Cenozoic colonisation of the Indian Ocean region by the Australian freshwater-originating glassperch family Ambassidae (Teleostei).

We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.

Effect of dietary prebiotics and probiotics on snakehead (Channa striata) health: Haematology and disease resistance parameters against Aeromonas hydrophila.

This study examined the effect of dietary prebiotics and probiotics after 16 weeks, followed by 8 weeks of post feeding trial with the control unsupplemented diet on haematological and immune response against Aeromonas hydrophila infection in Channa striata fingerlings. Fish were raised on a 40% protein and 12% lipid feed containing three commercial prebiotics (ß-glucan, GOS or galacto-oligosaccharide, MOS or mannan-oligosaccharide); and two probiotics- (Saccharomyces cerevisiae, Lactobacillus acidophilus), respectively and a control. Throughout the study, supplementation with dietary prebiotics and probiotics led to significant (P < 0.05) improvement in the red blood cells, white blood cells, packed cell volume, haemoglobin concentration and serum protein level and lysozyme activities; and these improvements were effective significantly (P < 0.05) when the fish were challenged with Aeromonas hydrophila at the dose of 2 × 106. The disease resistance against A. hydrophila was higher significantly (P < 0.05) in fish fed with probiotic feed supplements (L.acidophilus was highest) compared to prebiotics and control. The study is the first to report the absence of differences in sustaining the efficacies attained after intake of ß-glucan, GOS and MOS upon post-feeding with an unsupplemented feed, over a prolonged period.

A diminutive new species of cave-dwelling Wolf Snake (Colubridae: Lycodon Boie, 1826) from Peninsular Malaysia.

A newly discovered, diminutive, cave-dwelling, lowland species of the colubrid snake genus Lycodon Boie is described from a limestone cave along the Thai-Malaysian border in the state of Perlis, northwestern Peninsular Malaysia. Lycodon cavernicolus sp. nov. is most closely related to L. butleri Boulenger, an endemic, upland, forest-dwelling species from Peninsular Malaysia of the fasciatus group but is separated from L. butleri and all other species of the L. fasciatus group and the closely related L. ruhstrati group by having the combination of 245 (male) and 232 (female) ventral scales; 113 (male) and 92 (female) paired, subcaudal scales; a single precloacal plate; nine or 10 supralabials; 10 or 11 infralabials; a maximum total length of 508 mm (female); a relative tail length of 0.25-0.27; an immaculate venter in juveniles and dark-brown, posterior, ventral scale margins in adults; and dorsal and caudal bands in juveniles white. The discovery of L. cavernicolus sp. nov. adds to a rapidly growing list of newly discovered reptiles from karst regions and limestone forests of Peninsular Malaysia, underscoring the fact that these areas should be studied before they are quarried as they harbor a significant portion of the Peninsular Malaysia's herpetological diversity.

Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment.

A primary factor in population management and wildlife conservation is the delineation of population units derived from descriptions of population genetic structure. Yet, predicting factors that influence the patterns of gene flow in a population particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the mud crab Scylla olivacea examined based on a 542 bp segment of the mitochondrial DNA cytochrome c oxidase I gene among 91 individuals from six localities in the west and east coast of Peninsular Malaysia. In total 55 unique haplotypes were distinguished with 45 private haplotypes and a single common haplotype shared among all populations studied. The other ten haplotypes were shared among various populations. The sharing of this haplotype reflects the connection of the mangrove areas between east and west coast of Peninsular Malaysia. High haplotype diversity (h = 0.968 ± 0.021; mean ± SD) and low nucleotide diversity (π = 0.120 ± 0.015; mean ± SD) were displayed, which may be indicative of genetic bottleneck events. No significant phylogenetic lineages were recognized using neighbour-joining and maximum parsimony methods. Hierarchical AMOVA analysis indicated that 99.33 % of the genetic variation was contained within populations and 0.67 % occurred among populations, suggesting no geographical patterning among populations studied, supported by F st test. Mismatch distribution analysis showed that the observed distribution of the pairwise mutation differences among haplotypes was multimodal, which is not concordant with a sudden range expansion scenario. However, neutrality tests showed non-significant negative values suggesting that the populations studied may have experienced past population growth, but the expansion may have been restricted to separate local areas that resulted in the non-significant negative Fu's Fs and Tajima's D value. Overall, this present preliminary study was able to be a reference on the phylogenetic relationships and assessment of genetic structure of Scylla sp. in Malaysia.

