podoctids are conspecific.

A multilocus phylogeny of Podoctidae (Arachnida, Opiliones, Laniatores) and parametric shape analysis reveal the disutility of subfamilial nomenclature in armored harvestman systematics.

The taxonomy and systematics of the armored harvestmen (suborder Laniatores) are based on various sets of morphological characters pertaining to shape, armature, pedipalpal setation, and the number of articles of the walking leg tarsi. Few studies have tested the validity of these historical character systems in a comprehensive way, with reference to an independent data class, i.e., molecular sequence data. We examined as a test case the systematics of Podoctidae, a family distributed throughout the Indo-Pacific. We tested the validity of the three subfamilies of Podoctidae using a five-locus phylogeny, and examined the evolution of dorsal shape as a proxy for taxonomic utility, using parametric shape analysis. Here we show that two of the three subfamilies, Ibaloniinae and Podoctinae, are non-monophyletic, with the third subfamily, Erecananinae, recovered as non-monophyletic in a subset of analyses. Various genera were also recovered as non-monophyletic. As first steps toward revision of Podoctidae, the subfamilies Erecananinae Roewer, 1912 and Ibaloniinae Roewer, 1912 are synonymized with Podoctinae Roewer, 1912 new synonymies, thereby abolishing unsubstantiated subfamilial divisions within Podoctidae. We once again synonymize the genus Paralomanius Goodnight & Goodnight, 1948 with Lomanius Roewer, 1923 revalidated. We additionally show that eggs carried on the legs of male Podoctidae are not conspecific to the males, falsifying the hypothesis of paternal care in this group.

Phylogeny of the island archipelago frog genus Sanguirana: Another endemic Philippine radiation that diversified 'Out-of-Palawan'.

Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six nuclear loci and complete sampling for all known species. We use a time-calibrated Bayesian estimate of phylogeny and model-testing approach to biogeographic inference to infer ancestral areas and probable means of diversification. These analyses identify Sanguirana as an additional clade for which the 'Out-of-Palawan' biogeographic scenario is unambiguously preferred. This study lends additional support to recent work suggesting that a substantial portion of Philippine vertebrate megadiversity originated via colonization of the archipelago from the Palawan microcontinent, with subsequent invasion of oceanic islands (e.g., range expansion over Huxley's Modification of Wallace's Line), numerous instances of overwater dispersal, and geographic radiation across the archipelago.

Archipelago colonization by ecologically dissimilar amphibians: evaluating the expectation of common evolutionary history of geographical diffusion in co-distributed rainforest tree frogs in islands of Southeast Asia.

Widespread, co-distributed species with limited relative dispersal abilities represent compelling focal taxa for comparative phylogeography. Forest vertebrates in island archipelagos often exhibit pronounced population structure resulting from limited dispersal abilities or capacity to overcome marine barriers to dispersal. The exceptionally diverse Old World tree frogs of the family Rhacophoridae have colonized the forested island archipelagos of Southeast Asia on multiple occasions, entering the islands of Indonesia and the Philippines via a "stepping stone" mode of dispersal along elongate island chains, separated by a series of marine channels. Here we evaluate the prediction that two tightly co-distributed Philippine rhacophorids colonized the archipelago during concomitant timescales and in the same, linear, "island-hopping" progression. We use a new multilocus dataset, utilize dense genetic sampling from the eastern arc of the Philippines, and we take a model-based phylogeographic approach to examining the two species for similar topological patterns of diversification, genetic structure, and timescales of diversification. Our results support some common mechanistic predictions (a general south-to-north polarity of colonization) but not others (timescale for colonization and manner and degree of lineage diversification), suggesting differing biogeographic scenarios of geographical diffusion through the archipelago and unique and idiosyncratic ecological capacities and evolutionary histories of each species.

Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification.

The spectacular, virtually endemic radiation of Philippine semi-fossorial skinks of the genus Brachymeles represent one of the few radiations of scincid lizards to possess both fully limbed and limbless species. And yet, nothing is known of the phylogenetic relationships of this exceptional group. Morphologically similar body plans have made it difficult to assess species-level diversity, and the genus has long been recognized as one of the more modest radiations of southeast Asian lizards. However, recent large-scale survey efforts have resulted in the discovery of numerous new species, and taxonomic studies indicate that the diversity within the genus Brachymeles is grossly underestimated. In this study we provide the first robust estimate of phylogenetic relationships within the genus Brachymeles using a multi-locus dataset and nearly complete taxonomic sampling. We provide statistical tests of monophyly for all polytypic species and two widespread limb-reduced species and our results indicate wholesale deviations from past summaries and taxonomic evaluations of the genus. With few exceptions, we are able to reject the monophyly of all polytypic and widespread species, thereby validating the need for large-scale taxonomic revisions. Our results reveal that the limbless, monotypic, genus Davewakeum is nested within Brachymeles. Mapping of body form on our preferred phylogenetic tree suggests that limb-reduction and digit loss has occurred on multiple occasions in the history of the genus. A Bayesian reconstruction of ancestral areas indicates strong statistical support for a minimum of five major dispersal events that have given rise to a major component of the observed species diversity on separate Pleistocene aggregate island platforms of the archipelago.

