Fig. 2

Phylogenetic reconstruction of L. ircutianum subsp. crassifolium. The presented species tree (a) based on optimized allele partitions forms the consensus of 96 individual reconstructions with AllCoPol. Only clade frequencies of at least 0.5 are displayed. The histogram (b) illustrates the corresponding frequency distribution of averaged membership coefficients. The presented values refer to the first cluster only, i.e., a value of one denotes that an allele is consistently assigned to the same subgenome labeled as “P1” in the tree above. For comparison, an exemplary network inferred by the PhyloNet command InferNetwork_MP is shown (c). Both reticulating branches are annotated with their corresponding inheritance probabilities. The L. vulgare-group is marked with asterisk in (a) and (c)