Unveiling the Diversity of Periphytic Cyanobacteria (Cyanophyceae) from Tropical Mangroves in Penang, Malaysia.

Cyanobacteria are one of the most important groups of photoautotrophic organisms, contributing to carbon and nitrogen fixation in mangroves worldwide. They also play an important role in soil retention and stabilisation and contribute to high plant productivity through their secretion of plant growth-promoting substances. However, their diversity and distribution in Malaysian mangrove ecosystems have yet to be studied in detail, despite Malaysia hosting a significant element of remaining mangroves globally. In a floristic survey conducted in Penang, peninsular Malaysia, 33 morphospecies of periphytic cyanobacteria were identified and described for the first time from a mangrove ecosystem in Malaysia. Sixteen genera, comprising Aphanocapsa, Chroococcus, Chroococcidiopsis, Cyanobacterium, Desmonostoc, Geitlerinema, Leptolyngbya, Lyngbya, Microcystis, Myxosarcina, Oscillatoria, Phormidium, Pseudanabaena, Spirulina, Trichocoleus and Xenococcus, were obtained from field material growing on diverse natural and artificial substrata. Oscillatoriales was the dominant order with Phormidium the dominant genus at nine of the 15 sampling sites examined. Three of the morphospecies, Aphanocapsa cf. concharum, Xenococcus cf. pallidus and Oscillatoria pseudocurviceps, are rare and poorly known morphospecies worldwide. Chroococcus minutus, Phormidium uncinatum, P. amphigranulata, and some species of Oscillatoriales are considered as pollution indicator species. This study provides important baseline information for further investigation of the cyanobacterial microflora present in other mangrove areas around Malaysia. A complete checklist will enhance understanding of their ecological role and the potential for benefits arising from useful secondary metabolites or threats via toxin production to the ecosystem.

Multiple genetic lineages of anadromous migratory Mekong catfish Pangasius krempfi revealed by mtDNA control region and cytochrome b.

Population genetic structure of migratory fishes can reflect ecological and evolutionary processes. Pangasius krempfi is a critically important anadromous catfish in the Mekong River, and its migration pathways and genetic structure have attracted much interest. To investigate, we quantified the genetic diversity of this species using the control region (D-loop) and Cytochrome b (Cytb) of the mitochondrial genome. Fish were sampled (n = 91) along the Mekong tributaries from upstream to estuaries and coastal areas in the Mekong Delta and compared to three samples from Pakse (Laos). The D-loop haplotype (0.941 ± 0.014) and nucleotide diversity (0.0083 ± 0.0005) were high in all populations, but that of Cytb was low (0.331 ± 0.059 and 0.00063 ± 0.00011, respectively). No genetic difference was detected between populations, indicating strong gene flow and confirming a long migration distance for this species. Pangasius krempfi was not genetically structured according to geographical populations but was delineated into three haplogroups, suggesting multiple genetic lineages. The presence of haplogroups in each sampling location implies that migration downstream is random but parallel when the fish enter two river tributaries bifurcating from the main Mekong River. Individuals can also migrate along the coast, far from the estuaries, suggesting a longer migration path than previously reported, which is crucial for maintaining diverse genetic origin and migration pathways for P. krempfi.

Genotoxicity of heavy metals to the larvae of Chironomus kiiensis Tokunaga after short-term exposure.

