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The anchovy family (Engraulidae) holds significant economic and ecological value in seas around China, playing a crucial role in fisheries and marine ecosystems in these regions. This study analyzed the complete mitochondrial genome data of 18 Engraulidae species from seas around China, integrating molecular evidence to systematically investigate mitochondrial genome structure, codon usage patterns, and phylogenetic relationships within the family. The mitochondrial genomes of Engraulidae exhibited a highly conserved structure, characterized by significant A + T richness and variable control region lengths. Codon usage analysis in seven Thryssa species revealed that base composition, particularly GC content at the third codon position (GC3s), along with purifying selection, jointly influenced codon usage patterns. Phylogenetic analyses supported the division of the 18 species into two subfamilies, Engraulinae and Coiliinae, and highlighted variability in the phylogenetic placement of Setipinna depending on the inclusion of third codon positions. Furthermore, the genus Thryssa was supported to be polyphyletic: T. baelama and T. kammalensis formed one clade, while T. dussumieri, T. hamiltonii, T. setirostris, T. vitrirostris, and T. mystax constituted a separate branch. These findings provide novel molecular evidence for species identification and the taxonomic classification of Engraulidae, while offering a foundation for further exploration of their evolutionary relationships and systematic taxonomy. In this study, we utilized the complete mitochondrial genomes of 18 Engraulidae species to analyze their basic genomic features and reconstruct the phylogenetic relationships within the family. We examined the codon usage bias in the genus Thryssa, explored the evolutionary relationships among the species within the genus, and we also provide some insights into the taxonomic revision of this genus.

Small pelagic fishes in the Mediterranean Sea constitute about half of the total landings, of which almost one-third is European anchovy. Anchovy abundance mainly depends on early life stage and juvenile survival and growth, which are susceptible to shifts in environmental processes. Due to the commercial importance of this species, it is necessary to elucidate the processes affecting recruitment strength for effective fishery management, using environmental indices to set more appropriate harvesting limits. Here, we constructed a simple index to capture synchronicity between enrichment and retention/concentration processes, which are known to affect anchovy abundance, during the first year of life. Three ecosystems in the Mediterranean were examined: Gulf of Lions, Adriatic Sea, and Strait of Sicily. The synchronicity index (SI) represented the synergic evolution over time of the chlorophyll-a concentration (CHL, enrichment process) and mixed layer depth (MLD, concentration/retention processes), and was related with the abundance of anchovy recruits obtained from published survey reports. Considering different ecosystems, when the SI was significantly higher, anchovy recruitment was promoted. This result indicated SI is consistent across ecosystems in explaining anchovy abundance fluctuations and thus could be used to enhance fisheries management and extended to assess the impact of projected environmental changes.

In the Pacific Ocean, air and ocean temperatures, atmospheric carbon dioxide, landings of anchovies and sardines, and the productivity of coastal and open ocean ecosystems have varied over periods of about 50 years. In the mid-1970s, the Pacific changed from a cool \"anchovy regime\" to a warm \"sardine regime.\" A shift back to an anchovy regime occurred in the middle to late 1990s. These large-scale, naturally occurring variations must be taken into account when considering human-induced climate change and the management of ocean living resources.

Thrissina splendida sp. nov., described from 19 specimens collected from the coastal areas of Korea and China, is closely related to Thrissina adelae (Rutter 1897), both species having a long maxilla with the posterior tip beyond the pectoral-fin insertion and the snout tip above the eye center level, and similar ventral scute and fin-ray numbers. However, the former is characterized by lower total gill raker numbers on the first, second, third, and fourth gill arches, higher numbers of longitudinal series scale rows, transverse scales, and vertebrae, a shorter snout and lower jaw, a shorter distance between the dorsal and anal-fin origins, and 4th and 5th anal-fin rays, and distinct paired dark lines along the dorsum from the occiput to the caudal-fin base.

