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
Variation of male secondary sexual structures and the taxonomy of theritas lisus and relatives (lepidoptera, lycaenidae, eumaeini)
TL;DR: Variation of male secondary sexual structures, genitalia, and wing patterns in Theritas lisus (Stoll) and relatives is assessed to clarify the species level taxonomy, which is needed for a phylogenetic analysis.
Journal ArticleDOI
New species of leaf-mining Phyllonorycter (Lepidoptera Gracillariidae) from Siberia feeding on Caragana (Fabaceae).
TL;DR: It is shown that morphologically and genetically, Phyllonorycterivani has affinity to the haasi species group, a West Palearctic group with asymmetrical male genitalia, and that DNA barcode data weakly supports the Fabaceae-feeding species groups.
Journal ArticleDOI
Observations of Adelomyrmex (Hymenoptera: Formicidae) reproductive biology facilitated by digital field microscopy and DNA barcoding
TL;DR: It is reported how a combination of affordable digital field microscopes and DNA barcoding has allowed nest discovery and documentation and linked male and worker Adelomyrmex.
Dissertation
Effects of Andean geographic dynamics on the population history of Tococa-associated Azteca ants
Torres Jiménez,María Fernanda +1 more
TL;DR: A selection of images from around the world can be found at www.globenewspaper.org/publications/stable/index.asp.
Order Hymenoptera, family Braconidae Subfamily Microgastrinae from the Arabian Peninsula
TL;DR: The present paper records for the first time a significant number of genera and species for the Arabian Peninsula, including 12 new species of microgastrine wasps.
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.