Against all odds: reconstructing the evolutionary history of <Emphasis Type="Italic">Scrophularia</Emphasis> (Scrophulariaceae) despite high levels of incongruence and reticulate evolution

The figwort genus Scrophularia (Scrophulariaceae), widespread across the temperate zone of the Northern Hemisphere, comprises about 250 species and is a taxonomically challenging lineage displaying large morphological and chromosomal diversity. Scrophularia has never been examined in a large-scale phylogenetic and biogeographic context and represents a useful model for studying evolutionary history in the context of reticulation. A comprehensively sampled phylogeny of Scrophularia was constructed, based on nuclear ribosomal (ITS) and plastid DNA sequences (trnQ-rps16 intergenic spacer, trnL-trnF region) of 147 species, using Bayesian inference and maximum likelihood approaches. Selected individuals were cloned. A combination of coding plastid indels and ITS intra-individual site polymorphisms, and applying Neighbor-Net and consensus network methods for adequate examination of within-dataset uncertainty as well as among-dataset incongruence, was used to disentangle phylogenetic relationships. Furthermore, divergence time estimation and ancestral area reconstruction were performed to infer the biogeographic history of the genus. The analyses reveal significant plastid-nuclear marker incongruence and considerable amounts of intra-individual nucleotide polymorphism in the ITS dataset. This is due to a combination of processes including reticulation and incomplete lineage sorting, possibly complicated by inter-array heterogeneity and pseudogenization in ITS in the presence of incomplete concerted evolution. Divergence time estimates indicate that Scrophularia originated during the Miocene in Southwestern Asia, its primary center of diversity. From there, the genus spread to Eastern Asia, the New World, Europe, Northern Africa, and other regions. Hybridization and polyploidy played a key role in the diversification history of Scrophularia, which was shaped by allopatric speciation in mountainous habitats during different climatic periods.