Male secondary sexual characteristics, sexual selection, and molecular divergence in fanged ranid frogs of Southeast Asia

A group of Southeast Asian frogs of the family Ranidae are characterized by a suite of unusual secondary sexual characteristics. Males are larger than females, possess bony odontoid processes (fangs) and have enlarged heads. While all members of this clade are sexually dimorphic in this suite of characters, the degree of development of the secondary sexual characteristics in males varies widely across species. One of the most common species, Rana blythii Boulenger, has an extremely broad geographical range. This frog lacks an advertisement call in Borneo but calling has been reported in populations from peninsular Malaysia and Vietnam. This study examines the relationship between the expression of male secondary sexual characteristics, molecular divergence and number of speciation events in widely separated populations of R. blythii , and between R. blythii and other species of closely related fanged frogs belonging to the grunniens species group. Results from morphometric and sequence data indicate that (1) there is no correlation between morphological and molecular distance in these frogs and (2) there is no correlation between morphological distance and the number of speciation events separating taxa. Systematic analysis demonstrates that R. blythii , as currently recognized, is not a single species nor is it monophyletic.     

Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the asian and Australian faunal zones

The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.     

When Thailand was an island – the phylogeny and biogeography of mite harvestmen (Opiliones,Cyphophthalmi, Stylocellidae) in Southeast Asia

Aim To develop a comprehensive explanation for the biological diversity of Southeast Asia, especially in the Wallacea and Sundaland regions. This study focuses on a group of arachnids, mite harvestmen, which are thought to be an extremely old group of endemic animals that have been present in the region since most of its land supposedly formed part of the northern rim of the supercontinent Gondwana. Location Eastern Himalayas, Thai‐Malay Peninsula, Sumatra, Borneo, Java, Sulawesi, and New Guinea. Methods  Approximately 5.6 kb of sequence data were obtained from 110 South‐east Asian Cyphophthalmi specimens. Phylogenetic analyses were conducted under a variety of methods and analytical parameters, and the optimal tree was dated using calibration points derived from fossil data. Event based and paralogy‐free subtree biogeographical analyses were conducted. Results The Southeast Asian family Stylocellidae was recovered as monophyletic, arising on what is now the Thai‐Malay Peninsula and diversifying into three main clades. One clade (Meghalaya, here formally placed in Stylocellidae) expanded north as far as the eastern Himalayas, a second clade entered Borneo and later expanded back across the Sundaland Peninsula to Sumatra, and a third clade expanded out of Borneo into the entire lower part of Sundaland. Molecular dating suggested that Stylocellidae separated from other Cyphophthalmi 295 Ma and began diversifying 258 Ma, and the lineage that inhabits mostly Borneo today began diversifying between 175 and 150 Ma. Main conclusions The topology and molecular dating of our phylogenetic hypothesis suggest that Stylocellidae originated on Gondwana, arrived in Southeast Asia via the Cimmerian palaeocontinent, and subsequently diversified north, then south. Their present distribution in the Indo‐Malay Archipelago is explained largely by a diversification over the Sundaland Peninsula before western Sulawesi departed and the peninsula was extensively inundated.     

Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach

Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophorus were inferred from 1219 base positions of mitochondrial 12S and 16S rRNA genes. Results of the phylogenetic analyses incorporating data for representatives of other lygosomine genera indicated that the basal phylogenetic split within Tropidophorus separated a clade of continental Indochinese species exclusive of T. cocincinensis and T. microlepis from one comprising T. cocincinensis , T. microlepis and species from Borneo, Sulawesi and the Philippines. Of the latter group, the two continental species form the sister taxon to a clade comprising the island species. Diversification among species in Indochina and among Borneo, the Philippines and Sulawesi was likely concentrated in the Miocene, with no apparent dispersal among these regions during the Pleistocene. The body depression recognized in several Indochinese species is likely to have occurred twice in parallel as an adaptation to saxicolous habitats.     

