title: Sequence capture using RAD probes clarifies phylogenetic relationships and species boundaries in Primula sect. Auricula.
abstract: 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.
authors: Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, 8008 Zurich, Switzerland; Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address: flofloboucher@gmail.com.
authors: F C
authors: FC
authors: Boucher
authors: DISTAV, University of Genova, 16132 Genova, Italy.
authors: G
authors: G
authors: Casazza
authors: Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, 8008 Zurich, Switzerland.
authors: P
authors: P
authors: Szövényi
authors: Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, 8008 Zurich, Switzerland.
authors: E
authors: E
authors: Conti
mesh_terms: D005075:Biological Evolution; D018744:DNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D016013:Likelihood Functions; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D031825:Primula / Q000145:classification* / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: European Alpine system; Next-generation sequencing; Phylogenomics; Primula sect. Auricula; Species delimitations