Recent advances in DNA taxonomy

By A. Vogler, M. Monaghan. 2007

384 citations recorded by the source corpus.

Large-scale DNA sequencing of living species holds great promise in taxonomy, but has been controversial. In this article, we review the recent advances that follow the dramatic increase in data generation. We distinguish DNA taxonomy from DNA barcoding, where the former directly concerns the circumscription and delineation of species using evolutionary species concepts and the latter is a means of identifying a priori entities by sequence similarity. A key finding from recent studies in animals is that variation in mitochondrial DNA (mtDNA) is partitioned as tight clusters of closely related genotypes, which group specimens largely according to traditionally recognized species limits, and which are congruent with nuclear markers. This finding provides confidence to use sequence variation as the primary information for species delimitation in poorly known groups. A number of recent, large-scale studies support the power of mtDNA in species recognition, and previous application of molecular techniques to taxonomically complicated cases has likely led to an overestimate of the proportion of species with polyphyletic mtDNA haplotypes. The continued development of DNA taxonomy will lead to more refined sampling strategies and data analyses than those that are presently used. Sophisticated statistical methods of grouping have already been developed based on sequence similarity; yet, the units defined in this way have largely unknown evolutionary relevance. In future, a standard DNA taxonomic analysis will include broad sampling of the target taxa across their geographic range, followed by large-scale sequencing of representative samples for a DNA profile of the group, and algorithmic procedures for delineating species limits. The taxonomic system will be derived from the data rather than expert opinion, and hypothesized species entities can be tested against morphology, biogeography and other data, providing an evolutionary justification of the procedures used for species delimitation. Discrepancies between DNA and other data are used to refine species delimitations via a feedback loop that incorporates new data. We argue, however, that the use of DNA methodology in taxonomy (including DNA barcoding) will remain controversial until it is better founded in existing theory of evolutionary biology and phylogenetics.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/67bfd6585b8a154829879b6fdc76163a4efde853

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Citations in the corpus

Accelerated species inventory on Madagascar using coalescent-based models of species delineation. (2009, background): “This is a major short coming of existing approaches, as they may miss what is arguably the critical hierarchical level in the analysis—the species (Vogler and Monaghan 2007).”
The Application of Biotechnology to Orchids (2013, background): “DNA barcoding can be applied to identify species and to provide taxonomic information that would allow their evolutionary relevance to be clarified (Chase et al., 2005; Vogler and Monaghan, 2007).”
Biodiversity and phylogeography of Arctic marine fauna: insights from molecular tools (2011, background): “However, this example underscores the benefits of a combined molecular and morphological approach to taxonomy, particularly in diverse groups such as the polychaetes (cf., Vogler and Monaghan 2006; McManus and Katz 2009).”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, methodology): “Within this framework, and in line with the independently evolving species concept (De Queiroz, 2007) and the phylogenetic species concept, molecular species delimitation using DNA-barcoding serves as an excellent tool in modern taxonomy (Tautz et al., 2003; Vogler and Monaghan, 2007).”
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, background): “It is not clear to whom their advice is aimed, because their conclusions appear to blur the distinctions between DNA barcoding and DNA taxonomy, i.e. assigning unknowns to a preidentified reference library vs. species delimitation and description (Vogler & Monaghan 2007; Padial et al. 2010).”
The integrative future of taxonomy (2010, background): “Indeed, this progress is being made possible despite important impediments [9] because species taxonomy is resurging as a solid scientific discipline [10] that incorporates technological advances, such as virtual access to museum collections [11], high-throughput DNA sequencing [12], computer tomogr”
Cryptic species in ants (Hymenoptera: Formicidae) revisited: we need a change in the alpha taxonomic approach (2009, background): “A bad, untestable MOBAT could lead to an overestimation of mtDNA paraphyly (F UNK & O MLAND 2003, V OGLER & M ONAGHAN 2007) but, in the other extreme, underestimations could also result because such a MOBAT could opportunistically accept species de-limitations proposed by barcoding.”
Integrative taxonomy: a multisource approach to exploring biodiversity. (2010, background): “Given that it may not be knowable whether any hypotheses are correct under the hypothesis-driven approach, the discovery approach may be more appropriate in general because it has the potential to use the information available when inferring the number and demarcation of species present more fully t”
Current progress in DNA barcoding and future implications for entomology (2011, methodology): “Some researchers have envisioned “DNA taxonomy”, a concept of adopting DNA sequencing as a central criterion for taxonomic decisions and descriptions, and have proposed using DNA barcodes as the standard method of analysis (Blaxter 2003; Tautz et al. 2003; Vogler & Monaghan 2007).”
From ‘cryptic species’ to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera) (2010, background): “DNA sequence data have recently gained much popularity in taxonomic research and it is generally acknowledged today that they provide important evidence for delimiting species (Vogler & Monaghan 2007; Meier 2008).”
DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea) (2011, background): “Considering this, the phylogenetic species concept could also be applied, which defines a species as the smallest resolvable separately evolving lineage or the smallest diagnosable cluster (Vogler and Monaghan, 2007).”
ABGD, Automatic Barcode Gap Discovery for primary species delimitation (2012, background): “…data to clearly delimit species in what is called an integrative framework (Dayrat 2005; Will et al. 2005; Ah-rens et al. 2007; Miller 2007; Vogler & Monaghan 2007; Wiens 2007; Bond & Stockman 2008; Giraud et al. 2008; De´praz et al. 2009; Damm et al. 2010; Goetze 2010; O’Meara 2010;…”