Population genetic structure and demographic history of small yellow croaker, Larimichthys polyactis (Bleeker, 1877), from coastal waters of China

Small yellow croaker, Larimichthys polyactis (Bleeker, 1877), a commercially important benthopelagic fish, is widely distributed in the Bohai, Yellow and East China Seas. To evaluate the population genetic structure and demographic history of L. polyactis, we sequenced the complete mitochondrial deoxyribonucleic acid (mtDNA) control region (798 to 801 bp) in 127 individuals sampled from seven localities throughout its distribution region in China. A total of 136 polymorphic sites were detected, which defined 125 haplotypes. High haplotype diversity (1.000 ± 0.013 to 1.000 ± 0.034) and moderate nucleotide diversity (0.0112 ± 0.0061 to 0.0141 ± 0.0075) were detected in the species. The neighbor-joining tree of haplotypes was assigned into two closely related clades, but did not appear to have any geographic genealogic structure. Hierarchical molecular variance analysis (AMOVA), pair wise FST comparisons and the nearest-neighbor statistic (Snn) showed no significant genetic differences among populations in the Bohai, Yellow and East China Seas. The demographic history of L. polyactis was examined by using neutrality tests and mismatch distribution analysis, which revealed that the species had undergone a Pleistocene population expansion. The results based on the complete mtDNA control region sequences analysis indicate that within its distribution range, L. polyactis constituted a panmictic mtDNA gene pool. Factors such as dispersal capacity, ocean currents and insufficient evolution time could be responsible for the lack of population genetic differentiation in L. polyactis.Keywords: Larimichthys polyactis, mitochondrial control region, population genetic structure, demographi

Isolation and Characterization of New 24 Microsatellite DNA Markers for Golden Cuttlefish (Sepia esculenta)

Twenty-four microsatellite DNA markers were isolated and characterized for golden cuttlefish (Sepia esculenta) from a (GT)13—enriched genomic library. Loci were tested in 48 individuals from Jiaozhou bay of China. The numbers of alleles per locus ranged from two to 25 with an average of 10.3. The observed and expected heterozygosities ranged from 0.063 to 0.896 and from 0.137 to 0.953, with averages of 0.519 and 0.633, respectively. Six loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction and no significant linkage disequilibrium between loci pairs was detected. These microsatellite markers would be useful for analyzing the population genetic structure to make conservation and management decisions for S. esculenta

China is on the track tackling Enteromorpha spp forming green tide

Green tide management is supposed to be a long term fight rather than an episode during the 29th Olympic Games for China, since it has been gaining in scale and frequency during the past 3 decades in both marine and estuary environment all over the world. A number of rapid-responding studies including oceanographic comprehensive surveys along the coastline have been conducted during the bloom and post-bloom periods in 2008 by Chinese marine scientists. The preliminary results are as below: (1) phylogenetic analysis indicates that the bloom forming alga forms a clade with representatives of the green seaweed Enteromorpha linza, though, the alga has been identified as E. proliera by means of morphological; (2) the present data suggest that the bloom was originated from south of Yellow Sea, but not the severely affected area near Qingdao City; (3) pathways of reproduction for E. prolifera have approved to be multifarious, including sexual, asexual and vegetative propagation; (4) somatic cells may act as a propagule bank, which is supposed to be a very dangerous transmitting way for its marked movability, adaptability and viability; (5) pyrolysis of the alga showed that three stages appeared during the process, which are dehydration (18–20^o^C), main devolatilization (200–450^o^C) and residual decomposition (450–750^o^C), and activation energy of the alga was determined at 237.23 KJ•mol^-1^. Although the scarce knowlegde on E. prolifera not yet allow a fully understanding of the green tide, some of the results suggests possible directions in further green tide research and management

Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis).

The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis

Histological Characteristics of Fast and Slow Muscle Fibers in Skeletal Muscle of Fishes with Three Different Swimming Habits

Swimming is of great significance for the survival of fish and directly affects their ability to avoid predators and enemies, hunt and capture prey, carry out mating and reproduction, and migrate. The skeletal muscles of bony fish, which provide power for swimming and account for approximately 40%–60% of the body mass, can be divided into red and white muscle fibers. Red muscle fibers have a slow contraction, strong endurance, high mitochondria content, glycogen, and myoglobin; mainly employ aerobic metabolism; and effectively use oxygen to produce ATP. They are also known as slow-twitch muscle fibers, whose main function in fish is to provide stable and continuous power for the swimming process. White muscle fibers contract quickly but also tire rapidly and mainly use glycolic metabolism. They are also known as fast-twitch muscle fibers and, in fish, provide power for fast swimming behaviors (such as predation and escape).Many studies have indicated a strong correlation between fish swimming habits and the composition of slow and fast-twitch muscles. Most of these studies focused on the correlation between swimming motion and muscle fiber types, but differences in the histological characteristics of fast- and slow-twitch muscle fibers of fish with different swimming habits have rarely been reported. The histological characteristics of muscle fibers include shape, diameter, and density, which are important indicators describing the histological structure of the skeletal muscle in fishes. In this study, we selected three species (Scomber japonicus, Larimichthys crocea, and Paralichthys olivaceus) representing different swimming styles, to clarify the histological characteristics of fast- and slow-twitch muscle fibers, and compared them using hematoxylin-eosin staining of paraffin sections and morphometric methods.The staining showed that the transverse sections of the fast- and slow-twitch skeletal muscle fibers were irregular and the diameter of the fast-twitch muscle fibers was larger than that of the slow-twitch muscle fibers. In S. japonicus, a species engaged in sustained swimming, the fast-twitch muscles were multi-angular, whereas the slow-twitch muscle fibers were multi-columnar. In L. crocea, a species swimming in an extended style, the muscle fibers were long, oval, and had cells with round edges. In P. olivaceus, a species engaged in prolonged swimming, the fast-twitch muscle fibers were oblate and had more connective tissues than the slow-twitch fibers. The slow-twitch muscle fibers of S. japonicus and the fast-twitch muscle fibers of P. olivaceus were finer than the slow-twitch and fast-twitch muscle fibers of these two species, respectively. The longitudinal section of the muscle fibers in the three species were distributed in strips alternating with connective tissue. In addition, the muscle fibers in S. japonicus occupied a larger space and were more loosely arranged than those in the other two species. However, the muscular space between fibers of both types was smaller in P. olivaceus and the muscle cells were more closely arranged.Morphometric results showed that the diameters of fast-twitch muscle fibers were significantly larger than those of slow-twitch muscle fibers (P L. crocea [(205.43±12.63) unit/mm2] > S. japonicus [(118.92±10.74) unit/mm2]. The density of the fast-twitch muscle fiber of P. olivaceus was 2.31 and 1.34 times that of S. japonicus and L. crocea, respectively. The order of slow-twitch muscle fiber density was S. japonicus [(1 442.33±28.25) unit/mm2] > P. olivaceus [(1 073.92±39.40) unit/mm2] > L. crocea [(945.74±19.53) unit/mm2]. Furthermore, the slow-twitch muscle fiber density of S. japonicus was 1.53 and 1.34 times that of L. crocea and P. olivaceus, respectively. The above-described methodology and analysis of differences in the shape, diameter, and density in the skeletal muscle fibers of teleost fish with different swimming habits will provide basic data for further studies on the adaptive evolution and movement physiology of this taxonomic group

Integrative Metabolomics, Enzymatic Activity, and Gene Expression Analysis Provide Insights into the Metabolic Profile Differences between the Slow-Twitch Muscle and Fast-Twitch Muscle of <i>Pseudocaranx dentex</i>

The skeletal muscles of teleost fish encompass heterogeneous muscle types, termed slow-twitch muscle (SM) and fast-twitch muscle (FM), characterized by distinct morphological, anatomical, histological, biochemical, and physiological attributes, driving different swimming behaviors. Despite the central role of metabolism in regulating skeletal muscle types and functions, comprehensive metabolomics investigations focusing on the metabolic differences between these muscle types are lacking. To reveal the differences in metabolic characteristics between the SM and FM of teleost, we conducted an untargeted metabolomics analysis using Pseudocaranx dentex as a representative model and identified 411 differential metabolites (DFMs), of which 345 exhibited higher contents in SM and 66 in FM. KEGG enrichment analysis showed that these DFMs were enriched in the metabolic processes of lipids, amino acids, carbohydrates, purines, and vitamins, suggesting that there were significant differences between the SM and FM in multiple metabolic pathways, especially in the metabolism of energy substances. Furthermore, an integrative analysis of metabolite contents, enzymatic activity assays, and gene expression levels involved in ATP-PCr phosphate, anaerobic glycolysis, and aerobic oxidative energy systems was performed to explore the potential regulatory mechanisms of energy metabolism differences. The results unveiled a set of differential metabolites, enzymes, and genes between the SM and FM, providing compelling molecular evidence of the FM achieving a higher anaerobic energy supply capacity through the ATP-PCr phosphate and glycolysis energy systems, while the SM obtains greater energy supply capacity via aerobic oxidation. These findings significantly advance our understanding of the metabolic profiles and related regulatory mechanisms of skeletal muscles, thereby expanding the knowledge of metabolic physiology and ecological adaptation in teleost fish

<it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems

Abstract Background The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly tolerant of variations in salinity, temperature, and irradiance and are the main cause of green tides, which can have deleterious ecological effects. However, limited genomic information is currently available in this non-model and ecologically important species. Ulva linza is a species that inhabits bedrock in the mid to low intertidal zone, and it is a major contributor to biofouling. Here, we presented the global characterization of the U. linza transcriptome using the Roche GS FLX Titanium platform, with the aim of uncovering the genomic mechanisms underlying rapid and successful colonization of the coastal ecosystems. Results De novo assembly of 382,884 reads generated 13,426 contigs with an average length of 1,000 bases. Contiguous sequences were further assembled into 10,784 isotigs with an average length of 1,515 bases. A total of 304,101 reads were nominally identified by BLAST; 4,368 isotigs were functionally annotated with 13,550 GO terms, and 2,404 isotigs having enzyme commission (EC) numbers were assigned to 262 KEGG pathways. When compared with four other full sequenced green algae, 3,457 unique isotigs were found in U. linza and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both LhcSR and PsbS proteins and a C4-like carbon-concentrating mechanism were found, which may help U. linza survive stress conditions. At least 19 transporters for essential inorganic nutrients (i.e., nitrogen, phosphorus, and sulphur) were responsible for its ability to take up inorganic nutrients, and at least 25 eukaryotic cytochrome P450s, which is a higher number than that found in other algae, may be related to their strong allelopathy. Multi-origination of the stress related proteins, such as glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase and heat-shock proteins, may also contribute to colonization of U. linza under stress conditions. Conclusions The transcriptome of U. linza uncovers some potential genomic mechanisms that might explain its ability to rapidly and successfully colonize coastal ecosystems, including the land-specific genes; special photoprotective mechanism based on both LhcSR and PsbS; development of C4-like carbon-concentrating mechanisms; muti-origin transporters for essential inorganic nutrients; multiple and complex P450s; and glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase, and heat-shock proteins that are related to stress resistance.</p

DNA barcoding, identification, and validation of the pufferfish (Order: Tetraodontiformes) in China coastal waters

Abstract The order Tetraodontiformes are one of the most unique groups of teleostean fish, exhibiting highly derived and greatly diversified phenotypes. It is a difficult task for both professionals and nonprofessionals to accurately identify these species only according to morphological characteristics. DNA barcoding can identify species at the molecular level to overcome the limitations of morphological classification. In this study, we collected 616 specimens of pufferfish from the coastal waters of China. According to the morphological characteristics, they were preliminarily identified as 50 species. Further analysis using DNA barcodes identified these specimens as 46 species, belonging to 23 genera, 6 families. According to the species classification results of DNA barcoding, the three species identified by morphology as Takifugu pseudommus, Takifugu chinensis, and Takifugu rubripes should be the same species. Similarly, Lagocephalus wheeleri is the synonym of Lagocephalus spadiceus. Another important discovery of DNA barcoding analysis is that there are closer interspecific genetic distances within the genus Takifugu. If T. rubripes, T. pseudommus, and T. chinensis are taken as one species, the average interspecific to intraspecific genetic distance ratio of Takifugu is only 6.21 times, which does not reach the DNA barcoding threshold of more than 10 times proposed previously. Although the interspecific genetic distance in the genus Takifugu is relatively small, each species can be clustered into independent clades in the NJ tree. In conclusion, this study not only found that there are synonymous phenomena in the order Tetraodontiformes but also provided molecular evidence for the valid species names of Takifugu rubripes and Lagocephalus Spadiceus. The results can provide reliable DNA barcoding information for the identification of pufferfish species, help solve the problem of classification confusion in this order, and provide technical support for the identification of the original components of related commodities on the aquatic product market

Allelopathic interactions between the opportunistic species Ulva prolifera and the native macroalga Gracilaria lichvoides.

Allelopathy, one type of direct plant competition, can be a potent mechanism through which plant communities are structured. The aim of this study was to determine whether allelopathic interactions occur between the opportunistic green tide-forming species Ulva prolifera and the native macroalga Gracilaria lichvoides, both of which were collected from the coastline of East China sea. In laboratory experiments, the presence of G. lichvoides at 1.25 g wet weight L(-1) significantly inhibited growth and photosynthesis of U. prolifera at concentrations of 1.25, 2.50, and 3.75 g wet weight L(-1) (p<0.05) in both semi-continuous co-culture assays and in co-culture assays without nutrient supplementation. In contrast, although U. prolifera had a density effect on G. lichvoides, the differences among treatments were not significant (p>0.05). Culture medium experiments further confirmed that some allelochemicals may be released by both of the tested macroalgae, and these could account for the observed physiological inhibition of growth and photosynthesis. Moreover, the native macroalgae G. lichvoides was a stronger competitor than the opportunistic species U. prolifera. Collectively, the results of the present study represent a significant advance in exploring ecological questions about the effects of green tide blooms on the macroalgal community