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{"title"=>"Tropical Plant-Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes", "type"=>"journal", "authors"=>[{"first_name"=>"Carlos", "last_name"=>"García-Robledo", "scopus_author_id"=>"23093709600"}, {"first_name"=>"David L.", "last_name"=>"Erickson", "scopus_author_id"=>"7203015926"}, {"first_name"=>"Charles L.", "last_name"=>"Staines", "scopus_author_id"=>"6603746318"}, {"first_name"=>"Terry L.", "last_name"=>"Erwin", "scopus_author_id"=>"6701802648"}, {"first_name"=>"W. John", "last_name"=>"Kress", "scopus_author_id"=>"7006149645"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84872197921", "doi"=>"10.1371/journal.pone.0052967", "pui"=>"368093914", "pmid"=>"23308128", "scopus"=>"2-s2.0-84872197921", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"edcd6d53-33ce-3d52-a802-c911dcfa857a", "abstract"=>"Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt's sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.", "link"=>"http://www.mendeley.com/research/tropical-plantherbivore-networks-reconstructing-species-interactions-using-dna-barcodes", "reader_count"=>200, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>13, "Researcher"=>39, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>9, "Student > Master"=>30, "Other"=>4, "Student > Bachelor"=>19, "Lecturer"=>3, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>13, "Researcher"=>39, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>9, "Student > Master"=>30, "Other"=>4, "Student > Bachelor"=>19, "Lecturer"=>3, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Engineering"=>1, "Environmental Science"=>21, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>153, "Medicine and Dentistry"=>2, "Psychology"=>1, "Computer Science"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>153}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>21}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>2, "China"=>2, "Brazil"=>5, "United Kingdom"=>3, "Italy"=>1, "Mexico"=>1, "Kenya"=>1, "France"=>2, "Portugal"=>3, "Germany"=>2, "Spain"=>2}, "group_count"=>3}

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• {"id"=>"304581562127773696", "text"=>"Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes #cienciacriolla http://t.co/JAdceRiXpQ", "created_at"=>"2013-02-21T13:21:17Z", "user"=>"cdanielcadena", "user_name"=>"daniel cadena", "user_profile_image"=>"http://a0.twimg.com/profile_images/2369826125/9xkom6np5vcohr6zv9xg_normal.jpeg"}
• {"id"=>"305364410740912128", "text"=>"Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes http://t.co/Nvu7UAsmCF", "created_at"=>"2013-02-23T17:12:03Z", "user"=>"dlizcano", "user_name"=>"Diego J. Lizcano", "user_profile_image"=>"http://a0.twimg.com/profile_images/258599627/cabezaDanta_normal.jpg"}
• {"id"=>"316509324304347137", "text"=>"Beetles leaf-rollin', they feedin', tryin' to catch 'em interactin': Using DNA to work out plant-insect interactions: http://t.co/nF2gVsM7ru", "created_at"=>"2013-03-26T11:17:58Z", "user"=>"The_Episiarch", "user_name"=>"Tommy Leung", "user_profile_image"=>"http://a0.twimg.com/profile_images/2946280882/1ddf9e74fbbdc87e82d11eba0914fdc9_normal.png"}
• {"id"=>"317312048914632704", "text"=>"Tropical plant–herbivore networks reconstructed. New PLOS ONE paper by EOL Rubenstein fellow Carlos García-Robledo: http://t.co/WVWFbGTY7i", "created_at"=>"2013-03-28T16:27:42Z", "user"=>"eol", "user_name"=>"Encyclopedia of Life", "user_profile_image"=>"http://a0.twimg.com/profile_images/1697067756/follow_eol_on_twitter_normal.png"}
• {"id"=>"317491080759238658", "text"=>"What are beetles eating? In this paper they extract plant DNA from insects' stomachs and ID the plants they ate! http://t.co/odbBkpktGj", "created_at"=>"2013-03-29T04:19:07Z", "user"=>"nashturley", "user_name"=>"Nash Turley", "user_profile_image"=>"http://a0.twimg.com/profile_images/1249086569/nash_leaf_small_normal.JPG"}
