Takashi Yanagimoto

Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea

The population genetic structure and level of gene flow of Nibea albiflora from the Yellow Sea and the East China Sea were examined with a 479-bp segment of a mtDNA control region. In total, 65 samples were collected from three locations and 37 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the three populations ranged from 0.9130±0.0308 (Zhoushan) to 0.9926±0.0230 (Xiamen), and from 0.0073±0.0043 (Qingdao) to 0.0099±0.0057 (Xiamen). Analysis of molecular variance and pairwise FST revealed little genetic structure between the Yellow Sea and the East China Sea in N. albiflora. But based on the exact test of differentiation, the null hypothesis that N. albiflora within the Yellow Sea and the, East China Sea constitutes a panmictic mtDNA gene pool was rejected. This might be caused by the broad spawning areas but not by the Yangtze River outflow. Mismatch distribution revealed that N. albiflora has undergone population expansion, possibly before the last 85000–170000 years. The existence of high gene flow between stocks in the studied area was supported by our results. Annual migrations, larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.

Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

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; Θ(π)=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.

Deep phylogeographic break among white croaker Pennahia argentata (Sciaenidae, Perciformes) populations in North-western Pacific

The Quaternary cold periods in the North-western Pacific are thought to have greatly influenced the genetic structures of marine species. One hundred and thirty-two individuals of white croaker Pennahia argentata were sampled from 12 localities throughout its distribution range to estimate the demographic history and genetic structure based on mitochondrial DNA cytochrome b gene and control region sequences. Two distinct clades with net genetic divergence of 3% in the control region were detected, one in Chinese coastal waters and the other in Japanese coastal waters. These clades may have been isolated and diverged during Pleistocene low sea levels. Nucleotide diversity was much higher in the Chinese clade than in the Japanese clade. The demographic history of the two clades was examined using neutrality tests and mismatch analyses, and the results indicated Pleistocene population expansion in both clades. Molecular variance and pairwise FST analyses revealed significant differentiation between two Japanese populations and lack of genetic structure in the Chinese populations. The significant geographic structure in white croaker suggests a low level of dispersal in this species. The lack of phylogeographic structure in Chinese coastal waters may reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.

Remarkably low mtDNA control-region diversity and shallow population structure in Pacific cod Gadus macrocephalus

To investigate the genetic diversity and describe the population structure in Gadus macrocephalus, a 452 base pair (bp) fragment of the mitochondrial DNA control region was analysed in 259 individuals. The results showed remarkably low nucleotide diversity and a lack of genealogical structure. Small but significant genetic differentiations, however, were detected among north-western Pacific populations, but no large-scale regional differences were detected. These results indicate that populations of G. macrocephalus in the north-western Pacific are genetically subdivided and represent evolutionary lineages that should be managed individually.

Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north‐west Pacific

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life-history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair-wise F(ST) revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0.53, P < 0.001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration-drift equilibrium.

What maintains the central North Pacific genetic discontinuity in Pacific herring

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 (ΦST  = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (ΦST  = 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 (ΦST  = 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.

Lack of population genetic differentiation of a marine ovoviviparous fish Sebastes schlegelii in Northwestern Pacific

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.

Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region.

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.

Species identification of Alaska pollock, Gadus spp., and Micromesistius spp. in cod roe products using a PCR-based method

Fish species identification techniques for authentic food labeling were developed using species-specific PCR primers for cod roe products. A salted, seasoned fish roe product, karashimentaiko (chilli cod roe), is produced from the eggs of Alaska pollock, Theragra chalcogramma, according to the fair trade competition agreement authorized by the Fair Trade Commission of the Japanese government. To examine whether Alaska pollock ovaries or those of other fish species are being used as raw materials for the fish roe products, we developed species identification techniques using PCR amplification of a 255-bp fragment encoding the mitochondrial ATP synthase Fo subunit 6 (ATP6) gene with a species-specific primer set for Alaska pollock mitochondrial DNA. We also designed two species-specific primer sets corresponding to the mitochondrial ATP6 and cytochrome b (cytb) for Gadus spp. and Micromesistius spp. by PCR amplification of 332- and 223-bp fragments, respectively. We examined the species specificity of these PCR-based methods among nine commercially important Gadidae species.

Complete mitochondrial genome of Japanese Konosirus punctatus (Clupeiformes: Clupeidae)

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 fishes. Within the control region, we identified 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).