Phylogeography, geographic structure, genetic variation, and potential species boundaries in Philippine slender toads.

We investigated phylogeography of Philippine slender toads (genus Ansonia) and used a temporal framework for diversification, statistical tests of alternate topologies, and Bayesian approaches to test previous hypotheses concerning dispersal to, and colonization routes within, the southern Philippine island of Mindanao. Two species of Ansonia previously have been documented, with ranges separated by an east-west split corresponding to the approximate boundaries of Mindanao's paleoisland precursors. We present new mtDNA sequence data (1946 bp from genes encoding ND1, 16S rRNA and tRNALeu) for 105 Ansonia specimens sampled from 20 localities on Mindanao Island. Our data suggest that Philippine Ansonia is composed of at least eight, well-supported population lineages, structured into a minimum of four highly divergent mtDNA clades. One clade corresponds to Ansonia mcgregori, a range-restricted species apparently limited to the distal portion of the Zamboanga Peninsula of western Mindanao. Two morphologically indistinguishable, but genetically divergent, lineages possibly are undescribed cryptic species from western Mindanao. We recognize the five remaining lineages as Ansonia muelleri pending data from morphology or bioacoustics that might diagnose separate species among these lineages. Regardless of their species status, the five allopatric lineages of A. muelleri should be viewed as important genetic units for future genetic conservation planning.

Species boundaries and cryptic lineage diversity in a Philippine forest skink complex (Reptilia; Squamata; Scincidae: Lygosominae).

In the megadiverse conservation hotspot of the Philippines, biodiversity is not uniformly distributed throughout the archipelago, but hierarchically partitioned into islands and island groups that were conjoined during the mid- to late-Pleistocene. Few species groups are widely distributed throughout the archipelago, but some exceptions exist, such as the common scincid lizards of the Sphenomorphus jagori complex (including S. jagori, S. coxi, and S. abdictus). Using mtDNA haplotype data we test biogeographic and taxonomic predictions in these abundant, large-bodied, forest floor lizards and arrive at conclusions that differ significantly from both past, and current, appraisals of species diversity. In contrast to expectations based on existing taxonomy (three species, each with two subspecies), we find evidence of at least eleven highly divergent species lineages diagnosed by haplotypic variation. Each lineage corresponds to a biogeographically circumscribed distribution (i.e., isolated islands or geological components of islands), suggesting lineage cohesion and allopatric differentiation. Parametric bootstrapping tests reject taxonomic and biogeographic hypotheses and suggest a complex pattern of unpredicted relationships. Only one of the former species (S. jagori) appears as a monophyletic entity (including four allopatric, highly divergent lineages that we suspect may represent evolutionary species), and the remaining species are paraphyletic, necessitating a comprehensive future taxonomic revision. The pattern of biogeographic provincialism and hidden cryptic species diversity detected here leads us to suspect that even the most common, presumably well-studied, and widespread species complexes in the Philippines are in need of thorough analysis with modern genetic and phylogenetic techniques. Such studies of speciation genetics in these common, widely distributed groups may lead to a better understanding of the genetic underpinnings of biodiversity, allow for an enhanced appreciation of the evolutionary history of this model island archipelago, and enable more informed conservation planning in a global biodiversity hotspot.

Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification.

In the Philippines, Pleistocene sea level oscillations repeatedly connected and isolated neighboring islands. Hence, an understanding of the island platforms adjoined during periods of low sea level has led biologists to a suite of expectations that, taken together, represent a paradigm for the process of recent diversification in southeast Asia. We employ statistical tests of phylogenetic topology and population genetic analyses of widespread species of bent-toed geckos (Cyrtodactylus) to ascertain whether patterns of inter- and intra-specific diversity can be explained by a Pleistocene aggregate island model of diversification. Contrary to many classic studies of Philippine vertebrates, we find complex patterns that are only partially explained by past island connectivity. In particular, we determine that some populations inhabiting previously united island groups show substantial genetic divergence and are inferred to be polyphyletic. Additionally, greater genetic diversity is found within islands, than between them. Among the topological patterns inconsistent with the Pleistocene model, we note some similarities with other lineages, but no obviously shared causal mechanisms are apparent. Finally, we infer well-supported discordance between the gene trees inferred from mitochondrial and nuclear DNA sequences of two species, which we suspect is the result of incomplete lineage sorting. This study contributes to a nascent body of literature suggesting that the current paradigm for Philippine biogeography is an oversimplification requiring revision.

Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: systematic and biogeographic implications (Anura: Bufonidae).

We investigated the phylogenetic relationships and estimated the history of species diversification and biogeography in the bufonid genus Ansonia from Southeast Asia, a unique organism with tadpoles adapted to life in strong currents chiefly in montane regions and also in lowland rainforests. We estimated phylogenetic relationships among 32 named and unnamed taxa using 2461bp sequences of the mitochondrial 12S rRNA, tRNA(val), and 16S rRNA genes with equally-weighted parsimony, maximum likelihood, and Bayesian methods of inference. Monophyletic clades of Southeast Asian members of the genus Ansonia are well-supported, allowing for the interpretation of general biogeographic conclusions. The genus is divided into two major clades. One of these contains two reciprocally monophyletic subclades, one from the Malay Peninsula and Thailand and the other from Borneo. The other major clade primarily consists of Bornean taxa but also includes a monophyletic group of two Philippine species and a single peninsular Malaysian species. We estimated absolute divergence times using Bayesian methods with external calibration points to reconstruct the relative timing of faunal exchange between the major landmasses of Southeast Asia.

Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion?

Southeast Asia's widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomystax and its close relatives. Our expectation was that lineages on island archipelagos would exhibit more substantial geographic structure, corresponding to the geological history of terrestrial connectivity in this region, compared to the Asian mainland. Contrary to predictions, we found evidence of numerous highly divergent lineages from a limited area on the Asian mainland, but fewer lineages with shallower divergences throughout oceanic islands of the Philippines and Indonesia. Surprisingly and in numerous instances, lineages in the archipelagos span distinct biogeographical provinces. Phylogeographic analyses identified four major haplotype clades; summary statistics, mismatch distributions, and Bayesian coalescent inference of demography provide support for recent range expansion, population growth, and/or admixture in the Philippine and some Sulawesi populations. We speculate that the current range of P. leucomystax in Southeast Asia is much larger now than in the recent past. Conversion of forested areas to monoculture agriculture and transportation of agricultural products between islands may have facilitated unprecedented population and range expansion in P. leucomystax throughout thousands of islands in the Philippine and Indonesian archipelagos.

A new forest frog of the genus Platymantis (Amphibia: Anura: Ceratobatrachidae: subgenus Tirahanulap) from Leyte and Samar islands, eastern Philippines.

We describe a new species of frog of the genus Platymantis Günther (subgenus Tirahanulap), from the east-central regions of the Philippines. It belongs to the the previously-defined P. hazelae Group) based on morphological and bioacoustic datasets. The new species is phenotypically and ecologically most similar to members of Tirahanulap, an assemblage of small-bodied arboreal frogs inhabiting montane forests of the central and northern islands of the Philippine archipelago. The new species represents the first taxon in the Cloud Frog species known from the biogeographically unique Mindanao Pleistocene Aggregate Island Complex. Particularly susceptible to local extirpation following deforestation, all known species of Tirahanulap are important indicator species for environmental and conservation assessments, making this new species not only an exceptional addition to Philippine biodiversity but also an important symbol for conservation initiatives in the region.

Niche shifts and environmental non-equilibrium undermine the usefulness of ecological niche models for invasion risk assessments.

Niche shifts and environmental non-equilibrium in invading alien species undermine niche-based predictions of alien species' potential distributions and, consequently, their usefulness for invasion risk assessments. Here, we compared the realized climatic niches of four alien amphibian species (Hylarana erythraea, Rhinella marina, Hoplobatrachus rugulosus, and Kaloula pulchra) in their native and Philippine-invaded ranges to investigate niche changes that have unfolded during their invasion and, with this, assessed the extent of niche conservatism and environmental equilibrium. We investigated how niche changes affected reciprocal transferability of ecological niche models (ENMs) calibrated using data from the species' native and Philippine-invaded ranges, and both ranges combined. We found varying levels of niche change across the species' realized climatic niches in the Philippines: climatic niche shift for H. rugulosus; niche conservatism for R. marina and K. pulchra; environmental non-equilibrium in the Philippine-invaded range for all species; and environmental non-equilibrium in the native range or adaptive changes post-introduction for all species except H. erythraea. Niche changes undermined the reciprocal transferability of ENMs calibrated using native and Philippine-invaded range data. Our paper highlights the difficulty of predicting potential distributions given niche shifts and environmental non-equilibrium; we suggest calibrating ENMs with data from species' combined native and invaded ranges, and to regularly reassess niche changes and recalibrate ENMs as species' invasions progress.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia.

