Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water.

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community.

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.

Analysis of the Persistence and Particle Size Distributional Shift of Sperm-Derived Environmental DNA to Monitor Jack Mackerel Spawning Activity.

Environmental DNA (eDNA) analysis holds great promise as an efficient and noninvasive method to monitor not only the distribution of organisms but also their spawning activity. In eDNA analysis-based monitoring of spawning activity, the detection of sperm-derived eDNA is a key point; however, its characteristics and dynamics are completely unknown. The present study focuses on the persistence and particle size distribution (PSD) of eDNA derived from the sperm of Japanese jack mackerel. First, we investigated the time-dependent degradation and the PSD of sperm-derived eDNA by artificially adding sperm to seawater. Next, we kept fish in tanks and examined the changes in eDNA concentration and PSD before and after spawning. The results of two experiments showed that the degradation of sperm-derived eDNA proceeded rapidly, with PSD shifting to a smaller size regardless of the DNA region (Cyt b or ITS1). Additionally, it was shown that the nuclei and mitochondria released from sperm through degradation had a size distribution that was not simply dependent on each organelle size. These results will contribute to elucidating the characteristics and dynamics of eDNA specifically during the spawning season and to further developing eDNA analysis as a powerful tool for the monitoring of spawning activity.

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis.

Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture-based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture-based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population.

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3) and 41 (dada2) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA-based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods. Our results suggest that eDNA-based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

Real-time multiplex PCR for simultaneous detection of multiple species from environmental DNA: an application on two Japanese medaka species.

Information about species distribution is crucial to ecological studies. Environmental DNA (eDNA) analysis has recently been used to estimate the distribution of aquatic organisms. Several analytical methods including metabarcoding and species-specific PCR are being used for eDNA analysis. However, when only a few species are targeted, metabarcoding is not cost-effective because of the wasted consumption of read due to amplification of non-target species DNA. On the other hand, species-specific PCR requires tests to be repeated multiple times resulting in consuming more DNA templates, and experimental consumables. Here we propose a methodological framework for simultaneously detecting a few species using real-time multiplex PCR. We developed the species-specific primer-probe sets for two species of Japanese medaka (Oryzias latipes and o. sakaizumii), and we used them in the real-time multiplex PCR. In aquarium experiment, even when the species abundances were biased, both species were simultaneously detected in all samples. In a field survey, eDNA analysis and capture survey produced consistent results in all sampling sites, including sites with low fish densities. eDNA analysis using real-time multiplex PCR can be easily applied to other aquatic organisms, enabling a more cost-effective distribution survey of multiple target organisms.

Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance.

Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water temperature, and the relationship between eDNA degradation and bacterial abundance. This subject has not been well clarified, even though it is essential for improving the reliability of eDNA analysis. To determine the time- and water temperature-dependent degradation of eDNA, river water was sampled and eDNA concentrations were determined for ayu sweetfish (Plecoglossus altivelis altivelis) and common carp (Cyprinus carpio) at seven time points, over a 48-h period, and at three different water temperatures. The degradation of eDNA was modeled for each species using an existing exponential decay model with an extension to include water temperature effects. The degradation models were constructed for ayu sweetfish as Nt = 229,901.2 × exp [- (0.01062 × k - 0.07081) × t] and for common carp as Nt = 2,558.0 × exp [- (0.01075 × k - 0.07372) × t]. Nt is the DNA concentration at time t (elapsed time in hours) and k is the water temperature (°C). We also measured the concentration of eDNA derived from purified genomic DNA of the common carp, which was spiked into aquarium water without the target species, and we measured the bacterial abundance in the sample water after 12 and 24 h of incubation. Environmental DNA degradation was accelerated at higher water temperatures (generalized linear model, GLM; p < 0.001), but bacterial abundance did not have a significant effect on eDNA degradation (GLM, p = 0.097). These results suggest that the proper treatment of this temperature effect in data interpretations and adjustments would increase the reliability of eDNA analysis in future studies.

Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio.

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.

Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.

Recent studies in streams and ponds have demonstrated that the distribution and biomass of aquatic organisms can be estimated by detection and quantification of environmental DNA (eDNA). In more open systems such as seas, it is not evident whether eDNA can represent the distribution and biomass of aquatic organisms because various environmental factors (e.g., water flow) are expected to affect eDNA distribution and concentration. To test the relationships between the distribution of fish and eDNA, we conducted a grid survey in Maizuru Bay, Sea of Japan, and sampled surface and bottom waters while monitoring biomass of the Japanese jack mackerel (Trachurus japonicus) using echo sounder technology. A linear model showed a high R(2) value (0.665) without outlier data points, and the association between estimated eDNA concentrations from the surface water samples and echo intensity was significantly positive, suggesting that the estimated spatial variation in eDNA concentration can reflect the local biomass of the jack mackerel. We also found that a best-fit model included echo intensity obtained within 10-150 m from water sampling sites, indicating that the estimated eDNA concentration most likely reflects fish biomass within 150 m in the bay. Although eDNA from a wholesale fish market partially affected eDNA concentration, we conclude that eDNA generally provides a 'snapshot' of fish distribution and biomass in a large area. Further studies in which dynamics of eDNA under field conditions (e.g., patterns of release, degradation, and diffusion of eDNA) are taken into account will provide a better estimate of fish distribution and biomass based on eDNA.

