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1.  Hardy exotics species in temperate zone: can “warm water” crayfish invaders establish regardless of low temperatures? 
Scientific Reports  2015;5:16340.
The spreading of new crayfish species poses a serious risk for freshwater ecosystems; because they are omnivores they influence more than one level in the trophic chain and they represent a significant part of the benthic biomass. Both the environmental change through global warming and the expansion of the pet trade increase the possibilities of their spreading. We investigated the potential of four “warm water” highly invasive crayfish species to overwinter in the temperate zone, so as to predict whether these species pose a risk for European freshwaters. We used 15 specimens of each of the following species: the red swamp crayfish (Procambarus clarkii), the marbled crayfish (Procambarus fallax f. virginalis), the yabby (Cherax destructor), and the redclaw (Cherax quadricarinatus). Specimens were acclimatized and kept for 6.5 months at temperatures simulating the winter temperature regime of European temperate zone lentic ecosystems. We conclude that the red swamp crayfish, marbled crayfish and yabby have the ability to withstand low winter temperatures relevant for lentic habitats in the European temperate zone, making them a serious invasive threat to freshwater ecosystems.
doi:10.1038/srep16340
PMCID: PMC4648075  PMID: 26572317
2.  The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals 
Biology Open  2015;4(11):1583-1594.
ABSTRACT
The parthenogenetic all-female marbled crayfish is a novel research model and potent invader of freshwater ecosystems. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax, but its taxonomic status has remained unsettled. By cross-breeding experiments and parentage analysis we show here that marbled crayfish and P. fallax are reproductively separated. Both crayfish copulate readily, suggesting that the reproductive barrier is set at the cytogenetic rather than the behavioural level. Analysis of complete mitochondrial genomes of marbled crayfish from laboratory lineages and wild populations demonstrates genetic identity and indicates a single origin. Flow cytometric comparison of DNA contents of haemocytes and analysis of nuclear microsatellite loci confirm triploidy and suggest autopolyploidisation as its cause. Global DNA methylation is significantly reduced in marbled crayfish implying the involvement of molecular epigenetic mechanisms in its origination. Morphologically, both crayfish are very similar but growth and fecundity are considerably larger in marbled crayfish, making it a different animal with superior fitness. These data and the high probability of a divergent future evolution of the marbled crayfish and P. fallax clusters suggest that marbled crayfish should be considered as an independent asexual species. Our findings also establish the P. fallax–marbled crayfish pair as a novel paradigm for rare chromosomal speciation by autopolyploidy and parthenogenesis in animals and for saltational evolution in general.
Summary: The triploid marbled crayfish is a rare animal example of speciation by autopolyploidisation and parthenogenesis. It seems to be a particularly suitable model to study how much genetic and epigenetic change is necessary to create a new species.
doi:10.1242/bio.014241
PMCID: PMC4728364  PMID: 26519519
Marbled crayfish; Autopolyploidy; Parthenogenesis; Epigenetics; Chromosomal speciation; Saltational evolution
3.  Old divergences in a boreal bird supports long-term survival through the Ice Ages 
Background
Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species.
Results
In a sample of 113 individuals from 18 populations we identified 42 haplotypes of the mitochondrial cytochrome b gene, which separated into three clades: A - Alaska and mainland Eurasia (except Kamchatka); B - Kamchatka, Sakhalin and Hokkaido; and C - Honshu, Shikoku and Kyushu (i.e. Japan except Hokkaido). The oldest split among these clades, between A/B and C, is estimated to have taken place sometime between the mid Pliocene and early Pleistocene, and the second divergence, between clades A and B, in the early to mid Pleistocene. Within all of the three main clades, there are signs of population expansion.
Conclusions
The Arctic Warbler separated into three main clades in close succession around the Pliocene/Pleistocene border, with the two northern clades diverging last. All three clades probably experienced population bottlenecks during the Pleistocene as a result of range shifts and contractions, but nevertheless survived and maintained their integrities. Several other clades of Northeastern Palearctic birds are noted to have diversified during the Pliocene. In contrast, avian species or phylogroups presently occupying formerly glaciated North American ground are generally younger. The differences between these regions could be due to slower speciation rates in the Eastern Palearctic due to less fragmentation of forest habitats during glacial periods, or to longer survival of Eastern Palearctic clades as a result of less severe conditions in that region compared to northern North America. Several other Palearctic organisms show concordant biogeographical patterns to that of the Arctic Warbler, indicating common causes of their diversifications.
doi:10.1186/1471-2148-10-35
PMCID: PMC2848155  PMID: 20128930
4.  Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus 
Background
Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events.
Results
We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16 % and 22–32 %, respectively, for A. argenteus, and 12–17 % and 17–24 %, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1 %/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1 %/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP.
Conclusions
The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
doi:10.1186/s12862-015-0463-5
PMCID: PMC4571126  PMID: 26373638
5.  Invasive Crayfish Threaten the Development of Submerged Macrophytes in Lake Restoration 
PLoS ONE  2013;8(10):e78579.
Submerged macrophytes enhance water transparency and aquatic biodiversity in shallow water ecosystems. Therefore, the return of submerged macrophytes is the target of many lake restoration projects. However, at present, north-western European aquatic ecosystems are increasingly invaded by omnivorous exotic crayfish. We hypothesize that invasive crayfish pose a novel constraint on the regeneration of submerged macrophytes in restored lakes and may jeopardize restoration efforts. We experimentally investigated whether the invasive crayfish (Procambarus clarkii Girard) affects submerged macrophyte development in a Dutch peat lake where these crayfish are expanding rapidly. Seemingly favourable abiotic conditions for macrophyte growth existed in two 0.5 ha lake enclosures, which provided shelter and reduced turbidity, and in one lake enclosure iron was added to reduce internal nutrient loading, but macrophytes did not emerge. We transplanted three submerged macrophyte species in a full factorial exclosure experiment, where we separated the effect of crayfish from large vertebrates using different mesh sizes combined with a caging treatment stocked with crayfish only. The three transplanted macrophytes grew rapidly when protected from grazing in both lake enclosures, demonstrating that abiotic conditions for growth were suitable. Crayfish strongly reduced biomass and survival of all three macrophyte species while waterfowl and fish had no additive effects. Gut contents showed that crayfish were mostly carnivorous, but also consumed macrophytes. We show that P. clarkii strongly inhibit macrophyte development once favourable abiotic conditions for macrophyte growth are restored. Therefore, expansion of invasive crayfish poses a novel threat to the restoration of shallow water bodies in north-western Europe. Prevention of introduction and spread of crayfish is urgent, as management of invasive crayfish populations is very difficult.
doi:10.1371/journal.pone.0078579
PMCID: PMC3813481  PMID: 24205271
6.  New zoonotic cases of Onchocerca dewittei japonica (Nematoda: Onchocercidae) in Honshu, Japan 
Parasites & Vectors  2015;8:59.
Background
Zoonotic infections with Onchocerca species are uncommon, and to date only 25 clinical cases have been reported worldwide. In Japan, five previous zoonotic infections were concentrated in Oita, Kyushu (the southern island), with one previous case in Hiroshima in the western part of Honshu (the main island). The causative agent in Japan was identified as Onchocerca dewittei japonica Uni, Bain & Takaoka, 2001 from Japanese wild boars (Sus scrofa leucomystax Temminck, 1842). Here we report two infections caused by a female and male O. dewittei japonica, respectively, among residents of Hiroshima and Shimane Prefectures in the western part of Honshu.
Methods
In both cases, nodules were surgically removed. The parasites in nodules were identified on the basis of their histopathological characteristics. Identification was confirmed by sequencing the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from worms in the tissues used in the histological preparations.
Results
Case 1 was a 61-year-old woman from Hiroshima Prefecture who complained of a painful subcutaneous nodule on the back of her right hand. The causative agent was identified as a female O. dewittei japonica owing to transverse ridges on the cuticle and molecular analysis. Case 2 was a 78-year-old woman from Shimane Prefecture who had a painful nodule in the left temporal region. Histopathological characteristics and cox1 sequencing of the worm indicated that the causative agent was a male O. dewittei japonica.
Conclusions
For Cases 1 and 2, we diagnosed the causative agents as a female and male O. dewittei japonica, respectively. These findings indicate the spread of a zoonosis caused by O. dewittei japonica in the western part of Honshu, where wild boars have recently extended their habitats because of decreased annual snowfall, unused rice fields and a decline in the number of hunters in Japan. The O. dewittei japonica infection rate among wild boars was reported as 78% in Shimane Prefecture, in the western part of Honshu. Therefore, in the near future, zoonotic onchocercosis is likely to occur in Honshu as well as Kyushu, where wild boars, blackfly vectors and humans share the same habitat.
doi:10.1186/s13071-015-0655-2
PMCID: PMC4323255  PMID: 25623081
Filarioid; Global warming; Japanese wild boar; Onchocerca dewittei japonica; Vector-borne disease; Zoonosis
7.  Geographical Distribution of the Herpes Simplex Virus Type 1 BgKL Variant in Japan Suggests Gradual Dispersion of the Virus from Shikoku Island to the Other Islands 
Journal of Clinical Microbiology  2006;44(6):2109-2118.
Restriction endonuclease fragment length polymorphism (RFLP) is useful for the epidemiological study of herpes simplex virus type 1 (HSV-1). We report here the identification of a major BglII RFLP variant of HSV-1, designated BgKL, found in 27.0% of 636 HSV-1 clinical isolates. We have also established its geographic distribution in Japan. BgKL has an unusually large BglII K fragment. SalI cleavage analyses showed that 97% of BgKL variant isolates lack both the SalI C-J and the F-J cleavage sites and have an unusually large SalI D or E fragment, and 91% of the BgKL variants lack both SalI G and H fragments. Furthermore, 96% of BgKL isolates have an unusually small KpnI M fragment. Therefore, BgKL is a marker for these five mutations in most HSV-1 isolates and is a useful HSV-1 RFLP marker. The BgKL variant was found in 59% of HSV-1 isolates from Shikoku Island, 44% of HSV-1 isolates from the Chugoku region of Honshu Island, 31% of HSV-1 isolates from Kyushu Island, 0% of HSV-1 isolates from Okinawa Island, 49% of HSV-1 isolates from Osaka, 27% of HSV-1 isolates from Shiga, 13% of HSV-1 isolates from the Chubu Region, and 9% of HSV-1 isolates from the Tohoku Region of Honshu Island. Differences in the frequency of BgKL between the Shikoku-Chugoku-Osaka area (49%) and Kyushu, between Kyushu and Okinawa, between the Shikoku-Chugoku-Osaka area and Shiga, and between Shiga and Tohoku are all statistically significant. The BgKL frequency decreases in a geographical gradient suggest that this HSV-1 variant was dispersed from Shikoku to the surrounding regions and then to more distant regions. The BgKL frequency in Tokyo was similar to the nationwide average. These are the first data to suggest a geographic and demographic dispersion pattern of HSV-1. Implications for the epidemiology and diversification of HSV-1 are discussed.
doi:10.1128/JCM.02064-05
PMCID: PMC1489417  PMID: 16757606
8.  Host resistance does not explain variation in incidence of male-killing bacteria in Drosophila bifasciata 
Background
Selfish genetic elements that distort the sex ratio are found widely. Notwithstanding the number of records of sex ratio distorters, their incidence is poorly understood. Two factors can prevent a sex ratio distorter from invading: inability of the sex ratio distorter to function (failure of mechanism or transmission), and lack of drive if they do function (inappropriate ecology for invasion). There has been no test to date on factors causing variation in the incidence of sex ratio distorting cytoplasmic bacteria. We therefore examined whether absence of the male-killing Wolbachia infection in D. bifasciata in Hokkaido island of Japan, in contrast to the presence of infection on the proximal island of Honshu, was associated with failure of the infection to function properly on the Hokkaido genetic background.
Results
The male-killer both transmitted and functioned well following introgression to each of 24 independent isofemale inbred lines carrying Hokkaido genetic backgrounds. This was maintained even under stringent conditions of temperature. We therefore reject the hypothesis that absence of infection is due to its inability to kill males and transmit on the Hokkaido genetic background. Further trap data indicates that D. bifasciata may occur at different densities in Hokkaido and Honshu populations, giving some credence to the idea that ecological differentiation could be important.
Conclusions
The absence of the infection from the Hokkaido population is not caused by failure of the male-killer to function on the Hokkaido genetic background.
doi:10.1186/1471-2148-4-52
PMCID: PMC535909  PMID: 15571631
9.  Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology 
PLoS ONE  2012;7(2):e31757.
Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications.
doi:10.1371/journal.pone.0031757
PMCID: PMC3283663  PMID: 22363724
10.  Lanthanum from a Modified Clay Used in Eutrophication Control Is Bioavailable to the Marbled Crayfish (Procambarus fallax f. virginalis) 
PLoS ONE  2014;9(7):e102410.
To mitigate eutrophication in fresh standing waters the focus is on phosphorus (P) control, i.e. on P inflows to a lake as well as a lake's sediment as internal P source. The in-lake application of the lanthanum (La) modified clays – i.e. La modified bentonite (Phoslock) or La modified kaolinite, aim at dephosphatising the water column and at reducing the release of P from a lake's sediment. Application of these clays raises the question whether La from these clays can become bioavailable to biota. We investigated the bioavailability of La from Phoslock in a controlled parallel groups experiment in which we measured the La in carapace, gills, ovaries, hepatopancreas and abdominal muscle after 0, 14 and 28 days of exposure to Phoslock. Expressing the treatment effect as the difference of the median concentration between the two treatment groups (Phoslock minus control group) yield the following effects, the plus sign (+) indicating an increase, concentrations in µg g−1 dry weight: Day 14: carapace +10.5 µg g−1, gills +112 µg g−1, ovaries +2.6 µg g−1, hepatopancreas +32.9 µg g−1 and abodminal muscle +3.2 µg g−1. Day 28: carapace +17.9 µg g−1; gills +182 µg g−1; ovaries +2.2 µg g−1; hepatopancreas +41.9 µg g−1 and abodminal muscle +7.6 µg g−1, all effects were statistically significant. As La from Phoslock is bio-available to and taken up by the marbled crayfishes (Procambarus fallax f. virginalis), we advocate that the application of in-lake chemical water treatments to mitigate eutrophication should be accompanied by a thorough study on potential side effects.
doi:10.1371/journal.pone.0102410
PMCID: PMC4113486  PMID: 25068309
11.  Regional disparities in interferon therapy for chronic hepatitis C in Japan: a nationwide retrospective cohort study 
BMC Public Health  2015;15:566.
Background
Many patients with chronic hepatitis C have been treated with interferon (IFN) therapy in Japan, especially after the introduction of subsidies for medical expenses in 2008. However, its performance and outcome have never been evaluated. Therefore, a nationwide, mail-based, retrospective cohort study was conducted.
Methods
Regional disparities in the demographic features, treatment performance, and virological response were evaluated using an intent-to-treat design. The participating prefectures were classified into nine regions from north to south (Hokkaido/Tohoku, Kanto, Shin-etsu, Hokuriku, Tokai, Kinki, Chugoku, Shikoku, and Kyushu). Multivariate logistic regression analysis was performed to select predictive factors for treatment performance and outcome.
Results
From December 2009 to May 2013, 16,854 patients with chronic hepatitis C were registered from 37 prefectures in Japan (median age: 60 years; 50.4 % male; 74.8 % IFN-naïve; HCV genotype [1 or 2]/viral load [high (≥5 log IU/mL) or low (<5 log IU/mL)]: 1/high = 58.2 %, 1/low = 5.2 %, 2/high = 27.3 %, 2/low = 7.5 %; 83.4 % treated with peginterferon-α and ribavirin). Mean age, proportion of elderly patients (≥65 years), male sex, IFN-experienced, and HCV genotype were significantly different among the nine regions (all P < 0.001). Regional disparities were independently selected as one of the predictive factors for treatment performance and outcome in patients treated with peginterferon-α and ribavirin, which revealed two regions that required further investigation.
Conclusions
Regional disparities still exist in IFN therapy, and are strongly associated with treatment performance and outcome. Since the accessibility to medical resources for individual patients seemed to be different among the nine regions, public health actions should be focused on how to construct and properly manage consultation networks between base hospitals and local clinics, especially in those regions with low population density.
Electronic supplementary material
The online version of this article (doi:10.1186/s12889-015-1891-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12889-015-1891-2
PMCID: PMC4474553  PMID: 26088426
Treatment performance; Treatment outcome; Peginterferon-α; Ribavirin; Subsidy policy
12.  Prevalence of the Crayfish Plague Pathogen Aphanomyces astaci in Populations of the Signal Crayfish Pacifastacus leniusculus in France: Evaluating the Threat to Native Crayfish 
PLoS ONE  2013;8(7):e70157.
Aphanomyces astaci, the crayfish plague pathogen, first appeared in Europe in the mid-19th century and is still responsible for mass mortalities of native European crayfish. The spread of this parasite across the continent is especially facilitated by invasive North American crayfish species that serve as its reservoir. In France, multiple cases of native crayfish mortalities have been suggested to be connected with the presence of the signal crayfish Pacifastacus leniusculus, which is highly abundant in the country. It shares similar habitats as the native white-clawed crayfish Austropotamobius pallipes and, when infected, the signal crayfish might therefore easily transmit the pathogen to the native species. We investigated the prevalence of A. astaci in French signal crayfish populations to evaluate the danger they represent to local populations of native crayfish. Over 500 individuals of Pacifastacus leniusculus from 45 French populations were analysed, plus several additional individuals of other non-indigenous crayfish species Orconectes limosus, O. immunis and Procambarus clarkii. Altogether, 20% of analysed signal crayfish tested positive for Aphanomyces astaci, and the pathogen was detected in more than half of the studied populations. Local prevalence varied significantly, ranging from 0% up to 80%, but wide confidence intervals suggest that the number of populations infected by A. astaci may be even higher than our results show. Analysis of several individuals of other introduced species revealed infections among two of these, O. immunis and P. clarkii. Our results confirm that the widespread signal crayfish serves as a key reservoir of Aphanomyces astaci in France and therefore represents a serious danger to native crayfish species, especially the white-clawed crayfish. The prevalence in other non-indigenous crayfish should also be investigated as they likely contribute to pathogen transmission in the country.
doi:10.1371/journal.pone.0070157
PMCID: PMC3720925  PMID: 23894606
13.  Does Autocthonous Primary Production Influence Oviposition by Aedes japonicus japonicus (Diptera: Culicidae) in Container Habitats? 
Journal of medical entomology  2013;50(1):69-78.
Aedes (Finlaya) japonicus japonicus (Theobald) (Diptera: Culicidae) is recently invasive in North America and has expanded its range rapidly since 1998. Throughout its native and expanded range, Ae. j. japonicus larvae are commonly observed in many types of natural and artificial water-filled containers that vary in organic matter content and exposure to sunlight. Larvae are most often found in containers with decaying leaf material or algae, and we postulated that the added autocthonous primary production from algae could be both an important food source for larvae and an influential oviposition attractant to adult Ae. j. japonicus. We tested this hypothesis by placing plastic containers with varied levels of shading to manipulate algal density in the field, and then monitored oviposition by natural populations of Ae. j. japonicus. Over 99% of larvae hatching from eggs laid on the walls of our containers were Ae. j. japonicus, indicating that this species is a dominant colonizer of artificial containers in the study areas. Although full shading treatments effectively reduced algal biomass (significant reduction in chlorophyll a levels), at only one of three sites did this appear to affect Ae. j. japonicus oviposition. We conclude that algae in larval habitats are not a major factor in oviposition choices of adult Ae. j. japonicus females except when in situ primary production is high enough to substantially alter overall organic matter content cues.
PMCID: PMC4106285  PMID: 23427654
Aedes japonicus japonicus; algae; oviposition; container habitat
14.  Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping 
Breeding Science  2015;65(5):388-395.
Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.
doi:10.1270/jsbbs.65.388
PMCID: PMC4671699  PMID: 26719741
rice blast resistance; QTL; GWAS
15.  Macrogenomic Evidence for the Origin of the Black Fly Simulium suzukii (Diptera: Simuliidae) on Okinawa Island, Japan 
PLoS ONE  2013;8(8):e70765.
To determine the geographic origin of the black fly Simulium suzukii on Okinawa Island, Japan, macrogenomic profiles derived from its polytene chromosomes were compared with those of mainland and other insular populations of S. suzukii and of the isomorphic Simulium tani species complex. The Okinawan population is a chromosomally unique cytoform, designated ‘D,’ which is essentially monomorphic and differs by about 27 fixed rearrangements from the chromosomal standard sequence for the subgenus Simulium and by two fixed differences from its nearest known relative, representing the type of S. suzukii, on the main islands of Japan. Chromosomal band sequences revealed two additional, sympatric cytoforms of S. suzukii, designated ‘A’ and ‘B,’ each with species status, in Korea, and a third cytoform, designated ‘C,’ on Hokkaido, Japan. A new cytoform, ‘K,’ of S. tani from Malaysia, representing the type of S. tani, is more closely related to cytoforms in Thailand, as are populations from Taiwan previously treated as S. suzukii but more closely aligned with S. tani and newly recognized as cytoform ‘L’ of the latter nominal species. Rooting of chromosomal band sequences by outgroup comparisons allowed directionality of chromosomal rearrangements to be established, enabling phylogenetic inference of cytoforms. Of 41 macrogenomic rearrangements discovered in the five new cytoforms, four provide evidence for a stepwise origin of the Okinawan population from populations characteristic of the main islands of Japan. The macrogenomic approach applied to black flies on Okinawa Island illustrates its potential utility in defining source areas for other species of flies including those that might pose medical and veterinary risks.
