Genetic and morphological evidence for cryptic diversity in the <Emphasis Type="Italic">Careproctus rastrinus</Emphasis> species complex (Liparidae) of the North Pacific

The molecular phylogeny of the Careproctus rastrinus species complex is presented on the basis of sequence variations in the 16S rRNA and cytochrome b genes (1,447 base pairs) of mitochondrial DNA using specimens collected from across the North Pacific and its marginal seas, including the Sea of Japan, the Pacific coast of Japan, the Sea of Okhotsk, the Bering Sea, the Gulf of Alaska, and the Arctic Ocean. Gene flow and migration between geographic regions is apparently strictly restricted in the C. rastrinus species complex, as this phylogeny revealed nine genetically diverged groups in the C. rastrinus species complex, most of which corresponded well with major geographic regions. Most of the groups were different in terms of morphological characters. Five nominal species have been considered to be members of the complex and have been variously recognized as being valid or as synonyms of C. rastrinus, but the present genetic and morphological differences suggested that the C. rastrinus species complex represents far more divergence. Such cryptic diversity of the C. rastrinus species complex defined by geographic regions may be related to their low dispersal ability, because they bear large demersal eggs. The genetic divergence suggested that colder climates from the late Pliocene and the isolation of marginal seas during the Pleistocene may have driven the divergence of the C. rastrinus species complex.     

Genetic evidence supporting the existence of two distinct species in the genusGasterosteus around Japan

Synopsis The genetic and morphological features ofGasterosteus aculeatus were investigated for 29 populations around Japan. Allozyme analyses recognized two groups (Pacific Ocean group and Japan Sea group) that had distinct characteristic features, and showed high genetic differentiation between them (D = 0.482). The Pacific Ocean group had a wide range, from North America to Japan, along the Pacific coast. The distribution of the Japan Sea group was limited around the Sea of Japan and the Sea of Okhotsk. The distribution of these groups were found to be sympatric on the Pacific coast of Hokkaido Island, Japan. From this area, genetic analyses demonstrated that the sympatric populations of the two groups formed independent breeding stocks, and it is considered that the two groups were reproductively isolated from each other. Additionally, each group had distinctive morphological features of lateral plates and caudal keels in the sympatric area. These results suggested that these two groups of the threespine stickleback comprise different species and that the Japan Sea group is taxonomically distinguishable fromG. aculeatus.     

Taxonomic review of the genus <Emphasis Type="Italic">Cottiusculus</Emphasis> (Cottoidei: Cottidae) with description of a new species from the Sea of Japan

A taxonomic review of the cottid genus Cottiusculus Jordan and Starks 1904 established three species, C. nihonkaiensis sp. nov., C. schmidti, and C. gonez. Cottiusculus nihonkaiensis sp. nov., which had been previously confused with C. schmidti, is described on the basis of 32 specimens (44.8–77.9 mm, SL) collected from the Sea of Japan. The new species is very similar to C. schmidti in having a curved barbless uppermost preopercular spine and the lateral line extending past the caudal fin base, but is distinguishable as follows: nasal spines simple or sometimes weakly bicuspid (vs. deeply bicuspid in C. schmidti); first dorsal fin not elongated in either males or females (vs. elongated in males); ventral lateral and lateral line cirri present (vs. absent). The former is known from the Sea of Japan coasts of Hokkaido, Honshu, Kyushu and the Korean Peninsula, and Volcano Bay, Hokkaido, and the latter from the Pacific coast of Tohoku District, Japan. Cottiusculus gonez, known from the Sea of Japan, Sea of Okhotsk and Pacific coast of Hokkaido, is characterized by having a simple nasal spine, the uppermost preopercular spine almost straight with two small cusps dorsally, posterior cusp barbed, and the lateral line almost reaching to the caudal fin base. A lectotype of C. gonez is designated here. Sequence differences in the cytochrome b gene among the above three species of Cottiusculus are also presented.     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

Munnogonium affinissp. n.: A New Species of Isopod (Asellota: Paramunnidae) from the Coast of Korea,Sea of Japan

The new species Munnogonium affinisfrom the coast of Korea (the Sea of Japan) is described. This is the first record of the genus Munnogoniumfrom the western Pacific. The new species differs considerably from the four eastern Pacific American species of this genus and is most similar to M. maltiniifrom the Mediterranean Sea.     

