Repeated boat noise exposure damages inner ear sensory hair cells and decreases hearing sensitivity in Atlantic croaker (Micropogonias undulatus)

Anthropogenic noise is becoming a major underwater pollutant because of rapidly increasing boat traffic worldwide. But its impact on aquatic organisms remains largely unknown. Previous studies have focused mainly on high-frequency and impulsive noises (i.e. sonar); however, boat noise is more pervasive, continuous, and its highest intensity and component frequencies overlap the auditory bandwidth of most fishes. We assessed the impacts of boat noise on saccular sensory hair cell density and hearing thresholds of a soniferous species, Atlantic croaker (Micropogonias undulatus). In two laboratory experiments, individuals were subjected to simulated boat noise: a single 15-min exposure and 3 days of intermittent noise (simulating passing vessels). Immediately after both experiments, fish were either (1) tested for hearing sensitivity with auditory evoked potential (AEP) tests or (2) euthanized for fluorescent phalloidin and TUNEL labeling for hair cell density counts. Relative to controls, no differences were observed in auditory thresholds nor hair cell density between individuals subjected to a single 15-min noise exposure. However, fish from the 3-day experiment showed decreased sensory hair cell density, increased apoptotic cells, and higher hearing thresholds than control fish at 300, 800 and 1000 Hz. Our results demonstrate that impacts from boat noise depend upon the duration and frequency of exposure. For a species reliant on vocalization for communication, these impacts may hinder spawning success, increase predation risks and significantly alter the ecosystem.

Application of high-throughput sequencing to analyze the diet of black croaker (Atrobucca nibe) in southern coastal waters of Zhejiang

This study investigated the feeding habits of black croaker (Atrobucca nibe) to fully understand its role in the food web in southern coastal waters of Zhejiang, China. In total, 225 black croakers were collected in a bottom trawl survey, of which 195 were used for the stomach contents analysis and 30 for high-throughput sequencing (HTS). Both approaches showed that the main prey was shrimp, with Alpheus japonicus being the most predominant. In addition, black croaker also fed on other benthic species, suggesting that it was a demersal predator. Feeding intensity also varied with black croaker body length, as did prey preference, from small-sized species to larger species with increases in fish size; in addition, prey species were more diverse in the large-bodied prey group. Canonical correspondence analysis indicated that the feeding habit of black croaker was most significantly correlated with temperature and dissolved oxygen. HTS was shown to be a feasible high precision semi-quantitative analytical approach, although it must be combined with morphological methods to obtain more complete feeding data; thus, it could provide an effective scientific basis for feeding ecology studies of marine organisms.

Description of two new species of Diplectanum Diesing, 1858 (Monogenea: Diplectanidae) collected from Protonibea diacanthus (Lacepède, 1802) (Teleostei: Sciaenidae) from waters off northern Australia

Two new species of the family Diplectanidae Monticelli, 1903 from the gills of Protonibea diacanthus (Lacepède, 1802) (Teleostei: Sciaenidae) off the northern Australian coast are described. Previous studies have either morphological or genetic results, whereas this study combines morphological and advanced molecular methods to provide the first detailed descriptions for species of Diplectanum Diesing, 1858 from Australia utilising both methodologies. Two new species, Diplectanum timorcanthus n. sp. and Diplectanum diacanthi n. sp., are morphologically described and genetically characterised using the partial nuclear 28S ribosomal RNA gene (28S rRNA) and the internal transcribed spacer 1 (ITS1) partial sequence.

The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis

Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic−Indo−West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic−Indo−West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.

From development to taxonomy: the case of Sciaenacotyle pancerii (Monogenea: Microcotylidae) in the Mediterranean meagre

The microcotylid Sciaenacotyle pancerii is a pathogenic monogenean infecting Argyrosomus regius, a candidate for species diversification in the Mediterranean aquaculture. Life-history stages of S. pancerii commonly co-occur in field infections, but to date, morphological data have only been provided for oncomiracidia and adults although identifying life-history stages can be useful in infection management. A total of 114 specimens of S. pancerii were analysed to characterize the developmental events and to assess morphological and morphometric variations before and after maturity. The post-larval development of S. pancerii is characterized by: expansion and bifurcation of the gut, loss of the larval haptor, protandrous development of the genitalia and vitellaria formation. The size variability of larval hooks, hamuli and germanium of S. pancerii is firstly reported and dimensional ranges of parasite body, haptor, testes, posteriormost clamps and eggs are widened. The size of most of the diagnostic features of S. pancerii significantly increases after parasite maturity and therefore, only those specimens with more than 116 clamps should be considered for minimising development-related variability in size. The high number of clamps, their fast development and the asymmetry in their size and arrangement suggest that S. pancerii may use a mixed attachment strategy between the closely related microcotylids and heteraxinids. This combination of features may be host related and linked to the gill structure of the sciaenid fish and the phylogenetic position of the genus Sciaenacotyle; distant from other microcotylids while close to heteraxinid species.

Habitat transitions by a large coastal sciaenid across life history stages, resolved using otolith chemistry

Many coastal species move between estuarine and coastal environments throughout their life. Migration patterns develop as a result of ecology and evolution and must be understood to effectively manage harvested stocks. This study examined movements across estuarine and coastal marine habitats in adult Mulloway (Argyrosomus japonicus); a commercially, indigenous and recreationally harvested sciaenid of south-eastern Australia. Chemical profiles across the otolith (ear bone) were used to examine transitions between estuary and marine habitats over life history. Patterns in otolith Ba:Ca concentrations indicated that the majority of fish migrated between estuary and marine habitats, but a small proportion of fish appeared to remain in either the estuary or the marine habitat. Such movements may potentially be driven by a range of biological and environmental factors. This approach allows questions about the life history and habitat use of Mulloway to be addressed, which will aid management and provide a platform for future research on Mulloway, other sciaenid's and coastal migratory species.

