Out of Borneo, again and again: biogeography of the Stream Toad genusAnsoniaStoliczka (Anura: Bufonidae) and the discovery of the first limestone cave-dwelling species

Molecular phylogeny and historical biogeography of Cyclommatus stag beetles (Coleoptera: Lucanidae): Insights into their evolution and diversification in tropical and subtropical Asia

Cyclommatus stag beetles (Coleoptera, Lucanidae) are very interesting insects, because of their striking allometry (mandibles can be longer that the whole body in large males of some species) and sexual dimorphism. They mainly inhabit tropical and subtropical forests in Asia. To date, there has been no molecular phylogenetic research on how these stag beetles evolved and diversified. In this study, we constructed the first phylogenetic relationship for Cyclommatus using multi-locus datasets. Analyses showed that Cyclommatus is monophyletic, being subdivided into two well-supported clades (A and B). The clade A includes the island species from Southeast Asia, and the clade B is formed by the continental species. The divergent time estimates showed these beetles split from the outgroup around 43.10 million years ago (Mya) in the late Eocene, divided during the late Oligocene (around 24.90 Mya) and diversified further during the early and middle Miocene (around 18.19 Mya, around 15.17 Mya). RASP analysis suggested that these beetles likely originated in the Philippine archipelago, then dispersed to the other Southeast Asian archipelagoes, Indochina Peninsula, Southeast Himalayas, and Southern China. Moreover, relatively large genetic distance and stable morphological variations signified that the two clades reach the level of inter-generic differences, i.e., the current Cyclommatus should be separated in two genera: Cyclommatus Parry, 1863 including the clade A species, and Cyclommatinus Didier, 1927 covering the clade B species. In addition, the evidence we generated indicated these beetles’ diversification was promoted probably by both long-distance dispersal and colonization, supporting an “Upstream” colonization hypothesis. Our study provides insights into the classification, genetics and evolution of stag beetles in the Oriental region.

Biogeography of the Sunda Shelf revisited: Insights from Macaranga section Pruinosae (Euphorbiaceae)

The Southeast Asian region of Sundaland is among the world’s major biodiversity hotspots. The region’s biodiversity coupled with its complex and dynamic geographic and climatic histories makes it an ideal region to study the various factors that determine the diversification and distribution patterns of tropical biota. Here we investigate the biogeographic patterns in the partly myrmecophytic Macaranga section Pruinosae to reveal some of the factors that play a role in determining the distribution of biota in Sundaland. We used single nucleotide polymorphisms (SNP) data derived from GBS, a next generation sequencing technique, in maximum likelihood and cluster analyses to determine phylogenetic relationships and population structures within this taxonomic section. Bayesian inference based on secondary calibration points and ancestral area reconstruction analyses were performed to infer spatial–temporal origins of the major lineages in the section. The results from these analyses were further substantiated using nuclear microsatellite data obtained from a broader sample set of two widely distributed species within the section: Macaranga gigantea and Macaranga pruinosa. Phylogenetic and cluster analyses reveal four well-defined, discrete species groups within section Pruinosae, all of which but one originated in Borneo with the crown node dated at 3.58 mya. Biogeographic patterns within the species reveal a biogeographic barrier between east and west Sundaland besides bringing to light the role played by various geological factors, especially the Crocker Range, on Borneo. Patterns also reveal a biogeographic barrier between the Bangka/Belitung islands and Sumatra for ant-free, swamp-adapted species. This study provides evidence that geographic barriers, edaphic conditions, and ecological adaptations are tightly linked and that their mutual interaction determines the diversification and distribution of species.

An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.

PL, Lim KKP, Imbun PY, Anuar MSS. An investigation into the taxonomy of Abavorana luctuosa (Peters, 1871) (Anura, Ranidae) and the resurrection of Rana decorata Mocquard, 1890 from Borneo

The taxonomic status of the ranid frog Abavorana luctuosa (Peters, 1871) was investigated using a combination of molecular and morphological data. The analyses revealed that A. luctuosasensu lato is composed of two species in Borneo. One of these species agrees with the description of Rana decorata Mocquard, 1890 which is resurrected in the combination Abavorana decoratacomb. nov. (Mocquard, 1890). Abavorana decorata is recovered as the sister lineage to the remainder of Abavorana and differs by a 16.0–17.0 % uncorrected pairwise sequence divergence from its congeners A. nazgul and A. luctuosa, respectively. It is distinguishable morphologically from A. luctuosa and A. nazgul by its ventral pattern (bold, black and white reticulations on its venter along with bold banding on the underside of hind limbs vs. generally immaculate and spotted in the latter two species), and a prominent white streak beneath the eye and/or tympanum extending to the corner of the jaw. Abavorana decorata further differs from A. luctuosa by having a significantly wider head and snout, larger interorbital and tympanum diameters, longer femur in both sexes, and various combinations of other mensural characters. Both species are sympatric in Borneo and this discovery adds to a growing number of widespread Sundaic species shown to be species complexes with distinct forms in Borneo.

Two New Ansonia from Mountains of Borneo (Anura, Bufonidae)

Two lineages of stream toads in the genus Ansonia from Malaysian Borneo have long been suspected to be specifically distinct on the basis of molecular data. We assessed the taxonomic status of these lineages using morphological and additional genetic data. In mtDNA phylogeny, each lineage-one from Bario, Kelabit Highlands of Sarawak, the other from Mt. Mulu of Sarawak and the Crocker Range of Sabah-is separated from other congeners by large genetic distances, comparable with those observed between heterospecific species in the genus. These lineages are also morphologically distinguishable from other species, and are considered to represent valid, independently evolving species. We therefore describe them as A. kelabitensis sp. nov. and A. kanak sp. nov.

Two New Species of Ansonia from Thailand (Anura: Bufonidae)

The taxonomic status of two populations of stream toads of the genus Ansonia from Thailand, previously suspected to be specifically distinct on the basis of molecular data, are assessed using morphological and additional genetic data. In mtDNA phylogeny, each of the two Thai lineages, one from Pilok Subdistrict, Kanchanaburi, and another from Phuket Island, are separated from other congenerics from the Thai-Malay Peninsula by large genetic distances, comparable with those observed between other species in the genus. Although each of the two lineages is superficially similar to other species morphologically, they are distinguishable in several morphological traits and are considered to represent valid, independently evolving species. We therefore describe them as A. pilokensis sp. nov. and A. phuketensis sp. nov.

A new limestone-dwelling species of Micryletta (Amphibia: Anura: Microhylidae) from northern Vietnam

We report on a new species of the genus Micryletta from limestone karst areas in northern Vietnam, which is described on the basis of molecular and morphological evidence. Micryletta nigromaculata sp. nov. is restricted to narrow areas of subtropical forests covering karst massifs in Cat Ba National Park (Hai Phong Province) and Cuc Phuong National Park (Ninh Binh Province) at elevations of 90-150 m a.s.l. In the phylogenetic analyses, the new species is unambiguously positioned as a sister lineage to all remaining species of Micryletta. We also discuss genealogical relationships and taxonomic problems within the genus Micryletta, provide molecular evidence for the validity of M. erythropoda and discuss the taxonomic status of M. steinegeri. We suggest the new species should be considered as Endangered (B1ab(iii), EN) following the IUCN's Red List categories. A discussion on herpetofaunal diversity and conservation in threatened limestone karst massifs in Southeast Asia is provided.

A phylogenetic taxonomy of the Cyrtodactylus peguensis group (Reptilia: Squamata: Gekkonidae) with descriptions of two new species from Myanmar

A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar.

Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).