Taxonomy, distribution, and conservation status of a rare arboreal lizard, Bronchocela celebensis Gray, 1845 (Reptilia: Agamidae) endemic to Sulawesi, Indonesia.

Bronchocela celebensis Gray, 1845 is one of the rarest species of the genus, known only from less than 20 museum specimens collected from northern Sulawesi. It is often confused with its similar congener, B. cristatella, which occurs widely throughout the Indonesian Archipelago and Peninsular Malaysia, except on the Sulawesi mainland. Here, we examine the morphology of B. celebensis based on 46 museum specimens including freshly collected individuals, and redescribe the species based on the holotype (by monotypy). We studied the characters of B. celebensis with morphometric comparison to its allopatric congener B. cristatella from the adjacent islands of southern Sulawesi in Indonesia. Based on the current distribution pattern and the apparent threats, we update the conservation status of B. celebensis using the IUCN Red List Criteria and propose that it be considered as a Vulnerable (VU) species endemic to Sulawesi.

A new species of terrestrially-nesting fanged frog (Anura: Dicroglossidae) from Sulawesi Island, Indonesia.

Herein, we describe a new species of terrestrially-nesting fanged frog from Sulawesi Island, Indonesia. Though male nest attendance and terrestrial egg deposition is known in one other Sulawesi fanged frog (Limnonectes arathooni), the new species exhibits a derived reproductive mode unique to the Sulawesi assemblage; male frogs guard one or more clutches of eggs festooned to leaves or mossy boulders one to two meters above small slow-moving streams, trickles, or seeps. This island endemic has thus far been collected at three sites on Sulawesi: one in the Central Core of the island, and two on the Southwest Peninsula-south of the Tempe Depression (a major biogeographical boundary). The new Limnonectes has the smallest adult body size among its Sulawesi congeners-with a maximum snout-vent length of about 30 millimeters. Beyond its unique reproductive behavior and body size, the species is further diagnosed on the basis of advertisement call and genetic distance from sympatric fanged frogs. The discovery and description of the new species highlights the remarkable reproductive trait diversity that characterizes the Sulawesi fanged frog assemblage despite that most species in this radiation have yet to be formally described.

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.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi's Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.

Bewildering biogeography: Waves of dispersal and diversification across southern Wallacea by bent-toed geckos (genus: Cyrtodactylus).

Bent-toed Geckos, genus Cyrtodactylus, are one of the most diverse terrestrial vertebrate groups, and their range extends from South Asia into Australo-Papua and adjacent Pacific islands. Given the generally high faunal endemism on Wallacean islands, it is rather paradoxical that the diversity in these geckos appears to be so low (21 species in Wallacea, 15 in the Philippines) compared with continental shelf assemblages (>300 species on Sunda + Sahul Shelves + adjacent islands). To determine whether this shortfall was real or an artifact of historical undersampling, we analyzed mitochondrial DNA sequences of hundreds of southern Wallacean samples (Lesser Sundas + southern Maluku). After screening to guide sample selection for target capture data collection, we obtained a 1150-locus genomic dataset (1,476,505 bp) for 119 samples of southern Wallacean and closely related lineages. The results suggest that species diversity of Cyrtodactylus in southern Wallacea is vastly underestimated, with phylogenomic and clustering analyses suggesting as many as 25 candidate species, in contrast to the 8 currently described. Gene exchange between adjacent candidate species is absent or minimal across the archipelago with only one case of > 0.5 migrants per generation. Biogeographical analysis suggests that the hitherto unrecognized diversity is the result of at least three independent dispersals from Sulawesi or its offshore islands into southern Wallacea between 6 and 14 Ma, with one invasion producing small-bodied geckos and the other two or three producing larger-bodied geckos. The smaller-bodied laevigatus group appears to be able to coexist with members of either larger-bodied clade, but we have yet to find members of the two larger-bodied clades occurring in sympatry, suggesting that ecological partitioning or competitive exclusion may be shaping individual island assemblages.

Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].

A new high elevation species of Oreophryne Boettger (Anura: Microhylidae) from Sulawesi, Indonesia.

We examined the morphology of 50 specimens of Sulawesian Oreophryne and recognize a distinct, undescribed species. Based on morphological data and supported with phylogenetic analysis of the 16S rRNA gene, it is herein described and named as Oreophryne riyantoi sp. nov. The new species is diagnosed by having a combination of rounded snout in dorsal and lateral view, indistinct tympanum, narrow interorbital distance, small hands, small terminal discs on fingers and toes, toes without webbing, short legs, and dorsal surfaces of head, body and limbs irregularly tuberculated in life. It was found in leaf litter on the forest floor in extremely wet primary montane forest on Mount Mekongga at an altitude of 2528 m asl. The forest-dwelling habit of this terrestrial frog is unusual because other terrestrial Oreophryne occuring at high-altitude live in open grassy or fern dominated meadows. Four endemic species of Oreophryne are now known from Sulawesi. However, herpetological research activities, including high elevation surveys and additional taxonomic work, are necessary to achieve a comprehensive understanding of Oreophryne diversity and phylogeography in Sulawesi.

