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Find video protocols related to scientific articles indexed in Pubmed.
Lack of population genetic differentiation of a marine ovoviviparous fish Sebastes schlegelii in Northwestern Pacific.
Mitochondrial DNA
PUBLISHED: 10-01-2014
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Abstract Sebastes schlegelii is one of the fishes that aggregate around drifting seaweed during early development. To examine the population genetic structure of S. schlegelii, a 452-bp fragment of the mtDNA control region was sequenced and used to interpret life history characteristics and larval dispersal strategy. Two-hundred and twenty-one individuals from 13 sites across the entire range of S. schlegelii in China, Japan and Korea were analyzed. A neighbor-joining tree and network showed that there were no significant genealogical structures corresponding to sampling locations. AMOVA, pair-wise FST and exact test revealed no significant genetic differentiation among locations. The migration rate among locations was high based on the result of LAMARC. We conclude that larval dispersal with drifting seaweed and the current environmental factors may play an important role in shaping the contemporary phylogeographic pattern and genetic homogeneity of S. schlegelii.
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Population genetic structure of chub mackerel Scomber japonicus in the Northwestern Pacific inferred from microsatellite analysis.
Mol. Biol. Rep.
PUBLISHED: 09-22-2014
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Marine pelagic fishes are usually characterized by subtle but complex patterns of genetic differentiation, which are influenced by both historical process and contemporary gene flow. Genetic population differentiation of chub mackerel, Scomber japonicus, was examined across most of its range in the Northwestern Pacific by screening variation of eight microsatellite loci. Our genetic analysis detected a weak but significant genetic structure of chub mackerel, which was characterized by areas of gene flow and isolation by distance. Consistent with previous estimates of stock structure, we found genetic discontinuity between Japan and China samples. Local-scale pattern of genetic differentiation was observed between samples from the Bohai Sea and North Yellow Sea and those from the East China Sea, which we ascribed to differences in spawning time and migratory behavior. Furthermore, the observed homogeneity among collections of chub mackerel from the East and South China Seas could be the result of an interaction between biological characteristics and marine currents. The present study underlies the importance of understanding the biological significance of genetic differentiation to establish management strategies for exploited fish populations.
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The complete mitochondrial genome of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) from Japan.
Mitochondrial DNA
PUBLISHED: 01-14-2014
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Abstract The complete mitochondrial genome of marbled rockfish Sebastiscus marmoratus collected from Japan was determined by next-generation sequencing. The mitogenome is a circular molecule 17,301?bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The ETAS, central CSB and CSB were detected in the control region. The gene contents of the mitogenome are identical to those observed in most bony fishes.
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Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region.
Mitochondrial DNA
PUBLISHED: 04-02-2013
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Trachurus japonicus is a pelagic fish widely distributed from China, Korea to Japan. To examine the gene flow of T. japonicus between Chinese and Japanese coastal waters, eight populations were collected for the present study. Eighty-seven variable sites defined 168 haplotypes. The populations of T. japonicus showed high haplotype diversity (h) with a range from 0.964 ± 0.027 to 1.000 ± 0.016 and low nucleotide diversity with a range from 0.011 ± 0.006 to 0.015 ± 0.008. The topology of the neighbour-joining tree showed no significant genealogical branches or clusters corresponding to sampling localities. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. Both pairwise F st and analysis of molecular variance revealed no significant genetic differentiation throughout the range examined. The results of neutrality tests and mismatch distributions indicated that T. japonicus may experience a recent population demographic expansion.
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Complete mitochondrial genome of Japanese Konosirus punctatus (Clupeiformes: Clupeidae).
Mitochondrial DNA
PUBLISHED: 03-06-2013
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The long polymerase chain reaction and primer walking methods were employed for the complete mitochondrial genome (mitogenome) sequence of Japanese Konosirus punctatus. The mitogenome is a circular molecule 16,698 bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (L-strand replication origin and control region), the gene contents of which are identical to those observed in most bony ?shes. Within the control region, we identi?ed the termination-associated sequence domain, the central conserved sequence block domains (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-B), and the conserved sequence block domains (CSB-2 and CSB-3).
