Indo-West Pacific Ocean Research Articles

Elucidating the Mitogenomic Blueprint of Pomadasys perotaei from the Eastern Atlantic: Characterization and Matrilineal Phylogenetic Insights into Haemulid Grunts (Teleostei: Lutjaniformes).

The parrot grunt fish, Pomadasys perotaei, has a limited distribution in the Eastern Atlantic Ocean and is an important species in marine capture fisheries across several West African countries. Despite its ecological and economic significance, the mitogenomic information for this species is lacking. This study utilized next-generation sequencing to generate the de novo mitogenome of P. perotaei from Eastern Atlantic. The resulting mitogenome is 16,691 base pairs and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and an AT-rich control region (CR). Most of the PCGs exhibit nonsynonymous (Ka) and synonymous (Ks) substitution rates of less than '1', indicating strong negative selection across haemulid fishes. The control region of Pomadasys species contains four conserved domains, as seen in other teleost's, with polymorphic nucleotides that can be used to study population structures through the amplification of short mitochondrial gene fragments. Additionally, Bayesian phylogenetic analysis based on PCGs revealed a non-monophyletic clustering pattern of Pomadasys within the haemulid matrilineal tree. Overall, the structural characterization and phylogenetic analysis enhance our understanding of the genetic composition and evolutionary history of Pomadasys species from the Indo-West Pacific and Eastern Atlantic Oceans.

Mitogenomic Architecture of Atlantic Emperor Lethrinus atlanticus (Actinopterygii: Spariformes): Insights into the Lineage Diversification in Atlantic Ocean.

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.

Characterization of complete mitochondrial genome of Periclimenes brevicarpalis (Decapoda: Palaemonidae)

Periclimenes brevicarpalis is widely distributed in the Indo West Pacific oceans. The mitochondrial genome of P. brevicarpalis was sequenced and assembled firstly by next generation sequencing technology in our study. The complete mitochondrial genome of P. brevicarpalis was 16,673 bp in size, consisted of 22 transfer RNA genes, 13 protein coding genes and two ribosomal RNA genes. The contents of the four bases were C (25.62%), T (28.73%), A (31.64%), and G (14.01%). The result of phylogenetic analysis showed that P. brevicarpaliswas clustered with Anchistus australis. In conclusion, our research provided valuable data for phylogenetic analysis of the Palaemonidae family as the first report about mitochondrial genomes in Periclimenes.

Cryptic invasions of Pseudopolydora (Annelida: Spionidae), with description of a new species from Queensland, Australia

During surveys worldwide, we collected adult and larval specimens of Pseudopolydora Czerniavsky, 1881 similar to P. achaeta Radashevsky & Hsieh, 2000 and P. rosebelae Radashevsky & Migotto, 2009 far from their type localities in Taiwan and Brazil, respectively. Analysis of sequence data of five gene fragments: mitochondrial COI and 16S rDNA, nuclear 18S rDNA and 28S rDNA, and Histone 3 (3114 bp in total) of individuals from Nha Trang Bay (Vietnam), São Paulo (Brazil), Florida (USA), and the Caribbean Sea (Martinique) confirmed their conspecificity with P. achaeta from Taiwan. Based on the morphology, we also report this species for the first time for the East Sea (South Korea) and provide new records for the north-western part of the Sea of Japan (Russia). The analysis also showed the conspecificity of worms from Vietnam with P. rosebelae from Brazil. Based on the morphology, we also report P. rosebelae for the first time for the Caribbean Sea (Belize), South China Sea (Thailand), and Hawaii. Developed pelagic larvae of P. achaeta and P. rosebelae from Nha Trang Bay are described and illustrated. A worm from the Great Barrier Reef (Queensland, Australia) earlier identified as P. cf. rosebelae, is referred to the new species Pseudopolydora nivea sp. nov. Following our earlier hypothesis about the origin of Pseudopolydora in the Indo-West Pacific Ocean, we explain the occurrence of these worms, including Pseudopolydora floridensis Delgado-Blas, 2008, on the Atlantic coasts of North and South America by unintentional transportation in ballast water, followed by successful invasions. We assume that the penetration of warm waters of the East China Sea through the Korea Strait and the warming of the waters of the Sea of Japan have led to the extension of the range of tropical-subtropical P. achaeta to the north-western part of the Sea of Japan.