Geographical variation in age and growth of the endemic Australian sciaenid Atractoscion atelodus

Growth rates and other age-related population characteristics are essential parameters underpinning management of a stock. This is the first study to estimate length-at-age of Atractoscion atelodus (family Sciaenidae) in New South Wales (NSW), despite the species being exploited since the 1940s. The aim of the current study was to quantify the age-based biological characteristics of A. atelodus and in particular: (a) validate the use of sagittal otoliths to quantify age; (b) estimate the growth rates and longevity of males and females; (c) examine geographical variation in age and growth; (d) document the age composition in commercial landings and (e) estimate mortality rates. A. atelodus is relatively fast growing, reaching 40 cm fork length (L_F ) in the first year of life and living to at least 14 years. Growth was significantly different between sexes, with modelled asymptotic lengths of females (L_∞  = 84.6 cm L_F ) greater than males (L_∞  = 69.0 cm L_F ). Growth rates were also significantly different between northern and southern populations. Fish sampled from the southern region were younger and faster growing than those sampled in the northern region, supporting the counter-gradient growth theory and the influence of upwelling providing greater nutrient and food availability. The commercial fishery was predominantly based on young fish <3 years. with few (c. 5%) greater than 5 years. Fishing mortality estimates (F = 0.42) were similar to natural mortality estimates (M = 0.44). The age-based parameters estimated in the present study suggest that A. atelodus should be relatively resilient to fishing; nonetheless, the sizes and ages in landings are indicative of a stock heavily fished. The fishery is experiencing truncated age distributions and appears to be largely recruitment driven, increasing susceptibility to overexploitation. Determining geographical differences in growth rates of a population has important implications when considering impacts of anthropogenic drivers such as global warming and overexploitation and is important to determine in managing exploited fish populations.

Parasite assemblages of whitemouth croaker, Micropogonias furnieri: comparison between marine and brackish waters from the Argentine Sea

The whitemouth croaker, Micropogonias furnieri, a coastal demersal fish with wide distribution in the Southwest Atlantic Ocean, is a euryhaline species, inhabiting waters with a wide range in salinity. Here, the composition of parasite assemblages of M. furnieri caught along the coastal area off Mar del Plata, Argentina, was described and the infracommunity structure compared with fish from brackish waters to determine variations of its parasite communities due to fish migration between these environments. The relationships between the presence of parasites and the diet and ecological traits of this fish host were discussed. A total of 61 fish from Mar del Plata (MDP) were examined for parasites and compared with previously published data for whitemouth croakers from Mar Chiquita coastal lagoon (MCH), an estuarine system connected to the sea. Corynosoma australe, Dichelyne sciaenidicola, and Neopterinotrematoides avaginata were the most prevalent and abundant species in MDP. Comparisons of infracommunity descriptors showed that fish from MDP harbored a higher number of parasites, as well as richer and more diverse infracommunities than those of MCH. Significant differences occurred in the structure and composition of parasite assemblages of whitemouth croaker from MDP compared to those from MCH, in which Neomacrovalvitrema argentinensis, N. avaginata, Neobrachiella chevreuxii, D. sciaenidicola, and C. australe were the key discriminating species related to these differences. The present study provides comparative data, of great importance for the understanding of parasite-host-environment interactions, particularly in a host that alternates between brackish and marine waters during its life cycle.

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.

Boat noise affects meagre (Argyrosomus regius) hearing and vocal behaviour

Aquatic noise has increased in last decades imposing new constraints on aquatic animals' acoustic communication. Meagre (Argyrosomus regius) produce loud choruses during the breeding season, likely facilitating aggregations and mating, and are thus amenable to being impacted by anthropogenic noise. We assessed the impact of boat noise on this species acoustic communication by: evaluating possible masking effects of boat noise on hearing using Auditory Evoked Potentials (AEP) and inspecting changes in chorus sound levels from free ranging fish upon boat passages. Our results point to a significant masking effect of anthropogenic noise since we observed a reduction of ca. 20 dB on the ability to discriminate conspecific calls when exposed to boat noise. Furthermore, we verified a reduction in chorus energy during ferryboat passages, a behavioural effect that might ultimately impact spawning. This study is one of few addressing the effects of boat noise by combining different methodologies both in the lab and with free ranging animals.

Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

Spiny head croaker (Collichthys lucidus), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23 Mb, with a contig N50 of 74.92 kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24 Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24 Mb, with an improved scaffold N50 of 26.58 Mb. Based on our phylogenetic analysis, we observed that C. lucidus is much closer to Larimichthys crocea than Miichthys miiuy. We also predicted that many gene families were significantly expanded (p-value <0.05) in spiny head croaker; among them, some are associated with "calcium signaling pathway" and potential "inner ear functions." In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae.

