Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama.

The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish.

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

Distinctive color variation in Rhinolepadichthys geminus (Gobiesocidae: Diademichthyinae) from Alor Islands, Indonesia: morphological and molecular insights.

Rhinolepadichthys geminus, one of three recently described species in the genus Rhinolepadichthys (previously known as Lepadichthys lineatus complex), is characterized by several distinct diagnostic morphological and color features, including a pair of yellow stripes on the body ventral midline. However, one of three specimens recently collected from the Alor Islands, Indonesia, possessed a yellow circular line, instead of a pair of yellow stripes, indicating that the latter were not an invariable feature. Morphological and molecular evidence confirmed the identity of the specimen and intraspecific significance of the color variation.

Reduction in size-at-maturity in unprecedentedly strong cohorts of redfish (Sebastes mentella and S. fasciatus) in the Gulf of St. Lawrence and Laurentian Channel.

Life-history traits, such as size-at-maturity, are key parameters to model population dynamics used to inform fisheries management. Fishery-induced evolution, density-dependent effects, and global warming have been shown to affect size- and age-at-maturity, and resulting spawning stock biomass (SSB) in a wide range of commercial fish stocks. Marked changes in redfish biomass and environmental conditions in the Gulf of St. Lawrence and Laurentian Channel over the past decade called for a review and update of size-at-maturity for commercially important deepwater redfish Sebastes mentella and Acadian redfish Sebastes fasciatus stocks. Following a 25-year moratorium, local redfish biomass has recently reached unprecedented levels, co-occurring with an overall warming of bottom water temperatures. Our objectives were (1) to perform a histological assessment of redfish reproduction stages, including the validation and fine-tuning of a robust visual chart to facilitate monitoring of size-at-maturity and SSB in a transforming environment, and (2) to evaluate changes in size-at-maturity in unprecedentedly strong cohorts of redfish, and consequences for stock status assessment and fisheries management. Each specimen was genetically identified to species, and gonad reproduction stages were determined by histology and macroscopic appearances. The present study enabled a robust visual chart for continued and cost-effective monitoring of redfish reproduction stages to be refined and validated, and has shown a large decrease in redfish length when 50% of the individuals are considered mature that led to an increase in estimates of SSB during the 2011-2021 period for S. mentella and S. fasciatus. These changes modified the perception of stock status, thus having significant implications for fisheries management. Given that fishery-induced evolution and community structure changes along with global warming are affecting numerous stocks worldwide, the present study outlines a major and global challenge for scientists and resources managers. As shown by our results, the monitoring and frequent updates of life-history traits in transforming environments are needed to provide reliable science advice for sustainable fisheries.

Species of Dactylogyridae (Monogenoidea, Polyonchoinea) from the gills of haemulid and lutjanid fishes (Perciformes) from the Pacific coast of Mexico.

Examination of the gill lamellae of the Panama grunt Rhencus panamensis (Steindachner) (Haemulidae), golden snapper Lutjanus inermis (Peters), and yellow snapper Lutjanus argentiventris (Peters) (Lutjanidae) (Perciformes) from the coast of the Guerrero State (eastern Tropical Pacific) of Mexico revealed 5 species of Monogenoidea: Euryhaliotrema disparum n. sp. on R. panamensis; Haliotrematoides uagroi n. sp. on L. inermis; and E. anecorhizion Kritsky & Mendoza-Franco, 2012, E. fastigatum (Zhukov, 1976) Kritsky & Boeger, 2002, and E. paracanthi (Zhukov, 1976) Kritsky & Boeger, 2002 on L. argentiventris. Specimens found on R. panamensis were assigned within Euryhaliotrema as a new species possessing the atypical morphology of the male copulatory organ (i.e., a coiled tube with clockwise rings). Haliotrematoides uagroi n. sp. differs from Haliotrematoides striatohamus (Zhukov, 1981) Mendoza-Franco, Reyes-Lizama & Gonzalez-Solis, 2009 from Haemulon spp. (Haemulidae) from the Caribbean Sea (Mexico) in having inner blades on the distal shafts of the ventral and dorsal anchors. The present paper represents the first finding of a species of Euryhaliotrema (E. disparum n. sp.) on a species of Rhencus and the second species on a haemulid host, and H. uagroi n. sp. as the first monogenoidean species described on L. inermis. Euryhaliotrema anecorhizion, E. fastigatum, and E. paracanthi on L. argentiventris in the Pacific coast of Mexico represent new geographical records.

