Are the meiofaunal polychaetes Hesionides arenaria and Stygocapitella subterranea true cosmopolitan species? — results of RAPD‐PCR investigations

The interstitial meiofauna of sand beaches includes many species that are regarded as cosmopolites, on the basis of records from various sites throughout the world. There is a long-standing debate about the causes of such a distribution, but for most of these species it is still questionable whether they are in fact true species or 'merely' complexes of cryptic species. Here genetic differentiation is examined within and between two species considered typically cosmopolitan, Hesionides arenaria arenaria (Hesionidae) and Stygocapitella subterranea (Parergodrilidae), by RAPD-PCR analyses of specimens from diverse marine regions on two continents. For S. subterranea at three sites, on the North Sea coast (Sylt) and the US Atlantic (Massachusetts) and Pacific (Washington) coasts, with 14 primers 335 different DNA fragments were found: 20 diagnostic ones for the European animals, 17 for the animals from the American East Coast and 14 for those from the American West Coast. Five cluster procedures were used, all of which significantly distinguished the three populations as separate genetic clades; it is recommended that each be given species status. In contrast, the individual specimens of H. a. arenaria from eight European sites, between Skagerrak and the eastern Mediterranean (including the Canary Islands), and the North American Pacific coast, for which 468 different DNA fragments were amplified with 12 primers, do not form separate genetic clades. For no single population was it possible to demonstrate even one diagnostic character. Therefore the cosmopolitan nature of H. a. arenaria has been confirmed at the DNA level.     

Geographical distributions of mitochondrial DNA lineages reflect ancient directions of river flow: a case study of the Japanese freshwater shrimp Neocaridina denticulata denticulata (Decapoda: Atyidae)

The mitochondrial DNA phylogeographical structure of the freshwater atyid shrimp Neocaridina denticulata denticulata was investigated near the Yura and Kako Rivers in western Japan. To assess the biological significance of drainage evolution, fragments of 390 base pairs (bp) extending from the NADH dehydrogenase subunit 2 gene to the tryptophan transfer RNA gene were sequenced for 246 specimens from twenty locations. The phylogenetic tree detected two distinct clades corresponding to the region along the Sea of Japan and Seto Inland Sea, respectively. Geographical mapping of the two clades well reflected the river capture, in which the upper reaches of the Yura River draining into the Sea of Japan had been captured from the Kako River into the Seto Inland Sea. The clear pattern of mitochondrial DNA distribution may be accounted for by the ecological characteristics of species that minimize passive downstream drift, local adaptation, and mountain topography.     

Analysis of population clonal diversity using microsatellite markers in the salt marsh sedge Carex scabrifolia in western Japan

Carex scabrifolia, a perennial herb that commonly grows on sandbars in lagoons and tidal estuaries, is threatened by habitat reduction in some areas of Japan. Clonal diversity and the extent of gene flow among ten populations located along the Seto Inland Sea and the Japan Sea in western Japan were examined using six microsatellite loci. From 299 samples, we detected 77 multilocus genotypes. The mean number of alleles per population was 2.8 and the mean clonal diversity was 0.23. Many populations consisted of small patches, and the mean number of genets per patch was 2.0. The average number of alleles per locus and clonal diversity were positively correlated with the number of patches within a watershed. Gene flow was detected between the Ichikawa River and the Ohta River populations along the Seto Inland Sea, and weak differentiation among populations located along the Seto Inland Sea was observed. Our results suggest that effective conservation of C. scabrifolia populations should include maintaining all patches within a watershed regardless of population size, thus promoting genotype preservation.     

Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites

To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides , 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F _ST, global amova , and genetic admixture analysis identified three clusters — the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations — indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals ( P _SAxy) analyses between the Sea of Japan and the other samples, P _SAxy was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P _SAxy data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P _SAxy data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P _SAxy were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.     

