Identification of Rays through DNA Barcoding: An Application for Ecologists
Publication Date
June 11, 2012
Journal
PLOS ONE
Authors
Florencia Cerutti Pereyra, Mark G. Meekan, Nu Wei V. Wei, Owen O'shea, et al
Volume
7
Issue
6
Pages
e36479
DOI
https://dx.plos.org/10.1371/journal.pone.0036479
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0036479
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22701556
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372520
Europe PMC
http://europepmc.org/abstract/MED/22701556
Web of Science
000305337600003
Scopus
84862186847
Mendeley
http://www.mendeley.com/research/identification-rays-through-dna-barcoding-application-ecologists
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Mendeley | Further Information

{"title"=>"Identification of rays through DNA barcoding: An application for ecologists", "type"=>"journal", "authors"=>[{"first_name"=>"Florencia", "last_name"=>"Cerutti-Pereyra", "scopus_author_id"=>"55249978800"}, {"first_name"=>"Mark G.", "last_name"=>"Meekan", "scopus_author_id"=>"6701849401"}, {"first_name"=>"Nu Wei V.", "last_name"=>"Wei", "scopus_author_id"=>"55249792200"}, {"first_name"=>"Owen", "last_name"=>"O'Shea", "scopus_author_id"=>"35885816800"}, {"first_name"=>"Corey J.A.", "last_name"=>"Bradshaw", "scopus_author_id"=>"7102130752"}, {"first_name"=>"Chris M.", "last_name"=>"Austin", "scopus_author_id"=>"35576495400"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22701556", "doi"=>"10.1371/journal.pone.0036479", "sgr"=>"84862186847", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84862186847", "issn"=>"19326203", "pui"=>"364995636"}, "id"=>"132abb4a-4f20-3ac5-8309-956439c75e2f", "abstract"=>"DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the 'uarnak' complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.", "link"=>"http://www.mendeley.com/research/identification-rays-through-dna-barcoding-application-ecologists", "reader_count"=>138, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>4, "Researcher"=>26, "Student > Ph. D. Student"=>33, "Student > Postgraduate"=>5, "Student > Master"=>27, "Other"=>5, "Student > Bachelor"=>20, "Lecturer > Senior Lecturer"=>3, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>4, "Researcher"=>26, "Student > Ph. D. Student"=>33, "Student > Postgraduate"=>5, "Student > Master"=>27, "Other"=>5, "Student > Bachelor"=>20, "Lecturer > Senior Lecturer"=>3, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>15, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>92, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>1, "Chemistry"=>1, "Social Sciences"=>2, "Computer Science"=>2, "Earth and Planetary Sciences"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>92}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>15}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Puerto Rico"=>1, "United States"=>1, "Brazil"=>1, "Mexico"=>2, "United Kingdom"=>2, "Malaysia"=>1, "United Arab Emirates"=>1, "Australia"=>4, "Chile"=>1, "Iceland"=>1, "India"=>1}, "group_count"=>3}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/625795"], "description"=>"<p>Reduced view of the neighbour-joining tree based on COI sequence data using Kimura-two-parameter substitution model (left); the first part of the tree (right). Names in red are the sequences obtained in this study, the corrected nomenclature is in () and given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036479#pone.0036479.s002\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["rays"], "article_id"=>296286, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036479.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationship_of_rays_Part_I_/296286", "title"=>"Phylogenetic relationship of rays Part I.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-11 01:44:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/625928"], "description"=>"<p>Second part of the Neighbour-joining tree based on COI sequence data using Kimura-two-parameter substitution model (left); the second part of the tree (right). Names in red are the sequences obtained in this study, the corrected nomenclature is in () and given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036479#pone.0036479.s002\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["rays"], "article_id"=>296422, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036479.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationship_of_rays_Part_II_/296422", "title"=>"Phylogenetic relationship of rays Part II.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-11 01:47:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/324436", "https://ndownloader.figshare.com/files/324528", "https://ndownloader.figshare.com/files/324596"], "description"=>"<div><p>DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the <em>Neotrygon kuhlii</em> species complex and the <em>Aetobatus</em> species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the <em>‘uarnak’</em> complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.</p> </div>", "links"=>[], "tags"=>["rays", "dna", "ecologists"], "article_id"=>124017, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036479.s001", "https://dx.doi.org/10.1371/journal.pone.0036479.s002", "https://dx.doi.org/10.1371/journal.pone.0036479.s003"], "stats"=>{"downloads"=>3, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_Rays_through_DNA_Barcoding_An_Application_for_Ecologists/124017", "title"=>"Identification of Rays through DNA Barcoding: An Application for Ecologists", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-11 01:06:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/626067"], "description"=>"<p>Third part of the Neighbour-joining tree based on COI sequence data using Kimura-two-parameter substitution model (left); the third part of the tree (right). Names in red are the sequences obtained in this study, the corrected nomenclature is in () and given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036479#pone.0036479.s002\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["rays"], "article_id"=>296560, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036479.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationship_of_rays_Part_III_/296560", "title"=>"Phylogenetic relationship of rays Part III.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-11 01:49:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/626327"], "description"=>"<p>Means and ranges of K2P distance values (%) for the COI gene region at different taxonomic levels for the ray species analysed in this study.</p>", "links"=>[], "tags"=>["ranges", "k2p", "coi", "taxonomic", "levels", "ray", "analysed"], "article_id"=>296810, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036479.t001", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Means_and_ranges_of_K2P_distance_values_for_the_COI_gene_region_at_different_taxonomic_levels_for_the_ray_species_analysed_in_this_study_/296810", "title"=>"Means and ranges of K2P distance values (%) for the COI gene region at different taxonomic levels for the ray species analysed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-11 01:53:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/626165"], "description"=>"<p>Ningaloo Reef (NR), northern Indian Ocean (NIO), Great Barrier Reef (GBR), Japan (Jap), Southeast Asia (SEA);.</p>", "links"=>[], "tags"=>["scaling"], "article_id"=>296659, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Florencia Cerutti-Pereyra", "Mark G. Meekan", "Nu-Wei V. Wei", "Owen O'Shea", "Corey J. A. Bradshaw", "Chris M. Austin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036479.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_Scaling_MDS_of_Neotrygon_kuhlii_/296659", "title"=>"Multidimensional Scaling (MDS) of <i>Neotrygon kuhlii.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-11 01:50:59"}

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Relative Metric

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