Distribution of ribonucleic acid coliphages in south and east Asia.

We investigated the distribution of ribonucleic acid (RNA) coliphages in the Philippines, Singapore, Indonesia, India, and Thailand by collecting sewage samples from domestic drainage in November 1976. Of the 221 samples collected from domestic drainage, 50 contained RNA phages (52 strains). By serological analysis, 46 of the 52 strains were found to belong to group III. It can thus be said that the most prevalent RNA phages in Southeast Asia (at least, in the Philippines, Singapore, and Indonesia) were group III phages. Investigations of sewage samples collected from domestic drainage in Japan indicate that the most prevalent RNA phages in mainland Japan (north of Kyushu) are group II phages, whereas group III phages are predominant in the southern part of Japan (south of Amamiohshima Island). We therefore propose a borderline between Kyushu and Amamiohshima Island for the geographical distribution of RNA coliphages in the domestic drainage of South and East Asia. Moreover, one strain (ID2) was inactivated to some extent with the antisera of four groups of RNA phages. This is thought to be significant from the evolutionary viewpoint.     

Distribution of ribonucleic acid coliphages in raw sewage from treatment plants in Japan.

To determine the transmission cycle of ribonucleic acid (RNA) coliphages in their natural habitats, we investigated the distribution patterns of RNA phages in raw sewage collected from treatment plants in various localities in Japan. Most of the sewage samples contained group II and III phages. Samples from treatment plants in Sapporo, Tokyo, and Toyama contained appreciable amounts of group I phages in addition to the group II and III phages. As a whole, raw sewage from treatment plants in Japan contained RNA phages of the three groups in the ratio 1:2:5, group I/II/III. Based on the distribution patterns of RNA phages in sewage from domestic drainage in Japan proper (group II/III, 3:1), in animal feces and sewage from slaughter houses (mostly group I), and in human feces (group II/III, 1:1), it can be reasonably said that group I phages tend to be introduced from animal sources and group II and III phages tend to be introduced from human sources. Raw sewage from treatment plants in Japan consists mainly of human feces, sewage from domestic drainage, and industrial wastewater, and, in part, from slaughter houses. In fact, sewage from slaughter houses together with that from human sources flowed into the treatment plants of Tokyo as far as we could confirm.     

Two Genetically Distinct Lineages of the Sika Deer, Cervus nippon, in Japanese Islands: Comparison of Mitochondrial D-Loop Region Sequences

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705–824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.     

Distribution of RNA coliphages in Senegal, Ghana, and Madagascar

The distribution patterns of RNA coliphages (phages) in Senegal, Ghana, and Madagascar were investigated by collecting sewage samples from domestic drainage in November, 1980. In Senegal, among 65 sewage samples collected mainly from Dakar and its vicinity, 14 (22%) contained RNA phages (16 strains). By serological analysis, 13 of 16 strains were found to belong to group III. This is consistent with the distribution pattern of RNA coliphages in tropical and subtropical regions of Asia. In Ghana, however, among 106 samples collected from Accra, Suhum, and their vicinities, only seven (7%) contained RNA phages (seven strains) (groups I, II, and III [1:3:3]). In Madagascar, among 124 samples collected from Antananarivo, Moramanga, and their vicinities, seven (6%) contained RNA phages (seven strains) (groups I, II, III, and IV [1:1:1:4]). In spite of the low isolation frequency, it can be said that Madagascar appears to have a unique distribution pattern (abundance of group IV phages) which differs from that of any other countries we have examined. The generality of the distribution pattern of RNA phages in the tropical region (abundance of group III phages) was thus verified at least in Senegal.     