Summary The identification of larval fish has been an important morphological issue in marine biology due to the dramatic transformations that most species undergo from early larval stages to adulthood. Insufficient morphological diagnostic characters in larval fishes made it easy to misidentify them and a difficult process to key to genus and species level. The experiment aims to find out, by applying DNA barcoding, how consistent the morphological identifications can be among larval fish. Larval fish were mainly collected using plankton nets around mangrove areas in Pendas (Johor), Setiu (Terengganu), Pekan (Pahang) and Matang (Perak) Malaysia between April 2015 and October 2015. A total of 354 samples were morphologically identified, mostly to the family level and a few to the genus level. Larval fish ranged from 1.5 mm to 31 mm of total length, with the most abundant individuals being <3 mm. Among them, a total of 177 individuals were selected for DNA barcoding analyses. Molecular works involved polymerase chain reaction (PCR) and sequencing of mitochondrial Cytochrome c Oxidase I (COI) gene fragment (655 base pairs) methods. DNA barcoding enabled all samples to be identified down to species level. The overall genetic identities ranged from 91% to 100%. Morphological identification classified the specimens into 19 families and 11 genera while DNA barcoding identified them into 19 families 33 genera and 40 species. A comparison between the two methods showed a mismatched identification of 42.6% where the accuracy percentage for morphological identification was moderate for the family level (67.8%) but was low for genus level identification (30%). The DNA barcoding method also managed to successfully identify 86.4% of the samples up to their species level where morphological method has failed to do so. The most misidentified families in the study were Blenniidae, Sparidae, Apogonidae Ambassidae and Monachantidae while almost all samples from the family Gobiidae and Engraulidae were correctly identified to family level because of their distinct morphology. In conclusion, taxonomic studies of larval fish should continue using combination of both morphology and DNA barcoding methods. Morphological identification should be more conservative i.e., when in doubt, it is better to key only to family and not to the genus and species level. DNA barcoding is a better method for deeper taxonomic levels identification with the existence of robust sequence reference libraries and should be able to validate the accuracy of traditional larval fish identification.

The mitochondrial genome provides important information for phylogenetic analysis and an understanding of evolutionary origin. In this study, the mitochondrial genomes of Ilisha elongata and Setipinna tenuifilis were sequenced, which are typical circular vertebrate mitochondrial genomes composed of 16,770 and 16,805 bp, respectively. The mitogenomes of I. elongata and S. tenuifilis include 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), two ribosomal RNA (rRNA) genes and one control region (CR). Both two species' genome compositions were highly A + T biased and exhibited positive AT-skews and negative GC-skews. The genetic distance and Ka/Ks ratio analyses indicated that 13 PCGs were affected by purifying selection and the selection pressures were different from certain deep-sea fishes, which were most likely due to the difference in their living environment. Results of phylogenetic analysis support close relationships among Chirocentridae, Denticipitidae, Clupeidae, Engraulidae and Pristigasteridae based on the nucleotide and amino acid sequences of 13 PCGs. Within Clupeoidei, I. elongata and S. tenuifilis were most closely related to the family Pristigasteridae and Engraulidae, respectively. These results will help to better understand the evolutionary position of Clupeiformes and provide a reference for further phylogenetic research on Clupeiformes species.

Examination of numerous specimens characterised by predorsal scute, long maxilla, indented preopercle and pelvic scute lacking a spine and previously identified as (Dutt & Babu Rao, 1959) or Hardenberg, 1933, revealed four distinct species, true (distributed from the Bay of Bengal to Pakistan) and three new species, viz., (Taiwan to Java, Indonesia), (Strait of Malacca, from Penang , Malaysia, to Singapore) and (Bintan Island, Riau Archipelago, Indonesia). Characters separating the four species include numbers of gill rakers on each gill arch and vertebrae and pelvic fin and dorsal-fin ray lengths. Two molecular markers (mitochondrial cytochrome and cytochrome oxidase I genes) demonstrated the distinction of three of the species examined morphologically and enabled a reconstruction of their phylogenetic relationships. Each species was genetically divergent from the others by 3.5%-7.7% mean uncorrected distance in the mitochondrial cytochrome oxidase I gene.