Structural basis of DNA polymerase θ mediated DNA end joining.

DNA polymerase θ (Pol θ) plays an essential role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. However, the mechanisms by which Pol θ recognizes microhomologous DNA ends and performs low-fidelity DNA synthesis remain unclear. Here, we present cryo-electron microscope structures of the polymerase domain of Lates calcarifer Pol θ with long and short duplex DNA at up to 2.4 Šresolution. Interestingly, Pol θ binds to long and short DNA substrates similarly, with extensive interactions around the active site. Moreover, Pol θ shares a similar active site as high-fidelity A-family polymerases with its finger domain well-closed but differs in having hydrophilic residues surrounding the nascent base pair. Computational simulations and mutagenesis studies suggest that the unique insertion loops of Pol θ help to stabilize short DNA binding and assemble the active site for MMEJ repair. Taken together, our results illustrate the structural basis of Pol θ-mediated MMEJ.

Larval study revealed diversity and life-history traits of crypto-benthic eel gobies.

Because adult and juvenile eel gobies usually hide within the burrows of muddy substrates, their diversity and life history have not yet been fully elucidated. We investigated larval specimens of the eel gobies collected on Okinawa Island in southern Japan. The genus Trypauchenopsis was previously thought to consist of only one species, but our larval collection identified two species, Trypauchenopsis limicola and Trypauchenopsis intermedia, distinguished by their species-specific melanophore arrangements and differences in their fin-ray counts. Taenioides kentalleni were previously known from only two specimens worldwide. A third specimen of this species has now been added from the larval collection. In addition to the three species above, Taenioides gracilis and Caragobius urolepis were identified and the larval morphologies of the five species were described for the first time. All the larvae collected in the present study were at late postflexion stage. T. limicola, T. intermedia and T. gracilis were presumably collected in the estuaries and beaches when approaching their adult habitats at the end of pelagic life. They were 8.5-10.3 mm in standard length, and otolith analysis suggests that their pelagic larval durations are a little longer than 1 month (average 34-37 days). The larval occurrence suggested that the spawning season of T. limicola is May-December, when the water temperature is warmer than approximately 20°C. Our work reveals that studying the larval stage can provide new information on the taxonomy and life history of the elusive cryptobenthic fish.

Identification of enigmatic Mediterranean fish Gobius ater Bellotti, 1888 (Teleostei: Gobiidae) based on morphology from underwater photographs.

Gobius ater Bellotti, 1888 is the Mediterranean gobiid species whose live appearance has remained unknown the longest since its description. A goby observed in southern France in 2021 is here identified as G. ater based on a diagnosis of morphological characters visible on high-quality underwater photographs. Then, the authors provide the first description of colouration in live G. ater and a species diagnosis based on colouration. This diagnosis allows the authors to validate a previous photographic record, also from France. Reviewing all claims of G. ater, they argue that only seven records are unambiguously valid, including the two photographic records presented here.

The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators.

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae, and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species-particularly that of L. mariae-which may be important for conservation and management of this culturally and economically important clade of fishes.

Phylogenetics and the evolution of terrestriality in mudskippers (Gobiidae: Oxudercinae).

The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new resources and exploitation of untapped niches precipitating a major phylogenetic diversification. However, a paucity of fossils has left considerable uncertainties about phylogenetic relationships and the eco-morphological stages in this key transition in Earth history. Among extant actinopterygians, three genera of mudskippers (Gobiidae: Oxudercinae), Boleophthalmus, Periophthalmus and Periophthalmodon are the most terrestrialized, with vertebral, appendicular, locomotory, respiratory, and epithelial specializations enabling overland excursions up to 14 h. Unlike early stegocephalians, the ecologies and morphologies of the 45 species of oxudercines are well known, making them viable analogs for the initial vertebrate conquest of land. Nevertheless, they have received little phylogenetic attention. We compiled the largest molecular dataset to date, with 29 oxudercine species, and 5 nuclear and mitochondrial loci. Phylogenetic and comparative analyses revealed strong support for two independent terrestrial transitions, and a complex suit of ecomorphological forms in estuarine environments. Furthermore, neither Oxudercinae nor their presumed sister-group the eel gobies (Amblyopinae, a group of elongated gobies) were monophyletic with respect to each other, requiring a merging of these two subfamilies and revealing an expansion of phenotypic variation within the "mudskipper" clade. We did not find support for the expected linear model of ecomorphological and locomotory transition from fully aquatic, to mudswimming, to pectoral-aided mudswimming, to lobe-finned terrestrial locomotion proposed by earlier morphological studies. This high degree of convergent or parallel transitions to terrestriality, and apparent divergent directions of estuarine adaptation, promises even greater potential for this clade to illuminate the conquest of land. Future work should focus on these less-studied species with "transitional" and other mud-habitat specializations to fully resolve the dynamics of this diversification.