doi:10.1371/journal.pone.0070765
PMCID: PMC3739796  PMID: 23951001
16.  Adult Mortality Attributable to Preventable Risk Factors for Non-Communicable Diseases and Injuries in Japan: A Comparative Risk Assessment 
PLoS Medicine  2012;9(1):e1001160.
Using a combination of published data and modeling, Nayu Ikeda and colleagues identify tobacco smoking and high blood pressure as major risk factors for death from noncommunicable diseases among adults in Japan.
Background
The population of Japan has achieved the longest life expectancy in the world. To further improve population health, consistent and comparative evidence on mortality attributable to preventable risk factors is necessary for setting priorities for health policies and programs. Although several past studies have quantified the impact of individual risk factors in Japan, to our knowledge no study has assessed and compared the effects of multiple modifiable risk factors for non-communicable diseases and injuries using a standard framework. We estimated the effects of 16 risk factors on cause-specific deaths and life expectancy in Japan.
Methods and Findings
We obtained data on risk factor exposures from the National Health and Nutrition Survey and epidemiological studies, data on the number of cause-specific deaths from vital records adjusted for ill-defined codes, and data on relative risks from epidemiological studies and meta-analyses. We applied a comparative risk assessment framework to estimate effects of excess risks on deaths and life expectancy at age 40 y. In 2007, tobacco smoking and high blood pressure accounted for 129,000 deaths (95% CI: 115,000–154,000) and 104,000 deaths (95% CI: 86,000–119,000), respectively, followed by physical inactivity (52,000 deaths, 95% CI: 47,000–58,000), high blood glucose (34,000 deaths, 95% CI: 26,000–43,000), high dietary salt intake (34,000 deaths, 95% CI: 27,000–39,000), and alcohol use (31,000 deaths, 95% CI: 28,000–35,000). In recent decades, cancer mortality attributable to tobacco smoking has increased in the elderly, while stroke mortality attributable to high blood pressure has declined. Life expectancy at age 40 y in 2007 would have been extended by 1.4 y for both sexes (men, 95% CI: 1.3–1.6; women, 95% CI: 1.2–1.7) if exposures to multiple cardiovascular risk factors had been reduced to their optimal levels as determined by a theoretical-minimum-risk exposure distribution.
Conclusions
Tobacco smoking and high blood pressure are the two major risk factors for adult mortality from non-communicable diseases and injuries in Japan. There is a large potential population health gain if multiple risk factors are jointly controlled.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Worldwide, a small number of modifiable risk factors are responsible for many premature or preventable deaths. For example, having high blood pressure (hypertension) increases a person's risk of developing life-threatening heart problems and stroke (cardiovascular disease). Similarly, having a high blood sugar level increases the risk of developing diabetes, a chronic (long-term) disease that can lead to cardiovascular problems and kidney failure, and half of all long-term tobacco smokers in Western populations will die prematurely from diseases related to smoking, such as lung cancer. Importantly, the five major risk factors for death globally—high blood pressure, tobacco use, high blood sugar, physical inactivity, and overweight and obesity—are all modifiable. That is, lifestyle changes and dietary changes such as exercising more, reducing salt intake, and increasing fruit and vegetable intake can reduce an individual's exposure to these risk factors and one's chances of premature death. Moreover, public health programs designed to reduce a population's exposure to modifiable risk factors should reduce preventable deaths in that population.
Why Was This Study Done?
In 2000, the Japanese government initiated Health Japan 21, a ten-year national health promotion campaign designed to prevent premature death from non-communicable (noninfectious) diseases and injuries. This campaign set 59 goals to monitor and improve risk factor management in the Japanese population, which has one of the longest life expectancies at birth in the world (the life expectancy of a person born in Japan in 2009 was 83.1 years). Because the campaign's final evaluation revealed deterioration or no improvement on some of these goals, the Japanese government recently released new guidelines that stress the importance of simultaneously controlling multiple risk factors for chronic diseases. However, although several studies have quantified the impacts on life expectancy and cause-specific death of individual modifiable risk factors in Japan, the effects of multiple risk factors have not been assessed. In this study, the researchers use a “comparative risk assessment” framework to estimate the effects of 16 risk factors on cause-specific deaths and life expectancy in Japan. Comparative risk assessment estimates the number of deaths that would be prevented if current distributions of risk factor exposures were changed to hypothetical optimal distributions.
What Did the Researchers Do and Find?
