A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
TLDR
A persistent, species-level taxonomic registry for the animal kingdom is developed based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene.Abstract:
Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.read more
Citations
More filters
Journal ArticleDOI
North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae)
TL;DR: North-Western Palaearctic species of Pristiphora Latreille, 1810 are revised and the following 29 new synonymies are proposed: P. caraganae Vikberg & Prous, sp.
Journal ArticleDOI
Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale.
Andrea Galimberti,Giacomo Assandri,Davide Maggioni,Fausto Ramazzotti,Daniele Baroni,Gaia Bazzi,Ivan Chiandetti,Andrea Corso,Vincenzo Ferri,Mirko Galuppi,Luca Ilahiane,Gianandrea La Porta,Lorenzo Laddaga,Federico Landi,Fabio Mastropasqua,Samuele Ramellini,Roberto Santinelli,Giovanni Soldato,Salvatore Surdo,Maurizio Casiraghi +19 more
TL;DR: New insights are provided into the taxonomy of odonates and a valuable basis for future DNA and eDNA‐based monitoring studies are provided.
Journal ArticleDOI
Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding.
Sven Rossel,P. Martínez Arbizu +1 more
TL;DR: Assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans found that species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.
Journal ArticleDOI
Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding
Henrik Christiansen,Agnès Dettai,Franz Maximilian Heindler,Martin A. Collins,Guy Duhamel,Mélyne Hautecoeur,Dirk Steinke,Filip Volckaert,Anton Van de Putte,Anton Van de Putte +9 more
TL;DR: A dataset with previously unpublished cytochrome c oxidase I (COI) and rhodopsin gene sequences from specimens collected at various locations in the Southern Ocean is presented, providing a robust reference dataset for specimen identification, independently of incomplete morphological characters.
Journal ArticleDOI
Multiple components of plant diversity loss determine herbivore phylogenetic diversity in a subtropical forest experiment
Ming-Qiang Wang,Ming-Qiang Wang,Yi Li,Douglas Chesters,Perttu Anttonen,Helge Bruelheide,Jing-Ting Chen,Walter Durka,Peng-Fei Guo,Peng-Fei Guo,Werner Härdtle,Keping Ma,Stefan G. Michalski,Bernhard Schmid,Bernhard Schmid,Goddert von Oheimb,Chunsheng Wu,Naili Zhang,Qing-Song Zhou,Andreas Schuldt,Chao-Dong Zhu +20 more
TL;DR: The study shows that evolutionary dependencies determine the response of herbivore communities to changes in host plant diversity, and the need to address the consequences of current declines in insect abundances for ecosystem structure and functioning is underlined.
References
More filters
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Journal ArticleDOI
Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
TL;DR: A new graphical display is proposed for partitioning techniques, where each cluster is represented by a so-called silhouette, which is based on the comparison of its tightness and separation, and provides an evaluation of clustering validity.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
jModelTest 2: more models, new heuristics and parallel computing.
TL;DR: jModelTest 2: more models, new heuristics and parallel computing Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada.