Coalescing molecular evolution and DNA barcoding

The DNA barcoding concept (Woese et al . [Woese CR, 1990]; Hebert et al . [Hebert PDN, 2003]) has considerably boosted taxonomy research by facilitating the identification of specimens and discovery of new species. Used alone or in combination with DNA metabarcoding on environmental samples (Taberlet et al . [Taberlet P, 2012]), the approach is becoming a standard for basic and applied research in ecology, evolution and conservation across taxa, communities and ecosystems (Scheffers et al . [Scheffers BR, 2012]; Kress et al . [Kress WJ, 2015]). However, DNA barcoding suffers from several shortcomings that still remain overlooked, especially when it comes to species delineation (Collins & Cruickshank [Collins RA, 2012]). In this issue of Molecular Ecology , Barley & Thomson ([Barley A, 2016]) demonstrate that the choice of models of sequence evolution has substantial impacts on inferred genetic distances, with a propensity of the widely used Kimura 2‐parameter model to lead to underestimated species richness. While DNA barcoding has been and will continue to be a powerful tool for specimen identification and preliminary taxonomic sorting, this work calls for a systematic assessment of substitution models fit on barcoding data used for species delineation and reopens the debate on the limitation of this approach.