Research and Education Division

Kota Kinabalu, Malaysia

Research and Education Division

Kota Kinabalu, Malaysia
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Matsui M.,Kyoto University | Tominaga A.,Kyoto University | Tominaga A.,University of Ryukyus | Tominaga A.,Japan National Institute of Environmental Studies | And 11 more authors.
Molecular Phylogenetics and Evolution | Year: 2010

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, tRNAval, 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. Crown Copyright © 2009.


PubMed | Borneo Futures Project, Km 10, National University of Malaysia, Kent State University and 3 more.
Type: | Journal: BMC genomics | Year: 2015

Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxons range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84Ma.Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.


Nishikawa K.,Kyoto University | Matsui M.,Kyoto University | Yong H.-S.,University of Malaya | Ahmad N.,National University of Malaysia | And 11 more authors.
Molecular Phylogenetics and Evolution | Year: 2012

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. © 2012 Elsevier Inc.


Hamidy A.,Kyoto University | Hamidy A.,Indonesian Institute of Sciences | Matsui M.,Kyoto University | Shimada T.,Kyoto University | And 6 more authors.
Molecular Phylogenetics and Evolution | Year: 2011

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 2451bp 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. © 2011 Elsevier Inc.


Matsui M.,Kyoto University | Hamidy A.,Kyoto University | Hamidy A.,Indonesian Institute of Sciences | Murphy R.W.,Royal Ontario Museum | And 9 more authors.
Molecular Phylogenetics and Evolution | Year: 2010

By investigating genealogical relationships, we estimated the phylogenetic history and biogeography in the megophryid genus Leptobrachium (sensu lato, including Vibrissaphora) from southern China, Indochina, Thailand and the Sundaland. The genealogical relationships among the 30 named and unnamed taxa were estimated using 2009 bp of sequences from the mitochondrial DNA genes 12S rRNA, tRNAval, and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. The genus Leptobrachium was a well-supported monophyletic group that contained two major clades. One clade had three subclades primarily from disjunct regions including Borneo, Peninsular Malaysia and Java, and Thailand. The Bornean subclade included one species each from the Philippines and Sumatra. The other major clade consisted of two subclades, one from Indochina and the other from southern China (Vibrissaphora). Divergence times estimated an old evolutionary history of each subclade, one that could not be explained by the geohistory of Southeast Asian major landmasses. © 2010 Elsevier Inc. All rights reserved.


PubMed | Washington University in St. Louis, Research and Education Division, Dartmouth College, University of the Philippines at Diliman and Universiti Malaysia Sabah
Type: | Journal: Frontiers in integrative neuroscience | Year: 2014

The fovea is a declivity of the retinal surface associated with maximum visual acuity. Foveae are widespread across vertebrates, but among mammals they are restricted to haplorhine primates (tarsiers, monkeys, apes, and humans), which are primarily diurnal. Thus primates have long contributed to the view that foveae are functional adaptations to diurnality. The foveae of tarsiers, which are nocturnal, are widely interpreted as vestigial traits and therefore evidence of a diurnal ancestry. This enduring premise is central to adaptive hypotheses on the origins of anthropoid primates; however, the question of whether tarsier foveae are functionless anachronisms or nocturnal adaptations remains open. To explore this question, we compared the diets of tarsiers (Tarsius) and scops owls (Otus), taxa united by numerous anatomical homoplasies, including foveate vision. A functional interpretation of these homoplasies predicts dietary convergence. We tested this prediction by analyzing stable isotope ratios that integrate dietary information. In Borneo and the Philippines, the stable carbon isotope compositions of Tarsius and Otus were indistinguishable, whereas the stable nitrogen isotope composition of Otus was marginally higher than that of Tarsius. Our results indicate that species in both genera consumed mainly ground-dwelling prey. Taken together, our findings support a functional interpretation of the many homoplasies shared by tarsiers and scops owls, including a retinal fovea. We suggest that the fovea might function similarly in tarsiers and scops owls by calibrating the auditory localization pathway. The integration of auditory localization and visual fixation during prey detection and acquisition might be critical at low light levels.


Shimada T.,Aichi University of Education | Shimada T.,Kyoto University | Matsui M.,Kyoto University | Yambun P.,Research and Education Division | Sudin A.,Universiti Malaysia Sabah
Zootaxa | Year: 2011

Previous analyses of molecular and larval morphology have suggested that Meristogenys amoropalamus is composed of two cryptic species, but no diagnostic characters of their adult morphology have been reported. Here, we compared adult characters of these two species and found that they differed in iris colour (yellowish-green and sandy brown), tympanum size and relative limb length. Based on the results of analysis of DNA sequences of the type specimens and a discriminant analysis using 18 morphological variables, we conclude that the lineage with green irises is the true M. amoropalamus, and that the lineage with sandy brown irises is a new species, M. dyscritus sp. nov. In northern Sabah, M. dyscritus is distributed in altitudes lower than those of M. amoropalamus, but the distributional ranges of their larvae overlap in some streams. Meristogenys amoropalamus has larger and lighter-coloured ova, smaller clutch sizes and a more interstitial larval life than M. dyscritus. These differences suggest that M. amoropalamus has a more cryptic life during its larval period than M. dyscritus. Copyright © 2011.


Matsui M.,Kyoto University | Nishikawa K.,Kyoto University | Yambun P.,Research and Education Division
Zootaxa | Year: 2014

A new species of Leptolalax is described from Kinabalu National Park in western Sabah, Malaysian Borneo. The new species had been assigned to L. dringi, L. gracilis, or L. fritinniens in the past. It differs from all congeners, including these species, by a unique combination of morphological characters, including small body size, rounded snout, narrower interorbital than upper eyelid, basal toe webbing, smooth skin with tiny tubercles on dorsum and dorsal side of head, small pectoral glands, absence of supraaxillary glands and ventrolateral glandular ridges, spotted venter, advertisement call consisting of long series of 1-149 notes, each composed of three or four pulses, and dominant frequency at 6.90-7.35 kHz, without prominent frequency modulation. Copyright © 2014 Magnolia Press.


Shimada T.,Kyoto Gakuen University | Shimada T.,Kyoto University | Matsui M.,Kyoto University | Yambun P.,Research and Education Division | Sudin A.,Universiti Malaysia Sabah
Zoological Journal of the Linnean Society | Year: 2011

The genus Meristogenys (Anura: Ranidae), endemic to Borneo, presents serious taxonomic problems despite being one of the commonest frogs in the mountainous regions of this island. We investigated molecular and morphological variations in Meristogenys whiteheadi (Boulenger, 1887) using larval and adult specimens from Sabah and Sarawak (Malaysia). We found three allopatric lineages in this species. We regard each of these as a distinct species because they are separated by a large genetic distance, and do not form any monophyletic group. Their morphological characters indicate that the distributional range of M. whiteheadi s.s. is divided into two disjunct areas: Mt Kinabalu (northern Sabah) and northern Sarawak. The two other lineages occupy ranges between those of M. whiteheadi, and represent undescribed cryptic species. One of these, Meristogenys stigmachilus sp. nov., collected from the northern part of the Crocker Range, is distinguished from M. whiteheadi by black spots on the upper lip and dark dots scattered on the back. A second undescribed species, Meristogenys stenocephalus sp. nov., was collected mainly from the southern part of the Crocker Range, and is characterized by the large body size of males and a relatively narrow head. Meristogenys stenocephalus sp. nov. also differs from M. stigmachilus sp. nov. and M. whiteheadi in larval morphology, but larvae of the latter two cannot be differentiated morphologically. We discuss relative tibia length, a diagnostic specific characteristic in the genus Meristogenys, and the relationships between body size and sexual size dimorphism in this genus.© 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161, 157-183. © 2011 The Linnean Society of London.


Nishikawa K.,Kyoto University | Matsui M.,Kyoto University | Yambun P.,Research and Education Division
Current Herpetology | Year: 2012

A new unstriped Ichthyophis is described based on one adult male and five larval specimens collected from the northwestern slope of Mt. Kinabalu, Sabah, Malaysia. The new species is distinguished from all other unstriped congeners by a combination of characters that includes position of tentacles and number of annuli, scale rows, splenial teeth, and vertebrae. The anterior phallodeum morphology is described for the new species. The evolution of large larvae of unstriped Ichthyophis is discussed briefly. © 2012 by The Herpetological Society of Japan.

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