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
Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservation
Magdalini Christodoulou,Timothy D. O'Hara,Andrew F. Hugall,Sahar Khodami,Clara F. Rodrigues,Ana Hilário,Annemiek Vink,Pedro Martínez Arbizu +7 more
TL;DR: In this article, the authors used a fragment of the mitochondrial cytochrome c-oxidase subunit I (COI) subunit of ophiuroid material collected during eight scientific cruises from five exploration licence areas within the Clarion-Clipperton Zone (CCZ), one area being protected from mining, and the DISturbance and re-colonisation (DISCOL) Experimental Area (DEA), in the SE Pacific Ocean, was examined.
Journal ArticleDOI
Potentials and Challenges of Genomics for Breeding Cannabis Cultivars.
Gianni Barcaccia,Fabio Palumbo,Francesco Scariolo,Alessandro Vannozzi,Marcello Borin,Stefano Bona +5 more
TL;DR: The main advances in the genomic field of this species are resumed and a discriminant and polymorphic panel of SSR markers are provided as a valuable tool for future marker assisted breeding programs.
Journal ArticleDOI
A highly resolved food web for insect seed predators in a species-rich tropical forest.
Sofia Gripenberg,Yves Basset,Owen T. Lewis,J. Christopher D. Terry,S. Joseph Wright,Indira Simon,D. Catalina Fernández,Marjorie Cedeño‐Sanchez,Marleny Rivera,Marleny Rivera,Héctor Barrios,John W. Brown,Osvaldo Calderón,Anthony I. Cognato,Jorma Kim,Scott E. Miller,Geoffrey E. Morse,Sara Pinzón-Navarro,Donald L. J. Quicke,Robert K. Robbins,Juha-Pekka Salminen,Eero J. Vesterinen,Eero J. Vesterinen +22 more
TL;DR: The first food web quantifying trophic interactions between the majority of co‐occurring woody plant species and their internally feeding insect seed predators suggests that seed predators are unlikely to mediate indirect interactions such as apparent competition between plant species, but are consistent with their proposed contribution to maintaining plant diversity via the Janzen–Connell mechanism.
Journal ArticleDOI
With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast
Luisa M. S. Borges,Claudia Hollatz,Jorge Lobo,Ana Maria Cunha,Ana P. Vilela,Gonçalo Calado,Rita Coelho,Ana C. Costa,Maria S. G. Ferreira,Maria Helena Costa,Filipe O. Costa +10 more
TL;DR: Sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast, and there was a good concordance between morphological identification and DNA barcodes.
Journal ArticleDOI
Biodiversity, Evolution and Ecological Specialization of Baculoviruses: A Treasure Trove for Future Applied Research.
TL;DR: In this paper, a phylogenetic-concept-based approach was used to delimit 165 Baculovirus species, including 38 species derived from new genetic data, showing that besides selection during the infection process, baculoviruses diversification was influenced by tritrophic interactions, explained by their persistence on plants and interactions in the midgut during horizontal transmission.
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.