Perceived risk of nuclear power and other risks during the last 25 years in Japan.

The present study described the results of three "fixed-point" surveys on perceived risk related to a list of social and individual risk events during 25 years in Japan. Female clerical staff and researchers were asked to rank 30 items related to various types of technologies and human activities according to their subjective judgments on the order of perceived magnitude of risk in 1983, 1992, and 2007. A similar survey was undertaken for Japanese citizens using web-based questionnaires in 2007. In general, the risk perceptions of the Japanese people, irrespective of gender, age, and occupation, have been uniform during the last 25 years. The female clerical staffs have consistently judged nuclear power as most risky during the last 25 years, whereas researchers' judgment fluctuated with events such as the Chernobyl accident. The ranking of the risk of motor vehicles fell during the 25-y period, whereas those of health risks with food preservatives, x-rays, and antibiotics rose transiently in the 1992 survey. During the 15 years from 1992 to 2007, people tended to learn how to accommodate themselves to these technologies with low risks in exchange for high benefits, except in the case of nuclear power. Nuclear power was regarded as a high-risk item by the Japanese even before the Fukushima nuclear power plant accident in March 2011. This partly explains that the crisis inevitably provokes further high risk perception in Japan, although the overall health threat to the human population in Japan is estimated to be relatively limited so far.

[Factors impacting public acceptance of medical radiation exposure].

We undertook a survey to determine the public acceptance of medical radiation exposure throughout Japan, and 1,357 responses (67.9% response rate) were obtained using a two-stage systematic stratified random sampling method. The acceptance of exposure of children was generally similar to that of adults. For each of the attributes, 45-60% of the participants were accepting of exposure for cancer treatment and diagnosis, but only 30% were accepting of exposure for X-ray diagnoses of bone fractures and dental caries. In general, the presence of a child did not markedly affect women's acceptance of exposure. Factor analyses identified 3 factors influencing the acceptance of child exposure: symptomatic diseases to determine treatment, the possibility of high-risk diseases (or major organ diseases), and the association with cancer. Cluster analysis showed 4 clusters: a positive group regarding children's exposure for the diagnosis of bone fractures and dental caries (12.9% of all participants), a positive group for major organ disease and cancer (15.5%), a negative group excluding cancer (55.2%), and a positive group for all cases (16.4%). The cluster distributions revealed that mothers with 10-to 18-year-old firstborn children showed a tendency to accept the medical radiation exposure of their children in all cases.

Rapid and reliable diagnosis of murine myeloid leukemia (ML) by FISH of peripheral blood smear using probe of PU. 1, a candidate ML tumor suppressor.

BACKGROUND: Murine myeloid leukemia (ML) provides a good animal model to study the mechanisms of radiation-induced leukemia in humans. This disease has been cytogenetically characterized by a partial deletion of chromosome 2 with G-banding. For the rapid diagnosis of ML, this study reports a FISH method using spleen cells and peripheral blood smears from ML mice exposed to gamma rays and neutrons with PU.1, a candidate ML tumor suppressor, as a probe. RESULTS: Among mice that were tentatively diagnosed with ML by clinical findings and blood smear examination, 85% carried spleen cells showing the loss of PU.1 although the frequency of these abnormal cells varied among individuals. Mice with very low frequencies of cells showing the loss of one copy of PU.1 (one-PU.1 frequency) were later diagnosed pathologically not with ML but with blastic or eosinophilic leukemia. Some neutron-irradiated mice had cells showing translocated PU.1, although no pathological features differentiated these ML mice from ML mice expressing the simple loss of PU.1.The one-PU.1 frequency can be detected from spleen metaphase cells, spleen interphase cells, and blood smears. There was a good correlation between the one-PU.1 frequency in spleen metaphase cells and that in spleen interphase cells (r = 0.96) and between one-PU.1 frequency in spleen interphase cells and that in blood cells (r = 0.83). CONCLUSION: The FISH method was capable of detecting aberration of copy number of the PU.1 gene on murine chromosome 2, and using a peripheral blood smear is more practical and less invasive than conventional pathological diagnosis or the cytogenetic examination of spleen cells.

[Preliminary survey for communicating risk in medical exposure--perception of risk among nurses working in radiology].

A questionnaire survey was conducted on radiation risk and medical exposure, particularly in applications involving children. The survey was targeted at nurses (170 females) engaged in important roles in communicating risk regarding medical exposure. The questionnaire survey yielded the following findings. 1) A significant number of respondents associated the word "radiation" with "cancer treatment," "exposure," and "X-ray pictures." Perceptions about "food exposure" differed between respondents with children and those without. 2) Among the potential health problems posed by radiation, "effects on children," "cancer and leukemia," and "genetic effects" were perceived as the most worrisome. Significant differences in perception were noted regarding infertility between respondents with children and those without. 3) Concerning the effects of medical exposure on fetuses/children, only 10 percent of all respondents replied that they were not anxious about negative effects in either case. Among the respondents who felt uneasy about these aspects, most tended to assess exposed parts, doses, damage potentially suffered, timing of occurrence, and uncertainty, based on their professional experience and knowledge, to rationally distinguish acceptable risks from unacceptable ones and to limit concern to the unacceptable aspects.

Direct detection of p53 -/- thymocyte appearing at an early stage of radiation-induced thymic lymphomagenesis in p53 +/- heterozygous B10 mice.

PURPOSE: The appearance of tumor suppressor protein 53 (p53) -/- thymocytes at an early stage of radiation-induced lymphomagenesis was investigated in the p53 heterozygous (+/-) B10 mice following a single dose of irradiation, since most thymic lymphomas manifested the loss of the wild-type p53 allele and the loss of heterozygosity was thought to be an early event critical for radiation-induced thymic lymphomagenesis in p53 +/- mice. MATERIALS AND METHODS: The mice were exposed to a single dose (6 Gy) of irradiation to induce thymic lymphomas and, at various times after irradiation, treated with an extremely high dose (30 Gy) of whole-body irradiation to enrich p53 -/- thymocytes and, 24 h later, the remaining thymocytes were assayed for cell surface markers and p53 genotype. RESULTS: In a significant fraction of the p53 +/- mice 5 weeks after 6 Gy irradiation, there was a relative increase in the number of cluster of differentiation (CD) 4+CD8+ thymocyte subpopulation among thymocytes remaining after 30 Gy irradiation. The CD4+CD8+ double-positive (DP) thymocytes were shown to contain p53-/- cells, and the number of p53 -/- thymocytes was more than 10(5) in those individuals. CONCLUSIONS: The results clearly indicated that an extremely high dose (30 Gy) of whole-body irradiation enabled us to directly detect p53 -/- thymocytes in an abundant p53 +/- thymocyte population and that proliferative p53 -/- thymocytes develop in a CD4+CD8+ DP thymocyte subpopulation within a few weeks after a single dose (6 Gy) of irradiation.

An improved culture system of mouse peripheral blood lymphocytes for analysis of radiation-induced chromosome aberrations.

There is an incentive to develop a culture system of mouse peripheral blood lymphocytes (PBLs) to serve as models for studying genotoxic effects in humans exposed to mutagens, including ionizing radiation. However, many past approaches have been laborious, complex and only partly reproducible. In the present study, we established an improved culture system of mouse PBLs by removing blood and/or plasma, which was found to inhibit in vitro mitotic stimulation or proceeding cell cycles of lymphocytes. We compared the reactions of isolated PBLs to mitogens between the classical method and the present improved one. Then, we applied this method to the cytogenetic analysis using chemically induced premature chromosome condensation (PCC) as well as the conventional analysis, and demonstrated that the frequency of excess fragments observed in PCC cells might be useful to quantify the radiation-induced damages on chromosomes.

Effect of SCID mutation on the occurrence of mouse Pc-1 (Ms6-hm) germline mutations.

Mouse Pc-1 (Ms6-hm) is a hypervariable minisatellite locus that is unstable during intergenerational transmission. This hyper-instability of Pc-1 is useful for detecting germline mutation using a small number of experimental animals, although its molecular mechanism has not yet been elucidated. We examined the effect of severe combined immune deficiency (SCID) mutation on the spontaneous germline mutation at the Pc-1 locus using the CB17 mouse strain. Our results showed that the frequency of spontaneous germline mutation at Pc-1 in the offspring of wild-type parents was 9.7%. In F1 between SCID male and wild-type female, however, the frequency of germline mutation was drastically increased to 42.3%. When SCID female mice were mated with wild-type male, the frequency of germline mutation in F1 was slightly increased to 13.6%. These results suggest that DNA protein kinase catalytic subunit (DNA-PKcs), deficiency of which causes SCID mutation, plays an important role in the stable transmission of a genome containing hypervariable tandem repeats to progeny in male germ cells.