Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences
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{"title"=>"Using DNA metabarcoding to identify the floral composition of honey: A new tool for investigating honey bee foraging preferences", "type"=>"journal", "authors"=>[{"first_name"=>"Jennifer", "last_name"=>"Hawkins", "scopus_author_id"=>"56890449700"}, {"first_name"=>"Natasha", "last_name"=>"De Vere", "scopus_author_id"=>"23488430200"}, {"first_name"=>"Adelaide", "last_name"=>"Griffith", "scopus_author_id"=>"56890691000"}, {"first_name"=>"Col R.", "last_name"=>"Ford", "scopus_author_id"=>"55246627100"}, {"first_name"=>"Joel", "last_name"=>"Allainguillaume", "scopus_author_id"=>"6507115615"}, {"first_name"=>"Matthew J.", "last_name"=>"Hegarty", "scopus_author_id"=>"8748548300"}, {"first_name"=>"Les", "last_name"=>"Baillie", "scopus_author_id"=>"56890829200"}, {"first_name"=>"Beverley", "last_name"=>"Adams-Groom", "scopus_author_id"=>"16633743800"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84943229982", "sgr"=>"84943229982", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0134735", "pmid"=>"26308362", "isbn"=>"10.1371/journal.pone.0134735", "pui"=>"606225823"}, "id"=>"321d9a44-01d9-3b3a-95c1-5ed04328b957", "abstract"=>"Identifying the floral composition of honey provides a method for investigating the plants that honey bees visit. We compared melissopalynology, where pollen grains retrieved from honey are identified morphologically, with a DNA metabarcoding approach using the rbcL DNA barcode marker and 454-pyrosequencing. We compared nine honeys supplied by beekeepers in the UK. DNA metabarcoding and melissopalynology were able to detect the most abundant floral components of honey. There was 92% correspondence for the plant taxa that had an abundance of over 20%. However, the level of similarity when all taxa were compared was lower, ranging from 22-45%, and there was little correspondence between the relative abundance of taxa found using the two techniques. DNA metabarcoding provided much greater repeatability, with a 64% taxa match compared to 28% with melissopalynology. DNA metabarcoding has the advantage over melissopalynology in that it does not require a high level of taxonomic expertise, a greater sample size can be screened and it provides greater resolution for some plant families. However, it does not provide a quantitative approach and pollen present in low levels are less likely to be detected. We investigated the plants that were frequently used by honey bees by examining the results obtained from both techniques. Plants with a broad taxonomic range were detected, covering 46 families and 25 orders, but a relatively small number of plants were consistently seen across multiple honey samples. Frequently found herbaceous species were Rubus fruticosus, Filipendula ulmaria, Taraxacum officinale, Trifolium spp., Brassica spp. and the non-native, invasive, Impatiens glandulifera. Tree pollen was frequently seen belonging to Castanea sativa, Crataegus monogyna and species of Malus, Salix and Quercus. We conclude that although honey bees are considered to be supergeneralists in their foraging choices, there are certain key species or plant groups that are particularly important in the honey bees environment. The reasons for this require further investigation in order to better understand honey bee nutritional requirements. DNA metabarcoding can be easily and widely used to investigate floral visitation in honey bees and can be adapted for use with other insects. It provides a starting point for investigating how we can better provide for the insects that we rely upon for pollination.", "link"=>"http://www.mendeley.com/research/using-dna-metabarcoding-identify-floral-composition-honey-new-tool-investigating-honey-bee-foraging", "reader_count"=>120, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>25, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>2, "Student > Master"=>20, "Other"=>7, "Student > Bachelor"=>19, "Lecturer"=>4, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>25, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>2, "Student > Master"=>20, "Other"=>7, "Student > Bachelor"=>19, "Lecturer"=>4, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Environmental Science"=>15, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>74, "Medicine and Dentistry"=>2, "Arts and Humanities"=>3, "Veterinary Science and Veterinary Medicine"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>2, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>74}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>15}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "Germany"=>2}, "group_count"=>8}

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  • {"files"=>["https://ndownloader.figshare.com/files/2228173"], "description"=>"<p>Species and genera found in more than one honey sample for DNA metabarcoding and melissopalynology.</p>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523369, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0134735.t006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_and_genera_found_in_more_than_one_honey_sample_for_DNA_metabarcoding_and_melissopalynology_/1523369", "title"=>"Species and genera found in more than one honey sample for DNA metabarcoding and melissopalynology.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-26 03:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2228171"], "description"=>"<p>Values represent the percentage of the total number of pollen grains or sequence reads obtained for that honey. Taxa recorded using microscopy only based on the presence of a single pollen grain are not shown (these are provided in full in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134735#pone.0134735.s001\" target=\"_blank\">S1 Dataset</a>). Boxes outlined in red denote taxa with an abundance of 20% or over for either technique. Correlations between the relative abundance of taxa recorded with the two methods are assessed with Spearman Rank Correlations. Spearman’s Rho is shown with the corresponding p-value in brackets.</p>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523367, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0134735.g003", "stats"=>{"downloads"=>0, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plants_identified_using_DNA_metabarcoding_D_and_melissopalynology_M_for_nine_honeys_/1523367", "title"=>"Plants identified using DNA metabarcoding (D) and melissopalynology (M) for nine honeys.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-26 03:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2228172"], "description"=>"<p>Honey samples were provided by domestic beekeepers from hives located in gardens or smallholdings. The vegetation surrounding the hives was characterised based on descriptions from the beekeepers and observation of aerial images. H1 and H1_2 were two samples taken from the same hive.</p><p>The locations of the honey samples analysed using DNA metabarcoding and melissopalynology.</p>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523368, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0134735.t001", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_locations_of_the_honey_samples_analysed_using_DNA_metabarcoding_and_melissopalynology_/1523368", "title"=>"The locations of the honey samples analysed using DNA metabarcoding and melissopalynology.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-26 03:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2228170"], "description"=>"<p>The number of taxa detected (at family, genus or species level) is divided into those found with both techniques and those found using only one method. The taxa found using melissopalynology only are further subdivided into those where multiple pollen grains were found and those characterised with just a single grain. The values in the pie chart are the % of taxa within each category.</p>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523366, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0134735.g002", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_similarity_of_plant_taxa_found_in_nine_honey_samples_using_DNA_metabarcoding_and_melissopalynology_/1523366", "title"=>"The similarity of plant taxa found in nine honey samples using DNA metabarcoding and melissopalynology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-26 03:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2228174", "https://ndownloader.figshare.com/files/2228175", "https://ndownloader.figshare.com/files/2228176", "https://ndownloader.figshare.com/files/2228177"], "description"=>"<div><p>Identifying the floral composition of honey provides a method for investigating the plants that honey bees visit. We compared melissopalynology, where pollen grains retrieved from honey are identified morphologically, with a DNA metabarcoding approach using the <i>rbcL</i> DNA barcode marker and 454-pyrosequencing. We compared nine honeys supplied by beekeepers in the UK. DNA metabarcoding and melissopalynology were able to detect the most abundant floral components of honey. There was 92% correspondence for the plant taxa that had an abundance of over 20%. However, the level of similarity when all taxa were compared was lower, ranging from 22–45%, and there was little correspondence between the relative abundance of taxa found using the two techniques. DNA metabarcoding provided much greater repeatability, with a 64% taxa match compared to 28% with melissopalynology. DNA metabarcoding has the advantage over melissopalynology in that it does not require a high level of taxonomic expertise, a greater sample size can be screened and it provides greater resolution for some plant families. However, it does not provide a quantitative approach and pollen present in low levels are less likely to be detected. We investigated the plants that were frequently used by honey bees by examining the results obtained from both techniques. Plants with a broad taxonomic range were detected, covering 46 families and 25 orders, but a relatively small number of plants were consistently seen across multiple honey samples. Frequently found herbaceous species were <i>Rubus fruticosus</i>, <i>Filipendula ulmaria</i>, <i>Taraxacum officinale</i>, <i>Trifolium</i> spp., <i>Brassica</i> spp. and the non-native, invasive, <i>Impatiens glandulifera</i>. Tree pollen was frequently seen belonging to <i>Castanea sativa</i>, <i>Crataegus monogyna</i> and species of <i>Malus</i>, <i>Salix</i> and <i>Quercus</i>. We conclude that although honey bees are considered to be supergeneralists in their foraging choices, there are certain key species or plant groups that are particularly important in the honey bees environment. The reasons for this require further investigation in order to better understand honey bee nutritional requirements. DNA metabarcoding can be easily and widely used to investigate floral visitation in honey bees and can be adapted for use with other insects. It provides a starting point for investigating how we can better provide for the insects that we rely upon for pollination.</p></div>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523370, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0134735.s001", "https://dx.doi.org/10.1371/journal.pone.0134735.s002", "https://dx.doi.org/10.1371/journal.pone.0134735.s003", "https://dx.doi.org/10.1371/journal.pone.0134735.s004"], "stats"=>{"downloads"=>6, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Using_DNA_Metabarcoding_to_Identify_the_Floral_Composition_of_Honey_A_New_Tool_for_Investigating_Honey_Bee_Foraging_Preferences_/1523370", "title"=>"Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-26 03:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2228169"], "description"=>"<p>The location of the honey bee colonies from which honey was provided by domestic beekeepers.</p>", "links"=>[], "tags"=>["taxa", "rbcL DNA barcode marker", "melissopalynology", "Honey bees", "uk", "DNA metabarcoding", "DNA metabarcoding approach", "honey bees visit", "Honey Bee Foraging Preferences", "honey bees environment"], "article_id"=>1523365, "categories"=>["Uncategorised"], "users"=>["Jennifer Hawkins", "Natasha de Vere", "Adelaide Griffith", "Col R. Ford", "Joel Allainguillaume", "Matthew J. Hegarty", "Les Baillie", "Beverley Adams-Groom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0134735.g001", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_location_of_the_honey_bee_colonies_from_which_honey_was_provided_by_domestic_beekeepers_/1523365", "title"=>"The location of the honey bee colonies from which honey was provided by domestic beekeepers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-26 03:46:08"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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