Phylogenetic relationships of the mustache toads inferred from mtDNA sequences

Species of the genus Vibrissaphora are unique among all anurans in that males exhibit external cornified spines in the maxillary region during the breeding season. They were separated from species of the genus Leptobrachium based on this unique character. We construct a phylogeny using the 16S, ND4, and cytochrome b mitochondrial genes of 42 individuals from eight species of Vibrissaphora and five species of Leptobrachium from mainland China, Southeast Asia, and Hainan Island. Species of both Oreolalax and Scutiger were used as outgroups. The results indicate that: L. huashen and L. chapaense form a clade that is nested within Vibrissaphora, and L. hainanense is the sister taxon to the clade comprising all Vibrissaphora plus L. chapaense and L. huashen; V. boringiae is grouped with a clade consisting of V. leishanensis, V. liui, and V. yaoshanensis; and V. yaoshanensis is a species separate from V. liui. We propose taxonomic changes that reflect these findings. Also based on the resulting phylogenetic trees, we propose that the mustache toads originated in the trans-Himalayan region of southwest China, and that the evolution of maxillary spines, large body size, and reverse sexual size dimorphism in these frogs was influenced by intrasexual selection due to adopting a resource-defense polygyny mating system.     

Multiple invasions of the Ryukyu Archipelago by Oriental frogs of the subgenus Odorrana with phylogenetic reassessment of the related subgenera of the genus Rana

The genus Rana, notably diversified in Oriental regions from China to Southeast Asia, includes a group of cascade frogs assigned to subgenera Odorrana and Eburana. Among them, R. ishikawae and the R. narina complex represent the northernmost members occurring from Taiwan to the Ryukyu Archipelago of Japan. Relationships of these frogs with the continental members, as well as the history of their invasions to islands, have been unclear. The taxonomic status of Odorrana and related genera varies among authors and no phylogenetic reassessment has been done. Using partial sequences of mitochondrial 12S and 16S rRNA genes, we estimated phylogenetic relationships among 17 species of the section Hylarana including Odorrana and Eburana, and related species from the Ryukyus, Taiwan, China, Thailand, Malaysia, and Indonesia. We estimate that (1) Odorrana is monophyletic and encompasses species of Eburana and R. hosii, which is now placed in Chalcorana, (2) the ancestor of R. ishikawae separated from other Rana in the middle to late Miocene prior to its entry to the Ryukyu Archipelago, (3) the ancestor of the R. narina complex later diversified in continental Asia, and invaded the Ryukyu Archipelago through Taiwan, (4) the R. narina complex attained its current distribution within the Ryukyus through niche segregations, and (5) vicariance of R. hosii between Malay Peninsula and Borneo occurred much later than the divergence events in the R. narina complex. Current subgeneric classification of Rana, at least of Southeast Asian members, requires full reassessment in the light of phylogenetic relationships.     

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 2461 bp 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.     

The flea genus Sigmactenus (Siphonaptera: Leptopsyllidae): three new taxa from Sulawesi, updated identification key, and distribution map for all known species and subspecies

One new species and two new subspecies of fleas are described. These are S. sulawesiensis n. sp. from North and Central Sulawesi, S. alticola pilosus n. ssp. from Central Sulawesi, and S. alticola crassinavis n. ssp. from North Sulawesi. All three of these new taxa are ectoparasites of native, endemic murine rodents. Two of the new taxa, S. sulawesiensis and S. alticola crassinavis, coexist on the same mountain, Gunung Moajat, in North Sulawesi. The related S. alticola alticola, which becomes the nominate subspecies, parasitises the murine rodent Maxomys alticola in northern Borneo (Sabah) and it is hypothesized that Sigmactenus first colonized Sulawesi as an ectoparasite of ancestral Maxomys, or perhaps Rattus, as these murines dispersed from southeast Asia to Sulawesi; 15 endemic murine rodent species belonging to these two genera are known to currently inhabit Sulawesi. An identification key and distribution map are included for all known species and subspecies of Sigmactenus. In addition to the three new taxa and S. a. alticola, these include: S. celebensis from South Sulawesi, S. timorensis from Timor, S. toxopeusi from New Guinea, and S. werneri from the Philippines (Mindanao and Negros).     

