Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

A review of the genus Rusa in the indo-malayan archipelago and conservation efforts

Genus Rusa, belonging to the deer family Cervidae is native to the Indo-Malaya Archipelago (IMA). However, detailed information on the Rusa genus in the IMA is limited. This review provides comprehensive information on the Rusa genus in the IMA including, threats and conservation efforts. There are four species of deer in Rusa genus, which is Sambar deer (Rusa unicolor), Javan deer (Rusa timorensis), Visayan spotted deer (Rusa alfredi) and Philippine deer (Rusa marianna). Despite their wide distribution in the South Asian and Southeast Asian regions, they are under serious threats. Some conservation efforts that are being done to protect and conserve them among others are; (1) facilities protection, (2) habitat enrichment programme, (3) Ex-situ conservation, (4) legislations, and (5) captive breeding. Conservation through genetics is also an important step in conserving these species. Recommendations for conservation of the genus are also discussed; 1. maintenance of ecosystem. 2. more effective monitoring system on the existing protected area. 3. ex-situ conservation, and 4. habitat monitoring.     

Genetic variation,demographic history and phylogeography of tire track eel,Mastacembelus favus (Synbranchiformes: Mastacembelidae) in Southeast Asia

The complex climatic and geological history of Southeast Asia has been hypothesised to determine the most important aspects of the current phylogeographical structure and distribution of living organisms throughout the region. To test existing hypotheses, the genetic structure of the tire track eel, Mastacembelus favus, was investigated using 823 bp of mitochondrial DNA cytochrome b from 469 individuals from 51 localities encompassing its native range. The results classified all haplotypes into two major lineages, Lineage 1, which was further divided into Lineages 1a (lower Mekong, eastern Gulf of Thailand and Malay—Thai Peninsula), 1b (Banpakong River), 1c (Chao Phraya, Gulf of Thailand and Malay—Thai Peninsula) and 1d (Khlang Yai River), and Lineage 2, the upper reaches of the lower Mekong and the middle Mekong. Strong genetic discontinuities dated approximately 5 MYA were discovered in the Mekong with limited geographical overlap, suggesting a historically dissected drainage between two sections and species colonisation via different routes. The widespread Lineage 1 showed a strong signature of population expansion during the Pleistocene climate oscillation. Haplotype characteristics in the Malay—Thai Peninsula are hypothesised to result from postglacial dispersal from the Mekong and Chao Phraya through an extended Pleistocene drainage network.

     

High Connectivity in Rastrelliger kanagurta: Influence of Historical Signatures and Migratory Behaviour Inferred from mtDNA Cytochrome b

Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.     

Preliminary studies on cryopreservation of snakehead (Channa striata) embryos

This paper reports the findings of the ongoing studies on cryopreservation of the snakehead, Channa striata embryos. The specific objective of this study was to collect data on the sensitivity of C. striata embryo hatching rate to low temperatures at two different developmental stages in the presence of four different cryoprotectants. Embryos at morula and heartbeat stages were selected and incubated in 1 M dimethyl sulfoxide (Me₂SO), 1 M ethylene glycol (EG), 1 M methanol (MeOH) and 0.1 M sucrose solutions at different temperatures for a period of time. Embryos were kept at 24 °C (control), 15 °C, 4 °C and −2 °C for 5 min, 1 h and 3 h. Following these treatments, the embryos were then transferred into a 24 °C water bath until hatch to evaluate the hatching rate. The results showed that there was a significant decrease of hatching rate in both developmental stages following exposure to 4 °C and −2 °C at 1 h and 3 h exposure in each treatment. Heartbeat stage was more tolerant against chilling at −2 °C for 3 h exposure in Me₂SO followed by MeOH, sucrose and EG. Further studies will be conducted to find the best method to preserve embryos for long term storage.     