Sexual dimorphism and reproductive biology of the Asian bockadam snake (Cerberus schneiderii) in West Java.

Although they are among the most abundant snakes on Earth, and are heavily exploited for their skins and meat, Asian bockadams (or "dog-faced water snakes", Cerberus schneiderii) have attracted relatively little study across their wide geographic range. Based on dissection of 3,382 snakes brought to processing facilities in and around the city of Cirebon in West Java, Indonesia, we document facets of the biology of these mangrove-dwelling aquatic homalopsids. Females attain larger body sizes than do males, and are heavier-bodied (due in part to greater fat reserves) but have shorter tails relative to snout-vent length. Males showed testicular enlargement late in the year (August-November) but both reproductive and non-reproductive females were found year-round. Litters were large (3 to 45 offspring), especially in larger females. The commercial harvest falls mainly on adult snakes of both sexes, with seasonal variation in sex ratios. Life-history traits such as early maturation and frequent production of large litters render this species resilient to commercial harvesting. Future research should explore reasons for strong variation among facilities in the sex ratios of snakes, potentially identifying ways to focus the harvest on the sex (males) whose numbers are less critical for population viability.

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago.

The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.

Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia.

Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI- LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein familiesin T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusions: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom's toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.

Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia

Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI- LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein familiesin T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusions: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom's toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.(AU)

A tiny new species of Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from Belitung Island and Southeastern Sumatra, Indonesia.

A tiny new species of narrow-mouthed frog of the genus Microhyla is described from the island of Belitung and southeastern Sumatra, Indonesia. The most distinctive feature of the new frog is its diminutive adult size, snout-vent length ranging only from 12.3 to 15.8 mm in adult males. Phylogenetic analyses based a fragment of the mitochondrial 16S rRNA gene, along with detailed morphological and acoustic comparison differentiate the new taxon from all known congeners. The new species, formally described as Microhyla sriwijaya sp. nov., is a member of the M. achatina species group and the sister taxon to M. orientalis. It is diagnosable from other congeners by a combination of characters: (1) smaller male snout-vent size 16 mm; (2) snout obtusely rounded in dorsal view; (3) absence of mid-dorsal line and skin fold; (4) first finger reduced (finger I length less than half of finger II length); (5) dorsum with a prominent dark median mark extending posteriorly, narrow anteriorly near the level of the shoulder and expanding dorsolaterally up to the vent; margins of the dorsal marking concave with broad reddish-brown or orange colouration on either side; (6) foot webbing rudimentary, reaching just up to the first subarticular tubercle on all toes; (7) dorsal skin with prominent tubercles, especially in life; (8) tibiotarsal articulation of adpressed limb reaching beyond the snout tip; and (9) males produce a single type of call with pulsatile temporal structure, calls of relatively short duration ranging between 31.862.8 s, with two to three pulses delivered at a rate ranging between 32.236.0 pulses per second, and the mean overall dominant frequency of 4.3 kHz. The uncorrected pairwise genetic distances between Microhyla sriwijaya sp. nov. and all other known congeners are > 3.8% for the studied 16S gene fragment. The new species was discovered from wayside rural areas with oil palm plantations at four localities in the small island of Belitung (type locality), and from coffee plantation and secondary forest at Lampung in southeastern Sumatra. It is not known from any protected area and appears to be threatened due to tin mining activity, intensive logging, oil palm, and other commonly practiced agriculture activities.

Two new species of Megophrys Kuhl and Van Hasselt (Amphibia: Megophryidae) from Sumatra, Indonesia.

We evaluated the taxonomic status of the genus Megophrys in Sumatra using molecular and morphological data. Mitochondrial phylogenetic inference and morphological data revealed two undescribed species, one in southern SumatraM. selatanensis sp. nov. and one in northern SumatraM. acehensis sp. nov. We also detected a potential cryptic species within M. parallela, but refrain from describing this lineage here due to insufficient data. Genetic variation within Sumatran Megophrys is highly structured and will require additional geographic sampling to understand the interplay between geography and genetics in Sumatran Megophrys.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes.

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

A new Occidozyga from Sarawak, Malaysian Borneo (Anura: Dicroglossidae).