• {"id"=>"332178774936403968", "text"=>"¿Quién come a quién? \"Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes\" http://t.co/qyotJAyndg", "created_at"=>"2013-05-08T17:02:46Z", "user"=>"EvaAlloza", "user_name"=>"Eva Alloza", "user_profile_image"=>"http://a0.twimg.com/profile_images/2988330432/3ba4cccb8f5be98aa42cf35b0d281890_normal.jpeg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/277749", "https://ndownloader.figshare.com/files/277813", "https://ndownloader.figshare.com/files/277874"], "description"=>"<div><p>Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (<em>rbcL</em>, <em>trnH-psbA</em> and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (<em>rbcL</em> and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The <em>rbcL</em> locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt’s sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.</p> </div>", "links"=>[], "tags"=>["reconstructing", "interactions", "dna", "barcodes"], "article_id"=>114776, "categories"=>["Biochemistry", "Cell Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.s001", "https://dx.doi.org/10.1371/journal.pone.0052967.s002", "https://dx.doi.org/10.1371/journal.pone.0052967.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Tropical_Plant_Herbivore_Networks_Reconstructing_Species_Interactions_Using_DNA_Barcodes__/114776", "title"=>"Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-08 01:19:36"}
• {"files"=>["https://ndownloader.figshare.com/files/510643"], "description"=>"<p>First we assembled a DNA barcode library containing sequences of all potential host plants (<i>A</i>). After collecting insect herbivores in the field (<i>B</i>), we extracted plant DNA from gut contents (<i>C</i>). Host plant identifications were performed by comparing DNA sequences extracted from insect herbivores to sequences in the DNA barcode library using the BLAST algorithm and default search parameters (<i>D</i>).</p>", "links"=>[], "tags"=>["dna"], "article_id"=>181143, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diet_identification_using_DNA_barcodes_/181143", "title"=>"Diet identification using DNA barcodes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:19:03"}
• {"files"=>["https://ndownloader.figshare.com/files/510792"], "description"=>"<p><i>A</i>. Interactions recorded for two years during rainy and dry seasons (October 2008 - February 2009 and October 2010– February 2011). Each matrix element represents an association between an insect herbivore species (rows) and a host plant species (columns). Interactions in red were recorded during the second year of this study and selected for diet analyses. <i>B</i>. Sampling effort and accumulation curves of plant and insect herbivore species and their interactions at La Selva (Mean ± SD). Total number of host plants censused = 3092. Total number of insect herbivore records = 7359. Host plant species abbreviations: <u>Heliconiaceae.</u> Him = <i>Heliconia imbricata</i>. Hir = <i>H. irrasa</i>. Hla = <i>H. latispatha</i>. Hmr = <i>H. mariae</i>. Hmt = <i>H. mathiasiae</i>. Hpo = <i>H. pogonantha</i>. Hum = <i>H. umbrophila.</i> Hwa = <i>H. wagneriana</i>. <u>Zingiberaceae.</u> Ral = <i>Renealmia alpinia</i>. Rce = <i>R. cernua</i>. Rpl = <i>R. pluriplicata</i>. <u>Costaceae.</u> Cbr = <i>Costus bracteatus</i>. Clae = <i>C. laevis</i>. Clim = <i>C. lima</i>. Cmal = <i>C. malortieanus</i>. Cpu = <i>C. pulverulentus. </i><u>Marantaceae.</u> Ccl = <i>C. cleistantha</i>. Ccr = <i>C. crotalifera</i>. Cgy = <i>C. gymnocarpa</i>. Cha = <i>C. hammelii</i>. Cin = <i>C. inocephala</i>. Clas = <i>C. lasiostachya.</i> Cle = <i>C. leucostachys</i>. Clu = <i>C. lutea</i>. Cma = <i>C. marantifolia</i>. Csi = <i>C. similis</i>. Cve = <i>C. venusta</i>. Cwa = <i>C. warscewiczii</i>. Iel = <i>Ischnosiphon elegans</i>. Iin = <i>I. inflatus</i>. Ppr = <i>Pleiostachya pruinosa</i>. Cannaceae: Ctu = <i>Canna tuerckheimii</i>.</p>", "links"=>[], "tags"=>["rolled-leaf", "beetles", "associations", "zingiberales", "la", "selva", "costa"], "article_id"=>181276, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_comprehensive_survey_of_rolled_leaf_beetles_and_their_associations_with_Zingiberales_at_La_Selva_Biological_Station_Costa_Rica_/181276", "title"=>"A comprehensive survey of rolled-leaf beetles and their associations with Zingiberales at La Selva Biological Station, Costa Rica.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:21:16"}
• {"files"=>["https://ndownloader.figshare.com/files/510916"], "description"=>"<p>Diet identification was performed using the molecular markers: <i>A</i>. <i>rbcL</i> and <i>B</i>. ITS2. Each matrix element represents the associations between a rolled-leaf beetle species (rows) and a host plant (columns). N = interaction failed to be identified by the molecular marker. Taxonomic resolution of successful host plant identifications: O = Order, F = Family, G = Genus, S = Species. Total of sequences = 403 (DNA sequences extracted from insect gut contents are included in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052967#pone.0052967.s003\" target=\"_blank\">Supplement S1</a>). Plant species abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052967#pone-0052967-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["insect-host", "associations", "dna", "extracted", "rolled-leaf", "beetle"], "article_id"=>181405, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_insect_host_plant_associations_using_DNA_extracted_from_rolled_leaf_beetle_gut_contents_/181405", "title"=>"Identification of insect-host plant associations using DNA extracted from rolled-leaf beetle gut contents.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:23:25"}
• {"files"=>["https://ndownloader.figshare.com/files/511051"], "description"=>"<p>Rectangles represent insect herbivore and host plant species. Lines connect insect herbivores to their host plants. Line colors represent the taxonomic resolution at which each host plant association was identified. Rectangle size is proportional to its number of interactions. Host plant associations were inferred from <i>rbcL</i> and ITS2 DNA fragments. Fragments were compared to host plant DNA barcode libraries containing sequences of all potential hosts in the study area. Total of insect species = 19. Total of plant species = 28. Total of interaction = 74. (<i>see</i> matrix of associations in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052967#pone.0052967.s001\" target=\"_blank\">Table S1</a>).</p>", "links"=>[], "tags"=>["plant-herbivore", "dna", "extracted"], "article_id"=>181547, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstruction_of_a_tropical_plant_herbivore_network_using_DNA_extracted_from_insect_gut_contents_/181547", "title"=>"Reconstruction of a tropical plant-herbivore network using DNA extracted from insect gut contents.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:25:47"}
• {"files"=>["https://ndownloader.figshare.com/files/511189"], "description"=>"<p>Diet identifications were performed by comparing DNA sequences from insect gut contents with DNA barcode libraries containing sequences of all potential host plants present in the study area (identification probabilities used to estimate sampling efforts are included in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052967#pone-0052967-t001\" target=\"_blank\">Table 1</a>). <i>A</i>. <i>rbcL</i> DNA fragments allowed the identification of host plants to the family and genus taxonomic levels. <i>B</i>. ITS2 sequences identified insect hosts to the genus and species taxonomic levels.</p>", "links"=>[], "tags"=>["herbivore", "plants", "molecular", "markers"], "article_id"=>181684, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_effort_and_successful_identification_of_insect_herbivore_host_plants_using_two_molecular_markers_Mean_177_SD_/181684", "title"=>"Sampling effort and successful identification of insect herbivore host plants using two molecular markers (Mean ± SD).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-08 00:28:04"}
• {"files"=>["https://ndownloader.figshare.com/files/511270"], "description"=>"<p>Percent of success extracting plant DNA from gut contents and identification success of the resulting DNA sequences for the DNA barcodes <i>rbcL</i> and ITS2.</p>", "links"=>[], "tags"=>["extracting", "dna", "contents", "resulting", "sequences", "barcodes"], "article_id"=>181760, "categories"=>["Biochemistry", "Plant Biology"], "users"=>["Carlos García-Robledo", "David L. Erickson", "Charles L. Staines", "Terry L. Erwin", "W. John Kress"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052967.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_of_success_extracting_plant_DNA_from_gut_contents_and_identification_success_of_the_resulting_DNA_sequences_for_the_DNA_barcodes_rbcL_and_ITS2_/181760", "title"=>"Percent of success extracting plant DNA from gut contents and identification success of the resulting DNA sequences for the DNA barcodes <i>rbcL</i> and ITS2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-08 00:29:20"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime