Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus).

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.

Phylogeography of montane dragons could shed light on the history of forests and diversification processes on Sumatra.

Biogeographical evidence, both, for and against the "regional endemism paradigm" hypothesis has been uncovered across the Greater Sunda Region (Sundaland) of Southeast Asia. Additionally, there are competing hypotheses regarding how Pleistocene forests may have impacted biological patterns and processes in Sumatra. Using montane agamid lizards from Sumatra, we derived and analyzed a phylogenetic dataset, genetic divergence estimates, and contemporary distributional patterns among species. We tested whether (1) Sumatra's highland Draconinae diversification fits the regional endemism paradigm hypothesis and (2) Draconinae phylogeography provides biological evidence for Pleistocene forest extent at various points in history. Our results suggest in situ diversification was the main driver behind montane Draconinae lizard diversification in Sumatra, rejecting the "regional endemism paradigm". Contemporary distribution of endemic species and their genetic relationships may potentially provide biologicalevidence for determining more precise elevational lower limits of montane forests during the Pleistocene epoch. Our data suggests montane forests did not retreat more than 700-750 m during glacial maxima because lower retreating forests would have become interconnected, allowing for widespread dispersal, exchange of gene flow and sympatric distributions contemporarily. To the contrary, our divergence estimates show that cloud forest dragons have been isolated for millions of years, suggesting there may have been a continuous disconnect between some areas, predating the Pleistocene. There may also be other ecological and evolutionary factors that impacted Draconinae distributions, such as competition, making this an excellent system for testing questions regarding montane biogeography. Additionally, we provide the first phylogeny for a wide range of Sundaland agamid species and identify some biogeographic pressures that may have triggered montane Draconinae diversification in Sumatra.

Diversification of bent-toed geckos (Cyrtodactylus) on Sumatra and west Java.

Complex geological processes often drive biotic diversification on islands. The islands of Sumatra and Java have experienced dramatic historical changes, including isolation by marine incursions followed by periodic connectivity with the rest of Sundaland across highland connections. To determine how this geological history influenced island invasions, we investigated the colonization history and diversification of bent-toed geckos (genus Cyrtodactylus) on Sumatra and west Java. We used mitochondrial and nuclear sequence data to explore species boundaries, estimate phylogenetic relationships and divergence times, and to reconstruct ancestral range evolution. We found that Sumatran and Javan Cyrtodactylus were closely related to species from the Thai-Malay Peninsula, rather than from Borneo, and that Cyrtodactylus most likely dispersed to Sumatra three times during the late Oligocene and early Miocene. Similarly, Cyrtodactylus invaded west Java from Sumatra once in the early Miocene. Our results suggest that despite isolation by marine incursions during much of the Miocene, Cyrtodactylus dispersed to and from Sumatra and west Java likely via land bridges, and that in situ diversification occurred several times on Sumatra.

Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java.

Geological and climatological processes can drive the synchronous diversification of co-distributed species. The islands of Sumatra and Java have experienced complex geological and climatological histories, including extensive sea-level changes and the formation of valleys between northern, central, and southern components of the Barisan Mountain Range, which may have promoted diversification of their resident species. We investigate diversification on these islands using 13 species of the parachuting frog genus Rhacophorus. We use both mitochondrial and nuclear sequence data, along with genome-wide SNPs to estimate phylogenetic structure and divergence times, and to test for synchronous diversification. We find support for synchronous divergence among sister-species pairs from Sumatra and Java ∼9 Ma, as well as of populations of four co-distributed taxa on Sumatra ∼5.6 Ma. We found that sister species diverged in allopatry on Sumatra and conclude that divergence on Sumatra and Java was affected by sea-level fluctuations that promoted isolation in allopatry.

A taxonomic revision of Boiga multomaculata (Boie, 1827) and B. ochracea (Theobald, 1868), with the description of a new subspecies (Squamata, Serpentes, Colubridae).

