Defining operational taxonomic units using DNA barcode data

By Mark L. Blaxter, J. Mann, T. Chapman, F. Thomas, Claire Whitton, R. Floyd, Eyualem Abebe. Philosophical Transactions of the Royal Society B: Biological Sciences, 2005

856 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3fc473739cf38f65286b1f10120bf741d49c3cdd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Genetics

In Molecular Biology

Citations in the corpus

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective (2006, background): “It is apparent from Table 1 that the major sequence databases are not optimally suited to serve as barcoding engines as they presently stand; new techniques and strategies for data indexation and verification will have to be explored to address the above shortcomings [5,22].”
DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. (2006, methodology): “…that a similarity metric will also be needed for tree-based identification, we would argue that one may as well abandon the tree-based approaches and instead directly use the similarity metric as has been implemented in several recent algorithms (e.g., Blaxter et al., 2005; Steinke et al., 2005).”
Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose? (2018, background): “These sequences can be clustered to generate molecular operational taxonomic units (MOTU) (Blaxter et al. 2005) that closely reflect species or compared to reference databases to identify the associated taxa present in a sample (Porter et al. 2014). hokral@uoguelph.ca; 7mhajibab@uoguelph.ca; 8djbair”
DNA barcoding of Neotropical bats: species identification and discovery within Guyana (2007, background): “The incidence of overlooked taxa recognized in this fashion ranges from lows of 3% in groups that have seen much taxonomic work such as birds (Hebert et al. 2004b) or 5% in the Lepidoptera (Hajibabaei et al. 2006a) vs. > 200% in groups that have received little attention (Blaxter et al. 2005).”
Integrative taxonomy in two free-living nematode species complexes (2008, background): “Genomewide information has proven to be powerful for the separation of nematode sibling species (De Ley, 2000; Derycke et al., 2005), potentially even allowing the development of a DNA barcoding approach in nematology (Blaxter et al., 2005; Bhadury et al., 2006).”
A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms (2007, methodology): “1, Blaxter et al. (2005) advocate the use of a modiﬁed CLOBB algorithm (Parkinson et al., 2002) in combination with randomization of input order.”
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System (2013, methodology): “[24] were the first to apply this method to DNA barcode data for OTU recognition in animals, examining the impact of partitioning sequences at differing levels of sequence divergence.”
Co-variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica (2006, neutral): “These lineages also correspond with the MOTU concept (Floyd et al. 2002, Eyualem & Blaxter 2003, Blaxter et al. 2005), in that there are more than three nucleotide differences (in most cases many more) at the SSU locus between species .”
Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morhological tools (2008, background): “Molecular techniques and phylogenetic analyses can potentially overcome this problem, and barcoding appears to be a promising tool to assess biodiversity in free-living nematodes (Floyd et al., 2002; Blaxter et al., 2005; Bhadury et al., 2006).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, methodology): “Molecular Operational Taxonomic Unit (MOTU) Group identified through use of cluster algorithms and a predefined percentage sequence similarity (e.g., 97%; Blaxter et al., 2005).”
DNA Barcoding of Lepetodrilus Limpets Reveals Cryptic Species (2008, methodology): “Here we reportCOI barcodes for 20 ‘‘molecular operational taxonomic units’’ (MOTUs, Blaxter et al. 2005) that are currently nested within these nominal species.”
Indirect host effect on ectomycorrhizal fungi: Leaf fall and litter quality explain changes in fungal communities on the roots of co-occurring Mediterranean oaks (2010, methodology): “Ectomycorrhizal “operational taxonomic units” (OTUs) (Blaxter et al., 2005) were determined as follows: First, edited sequences were examined by BLAST searches against GenBank (http://www.”
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification (2008, background): “Evolutionary Bioinformatics 2008:4 amplifi cation from low-quantity samples such as herbarium specimens suggest that the much more easily amplifi ed ribosomal DNA will remain in frequent use for the foreseeable future (Tautz et al. 2003; Bruns and Shefferson, 2004; Blaxter et al. 2005).”
Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory (2009, background): “In many cases, divergent DNA sequences are observed that probably correspond to distinct, undescribed species, but a taxonomic analysis of these data are impracticable in the short term, especially in morphologically cryptic and highly diverse groups (32, 33).”
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications (2018, background): “Fungal metabarcoding struggles with very large numbers of operational taxonomic units (OTUs; 5) that cannot be identified to any meaningful taxonomic lineage be-* yond, e.g. the kingdom or phylum level (6).”