Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae)

Abstract

The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern. Our results show incongruences among methods. ABGD, PTP and mPTP trend towards a lower number of estimated species. Phylogenetic-coalescent methods with single threshold were majority congruent for a same number of lineages. On the other hand, algorithms with multiple thresholds tend to estimate a higher number of potential species. We do not endorse the use of single-locus for species delimitation, but we do reinforce that single-locus data is sufficient to flag many problems.

Does DNA barcoding offer meaningful insights into the diversity of the parrotfish of the genus Sparisoma (Scaridae)?

“…This topology requires at least well‐resolved nodes so that there is no variability in the length of the branches, resulting in biases that may underestimate or overestimate species diversity (Drummond & Suchard, ). The ABGD, which does not rely on a previous genealogical topology and solved internal nodes, was the method that delimited fewer ESUs in Sparisoma , corroborating with results, in which this method was not able to distinguish several pairs of species with known morphological differences (see Silva et al, ).…”

Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

“…Similar to other lichen genera and species complexes (e.g., Leavitt et al 2011cLeavitt et al , 2016Lücking et al 2014), including Peltigera sections Polydactylon and Peltigera, where the proportion of undiscovered biodiversity was unexpectedly high (half or more of the recovered species were potentially new; Magain et al 2017aMagain et al , b, 2018 support the recognition of 14 putative species for section Peltidea, of which nine are undescribed. The impact of the incongruence among loci and implemented methods on currently recognized species has previously been reported across various taxonomic groups, including fungi and, among them, the genus Peltigera (e.g., Singh et al 2014 and references therein;Wei et al 2016;Magain et al 2017a, b, 2018 andreferences therein;Da Silva et al 2018). In this study we detected a relatively high level of discrepancy and uncertainty in the species number and species boundaries, including cases of paraphyletic/polyphyletic entities, as well as nested and singleton species, especially in P. aphthosa (Fig.…”

Species identification and connectivity of marine amphipods in Canada’s three oceans

“…For example, da Silva et al . [ 60 ] noticed that ABGD and PTP produce lower estimates of snapper species diversity (based on the COI) than other methods. The relative performance of species delimitation methods has been examined in other studies [ 61 ].…”