A new timeframe for the diversification of Japan’s mammals

Aim The main Japanese islands are land‐bridge islands divided by the biogeographic division Blakiston’s Line and represent two natural laboratories for studying land‐bridge diversification. Colonization of the current mammal fauna has been dated to the middle to late Pleistocene using fossil evidence. The purpose of this paper is to apply a molecular clock to the genetic divergences between Japanese mammalian taxa and their sister mainland taxa to test the late Pleistocene land‐bridge colonization hypothesis. Location The main Japanese islands (Kyushu, Shikoku, Honshu and Hokkaido). Methods I used mitochondrial DNA (cytochrome b) and a species tree approach to estimate the divergence times of 24 Japanese non‐volant terrestrial mammal taxa and their mainland sister taxa using the program *beast . I then tested for evidence of non‐simultaneous divergence among these taxon‐pairs by controlling for expected coalescent stochasticity using the program Ms Bayes . Results Divergence events between taxa on Japan and their mainland sister taxa were significantly older than expected under the current paradigm, which is based on fossil data. Consistent with the land‐bridge colonization hypothesis, there was evidence of multiple divergence events. Main conclusions These results implicate a colonization timeframe that is older than posited by the current paradigm based on fossil evidence. However, these results are still consistent with the land‐bridge colonization hypothesis. Multiple periods of land‐bridge connectivity may account for the current mammalian fauna in Japan. In addition, half of the divergence time estimates in the Honshu–Shikoku–Kyushu region were clumped around 2.4 Ma, which might suggest a dramatic interchange period, concordant with a period of significant global cooling, when the first land bridge may have connected Japan to the mainland.     

Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: comparison of mitochondrial D-loop region sequences

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.     

Variation in flash speed of Japanese firefly,Luciola cruciata (Coleoptera: Lampyridae), identifies distinct southern “quick‐flash” population on Goto Islands,Japan

Luciola cruciata, a bioluminescent firefly endemic to Japan, communicates with species‐specific flashing patterns. Previous studies reported that flying males possess three distinct flashing frequencies: slow (4 s), intermediate (3 s) and fast (2 s). Our study focused on geographical variations in flashing patterns in the northwestern part of the Kyushu region of southern Japan (including its isolated islands) and their relationship to the mitochondrial COII region of firefly DNA. We found that “quick‐flash (1 s)” fireflies occur in the Goto Islands, at the western tip of Kyushu, and that, although they possess a unique haplotype, they do not differ much genetically from “fast‐flash” fireflies inhabiting mainland Kyushu. In contrast, although fireflies inhabiting the Tsushima and Iki Islands also possess a unique haplotype, their flashing patterns were the same (fast‐flash) as fireflies inhabiting mainland Kyushu. We determined that flash patterns of L. cruciata in Japan should be classified according to four flashing patterns: slow, intermediate, fast and quick.     

Faunal associations of the Rhopalocera of japan

The associations of the butterfly fauna of the Japanese islands of Hokkaido, Honshu, Kyushu, Shikoku and Ryukyu Rett are analysed with respect to one another and to the fauna of the far-east U.S.S.R. A faunal discontinuity exists between the fauna of Ryukyu Rett and all other areas. The fauna of Ryukyu Rett can be considered as being of the Oriental region, the faunas of the other Japanese islands as being of the Palaearctic region. This view was reinforced with conclusions drawn from MacArthus&Wilson's theory of island biogeography (1963, 1967). The divergence of die faunas of the Japanese islands is dependent on their isolation - the further the distance between islands, the greater the isolation and the greater the faunal divergence. Thus the fauna of all silands of Japan, except of the Ryukyu Rett, have a close association with the far-east Russian fauna. There is a greater similarity between these faunas than between the fauna of the islands of Hokkaido, Honshu, Kyushu and Shikoku with respect to that of Ryukyu Rett.     

Occurrence of two types of Hynobius naevius in Northern Kyushu, Japan (Amphibia: Urodela)

A survey to examine genetic variation among Hynobius naevius from four localities of Fukuoka Pref., northern Kyushu, Japan, resulted in the detection of two, sympatric, genetic types (A and B) that are clearly different in the allelic frequencies of four loci (ACOH-A, ACOH-B, ADH-A, and SOD-A) in each locality. Morphological investigations between the two genetic types also proved that they are clearly discriminated; the type A is about 75 mm in SVL, lacks mottling pattern on bluish purple dorsum, and possesses relatively short vomerine teeth series, while the type B is about 60 mm in SVL, and has light mottling on reddish purple ground color. These results strongly suggest that reproductive isolation occurs between these two types, and that they could be regarded as separate species. Populations from Toyota-cho, western Honshu, and Yabe-machi, central Kyushu, both close to Fukuoka Pref., were very similar to the types A and B, respectively. From these results, we consider that two evolutionary lineages that first evolved allopatrically in western Honshu and southern Kyushu secondarily contacted and became sympatric in the region of northern Kyushu.     

