Rosli Ramli

Enigmatic Phylogeny of Skuas (Aves: Stercorariidae)

Multiple sources of evidence show that the skuas (Aves: Stercorariidae) are a monophyletic group, closely related to gulls (Laridae). On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large–bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas (Otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta: Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere–breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter–generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.

Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species

Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.

Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region

Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform ‘b’ as valid species; indicated that S. xuandei, cytoform L, and morphoform ‘a’ contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G.

New zoonotic cases of Onchocerca dewittei japonica (Nematoda: Onchocercidae) in Honshu, Japan.

BackgroundZoonotic infections with Onchocerca species are uncommon, and to date only 25 clinical cases have been reported worldwide. In Japan, five previous zoonotic infections were concentrated in Oita, Kyushu (the southern island), with one previous case in Hiroshima in the western part of Honshu (the main island). The causative agent in Japan was identified as Onchocerca dewittei japonica Uni, Bain & Takaoka, 2001 from Japanese wild boars (Sus scrofa leucomystax Temminck, 1842). Here we report two infections caused by a female and male O. dewittei japonica, respectively, among residents of Hiroshima and Shimane Prefectures in the western part of Honshu.MethodsIn both cases, nodules were surgically removed. The parasites in nodules were identified on the basis of their histopathological characteristics. Identification was confirmed by sequencing the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from worms in the tissues used in the histological preparations.ResultsCase 1 was a 61-year-old woman from Hiroshima Prefecture who complained of a painful subcutaneous nodule on the back of her right hand. The causative agent was identified as a female O. dewittei japonica owing to transverse ridges on the cuticle and molecular analysis. Case 2 was a 78-year-old woman from Shimane Prefecture who had a painful nodule in the left temporal region. Histopathological characteristics and cox1 sequencing of the worm indicated that the causative agent was a male O. dewittei japonica.ConclusionsFor Cases 1 and 2, we diagnosed the causative agents as a female and male O. dewittei japonica, respectively. These findings indicate the spread of a zoonosis caused by O. dewittei japonica in the western part of Honshu, where wild boars have recently extended their habitats because of decreased annual snowfall, unused rice fields and a decline in the number of hunters in Japan. The O. dewittei japonica infection rate among wild boars was reported as 78% in Shimane Prefecture, in the western part of Honshu. Therefore, in the near future, zoonotic onchocercosis is likely to occur in Honshu as well as Kyushu, where wild boars, blackfly vectors and humans share the same habitat.

Onchocerca takaokai n. sp. (Nematoda: Filarioidea) in Japanese wild boars (Sus scrofa leucomystax): Description and molecular identification of intradermal females.

Human zoonotic onchocercosis is caused by Onchocerca dewittei japonica, parasitic in wild boars (Sus scrofa leucomystax) in Japan. Previously, microfilariae longer than those of Onchocerca dewittei japonica were observed in skin snips from wild boars during the study of O. dewittei japonica. Moreover, the third-stage larvae (L3) of these longer microfilariae were obtained from the blackfly Simulium bidentatum after experimental injections. Based on morphometric and molecular studies, similar L3 were found in blackflies during fieldwork in Oita, Japan. However, except for O. dewittei japonica, adult worms of Onchocerca have not been found in wild boars. In this study, we discovered adult females of a novel Onchocerca species in the skin of a wild boar in Oita, and named it Onchocerca takaokai n. sp. Females of this new species had longer microfilariae and differed from O. dewittei japonica in terms of their morphological characteristics and parasitic location. The molecular characteristics of the cytochrome c oxidase subunit 1 and 12S rRNA genes of the new species were identical to those of the longer microfilariae and L3 previously detected, but they differed from those of O. dewittei japonica at the species level. However, both species indicated a close affinity among their congeners and Onchocerca ramachandrini, parasitic in the warthog in Africa, was basal in the Suidae cluster of the 12S rRNA tree.

Geochemical study of volcanic and associated granitic rocks from Endau Rompin, Johor, Peninsular Malaysia.

Geochemical studies and modelling show that both volcanic and granitic magmas from the western part of the Johor National Park, Endau Rompin are different and probably have different sources. The geochemical plot suggests that both dacite/rhyolite and andesite probably have a common origin as in many of the geochemical plots, these two groups form a similar trend. Volcanic rocks have a transitional geochemical character between tholeiite and calc alkaline on a Y versus Zr plot. (La/Yb)N versus La and TiO2 versus Zr modelling show that the crystallization of both granitic and volcanic magmas are controlled by a different set of minerals. The rare earth elements (REE) patterns of some of the granite and volcanic samples have pronounced negative Eu anomaly indicating plagioclase fractionation. The difference between both profiles is that the granite samples show a concave shape profile which is consistent with liquids produced by partial melting of quartz feldspathic rocks containing amphibole among the residual phase. Both magmas were generated at a different time during the subduction of Sibumasu beneath the Indochina blocks.

The Effects of Water Parameters on Monthly Seagrass Percentage Cover in Lawas, East Malaysia

Seagrass is a valuable marine ecosystem engineer. However, seagrass population is declining worldwide. The lack of seagrass research in Malaysia raises questions about the status of seagrasses in the country. The seagrasses in Lawas, which is part of the coral-mangrove-seagrass complex, have never been studied in detail. In this study, we examine whether monthly changes of seagrass population in Lawas occurred. Data on estimates of seagrass percentage cover and water physicochemical parameters (pH, turbidity, salinity, temperature, and dissolved oxygen) were measured at 84 sampling stations established within the study area from June 2009 to May 2010. Meteorological data such as total rainfall, air temperature, and Southern Oscillation Index were also investigated. Our results showed that (i) the monthly changes of seagrass percentage cover are significant, (ii) the changes correlated significantly with turbidity measurements, and (iii) weather changes affected the seagrass populations. Our study indicates seagrass percentage increased during the El-Nino period. These results suggest that natural disturbances such as weather changes affect seagrass populations. Evaluation of land usage and measurements of other water physicochemical parameters (such as heavy metal, pesticides, and nutrients) should be considered to assess the health of seagrass ecosystem at the study area.

A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.

Foraging niche segregation in Malaysian babblers (Family: Timaliidae)

Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause’ law of competitive exclusion, which states two species occupying the same niche will not stably coexist.

A new case of zoonotic onchocercosis in northern Kyushu, Japan

A case of zoonotic onchocercosis has been found in a resident who lived in Iizuka City, Fukuoka Prefecture, Japan for some time. A 24-year-old male developed a painful nodule on the middle finger of his right hand. The nodule was surgically removed from the vagina fibrosa tendinis of the finger at Beppu Medical Center, Beppu City, Oita Prefecture in 2012. The causative agent was identified as a female Onchocerca dewittei japonica based on its histopathological characteristics. The identity of the filarioid has been confirmed by sequencing the cox1 gene. The present study indicates that the zoonotic onchocercosis caused by O. dewittei japonica has been concentrated in northeast Kyushu.