The endemic plant families and the palms of New Caledonia: a biogeographical analysis

This paper provides a panbiogeographical analysis of the endemic plant families and the palms of New Caledonia. There are three endemic plant families in New Caledonia and several genera that were previously recognized as endemic families. Of these taxa, some are sister to widespread Northern Hemisphere or global groups (Canacomyrica, Austrotaxus, Amborella). The others belong to trans‐Indian Ocean groups (Strasburgeria), trans‐tropical Pacific groups (Oncotheca) or Tasman Sea/Coral Sea groups (Phelline, Paracryphia) that are sister to widespread Northern Hemisphere or global groups. In palms, the four clades show allopatric regional connections in, respectively: (1) western Indonesia, Malaysia and Thailand; (2) Vanuatu/Fiji and the southern Ryukyu Islands near Taiwan; (3) the western Tasman/Coral Sea (eastern Australia, New Guinea and the Solomon Islands); and (4) the eastern Tasman/Coral Sea (Lord Howe and Norfolk Islands, New Zealand, Vanuatu, Fiji and the Solomon Islands). The four clades thus belong to different centres of endemism that overlap in New Caledonia. The patterns are attributed not to chance dispersal and adaptive radiation but to the different histories of the eight terranes that fused to produce modern New Caledonia. Trans‐tropical Pacific connections can be related to the Cretaceous igneous plateaus that formed in the central Pacific and were carried, with plate movement, west to the Solomon Islands and New Zealand, and east to Colombia and the Caribbean.     

Reproductive seasonality of the seaweed pipefish Syngnathus schlegeli (Syngnathidae) in the Seto Inland Sea, Japan

Latitudinal variations in fitness-related traits have been reported in a variety of organisms. Intraspecific comparison of such traits among populations living under different environmental conditions is an effective approach for elucidating the cause and consequences of such latitudinal variations. In the present study, population demography, seasonal changes in somatic and reproductive conditions, and the occurrence of egg-brooding males were investigated in the seaweed pipefish, Syngnathus schlegeli, collected monthly in the Seto Inland Sea, Japan, in order to estimate the reproductive season and mating pattern. The findings were then compared with those reported for a population in Otsuchi Bay, northern Japan. We found that the reproductive season is longer in the Seto Inland Sea population (March–November) than in the Otsuchi Bay population (May–October), although reproductive activity may temporarily cease during August in the Seto Inland Sea population. Males of the Seto Inland Sea population brooded eggs that were at the same developmental stage, suggesting that males mate with only one female in a single brooding episode (i.e., monogamy)—in contrast to the Otsuchi Bay population, where a portion of males brooded eggs consisting of multiple clutches at different developmental stages, suggesting that multiple females contribute to a single brood (i.e., polygamy). Additionally, we found that the standard lengths of both males and females are approximately 30?mm smaller in the Seto Inland Sea than in the Otsuchi Bay population. These results suggest that the multiple mating by males in a single brood and the larger body size in the Otsuchi Bay population are results of fecundity selection on life history and behavioral traits to adapt to the shorter reproductive season and lower reproductive efficiency in this relatively cold environment.     

The Melithaeidae (Cnidaria: Octocorallia) of the Ryukyu Archipelago: molecular and morphological examinations

The family Melithaeidae (Octocorallia: Alcyonacea) is distributed in the West Pacific, Indian Ocean and the Red Sea. They are most abundant in warmer waters but can also be found in temperate waters. At present six genera are assigned to this family (Melithaea, Mopsella, Clathraria, Acabaria, Wrightella and Asperaxis), however overlapping characteristics make this group's taxonomic identification difficult and their relationships unclear. There are only a few reports from the Ryukyu Archipelago in southern Japan of melithaeids and most other octocorals, despite the islands being an area of high octocoral diversity. To help resolve the taxonomic confusion in this family, samples from various Ryukyu Archipelago locations were collected and DNA sequences of nuclear 28S ribosomal DNA and mitochondrial cytochrome oxidase I (COI) were obtained. Additionally, SEM micrographs of the sclerites of specimens were taken to further confirm the molecular results. Three strongly supported clades were recovered from the COI and 28S rDNA analyses, corresponding to Melithaea, Acabaria, and Mopsella, and in most cases clades were clearly related with the sclerite shape reported for each genus. These results show clearly that molecular differences are present between the three genera, and also demonstrates the strong need of other molecular markers for resolving intra-generic phylogenies. Our results provide baseline data for future studies of this octocoral family, not only on taxonomy, but also with regards to their distribution in the Ryukyu Islands.     

Restricted gene flow and incipient speciation in disjunct Pacific Ocean and Sea of Cortez populations of a reef fish species, Girella nigricans

Abstract.— Population disjunctions have been proposed to play an important role in speciation processes. In this study, we have examined the possible role of the Pacific Ocean-Sea of Cortez disjunction as a contributing factor to cryptic speciation in a reef fish, the opaleye, Girella nigricans . Mitochondrial control region (D-loop) sequences (380 bp) of 117 individuals completely separated opaleye populations from the Pacific Ocean and the Sea of Cortez. Although opaleye exhibit pelagic larval stages that remain in the water column for several months, gene flow between the Pacific Ocean and the Sea of Cortez was found to be extremely limited ( F_ST = 0.84, Nm = 0.10). Whereas limited gene flow and reciprocal monophyly suggest that the observed physical and genetic disjunction are potentially contributing to the incipient speciation of Pacific and Sea of Cortez opaleye, moderate levels of D-loop sequence divergence (3.3%) and the absence of fixed allozyme markers challenge this idea. Pacific Coast populations also exhibited restricted gene flow levels ( F_ST = 0.25, Nm = 1.49) across Punta Eugenia, a recognized oceanographic boundary along the Baja California coast. Thus, opaleye individuals grouped into three clades: one clade in the Sea of Cortez, one Pacific clade south of Punta Eugenia, and one Pacific clade north of Punta Eugenia. Future work in this region will determine if our results can be generalized to other disjunct populations.     

A new species of Enterognathus (Copepoda, Cyclopoida, Enterognathidae) collected from the Seto Inland Sea, western Japan

A new species of the endoparasitic copepod Enterognathus (Cyclopoida, Enterognathidae) is described from a crinoid host in the Seto Inland Sea, western Japan. This is a third species of the genus and its first occurrence in the Pacific Ocean. The new species is distinguished from two previously known congeners by the morphology of the body somites, caudal rami, antennae and legs. Crinoid parasites belonging to Enterognathus and the closely related genus Parenterognathus have a broad distribution from the northeastern Atlantic through the Red Sea to the West Pacific.     

Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago

The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis on genome-wide single-nucleotide polymorphisms, genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 single-nucleotide polymorphisms to infer population history within the Miyako Islands, including Miyakojima, Irabu, and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 − 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about seven generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.     

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.     

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.     

A new species of the genus Arhynchite (Annelida,Echiura) from sandy flats of Japan,previously referred?to as Thalassema owstoni Ikeda, 1904

A new echiuran, Arhynchite hayaoi sp. n., is described from newly collected specimens from sandy flats of the Seto Inland Sea, Japan, together with many museum specimens, including those once identified as Thalassema owstoni Ikeda, 1904 or Arhynchite arhynchite (Ikeda, 1924). The new species is clearly distinguishable from its congeners by the smooth margin of gonostomal lips and lack of rectal caecum. Brief references are also made to the morphological distinction between the new species and Thalassema owstoni, originally described from the deep bottom on the Japanese Pacific coast.     

Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus)

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.     

Ancient drainage networks mediated a large‐scale genetic introgression in the East Asian freshwater snails

Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here, we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that the mtDNA haplotypes originated in the Lake Biwa endemic Semisulcospira species at the upstream side of the paleodrainage were frequently observed in the riverine Semisulcospira species at its downstream side. The genome‐wide DNA and morphological analyses consistently showed that there was no clear evidence of nuclear introgression between the Lake Biwa endemics and riverine species. These results suggest that the large paleodrainage had facilitated mitochondrial introgression and had broadly spread the introgressed mtDNA haplotypes to its downstream region around the Seto Inland Sea. Our study highlights the role of paleodrainages in shaping the genetic variation of freshwater organisms.     

Cryptic diversification of the swamp eel Monopterus albus in East and Southeast Asia, with special reference to the Ryukyuan populations

The swamp eel Monopterus albus is widely distributed in tropical and subtropical freshwaters ranging from Southeast Asia to East Asia, and is unique in its ability to breathe air through the buccal mucosa. To examine the genetic structure of this widespread species, molecular phylogenetic analyses of mitochondrial 16S rRNA sequence (514 bp) were conducted for 84 specimens from 13 localities in Southeast and East Asia. The analyses showed clearly that this species can be genetically delineated into three clades based on geographical populations [China–Japan (Honshu + Kyushu), Ryukyu Islands, and Southeast Asia clades], with each clade exhibiting its own reproductive behavior. Therefore, “M. albus” is believed to be composed of at least three species. The Southeast Asia clade with the highest genetic diversity may include more species. The Ryukyu clade was estimated to have diverged more than 5.7 million years ago, suggesting that the Ryukyuan “M. albus” is native. In contrast, in the China–Japan clade, all haplotypes from Japan were closely related to those from China, suggesting artificial introduction(s).     

Streaked horned lark <Emphasis Type="Italic">Eremophila alpestris strigata</Emphasis> has distinct mitochondrial DNA

The Streaked Horned Lark (STHL; Eremophila alpestris strigata) is a federal candidate for listing under the Endangered Species Act. We evaluated the conservation status and level of genetic diversity of the STHL using the complete mitochondrial ND2 gene. We sampled 32 STHLs from the southern Puget Sound region, the Pacific coast, and Whites Island in the Columbia River of Washington, and additional 68 horned larks from Alaska, alpine and eastern Washington, Oregon, California, and Asia (outgroups). Our Maximum Likelihood analysis of 32 haplotypes identified three geographically concordant clades in Pacific coast states: Pacific Northwest (alpine and eastern Washington, Alaska), Pacific Coast (western Washington, California), and Great Basin (eastern Oregon). Each of the three clades was supported by bootstrap values ≥86%. The distance among them varied from 0.72 to 0.79% nucleotide divergence excluding intraclade variation. The relationship among the clades was not resolved. AMOVA also showed significant structuring of haplotypes among the three clades. Differences among clades accounted for 75.7% of sequence variation, differences among localities within clades accounted for 12.1%, and differences among individuals within localities accounted for the remaining 12.2%. Although STHL populations were closely related to the Californian sample, they appeared unique and isolated. All pairwise F _st values involving the STHL samples were significant (except between themselves). STHLs appear to have remarkably low genetic diversity; all 32 STHLs shared the same haplotype. Even with small sample sizes, all other localities had multiple haplotypes. Because the STHL appears to be unique and isolated, and to have little genetic diversity our data suggest it should be a conservation priority.     

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.     

Gonad development of the sea anemone Anthopleura asiatica in clonal populations

Seasonal fluctuations in relative gonad volume and oocyte size of the sea anemone Anthopleura asiatica were examined in 3 unisexual (male) populations and one bisexual population in the Seto Inland Sea of Japan from December 1982 to December 1985. A distinct annual cycle of gonadal maturation with a peak in the summer was found in all of the populations, although they appeared to be sustained only by asexual reproduction. Spawning occured synchronously between the 2 sexes early in the fall in the bisexual population while it was one to one and a half months later in the unisexual populations.     

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.