We found a uniquely colored dicroglossid frog of the genus Occidozyga from western Sarawak, East Malaysia. It is divergent from other congeners in morphology and mtDNA sequences. In a molecular phylogeny, this species is the sister lineage to the continental species O. lima and O. martensii with weak support. The species is small with SVL 16-18 mm in males and 18-19 mm in females, without dorsolateral fold but with transverse wrinkles on dorsum, tips of fingers lacking disks but of toes with disks, only first and second toes webbed to disks, and orange-brown dorsum with dark brown band. We thus describe it as a new species.

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.

The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.

New insights on the systematics and reproductive behaviour in tree frogs of the genus Feihyla, with description of a new related genus from Asia (Anura, Rhacophoridae).

The taxonomy of the Asian tree frog genus Feihyla has been in a state of flux ever since its proposal in 2006. Allocation of species to Feihyla remains confusing, particularly with respect to the closely related genus Chirixalus (formerly Chiromantis sensu lato). At the same time, several Chirixalus species are known only from cursory descriptions and remain poorly studied. In this study, we review the systematics of the genus Feihyla and clarify the generic placement of its members along with all other species currently assigned to Chirixalus. Based on integrative evidence gathered from new collections, examination of types and original descriptions, morphological comparisons, phylogenetic relationships inferred from a multi-gene (three mitochondrial + two nuclear) 1,937 bp dataset, as well as reproductive modes including egg-laying, nesting behaviour, and clutch morphology, our results show that the six species formerly attributed to Feihyla represent three morphologically and phylogenetically distinct groups: (1) the type species of the genus, F. palpebralis, along with F. fuhua constitute the Feihyla palpebralis group or Feihyla sensu stricto; (2) F. inexpectata and F. kajau represent the Feihyla vittiger group and are closely related to the Feihyla palpebralis group; (3) 'F. hansenae' and 'F. vittata' constitute another distinct and reciprocally monophyletic lineage, more closely related to Chirixalus + Chiromantis. In light of long-standing taxonomic confusions and unresolved phylogenetic relationships, we propose recognition of a new genus to accommodate 'F. hansenae' and 'F. vittata' in order to stabilise the classification of several Asian rhacophorid species that have been frequently confused and transferred within the Chirixalus-Chiromantis-Feihyla complex. Based on integrative evidence, eight species previously attributed to the genus Chirixalus or Feihyla are formally transferred to Rohanixalus gen. nov., two Chirixalus members are allocated to Feihyla, and one synonymised with Rhacophorus bipunctatus. In addition, we report the first member of the tree frog family Rhacophoridae from the Andaman Islands of India-Rohanixalus vittatus, along with description of its male advertisement call, reproductive behaviour including parental care by the female, and larval morphology. Extended distributions are also provided for Rohanixalus species across Northeast India. The study further reveals the presence of potentially undescribed diversity in the new genus. Altogether, the revised classification and novel insights presented herein will facilitate a better working taxonomy for four phylogenetically distinct but morphologically related groups of Old World tree frogs.

Phylogeny and biogeography of Sumatra´s cloud forest lizards of the genus Dendragama and status of Acanthosaura schneideri.

Lizards of the genus Dendragama are endemic to the highland cloud forests of Sumatra's Barisan Mountain Range in western Indonesia, and recent studies have uncovered widespread diversity within the genus. Here, a suite of morphological characters and mitochondrial DNA are used to compare three geographically isolated populations of D. boulengeri from (1) Mount Kerinci in Jambi province, (2) Mount Marapi of west Sumatra, and (3) the Karo Highlands of north Sumatra. Additional phylogeographic analyses with two recently described sister species, D. australis and D. dioidema were conducted. Five genetically distinct clades of Dendragama, all distributed allopatrically of one another were identified and some are suspected to inhabit small distributions. Morphological and genetic data confirm the Karo Highlands population D. schneideri (previously Acanthosaura schneideri Ahl, 1926) should be revalidated from the synonymy of D. boulengeri. Dendragama schneideri is endemic to montane forests of the Karo Highlands surrounding Lake Toba in Sumatra Utara province. Pairwise genetic distances of 6-11% separate D. schneideri from congeners. Two distinct clades of D. boulengeri from Mount Kerinci and Mount Marapi were identified, which are 5.0% genetically distant from one another. Using morphological characters, we provide the first key for distinguishing between species of Dendragama. Based on biogeographic patterns and levels of genetic variation it is suspected that at least 18 other isolated cloud forest locations may hold new species or divergent populations of Dendragama but lack survey work. Collectively, these comparisons among populations of montane lizards further elucidate the complex biogeographic history of Sumatra's montane forest species and the first phylogeny of the genus Dendragama.