Guidelines for DNA taxonomy, with a focus on the meiofauna

Abstract

Describing biological diversity is a challenging endeavour, especially for the small, cryptic animals that make up the meiofauna. The field of DNA taxonomy, i.e., the use of DNA to delineate species boundaries, is rapidly growing and changing; herein we review the recent advances in the acquisition of DNA sequence data and the analytical tools for DNA-based species delimitation, with a focus on applications to the meiofauna. After providing general guidelines on the data collection and analysis steps (sampling design, sequencing, phasing of nuclear markers, and sequence alignment), we explain the rationale and usage of several widely used or promising methods developed for delineating species from single-locus data sets (distance-based DNA barcoding, automated barcode gap discovery, K/θ, generalized mixed Yule–coalescent models, Poisson tree process model, and haplowebs). As it is increasingly recognised that several loci are required to delineate species accurately, we then briefly outline multilocus species delimitation approaches (Structure, Structurama, Bayesian phylogenetics & phylogeography, SpedeSTEM, O’Meara’s heuristic search, and several newly published Bayesian approaches based on the multispecies coalescent).