First adult record of the barracudina Lestidiops extremus (Ege, 1953), based on a specimen from the Philippines (Teleostei: Paralepididae).

The adult morphology of Lestidiops extremus (Ege, 1953), a barracudina originally described based on postlarvae from Indonesia, has long been a mystery. An adult specimen collected from off the Philippines represents the first confirmed record of an adult of this species. Observations on the holotype and a detailed description of the adult are provided. The location of the pelvic-fin origin in the adult, clearly behind the posterior end of the dorsal-fin base, is unique within this genus and the entire subfamily Lestidiinae. The present find extends the known range of the species from northwestern New Guinea, Indonesia, to seas east of the Philippines.

Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters.

A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman's center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters.

Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing.

Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology.

The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.

Establishment and Characterization of a Novel Gill Cell Line, LG-1, from Atlantic Lumpfish (Cyclopterus lumpus L.).

The use of lumpfish (Cyclopterus lumpus) as a cleaner fish to fight sea lice infestation in farmed Atlantic salmon has become increasingly common. Still, tools to increase our knowledge about lumpfish biology are lacking. Here, we successfully established and characterized the first Lumpfish Gill cell line (LG-1). LG-1 are adherent, homogenous and have a flat, stretched-out and almost transparent appearance. Transmission electron microscopy revealed cellular protrusions and desmosome-like structures that, together with their ability to generate a transcellular epithelial/endothelial resistance, suggest an epithelial or endothelial cell type. Furthermore, the cells exert Cytochrome P450 1A activity. LG-1 supported the propagation of several viruses that may lead to severe infectious diseases with high mortalities in fish farming, including viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV). Altogether, our data indicate that the LG-1 cell line originates from an epithelial or endothelial cell type and will be a valuable in vitro research tool to study gill cell function as well as host-pathogen interactions in lumpfish.

Complete Mitochondrial Genome of Pseudocaranx dentex (Carangidae, Perciformes) Provides Insight into Phylogenetic and Evolutionary Relationship among Carangidae Family.

Pseudocaranx dentex (white trevally) which belongs to the Carangidae family, is an important commercial fishery and aquaculture resource in Asia. However, its evolution and population genetics have received little attention which was limited by the mitogenome information absence. Here, we sequenced and annotated the complete mitochondrial genome of P. dentex which was 16,569 bp in length, containing twenty-two tRNAs (transfer RNAs), thirteen PCGs (protein-coding genes), two rRNAs (ribosomal RNAs), and one non-coding region with conservative gene arrangement. The Ka/Ks ratio analysis among Carangidae fishes indicated the PCGs were suffering purify selection and the values were related to the taxonomic status and further influenced by their living habits. Phylogenetic analysis based on the PCGs sequences of mitogenomes among 36 species presented three major clades in Carangidae. According to the phylogenetic tree, we further analyzed the taxonomic confusion of Carangoides equula which was on the same branch with P. dentex but a different branch with Carangoides spp. We inferred Kaiwarinus equula should be the accepted name and belong to the independent Kaiwarinus genus which was the sister genus of Pseudocaranx. This work provides mitochondrial genetic information and verifies the taxonomic status of P. dentex, and further helps to recognize the phylogenetic relationship and evolutionary history of Carangidae.

Population-level morphological variation of Anisotremus interruptus (Gill, 1862) (Perciformes: Haemulidae) in the Tropical Eastern Pacific, with the description of two new species.