Mitochondrial DNA variation among worldwide populations of gypsy moths, Lymantria dispar

Gypsy moth populations from Japan, mainland Asia, Europe, Tunisia, and North America were analyzed for variation in mitochondrial DNA (mtDNA) sequences from three gene regions. These samples resolve into four groups, representing gypsy moths from (1) Okinawa, Japan, (2) Hokkaido, Japan, (3) Honshu and Kyushu, Japan and mainland Asia, and (4) Europe, Tunisia, and North America. Some patterns of geographic variation observed for mtDNA (for example, the distinctiveness of gypsy moths from Hokkaido, Japan) coincide with those observed by Goldschmidt from analyses of morphology, life history, and intersexuality. Other patterns (relative sequence homogeneity across Asia, Honshu, and Kyushu and reduced levels of variation in mainland Japan) do not.     

Fragmented environment affects birch leaf endophytes

The effect of environmental fragmentation on the species distribution and frequency of horizontally transmitted endophytic fungi in Betula pubescens and Betula pendula leaves was studied in an archipelago in southwestern Finland. The study system consisted of 14 islands, ranging in size and distance to the mainland, and five mainland sites. Endophytic fungi were grown out from surface-sterilized leaves. The frequency of endophytic fungi mainly depended on the size of the island, explaining 32-35% of the variation, and the distance to the mainland explaining 29-35% of the variation. The birch trees on the largest islands near the mainland had the highest endophyte frequencies. Fusicladium betulae, Gnomonia setacea and Melanconium betulinum were the most commonly isolated fungi. Foliar endophytes of birch trees are able to disperse to fairly fragmented areas, but their frequencies seem to depend on environmental isolation and size of the island.     

Terrestrial bird community patterns on the coralline islands of the Dahlak Archipelago, Red Sea, Eritrea

Aim This study aims to explain the patterns of species richness and nestedness of a terrestrial bird community in a poorly studied region. Location Twenty‐six islands in the Dahlak Archipelago, Southern Red Sea, Eritrea. Methods The islands and five mainland areas were censused in summer 1999 and winter 2001. To study the importance of island size, isolation from the mainland and inter‐island distance, I used constrained null models for the nestedness temperature calculator and a cluster analysis. Results Species richness depended on island area and isolation from the mainland. Nestedness was detected, even when passive sampling was accounted for. The nested rank of islands was correlated with area and species richness, but not with isolation. Idiosyncrasies appeared among species‐poor and species‐rich islands, and among common and rare species. Cluster analysis showed differences among species‐rich islands, close similarity among species‐poor and idiosyncratic islands, and that the compositional similarity among islands decreased with increasing inter‐island distance. Thus, faunas of species‐poor, smaller islands were more likely to be subsets of faunas of species‐rich, larger islands if the distance between the islands was short. Main conclusions Species richness and nestedness were related to island area, and nestedness also to inter‐island distances but not to isolation from the mainland. Thus, nestedness and species richness are not affected in the same way by area and distance. Moreover, idiosyncrasies may have been the outcome of species distributions among islands being influenced also by non‐nested distributions of habitats, inter–specific interactions, and differences in species distributions across the mainland. Idiosyncrasies in nested patterns may be as important as the nested pattern itself for conservation – and conservation strategies based on nestedness and strong area effects (e.g. protection of only larger islands) may fail to preserve idiosyncratic species/habitats.     