An overview of Miocene to Pleistocene methane-seep faunas from Taiwan: Paleoecology and paleobiogeographic implications

The invertebrate macrofauna of four methane-seep deposits of Miocene to Pleistocene age from Taiwan is taxonomically evaluated. The Neogene faunas, with one example each from the early and late Miocene and the Pliocene, consist exclusively of one or two large, infaunal lucinid bivalve genera per site, namely Meganodontia and Lucinoma. The former includes the large, charismatic Pliocene ‘Loripes’ goliath, which is here identified as belonging to the widespread, Neogene to Recent genus Meganodontia. The Pleistocene seep fauna is more diverse, includes extant species like the mytilid Gigantidas horikoshii and Meganodontia aff. acetabulum, unidentified species belonging to Lucinoma and the vesicomyid Isorropodon, and specimens resembling the enigmatic bivalve Sisonia frijellanae, described so far only from the late Miocene of the Philippines; the gastropods could not be identified below family level. The two Miocene seep faunules formed on the shelf of the Eurasian plate, the Pliocene faunule in an upper offshore setting in the Tainan foreland basin, whereas the Pleistocene site with its more diverse fauna formed closer to the shelf edge of the Tainan foreland basin. We suggest that water depth is the most likely driver of this difference in species diversity. The very negative δ13C signature of the seep carbonates of all fossil sites indicates the seepage of mostly biogenic rather than thermogenic methane, analogous to the extant seep sites around Taiwan. Biogeographically, the Miocene seep faunas show, with Meganodontia, links to seep faunas from lower to mid-latitudes worldwide (Caribbean Sea, Mediterranean Sea, Philippines, and New Zealand). From the Pliocene onward, biogeographic ties are more restricted to areas in the central Indo-West Pacific Ocean.

New perspectives on the genetic structure of dotted gizzard shad (Konosirus punctatus) based on RAD-seq

To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. Konosirus punctatus, which is a commercial fish species inhabiting the Indo-west Pacific Ocean, has shown an obvious annual global capture and aquaculture production decline due to climate changes and human activities. In the present study, restriction-site associated DNA sequencing (RAD-seq) was used to describe its genome-wide single nucleotide polymorphisms panel (SNPs). Among 146 individuals collected at nine locations scattered in China, Korea and Japan, a set of 632,090 SNPs were identified. Population genetic analysis showed that K. punctatus individuals were divided into two significant genetic clusters. Meanwhile, potential genetic differentiation between northern and southern population of K. punctatus was found. Treemix results indicated that gene flow existed among sampling locations of K. punctatus, especially from southern Japan to others. Moreover, candidate genes associated with habitat adaptations of K. punctatus were identified, which are involved in diverse physiological processes of K. punctatus including growth and development (e.g., KIDINS220, PAN3), substance metabolism (e.g., PGM5) and immune response (e.g., VAV3, CCT7, HSPA12B). Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of K. punctatus, which is beneficial to establish the management and conservation units of K. punctatus, guiding the rational use of resources, with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.

Mollusks (Gastropoda, Bivalvia) from Miocene cold-seep deposits in northern Italy: revisions and additions

Here, we report on 33 molluscan species from Miocene ’Calcari a Lucina’ hydrocarbon-seep deposits in northern Italy. Three new species are described: the chilodontaid gastropod Putzeysia diversii sp. nov., the lucinid bivalve Miltha (sensu lato) romaniae sp. nov., and Sisonia ultimoi sp. nov., a heterodont bivalve of uncertain taxonomic affinity. Fourteen species are described in open nomenclature. The common but enigmatic gastropod species Phasianema taurocrassa is here suggested to belong to the seguenzioid genus Cataegis. Most gastropod species are inhabitants of the deep-sea floor in general, and are not restricted (obligate) to sites of hydrocarbon-seepage. The gastropod Putzeysia diversii sp. nov. and the bivalve Sisonia ultimoi sp. nov. are the geologically oldest members of their genera known to date. While the genus Putzeysia is geographically restricted to the NE Atlantic Ocean and the Mediterranean Sea, Sisonia ultimoi sp. nov. represents another link of the Miocene Mediterranean seep fauna to that of the central Indo-West Pacific Ocean.

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean.

