DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

By R. Meier, Kwong Shiyang, Gaurav Vaidya, P. Ng. Systematic Biology, 2006

1,393 citations recorded by the source corpus.

Subfields: Ecology, Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e553ff7e5e965437cc9832bf66361f19bfbe076d

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Citations in the corpus

Integrating morphology and mitochondrial DNA for species delimitation within the spruce budworm (Choristoneura fumiferana) cryptic species complex (Lepidoptera: Tortricidae) (2010, background): “Alternatively, species can contain multiple divergent DNA lineages or, for that matter, polymorphic characters of any kind, where the extent of intraspecific variation is as high or higher than interspecific variation (e.g. Cognato, 2006; Meier et al., 2006).”
Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly (2010, methodology): “The indel-free regions of the ribosomal genes are then concatenated with the aligned protein-encoding gene sequences using sequencematrix (Meier et al., 2006; Vaidya et al., accepted).”
Testing the reliability of genetic methods of species identification via simulation. (2008, methodology): “…proportion of correct identifications of dipteran flies by the strict tree-based method calculated from Table 4 (revised identification criteria) in Meier et al. (2006), after removing singletons, plotted against the estimated ratio of intraspecific distance to distance to nearest heterospecific.”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, background): “How- ever, this potential universal standard gap has subsequently been found to be unreliable (Meyer & Paulay, 2005; Meier et al., 2006; Schmidt & Sperling, 2008) and is not accepted here.”
Towards a phylogenetic classification of reef corals: the Indo‐Pacific genera Merulina, Goniastrea and Scapophyllia (Scleractinia, Merulinidae) (2014, background): “In other words, a Goniastrea specimen from clade A1 or A3 cannot be reliably identified to species based on either ITS or IGR because its sequence will match the wrong species virtually all the time (Meier et al. 2006, 2008).”
DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species (2010, neutral): “…groups, e.g., North American birds (94%; Kerr et al. 2007), Australian fishes (100%; Ward et al. 2005) and Neotropical bats (93%; Clare et al. 2007), and contrasts with lower identification rates of COI in some invertebrate groups (e.g., Elias et al. 2007; Meier et al. 2006; Meyer and Paulay 2005).”
DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea) (2011, methodology): “5a12 (Meier et al., 2006) was used.”
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, background): “This is linked to the principal of the barcoding gap, which relies on individuals within a species being more similar to one another than to the closest individual of another species (Meyer & Paulay 2005; Meier et al. 2008).”
Biodiversity inventory and informatics in Southeast Asia (2010, background): “This level may not yet be sufficient for taxonomic needs (Meier et al. 2006), although next generation sequencing technologies should offer a large number of variable markers which will help improve resolution, even in recently evolved radiations.”
Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding (2012, methodology): “Tests of barcoding efﬁcacy include the following: species monophyly; ‘best close match’ (Meier et al. 2006); an inclusive threshold analysis similar to the method of specimen identiﬁcation used by BOLD; and nearest-neighbour identiﬁcation (cf. k -nearest neighbour of Austerlitz et al. 2009).”
Current progress in DNA barcoding and future implications for entomology (2011, background): “Meier et al. (2006) introduced distance-based criteria, in which a query sequence is assigned to a species of the best-matched barcode regardless of similarity (best match method) or when the degree of difference between the query and the best-matched barcode is less than 95% for all intraspecific…”
Accelerated species inventory on Madagascar using coalescent-based models of species delineation. (2009, background): “The former has been shown to be problematic (e.g., Meyer and Paulay 2005; Meier et al. 2006; Elias et al. 2007), in particular, if the reference database is incomplete (Paquin and Hedin 2004), and MOTUs may correspond to any hierarchical level, but not necessarily to the species category (Floyd et…”
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification (2008, background): “Criticism has been raised against the barcoding community for not taking these matters seriously enough (Wheeler, 2004; Will et al. 2005; Meier et al. 2006), and the present study lends further weight to the importance of these claims.”
DNA-based species delimitation in algae (2014, background): “For animals, the mitochondrial cytochrome oxidase I locus (COI or cox1) has been found to satisfy these criteria for most groups (Hebert et al., 2003) (but see Meier et al., 2006).”
The campaign to DNA barcode all fishes, FISH-BOL. (2009, background): “Meier et al. (2006) found that COI sequences generated only 70% success in species-level identification for Diptera using GenBank sequences, but many records in this repository are known to derive from misidentified specimens (Harris, 2003; Mitchell, 2008) and, or lack reference to the underlying…”
Cryptic genetic diversity in "widespread" Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. (2010, methodology): “Although genetic distances merely approximate differentiation between species (Meier et al., 2006; Meier et al., 2008) and alone are not diagnostic of species limits (Winker, 2009), these distances are consistent with species-level differentiation among birds (Kerr et al.”