The unholy trinity: taxonomy, species delimitation and DNA barcoding

Abstract

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings-Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…The main challenge to using distance‐based methods to species identification is that no single genetic distance threshold distinguishes all species (Ferguson, 2002; DeSalle et al., 2005; Little and Stevenson 2007; Wilson et al. 2011).…”

“…DNA polymorphism analysis is an approach that can potentially identify important diagnostic differences among sequences that are not detected by distance or tree‐based query assignment methods (DeSalle, Egan, & Siddall, 2005; Pettengill & Neel, 2010). This approach has not been previously applied for analyzing barcode sequences, and this is the first reported use here.…”

The Future of Phylogenetic Systematics in Conservation Biology: Linking Biodiversity and Society

“…DNA ) x individuals can be partitioned into clusters -potentially species -through a tree-like guidance. The new rationale is simple: to defi ne species, we need fi rst to recognize and delimit different groups of individuals, by contrasting their characters (Goldstein et al 2000 ;Pons et al 2006 ;Vogler and Monaghan 2006 ;O'Meara 2010 ;Pante et al 2015 ; but see DeSalle et al 2005 ). This phylogenetic perspective is still certainly new for many, although it is inexorably implemented in the most recent molecular methods used for biodiversity exploration and characterization, such as molecular species delimitation or metagenomics.…”

On-line relational and multiple relational SOM

“…The notion of DNA barcoding comprises a wide family of molecular and bioinformatics methods aimed at identifying biological specimens and assigning them to a species. According to the vast literature published during the past years on the topic, two separate tasks emerge for DNA barcoding: on the one hand, assign unknown observations to known species and, on the other hand, discover undescribed species, [50]. The second task is usually approached with the Neighbor Joining algorithm [51] which constructs a tree similar to a dendrogram.…”