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Molecular phylogeny of a red-snow-crab species complex using mitochondrial and nuclear DNA markers.
Zool. Sci.
PUBLISHED: 04-07-2011
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Nucleotide sequence variation of mitochondrial DNA COI and nuclear rRNA gene regions was used to reconstruct phylogenetic relationships for the red-snow-crab species complex, including the red snow crab, Chionoecetes japonicus, its nominal subspecies, C. japonicus pacificus, and the triangle tanner crab, C. angulatus. The topologies of the Bayesian and neighbor-joining (NJ) trees of the COI and of NJ trees of rRNA sequences placed C. japonicus and C. angulatus in a single clade. The net sequence divergence between these taxa was d(net) = 0.000 in COI, and strongly suggests that these taxa represent a single species. In contrast, haplotypes in C. j. pacificus clustered separately from the C. japonicus - C. angulatus clade. Net sequence divergence from C. japonicus - C. angulatus to C. j. pacificus was d(net) = 0.026 in COI, indicating that C. j. pacificus should be elevated to a separate species, C. pacificus. A 165 bp insert appeared in the rRNA gene of C. j. pacificus, but was absent in the remaining species of Chionoecetes. This autapomorphic condition in C. j. pacificus adds support for an independent evolution of this taxon. Evolutionary divergences between these taxa may reflect contrasting evolutionary process influenced by ocean bathymetry.
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Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.
Genetica
PUBLISHED: 09-21-2010
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Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5 end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.
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Demographic history and population structure of blackfin flounder (Glyptocephalus stelleri) in Japan revealed by mitochondrial control region sequences.
Biochem. Genet.
PUBLISHED: 01-03-2010
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The demographic history and population genetic structure of the blackfin flounder (Glyptocephalus stelleri) along coastal regions of Japan were investigated. Genetic variation in DNA sequences was examined from the first hypervariable region of the mitochondrial DNA control region. A high level of haplotypic diversity (h = 0.99 +/- 0.004) was detected, indicating a high level of intrapopulation genetic diversity. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. The demographic history of G. stelleri was examined using neutrality tests and mismatch distribution analysis, which also indicated a Pleistocene population expansion at about 124,100-413,400 years ago. Hierarchical molecular variance analysis and conventional population Fst comparisons revealed no significant genetic differentiation throughout the range examined.
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Isolation and cDNA cloning of an antibacterial L-amino acid oxidase from the skin mucus of the great sculpin Myoxocephalus polyacanthocephalus.
Comp. Biochem. Physiol. B, Biochem. Mol. Biol.
PUBLISHED: 03-15-2009
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The skin mucus of the great sculpin Myoxocephalus polyacanthocephalus showed both antibacterial and L-amino acid oxidase (LAO) activities. Antibacterial LAOs were purified from the skin mucus of the M. polyacanthocephalus by column chromatography and named MPLAO1, MPLAO2, and MPLAO3, based on the order of elution by ion-exchange high performance liquid chromatography. cDNA cloning of MPLAO3 revealed that the full-length cDNAwas 2659 bp and encoded the signal peptide (Met1-Ala26) and the mature protein (Val28-Phe520). A homology search using the BLAST program revealed that MPLAO3 shared sequence identity with LAO family proteins, and had 74% identity with the antibacterial LAO from the skin mucus of the rockfish Sebastes schlegeli. MPLAO3 catalyzed the oxidation of only L-lysine with a Km of 0.16 mM. MPLAO3 exhibited potent antibacterial activity against both Gram-positive and Gramnegative bacteria, and was most active against Aeromonas salmonicida JCM7874 with a minimum inhibitory concentration of 0.02 microg/mL. The antibacterial activity was attributable to H2O2, because the activity was completely lost in the presence of catalase. The antibacterial LAOs may be involved in the innate immunity of the great sculpin M. polyacanthocephalus skin.
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What maintains the central North Pacific genetic discontinuity in Pacific herring?
PLoS ONE
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Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (?(ST) ?= 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (?(ST) ?= 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (?(ST) ?= 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.
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Genetic stock structure of walleye pollock (Theragra chalcogramma) inferred by PCR-RFLP analysis of the mitochondrial DNA and SNP analysis of nuclear DNA.
Mar Genomics
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Walleye pollock, Theragra chalocogramma, is one of the most important species in the North Pacific and Bering Sea ecosystems. However genetic population structuring of walleye pollock is uncertain. In the present study, genetic variation of walleye pollock collected in several spawning areas ranging from the Japan Sea to the Gulf of Alaska was investigated by DNA analysis. Three regions of the spacer control region, the ND5 and ND6 region (ND complex), and the ND1 and 16S rRNA region (rDNA complex) were amplified using the polymerase chain reaction (PCR). Restriction fragment length polymorphism (RFLP) was conducted on these PCR products and composite haplotypes were calculated. Furthermore, several nuclear DNA regions (actin, Calmodulin, S7 ribosomal protein, creatin kinase, and SypI gene) were investigated to study the stock structure of walleye pollock. It was considered that Calmodulin gene was one of good genetic marker, therefore we conducted SNP analysis for Calmodulin gene by SnaPshot kits. In RFLP analyses, there were no area-specific fragment patterns in the three regions, control region, ND complex and rDNA complex of mtDNA. However compositions of the fragment patterns for the three digested sets, control region/HinfI, rDNA complex/MspI and ND complex/MspI indicated that there are significant differences between around the Japan (Sado-Funka Bay-Wakkanai-Rausu) and the Bering Sea (Western Bering Sea-Nabarin-Atka I.-Bogoslof I). Furthermore, in the case of haplotype frequency, composition showed also significant genetic difference between two areas. Moreover, in Calmodulin analyses, haplotype compositions were changing from western area to eastern area gradually and the results of AMOVA analysis showed that there are interesting differences between western Pacific, western Bering Sea, and eastern Bering Sea. Judging from these results, it was considered that there are three populations of walleye pollock in the Northern Ocean. However, area-specific pattern was not found in some populations in the Northern Ocean. Therefore, we suggested that these populations were related by weak gene flow, and the walleye pollock was formed with meta-population around the Japan and the Bering Sea.
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Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species).
Mol. Phylogenet. Evol.
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A previous analysis of Pacific herring mitochondrial (mt) DNA with Bayesian skyline plots (BSPs) was interpreted to reflect population growth in the late Pleistocene that was preceded by population stability over several hundred thousand years. Here we use an independent set of mtDNA control region (CR) sequences and simulations to test these hypotheses. The CR haplotype genealogy shows three deeply divided lineages, A, B and C, with divergences ranging from d=1.6% to 1.9% and with similar genetic diversities (h=0.95, 0.96, 0.94; ?(?)=0.011, 0.012, 0.014, respectively). Lineage A occurs almost exclusively in the NW Pacific and Bering Sea, but lineages B and C are co-distributed in the Northeastern Pacific. This distribution points to a historical allopatric separation between A and B-C across the North Pacific during Pleistocene glaciations. The origins of B and C are uncertain. One hypothesis invokes long-term isolation of lineage C in the Sea of Cortez, but the present-day lack of geographical segregation from lineage B argues for lineage sorting to explain the deep divergence between B and C. BSPs depict rapid population growth in each lineage, but the timing of this growth is uncertain, because of questions about an appropriate molecular clock calibration. We simulated historical demographies under a Pleistocene climate model using observed genetic parameters. BSPs for these sequences showed rapid population growth after the Last Glacial Maximum (LGM) 18-20 k years ago and a flat population history during previous climate fluctuations. Population declines during the LGM appear to have erased signals of previous population fluctuations.
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Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact.
PLoS ONE
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To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.
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