The analyses of molecular genetic data (mtDNA markers 16S, ND4, CYTB, and the nuclear marker c-mos) provided evidence that the Asian cat snake taxa Boiga multomaculata and B. ochracea actually represent a single species. They form mixed clades of low intraclade genetic differentiation. This evidence for conspecificy is supported by the lack of differentiation in all examined pholidotic and morphometric characters. Therefore, we formally place Dipsas ochracea Theobald, 1868 in the synonymy of Dipsas multomaculata Boie, 1827. We provide a summary of the tangled taxonomic history of the taxa involved in this study. Also, we resurrect Dipsadomorphus stoliczkae Wall, 1909 from synonymy of B. ochracea, for specimens exhibiting 21 midbody dorsal scale rows. Boiga stoliczkae is found in the Himalayas north and west of the Brahmaputra valley. Finally, based on the detection of historical genetic lineages within the newly defined species Boiga multomaculata we recognize three subspecies: Boiga multomaculata multomaculata (Boie, 1827), Boiga multomaculata ochracea (Theobald, 1868), and Boiga multomaculata septentrionalis n. ssp. which is distributed in northern Myanmar and Assam and Nagaland, India. We designate BMNH 1946.1.2.60 (1) as neotype of Dipsas ochracea Theobald, (2) as lectotype of D. ochraceus Günther, and (3) as lectotype of Boiga ochracea walli Smith, thereby making these names objective synonyms. Finally, we designate BMNH 94.12.31.55 as lectotype of Dipsadomorphus stoliczkae Wall.

A new species of the Cyrtodactylusquadrivirgatus complex (Chordata, Reptilia, Squamata, Gekkonidae) from Sumatra Barat, Indonesia.

Among the six species of Cyrtodactylus occurring in Sumatra, two species were described based on non-Sumatran type series, C.consobrinus and C.quadrivirgatus. The latter species was described originally from Thailand thus the wider distribution in Sumatra should be clarified taxonomically. Cyrtodactylusquadrivirgatus from Sumatra Barat was examined using both morphology and the Natrium Dehydrogenase Subunit 2 (ND2) gene to clarify its taxonomic status and phylogenetic placement. It was found that these specimens form a sister clade to all other species of the sworderi group from Peninsular Malaysia and the genetic distance ranges from 20-24.3%. This subset is herein described as a new species. The new species is readily distinguished from C.quadrivirgatus and other Sumatran species by a combination of characters: small size SVL 37.5-53.78 mm; longitudinal rows of dorsal tubercles 16-19; paravertebral tubercles 31-41; ventral scales 32-43; 24-49 enlarged precloacal and femoral scales; precloacal pores rarely present; no precloacal depression; two postcloacal tubercles on each side; 14-19 subdigital lamellae on forth toe; 9-15 supralabial scales; 9-12 infralabial scales; three or four internasal scales; and 3-6 gular scales that border the first pair of postmental scales. This work underscores the importance of clarifying widely distributed species for taxonomic validation.

Common but ignored: a new species of Cyrtodactylus (Chordata, Reptilia, Squamata, Gekkonidae) from lowland Sumatra Barat, Indonesia.

The lowland region of Sumatra Barat has received little attention in previous biodiversity studies. Past studies have mainly focused on highland habitat and conservation areas. However, many populations of Cyrtodactylus in the lowland habitats of Sumatra Barat were not correctly identified. A phylogenetic tree based on the NADH dehydrogenase subunit 2 (ND2) gene showed that the lowland Sumatran population is the sister group of the Malaysian lowland species, C.semenanjungensis, together nesting within the agamensis group. The genetic divergence within the Sumatra Barat population is 0-4.2% and 18.3-20% to C.semenanjungensis. Further examination of morphological characters revealed that they differed from the sister clade and other Sumatran Cyrtodactylus members by a unique combination of characters such as absence of tubercle on brachium, presence of tubercle on ventrolateral fold, 32-41 paravertebral tubercles, 38-46 ventral scales, enlarged femoral scales, presence of precloacofemoral pores and 22-23 subdigital lamellae under fourth toe. Based on the morphological and molecular evidence, the lowland Sumatran population is herein described as a new species, increasing the number of species in Sumatra to seven. More comprehensive and intensive sampling efforts would most likely yield further discoveries in the group of Sumatran Cyrtodactylus in the near future.