The influence of climatic and lunar drivers on landings cycles of the temperate Australian sciaenid (Atractoscion atelodus) at two temporal scales: A working hypothesis for future management of this resource

Commercial line-fishing catch rates of the endemic sciaenid Atractoscion atelodus in eastern-Australia were significantly affected by lunar phase. Periodic regression analysis indicated that catch rates were greatest during the full moon period and lowest during the new moon period. It is hypothesized that this observation is the result of the visual nocturnal feeding nature of A. atelodus, with schools of fish using the increased ambient light in the water column during the brighter part of the lunar phase to feed intensively. Increased feeding intensity during the brighter phase of the lunar month may also be related to spawning activity during the new moon phase; however this hypothesis remains to be tested. Annual commercial landings through a 71 year dataset (1950-2020) showed an approximately exponential decline, overlaid with periodic years of higher and lower landings. Such periods of higher landings were significantly positively correlated with coastal rainfall two and three years earlier, but not with rainfall in the same year or one, four or five years earlier. We hypothesize that increased coastal rainfall, likely in combination with unknown co-occurring factors, promotes increased recruitment success of A. atelodus, potentially through increased primary productivity in the nearshore marine environment. This translates into an increase in the fishable stock mainly two and three years later. If our hypothesis is correct, climate predictions of reduced rainfall in eastern Australia suggest a pessimistic outlook for this fishery.

Sexual dimorphism in the otolith shape of shi drum, Umbrina cirrosa (L.), in the eastern Mediterranean Sea: Fish size-otolith size relationships

Little is known about possible differences in sagitta otolith size and shape between sexes of the shi drum, Umbrina cirrosa, and relationships between their body and otolith size. Thus, this study aimed to fill this knowledge gap via examination of 414 sagittal otoliths from 108 male (total length 13.8-26.8 cm) and 99 female (13.5-26.7 cm) U. cirrosa caught between May 2017 and April 2018 in gillnets set at a depth of ~15 m in Mersin Bay, Eastern Mediterranean Sea. No statistical differences were observed between the shape indices of the left-sided and right-sided sagitta. However, there were significant differences in the size and shape of otoliths between males and females. The slopes of allometric power functions from otolith width × fish sizes gave significant differences between males and females (ANCOVA, P < 0.05). The relationship for length × weight of otoliths from both males and females showed isometric growth, whereas the relationship of otolith width × otolith weight showed positive allometry. Negative allometric growth was observed for the relationship otolith length × otolith width. In summary, this study revealed the presence of sexual dimorphism in the otolith shape of U. cirrosa, and the data on regression relationships of fish-otolith sizes can be used to estimate fish size from U. cirrosa otolith sizes.

Bilateral asymmetry in size of otolith of Otolithes ruber (Bloch & Schneider, 1801) collected from the marine waters of Iraq

The otolith length and width of adult teleost Otolithes ruber (Bloch & Schneider, 1801) were used to calculate the fluctuating asymmetry in these two characters. The results displayed that the amount of asymmetry of the otolith width was the highest between the two asymmetry values attained for the otolith of O. ruber. Further, the lowest level of asymmetry in the two otolith characters is at the fish length ranging between 150 and 180 mm and the highest at the fish length ranging between 461 and 2490 mm. The conceivable reason for the asymmetry in this species has been deliberated relative to different pollutants and their presence in the area. A tendency of increase in the asymmetry levels with the fish length was observed for the otolith length and width.

Acoustic Properties of the Otolith of the Large Yellow Croaker Larimichthys crocea (Perciformes: Sciaenidae)

The inner ears of fish contain three pairs of otoliths-lapilli, asterisci and sagittae-which play important roles in hearing and balance. However, acoustic properties and dynamic responses of fish otoliths are poorly understood. The large yellow croaker (Larimichthys crocea), like many species in the family Sciaenidae, is extremely sensitive to sound. The present study used L. crocea sagittae as the research subject and examined the variation in shear stress on sagittae under different acoustic stimuli. For the first time, the sound speed of the sagitta was measured using ultrasonic pulse-echo techniques, and the acoustic impedance and natural frequency of the sagitta were calculated. Larimichthys crocea adults (20-22 cm standard length, n = 10) had a sagitta density of 2781.5 ± 28.06 kg/m3, sound speed of 4828-6000 m/s and acoustic impedance range of 13.4-16.7 MPa·s/m, approximately 9-11 times that of seawater (1.48 MPa·s/m). The natural frequency of the sagitta was 76.4-95.5 kHz. The shape and structural details of sagittae were reconstructed by 3D scanner and the shear stress responses of sagittae under different acoustic stimulus were investigated based on a finite element model. The simulation results showed that the shear stress responses tended to increase and then decrease in the range of sciaenid hearing frequency from 200 to 1300 Hz, peaking at 800 Hz. The shear stress responses varied with the direction of acoustic stimulus and peaked when the incident direction was perpendicular to the inner surface of the otolith. These results provide important parameters that may be used to protect L. crocea from possible underwater noise damage, particularly during their spawning aggregations and over-wintering aggregations.

Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea)

High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.68–56.23% polymorphic SNP rate across species. A phylogenetic tree inferred by using the genotype data generated by NingXin-I confirmed the phylogenetic distance of the species in Sciaenidae. The performance of NingXin-I in large yellow croaker and the other species in Sciaenidae suggested high accuracy and broad application. The NingXin-I array should be valuable for quantitative genetic studies, such as genome-wide association studies (GWASs), high-density linkage map construction, haplotype analysis, and genome-based selection.

