Kouji Nakayama

Genetic differences among three colour morphotypes of the black rockfish, Sebastes inermis, inferred from mtDNA and AFLP analyses

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.

Molecular phylogenetic perspective on speciation in the genus Sebastes (Scorpaenidae) from the Northwest Pacific and the position of Sebastes within the subfamily Sebastinae

In the Northeast and the Northwest Pacific, 26 and 68 species of Sebastes occur, respectively, the similar appearance of some pairs of shallow coastal water species in the two regions having been interpreted as evidence either for migration of ancestral species or of morphological convergence. To distinguish between these competing hypotheses, a portion of the mitochondrial DNA (mtDNA) cytochrome b gene was sequenced from 23 species of Sebastes from the Northwest Pacific and phylogenetic trees constructed so as to include the existing data from Northeastern species of Sebastes. The results clearly indicated separate origins for external morphology in Northeast and Northwest Pacific species. The shallow coastal water species in the Northwest Pacific are thought to have diverged from about 9.8 MYA. Furthermore, the phylogenetic position of Sebastes was inferred among the subfamily Sebastinae, Helicolenus, Hozukius, Sebastes, and Sebastiscus, the results suggesting that Helicolenus and Hozukius are more closely related to Sebastes than Sebastiscus.

Diel and tidal changes in the distribution and feeding habits of Japanese temperate bass Lateolabrax japonicus juveniles in the surf zone of Ariake Bay

Japanese temperate bass Lateolabrax japonicus juveniles recruit to the surf zone and grow by feeding on commonly occurring coastal copepods. However, little is known about diel and tidal patterns in their migration and feeding habits. We sampled wild juveniles during the neap and spring tides, over periods of 24 h, with small seine nets in the sand flat of the eastern part of Ariake Bay, Kyushu, western Japan. In both the neap and spring tides, abundance of juveniles significantly increased during the daytime, being highest around the time of high tide. The relative gut fullness indices of juveniles drastically increased in the morning (0700–0900) and during the flood tide in the daytime, while major prey copepod (Paracalanus spp.) density in the ambient water was relatively constant. We summarized that L. japonicus juveniles would migrate to the surf zone after sunrise to feed on copepods, and then emigrate from the surf zone after sunset. The migratory behavior of L. japonicus juveniles would be influenced by light (daytime) and feeding activity influenced by both light (morning) and tidal condition (flood tide). The intertidal region of the tidal flat was recognized to be one of the important habitats for L. japonicus during their early life history.

Genetic variation and population structure of the Pacific cod Gadus macrocephalus in Korean waters revealed by mtDNA and msDNA markers

To investigate the extent of genetic differentiation among wild populations of the Pacific cod Gadus macrocephalus, we have examined genetic polymorphism at five locations within Korean waters [Boryeong in the West Sea (WC-BR); Jinhae Bay in the South Sea (SC-JH); Jumunjin (EC-JM), Jukbyeon (EC-JB), and Bangeojin (EC-BJ) off the eastern coast of Korea] using mitochondrial DNA (mtDNA) control region and microsatellite DNA (msDNA) markers. Nucleotide sequence analysis of 584 bp in the variable portion of the 5′ end of the mtDNA control region revealed 27 variable nucleotide sites among 184 individuals, which defined eight, three, and 11 haplotypes in the western, southern, and eastern coast populations, respectively. The mtDNA analysis revealed a low variability but significant local differentiation among populations from these three areas within Korean waters. msDNA analysis also revealed moderate polymorphism in the wild populations, with a mean of 13.8–22.6 alleles per locus for the five msDNA markers and observed (and expected) heterozygosities of 0.755 (0.825) for the WC-BR, 0.793 (0.810) for the SC-JH, 0.920 (0.905) for the EC-BJ, 0.783 (0.865) for the EC-JB, and 0.804 (0.812) for the EC-JM populations. Analysis of msDNA loci indicated that Pacific cod sampled at the WC-BR, SC-JH, and EC-JB sites belong to genetically distinct populations. However, no significant difference was found between the Pacific cod population from SC-JH and that from EC-BJ. Consequently, three genetically distinct populations, namely, WC-BR, SC-JH and EC-BJ, and EC-JB, were identified using msDNA analysis. These results indicate that genetically distinct populations of Pacific cod are present in Korean coastal waters where spawning aggregations occur.

Distribution of Japanese temperate bass, Lateolabrax japonicus, eggs and pelagic larvae in Ariake Bay

We collected eggs and larvae of the Japanese temperate bass, Lateolabrax japonicus, and present horizontal and temporal changes of distribution relative to development and growth during the species pelagic life history in Ariake Bay. Sampling was conducted from the inner to central region (11 sampling stations) of Ariake Bay using a plankton net (80 cm diameter, 0.5-mm mesh) from November 2000 to February 2001. Both eggs and larvae were collected most abundantly in mid-December. The CPUE of eggs in the surface layer was higher than the middle layer, which is in contrast to that at the larval stage. Most eggs were collected around the central and western regions of the bay. The distribution of eggs shifted vertically to the middle layer with development. Yolk-sac larvae were collected in the central region of the bay, and preflexion and flexion larvae were more abundantly collected in the inner region of the bay. The body length of larvae around the inner bay was larger than in the central region. The pelagic life history can be summarized as follows: eggs are distributed around the central region of the bay and eggs and larvae expand their distribution to the inner and shallower waters with growth. We conclude that the shift of vertical distribution in pelagic stages and the hydrographic features of the middle layer form one of the mechanisms enabling the inshore migration of L. japonicus.

Mitochondrial DNA Population Structure of the White-Spotted Charr (Salvelinus leucomaenis) in the Lake Biwa Water System

Abstract A phylogeographic analysis of mitochondrial DNA sequences was performed in order to elucidate the origin, dispersal process, and genetic structure of white-spotted charr in the Lake Biwa water system. Two haplotypes were most common in the Lake Biwa water system, and were also common in the adjacent inlet rivers of the Sea of Japan. These results suggest that in the glacial periods of the Pleistocene, white-spotted charr dispersed into the northern inlet rivers of Lake Biwa from adjacent inlet rivers of the Sea of Japan by watershed exchanges, colonizing the whole of the Lake Biwa water system. Mitochondrial DNA diversity contrasted sharply between the western and eastern parts of the system, suggesting that the populations in the western part might be more reduced than those in the eastern part in relation to the smaller habitat size. The high overall FST estimate (0.50), together with pairwise comparisons of FST, indicated significant genetic divergence between populations due to isolation and small population size. Hierarchical analysis (AMOVA) also showed that genetic variation was more pronounced among regions (28.39%) and among populations within regions (47.24%) than within populations (24.37%). This suggests that each population in and around the Lake Biwa water system should be treated as a significant unit for conservation and management.

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis.

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.

Genetic and morphological divergence within the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

Genetic and morphological divergence among the four subspecies in the Sebastes pachycephalus complex (S. pachycephalus pachycephalus, S. p. nigricans, S. p.nudus and S. p. chalcogrammus) was clarified. Principal coordinate analysis (PCoA) based on AFLP clearly divided 55 specimens of the complex into two groups, the S. p. pachycephalus–S. p. nigricans group (P-Ni group) and the S. p. nudus–S. p. chalcogrammus group (Nu-C group), although three specimens occupied intermediate positions. The minimum spanning network (MSN) based on partial sequences of the mitochondrial control region (mtCR) failed to separate either the P-Ni and Nu-C groups or the four subspecies into distinct clades, although restricted gene flow and genetic differentiation between the former were indicated by the FST estimation. Differences in morphological characters, including counts of pectoral fin rays and counts of dorsal fin spines lacking basal scales, were also evident between the two groups. However, little or no genetic or morphological difference was found between the two subspecies within each group. It was concluded that the P-Ni and Nu-C groups of the S. pachycephalus complex actually represent two different species, which is further supported by their sympatric distribution. Differences in dorsal body coloration and the presence or absence of brown spots on the ventral surface, which were formerly used to discriminate between four “subspecies,” may simply represent intraspecific variation. The three specimens occupying intermediate positions in the AFLP PCoA also occupied equivocal positions between the two species in the principal component analysis (PCA) based on morphometric characters, suggesting that they were hybrids between the two species. The star-shaped MSN of mtCR, which lacks distinct clades representing the two species, may be due to not only interspecific hybridization but also the sharing of ancestral haplotypes.

Distinct genetic isolation between “Kunimasu” (Oncorhynchus kawamurae) and “Himemasu” (O. nerka) in Lake Saiko, Yamanashi Prefecture, Japan, inferred from microsatellite analysis

The possibility of interspecific hybridization between Kunimasu (Oncorhynchus kawamurae) and Himemasu (Oncorhynchus nerka) was investigated in a large number of specimens, in a search for basic data relevant to conservation needs. A Bayesian-based clustering method using five microsatellite DNA loci separated 144 specimens from Lake Saiko, Yamanashi Prefecture, into two genetically distinct groups, corresponding to Kunimasu and Himemasu. Application of a threshold of individual proportion of membership of 0.90, so as to separate hybrids from purebreds, resulted in all specimens except two having high probability of purebred. These results implied that Kunimasu and Himemasu have been maintained as independent genetic entities in Lake Saiko.

Long-term patterns in the diets of Japanese temperate bassLateolabrax japonicus larvae and juveniles in Chikugo estuarine nursery ground in Ariake Bay, Japan

Larval and juvenile Japanese temperate bass (Lateolabrax japonicus) samples were collected from a wide range of spatial gradients (covering a distance of approximately 30 km) in Chikugo estuary, Ariake Bay, Japan over a period of 8 yr (1997–2004) in order to observe changes in diet. Gut contents were studied by separating, identifying, counting, and estimating the dry weight of prey organisms. Copepod samples were collected during each cruise to observe the numerical composition, abundance, and biomass in the estuary. Considerable spatial and temporal variations were observed in copepod distributions in ambient water and the diets of the fish. Two distinctly different copepod assemblages were identified in the estuary: One in the upper estuarine turbidity maximum (ETM), dominated by a single speciesSinocalanus sinensis and the other in the lower estuary consisting of a multispecies assemblage, dominated byOithona davisae, Acartia omorii, Paracalanus parvus, andCalanus sinicus. The gut content composition of the fish in the upper estuary was dominated byS. sinensis, while in the lower estuary, it consisted ofP. parvus, O. davisae, andA. omorii. Within the size group analyzed (13.0–27.0 mm SL), the smaller individuals were found to feed on a mixed diet composed of smaller prey. The diets gradually shifted to bigger prey composed predominantly ofS. sinensis for larger size groups. Greater proportions of empty guts were recorded in the smaller individuals and dropped with increasing fish size. Higher dry biomass of copepods in the environment, as well as higher dry weights of gut contents, were recorded in the upper estuary, indicating that the upper estuarine ETM areas are important nursery grounds for the early life stages of the Japanese temperate bass. The early life stages of the Japanese temperate bass are adapted to use the upstream nursery grounds and ascending to the nursery areas to useS. sinensis is one of the key survival strategies of the Japanese temperate bass in the Chikugo estuary.