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.     

Population subdivision of the brackish-water crab Deiratonotus cristatus on the Japanese coast

We investigated the genetic structure of populations of the brackish-water crab Deiratonotus cristatus (de Man, 1895) (family Camptandriidae) on the Japanese coast, together with morphological and the ecological variations. Genetic characteristics of the local populations based on mitochondrial DNA COI sequence data have revealed genetic differentiation between many populations, with the haplotype networks forming three geographical clades: a clade occurring on the Pacific coast, one occurring predominantly in northern Hokkaido, Kyushu and the Seto Inland Sea, and a third occurring in the Ryukyu Islands. Male pleopod morphology, carapace length relative to carapace width, and carapace width of adult crabs varied inconsistently among the geographic groups corresponding to the three clades. Life history traits were similar throughout, although differences in the breeding season were apparent between populations on the Pacific coast, and in the Seto Inland Sea and the Ryukyu Islands.     

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.     

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.     

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.     

海上丝路东海航线之濑户内海区域的景观振兴观察

濑户内海海域作为日本重要的商旅之路、近现代最大的新兴工业聚集地区以及海上丝路东海航线的延展,一直保有重要的文化意义和价值。国内现有研究分散于环境治理、工业布局、艺术活动等方面,但未能揭示该海域发展中社会、环境等因素的整体状况。为研究该海域的固有环境景观变迁问题,对日本社会各界与不同层面导入的濑户内海治理、振兴的研究及实践活动进行了综合考查。结合其历史信息与变迁过程,通过对相关法律法规及课题探讨的梳理,可发现,在统领于广义景观概念下的基础研究、创新研究、细节对策3个方面,对促进该区域的振兴工作有着显著的影响。同时其景观策略具有社会各界广泛参与的特征。     

Molecular Analysis of Ribosomal RNA Gene of Red Tide Algae Obtained from the Seto Inland Sea

Eleven clones from five species of the planktonic microalgae, (Chattonella antiqua, Chattonella marina, Heterosigma akashiwo, Alexandrium catenella, and Scrippsiella trochoidea), which were collected from the Seto Inland Sea in Japan and from Thailand, were subjected to nucleotide sequence analysis of the D1/D2 domain of the large subunit (LSU) of their ribosomal RNA genes. After amplification by polymerase chain reaction using degenerated primers, whole-nucleotide sequences for the D1/D2 domains of the LSU rRNA gene of 11 microalgae were analyzed. Phylogenic tree analysis using these nucleotide sequences showed each species located in a cluster corresponding to its morphological classification. The nucleotide sequence data for Chattonella spp. suggest that multiple clones of both Chattonella antiqua and Chattonella marina are present in the Seto Inland Sea and that red tide blooms of Chattonella spp. in different years may have contained different clones. Received September 6, 1999; accepted December 16, 1999.     

First report of the Asian seaweed <Emphasis Type="Italic">Sargassum filicinum</Emphasis> Harvey (Fucales) in California,USA

We report the occurrence of the brown seaweed Sargassum filicinum Harvey in southern California. Sargassum filicinum is native to Japan and Korea. It is monoecious, a trait that increases its chance of establishment. In October 2003, Sargassum filicinum was collected in Long Beach Harbor. In April 2006, we discovered three populations of this species on the leeward west end of Santa Catalina Island. Many of the individuals were large, reproductive and senescent; a few were small, young but precociously reproductive. We compared the sequences of the mitochondrial cox3 gene for 6 individuals from the 3 sites at Catalina with 3 samples from 3 sites in the Seto Inland Sea, Japan region. The 9 sequences (469 bp in length) were identical. Sargassum filicinum may have been introduced through shipping to Long Beach; it may have spread to Catalina via pleasure boats from the mainland.     

Production of Oikopleura dioica (Appendicularia) following a picoplankton 'bloom' in a eutrophic coastal area

The ecological importance of the appendicularian Oikupleuradioica as a picoplankton predator and a metazoan secondary producerwas assessed in summer 1995 in the Seto Inland Sea, Japan. Justafter the collapse of a red tide of Gymnodinium mikimotoi, theabundances of bacteria and picocyanobacteria increased rapidlyand attained values of     

Renewal of genetic composition of a lancelet, Branchiostoma belcheri, in the Seto Inland Sea, Japan

We studied renewal of genetic composition of a lancelet, Branchiostoma belcheri, at a station in the Seto Inland Sea, Japan, using random amplified polymorphic DNA (RAPD) technique. We detected a total of 49 DNA bands from 27 individuals of 5 seasonal samples. Among these, some were specific to individual or seasonal sample. There were no bands common to all individuals. We calculated the Band Sharing Index (BSI) values for each combination of individuals. BSI was in a wide range of 0.00-0.97 and the average BSI between the individuals of a sample was remarkably different from sample to sample (0.37-0.83). In cluster analysis on the basis of BSI, largely 3 clusters were constructed, which finally connected to a single cluster at as low as about 0.2 of BSI. Besides, many clusters were constructed exclusively by a seasonal sample. These results suggest a large gene pool of lancelets in this area, the remarkable differences in gene pool size among the samples and a seasonal renewal of genetic composition at a habitat.     

Natural hybridization between two Japanese medaka species (<Emphasis Type="Italic">Oryzias latipes</Emphasis> and <Emphasis Type="Italic">Oryzias sakaizumii</Emphasis>) observed in the Yura River basin,Kyoto, Japan

To determine the actual state of hybridization between two Japanese medaka species (Oryzias latipes and Oryzias sakaizumii) in their natural environment, we used nuclear DNA markers at 10 loci to analyze 215 individuals from eight wild populations in the middle reaches of the Yura River basin in Japan, where the two species are sympatric. Despite large genetic differentiation between the two species, reproductive isolation between them could not be confirmed. We also discussed the formation of the current distribution patterns of the two species and their hybridization zone in the Yura River basin.     

Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest

To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.     

Phylogeography of the bigeye chub Hybopsis amblops (Teleostei: Cypriniformes): early Pleistocene diversification and post‐glacial range expansion

The bigeye chub, Hybopsis amblops, is a member of the Central Highlands ichthyofauna of eastern North America. Phylogenetic analyses of the H. amblops species group based on a 1059 bp fragment of the mitochondrial DNA cytochrome b gene did not recover a monophyletic group. The inclusion of Hybopsis hypsinotus in the species complex is questionable. Within H. amblops, five strongly supported clades were identified; two clades containing haplotypes from the Ozark Highlands and three clades containing haplotypes from the Eastern Highlands and previously glaciated regions of the Ohio and Wabash River drainages. Estimates of the timing of divergence indicated that prior to the onset of glaciation, vicariant events separated populations east and west of the Mississippi River. East of the Mississippi River glacial cycles associated with the blocking and rerouting of the Teays River system caused populations to be pushed southward into refugia of the upper Ohio River. Following the most recent Wisconsinan glaciation, populations expanded northward into previously glaciated regions and southward into the Cumberland River drainage. In the Ozarks, west of the Mississippi River, isolation of clades appears to be maintained by the lack of stream capture events between the upper Arkansas and the White River systems and a barrier formed by the Arkansas River.     

Matrilinear phylogeography and demographical patterns of Rutilus rutilus: implications for taxonomy and conservation

A phylogeographic analysis of mitochondrial DNA sequence variation was carried out to infer the geographical distribution of the genealogical lineages and the historical demography of roach Rutilus rutilus (L.). A total of 265 individuals from 52 sites covering most of the Eurasian distribution range were sequenced for a 475 bp fragment of the mitochondrial cytochrome b gene. The monophyletic roach contained two deep clades that dated back to the Pliocene. The Ponto-Caspian clade comprised populations from Greece to Siberia with a likely palaeorefugium at the west coast of the Caspian Sea. This clade largely corresponds to individuals with morphological features described as Rutilus heckelii . The west European clade included individuals from central and western Europe with the Danube and Dniester basins as possible palaeorefugia. This clade largely corresponds to individuals with morphological features described as R. rutilus . A suture-zone of the two main lineages was observed along the coastal region of the Black Sea. The neutrality tests and the mismatch distributions indicated a demographic expansion during the Middle-Pleistocene for both clades.     

Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread 'mite harvestman' defies DNA taxonomy

Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi, Pettalidae), a widespread 'mite harvestman' endemic to the South Island of New Zealand, is found in leaf littler habitats throughout Nelson and Marlborough, and as far south as Arthur's Pass. We investigated the phylogeography and demographic history of A. denticulata in the first genetic population-level study within Opiliones. A total of 119 individuals from 17 localities were sequenced for 785 bp of the gene cytochrome c oxidase subunit I; 102 of these individuals were from the Aoraki subspecies A. denticulata denticulata and the remaining 17 were from the subspecies A. denticulata major. An extraordinarily high degree of genetic diversity was discovered in A. denticulata denticulata, with average uncorrected p-distances between populations as high as 19.2%. AMOVA, average numbers of pairwise differences, and pairwise F(ST) values demonstrated a significant amount of genetic diversity both within and between populations of this subspecies. Phylogenetic analysis of the data set revealed many well-supported groups within A. denticulata denticulata, generally corresponding to clusters of specimens from single populations with short internal branches, but separated by long branches from individuals from other populations. No haplotypes were shared between populations of the widespread small subspecies, A. denticulata denticulata. These results indicate a subspecies within which very little genetic exchange occurs between populations, a result consistent with the idea that Cyphophthalmi are poor dispersers. The highly structured populations and deep genetic divergences observed in A. denticulata denticulata may indicate the presence of cryptic species. However, we find a highly conserved morphology across sampling localities and large genetic divergences within populations from certain localities, equivalent to those typically found between populations from different localities. Past geological events may have contributed to the deep genetic divergences observed between sampling localities; additionally, the high divergence within populations of A. denticulata denticulata suggests that the rate of COI evolution may be accelerated in this taxon. In contrast, the larger subspecies A. denticulata major shows much less differentiation between and within sampling localities, suggesting that it may disperse more easily than its smaller counterpart. The fact that the remarkable genetic divergences within populations of A. denticulata denticulata from certain localities are equivalent to divergences between localities poses a challenge to the rapidly spreading practice of DNA taxonomy.     

