Human ribosomal protein (RP) gene sequences with respect to intron/exon structures and corresponding cDNA or genomic data of fish species were obtained from the GenBank database. Based on conserved exon sequences, 128 primer pairs for 41 genes were designed for exon-primed intron-crossing (EPIC) polymerase chain reaction (PCR). In reference to the draft genome sequences of the Pacific bluefin tuna (Thunnus orientalis), 12 primer pairs expected to amplify introns of the bluefin tuna with lengths of 500-1000 bp were selected and applied to six distantly related fish species belonging to the Orders Clupeiformes, Tetraodontiformes, Pleuronectiformes, Perciformes, Scorpaeniformes, and Anguilliformes. PCR amplification was observed for at least four species in each primer pair, and all fragments were larger than those expected for intronless amplification. Single fragment amplification was observed for at least seven primer pairs per species. Fragment sizes of the bluefin tuna for nine primer pairs corresponded to those expected from the genomic data. Thus, our primer pairs are potentially applicable to a wide variety of fish species and serve as an initial step for isolating single-copy nuclear DNA sequences.

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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.

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 Ϯ 0.0308 (Zhoushan) to 0.9926 Ϯ 0.0230 (Xiamen), and from 0.0073 Ϯ 0.0043 (Qingdao) to 0.0099 Ϯ 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 85 000-170 000 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.

An excess of low-frequency mutations is a ubiquitous characteristic of many marine species, and may be explained by three hypotheses. First, the demographic expansion hypothesis postulates that many species experienced a post-glacial expansion following a Pleistocene population bottleneck. The second invokes some form of natural selection, such as directional selection and selective sweeps. The third explanation, the reproductive skew hypothesis, postulates that high variation in individual reproductive success in many marine species influences genetic diversity. In this study, we focused on demography and reproductive success and the use of coalescent theory to analyse mitochondrial DNA sequences from the Japanese sardine. Our results show that population parameters estimated from both the site-frequency spectrum and the mismatch distribution of pairwise nucleotide differences refute the demographic expansion hypothesis. Further, the observed mismatch distribution, compared with the expectations of the reproductive skew hypothesis, supports the presence of multiple mergers in the genealogy. Many short external branches but few long terminal branches are found in the sardine genealogy. Model misspecification can lead to misleading contemporary and historical estimates of the genetically effective population sizes in marine species. The prevalence of reproductive skew in marine species influences not only the analysis of genetic data but also has ecological implications for understanding variation in reproductive and recruitment patterns in exploited species.