Search Results (53)

Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy–muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species. Full article

As important components of the equatorial current system in the Indian Ocean, Wyrtki jets (WJs) play a significant role in distributing heat and matter in the East and West Indian Oceans. By dividing the El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) events into several phases, we find that the spring branch exhibits positive (negative) anomalies during the El Niño (La Niña) decaying phase, while the fall branch exhibits negative (positive) anomalies during the El Niño (La Niña) developing phase. The spring and fall branches are characterized by negative (positive) anomalies under the influence of positive (negative) dipole events, and these anomalies are particularly pronounced during fall. This study systematically analyzes the characteristics of WJs under the interactions between the Indo-Pacific ocean and the atmosphere, based on the phase-locking characteristics of ENSO, and reveals the regulatory mechanisms underlying their different response patterns. Full article

The golden pompano ranks at the top of production in current China’s marine fish aquaculture; however, there has been long-standing controversy regarding its valid scientific name. Multiple latin names were used simultaneously to refer to golden pompano, such as Trachinotus ovatus, T. blochii, T. mookalee and T. anak. Moreover, two distinct morphological species are regarded as deserving the scientific name T. ovatus. In this study, we employed DNA barcoding to determine which particular species the “golden pompano” represents and to explore the potential synonyms and cryptic species within T. ovatus and its closely related species. We analyzed the DNA barcodes of golden pompano samples from various aquaculture farms in China’s main production regions, as well as most species within the genus Trachinotus. The phylogenetic analyses revealed that all T. ovatus sequences clustered into two divergent clades with a large genetic distance, and the two clades were geographically separated, being from the Indo-west Pacific and the East Atlantic regions, respectively. Based on the type locality information and historical distribution records, we support the validity of the naming of Trachinotus ovatus from the Indo-west Pacific, and the so-called Trachinotus ovatus from the East Atlantic may represent a cryptic species. All the golden pompano samples were clustered into the Indo-west Pacific T. ovatus clade, with a considerably small intragroup genetic distance, which suggests that the golden pompano in China should be identified as the species Trachinotus ovatus. The golden pompano, T. blochii and T. mookalee were completely separated into distinct monophyletic clades in the phylogenetic trees, which indicated that they are different species. The T. anak clustered with the monophyletic clade of Indo-west Pacific T. ovatus and the genetic distance between them was at the intraspecific difference level. This implied that the T. anak might be the junior synonym of T. ovatus. The species delimitations based on the ABGD and bPTP methods are in agreement with the findings from phylogenetic analyses. The above results help to form a consistent viewpoint regarding the naming of the golden pompano and provide new understandings for the taxonomy of the genus Trachinotus. Full article

Freshwater shrimps of the family Atyidae of New Guinea, including those from the Indonesian province of Papua, the Aru Islands, and the country of Papua New Guinea, are reviewed. A taxonomic synopsis is given to the 35 species identified so far, including two new species, namely Caridina iriana and C. yapenensis. Six species are recorded for the first time from New Guinea, namely Caridina mertoni, C. neglecta, C. brevicarpalis, C. endehensis, C. appendiculata, and C. cf. sikipozo. Seven landlocked species are found to be endemic to New Guinea, namely C. demani, C. cognata, C. fecunda, C. rouxi, C. buergersi C. elisabethae, and Parisia holthuisi. Biogeographically, apart from 11 species endemic to New Guinea, the majority of the amphidromous atyid shrimp species are found to be either restricted to the Island Chain of West Pacific (8 species) or restricted to the Indo-Australian Archipelago region, with New Guinea/Solomon Islands being the eastern and India/Sri Lanka being the western limits of their ranges (8 species), and five are restricted to the West Pacific, with Sulawesi/Philippines their western limit. Only three species are widely distributed in the Indo-West Pacific region. Descriptions/diagnoses for the new, taxonomically important or poorly known species, taxonomic discussions, habitat and distribution information for all species are presented. Full article

