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Polyploidy and hybridization are important processes in plant evolution, and often are connected to reproduction via asexually formed seed (apomixis). Apomictic polyploid complexes usually comprise a few sexual progenitor species, and numerous apomictic hybrid derivatives. In apomictic lineages, the lack of recombination and cross-fertilization can eventually result in numerous clonal hybrid lineages, which can fix certain morphological and ecological traits. However, facultative sexuality and crossings between lineages results in the formation of numerous morphological phenotypes (agamospecies) without regarding any evolutionary or genetic background. Adequate species concepts for apomictic plants are still under debate, but have remarkable influence on biodiversity estimations. To overcome the solely descriptive and impracticable classification of ill-founded "morphotypes", the project is aiming at a classification of apomictic lineages based on evolutionary concepts that are better comparable to sexual plant species. We analyze the Eurasian Ranunculus auricomus complex, a group comprising a handful of sexual species and more than 800 described agamospecies, by using a combination of different innovative methods: (1) Restriction site-associated DNA sequencing (RAD-seq), SNP mining and network-analyses are powerful tools for delimitation of closely related taxa and to test for origins and genetic coherence of described morphotypes, (2) target enrichment of nuclear genes combined to plastid genome skimming (Hyb-Seq) using coalescent approaches can resolve phylogenetic relationships of sexual and hybrid species, (3) ploidy screenings via flow cytometry detected new, undescribed diploid species, and will enable us to determine degree of facultative sexuality via flow cytometric seed screening (FCSS), and (4) geometric morphometrics of leaf shape and fruit characters and multivariate statistical analysis can objectively assess morphological differentiation and diversity. We will present first results from these approaches and discuss implications for reconstructing evolution and classification of the whole complex.