66 | wileyonlinelibrary.com/journal/jzs J Zool Syst Evol Res. 2020;58:66–78. © 2019 Blackwell Verlag GmbH Received: 7 February 2019 | Revised: 23 July 2019 | Accepted: 27 July 2019 DOI: 10.1111/jzs.12336 ORIGINAL ARTICLE A complex species complex: The controversial role of ecology and biogeography in the evolutionary history of Syllis gracilis Grube, 1840 (Annelida, Syllidae) Joachim Langeneck 1 | Fabio Scarpa 2 | Ferruccio Maltagliati 1 | Daria Sanna 3 | Michele Barbieri 1 | Piero Cossu 2 | Barbara Mikac 4 | Marco Curini Galletti 2 | Alberto Castelli 1 | Marco Casu 2 Joachim Langeneck and Fabio Scarpa contributed equally. Contributing authors: Joachim Langeneck (jlangeneck@biologia.unipi.it), Fabio Scarpa (fscarpa@uniss.it), Daria Sanna (darsanna@uniss.it), Michele Barbieri (michele.barbieri@for.unipi.it), Piero Cossu (picossu@uniss.it), Barbara Mikac (mikacbarbara@gmail.com), Marco Curini Galletti (curini@uniss.it), Alberto Castelli (alberto.castelli@unipi.it), Marco Casu (marcasu@uniss.it) 1 Dipartimento di Biologia, Università di Pisa, Pisa, Italy 2 Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy 3 Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy 4 Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Ravenna, Italy Correspondence Ferruccio Maltagliati, Dipartimento di Biologia, Università di Pisa, via Derna 1, 56126 Pisa, Italy. Email: ferruccio.maltagliati@unipi.it Abstract The cryptic diversity in the polychaete Syllis gracilis Grube, 1840, in the Mediterranean Sea was examined with an integrative morpho‐molecular approach. Individuals of S. gracilis were collected at eleven Mediterranean localities to provide an insight into the role of brackish environments in inducing cryptic speciation. The examination of morphological features combined with a molecular genetic analysis based on a partial sequence of the 16S rRNA gene highlighted discrepancies between morpho‐ logical and molecular diversity. Morphological data allowed to identify a morpho‐ type with short appendages occurring in coralline algae communities and another one with long appendages observed in brackish‐water environments and Sabellaria reefs. Multivariate analyses showed that sampling localities were the greatest source of morphological divergence, suggesting that phenotypic plasticity may play a role in local adaptations of S. gracilis populations. Molecular data showed the occurrence of four divergent lineages not corresponding to morphological clusters. Different species delimitation tests gave conflicting results, retrieving, however, at least four separated entities. Some lineages occurred in sympatry and were equally distributed in marine and brackish‐water environments, excluding a biogeographic or ecological explanation of the observed pattern and suggesting instead ancient separation be‐ tween lineages and secondary contact. The co‐occurrence of different lineages hin‐ dered the identification of the lineage corresponding to S. gracilis sensu stricto. The discrepancy between morphological and molecular diversity suggests that different environmental and biogeographic features may interact in a complex and unpredict‐ able way in shaping diversity patterns. An integrative approach is needed to provide a satisfactory insight on evolutionary processes in marine invertebrates. KEYWORDS Mediterranean Sea, mitochondrial DNA, phenotypic plasticity, polychaetes, species complex