Most data sets of ichthyoplankton contain a high frequency of zeros, and, not considering the possible inflation of zero counts, as in most studies, may result in incorrect model predictions. Thus, we modeled abundance of Engraulis anchoita eggs and larvae sampled during 18 oceanographic cruises conducted between 1974 and 2010 using zero-inflated (ZI) models. ZI models are mixture models with 2 components: (1) containing false zeros (due to design, survey or observer errors) modeled using a binomial generalized linear model (GLM); (2) containing abundance data that may produce zeros (true zeros), and modeled with a negative binomial GLM (ZINB). Although ZINB has been used in other areas of research, we are not aware of its previous use for ichthyoplankton. Common to larvae and eggs, the probability of false zeros was lowest in the southern area of the southeastern Brazilian Bight and higher at deeper station depths. The probability of false zeros was higher in 0.505 mm mesh-size samples than in 0.333 mm mesh only for eggs. Egg and larval abundance was negatively related to temperature in the count portion of the model; only larval abundance was negatively related to salinity. Egg abundance was higher in years sampled with 0.333 mm mesh under conditions of moderate/strong El Niño. The high interannual variability in the abundance and distribution of eggs emphasizes the importance of long-term studies to better understand patterns of fluctuations in the occurrence of ichthyoplankton that are related to environmental conditions.

Estuarine ecosystem conditions actively influence the early life stage of fishes. This study reports how environmental factors influenced the ichthyoplankton in a tropical estuary within an Environmental Protection Area by comparing the structure and composition of fish eggs and larval assemblages. A total of 1672 fish larvae and 486 fish eggs were collected. Higher densities of larvae were recorded for Engraulidae, Characidae, Clupeidae, Gerreidae, Mugilidae and Atherinopsidae, and higher egg densities of the families Mugilidae, Clupeidae and Engraulidae were found. The spatio-temporal variations were determined by the environmental predictors salinity, pH, dissolved oxygen and temperature, with salinity influenced by precipitation as one of the main predictors of the distribution of ichthyoplankton. During the rainy season, greater densities of eggs were recorded in the upper and intermediate zones, mainly Characidae and Engraulidae; in the dry season, in the lower zone, there was a greater density of larvae, particularly Atherinopsidae and Mugilidae. The information provided in the present study contributes to our knowledge of nursery habitat requirements for the initial development of marine migrant and resident species in tropical estuaries.

Anthropogenic perturbations and climate change have altered the zooplankton community structure in the Klang Strait during the past 30 years, in that the taxa of large-bodied crustaceans (Acartiidae, Calanidae, Pseudodiaptomidae) are being replaced by those of small-bodied crustaceans (Oithonidae, Ectinosomatidae), gelatinous jellyfish, and appendicularians. Since zooplankton constitutes the main larval food, we questioned: have bottom-up effects impacted larval fish feeding via the food chain? Larval fish that were sampled previously (1985–1986) and nearly three decades thereafter (2013–2014) were analysed for their dietary composition. Despite the dramatic replacements of zooplankton taxa due to escalating anthropogenic disturbances, the dominant copepod families, Paracalanidae, Oithonidae and Euterpinidae, remain the major prey for fish larvae. Dietary shifts in prey composition from before to after impact depend on the larval fish family and their ontogenetic stage. Dietary changes are observed in the Bregmacerotidae, Engraulidae, Gobiidae and Sciaenidae that opportunistically feed on the small-bodied copepods (oithonids and Parvocalanus crassirostris), whereas the Callionymidae, Clupeidae and Cynoglossidae naturally feed on these copepods even before these prey become numerically dominant with anthropogenic disturbance. There is no dietary shift in the Leiognathidae, exceptional in that they are specialists feeding mainly on detritus and polychaete larvae. Since the bottom-up effects are not comprehensive among fish families and dietary plasticity is evident, it is postulated that only the intolerant or non-adaptable larval species are adversely affected by the environmental perturbations.