Phylogeographic analysis reveals two periods of divergence in large-scaled redfin <Emphasis Type="Italic">Tribolodon hakonensis</Emphasis> (Pisces,Cyprinidae)

Analysis of mtDNA variation in one of the amphidromic Far Eastern redfins, Tribolodon hakonensis, revealed the presence of three considerably genetically different mtDNA phylogroups in the individuals from the Russian part of the range. These data suggest the presence of the two periods of divergent evolution in the history of the species examined. Comparison of the haplotype distributions from different phylogroups over the species range revealed geographic localization of only one phylogroup in the population samples from southern continental coastal regions of the Sea of Japan. At the same time, two other phylogroups were found in almost equal ratios in northern continental samples and near the Sakhalin Island. These results suggest that the first stage of the divergent evolution, which occured between Pliocene and Pleistocene, resulted in the formation of genetically isolated form (probably, a species) in the region of the Sea of Japan. The second, later period of divergence, probably associated with the separation of the Sea of Okhotsk from the Pacific Ocean then ended with the integration of earlier genetically separated forms into one species with the common gene pool.     

Genetic structure of threespine stickleback,Gasterosteus aculeatus,in Lake Harutori,Japan, with reference to coexisting anadromous and freshwater forms

Both anadromous and freshwater forms of threespine sticklebacks (Gasterosteus aculeatus) inhabit Lake Harutori on the pacific coast of eastern Hokkaido, Japan. Since the two groups of threespine sticklebacks, Pacific Ocean and Japan Sea groups, which showed high genetic differentiation between them, were sympatrically distributed on the Pacific Ocean coast of Hokkaido Island, the genetic structures of the two forms were examined in Lake Harutori. Allozyme analyses of the two forms showed that most specimens from Lake Harutori belonged to the Pacific Ocean group, with a few fish belonging to the Japan Sea group or representing hybrids between the two groups. Both anadromous and freshwater sticklebacks were detected in the Pacific Ocean group. There were no significant differences in allelic frequencies at 17 presumptive loci between the two forms. Analyses of genetic relationships among 5 populations showed that the freshwater population from Lake Harutori was genetically more closely related to the sympatric anadromous population than to the freshwater population from a neighboring river. These results suggested that anadromous and freshwater sticklebacks in Lake Harutori form a single breeding population, and that the two forms might represent a life-history polymorphism within a single population.     

Genetic structure of the beaked whale genus Berardius in the North Pacific,with genetic evidence for a new species

There are two recognized species in the genus Berardius, Baird's and Arnoux's beaked whales. In Japan, whalers have traditionally recognized two forms of Baird's beaked whales, the common “slate‐gray” form and a smaller, rare “black” form. Previous comparison of mtDNA control region sequences from three black specimens to gray specimens around Japan indicated that the two forms comprise different stocks and potentially different species. We have expanded sampling to include control region haplotypes of 178 Baird's beaked whales from across their range in the North Pacific. We identified five additional specimens of the black form from the Aleutian Islands and Bering Sea, for a total of eight “black” specimens. The divergence between mtDNA haplotypes of the black and gray forms of Baird's beaked whale was greater than their divergence from the congeneric Arnoux's beaked whale found in the Southern Ocean, and similar to that observed among other congeneric beaked whale species. Taken together, genetic evidence from specimens in Japan and across the North Pacific, combined with evidence of smaller adult body size, indicate presence of an unnamed species of Berardius in the North Pacific.     

A mitogenomic approach to the taxonomy of pollocks: <Emphasis Type="Italic">Theragra chalcogramma</Emphasis> and <Emphasis Type="Italic">T. finnmarchica</Emphasis> represent one single species

Background  

The walleye pollock (Theragra chalcogramma) and Norwegian pollock (T. finnmarchica) are confined to the North Pacific and North Atlantic Oceans, respectively, and considered as distinct species within the family Gadidae. We have determined the complete mtDNA nucleotide sequence of two specimens of Norwegian pollock and compared the sequences to that of 10 specimens of walleye pollock representing stocks from the Sea of Japan and the Bering Sea, 2 specimens of Atlantic cod (Gadus morhua), and 2 specimens of haddock (Melanogrammus aeglefinus).     

