Occurrence of the endangered species Nitellopsis obtusa (Charales,Charophyceae) in western Japan and the genetic differences within and among Japanese populations

Nitellopsis obtusa (Charales, Charophyceae) are widely distributed from Europe to Asia; however, this species has been recorded in only the five lakes in central Honshu in Japan. This species was thought to be extinct in Japan, but was rediscovered in limited areas of Lake Kawaguchi in central Honshu. More recently, we discovered more Japanese populations of N. obtusa in Lake Biwa in western Honshu, and it became clear that the species had a broader distribution in Japan than originally believed. In addition, although only male or female thalli have been collected at each lake, both male and female thalli were found from Lake Biwa. This is the first report of a potentially sexual population of N. obtusa in Japan. The DNA sequences of three chloroplast DNA markers, including both coding and non‐coding regions, were identical in all specimens from Lake Kawaguchi and Lake Nojiri (Central Honshu), and differed from those of Lake Biwa and German specimens. Although Japanese and German specimens were genetically similar, Japanese specimens displayed considerable genetic diversity according to locality.     

On the occurrence of Cebus flavius (Schreber 1774) in the Caatinga, and the use of semi-arid environments by Cebus species in the Brazilian state of Rio Grande do Norte

Cebus flavius is a recently rediscovered species and a candidate for the 25 most endangered primate species list. It was hypothesized that the distribution of C. flavius was limited to the Atlantic Forest, while the occurrence of C. libidinosus in the Rio Grande do Norte (RN) Caatinga was inferred, given its occurrence in neighboring states. As a result of a survey in ten areas of the RN Caatinga, this paper reports on four Cebus populations, including the first occurrence of C. flavius in the Caatinga, and an expansion of the northwestern limits of distribution for the species. This C. flavius population may be a rare example of a process of geographic distribution retraction, and is probably the most endangered population of this species. New areas of occurrence of C. libidinosus are also described. Tool use sites were observed in association with reports of the presence of both capuchin species.     

<Emphasis Type="Italic">Puccinia calystegiae-soldanellae</Emphasis>, a new rust species on <Emphasis Type="Italic">Calystegia soldanella</Emphasis> from Japan

A rust species on Calystegia soldanella in Japan has been treated as Puccinia convolvuli to date. However, morphological characteristics of specimens on C. soldanella collected from Japan are significantly different from those of specimens on other Calystegia and Convolvulus species from different areas of the world. It is proved by inoculation experiment that the rust on C. soldanella is specific to C. soldanella. Based on these results, Puccinia rust on C. soldanella from Japan is described as a new species, Puccinia calystegiae-soldanellae.     

Genetic structure of endangered Rhodiola sachalinensis

Rh. sachalinensis is a perennial,medicinal herb. The species is rare with apatchy distribution. Due to heavy disturbanceby human activities, it is now endangered.Allozyme analysis was employed to estimate itsgenetic diversity. Nineteen loci encoding 12enzyme systems were used. Rh.sachalinensis has a lower genetic variationwithin patches and higher differentiationbetween patches than other endangered, endemicspecies with limited distributions. The geneticdifferentiation between patches withingeographic regions is lower than that amonggeographic regions. Genetic drift is likely adominant factor contributing to the observedpattern of genetic structure. Because a higherdegree of genetic differentiation existsbetween patches in Rh. sachalinensis,more populations should be protected insitu, and samples from more populations shouldbe collected for ex situ conservation.     

The genetic population structure of lacustrine sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka,</Emphasis> in Japan as the endangered species

Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.     

Middle Devonian lycophyte <Emphasis Type="Italic">Protolepidodendron scharianum</Emphasis>: History of study and description of the holotype

The authorship of Protolepidodendron and its type species P. scharianum is discussed in accordance with the International Code of Botanical Nomenclature. The age and locality of the holotype are traced. For the first time, the morphology of the holotype and other specimens kept at the National Museum in Prague is described in detail as well as new materials collected in the Barrandien localities (Czech Republic).     

Origins of recently re‐established and newly discovered populations of the endangered butterfly Shijimiaeoides divinus (Lepidoptera: Lycaenidae) in Oita Prefecture,Japan

The endangered butterfly Shijimiaeoides divinus was believed to have been extirpated from Oita Prefecture, Kyushu, Japan, but was rediscovered in Taketa in recent years. This population is considered to have re‐established as a result of natural dispersal from Kumamoto, a neighboring prefecture located to the west of Oita. Furthermore, another population was recently found in Yufu, Oita Prefecture, which is an area where the species had never been recorded. To elucidate the origins of these two populations newly found from Oita Prefecture, their DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were compared with those of other S. divinus populations from Kumamoto Prefecture, Honshu and Korea. The results supported the hypothesis that the Taketa population originated from Kumamoto Prefecture. However, it was not clear whether this population originated from the natural dispersal or deliberate release of individuals. It was also found that the Yufu population was not established by the deliberate release of individuals from Honshu or Korea; however, it remained unclear whether the population of S. divinus was native to Yufu, or originated from other localities in Kyushu.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.     

Inferring species relationships among Camellia chrysanthoides and its closely related species for developing conservation strategies

Accurate species classification is important for developing conservation strategies for endangered species. Camellia chrysanthoides and its closely related species are currently threatened. However, the taxonomy of these species is complex and contentious. A total of 87 individuals from nine populations of C. chrysanthoides and its close relatives were collected and analyzed using two nuclear genes (PAL and waxy) and a chloroplast DNA fragment. Molecular and morphological evidence demonstrates that C. chrysanthoides and C. micrantha share floral traits and nuclear and chloroplast haplotypes, suggesting that they should be treated as a single species. Our nuclear results indicated that C. parvipetala is genetically close to C. chrysanthoides and C. micrantha. A barrier to gene flow between C. chrysanthoides and C. micrantha populations and the high number of private nuclear haplotypes in C. parvipetala suggest that C. chrysanthoides, C. micrantha and C. parvipetala should be recognized as three independent conservation units.     

Genetic diversity of the endangered coastal violet <Emphasis Type="Italic">Viola grayi</Emphasis> Franchet et Savatier (Violaceae) and its genetic relationship to the species in subsection <Emphasis Type="Italic">Rostratae</Emphasis>

Viola grayi, a coastal violet, is found on sandy seashores in limited regions in Japan, but not on rocky sea cliffs or in inland areas. This stemmed violet is classified in the subsection Rostratae. Because of recent human activity on sandy seashores, this species is now recorded as endangered. The present status of this species was surveyed and its genetic diversity was analyzed using 17 newly developed simple sequence repeat markers. The results are compared with those for two commonly found inland violet species in the same subsection, V. grypoceras and V. kusanoana. The coastal violet populations showed markedly lower genetic diversity than those of the common species, V. grypoceras, whereas V. kusanoana showed intermediate genetic diversity. About a half of the total genetic variation of V. grayi is found among populations in analysis of molecular variance. In contrast, only less than 25% of the total variation is found among populations for the two common violets. These three species showed a remarkably high inbreeding coefficient, which indicates high inbreeding under natural mating conditions, although these species have both chasmogamous and cleistogamous flowers. In a population-based dendrogram, V. grayi was clustered in a single and concise group, whereas V. grypoceras and V. kusanoana were found in somewhat discrete positions. In the Bayesian analysis of genetic structure of the coastal violet, delta K was the highest at K = 7, and the seven clusters almost correspond to seven populations studied here. Implications of the conservation of this endangered coastal violet are presented.     

New records of the rare deep-sea anglerfish Diceratias trilobus Balushkin and Fedorov (Lophiiformes: Ceratioidei: Diceratiidae) from the Western Pacific and Eastern Indian Oceans

Diceratias trilobus Balushkin and Fedorov, 1986, was described from a single female specimen, 122 mm standard length, collected from off the east of Honshu, Japan, in 1975. Since that time the holotype has remained the only known representative of the species. Recently, however, a number of additional specimens have become available. This new material is described below and compared with the holotype.     

Potential impacts on Japanese fauna of canestriniid mites (Acari: Astigmata) accidentally introduced with pet lucanid beetles from Southeast Asia

To develop a risk-assessment system for small organisms accidentally introduced with imported organisms, we investigated as a first case study parasitic canestriniid mites, which have been imported into Japan via pet lucanid beetles from Southeast Asia. We collected mites from pinned specimens of Japanese lucanids collected before 1999—when the Japanese government lifted a ban on the import of the beetles—and living mites from imported and native lucanid beetles collected after that. No foreign canestriniid was found on any of the native Japanese beetles. Because the mites collected from imported beetles were different from Japanese species, we conclude that the foreign mites have not yet established wild populations in Japan. However, because the Japanese mites migrate between hosts without host physical contact, introduced mites are assumed to be able to migrate from a foreign to Japanese host. In fact, possible contamination was observed in pet shops. We observed host switching in only one direction: Southeast Asian Canestrinia nr spectanda switched to Japanese Dorcus rectus, but Japanese Coleopterophagus berlesei never switched to Indonesian D. titanus. The foreign mites reproduced between 15°C and 25°C, suggesting that the mites could survive in mountainous sites in southern Japan and at low elevations in northern Japan. The ability of foreign parasitic canestriniids to infect and survive on Japanese hosts at temperatures characteristic of much of Japan leads us to conclude that these mites present a potential risk to Japanese endemic canestriniids as well as to native Japanese lucanids.     

