Recruitment Patterns and Environmental Sensitivity of Glass Eels of Anguilla japonica in the Yangtze Estuary, China.

The decline of Japanese eel (Anguilla japonica) populations in the Yangtze River estuary represents a critical conservation concern. Eleven-years of daily catch data during recruitment periods (i.e., January-April, 2012-2022) indicate that annual catch averaged from 153 to 1108 eels, and show a bimodal pattern in glass eel arrivals. Utilizing seasonal-trend decomposition and generalized additive models, we demonstrated a strong correlation between catch abundance, optimal water temperatures, and lunar cycles. An auto-regressive integrated moving average (ARIMA) model predicts an increase in glass eel numbers for 2023-2024 but also points to a concerning trend of delayed recruitment timing since 2016, attributable to the 0.48 °C per decade rise in sea surface temperatures. This delay correlates with a significant decrease in the average body weight of glass eels, suggesting potential energy deficits that may hinder successful upstream migration. This study not only furthers our understanding of glass eel recruitment dynamics but also underscores the urgent need for targeted conservation measures. Additionally, it highlights the importance of sustained, detailed monitoring to mitigate the detrimental effects of climate change on these eels, vital for preserving the Yangtze River's ecological integrity.

Resolving phylogenetic relationships and taxonomic revision in the Pseudogastromyzon (Cypriniformes, Gastromyzonidae) genus: molecular and morphological evidence for a new genus, Labigastromyzon.

The Pseudogastromyzon genus, consisting of species predominantly distributed throughout southeastern China, has garnered increasing market attention in recent years due to its ornamental appeal. However, the overlapping diagnostic attributes render the commonly accepted criteria for interspecific identification unreliable, leaving the phylogenetic relationships among Pseudogastromyzon species unexplored. In the present study, we undertake molecular phylogenetic and morphological examinations of the Pseudogastromyzon genus. Our phylogenetic analysis of mitochondrial genes distinctly segregated Pseudogastromyzon species into two clades: the Pseudogastromyzon clade and the Labigastromyzon clade. A subsequent morphological assessment revealed that the primary dermal ridge (specifically, the second ridge) within the labial adhesive apparatus serves as an effective and precise interspecific diagnostic characteristic. Moreover, the distributional ranges of Pseudogastromyzon and Labigastromyzon are markedly distinct, exhibiting only a narrow area of overlap. Considering the morphological heterogeneity of the labial adhesive apparatus and the substantial division within the molecular phylogeny, we advocate for the elevation of the Labigastromyzon subgenus to the status of a separate genus. Consequently, we have ascertained the validity of the Pseudogastromyzon and Labigastromyzon species, yielding a total of six valid species. To facilitate future research, we present comprehensive descriptions of the redefined species and introduce novel identification keys.

Revalidation and redescription of Sarcocheilichthys sciistius (Abbott, 1901) (Cypriniformes: Cyprinidae) from the northern China.

Sarcocheilichthys sciistius was originally described by Abbott in 1901. It was considered as a synonym of S. nigripinnis by later researchers. However, some recent studies suggested that S. nigripinnis from the Haihe River Basin and Yellow River Basin were different to S. nigripinnis distributed in southern China, and that these populations show a closer relationship with the Heilongjiang (Amur) River endemic speciesS. czerskii and S. soldatovi. In this study, we examined one hundred and twenty-five specimens from nine sites of six river basins. Based on morphological and molecular systematic studies, we confirmed S. sciistius is a valid species, and S. czerskii, S. soldatovi were synonyms of S. sciistius. Sarcocheilichthys sciistius can be distinguished from S. nigripinnis by having more lateral-line scales (4042 vs. 3840), shorter lower lip and different pectoral and pelvic fins color. The phylogenetic trees reconstructed by Bayesian Inference and Maximum Likelihood based on the Cyt b gene also support S. sciistius as a distinct species.

