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Fig. S1 Organization of the Triticum and Aegilops chloroplast genomes (expanded Fig. 1).

Fig. S2 Neighbor-joining phylogenetic tree of Emmer, Timppheevi, Speltoides and Sitopsis lineages based on synonymous substitutions in 70 concatenated protein coding sequences in SC blocks of the chloroplast genomes with Brachypodium, maize and Sorghum sequences as outgroups.

Fig. S3 Neighbor-joining phylogenetic tree of Emmer, Timppheevi, Speltoides and Sitopsis lineages based on concatenated SC sequences other than protein coding exons with barley sequence as an outgroup.

Fig. S4 Comparison of the best ML tree based on joined sequences of the LSC and SSC blocks and the NJ tree of Fig 2.

Fig. S5 Haplotype tree based on 10 chloroplast markers.

Table S1 Triticum and Aegilops species analyzed in this study.

Table S2 Plasmon and nuclear markers.

Table S3 Complete list of plasmon haplotypes and nuclear genotypes, and their prevalence in Emmer, Timopheevi, Speltoides and Sitopsis lineages (expanded Table 1).

Table S4 Divergence times calculated based on synonymous substitutions in 70 concatenated protein coding sequences (NJ method) and all substitutions (ML method) in SC blocks of the chloroplast genome.