How Many Loci Does it Take to DNA Barcode a Crocus?
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{"title"=>"How many loci does it take to DNA barcode a crocus?", "type"=>"journal", "authors"=>[{"first_name"=>"Ole", "last_name"=>"Seberg", "scopus_author_id"=>"6701539037"}, {"first_name"=>"Gitte", "last_name"=>"Petersen", "scopus_author_id"=>"7202922863"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"19240801", "sgr"=>"80053328730", "doi"=>"10.1371/journal.pone.0004598", "scopus"=>"2-s2.0-80053328730", "pui"=>"354309074", "isbn"=>"1932-6203 (Electronic)", "issn"=>"19326203"}, "id"=>"387bd14b-b34f-3a52-8c6b-f0c2c5e2c5ab", "abstract"=>"BACKGROUND: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.\\n\\nMETHODOLOGY AND PRINCIPAL FINDINGS: Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context.\\n\\nCONCLUSIONS/SIGNIFICANCE: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.", "link"=>"http://www.mendeley.com/research/loci-it-take-dna-barcode-crocus", "reader_count"=>161, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>18, "Researcher"=>36, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>47, "Student > Postgraduate"=>4, "Student > Master"=>20, "Other"=>5, "Student > Bachelor"=>7, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>18, "Researcher"=>36, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>47, "Student > Postgraduate"=>4, "Student > Master"=>20, "Other"=>5, "Student > Bachelor"=>7, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>13}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>4, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>13, "Mathematics"=>1, "Agricultural and Biological Sciences"=>127, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Computer Science"=>3, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>127}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>6}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"Ecuador"=>1, "United States"=>6, "United Kingdom"=>4, "Zambia"=>1, "Russia"=>1, "Spain"=>1, "Canada"=>4, "Netherlands"=>1, "Belgium"=>2, "Iran"=>1, "Norway"=>1, "China"=>1, "Brazil"=>2, "South Africa"=>1, "Italy"=>3, "France"=>1, "Germany"=>3}, "group_count"=>8}

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  • {"files"=>["https://ndownloader.figshare.com/files/907230"], "description"=>"*<p>Of 85 species. DNA was no longer available for <i>C. hartmannianus</i> Holmboe.</p>", "links"=>[], "tags"=>["plastid", "regions", "individually", "86"], "article_id"=>577691, "categories"=>["Ecology", "Evolutionary Biology", "Plant Biology"], "users"=>["Ole Seberg", "Gitte Petersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004598.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_variation_and_species_identification_ability_of_six_plastid_regions_individually_in_86_species_of_Crocus_/577691", "title"=>"Sequence variation and species identification ability of six plastid regions individually in 86 species of <i>Crocus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-25 02:08:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/907168"], "description"=>"<p>The extremely short branches make identification by cluster memberships difficult as does the “non-monophyly” of several species. Species that cannot be identified by any of the sequences used are marked in blue. The NJ tree is rooted with the two <i>Crocus</i> species that are sister group to the remaining <i>Crocus</i> species in the parsimony based phylogeny (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004598#pone.0004598.s001\" target=\"_blank\">figure S1</a>).</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "plant biology"], "article_id"=>577628, "categories"=>["Ecology", "Evolutionary Biology", "Plant Biology"], "users"=>["Ole Seberg", "Gitte Petersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004598.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_tree_of_Crocus_/577628", "title"=>"Neighbor-joining tree of <i>Crocus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-25 02:07:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/448691", "https://ndownloader.figshare.com/files/448719", "https://ndownloader.figshare.com/files/448727", "https://ndownloader.figshare.com/files/448732", "https://ndownloader.figshare.com/files/448743"], "description"=>"<div><h3>Background</h3><p>DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.</p><h3>Methodology and Principal Findings</h3><p>Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will – as is the case in crocus – undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached – even in a taxonomic context.</p><h3>Conclusions/Significance</h3><p>The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.</p></div>", "links"=>[], "tags"=>["loci", "dna", "barcode"], "article_id"=>148433, "categories"=>["Ecology", "Evolutionary Biology", "Cell Biology"], "users"=>["Ole Seberg", "Gitte Petersen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004598.s001", "https://dx.doi.org/10.1371/journal.pone.0004598.s002", "https://dx.doi.org/10.1371/journal.pone.0004598.s003", "https://dx.doi.org/10.1371/journal.pone.0004598.s004", "https://dx.doi.org/10.1371/journal.pone.0004598.s005"], "stats"=>{"downloads"=>10, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/How_Many_Loci_Does_it_Take_to_DNA_Barcode_a_Crocus_/148433", "title"=>"How Many Loci Does it Take to DNA Barcode a Crocus?", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-02-25 02:20:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/907077"], "description"=>"<p>The genus includes 86 known species, and the six regions (five proposed barcode regions plus <i>ndhF</i>) used here identify 79 species. The regions are added according to their ability to identify species. The performance of individual genes is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004598#pone-0004598-t002\" target=\"_blank\">Table 2</a>. The logarithmic trend line (y = 12.3 ln(x)−21.0) and the R<sup>2</sup> ( = 0.97) were calculated in Excel® and checked in JMP, Version 7. SAS Institute Inc., Cary, NC, 1989–2007.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "plant biology"], "article_id"=>577538, "categories"=>["Ecology", "Evolutionary Biology", "Plant Biology"], "users"=>["Ole Seberg", "Gitte Petersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004598.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationship_between_sequence_length_and_the_number_of_Crocus_species_identified_/577538", "title"=>"The relationship between sequence length and the number of <i>Crocus</i> species identified.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-25 02:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/907261"], "description"=>"<p>The best combination, i.e., the combination of the fewest number of sequences yielding the highest number of identified species, is marked in bold.</p>", "links"=>[], "tags"=>["plastid", "regions", "combinations", "86"], "article_id"=>577723, "categories"=>["Ecology", "Evolutionary Biology", "Plant Biology"], "users"=>["Ole Seberg", "Gitte Petersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004598.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_variation_and_species_identification_ability_of_six_plastid_regions_in_combinations_in_86_species_of_Crocus_/577723", "title"=>"Sequence variation and species identification ability of six plastid regions in combinations in 86 species of <i>Crocus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-25 02:08:43"}

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  • {"unique-ip"=>"14", "full-text"=>"14", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
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  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
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  • {"unique-ip"=>"18", "full-text"=>"23", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"18", "full-text"=>"17", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
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  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
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  • {"unique-ip"=>"14", "full-text"=>"17", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"16", "full-text"=>"18", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
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  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"17", "full-text"=>"16", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
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  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"15", "full-text"=>"11", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
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  • {"unique-ip"=>"10", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"16", "full-text"=>"22", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"19", "full-text"=>"17", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"18", "full-text"=>"21", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"14", "full-text"=>"14", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
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Relative Metric

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