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.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships.

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae).

New Guinea, the world's largest and highest tropical island, has a rich but poorly known biota. Papuascincus is a genus of skinks endemic to New Guinea's mountain regions, comprising two wide-ranging species and two species known only from their type series. The phylogeny of the genus has never been examined and the relationships among its species - as well as between it and closely related taxa - are hitherto unknown. We performed the first large-scale molecular-phylogenetic study of Papuascincus, including sampling across the genus' range in Papua New Guinea. We sequenced three mitochondrial and two nuclear markers from 65 specimens of Papuascincus and reconstructed their phylogenetic relationships. We also performed species-delimitation analyses, estimated divergence times and ancestral biogeography, and examined body-size evolution within the genus. Papuascincus was strongly supported as monophyletic. It began radiating during the mid-Miocene in the area now comprising the Central Cordillera of New Guinea, then dispersed eastward colonising the Papuan Peninsula. We found evidence of extensive cryptic diversity within the genus, with between nine and 20 supported genetic lineages. These were estimated using three methods of species delimitation and predominantly occur in allopatry. Distribution and body-size divergence patterns indicated that character displacement in size took place during the evolutionary history of Papuascincus. We conclude that the genus requires comprehensive taxonomic revision and likely represents a species-rich lineage of montane skinks.

Lizards of the lost arcs: mid-Cenozoic diversification, persistence and ecological marginalization in the West Pacific.

Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.

Early insularity and subsequent mountain uplift were complementary drivers of diversification in a Melanesian lizard radiation (Gekkonidae: Cyrtodactylus).

Regions with complex geological histories present a major challenge for scientists studying the processes that have shaped their biotas. The history of the vast and biologically rich tropical island of New Guinea is particularly complex and poorly resolved. Competing geological models propose New Guinea emerged as a substantial landmass either during the Mid-Miocene or as recently as the Pliocene. Likewise, the estimated timing for the uplift of the high Central Cordillera, spanning the length of the island, differs across models. Here we investigate how early islands and mountain uplift have shaped the diversification and biogeography of Cyrtodactylus geckos. Our data strongly support initial colonisation and divergence within proto-Papuan islands in the Early- to Mid-Miocene, with divergent lineages and endemic diversity concentrated on oceanic island arcs in northern New Guinea and the formerly isolated East-Papuan Composite Terrane. At least four lineages are inferred to have independently colonised hill- and lower-montane forests, indicating that mountain uplift has also played a critical role in accumulating diversity, even in this predominantly lowland lineage. Our findings suggest that substantial land in northern New Guinea and lower-montane habitats date back well into the Miocene and that insular diversification and mountain colonisation have synergistically generated diversity in the geologically complex Papuan region.

Neural basis of trigeminal chemo- and thermonociception in brown treesnakes, Boiga irregularis (Squamata: Colubridae).

To elucidate the nociceptive system of the brown treesnake, Boiga irregularis, we exposed isolated brown treesnake trigeminal neurons to thermal and chemical stimulation. We measured responses as changes in intracellular calcium using ratiometric fluorescent calcium imaging. Responses to aversive thermal and chemical identified several classes of putative nociceptors. Compounds that were aversive excited many trigeminal neurons, putative chemonociceptors. Identification as nociceptors was further supported by lack of activation by compounds that were not aversive. Brown treesnake neurons had thermal thresholds ranging from 32 to 49 °C. The distribution was discontinuous, with a population of thresholds from 32 to 45 °C and a population with thresholds > 48 °C. Thermal stimulation of 48 °C has been shown to be strongly aversive to brown treesnakes, is lethal, and suggests the presence of thermonociceptors. Thermal sensitivity of brown treesnake trigeminal neurons greatly overlaps with chemical sensitivity; only 1.1% of neurons were sensitive to only thermal stimulation. 50% of brown treesnake trigeminal neurons tested with both > 48 °C and cinnamaldehyde responded to both stimuli, identifying putative polymodal nociceptors. Although a previous study found brown treesnakes insensitive to capsicum extract containing capsaicin, brown treesnake trigeminal neurons responded to capsaicin. These findings are of evolutionary interest as well as providing potential insights into managing this significant pest species.

Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification.

Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas - New Guinea and its satellite islands, Australia and the Philippines. The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation. Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain. Here we reconstruct a phylogeny for Asterophryinae with greatly increased taxon and genetic sampling relative to prior studies. We use Maximum Likelihood and Bayesian Inference methods to produce the most robust and comprehensive phylogeny to date containing 155 species using 3 nuclear and 2 mitochondrial loci. We also perform a time calibration analysis to estimate the age of the clade. We find support for the monophyly of Asterophryinae as well as need for taxonomic reclassification of several genera. Furthermore, we find increased rates of speciation across the clade supporting the hypothesis of rapid radiation. Lastly, we found that adding taxa to the analysis produced more robust phylogenetic results over adding loci.

Systematics and biogeography of the Hylarana frog (Anura: Ranidae) radiation across tropical Australasia, Southeast Asia, and Africa.

We present an inclusive molecular phylogeny for Hylarana across its global distribution, utilizing two mitochondrial and four nuclear gene regions for 69 of the 97 currently described species. We use phylogenetic methods to test monophyly of Hylarana, determine relationships among ten putative subgenera, identify major clades, reconstruct biogeographic history, and estimate continental dispersal dates. Results support Hylarana as a monophyletic group originating approximately 26.9MYA and comprising eight clades that partly correspond to currently described subgenera plus two new groups. The African and Australasian species each form clades embedded within a paraphyletic Southeast Asian group. We estimate that Africa and Australasia were colonized by Hylarana s.l. from SE Asia approximately 18.7 and 10.8MYA, respectively. Biogeographic reconstructions also support three separate colonization events in India from Southeast Asia. Examination of museum specimens identified morphological characters useful for delineating subgenera and species. We herein elevate all supported subgenera to genus rank and formally describe two new genera to produce a revised taxonomy congruent with our new phylogenetic and biogeographic findings.

Congener diversity, topographic heterogeneity and human-assisted dispersal predict spread rates of alien herpetofauna at a global scale.

Understanding the factors that determine rates of range expansion is not only crucial for developing risk assessment schemes and management strategies for invasive species, but also provides important insight into the ability of species to disperse in response to climate change. However, there is little knowledge on why some invasions spread faster than others at large spatiotemporal scales. Here, we examine the effects of human activities, species traits and characteristics of the invaded range on spread rates using a global sample of alien reptile and amphibian introductions. We show that spread rates vary remarkably among invaded locations within a species, and differ across biogeographical realms. Spread rates are positively related to the richness of native congeneric species and human-assisted dispersal in the invaded range but are negatively correlated with topographic heterogeneity. Our findings highlight the importance of environmental characteristics and human-assisted dispersal in developing robust frameworks for predicting species' range shifts.

Phylogeny and phylogeography of Mantophryne (Anura: Microhylidae) reveals cryptic diversity in New Guinea.

New Guinea is one of five high biodiversity wilderness areas, and frog diversity is exceptionally large, with more than 400 species described to date. The microhylid frog genus Mantophryne is endemic to New Guinea and consists of four species, three of which have narrow geographic distributions and a fourth, M. lateralis, with a broad range that spans the eastern half of the island. Here, we sequence 104 Mantophryne samples for three mitochondrial and three nuclear loci to reconstruct the first phylogeny of the genus and to examine spatial patterns of diversity within M. lateralis. Results indicate that the wide-ranging M. lateralis is composed of at least nine geographically separated and well-supported lineages that represent putative species. Biogeographic analysis suggests that Mantophryne evolved on the eastern Papuan peninsula with subsequent dispersal westward, as well as overwater dispersal events to the Louisiade and D'Entrecasteaux archipelagos.

A revision of Gerrhopilus inornatus (Squamata: Gerrhopilidae) reveals a multi-species complex.

Melanesian blindsnakes of the genus Gerrhopilus have been little collected or researched. I examined specimens assigned in museums to Gerrhopilus inornatus and found considerable morphological diversity among them that indicates the presence of multiple species. I redescribe G. inornatus (Boulenger) based on the holotype and one additional specimen, and I describe six new species among specimens currently subsumed under that name from Papua New Guinea: Gerrhopilus flavinotatus sp. nov., Gerrhopilus lorealis sp. nov., Gerrhopilus papuanorum sp. nov., Gerrhopilus polyadenus sp. nov., Gerrhopilus slapcinskyi sp. nov., and Gerrhopilus wallachi sp. nov. Each species is currently known from only 1-3 specimens, and all but two are known only from single localities. In addition to traditional information on scale counts, habitus, and color patterns, I found the numbers and distributions of epidermal glands among the head shields to be especially useful for discriminating among species. The number of recognized Melanesian Gerrhopilus has increased tremendously in recent years, but the region has been poorly sampled for these snakes, and it is to be expected that additional species will be identified at such time as surveys can more effectively target these cryptic snakes.

Redescription of Lepidodactylus flaviocularis (Squamata: Gekkonidae), with the description of a new species from Makira Island, Solomon Islands.

Several species of geckos of the genus Lepidodactylus are endemic to the Solomon Islands and very poorly known. I redescribe one of these, L. flaviocularis, from Guadalcanal, based on examination of a second, newly obtained specimen and quantification of diagnostically useful features of the digits. I also describe a closely related new species from nearby Makira Island in the southern Solomon Islands. Both species are distinguished by their large number of undivided subdigital lamellae, extensive toe webbing, and a continuous row of enlarged precloacal/femoral scales. The new species is distinguished from L. flaviocularis by a number of scalational features and the color of the circumorbial scales. Both species are inhabitants of interior forest, and it remains uncertain whether they are naturally rare, rare due to interactions with invasive species, or simply have cryptic ecological habits, though the last seems most likely. Current evidence for both species is consistent with the taxon-cycle hypothesis, which posits ecological displacement to inland habitats of ancient island inhabitants by newer colonizers, but this remains to be critically tested. The limited pool of specimens available for both species necessitates assessing the IUCN conservation status of each as Data Deficient.

A new species of Lepidodactylus (Squamata: Gekkonidae) from Umboi Island, Papua New Guinea.

We describe a new species of Lepidodactylus from Umboi Island, just to the west of New Britain. It is a member of the Lepidodactylus guppyi Group and can be distinguished from all other Melanesian Lepidodactylus by aspects of digital scalation, digital webbing, enlarged femoral/precloacal scales, and color pattern. It is genetically distinct from its closest congeners, and genetic and morphological data indicate that the new species is most similar among named species to Lepidodactylus guppyi from the Solomon Islands, but it diverged from this species and other close relatives approximately 8 MYA or longer at a time prior to the existence of the island that it now occupies. The new species is known from only three individuals collected on a single tree, and efforts to find more animals in what seemed good habitat nearby were unsuccessful. This duplicates the pattern of apparent rarity seen for many Lepidodactylus species. Sufficient habitat exists on Umboi Island for arboreal geckos, suggesting that the species is not actually endangered but is ecologically cryptic. However, lack of needed information leads us to assess this species' conservation status as Data Deficient.

Collapse of the endemic lizard Podarcis pityusensis on the island of Ibiza mediated by an invasive snake.

The invasive snake Hemorrhois hippocrepis colonized the island of Ibiza (Balearic Islands) in 2003 as stowaways inside trunks of olive trees imported for gardening. It has quickly spread since 2010, posing a threat to the island's only remaining endemic vertebrate, the Ibiza wall lizard Podarcis pityusensis. We map the yearly expansion rate of the snake and estimate via transect surveys how severely it affects the distribution and abundance of the endemic lizard. As well, we surveyed 9 of 30 small lizard populations on islets surrounding Ibiza that have been isolated since the Last Glacial Maximum. Snakes had invaded 49% of Ibiza's land area by 2018, and censuses show a critical contrast in lizard abundance between areas with and without snakes; almost all censuses in areas without snakes show lizard presence whereas nearly all censuses in areas with H. hippocrepis lack lizard sightings. Moreover, at least one subspecies previously thriving on one of the offshore islets has become extinct, and there have been several snakes recorded swimming between Ibiza and the surrounding islets. Therefore, lizard populations have been dramatically reduced or have vanished within the range of the snake, and our results quantitatively support upgrading this species' threat level for extinction. This study can inform to programs to manage invasive snake populations and to conservation actions to recover the endemic lizard.

Cryptic extinction risk in a western Pacific lizard radiation.

Cryptic ecologies, the Wallacean Shortfall of undocumented species' geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term 'cryptic extinction risk'. The genus Lepidodactylus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work on Lepidodactylus showed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, in Lepidodactylus. From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk. Supplementary Information: The online version contains supplementary material available at 10.1007/s10531-022-02412-x.

Melanesia holds the world's most diverse and intact insular amphibian fauna.

Identifying hotspots of biological diversity is a key step in conservation prioritisation. Melanesia-centred on the vast island of New Guinea-is increasingly recognised for its exceptionally species-rich and endemic biota. Here we show that Melanesia has the world's most diverse insular amphibian fauna, with over 7% of recognised global frog species in less than 0.7% of the world's land area, and over 97% of species endemic. We further estimate that nearly 200 additional candidate species have been discovered but remain unnamed, pointing to a total fauna in excess of 700 species. Nearly 60% of the Melanesian frog fauna is in a lineage of direct-developing microhylids characterised by smaller distributions than co-occurring frog families, suggesting lineage-specific high beta diversity is a key driver of Melanesian anuran megadiversity. A comprehensive conservation status assessment further highlights geographic concentrations of recently described range-restricted threatened taxa that warrant urgent conservation actions. Nonetheless, by world standards, the Melanesian frog fauna is relatively intact, with 6% of assessed species listed as threatened and no documented extinctions; and thus it provides an unparalleled opportunity to understand and conserve a megadiverse and relatively intact insular biota.