Distribution of the Argentine ant, Linepithema humile, along the Seto Inland Sea, western Japan: Result of surveys in 2003–2005

The distribution of the Argentine ant, Linepithema humile, was investigated in 65 cities or towns along the Seto Inland Sea, western Japan in 2003–2005. Our results include all available information of their distribution in Japan until 2005. Argentine ants have invaded Aichi Prefecture (Tahara‐shi), Hyogo Prefecture (Kobe‐shi), Hiroshima Prefecture (Hiroshima‐shi, Fuchu‐cho, Hatsukaichi‐shi, Ono‐cho and Otake‐shi), and Yamaguchi Prefecture (Iwakuni‐shi and Yanai‐shi). The most widespread distribution was found around Hatsukaichi‐shi including the westernmost part of Hiroshima‐shi and the easternmost of Ono‐cho.     

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.     

Redescription and taxonomic status of Sinodiaptomus valkanovi , a common limnoplanktonic calanoid copepod in Japan, with comparison to the closely related S. sarsi

The limnoplanktonic calanoid copepod Sinodiaptomus valkanovi (Diaptomidae: Diaptominae) is redescribed in detail from Japan, where it commonly occurs in ponds and reservoirs especially around the Seto Inland Sea. The species has been referred to as a subspecies of S. sarsi outside Japan due to lack of subsequent morphological comparisons. Sinodiaptomus valkanovi is easily distinguishable from S. sarsi by having longer antennules in both sexes, a short projection on the right antennule segment 15 of the male, and a thumb-like posterodistal basal projection of the male left leg 5. These characters do not show significant variation, indicating differentiation at the species level. S. valkanovi is restricted to Japan, in contrast to the wide-range of it S. sarsi in Asian waters. The Bulgarian population, from which the species was originally described, and the North American population, which was formerly recorded as S. sarsi, are considered to have been introduced from Japan with aquatic plants such as water lilies.     

A new family of poecilostomatoid copepods (Umazuracolidae) based on specimens parasitic on the black scraper (Thamnaconus modestus) in Japan

Umazuracola elongatus n. gen., n. sp., is described based on specimens collected from the body surface of the black scraper, Thamnaconus modestus (Günther), taken from the Seto Inland Sea in western Japan. The new species belongs to a new family of the copepod order Poecilostomatoida. It is characterised by the reduction of the maxilliped and leg 1 in females and modification in both sexes of legs 2, 3, and 4 into robust attachment organs, with heavy, denticulate outer spines. Although the antenna, mandible, maxillule, and maxilla of U. elongatus resemble those of species of the "bomolochiform complex", a cladistic analysis revealed that phylogenetically this species is embedded in a different clade containing the polychaete-parasitizing families Entobiidae Ho, 1984 and Nereicolidae Claus, 1875.     

Surveillance of fish species composition using environmental DNA

Prompt and accurate methods for assessing the species composition of given areas are indispensable in addressing the rapid loss of biodiversity. Here, we propose a method for the surveillance of fish species composition in freshwater using environmental DNA as species markers. First, the applicability of the method was demonstrated through aquarium experiments. DNA was extracted from 120?ml aquarium water, and the degenerated primers targeting the fish mitochondrial cytochrome b gene were used for amplification. PCR-amplified fragments were analysed by random cloning, and all species reared in the aquarium were detected. Next, this method was applied to natural freshwater environments. Water samples were collected from three sites in the Yura River, Japan; DNA was concentrated from 2?l of environmental water, and then amplified and cloned. Up to four species of fish were detected by sequencing 47 randomly selected clones from a single water sample. Overall, the results were consistent with previous knowledge of fish habitat utilisation. Using this method, the surveillance of fish species composition can be conducted less laboriously than with traditional methods.