Seasonal distribution and migrations of Pacific cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> (Gadidae) in the northwestern part of the Sea of Japan and adjacent water areas

On the basis of materials collected in 32 expeditions in the northwestern part of the Sea of Japan from 1984 to 2009, seasonal and interannual dynamics of biomass of Pacific cod Gadus macrocephalus stock was analyzed. Seasonal variation of spatial and bathymetric distributions of this species is considered. The conclusion of the existence of seasonal migrations of cod along the continental coast is substantiated.     

Molecular identification of Anisakis simplex sensu stricto and Anisakis pegreffii (Nematoda: Anisakidae) from fish and cetacean in Japanese waters

Parasites morphologically consistent with Anisakis simplex sensu lato collected from the coast of Japan and Western North Pacific Ocean were examined by PCR-RFLP of the ITS region (ITS1, 5.8 subunit rRNA gene and ITS2) and mtDNA cox1. The RFLP patterns of rDNA generated by HinfI and HhaI showed that 100% of the larvae collected from Hokkaido and 94% of adults collected from Western North Pacific Ocean were identified as A. simplex sensu stricto. On the other hand, 97% of the larvae collected from Fukuoka prefecture were identified as A. pegreffii. A hybrid genotype was found in adults in Western North Pacific Ocean and larva in Fukuoka prefecture. These findings revealed that A. simplexs. str. is primarily distributed in the North Pacific Ocean and A. pegreffii is primarily distributed in the southern Sea of Japan. RFLP analysis of mtDNA cox1 showed different patterns between A. simplex s. str. and A. pegreffii after digestion with HinfI. This polymorphism obtained by RFLP analysis of mtDNA cox1 proved the usefulness as new genetic markers to distinguish two sibling species.     

Genetic similarity of disjunct populations of the giant sea bass Stereolepis gigas

Sequence variation in nuclear and mitochondrial genes of the giant sea bass Stereolepis gigas collected from the Pacific coast and the northern Sea of Cortez was examined. Restriction fragment length polymorphism analysis and direct sequencing showed extremely low mtDNA sequence diversity (13 closely related haplotypes with no evidence of geographical population subdivision). The mitochondrial haplotype mismatch distribution is consistent with a population expansion following the Last Pleistocene glaciation. Differences in single nucleotide polymorphism frequencies between Pacific and Sea of Cortez populations were detected at two of four nuclear loci, which may reflect natural selection or genetic drift in populations with low effective numbers of males. Although Pacific coast and Sea of Cortez populations of giant sea bass do not exhibit the mitochondrial phylogenetic break characteristic of many species with disjunct Pacific and Gulf populations, the possibility of genetic differentiation at nuclear loci suggests that a cautious approach to broodstock selection for captive breeding and restoration programmes be exercised.     

The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli

We used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both G_ST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.     

A concise review of geographic variation in adult body size in anadromous masu salmon, Oncorhynchus masou

Adult body size (size at maturity) is one of the key life history traits and is well known to sometimes correlate with latitude in anadromous salmonids. However, it is poorly understood whether geographic size patterns except for latitudinal trends occur or why such patterns have been shaped. The present paper briefly reviewed body size variation between anadromous returns of masu salmon Oncorhynchus masou in the Okhotsk group (10 populations along the Sea of Okhotsk coast), the Pacific group (2 populations along the Pacific Ocean coast) and the Sea of Japan group (24 populations along the Sea of Japan coast). The Okhotsk group was smaller than the Sea of Japan group. Although the statistical analysis detected no differences among the remaining combinations, the Okhotsk group was possibly smaller than the other groups because the size of the Pacific group seemed to be within range of the Sea of Japan group but tended to be larger than that of the Okhotsk group. Future research should first test whether size at maturity genetically differs between the Okhotsk group and the other two groups to explore further evolutionary factors shaping geographic size variation.     

Extensive Introgression of Mitochondrial DNA Found between two Genetically Divergent Forms of Threespine Stickleback, Gasterosteus Aculeatus, around Japan

The genetic structure and phylogenetic relationships of Gasterosteus aculeatus around Japan were investigated for 15 populations of the Japan Sea and Pacific Ocean forms previously detected by allozyme analyses. PCR-RFLP analysis of mtDNA ND5/6 gene indicated two major divergent clades: (1) Alaskan population and (2) Russian and Japanese populations. Japanese populations were clearly subdivided into G. aculeatus populations and hariyo (G. aculeatus leiurus). However, the relationships among Japanese G. aculeatus populations did not support the genetic divergence between Japan Sea and Pacific Ocean forms shown by allozyme analyses. This suggests that mtDNA genetype similarity between the two forms could have resulted from complete replacement of mtDNA from one form to the other. MtDNA introgression is possible in two direction: from Japan Sea form to Pacific Ocean form and the reverse. The haplotype composition of each population observed in the present study suggests that the second direction is more likely. The migrant number of females per generation (Nm) between populations of the two forms was remarkablely large (9.083–infinite), suggesting that gene flow is taking place between the populations at the present time or might have occurred until recent years.     

Population structure of the sailfin sandfish, Arctoscopus japonicus (Trichodontidae), in the Sea of Japan

We analyzed patterns of genetic diversity in the sailfin sandfish (Arctoscopus japonicus), focusing on population subdivisions within the Sea of Japan. We observed 270 specimens from nine sampling sites in 1999–2000, i.e., seven sites in the Sea of Japan and two sites from the Pacific coast of Hokkaido. An additional site (30 specimens) was sampled from eastern Korea in the spawning season of 2004 for comparison. Forty haplotypes, compiled into three haplogroups (A–C), were detected based on the comparison of a 400-bp sequence of the anterior part of the mitochondrial control region. In accordance with previous hypotheses from morphological and molecular analyses, genetic discontinuity between the Sea of Japan and the Pacific coast of Hokkaido was conspicuous. Within the Sea of Japan, eight sampling sites were not genetically uniform, and most of the variations among sites were detected between eastern Korea [the “eastern Korea” (EK) population: distributed from the Korean Peninsula to Mishima, Yamaguchi Prefecture] and the other sites along the coast of Japan [the “western Japan” (WJ) population: from Oki Islands to western Hokkaido] (Φ _CT  = 0.096, P = 0.0183). The WJ population, having lower genetic variability, showed significant departure from neutrality, indicating influences through a recent population expansion. The period of the expansion can be estimated to have begun on the order of 10⁴ years ago. We consider that the present Japan Sea populations have been formed through the invasion of a small ancestral stock to the Sea of Japan and its population expansion during the last glacial period or later. On the other hand, we failed to detect distinct evidence of a population expansion in the EK population. Haplogroup C, detected in a high frequency in this population, was estimated to have mixed with haplogroup A after rapid differentiations of the latter. Therefore, the EK population, strongly influenced by such a mixture, might possess haplogroup C in a higher frequency and a different haplotype composition from the WJ population.     

Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north‐western Pacific: effect of past population expansion and contemporary gene flow

Aim Phylogeographical patterns of marine organisms in the north‐western Pacific are shaped by the interaction of past sea‐level fluctuations during glacial maxima and present‐day gene flow. This study examines whether observed population differentiation in the barnacle Chthamalus challengeri, which is endemic to the north‐western Pacific, can be explained by the interactions between historical glacial events and patterns of contemporary gene flow. Location Eleven locations in the north‐western Pacific. Methods Partial sequences of mitochondrial cytochrome c oxidase subunit I (COI), 12S, 16S and nuclear internal transcribed spacer 1 (ITS1) were obtained from 312 individuals. Parsimony haplotype networks and analysis of molecular variance (AMOVA) were used to determine whether the observed genetic structure corresponds to marine provinces (Kuroshio Current and China Sea Coastal Provinces), zoogeographical zones (oriental and Japan warm‐temperate zones) and/or potential refugial areas (Sea of Japan and East China Sea) in the north‐western Pacific. Neutrality tests, mismatch distribution analysis and Bayesian skyline plots were used to infer the demographic history of C. challengeri. Results In total, 312, 117, 182 and 250 sequences were obtained for COI, 12S, 16S and ITS1, respectively. A panmictic population was revealed, which did not conform to the ‘isolation by distance’ model. None of the a priori population groupings based on marine provinces, zoogeographical zones or potential refugial areas was associated with observed genetic patterns. Significant negative values from neutrality tests and the unimodal mismatch distribution and expansion patterns in Bayesian skyline plots for the COI and 16S data sets indicate a population expansion in the mid‐Pleistocene (c. 200 ka). Information from the fossil record suggests that there has been a northward range shift of this species from the East China Sea or the Palaeo‐Pacific coast of Japan to the Sea of Japan since the mid‐Pleistocene. Main conclusions Chthamalus challengeri has experienced a population expansion and range shift since the mid‐Pleistocene. The observed lack of population differentiation can be explained by this past population expansion and present‐day wide‐scale larval dispersal (owing to the long planktonic larval duration) across marine provinces, which have led to the successful establishment of the species in different zoogeographical zones and habitats.     