The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

Evidence of Distinct Genetic Stocks of the Bottlenose Wedgefish (Rhynchobatus australiae) in the Indo-West Pacific

Populations of the bottlenose wedgefish (Rhynchobatus australiae) in the Indo-West Pacific (IWP) have declined by nearly 80% in recent decades. In response, IWP countries are establishing sanctuaries to provide refuge for the fish. However, little is known about the genetic stock structure of the fish in the region. Hence, this study analysed partial sequences (610 base pairs) of the cytochrome oxidase subunit (COI) gene from eight bottlenose wedgefish populations in the IWP to assess the genetic stock structure of the fishery. The sequences revealed that Western Indian Ocean (WIO) populations are genetically distinct from those in the West Pacific (WP) (FCT = 0.24, p = 0.01) and Australia (FCT = 0.88, p = 0.01). Similarly, WP populations were genetically distinct from Australian populations (FCT = 0.42, p = 0.01). This suggests that the IWP contains three genetically distinct stocks of the bottlenose wedgefish: the WIO, WP, and Australia. The indices of genetic diversity and population size showed that the WIO stock has low genetic diversity and population size when compared to the WP and Australia. This shows that efforts to establish elasmobranch sanctuaries in the IWP should take into account the three identified stocks, with priority given to the WIO.
 Keywords: Restricted gene flow, genetic connectivity, elasmobranch sanctuaries, Indo-West Pacific Ocean

Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands.

Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H. leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora. Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous research from the Indo-West Pacific Ocean region, we conclude that Okinawan LEC sea cucumber populations have been and are being impacted by high levels of direct (e.g., overexploitation, as well as coastal development) and indirect anthropogenic pressure (e.g., decreasing water quality). To address the current situation, repeated monitoring and more detailed investigations to reveal the drivers that determine LEC sea cucumber species aggregations and population densities are urgently needed, along with more robust management of remaining LEC sea cucumber populations.

Genome-wide SNPs reveal fine-scale genetic structure in ornate spiny lobster Panulirus ornatus throughout Indo-West Pacific Ocean

Abstract Genome-wide, single nucleotide polymorphism (SNP) typing can improve the management of valuable marine species by delineating finer scale population structure compared with traditional markers. This approach was applied to the spiny lobster, Panulirus ornatus distributed in the Indo-West Pacific and is one of the most highly valuable seafood products in the world. A total of 3008 SNPs was generated from DArTseq sequencing of 224 lobsters sampled at 13 locations across the Indo-Pacific. SNPs revealed a highly significant genetic structure among samples (analysis of molecular variance FST = 0.046). Pairwise genetic comparison showed significant differences among the majority of sampling locations. Outlier loci (including an outlier SNP mapped to the CASc gene with different allele frequencies among sampling locations) revealed highly significant pairwise differentiation, especially a genetic break between regional populations in northern Australia and South East Asia. Significant pairwise differences in outliers among sampling locations, even over small geographic scales, suggest a possible role of local adaptation on the population structure. Genetic differences identified among samples from northern Australia and South East Asia are sufficient to refute the single-stock hypothesis proposed using conventional genetic markers. The results of genome-level SNPs identify five management units across the species’ range, with significant implications for the future fisheries management and aquaculture development of this species.

Possible Linkage Between Tropical Indian Ocean SST Anomalies and the Date of First and Last Tropical Cyclones Landfalling in the Chinese Mainland

Bases on the NCEP / NCAR reanalysis products, HadISST dataset, and data of tropical cyclone (TC)landfalling in the Chinese mainland during 1960-2019, the possible impacts of Indian Ocean Dipole (IOD) mode andIndian Ocean basin (IOB) mode on the last-TC-landfall date (LLD) and first-TC-landfall date (FLD), respectively, areinvestigated in this study. The LLD is in significantly negative correlation with autumn IOD on the interannual time-scale and their association is independent of El Niño-Southern Oscillation (ENSO). The LLD tends to be earlier when theIOD is positive while becomes later when the IOD is negative. An anomalous lower-level anticyclone is located aroundthe Philippines during October-November, resulting from the change of Walker circulation over the tropical Indo-westPacific Ocean forced by sea surface temperature (SST) anomalies related to a positive IOD event. The Philippinesanticyclone anomaly suppresses TCs formation there and prevents TCs from landfalling in the Chinese mainland due tothe anomalous westerly steering flows over southeast China during October-November, agreeing well with the earlierLLD. However, the robust connection between spring IOB and FLD depends on ENSO episodes in preceding winter.There is an anticyclonic anomaly around the Philippines caused by the tropical SST anomalies through modulating theWalker circulation during May-June when the IOB is warming in the El Niño decaying phase. Correspondingly, the TCsgenesis is less frequent near the Philippines and the mid-level steering flows associated with the expanded westernPacific subtropical high are disadvantageous for TCs moving towards southeast China and making landfall during May-June, in accordance with the later FLD. By contrast, cooling IOB condition in spring of a La Niña decaying year andnegative IOD cases during autumn could produce a completely reversed atmospheric circulation response, leading to anearlier FLD and a later LLD over the Chinese mainland, respectively.

