From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus

Abstract.—Allopolyploidization accounts for a significant fractionof speciation events inmanyeukaryotic lineages.However, existingphylogenetic anddatingmethods require tree-like topologies andareunable tohandle thenetwork-likephylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (no