Examination of the original descriptions and available type specimens of nominal species previously regarded as synonyms of Thrissina mystax (Bloch and Schneider, 1801), and many non-type specimens representing an extensive geographic range, confirmed the validities of T. mystax, Thrissina porava (Bleeker, 1849), and Thrissina valenciennesi (Bleeker, 1866). Additionally, Engraulis poorawah Bleeker, 1872, a nominal species previously regarded as a junior synonym of T. mystax, is recognized as a junior synonym of Thrissina malabarica (Bloch, 1795). Diagnoses and detailed color descriptions are given for all of the valid species, in addition to clarification of their taxonomic histories, and neotype designation for T. porava. The phylogenetic relationships among 15 species of Thrissina (including T. porava and T. valenciennesi but not T. mystax) were reconstructed from the mitochondrial cytochrome oxidase I (COI) gene. T. porava and T. valenciennesi were not recovered as a monophyletic group, instead being divergent from each other and the other species of Thrissina by 12.4% and >11.7% mean uncorrected distances, respectively, confirming their reciprocal validity.
Examination of numerous specimens characterised by predorsal scute, long maxilla, indented preopercle and pelvic scute lacking a spine and previously identified as Stolephorusbengalensis (Dutt & Babu Rao, 1959) or Stolephorusinsularis Hardenberg, 1933, revealed four distinct species, true S.bengalensis (distributed from the Bay of Bengal to Pakistan) and three new species, viz., Stolephoruseldorado sp. nov. (Taiwan to Java, Indonesia), Stolephorusdiabolus sp. nov. (Strait of Malacca, from Penang , Malaysia, to Singapore) and Stolephoruseclipsis sp. nov. (Bintan Island, Riau Archipelago, Indonesia). Characters separating the four species include numbers of gill rakers on each gill arch and vertebrae and pelvic fin and dorsal-fin ray lengths. Two molecular markers (mitochondrial cytochrome b and cytochrome oxidase I genes) demonstrated the distinction of three of the species examined morphologically and enabled a reconstruction of their phylogenetic relationships. Each species was genetically divergent from the others by 3.5%-7.7% mean uncorrected distance in the mitochondrial cytochrome oxidase I gene.
The Bengal Spined Anchovy, Stolephorus taurus sp. nov. is described from 21 specimens from the northern Bay of Bengal. The new species closely resembles Stolephorus dubiosus Wongratana, 1983, which is redescribed. Both species have a predorsal scute, spine on the pelvic scute, long maxilla posteriorly slightly short of or just reaching the posterior margin of the opercle, 25 or more gill rakers on the lower limb of the first gill arch, and double black lines on the dorsum posterior to the dorsal fin. However, the new species differs from S. dubiosus in having a longer pelvic fin with the posterior tip of the depressed fin beyond vertical through the dorsal-fin origin (vs. usually not reaching to vertical through dorsal-fin origin), longer pectoral fin, second dorsal-and third dorsal-fin rays, second anal-and third anal-fin rays, and greater interorbital width. Stolephorus taurus sp. nov. is closely related to Stolephorus baganensis Delsman, 1931 and S. dubiosus, although at least 2% mean p-distance divergence in the mitochondrial cytochrome c oxidase subunit I (COI) gene separates each of the three species. A phylogenetic reconstruction of the evolution of the number of prepelvic scutes within Stolephorus indicated that having six scutes was the most likely ancestral condition in the genus, and was later reduced in the evolution of Stolephorus to five or four scutes. One such reduction occurred recently in the lineage of Stolephorus taurus sp. nov.
The taxonomic status of the Southeast Asian spotted barb, Barbodes binotatus (Teleostei: Cyprinidae), has puzzled researchers because of large but inconsistent geographic variation of its body melanin marking pattern. In this study, the authors appraise the differentiation of B. binotatus and two closely related species, Barbodes rhombeus and saddle barb, Barbodes banksi, in Peninsular Malaysia using mitochondrial and nuclear markers. The results of this study reveal that the Peninsular Malaysia populations of each of the three species form largely reciprocal monophyletic lineages that differ from each other by a minimum of 2.3% p-genetic distance using COI gene. Nonetheless, specimens of B. binotatus in Peninsular Malaysia are only distantly related to specimens of B. binotatus in Java (type locality). The monophyly of B. banksi is not refuted although specimens of Peninsular Malaysia are genetically distinct from those of Sarawak (type locality). The authors discuss alternative hypotheses whether each of these three valid species is a single species or each of the main five genetic lineages revealed in this study represents a distinct species. Preliminary investigations reveal a mito-nuclear discordance at one locality in Peninsular Malaysia where B. binotatus and B. banksi co-occur. Further studies should inform on the extent of reproductive porousness between these two lineages and others.
Sébastien Lavoué, Sahat Ratmuangkhwang, Hsuan-Ching Ho, Wei-Jen Chen, and Mohd Nor Siti Azizah (2018) Longfin herrings form a monophyletic, circumtropically distributed family of mostly marine teleost fishes, the Pristigasteridae (Clupeoidei), that includes 38 species classified into nine genera and three main lineages (the Pelloninae, Pristigasterinae, and the genus Ilisha). The external morphology and osteology of the Pristigasteridae provide only a few, sometimes conflicting, informative characters which makes it difficult to reconstruct their phylogeny, but their swimbladder (a visceral gas-filled chamber that has several important functions in the Teleostei) appears to be highly specialized and variable among species. In particular, the swimbladder of most Indo-West Pacific pristigasterid species exhibits one or paired post-coelomic extensions, whereas New World species do not. The presence of these extensions conflicts with the current systematic classification, as they are only found in subsets of different taxa. To examine this conflict, the most comprehensive molecular phylogenetic tree of the Pristigasteridae to date was built using six molecular markers and 21 species. This tree deeply disagreed with the current classification in that it indicated that the subfamilies Pelloninae and Pristigasterinae are not monophyletic and neither are the genera Ilisha, Pellona, and Opisthopterus. Using this tree to infer the evolution of the post-coelomic extensions, it was found that their absence is the ancestral condition in the Pristigasteridae. Indo-West Pacific species with post-coelomic extensions evolved later and form a monophyletic group, inside which species with only one extension form a monophyletic group. The consequences of our findings on the evolution and classification of Pristigasteridae are discussed. We suggest that only species of Pristigasteridae having one or paired post-coelomic extensions should be included in the genus Ilisha.
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010-2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species-stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.
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.
The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.
Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA3/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.