Taxonomic revision of shrews of the genus Crociduras from the Sunda Shelf and Sulawesi with description of two new species (Mammalia: Soricidae)

The skulls of 387 shrews of the genus Crocidura sampled in peninsular Malaysia, Sumatra, Borneo, Java and Sulawesi were submitted to principal component and stepwise discriminant analyses. These analyses helped to delineate morphological taxa in this species-rich genus of mammals. Most morphologic groups could be attributed to described species, except one taxon from Sumatra and one from Sulawesi, which are described and named as new. Most of the 21 species recognized in this paper are endemic to one major island. Although Sulawesi has never been connected to the mainland, it supports at least six species, followed by Sumatra (5–6 species), Java and the Malay Peninsula (4 spp) and Borneo (3 spp). C. monticola is apparently the only widespread species whose distribution range covers the entire Malay Archipelago except the Philippines and Sulawesi. In contrast, the continental C. fuliginosa enters only marginally into the Sunda Shelf: its southernmost record is on the Malay Peninsula. This interpretation is completely different from the classical view that C. fuliginosa is a cosmopolitan species occupying the whole of Southeast Asia. Identification keys, tables of measurements and discriminant functions provided in this work may aid in identification of the various species and subspecies of Crocidura living in the Malaya Archipelago.     

Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

We investigated the phylogenetic relationships and estimated the history of species diversification and character evolution in two ichthyophiid genera: Caudacaecilia and Ichthyophis. We estimated the phylogenetic relationships of 67 samples from 33 localities in Southeast Asia from 3840-bp sequences of the mitochondrial 12S rRNA, 16S rRNA, and cyt b genes using Bayesian inference, maximum likelihood, and maximum parsimony methods. The Southeast Asian samples formed a well-supported clade differentiated from a South Asian sample. The Southeast Asian clade was divided into two subclades, one containing samples from South China, Indochina, Malay Peninsula, and Java. The other consisted of samples from Borneo and the Philippines. Neither Caudacaecilia nor Ichthyophis was monophyletic, nor did samples with or without light stripes lateral to the body form clades. We found several distinct sympatric lineages and undescribed species, especially from Sundaland.     

Morphological and genetic discordance in two species of Bornean Leptobrachium (Amphibia, Anura, Megophryidae)

Recent phylogenetic studies of Southeast Asian megophryid Leptobrachium, while clarifying (1) distinct specific status of three Philippine populations and (2) high genetic diversities within Bornean Leptobrachium montanum, posed two questions, (1) relationships and divergence histories of two Philippine species and Bornean Leptobrachium gunungense, and (2) possible discordance between phylogenetically and morphologically defined lineages. In order to solve these questions, and especially reviewing current taxonomy of Bornean species, we estimated the phylogenetic relationships of endemic Bornean species together with their putative relatives from Philippines and Sumatra, using 2451 bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA genes. With respect to Leptobrachium hasseltii and Leptobrachium chapaense, lineages from Borneo, Philippines, and Sumatra formed a monophyletic group with Leptobrachium lumadorum from Mindanao as the basal clade, while two other Philippine species from Palawan and Mindoro formed a clade and nested in Bornean lineages. Sister species relationship of the two Philippine species and L. gunungense is not supported, rejecting the hypothesis of Philippine origin of L. gunungense. Phylogeny does not conform to morphological variation, and the topotypic L. montanum and one lineage of Leptobrachium abbotti are genetically very close despite their clear difference in ventral color pattern. Furthermore, each of these species forms a paraphyletic group and contains several lineages, each of which is a candidate of good species. These results clearly indicate that current taxonomy of Bornean species based on several morphological characteristics requires complete revision. Detailed studies on adult and larval morphology, as well as acoustic characteristics, are necessary to evaluate the taxonomic status of all lineages recovered.     

Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids

Aim To test the hypothesis that continental drift drives diversification of organisms through vicariance, we selected a group of primitive arachnids which originated before the break‐up of Pangaea and currently inhabits all major landmasses with the exception of Antarctica, but lacks the ability to disperse across oceanic barriers. Location Major continental temperate to tropical landmasses (North America, South America, Eurasia, Africa, Australia) and continental islands (Bioko, Borneo, Japan, Java, New Caledonia, New Guinea, New Zealand, Sri Lanka, Sulawesi, Sumatra). Methods Five kb of sequence data from five gene regions for more than 100 cyphophthalmid exemplars were analysed phylogenetically using different methods, including direct optimization under parsimony and maximum likelihood under a broad set of analytical parameters. We also used geological calibration points to estimate gross phylogenetic time divergences. Results Our analyses show that all families except the Laurasian Sironidae are monophyletic and adhere to clear biogeographical patterns. Pettalidae is restricted to temperate Gondwana, Neogoveidae to tropical Gondwana, Stylocellidae to Southeast Asia, and Troglosironidae to New Caledonia. Relationships between the families inhabiting these landmasses indicate that New Caledonia is related to tropical Gondwana instead of to the Australian portion of temperate Gondwana. The results also concur with a Gondwanan origin of Florida, as supported by modern geological data. Main conclusions By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats, but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted. Our results strongly support the presence of a circum‐Antarctic clade of formerly temperate Gondwanan species, a clade restricted to tropical Gondwana and a Southeast Asian clade that originated from a series of early Gondwanan terranes that rifted off northwards from the Devonian to the Triassic and accreted to tropical Laurasia. The relationships among the Laurasian species remain more obscure.     

Clambidae of Sulawesi with reference to the biogeography of the Sunda Islands (Coleoptera, Eucinetoidea)

Abstract. Eight new species of Clambidae from Sulawesi (Celebes), and two new species and a new subspecies from Borneo and Sumatra are described. The emerging distribution patterns reflect the long-standing isolation of Sulawesi from the rest of the Sunda Islands and from the Asian continent. The clambid fauna of Borneo, Sumatra and the Malayan Peninsula indicates close faunal-historic contacts.     

猪科的系统发育与系统地理分化

猪科动物是最为昌盛的哺乳动物之一,但它们的分类及系统发育关系却尚待解决。为此,用PCR直接测序法测定了一个红河猪(Potamochoerusporcus)、一个马来西亚野猪(Susbarbatus)以及数头欧亚野猪(Susscorfa)线粒体细胞色素b全序列1140bp。结合从GenBank中获得的其他猪科物种胞色素b序列,用邻接法和最大简约法构建了猪科物种的系统发育关系,其结果显示苏拉威西鹿猪与其他猪科物种为姐妹群的关系。非洲物种疣猪和河猪聚为一枝,而欧亚猪属物种聚为另一支。各物种在系统发育关系中的位置与它们的地理分布对应。猪属物种可以被划分为3个种组:分布于菲律宾群岛、苏拉威西岛及其邻近岛屿的猪属物种形成一个种组,包括苏拉威西岛疣猪、菲律宾疣猪和印度尼西亚疣猪;欧亚野猪种组,包括欧亚野猪和姬猪;须猪和爪哇疣猪形成一个种组。     

Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae)

We investigated the phylogenetic relationships among 20 species of Oriental torrent frogs in the genus Amolops and its allies from China and Southeast Asia based on 1346-bp sequences of the mitochondrial 12S and 16S rRNA genes. Oriental species of the tribe Ranini form a monophyletic group containing 11 clades (Rana temporaria + Pseudoamolops, R. chalconota, four clades of Amolops, Meristogenys, three clades of Huia species, and Staurois) for which the phylogenetic relationships are unresolved. The genus Amolops consists of southern Chinese, southwestern Chinese, Thai, and Vietnamese-Malaysian lineages, but their relationships are also unresolved. The separation of southern and southwestern lineages within China conforms to previous morphological and karyological results. Species of Huia do not form a monophyletic group, whereas those of Meristogenys are monophyletic. Because P. sauteri is a sister species of R. temporaria, distinct generic status of Pseudoamolops is unwarranted.     