Taxonomic review of East Asian <Emphasis Type="Italic">Pleuronichthys</Emphasis> (Pleuronectiformes: Pleuronectidae), with description of a new species

A review of East Asian frog flounders, genus Pleuronichthys (family Pleuronectidae), recognized Pleuronichthys japonicus sp. nov. and P. cornutus (Temminck and Schlegel 1846). Pleuronichthys japonicus sp. nov. is characterized by small, dark, rounded spots or marbled markings on the ocular side of the body, rounded cycloid scales somewhat irregularly arranged, usually 12 abdominal vertebrae, 67–80 (modally 75) dorsal-fin rays, 48–59 (modally 55) anal-fin rays, and a short branch of the supratemporal lateral line usually present on both sides. Pleuronichthys cornutus is characterized by densely distributed small, dark, irregular spots on the ocular side of the body, elongate cycloid scales somewhat regularly arranged, usually 13 abdominal vertebrae, 72–88 (modally 77) dorsal-fin rays, 52–65 (modally 58) anal-fin rays, and a branch of the supratemporal lateral line usually absent on both sides. Whereas P. cornutus is distributed from Miyagi Prefecture (Tohoku District) southward along the Pacific coast of Japan to the Bungo Channel, from Akita Prefecture (Tohoku District) southward along the Sea of Japan coast through the Tsushima Strait to the East China Sea, Yellow and Bohai Seas, the Taiwan Strait, and northern Chinese coast of the South China Sea, P. japonicus is distributed from southern Hokkaido southward along the Sea of Japan and Pacific coasts of Japan to the southern East China Sea. Geographic variations were found in caudal vertebrae and anal-fin ray counts, and caudal-peduncle depth in P. cornutus, and in ocular side body coloration, body depth, and head length in P. japonicus. Pleuronichthys lighti Wu 1929 was regarded as a junior synonym of P. cornutus.     

Genetic Differentiation Inferred from Data on Restriction Analysis of Mitochondrial DNA in the Northern and Southern Forms of the Dolly Varden Char

Restriction fragment length polymorphism of the ATPase6/ND4L and cytochrome b regions of mitochondrial DNA (mtDNA) was studied in populations of the northern and southern forms of the Dolly Varden char Salvelinus malma from the Asian coast of the northern part of the Pacific Ocean. Seven genotypes of mtDNA were found, of which AAAA/ACCC and BBAC/ACEC characterize the northern and southern groups of populations, respectively. By the identity test, the studied populations of the Chukotka and Kamchatka peninsulas and the northern coast of the Sea of Okhotsk significantly differed from the studied populations of Sakhalin Island, Primorye, and Kuril Islands.     

Fine-scale population genetic structure in Alaskan Pacific halibut (<Emphasis Type="Italic">Hippoglossus stenolepis</Emphasis>)

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine microsatellite loci, significant heterogeneity was detected between Aleutian Island Pacific halibut and fish from the other two regions (F _ST range = 0.007–0.008). Significant F _ST values represent the first genetic evidence of divergent groups of halibut in the central and western Aleutian Archipelago. No significant genetic differences were found between Pacific halibut in the Gulf of Alaska and the Bering Sea leading to questions about factors contributing to separation of Aleutian halibut. Previous studies have reported Aleutian oceanographic conditions at deep inter-island passes leading to ecological discontinuity and unique community structure east and west of Aleutian passes. Aleutian Pacific halibut genetic structure may result from oceanographic transport mechanisms acting as partial barriers to gene flow with fish from other Alaskan waters.