Sequence capture using RAD probes clarifies phylogenetic relationships and species boundaries in Primula sect. Auricula

Species-rich evolutionary radiations are a common feature of mountain floras worldwide. However, the frequent lack of phylogenetic resolution in species-rich alpine plant groups hampers progress towards clarifying the causes of diversification in mountains. In this study, we use the largest plant group endemic to the European Alpine system, Primula sect. Auricula, as a model system. We employ a newly developed next-generation-sequencing protocol, involving sequence capture with RAD probes, and map reads to the reference genome of Primula veris to obtain DNA matrices with thousands of SNPs. We use these data-rich matrices to infer phylogenetic relationships in Primula sect. Auricula and examine species delimitations in two taxonomically difficult subgroups: the clades formed by the close relatives of P. auricula and P. pedemontana, respectively. Our molecular dataset enables us to resolve most phylogenetic relationships in the group with strong support, and in particular to infer four well-supported clades within sect. Auricula. Our results support existing species delimitations for P. auricula, P. lutea, and P. subpyrenaica, while they suggest that the group formed by P. pedemontana and close relatives might need taxonomic revision. Finally, we discuss preliminary implications of these findings on the biogeographic history of Primula sect. Auricula. (C) 2016 Elsevier Inc. All rights reserved.