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  • Wiley  (48)
  • Englisch  (48)
  • 1
    Online-Ressource
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    Nuclear internal transcribed spacer‐1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio
    Wiley ; 2017
    In:  Molecular Ecology Resources Vol. 17, No. 2 ( 2017-03), p. 324-333
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 17, No. 2 ( 2017-03), p. 324-333
    Kurzfassung: 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 .
    Materialart: Online-Ressource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2017.17.issue-2
    DOI: 10.1111/1755-0998.12586
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2017
    ZDB Id: 2406833-0
    SSG: 12
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  • 2
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    Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
    Wiley ; 2020
    In:  Molecular Ecology Resources Vol. 20, No. 5 ( 2020-09), p. 1248-1258
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 20, No. 5 ( 2020-09), p. 1248-1258
    Kurzfassung: 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.
    Materialart: Online-Ressource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v20.5
    DOI: 10.1111/1755-0998.13165
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 2406833-0
    SSG: 12
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  • 3
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    Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA
    Wiley ; 2017
    In:  Molecular Ecology Resources Vol. 17, No. 6 ( 2017-11)
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 17, No. 6 ( 2017-11)
    Kurzfassung: The advent of environmental DNA ( eDNA ) analysis methods has enabled rapid and wide‐range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel ( Trachurus japonicus ), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish. Long DNA fragments showed a higher decay rate than short fragments. Next, we measured the eDNA copy numbers of long and short DNA fragments using field samples, and compared them with fish biomass as measured by echo intensity. Although a previous study suggested that short eDNA fragments could be overestimated because of nontarget eDNA from a nearby fish market and carcasses, the eDNA concentrations of long fragments were correlated with echo intensity. This suggests that the concentration of longer eDNA fragments reflects fish biomass more accurately than the previous study by removing the effects of the fish market and carcasses. The length‐related differences in eDNA have a substantial potential to improve estimation of species biomass.
    Materialart: Online-Ressource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2017.17.issue-6
    DOI: 10.1111/1755-0998.12685
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2017
    ZDB Id: 2406833-0
    SSG: 12
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  • 4
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    Environment–KHV–carp–human linkage as a model for environmental diseases
    Wiley ; 2011
    In:  Ecological Research Vol. 26, No. 6 ( 2011-11), p. 1011-1016
    Details
    In: Ecological Research, Wiley, Vol. 26, No. 6 ( 2011-11), p. 1011-1016
    Kurzfassung: To predict outbreaks of infectious disease and to prevent epidemics, it is essential not only to conduct pathological studies but also to understand the interactions between the environment, pathogen, host and humans that cause and spread infectious diseases. Outbreaks of mass mortality in carp caused by Cyprinid herpesvirus 3 (CyHV‐3), formerly known as koi herpesvirus (KHV), disease have occurred worldwide since the late 1990s. We proposed an environment–KHV–carp–human linkage as a conceptual model for “environmental diseases” and specify research subjects that might be necessary to construct and shape this linkage.
    Materialart: Online-Ressource
    ISSN: 0912-3814 , 1440-1703
    URL: Article
    DOI: 10.1007/s11284-011-0881-9
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2011
    ZDB Id: 2023900-2
    SSG: 12
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  • 5
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    On‐site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation
    Wiley ; 2016
    In:  Ecological Research Vol. 31, No. 6 ( 2016-11), p. 963-967
    Details
    In: Ecological Research, Wiley, Vol. 31, No. 6 ( 2016-11), p. 963-967
    Kurzfassung: Environmental DNA (eDNA) analysis is an innovative tool for determining the distribution or abundance of aquatic macroorganisms. However, because eDNA degrades rapidly in water, long delays between sampling and analysis may hinder eDNA quantification. In the present study, we developed a portable filtration system that enables on‐site (and on‐the‐road) filtration of water samples. Degradation rates of eDNA within 6 h were compared using water from an outdoor pond that was subjected to (1) on‐site filtration, (2) transportation of water on ice, and (3) transportation of water at ambient temperature. Groups 2 and 3 were filtered in the laboratory 6 h after sampling. The concentration of eDNA was determined as the copy number of the mitochondrial cytochrome b gene of two fish species using real‐time polymerase chain reaction. The portable filtration system offers the following benefits: (1) the eDNA concentration is preserved as is at the time of sampling, permitting higher accuracy of eDNA quantification, (2) use of a disposable sealed plastic bag reduces the risk of contamination and ensures on‐the‐road filtration, (3) time is saved because filtration can be accomplished when driving between sampling sites.