Blubber fatty acid compositions in different geographic populations of finless porpoise in Chinese waters: implications for thermal adaptation.

The stratification of blubber fatty acids (FAs) is a widely used strategy in marine mammals and can be influenced by many factors, including their diet, environmental temperature, and physiological status. There are 3 distinct finless porpoise species/subspecies in Chinese coastal and inland waters in a wide range from 20°N to 40°N. The biochemical stratification of the blubbers of finless porpoises in different regions may provide valuable information for understanding their environmental adaptations. The FA compositions of 4 geographic populations of finless porpoise (FP) collected from the Bohai Gulf, East China Sea, South China Sea, and Yangtze River were therefore analyzed and compared. The blubber FA compositions of finless porpoises were dominated by ΣMUFAs, followed by ΣSFAs and ΣPUFAs, and were generally consistent with those of other cetaceans. The blubber of finless porpoises was significantly stratified with increasing levels of ΣMUFAs and decreasing levels of ΣSFAs and ΣPUFAs from the inner to the outer layers. The 3 marine populations shared more similarities in their FA compositions and stratifications compared to the freshwater porpoises, particularly regarding the PUFAs in the inner layers, which might have been mainly influenced by the diet compositions of marine and freshwater porpoises. Contrary to what was expected, in the 3 marine populations, the SFA and MUFA levels showed opposite correlations (negative and positive, respectively) with habitat temperatures, possibly indicating an adaptation mechanism in finless porpoises characterized by a trade-off between the insulation and fluidity properties of the blubber through the adjustment of the compositions and gradients of MUFAs and SFAs across the blubber depth in response to environmental temperature/latitude changes.

Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis).

Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.

Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes.

Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.

Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses.

BACKGROUND: The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. RESULTS: We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. CONCLUSIONS: This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

Genetic diversity and structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis).

Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θπ = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.

SINE Retrotransposon variation drives Ecotypic disparity in natural populations of Coilia nasus.

BACKGROUND: SINEs are a type of nonautonomous retrotransposon that can transpose from one site to be integrated elsewhere in an organism genome. SINE insertion can give rise to genetic variants and regulate gene expression, allowing organisms to acquire new adaptive capacity. Studies on this subject have focused on the impacts of SINEs on genes. However, ecological disparities in fish have not yet been explained by SINEs. RESULTS: New SINEs were isolated from Coilia nasus, which has two ecotypes-migratory and resident-that differ in their spawning and migration behaviors. The SINEs possess two structures that resemble a tRNA gene and a LINE retrotransposon tail. Comparison of olfactory tissue transcriptomes, intact SINE transcript copies were detected in only the migratory fish at the initial retrotransposition stage. The SINE DNA copy numbers were higher in the resident type than in the migratory type, while the frequency of SINE insertion was higher in the migratory type than in the resident type. Furthermore, SINE insertions can lead to new repeats of short DNA fragments in the genome, along with target site duplications. SINEs in the resident type have undergone excision via a mechanism in which predicted cleavage sites are formed by mutations, resulting in gaps that are then filled by microsatellites via microhomology-induced replication. CONCLUSIONS: Notably, SINEs in the resident type have undergone strong natural selection, causing genomic heteroplasmy and driving ecological diversity of C. nasus. Our results reveal possible evolutionary mechanisms underlying the ecological diversity at the interface between SINE mobilization and organism defense.

New insights on geographical/ecological populations within Coilia nasus (Clupeiformes: Engraulidae) based on mitochondrial DNA and microsatellites.

The Coilia nasus is an important fish species, which is of commercial values in China. In order to manage the fisheries resources and the development of sustainable fishing strategies to protect this species, 11 microsatellite loci polymorphisms and mtDNA COI sequences were used to examine the genetic diversity of C. nasus in Japan and China. In total, the 40 COI haplotypes and 93 microsatellite alleles were detected. The mtDNA phylogeny did not support population grouping, but the distribution patterns of mtDNA haplotypes and the results of STRUCTURE analysis based on microsatellite indicated a degree of genetic isolation in this species. Our study suggested that the lack of a population genetic structure might result in its amphidromous life cycle, and the geographical distance and habitat fragments might cause isolated populations. Thus, the sampling populations of C. nasus in Japan and China could be divided as four geographical/ecological populations.

Identification of olfactory receptor genes in the Japanese grenadier anchovy Coilia nasus.

Olfaction is essential for fish to detect odorant elements in the environment and plays a critical role in navigating, locating food and detecting predators. Olfactory function is produced by the olfactory transduction pathway and is activated by olfactory receptors (ORs) through the binding of odorant elements. Recently, four types of olfactory receptors have been identified in vertebrate olfactory epithelium, including main odorant receptors (MORs), vomeronasal type receptors (VRs), trace-amine associated receptors (TAARs) and formyl peptide receptors (FPRs). It has been hypothesized that migratory fish, which have the ability to perform spawning migration, use olfactory cues to return to natal rivers. Therefore, obtaining OR genes from migratory fish will provide a resource for the study of molecular mechanisms that underlie fish spawning migration behaviors. Previous studies of OR genes have mainly focused on genomic data, however little information has been gained at the transcript level. In this study, we identified the OR genes of an economically important commercial fish Coilia nasus through searching for olfactory epithelium transcriptomes. A total of 142 candidate MOR, 52 V2R/OlfC, 32 TAAR and two FPR putative genes were identified. In addition, through genomic analysis we identified several MOR genes containing introns, which is unusual for vertebrate MOR genes. The transcriptome-scale mining strategy proved to be fruitful in identifying large sets of OR genes from species whose genome information is unavailable. Our findings lay the foundation for further research into the possible molecular mechanisms underlying the spawning migration behavior in C. nasus.

Complete mitochondrial genome of Ophichthus rotundus (Anguilliformes: Ophichthidae).

The complete mitochondrial genome of Ophichthus rotundus was sequenced in this study. The genome sequence is 17,785 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. Overall base composition is 30.59% A, 24.94% T, 17.01% G, and 27.46% C. The result of phylogenetic analysis indicates that O. rotundus mitogenome is close to that of M. maculosus, which are nested within the family Ophichthidae.

Complete mitochondrial DNA sequence of Brachysomophis crocodilinus (Anguilliformes: Ophichthidae).

Brachysomophis crocodilinus belongs to the family Ophichthidae, the complete mitochondrial genome of which was sequenced in this study. The mitochondrial genome of B. crocodilinus is of 17,818 bp in length, with overall base composition of 32.11% A, 24.69% T, 16.22% G, and 26.98% C. The genome content includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. The result of phylogenetic analysis indicates that B. crocodilinus mitogenome is close to that of Ophisurus macrorhynchos, which are nested within the family Ophichthidae.

Spatial genetic structure of the cyprinid fish Onychostoma lepturum on Hainan Island.

Population genetic structure of Onychostoma lepturum on Hainan Island was investigated based on mitochondrial CR + cyt b region in 63 specimens collected from four populations. Population analyses indicated significant genetic structure (FST = 0.749) and displayed a significant relationship between phylogeny and geography (NST = 0.750 and GST = 0.140). Thirty-one mtDNA haplotypes were classified into four lineages, and these lineages had an almost allopatric distribution. The results of a statistical dispersal-vicariance analysis suggest that the ancestral populations were distributed widely on Hainan Island, and the rising of the central mountainous area of Hainan Island, the Wuzhi and Yinggeling Mountain Range, separated these four drainages into independent lineages. According to a spatial analysis of molecular variance analysis, we divided these populations into three units: ND, CH and WQ + LS, running into Qiongzhou Strait, the Gulf of Tokin and the South China Sea, respectively. According to our study, the exposure of straits and shelf under water retreat gave chances for population dispersion during the glaciations.