Discrimination of two Japanese water pennies,Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter (Coleoptera: Psephenidae), based on laboratory rearing and molecular taxonomy

Two psephenid beetles, Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter, are common species on the main islands of Japan (i.e. Honshu, Shikoku and Kyushu), but diagnostic characters for larval identification are unknown. Two types of field‐collected Eubrianax larvae from Honshu and Kyushu were discriminated based on the distributions of granules on the dorsal surface. These larvae were assigned to E. granicollis and E. ramicornis by comparing them with larvae of the two species obtained via laboratory rearing. The two species were also identified unambiguously on the basis of their mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Larval and pupal morphology are described based on laboratory‐reared specimens.     

生境片段化对千岛湖地表甲虫物种多样性的影响

在千岛湖片段化景观中选取20个陆桥岛屿和8个大陆样点,从2012年7月到2014年4月,按季度(春、夏、秋季)6次采用巴氏陷阱法收集地表甲虫,分析其物种多度、组成、多样性和季节动态,以及不同岛屿上的地表甲虫的物种多样性与岛屿面积和隔离度等岛屿空间特征的关系.结果表明: 共收集记录到地表甲虫26科101种3370头.大陆和大岛地表甲虫的物种丰富度有显著差异,且小岛地表甲虫密度显著高于大陆;大陆地表甲虫的物种组成变化较大,而岛屿上分布的地表甲虫的物种组成则变化较小.地表甲虫的物种丰富度与岛屿面积呈显著正相关,密度与隔离度呈显著正相关.夏季岛屿上地表甲虫物种丰富度高于春秋两季,岛屿与大陆样地的Shannon指数、Simpson指数和Pielou均匀度指数均在夏季最高、秋季最低.     

Geographic allozyme variation in the Japanese clouded salamander, Hynobius nebulosus (Amphibia: Urodela)

Using starch gel electrophoresis, geographical enzyme variation was surveyed in 46 populations of the Japanese salamander Hynobius nebulosus , which occurs widely in western Japan. This species exhibits substantial local genetic differentiation and is more diverse in inland regions than on small islands. In several different analyses, two groups of populations, one from Kyushu Island to the westernmost part of Chugoku district, Honshu (western group), and another from Shikoku through Kinki to Chubu district, Honshu (eastern group), were consistently recognized. Most of the remaining populations were placed in two less clearly-defined groups: the montane group from the Chugoku Mountains and the Chugoku group from the coastal regions of Chugoku district. The divergence patterns of H. nebulosus are thought to be related to the geological history of its range. The populations near the boundary of the western group were found to share several alleles that were predominant on both sides of the boundary, indicating past secondary contact. Differentiation in the montane group did not follow the isolation by distance model, probably because several populations included were genetically mixed with lowland populations of the Chugoku group.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 311–330.     

F-specific RNA bacteriophages and sensitive host strains in faeces and wastewater of human and animal origin

Faeces of humans, pigs, cattle and chickens were investigated for the presence of somatic coliphages, F-specific bacteriophages and Escherichia coli strains sensitive to infection by F-specific phages. Attention was given to the possible effect of age and use of antibiotics on the prevalence of the FRNA phages and sensitive E. coli strains. Somatic coliphages were often detected in high numbers in all types of faeces. In contrast, FRNA phages were rarely detected in faeces from humans and cattle but more often in faeces from pigs and adult chickens. Samples from young chickens (with or without antibiotics) were consistently positive for FRNA phages (up to 3 x 10(6) pfu/g). F-specific RNA phages were found in substantial numbers (greater than 10(3) pfu/ml) in a variety of wastewaters: domestic, hospital, slaughterhouses and occasionally in 'grey water'. Their origin in wastewater was not clear. Strains from faeces usually belonged to serogroups I and IV. These types were also found in wastewater, as were group II and III strains. Serogroup II phages were abundant in wastewater of human origin but rare in faeces. Escherichia coli strains sensitive to infection by F-specific phages were common in faeces (overall 290/1081: 27%). No strains with fully depressed F-pilus synthesis were detected among the sensitive strains. It is concluded that the occurrence of F-specific RNA bacteriophages in water points to sewage pollution rather than faecal pollution; the mechanism of replication of these organisms in wastewater is not understood.     