Whos your daddy? On the identity and distribution of the paternal hybrid ancestor of the parthenogenetic gecko Lepidodactylus lugubris (Reptilia: Squamata: Gekkonidae).

The widespread parthenogenetic gecko Lepidodactylus lugubris is comprised of several clonal lineages, at least one of which has been known for some time to have originated from hybridization between its maternal ancestor, Lepidodactylus moestus, and a putatively undescribed paternal ancestor previously known only from remote islands in the Central Pacific. By integrating new genetic sequences from multiple studies on Lepidodactylus and incorporating new genetic sequences from previously sampled populations, we recovered a phylogenetic tree that shows a close genetic similarity between the generally hypothesized paternal hybrid ancestor and a recently described species from Maluku (Indonesia), Lepidodactylus pantai. Our results suggest that the paternal hybrid ancestor of at least one parthenogenetic clone of L. lugubris is conspecific with L. pantai and that the range of this species extends to Palau, the Caroline Islands, the Kei Islands, Wagabu, and potentially other small islands near New Guinea. Deeper genetic structure in the western (Palau, Maluku) versus eastern (eastern Melanesia, Micronesia, Polynesia) part of this species range suggests that the western populations likely dispersed via natural colonization, whereas the eastern populations may be the result of human-mediated dispersal. The potential taxonomic affinities and biogeographic history should be confirmed with further morphological and genetic analyses, including research on L. woodfordi from its type locality, which would have nomenclatural priority if found to be conspecific with L. pantai. We recommend referring to the wide-ranging sexual species as Lepidodactylus pantai until such a comparison can be made.

Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): evidence from mitochondrial and nuclear markers.

The Papuan region, comprising New Guinea and nearby islands, has a complex geological history that has fostered high levels of biodiversity and endemism. Unfortunately, much of this diversity remains undocumented. We examine the evolutionary relationships of the venomous snake genus Aspidomorphus (Elapidae: Hydrophiinae), a Papuan endemic, and document extensive cryptic lineage diversification. Between Aspidomorphus species we find 22.2-27.9% corrected cyt-b sequence divergence. Within species we find 17.7-23.7% maximum sequence divergence. These high levels of genetic divergence may have complicated previous phylogenetic studies, which have had difficulty placing Aspidomorphus within the subfamily Hydrophiinae. Compared to previous studies, we increase sampling within Hydrophiinae to include all currently recognized species of Aspidomorphus and increase species representation for the genera Demansia and Toxicocalamus. We confirm monophyly of Aspidomorphus and resolve placement of the genus utilizing a set of seven molecular markers (12S, 16S, cyt-b, ND4, c-mos, MyHC-2, and RAG-1); we find strong support for a sister-group relationship between Aspidomorphus and a Demansia/Toxicocalamus preussi clade. We also use one mitochondrial (cyt-b) and one nuclear marker (SPTBN1) to document deep genetic divergence within all currently recognized species of Aspidomorphus and discuss the Solomon Island Arc as a potential center of divergence in this species. Lastly, we find high levels of concordance between the mtDNA and nuDNA markers used for inter-species phylogenetic reconstruction.

A new species of Lobulia (Squamata: Scincidae) from Papua New Guinea.

I describe a new skink of the genus Lobulia from Mt. Simpson in southeasternmost New Guinea. This species differs from all other members of the genus in having only three pairs of enlarged chin shields and only the first pair in medial contact. It is most similar in scalation to L. elegans but is readily distinguished from that species by its color pattern, body size and shape, and numbers of lamellae. Morphological data on L. elegans have not been reported since the description of the holotype in 1897, so I provide a redescription of that species based on six specimens-including the holotype-of certain conspecificity and from within approximately 100 km of the type locality at Mt. Victoria. I also elevate Lygosoma elegantoides lobulus from synonymy with Lobulia elegans, from which it is readily distinguished on the basis of scalational and color-pattern features. The resurrected L. lobulus and the new species from Mt. Simpson represent the seventh and eighth recognized species of Lobulia, and the Mt. Simpson species is the fifth member of the Papuan herpetofauna that is apparently endemic to Mt. Simpson. Mt. Simpson appears to be a moderate center of local endemism within southeastern New Guinea.