A Checklist of the Herpetofauna of Nusa Kambangan Island, Central Java, Indonesia.

An inventory of herpetofauna species from western part of Nusa Kambangan Island, Central Java, Indonesia, is presented. There are 43 herpetofauna species reported (16 amphibians and 27 reptiles). This study confirmed new distribution record and list some of threatened species. In light of the imminent human disturbances on Nusa Kambangan Island, a conservation plan is urgently needed.

Postmating isolation and evolutionary relationships among Fejervarya species from Lesser Sunda, Indonesia and other Asian countries revealed by crossing experiments and mtDNA Cytb sequence analyses.

To evaluate the degree of postmating isolation and the evolutionary relationships among frog species in the genus Fejervarya from Indonesia (Lesser Sunda), Bangladesh, China, and Japan, crossing experiments and molecular phylogenetic analyses were carried out. Crossing experiments revealed that reciprocal hybrids among F. iskandari, F. verruculosa, and F. sp. large type and between F. multistriata and F. kawamurai are viable through metamorphosis, while those between the F. iskandari group and F. limnocharis group were completely or partially inviable at the tadpole stage and those between Southeast Asian and South Asian Fejervarya groups were completely inviable at the embryonic stage. The mature reciprocal hybrids between F. iskandari and F. verruculosa from Lesser Sunda, Indonesia, showed some degree of abnormality in spermatogenesis. In phylogenetic analyses based on mtDNA Cytb sequences, F. iskandari formed a sister clade with F. verruculosa from Lesser Sunda, Indonesia, with 8.1% sequence divergence. F. multistriata from China formed a clade with populations of F. limnocharis in Thailand, Malaysia, and Indonesia (topotype), and these taxa showed sister relationships to F. kawamurai from Japan with 8.9% sequence divergence. Fejervarya sp. small type from Bangladesh formed a clade with the other South Asian members of the Fejervarya group and formed a sister clade with the Southeast Asian Fejervarya group, with 23.1% sequence divergence in the Cytb gene. These results showed that the degree of postmating isolation reflects molecular phylogenetic relationships and that F. iskandari and F. verruculosa from Indonesia (Lesser Sunda) are reproductively isolated by abnormalities in spermatogenesis and show genetic differentiation.

Taxonomic status of three types of Fejervarya cancrivora from Indonesia and other Asian countries based on morphological observations and crossing experiments.

Although the crab-eating frog Fejervarya cancrivora is one of the most widely distributed species in Asian region, taxonomic relationships among different populations remain unclarified. In this study, we attempted to elucidate the taxonomic status of F. cancrivora from Indonesian and other Asian populations. Five populations of F. cancrivora from Selangor (Malaysia), Cianjur (Java, Indonesia), Trat (Thailand), Khulna (Bangladesh), and Makassar (Sulawesi, Indonesia) were morphologically observed and subjected to crossing experiments. Principal component and clustering analyses revealed that these five populations could be organized into three groups corresponding to three observed morphological types: a Selangor and Cianjur group (large-type), a Trat and Khulna group (mangrove-type), and a Makassar group (Sulawesi-type). The limited crossing experiments revealed that hybrids between Selangor females and Cianjur and Trat males developed normally, whereas hybrids between Selangor females and Khulna males showed incomplete gametic isolation. Histological observations of the testes of mature males revealed the presence of pycnotic nuclei in the hybrids between Selangor females and Khulna males in addition to normal bundles of spermatozoa. In contrast, no pycnotic nuclei were observed in the Selangor controls. Although meiotic metaphases in the controls were normal, those in hybrids showed several abnormalities, such as the appearance of univalents and an increase in rod-shaped bivalents. Based on our findings from the morphological observations and crossing experiments, we conclude that each of three identified types represents a distinct species. We propose that the large-type is F. cancrivora, the mangrove-type is F. moodiei, and the Sulawesi-type represents an undescribed species.