The influence of rainfall on recruitment success and commercial catch for the large sciaenid, Argyrosomus japonicus, in eastern Australia

Freshwater flows into estuaries influence fish populations through effects on recruitment, growth and mortality. We compared year class strength of a large sciaenid Argyrosomus japonicus with rainfall through a 16-year period in southeastern Australia, to understand the influence of freshwater input on this estuary-dependent and depleted population. Relative year class strength, estimated by back-calculating age composition data from commercial fishery landings, was positively related to rainfall within estuarine catchments (R² = 52%). Commercial estuarine landings from a separate 29-year dataset were positively related to rainfall two and three years earlier (R² = 21% and 44%, respectively). Year class strength of a key prey species, the penaeid prawn Metapenaeus macleayi, was also related to year class strength of A. japonicus (R² = 39%), suggesting that rainfall influences recruitment of A. japonicus by affecting food availability. Several years of above average rainfall may be required to promote recruitment substantial enough to rebuild the population.

Sound production in the Meagre, Argyrosomus regius (Asso, 1801): intraspecific variability associated with size, sex and context

Background

Many fish taxa produce sound in voluntary and in disturbance contexts but information on the full acoustic repertoire is lacking for most species. Yet, this knowledge is critical to enable monitoring fish populations in nature through acoustic monitoring.

Methods

In this study we characterized the sounds emitted during disturbance and voluntary contexts by juvenile and adult meagre, Argyrosomus regius, in laboratory conditions. Breeding sounds produced by captive adults were also compared with meagre sounds registered in the Tagus estuary (Lisbon, Portugal) from unseen fish during the breeding season.

Results

The present dataset demonstrates for the first time that in this species dominant frequency is inversely related to fish size, and that sounds vary according to sex, context and age. Sounds from captive breeding adults were similar to sounds recorded in the field.

Discussion

Our findings indicate that A. regius sound features carry information about size, sex, age and motivation. This variability could potentially be used to identify meagre in the field and to infer about ontogenetic phase (i.e., juveniles vs. adults, and variation with size) and motivation (e.g., spawning). Future studies should confirm sex differences and ascertain the influence of water temperature on acoustic features.

Reproductive Biology of Johnius taiwanensis (Perciformes: Sciaenidae) in Fujian Waters, Southern China

Johnius taiwanensis is a newly described species from the Family Sciaenidae (Perciformes). The species is commonly found in shallow coastal waters along both sides of the Taiwan Strait, on the west sides of Zhejiang, Fujian, Guangdong and Hong Kong and east side of Taiwan, and has been misidentified for decades. We studied the reproductive biology of J. taiwanensis from Fujian coastal waters, southern China, using gonadosomatic index (GSI) and gonad histology analyses. Monthly sampling from July 2016 to October 2017 was conducted and a total of 638 specimens were collected, ranging from 7.3 to 19.0 cm standard length (SL). Gonad histology suggested that the spawning activity of J. taiwanensis females and males lasted from April to October, and the peak spawning months for females was July to September. Mature females and males were 12.5 and 11.8 cm SL, respectively, while the estimated sizes at 50% maturity were 12.0 cm and 10.9 cm SL, respectively. Vitellogenic stage oocytes (O3) and post-ovulatory follicles (POF) or hydrated oocytes (HO) were observed, and POF and O3 in ovaries indicated that J. taiwanensis spawns multiple times each spawning season. HO or both HO and POF were observed in ovaries collected from one same location in May 2017 and August 2016.

Characterization of the complete mitochondrial genome sequence of Nibea diacanthus and its phylogenetic implication

The blackspotted croaker (Nibea diacanthus) is an important food fish of Indo-West Pacific and China. To study the phylogenetic status, we sequenced the complete mitochondrial genome of N. diacanthus. The mitogenome is 16,532 bp in length and composed of 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. The gene composition and the structural arrangement of N. diacanthus complete mtDNA were identical to most of other vertebrates. The phylogenetic analysis using the complete mitochondrial genome revealed that the N. diacanthus might be separated from Nibea genera of Argyrosominae, which was inconsistent with that based on morphology. The complete mitogenome data would be useful for the evolution and conservation genetic studies of Sciaenidae.

nov

Two species, Otolithes ruber and Otolithes cuvieri, are currently recognized in the sciaenid genus Otolithes. Recent findings suggest that Otolithes ruber likely has multiple genetically and morphologically distinct lineages and one of them, Otolithes sp. West Indian Ocean II group (WIO II group), has been previously identified in the Arabian Gulf. In this study, the specimens of Otolithes sp. collected from the western Arabian Gulf were examined using an integrative approach by combining mitochondrial cytochrome c oxidase 1 gene, morphological characteristics, and otolith-shape analyses. Three groups were found to have small within-group and large between-group genetic distance: the Otolithes sp. Western Arabian Gulf (WA) group, and the Otolithes sp. WIO II groups type A and type B. Accordingly, three primary species hypotheses were proposed. Evidence from conventional morphological comparisons, multivariate statistical analysis, geometric morphometric landmark analysis on morphological characteristics, and otolith shape analysis based on wavelet transformation all favor the hypothesis that the Otolithes sp. WA group is a distinct lineage. For this new species, the name Otolithes arabicus sp. nov. is proposed. A detailed description of Otolithes arabicus sp. nov. and a key to identifing species in the genus Otolithes are also provided. However, the primary species hypotheses for Otolithes sp. West Indian Ocean II group type A and type B cannot be fully supported because of partial congruence, which may result from recent divergence.

