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Fig. S1 Generalization of the probability of incorrect consensus calling as a function of depth of coverage and size of the matrix.

Fig. S2 Log10-transformed mean values of the depth of coverage for the regions used in the phylogenetic analyses.

Fig. S3 Depth of coverage, dC, for the regions used in the phylogenetic analyses.

Fig. S4 Density plot showing the number of assembled sites covering matrix characters as a function of consensus miscalling probability.

Fig. S5 Phylogeny of Aquilegia showing all accessions used in the present work.

Fig. S6 Consensus phylogram from the MB analysis conducted on the data set including the indel matrix.

Fig. S7 Best-scoring ML tree based on a reduced data set including one accession for each European Aquilegia taxon.

Fig. S8 Results of the PCO-MC clustering analysis including Aquilegia accessions for the European species and for the closest Asian clades as inferred from the obtained phylogeny.

Fig. S9 Phylogeny of the Ranunculaceae data set.

Fig. S10 Chronogram obtained with BEAST for the Ranunculaceae data set.

Fig. S11 Chronogram obtained with BEAST for the Aquilegia data set.

Table S1 Studied taxa, voucher information and MIDs sequences used in 454 sequencing

Table S2 PCR primers used in this study

Table S3 Depth of coverage of the variants found among the Aquilegia accessions

Methods S1 Amplicon sequencing with Roche 454.

Methods S2 Assembly and estimation of error rates and reliability of the phylogenetic matrix: Methods, Generalization, and Results.