The genotoxic effects of increasing concentrations (below lethal concentration [LC50]) of cadmium ([Cd] 0.1, 1 and 10 mg/L), copper ([Cu] 0.2, 2 and 20 mg/L) and zinc ([Zn] 0.5, 5 and 50 mg/L) on Chironomus kiiensis were evaluated using alkaline comet assay after exposure for 24 h. Both the tail moment and the olive tail moment showed significant differences between the control and different concentrations of Cd, Cu and Zn (Kruskal-Wallis, p < 0.05). The highest concentration of Cd was associated with higher DNA damage to C. kiiensis larvae compared with Cu and Zn. The potential genotoxicity of these metals to C. kiiensis was Cd > Cu > Zn.

Protective effects of dietary supplementation of probiotic Bacillus licheniformis Dahb1 against ammonia induced immunotoxicity and oxidative stress in Oreochromis mossambicus.

The goal of this study was to assess the efficacy of probiotics in mitigating ammonia-induced toxicity in fish. Fish were divided into four groups: control, only probiotic, only ammonia, and combined ammonia + probiotic. For 8 weeks, the Oreochromis mossambicus were exposed to waterborne ammonia at 1.0 mg L-1 and/or dietary Bacillus licheniformis Dahb1 at 107 cfu g-1. After the 4th and 8th weeks, the fish were evaluated for growth performance, enzymatic and non-enzymatic antioxidant activities (superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) reduced glutathione (GSH), neurotoxicity (acetylcholinesterase - AChE), non-specific immune responses (lysozyme (LYZ), myeloperoxidase (MPO), reactive nitrogen and oxygen species (RNS and ROS) and oxidative stress effects (lipid peroxidation (LPO), DNA damage)). Our results showed that in the absence of waterborne ammonia exposure, B. licheniformis Dahb1 significantly improved growth performance, enzymatic and non-enzymatic antioxidant capacity, AChE activity, non-specific immune response and decreased oxidative stress effect. Ammonia exposure resulted in significantly lower growth performance, reduced enzymatic and non-enzymatic antioxidant ability, decreased AChE activity, decreased non-specific immune response and increased oxidative stress effect. When O. mossambicus were exposed to ammonia, supplementation with B. licheniformis Dahb1 in the diet significantly increased survival, indicating that it may have a significant protective effect against ammonia toxicity by enhancing enzymatic and non-enzymatic antioxidant ability, activity of AChE, non-specific immune response and reduced oxidative stress effect. According to our findings, diet supplementation of B. licheniformis Dahb1 (107 cfu g-1) has the potential to combat ammonia toxicity in O. mossambicus.

Low morphological and genetic variation within the glass-perchlet Parambassis siamensis (Teleostei: Ambassidae) in Peninsular Malaysia.

We compare several populations of the glass-perchlet Parambassis siamensis (Fowler 1937) (Teleostei: Ambassidae) sampled throughout Peninsular Malaysia to determine their degree of differentiation, using both morphological and molecular characters. Our morphological analyses do not show evidence for the presence of more than one species, with the range of morphometric and meristic characters overlapping among populations. Our genetic analysis using partial sequences of the mitochondrial gene coding for the protein cytochrome c oxidase I (COI) reveals the existence of two clades that diverge from each other by a minimum uncorrected p-distance of 2.2%. The first clade comprises of specimens from south-eastern Peninsular Malaysia (Pahang and Endau-Rompin River basins) along with those from Cambodia (lower Mekong River). The second clade comprises of specimens from western Peninsular Malaysia (Selangor, Kurau, Perak, Muda and Kerian River basins) and north-eastern Peninsular Malaysia (Terengganu River basin), along with those from Chao Phraya River basin nearby Bangkok (type locality of P. siamensis). The presence of specimens with numerous melanophores on body sides in each of these two clades indicates that body marking pattern is not a valuable taxonomic character. This finding supports the conclusion that Chanda punctulata Fraser-Brunner 1955 is a junior synonym of P. siamensis. Altogether, our results support the hypothesis that all populations of P. siamensis in Peninsular Malaysia (along those from Chao Phraya and lower Mekong basins) are conspecific, comprising two genetically distinct, although close lineages. We further discuss the phenotypic plasticity within P. siamensis in relation to lotic and lentic habitats. Finally, we briefly discuss some implications for biogeography and possible causes explaining the distribution pattern.

Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment.

The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

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.

Interactive effects of freshwater acidification and selenium pollution on biochemical changes and neurotoxicity in Oreochromis mossambicus.

Effect of selenium and acidification in freshwater environment was assessed solitary but no reports are available on the impacts of both factors act together. In the present study, effects of combined simultaneous exposure to selenium (Se) and low pH were assessed in Mozambique tilapia, Oreochromis mossambicus. Responses were measured based on antioxidant defenses (enzymatic SOD, CAT, GPx and non-enzymatic GSH), biotransformation enzyme (GST), metallothionein levels (MT), oxidative damage (LPO, CP), Na+/K+-ATPase (NKA) activity in gills and liver tissues and neurotoxicity (acetylcholinesterase, AChE) response in brain tissue. Fish were exposed to combined treatment at different pH levels (7.5, control (optimum pH for tilapia growth); 5.5, low pH) and Se concentrations (0, 10, and 100 µg L-1). Toxicity levels of Se were not significantly different under control and low pH indicating that pH did not affect Se toxicity. Levels of GSH and MT were enhanced in Se-exposed fish at both pH. Combined effects of high Se concentration and low pH decreased SOD and CAT activities and increased those of GPx and GST. However, organisms were not able to prevent cellular damage (LPO and CP), indicating a condition of oxidative stress. Furthermore, inhibition of Na+/K+-ATPase activity was showed. Additionally, neurotoxicity effect was observed by inhibition of cholinesterase activity in organisms exposed to Se at both pH conditions. As a result, the combined stress of selenium and freshwater acidification has a slight impact on antioxidant defense mechanisms while significantly inhibiting cholinesterase and Na+/K + -ATPase activity in fish. The mechanisms of freshwater acidification mediating the toxic effects of trace non-metal element on freshwater fish need to investigate further.

Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean.

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

Distribution of chironomidae (Insecta: Diptera) in polluted rivers of the Juru River Basin, Penang, Malaysia.

The influence of physical and chemical parameters on the abundance and diversity of chironomids was studied in six rivers with moderate to highly polluted water in the Juru River Basin. The rivers: Ceruk Tok Kun (CTKR) as reference site, and polluted rivers of Pasir (PR), Juru (JR), Permatang Rawa (PRR), Ara (AR) and Kilang Ubi (KUR) were sampled over a period of five months (November 2007-March 2008). Nine chirnomid species: Chironimus kiiensis, C. javanus, Polypedilum trigonus, Microchironomus sp., Dicrotendipes sp., Tanytarsus formosanus, Clinotanypus sp., Tanypus punctipennis and Fittkauimyia sp. were identified. Assessment of their relationships with several environmental parameters was performed using the canonical correspondence analysis (CCA). Tanytarsus formosanus was the most dominant in the relatively clean CTKR and moderately polluted JR with mean densities of 19.66 and 25.32 m(-2), respectively while C. kiiensis was abundant in more polluted rivers. Tanytarsus formosanus, Dicrotendipes sp. and Microchironomus sp. were grouped under moderate to high water temperature, total organic matter (TOM), total suspended solids (TSS), velocity, pH, phosphates and sulphates. However, Tanypus punctipennis, Fittkauimyia sp., and Clinotanypus sp. were associated with high contents of river sediment such as TOM, Zn and Mn and water ammonium-N and nitrate-N and they were associated with higher dissolved oxygen (DO) content in the water. Chironomus kiiensis, C. javanus and P. trigonus showed positive relationships with TOM, ammonium-N and nitrate-N as well as trace metals of Zn, Cu and Mn. These three species could be considered as tolerant species since they have the ability to survive in extreme environmental conditions with low DO and high concentrations of pollutants. Based on the water parameter scores in all rivers, the highest diversity of chironomid larvae was reported in CTKR. With higher concentrations of organic and/or inorganic pollutants as reported in PPR, KUR and AR, the chironomid larval diversity decreased, and the abundance of tolerant species, mainly Chironomus spp., increased.