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12.

The curious case of the endemic freshwater crocodile Crocodylus mindorensis as incidental host of marine fish acanthocephalan.

We performed the first host-parasite survey of the Philippine crocodile, Crocodylus mindorensis, a critically endangered species for which ecological information is lacking. We collected by gastric lavage samples of the stomach contents of crocodiles (n = 10) residing at the Palawan Wildlife Rescue and Conservation Center in Puerto Princesa, Palawan, Philippines. The only parasite detected was an acanthocephalan, which was identified as Neorhadinorhynchus nudus (n = 68), a parasite typically found in the marine fish species consumed by three crocodile individuals. Given the known hosts of N. nudus, its parasitism of C. mindorensis in captivity is likely established by consumption of marine fish. Our findings have implications for the conservation management of C. mindorensis, particularly in terms of preventing introduction of parasites that could lead to development of infectious disease or alter the fitness of captive animals.

A new species of Pseudogekko (Squamata: Gekkonidae) from the Romblon Island Group, Central Philippines.

We describe a new species of lizard in the genus Pseudogekko from Sibuyan and Tablas islands in the Romblon Island Group of the central Philippines. The new species is diagnosed from other Philippine Pseudogekko by body size and shape, color pattern, and multiple differences in scale characteristics. Pseudogekko isapa sp. nov. has been collected only twice from leaves of shrubs in forested habitat on Sibuyan and Tablas islands. The distinctive new species of false gecko is undoubtedly endemic to this single, isolated island group. The fact that populations of such a distinctive new species of Pseudogekko has escaped notice of herpetologists on the reasonably well-studied and largely protected Sibuyan Island further emphasizes the secretive and forest-dependent habits of Philippine false geckos. These characteristics of their behavior and natural history render them difficult to study and challenge biologists' efforts to accurately assess their conservation status.

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands.

We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.

Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) II: a new species from the northern Philippines.

We describe a new digitless scincid lizard of the genus Brachymeles from northern Luzon and Camiguin Norte islands in the Philippines. This species belongs to the Brachymeles bonitae Complex, and both molecular and morphological data confirm that this species is distinct from all other congeners. Formerly considered to be a single widespread species, this group of species has been the focus of recent systematic reviews. Here we describe a new species in the B. bonitae Complex, recognized currently to constitute five species. Brachymeles ilocandia sp. nov. is the second digitless and the seventeenth non-pentadactyl species in genus. The description of this species brings the total number of species in the genus to 40, and provides new insight into unique distribution patterns of species of the northern Philippines.

A new species of limestone karst inhabiting forest frog, genus Platymantis (Amphibia: Anura: Ceratobatrachidae: subgenus Lupacolus) from southern Luzon Island, Philippines.

We describe a new species of limestone karst dwelling forest frog of the genus Platymantis from the Quezon Protected Landscape in southeastern Luzon Island, Philippines. We assign Platymantis quezoni, sp. nov., to the diverse assemblage of terrestrial species in the Platymantis dorsalis Group, subgenus Lupacolus on the basis of its body size and proportions, only slightly expanded terminal discs of the fingers and toes, and its terrestrial microhabitat. The new species is distinguished from these and all other Philippine congeners by features of its external morphology, its restriction to a distinctive limestone karst microhabitat, and its advertisement call, which is unique among frogs of the family Ceratobatrachidae. Several distinguishing morphological characters include its moderate body size (22.1-33.9 mm SVL for 16 adult males and 32.4-39.7 mm SVL for five adult females), slightly expanded terminal discs of the fingers and toes, smooth skin with limited dermal tuberculation, and a dorsal color pattern of mottled tan to dark brown with black blotches. The new species is the sixth Philippine Platymantis known to occur exclusively on limestone karst substrates (previously known karst-obligate species include: P. bayani, P. biak, P. insulatus, P. paengi, and P. speleaus). Recently accelerated discovery of limestone karst anurans across the Philippines suggests that numerous additional species may await discovery on the hundreds of scattered karst formations throughout the archipelago. This possibility suggests that a major conservation priority in coming years will be to study, characterize, describe, and preserve the endemic species supported by this patchy, unique and imperiled type of forest ecosystem in the Philippines.