Neither Diplectanum nor specific: a dramatic twist to the taxonomic framework of Diplectanum (Monogenea: Diplectanidae)

The taxonomy of the genus Diplectanum has been exclusively based on morphological features, with 28 nominal species parasitic on perciform fishes recognised. We used molecular data, to our knowledge for the first time, to evaluate the taxonomic framework of Diplectanum, infer the relationships amongst species attributed to this genus, re-assess the degree of host specificity and explore the population genetic structure of Diplectanum spp. parasitising Mediterranean sciaenids, which are potential target fish species for aquaculture diversification in the region. A minimum of 10 specimens of Diplectanum spp. were sequenced per host species (Argyrosomus regius, Sciaena umbra, Umbrina canariensis and Umbrina cirrosa) and locality (Burriana, Sant Carles de la Ràpita and Santa Pola (Spain)) together with five individuals of the type species Diplectanum aequans. Sequences of partial 28S rDNA and internal transcribed spacer region of Diplectanum spp. were analysed together with those from other Diplectanidae spp. in GenBank using Bayesian inference and maximum likelihood phylogenetic methods. Population genetic analyses were performed using cytochrome c oxidase subunit I gene sequences for a diplectanid species with a wide distribution across host species and localities. Results showed that Diplectanum was not monophyletic, nor were the specimens infecting sciaenids. Instead they formed two separate clades, 26.1-28.6% divergent for the internal transcribed spacer and 13.2-16.9% for the 28S region from D. aequans. Altogether, our results suggest that these specimens represent two distinct new genera from Diplectanum and five putative species with low host specificity. It is likely that morphological variability has led to the description of more species than were detected by molecular methods. In contrast to other monogeneans, Diplectaninae gen. spp. are chiefly generalists. Nonetheless, intraspecific genetic divergence in the internal transcribed spacer region of Diplectaninae gen. spp., and population genetic analyses of one presumed generalist species, Diplectaninae gen. sp. 1.2, showed significant variation between subpopulations living on different hosts. The intraspecific genetic structure by host also suggests different cross-infection potential amongst sciaenid species.

Molecular phylogeny of the Sciaenidae based on the complete mitochondrial sequences

In this study, 45 complete mitochondrial genomes of Sciaenidae species obtained from GenBank were analyzed. Our results suggested that mitochondrial genomes could be an effective marker for resolving the phylogeny of Sciaenidae species. Phylogenetic relationships indicated that Johnius species are more ancient species among all the species that were used in this analysis because Johnius species stands on the root of the polygenetic tree. However, Collichthys niveatus could not separate from Larimichthys polyactis based on the complete mtDNA which indicate that these two species needs further study in the future.

Characterization of the Complete Mitochondrial Genome Sequences of Three Croakers (Perciformes, Sciaenidae) and Novel Insights into the Phylogenetics

The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.

Complete mitochondrial genome and the phylogenetic position of the blackmouth croaker Atrobucca nibe (Perciformes: Sciaenidae)

In this study, the complete mitogenome of the blackmouth croaker Atrobucca nibe was obtained. Its mitogenome is 16,842 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.2% A; 31.2% C; 16.4% G and 25.2% T. Sizes of the 22 tRNA genes range from 66 to 74 bp. One start codons (ATG) and three stop codons (TAG, AGA, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 20 species (including A. nibe) from the family Sciaenidae, all nodes were strongly supported. The result suggested that A. nibe was subsequent to the group with genera Otolithes, Chrysochir, Megalonibea, Pennahia, Nibea, Dendrophysa, and Johnius.

Complete mitochondrial genome and the phylogenetic position of the Caroun croaker Johnius carouna (perciformes: Sciaenidae)

In this study, the complete mitogenome of the Caroun croaker Johnius carouna was obtained. Its mitogenome is 18,752 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. carouna, same as another two Johnius species available in GenBank, J. distinctus (MF083699) and J. grypotus (KC491206). The overall nucleotide composition is: 24.2% A; 18.0% C; 21.4% G, and 36.4% T. Sizes of the 23 tRNA genes range from 67 to 75 bp. One start codons (ATG) and three stop codons (TAG, AGG, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 21 species (including J. carouna) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. carouna was placed as sister to the silver croaker J. grypotus of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.

Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring

Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.

Comparative cytogenetics in three Sciaenid species (Teleostei, Perciformes): evidence of interspecific chromosomal diversification

Background

Species belonging to the Sciaenidae family present a karyotype composed by 48 acrocentric chromosomes and are thus considered a striking example of chromosomal conservation. In this family, three species are extensively studied including Larimichthys crocea, Larimichthys polyactis and Nibea albiflora due to their importance in fishery and aquaculture in East Asia. Despite abundant data of population genetics available for some of them, cytogenetic information on these species is still scarce and obtained by conventional cytogenetic protocols. Therefore, a more detailed cytogenomic investigation was performed in these species to analyze their karyotype differentiation using conventional staining techniques and fluorescence in situ hybridization to map several repetitive DNAs.

Results

The three species showed a slight karyotype differentiation with 4sm + 2st + 42a in L. polyactis, 20st + 28a in L. crocea and 48a in N. albiflora. Additionally, the mapping of repetitive sequences further revealed a number of interspecific differences among them. Particularly, 18S and 5S rDNA sites showed syntenic arrangements in N. albiflora and non-syntenic arrangements in both Larimichthys species. The microsatellites (CA)₁₅ and (GA)₁₅ showed conspicuous terminal clusters in some chromosomes of all species. On the other hand, (CGG)₁₀ repeats, Rex6 elements and U2 snRNA displayed a scattered distribution on the chromosomes.

