Low mtDNA Cytb diversity and shallow population structure of Eleutheronema tetradactylum in the East China Sea and the South China Sea

Eleutheronema tetradactylum is an economically important fish species in China water. To investigate the genetic diversity and describe population structure of it, an 1151 base pair (bp) fragment of the mitochondrial DNA Cytb sequence was analyzed in 120 individuals from four populations in the East China Sea and the South China Sea. A total of 16 haplotypes were defined by 24 variable nucleotide sites. High level of haplotype diversity and low nucleotide diversity were observed in all populations. The results of AMOVA detected that 89.44% of the genetic variation occurred within populations. Significant genetic differentiations were detected among populations (0.05097, P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggested no recent population expansion happened. The present results provided new information for genetic assessment, fishery management and conservation of this species.     

Genetic diversity and population differentiation in the yellow drum Nibea albiflora along the coast of the China Sea

Nibea albiflora (yellow drum) is an important seafood fish species in East Asia. We explored the population genetic variation of N. albiflora along the coastal waters of the China Sea using microsatellite markers to facilitate a selective breeding programme that is undertaken in China. A total of 256 alleles were detected at 12 loci in four wild populations. A high level of genetic diversity was observed with the mean number of alleles and the observed and expected heterozygosity in each population ranging from 7.917 to 14.083, 0.701 to 0.764 and 0.765 to 0.841, respectively. Pairwise fixation index (F_ST) analysis indicated significant but weak genetic differentiation among populations from four localities (F_ST?=?0.030, P?<?0.01), which was also confirmed by analysis of molecular variance (AMOVA). Significant genetic differentiation was detected between Ningde and the other populations (F_ST?=?0.047–0.056, P?<?0.01). Structure analysis suggested that N. albiflora within the examined range might be composed of two stocks. The data of the present study revealed high genetic diversity and low genetic differentiation among the N. albiflora populations along the coast of the China Sea. This baseline information could be valuable for future selective breeding programmes of N. albiflora.     

Microsatellite analysis of the genetic relationships between wild and cultivated giant grouper in the South China Sea

The giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia. In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different populations. The expected heterozygosity varied from 0.131 to 0.855 with a mean value of 0.623 and the observed heterozygosity varied from 0.145 to 0.869 with a mean value of 0.379. The allelic richness and heterozygosity studies revealed that the genetic diversity of the cultured population was significantly reduced when compared with that of the wild population. The F_is, pairwise F_st values, analysis of molecular variance (AMOVA), three-dimensional factorial correspondence analysis and structure analysis revealed significant population differentiation between the cultured stocks and the wild populations, among the three cultured populations and between the two wild populations. These differences may be caused by random genetic drift, the effects of artificial selection and founder effects. Our results will be useful in the management of cultured stocks and conservation of wild populations of the giant grouper.     

Determination of genetic diversity of wild and cultured topmouth culter (Culter alburnus) inhabiting China using mitochondrial DNA and microsatellites

The topmouth culter (Culter alburnus) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding its genetic diversity and population structure, thus hindering the effective management of this fish stock. Understanding the genetic diversity of wild and cultured topmouth culter populations is highly relevant for successful hatchery management. This study evaluated the genetic diversity and structure of five wild and two cultured populations of topmouth culter in China by using microsatellites and mitochondrial DNA. The genetic diversity of wild populations was found to be lower than that of cultured populations. This finding indicates that wild topmouth culter resources should be protected to prevent further degeneration and extinction. Moreover, it demonstrated that cultured populations have greater breeding potential than wild ones. Subdivisions among wild populations were observed, which should be considered as different units for conservation and hatchery management.     

Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data

The large yellow croaker Larimichthys crocea is an important commercial marine fish species in China. However, information about the population structure of this species is limited. In the present study, mitochondrial DNA (mtDNA) control region was sequenced from four populations of the yellow croaker in the southern Yellow Sea, East China Sea and South China Sea to investigate the genetic structure of this species. A total of 54 haplotypes were detected among 62 individuals of large yellow croaker. High levels of population genetic diversity were observed. Among the four populations, the haplotype diversity was between 0.9895 ± 0.0193 (Xiamen) and 1.0000 ± 0.0524 (Lvsi, Zhoushan). The nucleotide diversity ranged from 0.0208 ± 0.0108 (Xuwen) to 0.0246 ± 0.0138 (Lvsi). The results of AMOVA detected no significant differences among populations. The conventional F_ST statistics were negative and insignificant values. These indicated lack of population genetic structure throughout the Yellow Sea, East China Sea and South China Sea, and random mixing of individuals among the samples. Biological characters of large yellow croaker and lack of physical barrier in the studied area could be the reasons for lack of genetic structure in this species.     

Genetic divergence and historical demography in the endangered large yellow croaker revealed by mtDNA

Due to high level of fishing, many marine fish species are in danger of becoming extinct. The large yellow croaker, Larimichthys crocea, was once an important commercial marine species in China. At present, this croaker is seldom captured in the wild. In this work, mitochondrial DNA data was obtained from five populations of the yellow croaker from the Yellow Sea and the East China Sea to investigate their genetic divergence and demographic history. Results of phylogenetic analysis suggest two genetic lineages for this croaker, although the divergence was relatively shallow. This might reflect the effects of glacial isolation on population structure. Furthermore, our Bayesian based approach showed that the effective population size for both genetic lineages experienced recent sharp decline. This study provides new insights into the genetic divergence and historical demography of this croaker. Strict measures must be taken to protect this species.     

Decreasing genetic diversity in wild and captive populations of endangered Itasenpara bittering (Acheilognathus longipinnis) in the Himi region,central Japan,and recommendations for conservation

Biodiversity is increasingly declining as a result of direct human impact and structural alteration of ecosystems resulting from changes in human life styles. Itasenpara bittering (Acheilognathus longipinnis), which has been maintained in floodplain and paddy fields, is a threatened cyprinid fish endemic to central Japan. To aid in the preservation of this species, information on genetic diversity and demographic variables in wild and captive populations was obtained using microsatellite DNA analysis. Temporal changes in genetic diversity and effective population size (N _e) tended to be relatively stable in the wild Moo River population, although lower values were detected in the wild Busshouji River population, suggesting an extremely high risk of extinction in the latter. Captive populations derived from the Busshouji River population demonstrated significant genetic divergence even among intrapopulational cohorts, suggesting the influence of genetic drift caused by geographic isolation and small population size. Active maintenance of genetic diversity in captive population is a necessary part of conservation programs, as are continuous addition of wild individuals and replacement of individuals among captive populations. In addition, increasing or maintaining suitable floodplain areas and artificial habitats such as paddy fields might contribute to the conservation of genetic diversity in the Itasenpara bittering.     

Significant genetic differentiation between the Yellow Sea and East China Sea populations of cocktail shrimp Trachypenaeus curvirostris revealed by the mitochondrial DNA COI gene

The cocktail shrimp Trachypenaeus curvirostris is an ecologically and economically important shrimp species in the Yellow Sea and East China Sea. However, there is no information about its population genetic structure. The population genetic structure and level of gene flow of T. curvirostris from the Yellow Sea and the East China Sea were studied with a 658-bp segment of mtDNA COI gene. In total, 85 individuals were collected from five locations and 13 haplotypes were obtained. The genetic variation of COI gene in five populations was moderate, giving an overall haplotype diversity of 0.6888 ± 0.0432 and nucleotide diversity of 0.0069 ± 0.0038. Conflicting to our expectation, significant genetic differentiation was detected in this species. The result revealed two genetically divergent lineages, displaying clear different geographical distributions in the studied area. The significant genetic differentiation between the Yellow Sea and East China Sea populations might be caused by the Yangtze River outflow. Mismatch distribution revealed that T. curvirostris had undergone population range expansion, possibly before 103,400–109,700 years ago in the last interglaciation, rejecting the sudden demographic expansion.     

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F _ST statistic and a phylogeographic method. A significant nonzero F _ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500?C800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.     