The Complete Mitochondrial Genome of Plectorhinchus Chaetodonoides (Perciformes: Haemulidae)

Plectorhinchus chaetodonoides Lacepède, 1801 is a widespread multicolored sweetlips fish found in the Indo-West Pacific Ocean where its appearance and color patterns drastically change during growth. In this study, the whole mitochondrial genome of P. chaetodonoides was sequenced which revealed it is 16,546 bp long and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one noncoding regulatory region. The GC content of the whole genome was 47.5% and 48.2%, 46.3%, 46.8%, 42.5% in the protein coding genes, tRNAs, rRNAs, and control regions, respectively. Molecular phylogenetic analysis resolved P. chaetodonoides as closely associated with Diagramma pictum and nested within a clade of Haemulidae that is allied with species from the Lutjanidae, Kyphosidae, Teraponidae, and Sciaenidae families. These results provide an essential genomic resource for future evolutionary and conservation studies of P. chaetodonoides as well as the Haemulidae family.

Population subdivision promoted by a sea-level-change-driven bottleneck: A glimpse from the evolutionary history of the mangrove plant Aegiceras corniculatum.

Historic climate changes drive geographical populations of coastal plants to contract and recover dynamically, even die out completely. Species suffering from such bottlenecks usually lose intraspecific genetic diversity, but how do these events influence population subdivision patterns of coastal plants? Here, we investigated this question in the typical coastal plant: mangrove species Aegiceras corniculatum. Inhabiting the intertidal zone of the tropical and subtropical coast of the Indo-West Pacific oceans, its populations are deemed to be greatly shaped by historic sea-level fluctuations. Using dual methods of Sanger and Illumina sequencing, we found that the 18sampled populations were structured into two groups, namely, the "Indo-Malayan" group, comprising three subgroups (the northern South China Sea, Gulf of Bengal, and Bali), and the "Pan-Australasia" group, comprising the subgroups of the southern South China Sea and Australasia. Based on the approximate Bayesian computations and Stairway Plot, we inferred that the southern South China Sea subgroup, which penetrates the interior of the "Indo-Malayan" group, originated from the Australasia subgroup, accompanied by a severe bottleneck event, with a spot of gene flow from both the Australasia and "Indo-Malayan" groups. Geographical barriers such as the Sundaland underlie the genetic break between Indian and Pacific Oceans, but the discontinuity between southern and northern South China Sea was originated from genetic drift in the bottleneck event. Hence, we revealed a case evidencing that the bottleneck event promoted population subdivision. This conclusion may be applicable in other taxa beyond coastal plants.

Higher Genetic Diversity of the Common Sea Cucumber Holothuria (Halodeima) atra in Marine Protected Areas of the Central and Southern Ryukyu Islands

Recently, sea cucumbers (Echinodermata: Holothuroidea) have been over-exploited in many areas of the world, including in the Ryukyu Islands, southern Japan, due to increases in their economic importance. Nevertheless, management and protection of sea cucumbers are insufficient worldwide. The black sea cucumber Holothuria (Halodeima) atra Jaeger, 1833, inhabits a large range across the Indo-West Pacific Ocean and is a widely harvested species. Here we conducted population genetic analyses on H. atra using partial mitochondrial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) to examine 11 different populations around three island groups in the middle Ryukyus; Okinawajima Island, the Kerama Islands, and the Sakishima Islands, all within Okinawa Prefecture. We found 27 haplotypes for COI and 16 haplotypes for 16S. Locations within national and quasi-national parks (Zamami Island, Keramas, and Manza, Okinawajima; managed by the national Ministry of Environment and Okinawa Prefecture, respectively) had the highest number of haplotypes, whereas locations with less management and more anthropogenic pressure had lower numbers The mean of all samples' genetic diversity indices was moderate with regards to both haplotype and nucleotide diversity. According to our results, Zamami Ama was the most genetically diverse location based on both markers used, likely because it is located within Kerama-Shoto National Park with comparatively stricter regulations than most other locations. Based on our COI sequences, three-quarters of the locations with the highest haplotype diversity were found to be distant from Okinawajima Island, indicating that the genetic diversity of H. atra was reduced around Okinawajima Island. Our results possibly reflect negative impacts from anthropogenic pressures such as over-harvesting and coastal development, although future comprehensive research including sequences of nuclear loci is needed to confirm this hypothesis.

