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.

Keywords:

• Beast
• COI
• GMYC
• mtDNA
• species delimitation

Acknowledgements

An earlier version of this manuscript was presented as a class seminar at Museu Paraense Emílio Goeldi. We are grateful to all colleagues for ideas and discussions that improved our work.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

P.L.V.P. was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/BJT 313680/2014-0, 400252/2014-77).