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
Ultraconserved element phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)
Journal ArticleDOI
A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae).
TL;DR: The effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe to generate an extensive reference library of DNA Barcodes for carabids.
Journal ArticleDOI
Diptera of Canada.
Jade Savage,Art Borkent,Fenja Brodo,Jeffrey M. Cumming,Gregory R. Curler,Douglas C. Currie,Jeremy R deWaard,Joel F. Gibson,Martin Hauser,Louis Laplante,Owen Lonsdale,Stephen A. Marshall,James E. O'Hara,Bradley J. Sinclair,Jeffrey H. Skevington +14 more
TL;DR: A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979).
Journal ArticleDOI
Springtail phylogeography highlights biosecurity risks of repeated invasions and intraregional transfers among remote islands.
Helena P. Baird,Katherine L. Moon,Charlene Janion-Scheepers,Charlene Janion-Scheepers,Steven L. Chown +4 more
TL;DR: Analysis of the phylogeographic structure of an indigenous and an invasive springtail species, each distributed across multiple remote sub‐Antarctic islands, highlights the need for improved intraregional biosecurity among remote island systems, where the policy focus to date has been on external introductions.
Journal ArticleDOI
High incidence of mislabeling and a hint of fraud in the ceviche and sushi business
Ximena Velez-Zuazo,Joanna Alfaro-Shigueto,Ulises Rosas-Puchuri,Chiara Guidino,Andrea Pasara-Polack,Juan Carlos Riveros,Jeffrey C. Mangel +6 more
TL;DR: In this paper, DNA barcode sequencing of 364 samples collected from fresh and frozen fish fillets and ready-to-eat dishes (i.e., ceviche, sushi, and sashimi) was performed in restaurants, supermarkets, and fish retail markets from September 2017 and October 2018, in Peru.
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.