F-specific RNA bacteriophages and sensitive host strains in faeces and wastewater of human and animal origin

Faeces of humans, pigs, cattle and chickens were investigated for the presence of somatic coliphages, F-specific bacteriophages and Escherichia coli strains sensitive to infection by F-specific phages. Attention was given to the possible effect of age and use of antibiotics on the prevalence of the FRNA phages and sensitive E . coli strains. Somatic coliphages were often detected in high numbers in all types of faeces. In contrast, FRNA phages were rarely detected in faeces from humans and cattle but more often in faeces from pigs and adult chickens. Samples from young chickens (with or without antibiotics) were consistently positive for FRNA phages (up to 3 × 10⁶ pfu/g). F-specific RNA phages were found in substantial numbers (> 10³ pfu/ml) in a variety of wastewaters: domestic, hospital, slaughterhouses and occasionally in 'grey water'. Their origin in wastewater was not clear. Strains from faeces usually belonged to serogroups I and IV. These types were also found in wastewater, as were group II and III strains. Serogroup II phages were abundant in wastewater of human origin but rare in faeces. Escherichia coli strains sensitive to infection by F-specific phages were common in faeces (overall 290/1081: 27%). No strains with fully derepressed F-pilus synthesis were detected among the sensitive strains. It is concluded that the occurrence of F-specific RNA bacteriophages in water points to sewage pollution rather than faecal pollution; the mechanism of replication of these organisms in wastewater is not understood.     

Comments on cephalometrical configurations of the Japanese

Cephalometrical configurations of Japanese people were investigated on two hundred and sixteen groups living on the four main islands of Japan: Hokkaido, Honshu, Shikoku, and Kyushu. The Japanese in Honshu were divided geographically into a narrow-featured eastern major group and a broad-featured western major group. A physical characteristic of Japanese living in the western mid-Honshu was the lengthened feature of their cephalic measurement, an influence of a long-headed group of Korean people; Japanese residents in eastern mid-Honshu, however, showed the result of mixing with a short-headed group of Korean people. Japanese people living in Hokkaido, the northernmost island, and in the Ryukyu Islands in the South of Japan, presented no important finding which suggests their influence on the physical characteristics of the Japanese. Ongoing studies indicating physical relationships between Kyushu or Shikoku residents and Honshu residents, are as yet insufficient.     

Colony and population genetic structure of the Formosan subterranean termite,Coptotermes formosanus,in Japan

Subterranean termites have unusual plasticity in their breeding systems. As a result of their cryptic foraging and nesting habits, detailed information on the numbers and types of reproductive individuals in colonies has been difficult to obtain. In this study, we used microsatellite markers to infer the major features of the breeding system of the Formosan subterranean termite, Coptotermes formosanus, in southern Japan, where it is believed to have been introduced from China. A total of 30 colonies was sampled from two islands (Kyushu and Fukue) located 100 km apart. Twenty workers from each colony were genotyped at six microsatellite loci. Analysis of worker genotypes within colonies indicated that 27 colonies (90%) were simple (Mendelian) families. The remaining three colonies, all from Kyushu, were consistent with being extended families having begun as simple families but being currently headed by multiple neotenic (secondary) reproductives descended from the original king and queen. Workers from simple families in both populations were significantly inbred (FIT = 0.10 for Kyushu and 0.46 for Fukue) and highly related to their nestmates (coefficient of relatedness, r = 0.59 for Kyushu and 0.77 for Fukue), suggesting that many simple-family colonies were headed by closely related reproductives, especially in the Fukue population. This conclusion is supported by the high coefficient of relatedness between nestmate reproductives in simple-family colonies (r = 0.23 for Kyushu and 0.61 for Fukue) based on genotypes inferred from their worker offspring. There was moderate genetic differentiation (FST = 0.12) between the two populations, suggesting rather restricted gene flow between them. There was no significant isolation by distance among colonies, as might be expected given the limited dispersal of reproductives, presumably because of the frequent movement of colonies by humans. Finally, there was no evidence of a recent bottleneck, a finding possibly consistent with the more than 300-year history of this species in Japan.