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This study analyzes intraand interspecific chloroplast DNA sequence variation of diploid and polyploid species belonging to the Triticum-Aegilops complex. Particularly informative data were obtained from noncoding regions of cpDNA including base pair substitutions, insertion/deletions (indels) (50 loci pooled), microsatellites (7 loci pooled), and an inversion. Nine out of thirteen diploid Triticum-Aegilops species were successfully identified and genotyped using these data. Sixty-two haplotypes were detected in 115 accessions of 13 diploid species. Because of the large number of characters examined, novel deep relationships within and among diploid Triticum-Aegilops species could be evaluated. Phylogenetic trees for the genus Triticum-Aegilops were rooted with Hordeum vulgare and Dasypyrum villosum as outgroups and the results were compared to previous studies. The following inferences were made: (1) Aegilops species should be included in Triticum; (2) groups D, T, M, N, U and subsection Emarginata of section Sitopsis underwent speciation concurrently, but most diploid species evolved independently; (3) Ae. mutica does not occupy a basal position in Triticum-Aegilops; (4) Ae. speltoides is in a basal position and differs significantly from other Sitopsis species; (5) Ae. caudata is polyphyletic in all trees; (6) the genus Aegilops is paraphyletic and includes Secale; (7) origin of polyploid species generally follow those reported previously including several dior polyphyletic origin; (8) T. dicoccoides and T. araraticum formed a cluster and this, further, formed a cluster with Ae. speltoides.

Phylogeny of Aegilops and Triticum inferred from sequence data of cpDNA