Reassessment of species distribution and occurrence of mud crab (Scylla spp., Portunidae) in Malaysia through morphological and molecular identification.

This study utilized genetic and morphometric approaches to assess the molecular and morphometric differentiation among commercially important species of mud crab. Molecular investigations were derived from 542 bp mitochondrial DNA COI on 249 individuals within genus Scylla from nine states in Malaysia represents four marine regions; South China Sea, Sulu Sea, Straits of Singapore and Straits of Malacca. Four specimens were obtained from Indonesia to give a robust analysis in this study. For species delimitation, Automatic Barcode Gap Discovery (ABGD) method on a web interface was employed. Analysis on phylogenetics was implemented utilizing Neighbour joining (NJ) and Maximum Parsimony (MP) methods. The inter- and intraspecies genetic distances (Ds ) was computed using Kimura 2-parameter distance and executed in MEGA version 5.05. All samples were genetically and morphologically identified and clustered into four distinct species. Among the species, S. olivacea was the most abundant (n = 111), on the other hand the occurrence of S. paramamosain in Malaysia was very low (n = 29). No single individual of S. serrata from Malaysia was recorded in this study. Both genetic distance and phylogenetic approaches exhibited a correlative monophyletic association among all specimens analysed. This present study is crucial as it reports the reassessment of all species within genus Scylla in Malaysia, eventually could be employed as a reference source for subsequent research mainly on mariculture and other conservation efforts for the species.

Phylogeography of the Japanese scad, Decapterus maruadsi (Teleostei; Carangidae) across the Central Indo-West Pacific: evidence of strong regional structure and cryptic diversity.

The Japanese scad Decapterus maruadsi (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome b gene. Genetic homogeneity within the Sundaland region's population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity (π = 0.001-0.003) but high haplotype diversity (h = 0.503-0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by FST, AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of D. maruadsi in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

Correction: Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

[This corrects the article DOI: 10.1371/journal.pone.0176623.].

Dietary Prebiotics and Probiotics Influence the Growth Performance, Feed Utilisation, and Body Indices of Snakehead (Channa striata) Fingerlings.

This study used a two-phase feeding trial to determine the influence of selected dietary prebiotics and probiotics on growth performance, feed utilisation, and morphological changes in snakehead (Channa striata) fingerlings as well as the duration of these effects over a post-experimental period without supplementation. Triplicate groups of fish (22.46 ±0.17 g) were raised on six different treatment diets: three prebiotics (0.2% ß-glucan, 1% galacto-oligosaccharides [GOS], 0.5% mannan-oligosaccharides [MOS]), two probiotics (1% live yeast [Saccharomyces cerevisiae] and 0.01% Lactobacillus acidophilus [LBA] powder) and a control (unsupplemented) diet; there were three replicates for each treatment. All diets contained 40% crude protein and 12% crude lipid. Fish were fed to satiation three times daily. No mortalities were recorded during Phase 1; however, 14% mortality was documented in the control and prebiotic-amended fish during Phase 2. At the end of Phase 1, growth performance and feed utilisation were significantly higher (p<0.05) in the LBA-treated fish, followed by live yeast treatment, compared with all other diets tested. The performance of fish on the three prebiotic diets were not significantly different from one another but was significantly higher than the control diet. During Phase 2 (the post-feeding phase), fish growth continued until the 6th week for the probiotic-based diets but levelled off after four weeks for the fish fed the prebiotic diets. The feed conversion ratio (FCR) was higher in all treatments during the post-feeding period. The hepatosomatic index (HSI) did not differ significantly among the tested diets. The visceral somatic index (VSI) and intraperitoneal fat (IPF) were highest in the LBA-based diet and the control diet, respectively. The body indices were significantly different (p<0.05) between Phases 1 and 2. This study demonstrates that probiotic-based diets have a more positive influence on the growth, feed utilisation, and survival of C. striata fingerlings compared with supplementation with prebiotics.

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.