Conclusions

Although the three Sciaenid species examined displayed a general pattern of karyotypic conservatism, we explored chromosomal diversification among them. The diversificated karyotypic macrostructure is followed by intergeneric evolutionary diversification of the repetitive sequences. The data indicate some degree of intergeneric evolutionary diversification at chromosomal level, and suggest the evolutionary dynamics among Sciaenid species, higher than previously thought. The present cytogenetic data provide new insight into the chromosomal diversification in Sciaenidae, and contribute to inferring the chromosomal rearrangements and trends of karyotype evolution in this fish group.

Three monogeneans parasitic on marine sciaenid fish from Peru including description of Cynoscionicola veranoi n. sp. (Microcotylidae), and redescription of C. americanus Tantaleán, Martínez and Escalante, 1987 and Hargicotyle sciaenae Oliva and Luque, 1989 (Diclidophoridae)

Cynoscionicola veranoi n. sp. (Monogenea: Microcotylidae) is described based on specimens collected from the gills of lorna drum Sciaena deliciosa (Tschudi, 1846) (Sciaenidae) from Peru. The new species can be differentiated from the other congeneric species by the combination of the following characteristics: (1) haptor with two types of clamps, (2) number and shape of the spines in anterolateral pouches of genital atrium (10-11 curved spines and 3-4 short and bifid spines with a knob in each lateral margin), (3) number and shape of the spines in posterolateral pouches of genital atrium (13-18 bifid spines), (4) 4-6 small spherical unarmed pouches in the genital atrium, and (5) 10-15 testes. In addition, a redescription of Cynoscionicola americanus Tantaleán, Martínez and Escalante, 1987 and Hargicotyle sciaenae Oliva and Luque, 1989 (Diclidophoridae) based on examination of type material and newly collected specimens from snakehead kingcroaker Menticirrhus ophicephalus (Jenyns, 1840) and S. deliciosa (type hosts), respectively, are provided herein.

Complete mitochondrial genome and the phylogenetic position of the Pawak croaker Pennahia pawak (Perciformes: Sciaenidae)

In this study, the complete mitogenome of the Pawak croaker Pennahia pawak was first determined. This mitogenome is 16,408 bp in length, and consists of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.7% A, 29.5% C, 15.9% G, and 26.9% T. Sizes of the 22 tRNA genes range from 66 to 75 bp. One start codons (ATG) and two stop codons (AGA and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 17 species (including P. pawak) from the family Sciaenidae, all nodes were strongly supported. The phylogenetic results suggested that P. pawak has the closest relationship to the silver croaker P. argentata, a species from the same genus.

Effects of release procedures on the primary stress response and post-release survival and growth of hatchery-reared spotted seatrout Cynoscion nebulosus

To help explain the apparent poor post-release success of hatchery-reared (HR) spotted seatrout Cynoscion nebulosus, this study examined the effects of handling, transport and release procedures on the stress response of two age classes [48 and 80 day post-hatch (dph)] of HR C. nebulosus, as measured by cortisol concentrations and the post-release survival and growth of 48 and 80 dph HR C. nebulosus. As a proxy for stress, tissue cortisol was measured at various times during the handling, tagging (80 dph), transport, acclimation and release process. To consider the implications of the pre-release stressors, growth and survival were monitored in separate field experiments for each age class of acclimated post-transport C. nebulosus using control C. nebulosus that only experienced anaesthesia, transport, acclimation and a net release v. experimental C. nebulosus that underwent the entire routine procedure, including anaesthesia, tagging, transport, acclimation and gravity release through a pipe. For 48 dph C. nebulosus, mean cortisol varied significantly throughout handling and transport, increasing more than six-fold from controls before decreasing in mean concentration just prior to release. For 80 dph C. nebulosus, cortisol varied throughout handling, tagging and transport, first increasing more than three-fold compared with control C. nebulosus, before decreasing and rising slightly just prior to release. For 48 dph C. nebulosus within field enclosures, survival was high and similar for control and experimental groups; experimental C. nebulosus, however, were shorter, lighter and lower in condition than control C. nebulosus. For 80 dph C. nebulosus within field enclosures, fewer experimental C. nebulosus survived and those that did survive were of lower condition than C. nebulosus from the control group. Small untagged C. nebulosus may survive the release procedure better than larger C. nebulosus carrying a coded-wire tag. These findings document some ways in which pre-release practices may translate into detrimental effects on post-release success of HR C. nebulosus.

Complete mitochondrial genome and the phylogenetic position of the tigertooth croaker Otolithes ruber (Perciformes: Sciaenidae)

In this study, the complete mitogenome of the tigertooth croaker Otolithes ruber was first determined. This mitogenome is 16,589 bp in length, and consists of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.4% A; 29.1% C; 16.1% G and 27.4% T. Sizes of the 22 tRNA genes range from 66 to 74 bp. Four start codons (ACG, CTG, GTG and ATG) and three stop (AGA, TAG and TAA/TA/T) codons were detected in 13 protein-coding genes. In the Bayesian treebased on the complete mitogenomes of 18 species (including O. ruber) from the family Sciaenidae, all nodes were strongly supported. The phylogenetic results suggested that O. ruber was closed to the black-spotted croaker Protonibea diacanthus.