The complete mitochondrial genome of the Neophocaena asiaeorientails sunamrei (Phocaenidae: Neophocaena).

The complete sequence of the mitochondrial DNA (mtDNA) of the East Asian finless porpoise (Neophocaena asiaeorientails sunamrei) has been completed and annotated in this study. The circular genome is 16 385 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding areas. Ten protein-coding genes use ATG as the initiation codon, except that ND2 started with ATT, and ND3 and ND5 started with ATA. Canonical TAA and TAG termination codons are found in seven protein-coding genes, the remaining four (ND4, ND2, ND3, and COIII) have incomplete termination codons (T or TA), in addition, the COI ends with AGG, and the Cyt b ends with AGA. On the neighbor-joining phylogenetic tree, these results show that the relationship of Phocoenidae is closer with Delphinidae.

Identification of a uniquely expanded V1R (ORA) gene family in the Japanese grenadier anchovy (Coilia nasus).

A number of studies have suggested that olfaction plays an important role in fish migration. Fish use several distinct families of olfactory receptors to detect environmental odorants, including MORs (main olfactory receptors), V1Rs (vomeronasal type-1 receptors), V2Rs (vomeronasal type-2 receptors), TAARs (trace amine-associated receptors), and FPRs (formyl peptide receptors). The V1Rs have been reported to detect pheromones, and a pheromone hypothesis for the spawning migration of anadromous fish has been proposed. Examining whether Coilia nasus relies on V1R-mediated olfaction for spawning migration is important for understanding the molecular basis of spawning migration behavior. Here, we explored the V1R gene family in anadromous C. nasus. Six V1R genes previously reported in other teleost fish were successfully identified. Interestingly, we detected the largest V1R repertoire in teleost fish from C. nasus and identified a species-specific expansion event of V1R3 gene that has previously been detected as single-copy genes in other teleost fish. The V1R loci were found to be populated with repetitive sequences, especially in the expanded V1R3 genes. Additionally, the divergence of V1R3 genetic structures in different populations of C. nasus indicates the copy number variation (CNV) in V1R3 gene among individuals of C. nasus. Most of the putative C. nasus V1R genes were expressed primarily in the olfactory epithelium, consistent with the role of the gene products as functional olfactory receptors. Significant differences in the expression levels of V1R genes were detected between the anadromous and non-anadromous C. nasus. This study represents a first step in the elucidation of the olfactory communication system of C. nasus at the molecular level. Our results indicate that some V1R genes may be involved in the spawning migration of C. nasus, and the study provides new insights into the spawning migration and genome evolution of C. nasus.

The population history of Garra orientalis (Teleostei: Cyprinidae) using mitochondrial DNA and microsatellite data with approximate Bayesian computation.

BACKGROUND: The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass's phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci. RESULTS: In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China. CONCLUSION: Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.

Complete mitochondrial DNA sequence of Pseudogastromyzon changtingensis (Osteichthyes: Gastromyzontidae).

Pseudogastromyzon changtingensis belonging to the family Gastromyzontidae is a good model for phylogeny and zoogeography research. In the present paper, the sequenced mitochondrial genome of P. changtingensis is of 16573 bp in length, and encodes 13 typical protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The result of phylogenetic analysis demonstrates that P. changtingensis is close to that of P. fasciatus.

Complete mitochondrial genome of Pseudogastromyzon fasciatus (Osteichthyes: Gastromyzontidae).

Pseudogastromyzon fasciatus belonging to the family Gastromyzontidae is a good model for phylogeny and zoogeography research. The complete mitochondrial genome of P. fasciatus was sequenced in this study. The genome sequence is 16,563 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region. Overall base composition is 29.70% A, 25.16% T, 16.53% G, and 28.60% C. The result of phylogenetic analysis indicates that P. fasciatus mitogenome is close to that of P. myersi.