Youn-Ho Lee

Population genetic structure and demographic history of the fat greenling Hexagrammos otakii

Fat greenling (Hexagrammos otakii) is an important commercial fish in the Northwestern Pacific, being distributed along the coastal waters of the East/Japan Sea and the Yellow Sea. To investigate population genetic structure and demographic history of this species, one hundred and fifty five individuals were collected from five localities in the distribution range of the species and sequence variations in the mitochondrial genes COI, COIII-ND3-ND4L, and cytochrome b were examined. For all the genes in every sampling location, the nucleotide diversities were very low (0.001 ∼ 0.005) although the haplotype diversities were relatively high, 0.55 ∼ 0.81 for COI, 0.79 ∼ 0.84 for COIII-ND3-ND4L, and 0.95 ∼ 0.97 for cytochrome b. Hierarchical analysis of molecular variance (AMOVA), the conventional population statistic FST, and exact test of population differentiation revealed no significant genetic structuring among the samples, indicating that fat greening is panmictic throughout the range of its distribution. Neutrality tests such as Tajima’s D and Fu’s FS statistics and mismatch distribution analyses suggested that fat greening has undergone the demographic history of population expansion during the late Pleistocene period approximately 91,000 ∼ 327,000 years ago. The star-burst patterns of haplotype networks and low nucleotide diversities also indicated recent population expansion. These results help establish the fisheries management strategy for fat greenling in the Northwestern Pacific.

Complete mitochondrial genome of sea urchin: Mesocentrotus nudus (Strongylocentrotidae, Echinoida)

The complete nucleotide of mitochondrial DNA of a sea urchin Mesocentrotus nudus was determined for the first time. It is 15,709 bp in length, containing 2 rRNA, 22 tRNA and 13 protein-coding genes generally found in other echinoderm species. The gene order and structure of the genome are identical to those of other Strongylocentrotidae species. The genome was composed of 29.3% A, 23.4% C, 29.5% T and 17.8% G, showing a slight AT bias (58.8%). The G is the least used base and markedly lower at the third codon position (12.74%). Twelve of the 13 mitochondrial protein-coding genes use ATG as their start codon while the ATP8 gene starts with GTG. The control region is 125 bp in length and contains a G-stretch of 19 nucleotides, a typical DNA structure of the echinoid mitochondrial genomes.

DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups

Abstract The analysis of variation among 203 nucleotide sequences of Co-1 gene (DNA-barcode) for 45 species, 31 genera and 7 families of the order Perciformes from the Far Eastern seas of Russia has been performed. As a result, 42 species (93.3%) can be unambiguously identified using molecular DNA-barcode at Co-1, whereas more variable markers are required for other species (6.7%): Stichaeus grigorjewi, S. nozawae, and Lumpenus sagitta. The latter includes as well 2 morphologically distinct (by number of vertebrae) but genetically unresolved species, L. sagitta (Sea of Okhotsk) and L. fabricii (Bering Sea). In addition, within this genus morphologically poorly characterized but genetically well-distinguished cryptic species has been detected. Amphi-Pacific distribution is in question relative to L. sagitta. Cryptic diversity was observed in the genus Ammodytes.

Population panmixia and the Pleistocene demographic expansion of spotty belly greenling Hexagrammos agrammus in the East Sea and Northwest Pacific

The population genetic structure and historical demography of spotty belly greenling, Hexagrammos agrammus, which has limited distribution in the Northwest Pacific, was assessed with partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and the control region (D-loop). A total of 103 individuals were collected from four sites located at the Korea Strait (Southern coast of Korea) and the East coast of Korea and two places in the Pacific coast of Japan. For all the populations, nucleotide diversities were low (0.006–0.009) while the haplotype diversities were as high as 0.92 to 0.97, indicating that the fish has undergone a recent population expansion after experiencing bottleneck. Star-shaped patterns of haplotype networks as well as the significant negative values of Tajima’s D and Fu’s FS corroborate the recent population expansion. Mismatch distribution analysis reveals that the demographic expansion of the species started during the 2nd half of the Middle Pleistocene Series approximately 141,000–406,000 years ago. Hierarchical analysis of molecular variance (AMOVA), the pairwise population statistics (FST), and the exact test of haplotype differentiation demonstrate no significant genetic differentiation among populations investigated, suggesting that spotty belly greenling is panmictic in the East Sea and the Pacific coast of Japan.

The complete mitochondrial genome of the marine polychaete: Perinereis aibuhitensis (Phyllodocida, Nereididae)

Abstract We determined the complete mitochondrial genome sequence of the marine polychaete Perinereis aibuhitensis (Grube, 1878) (Phyllodocida, Nereididae), a dominant species in the mudflat of the West Pacific and Indian Ocean. The complete genome of P. aibuhitensis is 15,852 bp in size including 13 protein coding genes (PCGs), 2 rRNA and 22 tRNA with the same gene order and structure as those of other Nereididae species. The nucleotide composition is 29.5% A, 21.2% C, 14.1% G, 35.2% T, showing a high content of A + T with G being used least in the third codon position (6.7%). All PCGs use ATG as the start codon while for the stop codon COI and ND1 use incomplete codon of T. The mitogenome sequence of P. aibuhitensis is second to that of P. nuntia known in the genus Perinereis, which will provide useful information for understanding evolutionary history of the genus Perinereis within the family Nereididae.

The complete mitochondrial genome of the Longnose skate: Raja rhina (Rajiformes, Rajidae)

Abstract The complete sequence of mitochondrial DNA of a longnose skate, Raja rhina was determined for the first time. It is 16,910 bp in length containing 2 rRNA, 22 tRNA and 13 protein coding genes with the same gene order and structure as those of other Rajidae species. The nucleotide of L-strand is composed of 30.1% A, 27.2% C, 28.5% T and 14.2% G, showing a slight A + T bias. The G is the least used base and markedly lower at the third codon position (5.4%). Twelve of the 13 protein coding genes use ATG as their start codon while the COX1 starts with GTG. As for stop codon, only ND4 shows incomplete stop codon TA. This mitogenome is the first report for a species of the genus Raja, and providing a valuable resource of genetic information for understanding the phylogenetic relationship and the evolution of the genus Raja as well as the family, Rajidae.

Complete mitochondrial genome of the mottled skate: Raja pulchra (Rajiformes, Rajidae)

Abstract The complete sequence of mitochondrial DNA of a mottled skate, Raja pulchra was sequenced as being circular molecules of 16,907 bp including 2 rRNA, 22 tRNA, 13 protein-coding genes (PCGs), and an AT-rich control region. The organization of the PCGs is the same as those found in other Rajidae species. The nucleotide of L-strand is composed of 29.8% A, 28.0% C, 27.9% T, and 14.3% G with a bias toward A + T slightly. Twelve of 13 PCGs are initiated by the ATG codon while COX1 starts with GTG. Only ND4 harbors the incomplete termination codon, TA. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA with the exception of which has a reduced DHU arm. This mitogenome will provide essential information for better phylogenetic resolution and precision of the family Rajidae and the genus Raja as well as for establishment of a fish stock recovery plan of the species.

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 FST statistic and a phylogeographic method. A significant nonzero FST 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 500–800 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.

The complete mitochondrial genome of the marine polychaete: Hediste diadroma (Phyllodocida, Nereididae)

Abstract The mitogenome sequence of a polychaete Hediste diadroma (Phyllodocida, Nereididae) was determined first in the genus Hediste. The circular genome is 15,765bp in size including 13 protein-coding genes (PCGs), 2 rRNA and 22 tRNA of which the order and structure is same as those of other Nereididae species. All PCGs use ATG as the start codon while for the stop codon, COI, ND5 and ND1 use an incomplete codon of T. The genome consists of 32.4% A, 18.2% C, 14.2% G, 35.2% T, showing a high content of A + T similar to the other Phyllodocid polychaetes.

The F type mitochondrial genome of hard-shelled mussel: Mytilus coruscus (Mytiloida, Mytilidae).

Abstract We determined the complete mitochondrial genome of the female hard-shelled mussel Mytilus coruscus (Gould, 1869) (F type). The F type genome is composed of 16,642 bp in length including 12 protein coding genes (PCGs), 2 rRNA and 23 tRNA with the same gene content and order as the other Mytilus species which is characterized by the absence of the ATPase8 gene and addition of tRNAMet (AUA). The nucleotide composition of the genome shows that the percentage of A+T (63.2%) is higher than those of M. edulis complex species (M. edulis, M. galloprovincialis, M. trossulus) but lower than that of M. californianus. The F type mitochondrial genome of M. coruscus will provide useful information on the evolutionary history of the Mytilus species in the family Mitilidae.