The researchers obtained data on exposure to the selected risk factors from the 2007 Japanese National Health and Nutrition Survey and from epidemiological studies, and information on the number of deaths in 2007 from different diseases from official records. They used published studies to estimate how much each factor increases the risk of death from each disease and then used a mathematical formula to estimate the effects of the risk factors on the number of deaths in Japan and on life expectancy at age 40. In 2007, tobacco smoking and high blood pressure accounted for 129,000 and 104,000 deaths, respectively, in Japan. Physical inactivity accounted for 52,000 deaths, high blood glucose and high dietary salt intake accounted for 34,000 deaths each, and alcohol use for 31,000 deaths. Life expectancy at age 40 in 2007 would have been extended by 1.4 years for both sexes, the researchers estimate, if exposure to multiple cardiovascular risk factors had been reduced to calculated optimal distributions, or by 0.7 years if these risk factors had been reduced to the distributions defined by national guidelines and goals.
What Do These Findings Mean?
These findings identify tobacco smoking and high blood pressure as the major risk factors for death from non-communicable diseases among adults in Japan, a result consistent with previous findings from the US. They also indicate that simultaneous control of multiple risk factors has great potential for producing health gains among the Japanese population. Although the researchers focused on estimating the effect of these risk factors on mortality and did not include illness and disability in this study, these findings nevertheless identify two areas of public health policy that need to be strengthened to improve health, reduce death rates, and increase life expectancy among the Japanese population. First, they highlight the need to reduce tobacco smoking, particularly among men. Second and most importantly, these findings emphasize the need to improve ongoing programs designed to help people manage multiple cardiovascular risk factors, including high blood pressure.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001160.
The US Centers for Disease Control and Prevention provides information on all aspects of healthy living
The World Health Report 2002—Reducing Risks, Promoting Healthy Life provides a global analysis of how healthy life expectancy could be increased
The American Heart Association and the American Cancer Society provide information on many important risk factors for noncommunicable diseases and include some personal stories about keeping healthy
Details about Health Japan 21 are provided by the Japanese Ministry of Health, Labour and Welfare. Further details about this campaign are available from the World Health Organization
MedlinePlus provides links to further resources on healthy living and on healthy aging (in English and Spanish)
doi:10.1371/journal.pmed.1001160
PMCID: PMC3265534  PMID: 22291576
17.  Biogeographical Consequences of Cenozoic Tectonic Events within East Asian Margins: A Case Study of Hynobius Biogeography 
PLoS ONE  2011;6(6):e21506.
Few studies have explored the role of Cenozoic tectonic evolution in shaping patterns and processes of extant animal distributions within East Asian margins. We select Hynobius salamanders (Amphibia: Hynobiidae) as a model to examine biogeographical consequences of Cenozoic tectonic events within East Asian margins. First, we use GenBank molecular data to reconstruct phylogenetic interrelationships of Hynobius by Bayesian and maximum likelihood analyses. Second, we estimate the divergence time using the Bayesian relaxed clock approach and infer dispersal/vicariance histories under the ‘dispersal–extinction–cladogenesis’ model. Finally, we test whether evolutionary history and biogeographical processes of Hynobius should coincide with the predictions of two major hypotheses (the ‘vicariance’/‘out of southwestern Japan’ hypothesis). The resulting phylogeny confirmed Hynobius as a monophyletic group, which could be divided into nine major clades associated with six geographical areas. Our results show that: (1) the most recent common ancestor of Hynobius was distributed in southwestern Japan and Hokkaido Island, (2) a sister taxon relationship between Hynobius retardatus and all remaining species was the results of a vicariance event between Hokkaido Island and southwestern Japan in the Middle Eocene, (3) ancestral Hynobius in southwestern Japan dispersed into the Taiwan Island, central China, ‘Korean Peninsula and northeastern China’ as well as northeastern Honshu during the Late Eocene–Late Miocene. Our findings suggest that Cenozoic tectonic evolution plays an important role in shaping disjunctive distributions of extant Hynobius within East Asian margins.
doi:10.1371/journal.pone.0021506
PMCID: PMC3125272  PMID: 21738684
18.  Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory 
Heredity  2011;107(4):338-348.
We aimed to reveal the effects of range expansion and subsequent lineage admixture from separated glacial refugia on genetic diversity of Kalopanax septemlobus in Japan, by combining nuclear microsatellite data and ecological niche modelling. Allelic richness and gene diversity were compared at the population and regional level. We also statistically examined these indices as a function of population accessibility to the last glacial maximum (LGM) palaeodistribution reconstructed by ecological niche modelling to test a simple range expansion scenario from glacial refugia. Genetic diversity was highest in the populations of southern Japan and gradually decreased towards the north. However, an additional centre of genetic diversity, when measured as gene diversity, was found in northern Honshu Island, where distinct lineages were shown to be in contact. Positive effects of population accessibility to the LGM range were detected in both diversity indices at different spatial scales. The combined data support independent postglacial range expansions towards the north from the edge populations on the exposed coastal shelf of Pacific and Sea of Japan in northern Honshu during the LGM, which subsequently resulted in markedly low genetic diversity in the northernmost extant range, Hokkaido. The regional increase in gene diversity in northern Honshu is likely to be the result of postglacial lineage admixture. Relative difference in the spatial scales best relating population genetic diversity with the LGM distribution can be explained by a higher rate of allelic richness diversity loss during range expansions and stronger effects of lineage admixture on gene diversity.
doi:10.1038/hdy.2011.20
PMCID: PMC3182501  PMID: 21427749
accessibility to palaeodistribution; ecological niche model; exposed coastal landscape; lineage admixture; nuclear microsatellite; postglacial colonisation
19.  Population Genetic Structure and Post-Establishment Dispersal Patterns of the Red Swamp Crayfish Procambarus Clarkii in China 
PLoS ONE  2012;7(7):e40652.