Evidence of the existence of a toxic form of Cylindrospermopsis raciborskii (Nostocales,Cyanobacteria) in Japan

Cylindrospermopsis raciborskii is a common, bloom‐forming, planktonic, freshwater cyanobacterium. Toxic populations producing cylindrospermopsin can cause water‐safety problems. Although C. raciborskii is distributed worldwide, the presence of cylindrospermopsin‐producing strains of C. raciborskii was initially reported only in Australia and recently in Thailand. Here, we report the isolation of a toxic strain of C. raciborskii (ISG9) from a freshwater sample collected in Okinawa in 2008. This is the first report describing toxin expression in this species in Japan, detected from a subtropical area. The C. raciborskii species is known to produce cylindrospermopsin as a dominant toxin; however, in this new isolate, the dominant toxin expressed was deoxy‐cylindrospermopsin. The discovery of a toxic strain of C. raciborskii in southern Japan emphasizes the need for basic monitoring schemes for this species in water supplies located in the temperate regions of Japan because of its possible expansion and distribution to other geographic areas.     

A first record of anchialine crab of the genus Orcovita Ng and Tomascik, 1994 (Decapoda: Brachyura: Varunidae) from Japan, with description of the species

Orcovita miruku, new species, is described from Ishigaki Island, southern Ryukyu Islands, Japan. Orcovita miruku is easily distinguished from the other congeners by the presence of three teeth (including external orbital angle) on the anterolateral margin of the carapace. Orcovita angulata may be allied to O. miruku, but there are a number of differences in the characters of the carapace and the ambulatory legs. The holotype, obtained from an anchiline pool in a limestone excavation, is the only specimen collected thus far, and this is the first record of an anchiline crab from Japan.     

Management units of the endangered herb Primula sieboldii based on microsatellite variation among and within populations throughout Japan

To promote programs for the conservation and restoration of the endangered species Primula sieboldii, we examined genetic variation at eight microsatellite loci among and within 32 remnant wild populations throughout Japan. Total allelic diversity within a population was higher in larger populations, but not so after rarefaction adjustment. The positive relationship between population size and the inbreeding coefficient may suggest that more heterozygous genets tend to survive the habitat contraction possibly because of the higher fitness associated with heterozygosity. By principal coordinate analysis and Bayesian analysis, we detected four genetic groups (Hokkaido, northern Honshu, central Honshu, and western Japan), which could be recognized as management units of P. sieboldii. If supplementation with plants from other populations were planned, it should be conducted among populations which belong to the same management unit and which are likely to represent the same adaptive variation.     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

The coralline genera Sporolithon and Heydrichia (Sporolithales,Rhodophyta) clarified by sequencing type material of their generitypes and other species

Interspecific systematics in the red algal order Sporolithales remains problematic. To re‐evaluate its species, DNA analyses were performed on historical type material and recently collected specimens assigned to the two genera Sporolithon and Heydrichia. Partial rbcL sequences from the lectotype specimens of Sporolithon ptychoides (the generitype species) and Sporolithon molle, both from El Tor, Egypt, are exact matches to field‐collected topotype specimens. Sporolithon crassum and Sporolithon erythraeum also have the same type locality; material of the former appears to no longer exist, and we were unable to PCR amplify DNA from the latter. A new species, Sporolithon eltorensis, is described from the same type locality. We have not found any morpho‐anatomical characters that distinguish these three species. No sequenced specimens reported as S. ptychoides from other parts of the world represent this species, and likely reports of S. ptychoides and S. molle based on morpho‐anatomy are incorrect. A partial rbcL sequence from the holotype of Sporolithon dimotum indicates it is not a synonym of S. ptychoides, and data from the holotype of S. episporum confirm its specific recognition. DNA sequences from topotype material of Heydrichia woelkerlingii, the generitype species, and isotype material of Heydrichia cerasina confirm that these are distinct species; the taxon reported to be H. woelkerlingii from New Zealand is likely an undescribed species. Type specimens of all other Sporolithon and Heydrichia species need to be sequenced to confirm that they are distinct species; morpho‐anatomical studies have proved inadequate for this task.     

Allozyme Variation among Populations of Rana pirica (Amphibia: Anura)

Genetic variation of Rana pirica , an east Asian brown frog of the R. temporaria group, was elucidated by analysing 140 specimens from 11 populations from Hokkaido and Sakhalin, both locating near the eastern coasts of the Asian continent, and 12 specimens of R. ornativentris from Honshu, Japan mainland, as an outgroup, through horizontal starch gel electrophoresis. Rana pirica shows relatively low genetic differentiation, and high genetic affinities are found between Hokkaido and Sakhalin populations. Populations from these islands are morphologically somewhat differentiated but should be regarded as conspecific. Degree of genetic divergence among populations of amphibian species from Hokkaido, including R. pirica , is not so extensive as that reported for species from Japan mainland and relatively recent formation of amphibian fauna in Hokkaido is suggested.