Length‐weight relationships and condition factors of two threatened fishes,Rasbora tawarensis and Poropuntius tawarensis,endemic to Lake Laut Tawar,Aceh Province,Indonesia

Studied were the length‐weight relationships (LWRs) and condition factors of two threatened species, Rasbora tawarensis and Poropuntius tawarensis, endemic to Lake Laut Tawar. The objective of the present study was to establish baseline data on LWRs of the two endemic fishes. The growth pattern for both species was predicted using a Linear Allometric Model (LAM) of length‐weight relationship and Fulton’s condition factor (K_TL) as well as Relative Weight (W_r). The b value of R. tawarensis was relatively similar between females and males, while the b value of female P. tawarensis was slightly higher than in males. Nevertheless, both R. tawarensis and P. tawarensis showed an allometric negative growth pattern. The average K_TL value of R. tawarensis was 1.85 and 1.73 for females and males, respectively, while P. tawarensis had values of 2.44 and 2.41 for females and males, respectively. In addition, the average W_r values of R. tawarensis were 98.9 and 100.45 for females and males respectively, while 102.30 for female and 102.96 for male P. tawarensis, indicating that the condition factors of P. tawarensis were higher than in R. tawarensis.     

Sensitivity and specificity of the micronucleus test in hypotonic-swollen mononuclear leukocytes compared to the micronucleus test in binucleated lymphocytes to assess chromosomal breaks

OBJECTIVE: To examine the sensitivity and specificity of the micronucleus (MN) test on swollen mononuclear cells compared to that in binucleated lymphocytes. STUDY DESIGN: This is a cross-sectional experimental study. Samples were taken from patients who had a malignancy who were scheduled to receive chemotherapy; samples were taken before and after the chemotherapy regimen began. The MN tests on swollen mononuclear cells and binucleated lymphocytes were performed on every sample. Proportions of micronucleated cells/cells screened were noted and interpreted as positive or negative results. The results of both tests were compared to get the sensitivity and specificity of the MN test on swollen mononuclear cells. RESULTS: Of 59 samples obtained, 54 were included in this study. The results showed that the sensitivity of the MN test on swollen mononuclear cells compared to that on binucleated lymphocytes was 89% and specificity was 78%. CONCLUSION: The MN test on swollen mononuclear cells was able to detect chromosomal breaks caused by chronic clastogen exposure.     

DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes)

Background

DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.

Methodology/Principal Findings

Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32–4.82%) than mean estimates (0.24–0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region''s suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata.

Conclusion/Significance

This study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.     

Constructing interpretive ethnicity in between two nations: television and diasporic discourses of identity in Malaysia

This article discusses the interpretation of television in relation to ethnic identity embraced by the female members of Javanese diaspora in Malaysia. The Javanese diaspora in this context refers to the descendants of the colonial Javanese migrants from Indonesia. In contemporary Malaysia, they are considered as Malays, but essentially they retain some cultural identifications of Javanese ethnicity, especially the language. As Malaysia becomes one of the destinations for Indonesian migrant labour and popular culture, the Javanese diaspora are certainly exposed to manifold images of their ethnic origin. Through the audience ethnography in a Javanese community of Selangor, this article reveals that the Malaysian Javanese women negotiate both representative and distant images of Javanese identity on television. Their interpretation of ethnic identity from television represents the notion of ‘interpretive ethnicity’.     

The vesicular-arbuscular (VA) mycorrhiza and its effects on growth of vegetatively propagated Theobroma cacao L.

A greenhouse experiment was conducted to study the effects of mycorrhizal inoculation on growth and nutrient uptake of vegetatively propagated cocoa plants from the Sabah hybrid (NA 33 × PA 7) raised on unsterilized Munchong soils. Inoculation with mixed species of Scutellospora and Glomus, resulted in higher dry matter yield and stem diameter of mycorrhizal plants obtained through budding, air layering or marcotting (a form of asexual plant propagation using vegetative parts and the selection of a healthy branch and scraping off the bark at the lower end of the branch, forcing it to root by covering it with a ball of soil) and stem cutting. Budded and marcotted mycorrhizal plants gave a significant increase in P content of shoots. In contrast, only budded mycorrhizal plants (on both young and old rootstocks) gave a significantly higher Ca concentration in tops, compared to uninoculated plants.