The red swamp crayfish (Procambarus clarkii) was introduced to China in the early 20th century. It has been spread to almost all forms of fresh water bodies including lakes, rivers and even paddyfields in most provinces of China. To clarify issues such as the initial entry point(s), dispersal pattern, genetic diversity and genetic structure of Procambarus clarkii in China, the genetic structure and diversity of P. clarkii populations at 37 sampling sites (35 from China, one from the USA and one from Japan) were analyzed using both mitochondrial gene sequences (COI and 16S rRNA) and 12 nuclear microsatellites. Multiple tests including phylogenetic analyses, Bayesian assignment and analysis of isolation by distance showed that (i) the population from Japan and those collected from China, particularly from NanJing (BGt and XG) and its some neighboring sites (CJr, NT and NB), have similar genetic composition, (ii) relatively high genetic diversity was detected in Chinese populations, (iii) the P. clarkii populations in China did not experience significant population expansions. Taken together, Nanjing, Jiangsu province is the presumed initial entry point, and human-mediated dispersal and adaptive variation are likely responsible for the observed genetic pattern of P. clarkii in China.
doi:10.1371/journal.pone.0040652
PMCID: PMC3393698  PMID: 22808222
20.  Transmission dynamics of hepatitis E among swine: potential impact upon human infection 
Background
Hepatitis E virus (HEV) infection is a zoonosis for which pigs play a role as a reservoir. In Japan, the infection has been enzootic in swine. Clarifying the detailed mechanisms of transmission within farms is required in order to facilitate an understanding of the age-specific patterns of infection, especially just prior to slaughter.
Results
Here we reanalyze a large-scale seroprevalence survey dataset from Japanese pig farms to estimate the force of infection. The forces of infection of swine HEV were estimated to be 3.45 (95% confidence interval: 3.17, 3.75), 2.68 (2.28, 3.14) and 3.11 (2.76, 3.50) [×10-2 per day] in Hokkaido, Honshu and Kyushu, respectively. The estimates with our model assumptions indicated that the average ages at infection ranged from 59.0–67.3 days and that the basic reproduction number, R0, was in the order of 4.02–5.17. Sensitivity analyses of age-specific incidence at different forces of infection revealed that a decline in the force of infection would elevate the age at infection and could increase the number of virus-excreting pigs at the age of 180 days.
Conclusion
Although our estimates imply that more than 95% of pigs are infected before the age of 150 days, the model shows that a decline in the force of infection could increase the risk of pig-to-human transmission. If the force of infection started to decline, it might be necessary to implement radical countermeasures (e.g. separation of uninfected pigs from infected herds beginning from the end of the suckling stage) to minimize the number of virus-positive pigs at the finishing stage.
doi:10.1186/1746-6148-3-9
PMCID: PMC1885244  PMID: 17493260
21.  Where to deliver baits for deworming urban red foxes for Echinococcus multilocularis control: new protocol for micro-habitat modeling of fox denning requirements 
Parasites & Vectors  2014;7:357.
Background
Deworming wild foxes by baiting with the anthelmintic praziquantel is being established as a preventive technique against environmental contamination with Echinococcus multilocularis eggs. Improvement of the cost-benefit performance of baiting treatment is required urgently to raise and maintain the efficacy of deworming. We established a spatial model of den site selection by urban red foxes, the definitive host, to specify the optimal micro-habitats for delivering baits in a new modeling approach modified for urban fox populations.
Methods
The model was established for two cities (Obihiro and Sapporo) in Hokkaido, Japan, in which a sylvatic cycle of E. multilocularis is maintained. The two cities have different degrees of urbanization. The modeling process was designed to detect the best combination of key environmental factors and spatial scale that foxes pay attention to most (here named ‘heeding range’) when they select den sites. All possible models were generated using logistic regression analysis, with “presence” or “absence” of fox den as the objective variable, and nine landscape categories customized for urban environments as predictor variables to detect the best subset of predictors. This procedure was conducted for each of ten sizes of concentric circles from dens and control points to detect the best circle size. Out of all models generated, the most parsimonious model was selected using Akaike’s Information Criterion (AIC) inspection.
Results
Our models suggest that fox dens in Obihiro are located at the center of a circle with 500 m radius including low percentages of wide roads, narrow roads, and occupied buildings, but high percentages of green covered areas; the dens in Sapporo within 300 m radius with low percentages of wide roads, occupied buildings, but high percentages of riverbeds and green covered areas. The variation of the models suggests the necessity of accumulating models for various types of cities in order to reveal the patterns of the model.
Conclusions
Our denning models indicating suitable sites for delivering baits will improve the cost-benefit performance of the campaign. Our modeling protocol is suitable for the urban landscapes, and for extracting the heeding range when they select the den sites.
Electronic supplementary material
The online version of this article (doi:10.1186/1756-3305-7-357) contains supplementary material, which is available to authorized users.
doi:10.1186/1756-3305-7-357
PMCID: PMC4262088  PMID: 25095789
Echinococcus multilocularis; Baiting strategy; Cost-benefit performance; Vulpes vulpes; Urban red fox; Den site selection; Key environmental factors; Key spatial scale; Requisite spatial scale; Heeding range
22.  Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region 
Breeding Science  2015;65(5):403-410.
Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.
doi:10.1270/jsbbs.65.403
PMCID: PMC4671701  PMID: 26719743
genome-wide association mapping; local population; Oryza sativa L.; plant breeding programs; rice
23.  Current status of therapy for breast cancer worldwide and in Japan 
The results of clinical trials conducted in Europe and North America have been incorporated into treatment strategies for breast cancer in Japan. Despite the use of similar treatment regimens, why has mortality from breast cancer been increasing in Japan? Procedures for surgical treatment and sentinel lymph node biopsy in breast cancer do not differ between Japan and Western countries, but the strategies for radiotherapy differ slightly. Hormonal therapy is now selected on the basis of scientific evidence, and similar regimens are used in Japan and Western countries. As for postoperative adjuvant chemotherapy, an anthracycline plus cyclophosphamide and taxane-based regimens are standard treatments in Japan and Western countries. In 2009, however, the results of two large clinical studies designed to determine whether intravenous or oral treatment was superior for postoperative adjuvant chemotherapy were reported in Japan. Both studies showed that relapse-free survival and overall survival (OS) at 5 years after surgery were similar for a combination of cyclophosphamide, methotrexate, and 5-fluorouracil and for tegafur/uracil. Many chemotherapeutic agents that are used to treat recurrent or metastatic breast cancer have not yet been approved in Japan. As for molecular targeted therapy, some agents that target the human epidermal growth factor receptor family have been approved in Japan, whereas angiogenesis inhibitors have not. The results of many clinical trials have been incorporated into clinical practice in Japan, therefore, the outcomes of breast cancer therapy have surpassed those in other countries. Many pivotal clinical trials have been conducted outside Japan. Treatment regimens that have been developed on the basis of these studies might be suitable for the management of breast cancer in Western women, but not for Japanese women because of differences in genetic factors, physique, body mass index, pharmacokinetics, and drug metabolism. Such regimens should be modified on the basis of the characteristics of breast cancer in Japan to develop treatment that is optimally suited for Japanese women. In particular, local studies of pharmacokinetics, pharmacodynamics, and optimal dose levels and treatment intervals should be carefully performed. The establishment of treatment regimens optimally suited for Japanese patients with breast cancer could put the brakes on the trend towards increasing mortality from breast cancer in Japan.
doi:10.5306/wjco.v2.i2.125
PMCID: PMC3095468  PMID: 21603322
Breast cancer; Breast-conservation therapy; Hormonal therapy; Chemotherapy; Molecular targeted therapy
24.  Invasion Biology of Aedes japonicus japonicus (Diptera: Culicidae) 
Aedes japonicus japonicus (Theobald) (Diptera: Culicidae) has recently expanded beyond its native range of Japan and Korea into large parts of North America and Central Europe. Population genetic studies begun immediately after the species was detected in North America revealed genetically distinct introductions that subsequently merged, likely contributing to the successful expansion. Interactions, particularly in the larval stage, with other known disease vectors give this invasive subspecies the potential to influence local disease dynamics. Its successful invasion likely does not involve superior direct competitive abilities, but it is associated with the use of diverse larval habitats and a cold tolerance that allows an expanded seasonal activity range in temperate climates. We predict a continued but slower expansion of Ae. j. japonicus in North America and a continued rapid expansion into other areas as this mosquito will eventually be considered a permanent resident of much of North America, Europe, Asia, and parts of Hawaii.
doi:10.1146/annurev-ento-011613-162012
PMCID: PMC4106299  PMID: 24397520
Aedes japonicus or Ochlerotatus japonicus; invasive mosquitoes; disease vectors; container habitats; mosquito larvae interactions
25.  Recently discovered Aedes japonicus japonicus (Diptera: Culicidae) populations in The Netherlands and northern Germany resulted from a new introduction event and from a split from an existing population 
Parasites & Vectors  2015;8:40.
Background
Originally native to East Asia, Aedes japonicus japonicus, a potential vector of several arboviruses, has become one of the most invasive mosquito species in the world. After having established in the USA, it is now spreading in Europe, with new populations emerging. In contrast to the USA, the introduction pathways and modes of dispersal in Europe are largely obscure.
Methods
To find out if two recently detected populations of Ae. j. japonicus in The Netherlands and northern Germany go back to new importations or to movements within Europe, the genetic makeup of mosquito specimens from all known European populations was compared. For this purpose, seven microsatellite loci from a representative number of mosquito specimens were genotyped and part of their mitochondrial nad4 gene sequenced.
Results
A novel nad4 haplotype found in the newly discovered Dutch population of Ae. j. japonicus suggests that this population is not closely related to the other European populations but has emanated from a further introduction event. With five nad4 haplotypes, the Dutch population also shows a very high genetic diversity indicating that either the founder population was very large or multiple introductions took place. By contrast, the recently detected North German population could be clearly assigned to one of the two previously determined European Ae. j. japonicus microsatellite genotypes and shows nad4 haplotypes that are known from West Germany.
Conclusion
As the European populations of Ae. j. japonicus are geographically separated but genetically mixed, their establishment must be attributed to passive transportation. In addition to intercontinental shipment, it can be assumed that human activities are also responsible for medium- and short-distance overland spread. A better understanding of the processes underlying the introduction and spread of this invasive species will help to increase public awareness of the human-mediated displacement of mosquitoes and to find strategies to avoid it.
doi:10.1186/s13071-015-0648-1
PMCID: PMC4311435  PMID: 25608763
Aedes japonicus japonicus; Asian bush mosquito; Europe; Microsatellites; Population genetics; nad4 haplotypes

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