One year of monthly sampling in some lagoons of the Po Delta and a pond in the Comacchio Valleys helped fill a gap in the knowledge of the primary producers of these degraded environments, focusing on the competition between macrophytes and phytoplankton. Key water column and surface sediment parameters showed a strong association with the different primary producers, explaining the main factors influencing the dominance of one group over the other. Phytoplankton, recorded as Chlorophyll-a and Phaeophytin-a, and Chlorophyceae among the macrophytes, dominated in conditions of high water turbidity and elevated nutrient concentrations. In contrast, macrophytes, particularly Rhodophyceae, their abundance, total biomass, and number of taxa. prevailed in clear, oxygenated waters. Under optimal conditions, sensitive macroalgae and aquatic angiosperms were also present. Additionally, the current list of macroalgal taxa has been updated, highlighting the dominance of some nonindigenous species (NIS) that had not been recorded before the 2000s. Specifically, Gracilaria vermiculophylla and Ulva australis, native to the North West Pacific (Japan, Korea, China, and Vietnam) and to South Australia, as well as the Indo-West Pacific (India, South Africa, Japan, and Korea), respectively, are now the most frequent and abundant taxa in these lagoons. Full article

The Indo-West Pacific scombrid genus Rastrelliger Jordan & Starks is reviewed. Formerly, the genus was considered to contain three valid species, viz., R. brachysoma (Bleeker, 1851) known from the south-east coast of India to Samoa Islands; R. faughni Matsui, 1967 reported from the south-east coast of India to Fiji; and R. kanagurta (Cuvier, 1816), the most widespread species known from the east coast of Africa and the Persian/Arabian Gulf east to Tonga. Herein, R. chrysozonus (Rüppell, 1836), restricted to the Red Sea, is resurrected from the synonymy with R. kanagurta and both species are redescribed in detail, based on an integrative morphological and molecular assessment. Consequently, Scomber microlepidotus Rüppell, 1836 is moved from the synonymy with R. kanagurta to synonymy with R. chrysozonus. Rastrelliger chrysozonus differs from R. kanagurta primarily by a longer upper jaw. Rastrelliger brachysoma differs from the other three species by a deeper body, a deeper caudal peduncle, and a very long intestine. Rastrelliger faughni differs from the other three species in having a more slender body, usually X spines in the first dorsal fin (versus IX spines), shorter and fewer gill rakers, a shorter maxilla, and a shorter intestine. The phylogenetic analysis of mitochondrial genes of all Rastrelliger species also demonstrated that R. chrysozonus forms a well divergent evolutionary lineage, with R. kanagurta being its closest relative. In addition to the redescriptions of R. chrysozonus and R. kanagurta, brief species accounts for R. brachysoma and R. faughni and the key to the four species are provided. Full article

Acanthocepola indica, a deep-sea snake fish, is primarily found in the Indo-west Pacific region, including India, Korea, Japan, and the South China Sea. The taxonomic classification of A. indica based on morphological characteristics remains inaccurate and unclear. In this study, we utilized next-generation sequencing to generate comprehensive genomic data for A. indica. The estimated genome size of A. indica was 422.95 Mb, with a heterozygosity ratio of 1.02% and a sequence repeat ratio of 22.43%. Our analysis suggested that A. indica is diploid, and the draft genome assembly consists of 1,059,784 contigs with a contig N50 of 1942 bp. We identified a total of 444,728 simple sequence repeats in the genome of A. indica. Furthermore, we successfully assembled the complete mitochondrial genome (16,439 bp) of A. indica, which included 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on mitochondrial genomes revealed that A. indica is closely related to Acanthocepola krusensternii and Cepola schlegelii, providing evidence that the family Cepolidae belongs to the order Priacanthiformes. Population size dynamics analysis indicated that A. indica experienced a bottleneck effect during the Pleistocene Glacial Epoch, likely due to the changes in glacial cycles and sea level fluctuations since ~800 Kya. Full article

