Submitted version (preprint).This is the pre-peer reviewed version of the following article: Smolina, I., Kollias, S., Poortvliet, M., Nielsen, T.G., Lindeque, P., Castellani, C., ... Hoarau, G.G. (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources, 14(5), 1072-1079, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.12241. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html).