Genetic analysis of the populations of Japanese anchovy Engraulis japonicus from the Yellow Sea and East China Sea based on mitochondrial cytochrome b sequence

Japanese anchovy Engraulis japonicus was not only a commercial species but also a key link in the marine food chain in the Yellow Sea and East China Sea. However, in recent years, E. japonicus experienced a deep recession caused by over fishing. Therefore, determination of population genetic structure is essential to underpin resource recovery and to aid delineating and monitoring populations for fishery management. In this study, sequence variation of a 402-bp fragment of mitochondrial cytochrome b (cyt b) gene from ten populations of E. japonicus in the Yellow Sea and East China Sea was determined, detecting 73 haplotypes. Haplotype diversities and nucleotide diversities for the ten populations ranged from 0.4706 ± 0.1177 (D) to 0.9935 ± 0.210 (WH), and from 0.0014 ± 0.0013 (D) to 0.0090 ± 0.0053 (WH), respectively. Analysis of molecular variance (AMOVA) showed no significant differences at all hierarchical levels, and almost all F_ST values were non-significant, indicating no significant population genetic structure in the Yellow Sea and East China Sea. Two indistinct clades with low support values were detected and the analysis of haplotype frequency distribution showed no significant geographic differences among populations. These results supported the null hypothesis that E. japonicus within the Yellow Sea and East China Sea constituted a panmictic mtDNA gene pool. Based on the present study, the existence of separate genetic stocks in the Yellow Sea and East China Sea were not detected. Strong dispersal capacity of planktonic larvae, and ocean current could be the reasons for genetic homogeneity in this species in the Yellow Sea and East China Sea.     

Genetic diversity and differentiation of the Korean starry flounder (Platichthys stellatus) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis

The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.     

Mitochondrial control region variability of baiji and the Yangtze finless porpoises,two sympatric small cetaceans in the Yangtze river

BaijiLipotes vexillifer (Miller, 1918) and the Yangtze finless porpoiseNeophocaena phocaenoides asiaeorientalis (Pilleri and Gihr, 1972) are two sympatric small cetaceans inhabiting the middle and lower reaches of the Yangtze River. In this study, a fragment (420–428 bp) of the mitochondrial control region was sequenced to provide the first comparative survey of genetic variability and population structure in these two endangered species, with samples of finless porpoises from the Yellow/Bohai Sea, East China Sea, and South China Sea also included. Low values of haplotype diversity and nucleotide diversity were found for both species, especially for the baiji and the Yangtze River and South China Sea populations of finless porpoises. The analysis of molecular variance (AMOVA) supported a high level of overall genetic structure among three porpoise populations in Chinese waters, with greatest differences found between either the Yangtze River population or the Yellow Sea population and the South China Sea population. The differentiation between the Yangtze and Yellow Sea populations was not significant, and the males have higher genetic differentiation than the females, suggesting a significant female-biased dispersal between these two populations. This study showed that the Yangtze finless porpoise, unlike the sympatric baiji, was not a genetically isolated population. The Yangtze and Yellow Sea porpoises should be included in the same management unit, but further studies using more samples and especially based on more molecular markers are urgently needed to confirm this.     

Genetic diversity and population structure of the roughskin sculpin (<Emphasis Type="Italic">Trachidermus fasciatus</Emphasis> Heckel) inferred from microsatellite analyses: implications for its conservation and management

Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F _ST estimates were significant after false discovery rate correction (overall average F _ST = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.     

Genetic diversity and population structure of the Asian green mussel Perna viridis in South China Sea based on microsatellite markers

The green mussel, Perna viridis is ecologically and economically important in the coastal region of the South China Sea. Determining its population genetic structure at this fine geographic scale will help sustainable management of natural stocks. In this study, we examined the genetic diversity and population genetic structure of P. viridis from four locations in the South China Sea (n = 45–48) using nine microsatellite loci. The results showed moderate levels of genetic diversity in all four samples (mean A = 13.222–14.000, mean A_e = 7.092–7.571, mean A_r = 12.894–13.746, mean H_o = 0.596–0.656, mean H_e = 0.690–0.733) and a large effective population size estimate for the pooled sample (total N_e estimates = infinity, 95% CI = 1869.0-infinity). We did not detect any sign of recent bottleneck events in P. viridis populations in the South China Sea. The conventional and a model-based analysis reveal low, non-significant genetic divergence among the four samples (F_ST = − 0.001–0.005, P > 0.05/6). The results obtained from this study can provide valuable genetic information for the conservation and fishery management of P. viridis by retaining the high N_e estimates.     

Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences

Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F_ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation.     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Genetic diversity and population structure of the northern snakehead (<Emphasis Type="Italic">Channa argus</Emphasis> Channidae: Teleostei) in central China: implications for conservation and management

Major threats to freshwater fish diversity now include loss of native genetic diversity as a consequence of translocations of fishes between sites and from hatcheries to sites, and small effective population sizes resulting from overfishing and/or habitat loss. Ten polymorphic microsatellite markers were employed to evaluate genetic diversity, population genetic structure and gene flow amongst nine populations of the ecologically and economically important fish, the northern snakehead (Channa argus), in three river systems in central China. Multiple analyses revealed evidence of high genetic diversity and pronounced subdivision based on both regional separation and on river systems. A lack of evidence of genetic bottleneck over recent generations was consistent with the long-term stability of population size and contemporary distribution. The effective population sizes for most C. argus populations were small, suggesting the need for future conservation efforts focusing on these populations. Different lines of evidence point to the local enhancement of stocks by both aquaculture-reared fish and the transfer of wild fish. This study illustrates how human activities may affect genetic diversity and population genetic structure of C. argus populations, and highlights the need for new management regimes to protect native freshwater fish genetic diversity.     

Genetic diversity and population structure of the ark shell Scapharca broughtonii along the coast of China based on microsatellites

As a commercially important species in East Asia, the natural resources of Scapharca broughtonii have been suffering from severe population decline across its main habitats. In China, recovery efforts for S. broughtonii are in progress. To provide scientific bases for fisheries management and conservation program, genetic diversity and population structure of seven wild populations of S. broughtonii from the northern China coast was assessed using seven microsatellite loci in this study. High genetic diversity was present in all the seven populations, as observed in mean allelic richness per locus (11.3–12.5), and average expected heterozygosity (0.835–0.867). No significant difference in allelic richness or expected heterozygosity was observed among the seven populations. Pairwise F_ST estimates and NJ tree topologies based on D_C distances indicated that the seven populations fell into two groups, showing a clear division between the populations from the south and north of the Shandong Peninsula. Genetic differentiation was further analyzed using AMOVA and assignation tests. Genetic barrier analysis using Monmonier algorithm also confirmed that the Shandong Peninsula was the putative barrier separating the northern and southern populations. In addition, marine currents probably play an important role in high gene flow among three populations from the same marine gyre.     

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major,Temminck et Schlegel) Populations in Japan

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F_ST = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.     

Genetic diversity and genetic structure of the endangered Manchurian trout, <Emphasis Type="Italic">Brachymystax lenok tsinlingensis</Emphasis>, at its southern range margin: conservation implications for future restoration

The Manchurian trout, Brachymystax lenok tsinlingensis (family: Salmonidae), is a cold freshwater fish endemic to Northeast Asia. South Korean populations of this species, which comprise its southern range limit, have recently decreased markedly in size and are now becoming critically endangered. We assessed the current population status of this species in South Korea by estimating the levels of genetic diversity and genetic structure of five natural and four restored populations using mitochondrial DNA (mtDNA) control region sequences and eight nuclear microsatellite loci. Levels of within-population genetic diversity were low, suggesting that past effective population sizes (N _e) have been small. Each population had one or a maximum of two mtDNA haplotypes. Microsatellite allelic richness (AR) was significantly higher for natural populations (mean AR?=?3.51; 95% confidence interval, 3.00–4.03) than for restored populations (mean AR?=?2.61; 2.38–2.98). South Korean populations were significantly genetically isolated from one another, with private mtDNA haplotypes and microsatellite alleles, suggesting that limited gene flow has been occurring among populations. A mtDNA phylogeny revealed that South Korean lineages were more closely related to those of China than to those of North Korea and Russia. Overall, we suggest that future restoration efforts aimed at South Korean populations should consider the genetic characteristics reported here, which should help to fulfil effective conservation strategies for this highly cherished species. Our results will inform other conservation efforts, including assisted migration of freshwater fish populations at the equatorial end of the geographical range limit of the species.