The evolutionary history of emperors, particularly in the Atlantic and Indo-West Pacific Oceans, remains largely unmapped. This study explores the maternal lineage evolution of Lethrinids by examining the complete mitogenome of Lethrinus atlanticus, which is endemic to the Eastern Atlantic Ocean. Utilizing advanced next-generation sequencing, we found that the mitogenome spans 16,789 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and an AT-rich control region (CR). Our analysis indicates a preference for AT base pairs in the L. atlanticus mitogenome (53.10%). Most PCGs begin with the ATG codon, except for COI, which starts with GTG. Relative synonymous codon usage reveals high frequencies for alanine, leucine, proline, serine, and threonine. The ratio of nonsynonymous to synonymous substitutions suggests strong negative selection across all PCGs in Lethrinus species. Most transfer RNAs exhibit typical cloverleaf structures, with the exception of tRNA-serine (GCT), which lacks a dihydrouracil stem. Comparative analysis of conserved sequence blocks across the CRs of three Lethrinus species shows notable differences in length and nucleotide composition. Phylogenetic analysis using concatenated PCGs clearly distinguishes all Lethrinus species, including L. atlanticus, and sheds light on the evolutionary relationships among Spariformes species. The estimated divergence time of approximately 20.67 million years between L. atlanticus and its Indo-West Pacific relatives provides insights into their historical separation and colonization during the late Oligocene. The distribution of Lethrinids may be influenced by ocean currents and ecological factors, potentially leading to their speciation across the Eastern Atlantic and Indo-West Pacific. This study enhances our understanding of the genetic diversity and phylogenetic relationships within Lethrinus species. Further exploration of other emperor fish mitogenomes and comprehensive genomic data could provide vital insights into their genetic makeup, evolutionary history, and environmental adaptability in marine ecosystems globally. Full article

The spotted eagle ray Aetobatus ocellatus (Kuhl, 1923) has a widespread Indo-West Pacific distribution and displays substantial population genetic structuring. Genetic data are crucial for understanding the species’ diversity, connectivity, and adaptation. However, molecular genetic information on A. ocellatus from Melanesia is lacking, which impedes our understanding of gene flow among geographic regions. In this study, we sampled 45 A. ocellatus, primarily from Fiji’s largest fish market in the capital, Suva. Mitochondrial DNA Cytochrome C Oxidase subunit I (COI) barcoding was used for species identification, and DArT-seqTM technology was applied to assess the nuclear genetic diversity. Barcoding of the COI gene showed a 98.6% to 99.8% similarity to A. ocellatus reference sequences in the Barcode of Life Data System, and the 45 individuals were represented by three major evolutionary haplotype clusters. Genotyping resulted in 24,313 Single-Nucleotide Polymorphisms (SNPs) which were quality-filtered to 7094 SNPs per individual. The observed heterozygosity level was 0.310. The inbreeding coefficient was positive, and genotyping identified one full-sibling pair and one half-sibling pair from the 45 individuals. Additionally, eagle rays exhibit polychromatic patterns, and at least three ventral pattern variations were recorded in specimens from the market. Collectively, our main findings characterize the genetic profile of A. ocellatus in Fiji and can help to understand the diversification of this species within the region. Full article

Climate change (CC) represents an increasing threat to mangroves worldwide and can amplify impacts caused by local anthropogenic activities. The direct effects of CC on mangrove forests have been extensively discussed, but indirect impacts such as the alteration of ecological processes driven by specific functional groups of the biota are poorly investigated. Ecological roles of key functional groups (FGs) in mangroves from the Atlantic–Caribbean–East Pacific (ACEP) and Indo-West Pacific (IWP) regions are reviewed, and impacts from CC mediated by these FGs are explored. Disruption by CC of ecological processes, driven by key FGs, can reinforce direct effects and amplify the loss of ecological functionality and further degradation of mangrove forests. Biogeochemistry mediator microbiotas of the soil, bioturbators, especially semiterrestrial crabs (Ocypodoids and Grapsoids) and herbivores (crustaceans and Insects), would be the most affected FG in both regions. Effects of climate change can vary regionally in the function of the combination of direct and indirect drivers, further eroding biodiversity and mangrove resilience, and impairing the predictability of ecosystem behaviour. This means that public policies to manage and conserve mangroves, as well as rehabilitation/restoration programs, should take into consideration the pressures of CC in specific regions and the response of key FGs to these pressures. Full article

