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The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next‐generation monitoring. With this objective, we present the results of a large‐scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA‐based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses. The fish fauna of the beibu gulf, one of the largest sea food hubs in Southeast Asia, is characterized here by DNA barcoding. The 1080 DNA barcodes analyzed show concordance between morphological identifications and DNA‐based species delimitation. Lower level of diversity detected here compared to historical observations is concordant with the stock collapses previously described in the literature for the area. This study opens new perspectives by enabling next‐generation monitoring of the 285 species DNA barcoded here.

Orange‐spotted groupers (Epinephelus coioides) are commercially important fish species that inhabit coral reef areas and are distributed across tropical coastal regions throughout the Indo‐West Pacific Oceans. This study aims to assess the phylogeographic structure of E. coioides by analyzing 180 individuals collected from six locations along the coast of mainland China and Hainan Island, using the mitochondrial Cyt b gene and 17 microsatellite DNA markers. The mitochondrial DNA analysis revealed high haplotype diversity (0.882), while the microsatellite DNA data showed an average of 8.677 alleles among the six populations, indicating that all populations exhibit a high level of genetic diversity. The presence of two distinct evolutionary lineages of E. coioides, along with the lack of significant genealogical structures corresponding to sampling localities, suggests that isolation in marginal seas during glaciation with lower sea levels shaped their phylogeographic distribution patterns. The results from STRUCTURE, PCoA, and pairwise FST revealed significant genetic differentiation in the Lingshui region (LS population) compared to other populations, suggesting that the Lingshui region, adjacent to deep‐sea areas, remained isolated during glacial periods as it was not connected to the continental shelf of mainland China. Analysis of demographic history using ABC revealed that E. coioides experienced historical lineage diversification and admixture due to secondary contact. This study aims to assess the phylogeographic structure of E. coioides by analyzing 180 individuals collected from six locations along the coast of mainland China and Hainan Island, using the mitochondrial Cyt b gene and 17 microsatellite DNA markers. The results from STRUCTURE, PCoA, and pairwise FST revealed significant genetic differentiation in the Lingshui region (LS population) compared to other populations, suggesting that the Lingshui region, adjacent to deep‐sea areas, remained isolated during glacial periods as it was not connected to the continental shelf of mainland China.

Despite concerns about overfishing and the potential impact of release programs on wild populations, our study of 3116 individuals from 13 wild populations and 2787 individuals from two cultured populations in Zhejiang and Fujian provinces spanning 2008 to 2023 reveals a relatively stable genetic diversity in Larimichthys crocea. Surprisingly, the genetic diversity of wild large yellow croaker populations has remained consistent over the years, suggesting minimal influence from population declines due to overfishing. With the exception of populations in Sansha Bay and Luoyuan Bay, no significant genetic differences were observed among wild populations, indicating a single panmictic genetic population across the East and South China seas. Notably, significant genetic differentiation exists between cultured and wild populations, suggesting a possible limited genetic adaptation of cultured‐released individuals to the wild environment. The genetic differences observed between the Sansha Bay, with its adjacent Luoyuan Bay populations, and other wild populations underscore the dual effects of habitat environment and farming activities on the genetic structure of large yellow croaker. Our findings suggest that, despite declines in population numbers due to overfishing and expands extensive cultured releases, the genetic diversity of L. crocea populations remains largely unaffected. Moreover, the L. crocea population along the Chinese coast appears to form a single panmictic population with considerable genetic diversity. The genetic diversity of wild large yellow croaker populations has remained consistent over the years, suggesting minimal influence from population declines due to overfishing. A limited genetic adaptation of cultured‐released individuals to the wild environment. Moreover, the L. crocea population along the Chinese coast appears to form a single panmictic population with considerable genetic diversity.

Oceanic currents, biological traits, and geological evidence from historical climate change have shaped the distribution of genetic diversity and demographic history in Macrobrachium japonicum. In this study, we investigated the phylogeographic structures and demographic history of M. japonicum in Taiwan and the Ryukyu Islands by the partial mitochondrial COI gene. The topology of the haplotype minimum-spanning network revealed a star-like structure, which suggested a recent range expansion. With the apparent lack of strong dispersal barriers to gene flow between ocean basins, amphidromous prawns, as marine organisms with larvae of high dispersal abilities, are generally expected to show genetic homogeneity. Divergence data suggested that M. japonicum populations diverged 0.462 ± 0.164 myr. Complex patterns of asymmetrical gene flow indicate that variation in dispersal ability is affected by the dominant Kuroshio Current systems of the Pacific Ocean. Analysis of its demographic history revealed that M. japonicum underwent a decline in size following a recent population expansion based on ABC analysis. Bayesian skyline plot analyses of all populations indicated that the expansion of M. japonicum was estimated to have occurred in 175 Kya and that the effective population size rapidly increased by approximately 50 Kya. The results of this study may offer both practical and theoretical value for the further study of conservation genetics, management, and sustainable resource utilization.