Complete mitochondrial genome and the phylogenetic position of the bighead pennah croaker Pennahia macrocephalus (Perciformes: Sciaenidae)

The complete mitogenome of the bighead pennah croaker Pennahia microcephalus was first determined in this study. It is 16,508 bp in length with the typical gene order and transcriptional direction in vertebrates containing 37 genes. The overall nucleotide composition is 27.5% A; 31.2% C; 16.0% G, and 25.3% T. The sizes of the 22 tRNA genes range from 68 to 75 bp. Two start (ATC and ATG) and three stop (AGA, TAG, and TAA/TA/T) codons were found in the protein-coding genes. In the Bayesian tree, all nodes were strongly supported based on the complete mitogenomes of 16 species from the family Sciaenidae. The phylogenetic results suggested P. macrocephalus has the closest relationship to the silver croaker P. argentata, a species from the same genus.

Acoustic Communication in Fishes and Potential Effects of Noise

Many soniferous fishes such as cods and groupers are commercially important. Sounds are produced during courtship and spawning, and there is the potential for aquatic noise to interfere with critical behaviors and affect populations. There are few data on the response of wild populations of sound-producing fishes to acoustic noise. New motion and sound exposure fish tags could be used to assess the behavioral responses of large numbers of fish to noise exposure. Many factors, such as fishing mortality and environmental variability in prey supply, could also affect populations and potentially interact with the behavioral responses to noise.

Complete mitochondrial genome sequence for the cuneate drum Nibea miichthioides (Perciformes, Sciaenidae) and its phylogeny

The cuneate drum, Nibea miichthioides, is a native sciaenid species with relevant commercial importance in China. However, the wild resource represented by this species has been severely damaged owing to overfishing and water pollution. For conserving and recovering the species through appropriate measures, genetic studies on the population are necessary. The complete mitochondrial genome of N. miichthioides is a supplement to the mitogenome database for giant croakers and can be used to address taxonomic problems and phylogenetic relationships in Sciaenidae. In this study, we sequenced and characterized the complete mitochondrial genome of N. miichthioides. The full length of the complete mitochondrial DNA was 16,490 bp. It contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. All 21 tRNA genes can fold into a typical cloverleaf structure except for tRNA^Ser (AGY), which lacks a dihydrouridine arm. The phylogenetic analysis using the complete mitochondrial genome revealed that N. miichthioides, A. amoyensis, N. japonica and A. japonicus might be grouped in Argyrosomus, but not belonged to Nibea of Argyrosominae, which was highly consistent with the proposal of Talwar. This investigation provides an effective molecular tool for genetic research on and protection of this endangered species.

Long-term monitoring of captive red drum Sciaenops ocellatus reveals that calling incidence and structure correlate with egg deposition

In the present study, quantitative data were collected to clarify the relationship between calling, call structure and eggs produced in a captive population of red drum Sciaenops ocellatus. Sciaenops ocellatus were held in four tanks equipped with long-term acoustic loggers to record underwater sound throughout a simulated reproductive season. Maximal sound production of captive S. ocellatus occurred when the photoperiod shifted from 13·0 to 12·5 h of light, and the water temperature decreased to c. 25° C. These captive settings are similar to the amount of daylight and water temperatures observed during the autumn, which is the primary spawning period for S. ocellatus. Sciaenops ocellatus exhibited daily patterns of calling with peak sound production occurring in the evenings between 0·50 h before dark and 1·08 h after dark. Spawning occurred only on evenings in which S. ocellatus were calling, and spawning was more productive when S. ocellatus produced more calls with longer durations and more pulses. This study provides ample evidence that sound production equates to spawning in captive S. ocellatus when calls are longer than 0·8 s and contain more than seven pulses. The fact that more calling, longer calls and higher sound pressure levels are associated with spawns that are more productive indicates that acoustic metrics can provide quantitative information on spawning in the wild.

Sound production by the Shi drum Umbrina cirrosa and comparison with the brown meagre Sciaena umbra: a passive acoustic monitoring perspective

Sounds produced by the Shi drum Umbrina cirrosa were short trains of pulses with an average pulse period of 180 ms, pulse duration of c. 40 ms and an average peak frequency of 400 Hz; average values of acoustical properties differed from those recorded from the brown meagre Sciaena umbra in previous studies. The present study provides a preliminary tool for discriminating between these two species while conducting passive acoustic monitoring. The potential effects of ontogeny on sound production in both species are discussed and recommendations are made for further research.

Complete mitochondrial genome of the golden drum Chrysochir aurenus (Perciformes, Sciaenidae) and its phylogeny

The golden drum (Chrysochir aurenus) is an important food fish of Indo-West Pacific and China. To study the phylogenetic status, we sequenced the complete mitochondrial genome of C. aurenus. The mitogenome is 16 505 bp in length and composed of 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and a control region. The gene composition and the structural arrangement of C. aurenus complete mtDNA were identical to most of other vertebrates. The phylogenetic analysis using the complete mitochondrial genome revealed that the C. aurenus might be grouped in different genera of Argyrosominae, but not belonged to Otolithinae, which was highly consistent with that based on the morphology. The present study will be helpful for the evolution and conservation genetic studies of C. aurenus.

Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications

To understand the systematic status of Bahabataipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the

extended termination associated sequence domain

(ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahabataipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahabataipingensis is the sister taxon of Miichthysmiiuy, and those two are sister to Collichthys plus Larimichthys.

Complete mitochondrial genome of the giant croaker Nibea japonica (Perciformes, Sciaenidae) and phylogenetic analysis of the Sciaenidae

The giant croaker Nibea japonica (Perciformes, Sciaenidae) is an important economic fish distributing in the East China Sea, South China Sea, and Japan southern coast. In this study, the complete mitochondrial genome of N. japonica was firstly determined. It is 16 496 bp-length and consists of 22 tRNA genes, 13 protein-coding genes, two rRNA genes, and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. Phylogenetic analysis revealed that N. japonica, A. amoyensis, and other seven fish first clustered into the Argyrosominae clade. It is consistent with the taxonomic status. Then, the Argyrosominae, Pseudosciaeninae, and Sciaeniae formed the sister group, while the Johniinae became a separate clade, which is inconsistent with the previous phenotypic report. It is suggested that the researches of single gene and taxionomic might lose some significant evolutionary characters. This study will contribute to phyogenetic analysis of the Sciaenidae and the natural resources conservation.

Movement patterns, habitat use and site fidelity of the white croaker (Genyonemus lineatus) in the Palos Verdes Superfund Site, Los Angeles, California

White croaker (Genyonemus lineatus family: Sciaenidae) are a schooling, benthic foraging fish historically associated with soft sediment and wastewater outfalls in southern California. While they are often used as an indicator species due to their high organochlorine contaminant loads, little is known of their movements in relation to contaminated habitats. A Vemco Positioning System acoustic telemetry array was used to collect fine-scale movement data and characterize the site fidelity, area use, and dispersal of 83 white croaker on the Palos Verdes Shelf Superfund Site, California over 27 months. White croaker generally demonstrated low residency and recurrence to the Palos Verdes Shelf, and were observed to be largely nomadic. However, individual behavior was highly variable. Although the entire monitored shelf was visited by tagged white croaker, habitats in 0-200 m proximity to wastewater outfalls and between 25 and 35 m depth were used most frequently. Approximately half of white croaker migrated into Los Angeles and Long Beach Harbors; areas where they may be targeted by subsistence fishers. A model framework for incorporating fish movement data into contaminant exposure estimates was developed to better understanding organochlorine contaminant exposure for planning future remediation and monitoring.

A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae)

Widely distributed groups of living animals, such as the predominantly marine fish family Sciaenidae, have always attracted the attention of biogeographers to document the origins and patterns of diversification in time and space. In this study, the historical biogeography of the global Sciaenidae is reconstructed within a molecular phylogenetic framework to investigate their origin and to test the hypotheses explaining the present-day biogeographic patterns. Our data matrix comprises six mitochondrial and nuclear genes in 93 globally sampled sciaenid species from 52 genera. Within the inferred phylogenetic tree of the Sciaenidae, we identify 15 main and well-supported lineages; some of which have not been recognized previously. Reconstruction of habitat preferences shows repeated habitat transitions between marine and euryhaline environments. This implies that sciaenids can easily adapt to some variations in salinity, possibly as the consequence of their nearshore habitats and migratory life history. Conversely, complete marine/euryhaline to freshwater transitions occurred only three times, in South America, North America and South Asia. Ancestral range reconstruction analysis concomitant with fossil evidence indicates that sciaenids first originated and diversified in the tropical America during the Oligocene to Early Miocene before undergoing two range expansions, to Eastern Atlantic and to the Indo-West Pacific where a maximum species richness is observed. The uncommon biogeographic pattern identified is discussed in relation to current knowledge on origin of gradients of marine biodiversity toward the center of origin hypothesis in the Indo-West Pacific.

The complete mitochondrial genome of Nibea coibor (Perciformes: Sciaenidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Nibea coibor has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is 16,509 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D and CSB-C), and the conserved sequence block domains (CSB-2, CSB-3).

The complete mitochondrial genome of the blackspotted croaker Protonibea diacanthus (Perciformes, Sciaenidae)

We present the complete mitochondrial genome of Protonibea diacanthus in this study. The mitochondrial genome is 16,535 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand are 31.09% of G, 27.54% of T, 25.34% of A and 16.03% of C. All the protein-coding genes start with ATG initiation codon except ATP6 with GTG, and 5 types of inferred termination codons are AGA (COXI and COXII), T (ND3, ND4, Cytb), TA (ND2, COXIII and ATP6), TAA (ND1, ATP8 and ND4L) and TAG (DN5 and ND6). There are 14 intergenic spacers and 7 gene overlaps. The tandem repeat sequence is observed in 12S-rRNA, 16S-rRNA, tRNA(Trp), tRNA(Ala), COXIII, ND4L and ND4 genes. Gene arrangement and distribution are consistent with the typical vertebrates.

The complete mitochondrial genome of Nibea coibor (Perciformes, Sciaenidae)

We present the complete mitochondrial genome of Nibea coibor in this study. The mitochondrial genome is 16,502 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand were 31.62% of G, 26.88% of T, 25.19% of A and 16.31% of C. Three types of initiation codons are ATA (ATP6), ATG (ND2, COXI, COXII, ATP8, COXIII, ND3, ND4L, ND4, ND5, ND6, Cytb) and GTG (ND1), and 3 types of termination codons are AGA (COXI), T (ND2, COXII, ND3, ND4) and TAA (ATP6, ATP8, COXIII, ND4L, ND5, ND6, Cytb, ND1). There are 13 intergenic spacers, 7 gene overlaps and no tandem repeat sequence. Gene arrangement and distribution are consistent with the typical vertebrates.

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.