BioNames: linking taxonomy, texts, and trees

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Abstract

BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic “dashboard” where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question “what is this taxon?” BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org.

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Most cited references 52

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Kurt Bollacker, Colin Evans, Praveen Paritosh … (2008)

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How many species are there on Earth?

R M May (1988)

This article surveys current answers to the factual question posed in the title and reviews the kinds of information that are needed to make these answers more precise. Various factors affecting diversity are also reviewed. These include the structure of food webs, the relative abundance of species, the number of species and of individuals in different categories of body size, along with other determinants of the commonness and rarity of organisms.

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Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

Miguel Vences, Meike Thomas, Arie van der Meijden … (2005)

Background Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. Results Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%), with low degrees of pairwise haplotype divergence within populations (0–1%). Conclusion We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

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Roderic D.M. Page

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Journal ID (nlm-ta): PeerJ

Journal ID (iso-abbrev): PeerJ

Journal ID (pmc): PeerJ

Journal ID (publisher-id): PeerJ

Title: PeerJ

Publisher: PeerJ Inc. (San Francisco, USA )

ISSN (Electronic): 2167-8359

Publication date (Electronic): 29 October 2013

Publication date Collection: 2013

Volume: 1

Electronic Location Identifier: e190

Affiliations

[-1]Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, Graham Kerr Building, University of Glasgow , Glasgow, UK

Article

Publisher ID: 190

DOI: 10.7717/peerj.190

PMC ID: 3817598

PubMed ID: 24244913

SO-VID: 6f5df110-251e-4351-bc41-3a334a334ea1

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 28 August 2013

Date accepted : 8 October 2013

Funding

Funded by: Encyclopedia of Life (EOL)

Funding for initial web interface development was provided by the Encyclopedia of Life (EOL). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

BioNames: linking taxonomy, texts, and trees

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Most cited references 52

Freebase

How many species are there on Earth?

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

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