Geological events, landscape features, and climate fluctuations have shaped the distribution of genetic diversity and evolutionary history in freshwater fish, but little attention has been paid to that around the Gulf of Tonkin; therefore, we investigated the phylogeographic structure of the dwarf snakehead (Channa gachua) on Hainan Island and mainland China, as well as two populations in Vietnam. We attempted to elucidate the origins of freshwater fish in South Hainan by incorporating genetic data from DNA markers on both the mitochondrial cytochrome b gene (cyt b) and the nuclear recombination‐activating gene 1 (RAG‐1). Mitochondrial phylogenetic analysis identified two major lineages (lineages A and B), which may represent separate species. Divergence data suggested that C. gachua populations diverged between 0.516 and 2.376 myr. The divergence of the two cryptic species is congruent with sea‐level rise, which subsequently isolated Hainan from the mainland. During the Pleistocene glaciations, the entire region of the Gulf of Tonkin and the Qiongzhou Strait became part of the coastal plain of the Asian continent, which might have resulted in the current distribution patterns and dispersal routes of C. gachua populations. The formation of three sublineages in lineage A indicated that the Gulf of Tonkin was a geographical barrier between Hainan Island and mainland China but not between Vietnam and Hainan Island. The results of this study may help to elucidate the origins of freshwater fish in South Hainan and the phylogeographic structure of C. gachua. During the Pleistocene glaciations, the entire region of the Gulf of Tonkin and the Qiongzhou Strait became part of the coastal plain of the Asian continent, which might have resulted in the current distribution patterns and dispersal routes of C. gachua populations.

Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.

The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.

A new cyprinid fish, Opsariichthys rubriventris sp. nov., is described from the Xizhijiang River, a tributary of the Pearl River basin in Huizhou City, Guangdong Province, southern China. The species is distinguished from all other congeners by the following combination of characters: predorsal scales 13–14; lower jaw projecting slightly beyond upper jaw; cheek with two mainly longitudinal rows of tubercles; and lower jaw, belly, pectoral fin, and anterior margin of anal fin in adult males being reddish-orange. The principal component analysis result of the morphological data indicated that O. rubriventris sp. nov. could be clearly distinguished fromfour other congeners. The phylogenetic analysis conducted in this study, utilizing both Maximum Likelihood (ML) and Bayesian Inference (BI) methods, supported the monophyly of the novel species O. rubriventris sp. nov. at the species level. Additionally, the genetic distance analysis revealed that O. rubriventris sp. nov. exhibits a genetic distance ranging from 0.14 to 0.16 with its congeneric species, further affirming its taxonomic status.

The genetic structure and demographic history of marine organisms are influenced by biological and ecological features, oceanic currents, and the paleo-geological effects of sea-level fluctuations. In this study, we used mitochondrial COI + 16S gene analysis to investigate the phylogeographic pattern and demography of Monodonta labio and M. confusa in Taiwan, the Ryukyu Islands, Japan, mainland China, and Korea. Our genetic analysis identified two major lineages that were not evident from the distribution patterns of different populations. The Taiwan Strait, which acted as a land bridge during Pleistocene glaciations, and the lack of strong dispersal barriers to gene flow between ocean basins after glaciations shaped the phylogeographic pattern. The genetic differentiation in the Ryukyu Islands was influenced by the specialist-generalist variation hypothesis and the Kuroshio Current. Bayesian skyline plot analyses suggested that the effective population size of M. labio and M. confusa rapidly increased approximately 0.1 and 0.075 million years ago, respectively. Our approximate Bayesian computation analysis suggested that all M. labio and M. confusa populations experienced a decline in population size following a recent population expansion and constant size, respectively. Our study provides a baseline for future investigations of the biogeographical patterns of marine gastropods in the Northwest Pacific and offers valuable insights for the management, sustainable resource utilization, and conservation of this species.

To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China. Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades. The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups.