Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan
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{"title"=>"Environmental DNA as a 'snapshot' of fish distribution: A case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan", "type"=>"journal", "authors"=>[{"first_name"=>"Satoshi", "last_name"=>"Yamamoto", "scopus_author_id"=>"55475457600"}, {"first_name"=>"Kenji", "last_name"=>"Minami", "scopus_author_id"=>"36192020400"}, {"first_name"=>"Keiichi", "last_name"=>"Fukaya", "scopus_author_id"=>"36600352500"}, {"first_name"=>"Kohji", "last_name"=>"Takahashi", "scopus_author_id"=>"55500728600"}, {"first_name"=>"Hideki", "last_name"=>"Sawada", "scopus_author_id"=>"9942596900"}, {"first_name"=>"Hiroaki", "last_name"=>"Murakami", "scopus_author_id"=>"57169451400"}, {"first_name"=>"Satsuki", "last_name"=>"Tsuji", "scopus_author_id"=>"57169539800"}, {"first_name"=>"Hiroki", "last_name"=>"Hashizume", "scopus_author_id"=>"57169758400"}, {"first_name"=>"Shou", "last_name"=>"Kubonaga", "scopus_author_id"=>"57170693300"}, {"first_name"=>"Tomoya", "last_name"=>"Horiuchi", "scopus_author_id"=>"57169564700"}, {"first_name"=>"Masamichi", "last_name"=>"Hongo", "scopus_author_id"=>"57169861300"}, {"first_name"=>"Jo", "last_name"=>"Nishida", "scopus_author_id"=>"57169887900"}, {"first_name"=>"Yuta", "last_name"=>"Okugawa", "scopus_author_id"=>"57170086600"}, {"first_name"=>"Ayaka", "last_name"=>"Fujiwara", "scopus_author_id"=>"57169694300"}, {"first_name"=>"Miho", "last_name"=>"Fukuda", "scopus_author_id"=>"57169422400"}, {"first_name"=>"Shunsuke", "last_name"=>"Hidaka", "scopus_author_id"=>"57169812800"}, {"first_name"=>"Keita W.", "last_name"=>"Suzuki", "scopus_author_id"=>"37063845200"}, {"first_name"=>"Masaki", "last_name"=>"Miya", "scopus_author_id"=>"7005173446"}, {"first_name"=>"Hitoshi", "last_name"=>"Araki", "scopus_author_id"=>"7201945546"}, {"first_name"=>"Hiroki", "last_name"=>"Yamanaka", "scopus_author_id"=>"35369497900"}, {"first_name"=>"Atsushi", "last_name"=>"Maruyama", "scopus_author_id"=>"7102913001"}, {"first_name"=>"Kazushi", "last_name"=>"Miyashita", "scopus_author_id"=>"7202708298"}, {"first_name"=>"Reiji", "last_name"=>"Masuda", "scopus_author_id"=>"7101661522"}, {"first_name"=>"Toshifumi", "last_name"=>"Minamoto", "scopus_author_id"=>"25639837900"}, {"first_name"=>"Michio", "last_name"=>"Kondoh", "scopus_author_id"=>"7005073407"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"608947562", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0149786", "scopus"=>"2-s2.0-84960929379", "pmid"=>"26933889", "sgr"=>"84960929379"}, "id"=>"cd636b68-5663-3c18-bff3-73e6b4fa15c6", "abstract"=>"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 R2 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.", "link"=>"http://www.mendeley.com/research/environmental-dna-snapshot-fish-distribution-case-study-japanese-jack-mackerel-maizuru-bay-sea-japan-1", "reader_count"=>155, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Researcher"=>43, "Student > Doctoral Student"=>4, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4807549"], "description"=>"<p>Y-axis indicates vertical distance between surface- and bottom-sampling positions, i.e., the coefficient value of the class of 3.5–8.5 m was calculated using samples obtained at stations where water depth is 3.5–8.5 m. Correlation coefficient was relatively high when using samples from shallower stations, while it was low when using samples from deeper stations. This figure was depicted based on eDNA concentrations of filter series 1.</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093604, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Correlation_coefficient_between_eDNA_concentration_in_surface_and_bottom_waters_/3093604", "title"=>"Correlation coefficient between eDNA concentration in surface and bottom waters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807447"], "description"=>"<p>Location of Maizuru Bay, sampling stations and cruise track in Maizuru Bay (a) and a picture of the target species, jack mackerel (b). Gray areas indicate land masses and gray lines indicate depth contours with an interval of 4 m.</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093514, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Research_site_and_target_species_/3093514", "title"=>"Research site and target species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807558"], "description"=>"<p>Selected explanatory variables, selected size of water column, and estimated partial regression coefficient of ‘echo’ for each filter series.</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093613, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Selected_explanatory_variables_selected_size_of_water_column_and_estimated_partial_regression_coefficient_of_echo_for_each_filter_series_/3093613", "title"=>"Selected explanatory variables, selected size of water column, and estimated partial regression coefficient of ‘echo’ for each filter series.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807519"], "description"=>"<p>a, data from all research areas; b, data within 150 m of St. 2; c, data within 150 m of St. 27. Bars indicate the mean echo intensity (the average of s<sub>v</sub>) of each depth interval. Dashed lines indicate frequency distribution of water depth. Number below station names indicates the mean water depth.</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093583, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Vertical_distributions_of_echo_intensity_and_the_sea_bottom_/3093583", "title"=>"Vertical distributions of echo intensity and the sea bottom.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807402", "https://ndownloader.figshare.com/files/4807411", "https://ndownloader.figshare.com/files/4807414", "https://ndownloader.figshare.com/files/4807417", "https://ndownloader.figshare.com/files/4807423", "https://ndownloader.figshare.com/files/4807429", "https://ndownloader.figshare.com/files/4807432"], "description"=>"<div><p>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 (<i>Trachurus japonicus</i>) using echo sounder technology. A linear model showed a high <i>R</i><sup>2</sup> 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.</p></div>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093490, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0149786.s001", "https://dx.doi.org/10.1371/journal.pone.0149786.s002", "https://dx.doi.org/10.1371/journal.pone.0149786.s003", "https://dx.doi.org/10.1371/journal.pone.0149786.s004", "https://dx.doi.org/10.1371/journal.pone.0149786.s005", "https://dx.doi.org/10.1371/journal.pone.0149786.s006", "https://dx.doi.org/10.1371/journal.pone.0149786.s007"], "stats"=>{"downloads"=>3, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Environmental_DNA_as_a_Snapshot_of_Fish_Distribution_A_Case_Study_of_Japanese_Jack_Mackerel_in_Maizuru_Bay_Sea_of_Japan/3093490", "title"=>"Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807489"], "description"=>"<p>Vertical bar on the cruise track (gray line) indicates local s<sub>a</sub> values (i.e., fish biomass observed using quantitative echo sounder), which is the integrated s<sub>v</sub> of a water column with a cross-sectional area of 1 m<sup>2</sup>. This figure is depicted according to s<sub>a</sub> extracted every 80-m intervals. Note that this figure shows a summary of field observation using echo sounder. We used s<sub>v</sub> values rather than s<sub>a</sub> values as index of fish biomass in regression analyses (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149786#pone.0149786.s001\" target=\"_blank\">S1 Fig</a>).</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093556, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Observed_fish_biomass_using_echo_sounder_/3093556", "title"=>"Observed fish biomass using echo sounder.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807537"], "description"=>"<p>Relationships among eDNA concentrations (only results from filter series 1 are shown), local echo intensity (‘echo’ in regression analysis) and a measure of the inverse of distance between sampling stations and the fish market (‘inv-dist’ in regression analysis). Regression surfaces (blue), which were assessed using linear regression analysis, are indicated. Upper panels show the results of all data (a, surface water; b, bottom water) and lower panels show the results of data without outliers (c, surface water; d, bottom water).</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093592, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Regression_surface_/3093592", "title"=>"Regression surface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4807465"], "description"=>"<p>Based on CytB gene copy number in a 2 μL template DNA solution at the 47 sampling station, spatial variation of jack mackerel eDNA in west Maizuru Bay was estimated by approximation. The level of the approximate eDNA concentration is indicated by colors between red (relatively high concentration) and blue (low concentration). White areas suggest that the concentration approximated using a regularized spline is ≤ 0. Spatial approximation was performed using a regularized spline with a tension parameter of 40.</p>", "links"=>[], "tags"=>["biomas", "Maizuru Bay", "echo intensity", "eDNA concentration", "fish distribution", "surface water samples", "outlier data points", "water sampling sites", "Japanese Jack Mackerel"], "article_id"=>3093535, "categories"=>["Biochemistry", "Genetics", "Molecular Biology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Satoshi Yamamoto", "Kenji Minami", "Keiichi Fukaya", "Kohji Takahashi", "Hideki Sawada", "Hiroaki Murakami", "Satsuki Tsuji", "Hiroki Hashizume", "Shou Kubonaga", "Tomoya Horiuchi", "Masamichi Hongo", "Jo Nishida", "Yuta Okugawa", "Ayaka Fujiwara", "Miho Fukuda", "Shunsuke Hidaka", "Keita W. Suzuki", "Masaki Miya", "Hitoshi Araki", "Hiroki Yamanaka", "Atsushi Maruyama", "Kazushi Miyashita", "Reiji Masuda", "Toshifumi Minamoto", "Michio Kondoh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149786.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Spatial_approximation_of_jack_mackerel_eDNA_concentration_/3093535", "title"=>"Spatial approximation of jack mackerel eDNA concentration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-03-02 07:33:41"}

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{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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