Unraveling cryptic diversity among shallow-water tonguefishes (Pleuronectiformes: Cynoglossidae: Symphurus) from the Indo-West Pacific region, with descriptions of five new species.

Species of Symphurus (Pleuronectiformes: Cynoglossidae) are relatively small-sized tonguefishes occurring worldwide in tropical, subtropical, and warm-temperate seas. In the Indo-West Pacific Ocean, species of Symphurus inhabiting waters shallower than 200 m are rarely reported; only five have been described, S. microrhynchus (Weber, 1913), S. holothuriae Chabanaud, 1948, S. monostigmus Munroe, 2006, S. leucochilus Lee et al. 2014, and S. longirostris Lee et al. 2016. Examination of museum and recently collected specimens yielded over 100+ Symphurus captured in relatively shallow waters off Japan, Papua New Guinea, the Philippines, Taiwan, and Vietnam. All of these specimens, except S. monostigmus (with 14 caudal-fin rays), were originally tentatively identified as S. microrhynchus because of shared similarities (small size, low meristic values, 12 caudal-fin rays, shared pigmentation traits). Detailed comparisons revealed that, although similar, specimens from allopatric locations have small differences in meristic, morphometric and pigmentation features. In previous literature, these small differences were thought to represent intraspecific variation among populations of a widespread species, S. microrhynchus. However, further study, including molecular data, has revealed that such minor differences among specimens from allopatric locations actually represent interspecific, and not population-level, variations. Where available, molecular differences among these allopatric populations, in contrast to the morphological features, were significantly different (9.0 to 26.3%), providing additional strong support for the hypothesis that more than one species is represented among fishes examined. Combined data from morphological and molecular characters, and species delimitation analysis, reveal that five, undescribed, cryptic species should be recognized: S. brachycephalus n. sp. from Vietnam, S. hongae n. sp. from Taiwan, S. leptosomus n. sp. from the Philippines, S. polylepis n. sp. from Papua New Guinea, and S. robustus n. sp. from Japan. Also, based on new information, the previous decision to place S. holothuriae Chabanaud in the synonymy of S. microrhynchus was determined to be premature. This species should be recognized as valid until additional specimens are captured and the taxonomic status of this nominal species re-evaluated. At least 10 species of Indo-West Pacific shallow-water Symphurus are now known. Eight are members of the Symphurus microrhynchus species complex with hypothesized closer relationship to each other than to the other two species of shallow-water tonguefishes. Included in this study are redescriptions of S. microrhynchus and S. holothuriae based on their holotypes, including an expanded number of morphological characters not previously used to diagnose these species; redescriptions are also provided for comparative purposes of three other shallow-water species; five new cryptic species are described; and lastly, detailed comparisons and an identification key to all 10 species of shallow-water Symphurus occurring in the Indo-West Pacific Ocean are provided. Two additional populations are also identified that likely represent other undescribed taxa belonging to the S. microrhynchus species complex. Adequate specimens are not available at this time to formally describe these nominal species. This study contributes further understanding about species diversity within Symphurus inhabiting shallow waters of the Indo-West Pacific Ocean. Several other nominal species of small-sized cynoglossid and soleid flatfishes are currently considered to have widespread distributions in the Indo-West Pacific. Many of these species also have junior synonyms available based on nominal species described from allopatric sites within their geographic ranges. How many of these presumed populations of widespread species will be resurrected from synonymy once additional specimens and their genetic information becomes available remains an interesting question for future study.

The complete mitochondrial genome of Diagramma pictum (Perciformes: Haemulidae)

The painted sweetlips Diagramma pictum (Thunberg 1792) is an important fish for commercial fisheries which is widely distributed in the Indo-West Pacific Ocean. It can change its external coloration and pattern during their lives. The complete mitochondrial genome of D. pictum was determined in this study. The genome was 16,531 bp in length and consisted of 13 protein coding genes, 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and one noncoding control region. The overall base composition was estimated to be A: 27.5%; T: 24.7%; C: 30.9% and G: 16.9% with AT bias of 52.2%. The molecular phylogenetic result revealed that D. pictum did not form an independent branch but was tightly clustered inside the Plectorhinchus groups, closely related to the species Plectorhinchus chaetodonoides, indicating the close relationships between genera Diagramma and Plectorhinchus. These results may provide important genomic information for species evolution and mitogenome based phylogenetic analyses of D. pictum in the family Haemulidae.