    Materialart: Online-Ressource
    ISSN: 0912-3814 , 1440-1703
    URL: Article
    DOI: 10.1007/s11284-016-1400-9
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2016
    ZDB Id: 2023900-2
    SSG: 12
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  • 6
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    Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt ( Spirinchus lanceolatus )
    Wiley ; 2020
    In:  Environmental DNA Vol. 2, No. 2 ( 2020-04), p. 130-139
    Details
    In: Environmental DNA, Wiley, Vol. 2, No. 2 ( 2020-04), p. 130-139
    Kurzfassung: Monitoring reproductive migration is essential for the conservation of anadromous species. Shishamo smelt ( Spirinchus lanceolatus) is endemic to Hokkaido, the northernmost large island in Japan. S. lanceolatus is an anadromous species that is known to migrate into rivers for a very short period in early winter. While this species has a special value for local fisheries, the catch amount has drastically declined in the last few decades. Information about S. lanceolatus reproductive migration dynamics is limited, which prevents them from being efficiently managed as a resource. In this study, we used environmental DNA (eDNA) methods as a noninvasive molecular tool for estimating presence/absence and abundance/biomass of S. lanceolatus during their migration into rivers. We developed a species‐specific qPCR system for S. lanceolatus , examining (a) temporal variation in S. lanceolatus eDNA concentrations compared with catch data gathered by traditional methods and (b) variability of migratory patterns among river systems. In a core river for their spawning migration, we consistently detected S. lanceolatus eDNA throughout the spawning season, and the temporal distribution of eDNA concentration was consistent with that of the number of migrating S. lanceolatus estimated by catch survey data. In addition, we were able to detect S. lanceolatus eDNA even from rivers without any official record of their migration. Among rivers with eDNA detection, the relative eDNA concentrations varied, indicating that the population biomass differs largely among the river populations. Our study suggests that eDNA detection systems are useful for tracking reproductive migration of S. lanceolatus at fine spatio‐temporal scales.
    Materialart: Online-Ressource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    URL: Article
    DOI: 10.1002/edn3.v2.2
    DOI: 10.1002/edn3.50
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 3001165-6
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  • 7
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    Discovery of an unrecorded population of Yamato salamander ( Hynobius vandenburghi ) by GIS and eDNA analysis
    Wiley ; 2019
    In:  Environmental DNA Vol. 1, No. 3 ( 2019-09), p. 281-289
    Details
    In: Environmental DNA, Wiley, Vol. 1, No. 3 ( 2019-09), p. 281-289
    Kurzfassung: Biodiversity loss is a serious environmental problem, and human activities might be primarily responsible for the marked decline in animal populations globally. Amphibians, in particular, have significantly decreased in number in recent decades. One example is the endangered Yamato salamander ( Hynobius vandenburghi ), which is distributed in Central Japan and has a very restricted distribution in Gifu Prefecture. Aims We aimed to discover new populations of H. vandenburghi using a combination of GIS and environmental DNA (eDNA) analysis. Materials & Methods Firstly, we designed two primer sets for amplifying Hynobius species targeting mitochondrial 12S rRNA and cytochrome b genes. Next, we performed aquarium experiments to detect H. vandenburghi DNA in aquarium water. We also conducted sequential eDNA detection surveys in five known habitats in Gifu City, Japan, 17 times from January to August 2016. Following these basic eDNA studies, we used GIS to characterize the vegetation and topography of known habitats of H. vandenburghi . We collected water samples in the potential habitats identified by GIS and analyzed eDNA for the presence of H. vandenburghi using the designed primers. Finally, we conducted physical collection surveys in these potential habitats. Results We successfully developed two Hynobius‐specific primer sets and detected H. vandenburghi eDNA in aquarium water. The eDNA of the target species was detected in almost all (94%–100%) samples from four habitats, whereas only 29% of samples were positive for one habitat. We identified five potential habitats by GIS analysis. The DNA of H. vandenburghi was detected in three of five potential habitats. Finally, we discovered a new population in one of the potential sites. Discussion Our approach combining GIS and eDNA enabled the detection of novel population of an endangered amphibian species. This study was conducted by high school students under the supervision of teachers with the help of university researchers, suggesting the applicability of eDNA studies as a tool of citizen science. Conclusion The combination of GIS and eDNA will allow to detect cryptic populations on which conservation efforts may be focused and to alert people to the need for conservation action.
    Materialart: Online-Ressource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    URL: Article
    DOI: 10.1002/edn3.v1.3
    DOI: 10.1002/edn3.31
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2019
    ZDB Id: 3001165-6
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  • 8
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    Detection of herbivory: eDNA detection from feeding marks on leaves
    Wiley ; 2020
    In:  Environmental DNA Vol. 2, No. 4 ( 2020-10), p. 627-634
    Details
    In: Environmental DNA, Wiley, Vol. 2, No. 4 ( 2020-10), p. 627-634
    Kurzfassung: Many techniques have been developed to investigate the interactions between plants and herbivorous insects in natural environments and are generally used to determine either (a) which plant species are eaten by a specific herbivorous insect or (b) which herbivorous insect species are herbivores of a specific plant. The former problem is usually addressed by the direct observation of feeding and microscopic observation of gut contents and excrements, as well as the application of DNA‐barcoding techniques. However, the latter problem has typically been addressed using time‐consuming methods, such as direct observation and rearing. Therefore, more efficient techniques are needed for identifying and quantifying the interactions of plants with herbivorous insects. The present study demonstrates that the environmental DNA (eDNA) of herbivorous insects can be recovered from leaves with external foliage feeding marks. Mitochondrial DNA fragments of herbivorous insects were detected from insect‐exposed leaves using primer sets that amplified the DNA of target species. The amplification rate of the herbivorous insect DNA was positively associated with the rim length of feeding marks, which suggests that most of the insect DNA came from the feeding marks. Additionally, we showed that this method has the potential to detect eDNA from field‐collected leaves. This time‐efficient approach will contribute to the detection of plant–insect herbivore interactions.
    Materialart: Online-Ressource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    URL: Article
    DOI: 10.1002/edn3.v2.4
    DOI: 10.1002/edn3.113
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 3001165-6
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  • 9
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    Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods
    Wiley ; 2018
    In:  Freshwater Biology Vol. 63, No. 6 ( 2018-06), p. 569-580
    Details
    In: Freshwater Biology, Wiley, Vol. 63, No. 6 ( 2018-06), p. 569-580
    Kurzfassung: We present a performance evaluation of environmental DNA ( eDNA ) metabarcoding with MiFish‐U/E primers to investigate local and regional diversities of stream fish species to examine potential effectiveness, limits and future remedies of this technique in large‐scale monitoring. We hypothesised that eDNA inferences are more consistent with fish assemblages observed upstream than downstream due to a directional flow of river water. River water was sampled at 102 sites in 51 rivers around Lake Biwa in the central part of Honshu Island, Japan, within 10 person‐days, and fish species compositions inferred from eDNA and existing observational data were compared. Observation sites were chosen from the observational data that were within a certain distance (buffer range) of a water‐sampling site along a river trajectory. The hypothesis of the detection bias of eDNA towards upstream assemblage was tested by comparing results with all of the observational data, data from a higher elevation and data from a lower elevation. The Jaccard dissimilarity index was plotted between the observational data and the eDNA estimates against the buffer range; the buffer range with minimum dissimilarity was chosen. When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 86.4% of the species reported (38/44), as well as two additional species. eDNA results also showed patterns consistent with known upstream–downstream turnover of related species and biogeographical assemblage patterns of certain species. Our 10‐person‐days survey using the metabarcoding technique enabled us to obtain as much regional fish diversity data including the hypothesised pattern of eDNA detection with an upstream bias as the accumulated observational data obtained through greater amounts of time, money and labour. The problems regarding false‐positive/negative detection were suggested in our survey; however, these should be decreased or removed by modifying the sampling methods and experimental procedures in future works. Therefore, we concluded this new tool to enable monitoring that has never been implemented, such as cross‐nation, and even whole‐Earth monitoring with the data at yearly, seasonal or finer temporal scales.
    Materialart: Online-Ressource
    ISSN: 0046-5070 , 1365-2427
    URL: Issue
    URL: Article
    DOI: 10.1111/fwb.2018.63.issue-6
    DOI: 10.1111/fwb.13094
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2018
    ZDB Id: 2020306-8
    ZDB Id: 121180-8
    SSG: 12
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  • 10
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    Suppression of environmental DNA degradation in water samples associated with different storage temperature and period using benzalkonium chloride
    Wiley ; 2020
    In:  Limnology and Oceanography: Methods Vol. 18, No. 8 ( 2020-08), p. 437-445
    Details
    In: Limnology and Oceanography: Methods, Wiley, Vol. 18, No. 8 ( 2020-08), p. 437-445
    Kurzfassung: Environmental DNA (eDNA) is a useful tool for biological monitoring of a target species by detecting DNA contained in environmental samples. However, the suppression of eDNA degradation after sample collection is a major issue when estimating the presence of a target species. Recently, benzalkonium chloride (BAC) was shown to dramatically suppress the degradation of eDNA in fish species from freshwater environments. However, the effect of this inexpensive reagent has not yet been tested in the other fish and shellfish species. We examined changes in eDNA concentrations for three target species ( Corbicula japonica , Lateolabrax japonicus , and Anguilla japonica ). eDNA was measured in samples containing added BAC. The effects of storage temperature (25°C, 4°C, and −30°C) and storage periods (periods up to 21 d) were also measured to determine how sample degradation was affected. We observed that BAC addition was effective in suppressing eDNA degradation, and its influence was similar among species but not storage temperatures. The concentrations of eDNA with BAC for all three species did not decrease with storage period, except for L. japonicus at 25°C and 4°C. Our results suggest that BAC affects eDNA degradation universally for a variety of species inhabiting both freshwater and brackish water.
    Materialart: Online-Ressource
    ISSN: 1541-5856 , 1541-5856
    URL: Issue
    URL: Article
    DOI: 10.1002/lom3.v18.8
    DOI: 10.1002/lom3.10374
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 2161715-6
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