Ranging behaviour,activity, habitat use,and morphology of the Malay civet (Viverra tangalunga) on Peninsular Malaysia and comparison with studies on Borneo and Sulawesi

The Malay civet (Viverra tangalunga) is found throughout Southeast Asia, but there have been very few studies on its natural history and ecology. We present here the results from the first radio telemetry study of this species on Peninsular Malaysia and compared our findings to similar studies on Borneo and Sulawesi. From August 2004 to August 2006, we captured 11 Malay civets in Krau Wildlife Reserve and radio-tracked seven adults (four males and three females). The mean weight of males (6.6 kg) was significantly higher than females (5.8 kg). Both sexes on Peninsular Malaysia were larger than their counterparts on Borneo and Sulawesi. There was no significant difference between the mean sizes of male and female home ranges on Peninsular Malaysia; the mean home range size for both sexes was 143 ha (95% MCP), which was larger than the mean range size recorded on Borneo and Sulawesi. We found that the Malay civet is a solitary, territorial species on Peninsular Malaysia: mean range overlap was 15% for males and 0% for females, and the home range of each male overlapped one or two females. Malay civets were mainly nocturnal, with some periods of rest during the night; daytime rest sites were within dense ground cover. Lowland forest is an essential habitat for this species; although Malay civets were sometimes found in plantations, they did not venture far from forested habitat.     

A Novel Reproductive Mode in Frogs: A New Species of Fanged Frog with Internal Fertilization and Birth of Tadpoles

We describe a new species of fanged frog (Limnonectes larvaepartus) that is unique among anurans in having both internal fertilization and birth of tadpoles. The new species is endemic to Sulawesi Island, Indonesia. This is the fourth valid species of Limnonectes described from Sulawesi despite that the radiation includes at least 15 species and possibly many more. Fewer than a dozen of the 6455 species of frogs in the world are known to have internal fertilization, and of these, all but the new species either deposit fertilized eggs or give birth to froglets.     

Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis)

One group of mantellid frogs from Madagascar (subgenus Pandanusicola of Guibemantis) includes species that complete larval development in the water-filled leaf axils of rainforest plants. This group consists of six described species: G. albolineatus, G. bicalcaratus, G. flavobrunneus, G. liber, G. pulcher, and G. punctatus. We sequenced the 12S and 16S mitochondrial rRNA genes ( approximately 1.8 kb) from multiple specimens (35 total) of all six species to assess phylogenetic relationships within this group. All reconstructions strongly supported G. liber as part of the Pandanusicola clade, even though this species does not breed in plant leaf axils. This result confirms a striking reversal of reproductive specialization. However, all analyses also indicated that specimens assigned to G. liber include genetically distinct allopatric forms that do not form a monophyletic group. Most other taxa that were adequately sampled (G. bicalcaratus, G. flavobrunneus, and G. pulcher) likewise consist of several genetically distinct lineages that do not form monophyletic groups. These results suggest that many of the recognized species in this group are complexes of cryptic species.     

Theloderma licin McLeod and Ahmad, 2007 （Lissamphibia： Anura： Rhacophoridae）, a New Frog Record for Borneo

A new record of the rhacophorid frog, Theloderma licin is reported from Gunung Serambu, in the Bau region of western Sarawak, East Malaysia, which comprises the first published record of the species from the Sundaic island of Borneo. The species was previously known from the Malay Peninsula （southern Peninsular Thailand and Peninsular Malaysia）. Species of Theloderma are widespread in mainland and insular Southeast Asia, their arboreal habits perhaps contributing to our perception of rarity.     

Cyanoneuron (Rubiaceae) in Sulawesi? Reaffirmation of a Bornean endemic genus as a cautionary example on the use and interpretation of natural history specimen data

Cyanoneuron, a genus of five species in the Rubiaceae, was described from Borneo and Sulawesi. We show that the occurrence of the genus in Sulawesi was probably derived from careless specimen labeling, and that Cyanoneuron should be considered endemic only to Borneo according to present knowledge. Erroneous collection localities in natural history specimen data can lead to the wrong interpretation of species distribution patterns, so care should be taken to verify specimen records before they are used.