The family Haemulidae is a wide-ranging group of marine fishes that are of significant commercial value in the Tropical Eastern Pacific (TEP). Phylogenetic studies on the species Anisotremus interruptus have revealed high levels of genetic diversity as well as divergence among populations in the TEP, which suggests that the taxonomic diversity of A. interruptus could be underestimated. Anisotremus interruptus has a large distribution, ranging from central Baja California, Mexico to northern Peru, including all oceanic islands except Clipperton. Recent genetic studies on this taxon indicate the presence of a species complex of at least three distinctive lineages. We performed a comparative study of the population-level meristic and morphometric variation of A. interruptus in the TEP to evaluate and identify possible morphological features concordant with the genetic differentiation of populations. Our results provide evidence of the presence of two new species of the genus Anisotremus, A. perezponcedeleoni sp. n. from the Revillagigedo Archipelago and A. espinozai sp.n. from Galapagos Archipelago-Cocos Island.

Five new species of Western Atlantic stardrums, Stellifer (Perciformes: Sciaenidae) with a key to Atlantic Stellifer species.

Five new species of Stellifer are described from the Caribbean Sea and tropical southwestern Atlantic. Among the previously recognized stelliferine genera, Stellifer is unique by having a pair of variably developed appendages on the posterior margin of the anterior gas chamber, which is lacking in Bairdiella, Corvula, Elattarchus, Odontoscion and Ophioscion. However, recent genetic studies indicated that Stellifer and Ophioscion are not monophyletic. The genus Ophioscion Gill, 1863 is recognized herein as a junior synonym of Stellifer Oken, 1817. Of the five new species described, Stellifer cervigoni n. sp., S. collettei n. sp., and S. musicki n. sp. have a pair of knob-like diverticula along the posterior margin of the anterior gas chamber, which is absent in S. macallisteri n. sp., and S. menezesi n. sp. Stellifer cervigoni n. sp. is found along the southern Caribbean coast of Colombia and Venezuela; it can be distinguished from other species by having a jet-black roof of mouth and inner opercular lining. Stellifer collettei n. sp. is found from Surinam to southeastern Brazil, while S. musicki n. sp. is endemic to northern Brazil. Stellifer macallisteri n. sp. has an oblique, terminal mouth and it is found in Colombia, Venezuela and Dominican Republic. Stellifer menezesi n. sp. has a subterminal mouth and is found from northeastern to southeastern Brazil. These results bring the number of valid species of Stellifer in the Atlantic to 18, and a key to the identification of these species is included.

A review of the Glossogobius giuris complex in Australia, with wider discussion on nomenclature and possible synonymies.

Two species that had previously been referred to as Glossogobius giuris from Australia are redescribed and tentatively treated as Glossogobius giuris and Glossogobius laticeps. The two species are largely allopatric in Australia with G. laticeps found on the east coast of Queensland and some rivers of the Northern Territory, while G. giuris is distributed from the Northern Territory to rivers of the west coast of Western Australia. The two species are known to be genetically distinct and with some differences in colour patterns. Morphological features separating the species are minor and there is considerable overlap in many of the characters separating them. High variation in the Hammersley Ranges and Kimberley region of Western Australia further complicates separation of the species. The status of the Glossogobius giuris group from India is discussed as a key area to resolving an overall "giuris" species complex. Information is provided on the current identity of a number of species that had previously been considered synonyms of Glossogobius giuris. Extant types and difficulties assigning the types of known species are also discussed. A key is provided to aid identification of Australian species of Glossogobius.

Description of a new eelpout Pachycara angeloi sp. nov. (Perciformes: Zoarcidae) from deep-sea hydrothermal vent fields in the Indian Ocean.

A new species of eelpout genus Pachycara Zugmayer, 1911 is described based on five specimens caught at a depth of 24193275 m along the Central and Southeast Indian Ridges in the Indian Ocean. The specimens were collected during the INDEX cruises in 2016, 2018 and 2019, respectively. The new species is distinguished from its congeners by the following combination of characters: scales and pelvic fins absent; lateral line configuration mediolateral; dorsal fin origin associated with vertebrae 79 with no free predorsal pterygiophores; vertebrae 2728 + 5759 = 8587; dorsal-fin rays 7880, anal-fin rays 5862; pectoral fin rays 1315. DNA sequences of a mitochondrial COI gene fragment showed low intra-specific variation ranging from 00.3 % sequence divergence and do not reflect different vent sites. This is the 29th species of Pachycara, which is the fifth to be described from specimens collected only from chemosynthetic environments and the sixth known from the Indian Ocean.