Multilocus phylogeny and systematics of Iberian endemic Squalius (Actinopterygii, Leuciscidae)

Inferring the evolutionary history of a group of species can be challenging given the many factors involved. In recent years, the increased availability of sequences of multiple genes per species has spurred the development of new methodologies to analyse multilocus data sets. Two approaches that analyse such data are concatenated supermatrix and coalescent-based species-tree analyses. In this study, we used both of these methods to infer the phylogenetic relationships of Iberian species of the genus Squalius from one mitochondrial and six nuclear genes. We found mitonuclear discordance in the phylogenetic relationships of the group. According to the mitochondrial gene analysis, all species were recovered as monophyletic except S. pyrenaicus; besides, in the concatenated supermatrix analysis of the nuclear markers, this species resolved as polyphyletic with three divergent evolutionary lineages. The coalescent-based nuclear species-tree analysis rendered a well-resolved phylogeny compared with the supermatrix analysis, which was unable to discern between S. carolitertii, S. castellanus and one of the evolutionary lineages of S. pyrenaicus. This result is likely due to the better integration of population uncertainty in the coalescent approach. Furthermore, Bayesian multilocus species delimitation analyses based on a BPP approach strongly supported the distinct nuclear lineages as different species. Nevertheless, the supermatrix analysis was able to obtain well-supported relationships in the divergent lineages with low numbers of individuals. Our study highlights the usefulness of different analytical methodologies to obtain a more complete picture of the evolutionary history of taxa, especially when discordant patterns among genes are found.We thank P. Garzón, J.L. González and B. Prieto, for field assistance within the Project ‘Basis for the monitoring of Spanish Freshwater Fishes' supported by MARM (Ministerio de Medio Ambiente y Medio Rural y Marino) in which part of the samples used in this study was collected. L. Alcaraz helped with laboratory procedures. This study has been also supported by the Spanish Ministry of Science and Innovation (CGL2010‐15231BOS) and by the management commission funded by the Duero Hydrographic Confederation in Spain (Análisis y estudios filogeográficos y de variabilidad genética de endemismos ibéricos de ciprínidos: Life13 nat/es/000772 ‘Actuaciones para la protección y conservación de ciprínidos ibéricos de interés comunitario'). S. Perea was awarded with the Angel Cabrera Prize to the best predoctoral CV in 2015 granted by the Biodiversity and Evolutionary Department of the Museo Nacional de Ciencias Naturales—CSIC, which covered part of the laboratory expenses of this study