The taxonomy of the family Mugilidae has historically posed challenges, marked by discrepancies between described and valid species, compounded by cryptic diversity and a similar external appearance. Previous studies left four of six lineages unidentified within Crenimugil, including Crenimugil sp. A and Crenimugil sp. B. The goal of this study is to provide a detailed revision of species assigned to Crenimugil by examining specimens from the Red Sea, which is the type locality of Mugil crenilabis, Mugil seheli and Mugil tade, which were here genetically analyzed. After demonstrating that the genus contains nine monophyletic lineages and Moolgarda pura is a valid nominal species, the mugilid genus Moolgarda is restored. Consequently, Moolgarda has priority over Crenimugil and Valamugil. Additional morphological analyses of specimens from the Red Sea assigned to Moolgarda sp. A and Moolgarda sp. B identified them as representing Moolgarda seheli and Moolgarda crenilabis, respectively. A phylogenetic analysis, including new DNA barcodes, confirmed a wide distribution range of both species in the Indo-West Pacific. The identity of the lineage previously identified as Crenimugil crenilabis remains doubtful, and it is referred to as Moolgarda cf. crenilabis here. A third lineage, previously named Crenimugil buchanani, is re-described as Moolgarda tade, a species originally reported from the Red Sea with a long history of taxonomic confusion. The species is widely distributed in the Indo-West Pacific and distinguished from other congeners by falcate second dorsal and anal fins that are distinctly higher than the first dorsal fin. A detailed description of the Red Sea specimens of M. crenilabis, M. seheli and M. tade is provided, with comments to other unnamed lineages. Full article

We document aggregations of an undescribed benthic solitary tunicate of the family Pyuridae from the Arabian Sea. This new genus was found forming dense thickets in shallow rocky substrates around Masirah Island and the Dhofar area in Oman. Such aggregations of tunicates have not been reported before from coral reefs in the Indo-West Pacific region and the Atlantic. This observation contributes to our understanding of the ecology and biogeography of ascidians, setting the stage for a comprehensive species description and in-depth analysis of this species. Full article

The genus Dichichthys was resurrected for five species previously allocated to the genus Parmaturus in the family Pentanchidae. Supraorbital crests on the chondrocranium distinguish Dichichthys from Parmaturus and other members of the family Pentanchidae. A new family, Dichichthyidae, has been proposed to contain Dichichthys. The sequence of the NADH2 mitochondrial gene confirms the placement of Dichichthys outside of the Pentanchidae family, as well as separate from the Atelomycteridae and Scyliorhinidae families. Dichichthys albimarginatus was described using a holotype collected off the coast of New Caledonia. A second juvenile specimen collected off the coast of Papua New Guinea was tentatively assigned as D. cf. albimarginatus. Dichichthys bigus is known from the holotype collected in the Coral Sea off the coast of Queensland, Australia. A new, parasite-afflicted underwater observation was reported further north of Queensland. The type species Dichichthys melanobranchus, previously only known from juvenile specimens, was redescribed based on adult specimens. Dichichthys nigripalatum is known from the holotype collected off Sumbawa, Indonesia, and a tentatively identified photo record from West Java. Dichichthys satoi n. sp. is described from the West Norfolk Ridge and off the North Island of New Zealand. Members of the genus Dichichthys have unique curved egg cases which have pliable ridges made up of numerous fibres and long coiled tendrils on the posterior end. Full article

Coral-dwelling gall crabs (Cryptochiridae) are common inhabitants of scleractinian corals. Several species have been described as new in recent years, including Lithoscaptus doughnut, which was described from Hong Kong based on a single female retrieved from the coral Plesiastrea peroni. Here we extend the distribution range of L. doughnut with nine additional localities throughout the Indo-West Pacific, from the Red Sea to the Coral Triangle and Japan. We describe a male specimen of L. doughnut for the first time, based on a specimen from Malaysia, and provide photographs of life and preserved material. Haplotype networks based on COI mtDNA (n = 12) and 16 rRNA sequences (n = 12) were created. We retrieved eleven COI haplotypes and six 16S haplotypes, however no clear geographic distribution pattern was discerned. Intraspecific variation in L. doughnut was 1.4% for COI and 0.2% for 16S. Lastly, the first colour photos and records of associated parasites of this species are provided. Full article

Salmoneus sultanus sp. nov. is described based on several specimens collected on the exposed shores of Masirah Island and Dhofar, Oman, a region characterised by seasonal upwellings cooling water temperature to less than 23 °C. The new species is compared with the morphologically most similar congeners present in the north-western Indian Ocean, e.g., S. latirostris (Coutière, 1897), S. cristatus (Coutière, 1897), S. serratidigitus (Coutière, 1897), and S. chadwickae Ďuriš and Horká, 2016; the latter species is recorded for the first time from Oman. The conspicuous colour pattern of S. sultanus sp. nov. appears to be diagnostic, differing greatly from that of S. latirostris, S. cristatus, S. serratidigitus, and S. chadwickae. Full article