Setting-up a methodological pipeline for species delimitation and species network reconstruction in polyploid complexes

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Hybridisation, whole-genome duplication (autopolyploidy), and the combination of both (allopolyploidy) are paramount processes in the evolution of and species formation in flowering plants. Gene flow at the diploid and polyploid level, multiple formation of polyploid species, often under reciprocal parentage, and the young age of polyploid species radiations account for the taxonomy of polyploid complexes being the ultimate challenge for a DNA-based, phylogenetic species delimitation approach. Additionally, reconstructions of the evolutionary history of polyploid complexes are still hampered by the lack of explicit methods for the reconstruction of reticulate (species) phylogenies. Our present project proposal aims at the development, establishment, and evaluation of a methodological pipeline allowing the fast discovery and delimitation of evolutionary significant units (species) and the reconstruction of species trees and networks in polyploid complexes using genomic, morphological, and geographic distribution data (including climatic niches). Our approach will be exemplified in the polyploid complex of Leucanthemum Mill. (ox-eye daisy; Compositae), which comprises around 43 species with ploidy levels between 2x and 22x. Molecular data for the multi-species coalescent species delimitation (MSCSD) and species network reconstructions will be provided by two next-generation sequencing (NGS) methods: (a) GBS/RADseq information via Illumina sequencing for population genetic analyses, especially for the detection of actual hybridisation among taxa, and (b) PacBio single-molecule sequencing of single-copy nuclear markers for species network reconstructions and the testing of species delimitation hypothesis. The core package of our proposed project will deal with the creation of novel bioinformatic tools for the application of species delimitation and species tree reconstruction methods at polyploid levels. Besides validation of our proposed work-flow with other groups of the SPP working in polyploid complexes in plants, a general discussion of methodological and philosophical issues connected with species delimitation concepts and applicability of our approach in other organism groups is envisaged.