Exploring the phylogenetic relationships in Santolina (Asteraceae): a taxonomically complex genus endemic to the Mediterranean Basin

Rapid divergence, introgressive hybridisation and polyploidization often result in taxonomically and evolutionary complex groups with weakly geographically and/or morphologically defined species. In these groups, the difficulty to classify species in stable and coherent taxa strongly affects the implementation of conservation measures for threatened, rare or endemic evolutionary significant units, thus, to preserve the processes that lead to the generation of biodiversity. The genus Santolina L. (Asteraceae, Anthemidae), endemic to the western part of the Mediterranean basin, has a long taxonomic history since Linnaeus (1753) described the genus. According to a recent taxonomic revision, the whole genus comprises roughly 30 taxa, most of which are divided in two morphological complexes: the rosmarinifolia one, which includes eleven taxa endemic to Iberian Peninsula and North Africa and was subject of extensive systematic and phylogenetic analysis, and the chamaecyparissus one, which includes fourteen taxa mainly narrow endemics occurring in Spain, France, and Italy. In addition, four taxa are not included in either complex. In this study, for the first time we presented a genome-wide phylogenetic analysis of the whole genus based on RADseq. We also investigated diversity structure by computing a co-ancestry matrix using RADpainter software. To assess evidence of introgression between species, we used Dsuite package performing the ABBA-BABA test. Our phylogeny corroborates the results of previous morphological analyses, confirming the existence of two main clades: the rosmarinifolia clade, which is monophyletic; and the chamaecyparissus clade which is monophyletic if the allopolyploid S. villosa is excluded. Santolina villosa (chamaecyparissus complex) shares common ancestor with species of S. rosmarinifolia complex. Taxa belonging to rosmarinifolia clade shown high level of co-ancestry supporting the phylogenetic closeness of these species. Taxa of chamaecyparissus clade are genetically more heterogeneous and form multiple subclusters. The ABBA-BABA tests found that the degree of introgression varies among taxa, being generally high between taxa of the chamaecyparissus clade and the rosmarinifolia clade. The introgression between the two early diverging lineages (i.e., S. rosmarinifolia and S. chamaecyparissus clades) was probably a crucial factor supplying the genetic diversity required for the radiation of Santolina lineages, particularly in the sympatric species of the rosmarinifolia clade. In conclusion, we build the first evolutionary hypothesis for Santolina chamaecyparissus complex, which yields a much-increased understanding of phylogenetic relationships in this group. Taken together our results set the stage for further investigations of the biogeographic history of this circum-Mediterranean group.