Genetic diversity and population structure of cutlassfish (Lepturacanthus savala) along the coast of mainland China, as inferred by mitochondrial and microsatellite DNA markers

Cutlassfish (Lepturacanthus savala) is a commercially important fish species that is distributed in the tropical coastal area throughout the Indo-West Pacific Oceans. However, there have been few genetic studies on this species. Therefore, based on mitochondrial COI gene and thirteen microsatellite DNA markers that have been successfully developed by predecessors, the objective of this study is to assess the genetic diversity and structure of L savala for the first time, using 172 individuals collected from six locations along the coast of mainland China during 2019. High levels of haplotype diversity (0.94) in mitochondrial DNA and the average number of alleles among the six populations ranged from 10.3 to 14.0 in microsatellite DNA data, which showed that all population exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA) showed that did not indicate any significant genetic differentiation among groups with no relation to the geographic area. The significant genetic differentiation was found in LYG and BH populations revealed that the prevention of gene flow caused by the Yangtze River and the Qiongzhou Strait. The results of STRUCTURE suggested that all populations were admixtures of two clusters, which could be explained only by the high migratory ability of L. savala resulting in extensive gene flow. Analysis of demographic history revealed that L. savala undergo historical lineage diversification and admixture due to the secondary contact based on ABC analysis, and no evidence for recent population bottlenecks were detected. Such study is both practical and theoretical value for genetic improvement, conservation, management, and sustainable resource utilization.

Taxonomy of the Genus Halophila Thouars (Hydocharitaceae): A Review.

The seagrass genus Halophila Thouars has more than twenty described species and is predominately distributed over a wide geographic range along the tropical and the warm temperate coastlines in the Indo-West Pacific Oceans. A brief history of the Halophila taxonomic development is presented. Based on reproductive and vegetative morphology, the genus is divided into eight sections including three new sections: section Australes, section Stipulaceae and section Decipientes. A rewritten taxonomic description of the type species for the genus Halophila, H. madagascariensis Steudel ex Doty et B.C. Stone, is provided. The lectotype of H. engelmannii Asch. as well as neotypes of H. hawaiiana Doty et B.C. Stone and H. spinulosa (Br.) Asch. are designated. Furthermore, H. ovalis ssp. bullosa, ssp. ramamurthiana and ssp. linearis together with H. balforurii have been recognised as distinct species. Nomenclature, typification, morphological description and botanical illustrations are presented for each taxon. Recent molecular phylogenetic surveys on certain Halophila taxa are also discussed. Field surveys for the deep water Halophila in West Pacific regions are suggested. Morphological studies combined with molecular investigations for the Halophila on the east coast of Africa and the West Indian Ocean are urgently needed and highly recommended.

Colour variation of the intertidal hermit crabClibanarius virescensconsidering growth stage, geographic area in the Indo–West Pacific Ocean, and molecular phylogeny

AbstractMembers ofClibanarius virescensshow considerable intraspecific colour variation, including colouration of the second/third pereopods (green/white) and the dactyls of the second/third pereopods (with or without dark bands/patches). However, factors inducing these colour variations have not yet been elucidated. Here, we investigated the occurrence of colour variation in this species with particular emphasis on change of colouration associated with growth stage and region in specimens from tropical/subtropical to warm temperate areas in the Indo–West Pacific, including evidence from molecular phylogeny based on the cytochrome c oxidase subunit I (COI). We have, then, clarified that the colouration on the pereopod dactyls gradually changed from solid colour (yellow/white) to having dark-coloured area(s) or transverse band(s) as a result of the growth stage. The frequency of occurrence of the solid colour dactyls was higher than those of other colour types in tropical regions. Our results also indicated that the white ambulatory leg type was the colouration type that was frequently seen in juvenile stages. However, significant genetic differences were not detected between each colouration determined by molecular analysis of samples from 14 localities in the Indo-West Pacific region; in contrast, two genetically differentiated regional populations (North Australia; Phuket, Thailand; and Lombok, Indonesia) were detected. The present study, therefore, emphasizes the necessity for further study on the colour variation of marine animals focusing on growth stages and regional differences, with molecular data to facilitate the research on adaptation and/or speciation, especially in geographically widely distributed species.