Jointed goatgrass (Aegilops cylindrica Host; 2n=4x=28; CCDD) is an agriculturally important species both as a weed and as a genetic resource for wheat (Triticum aestivum L.; 2n=6x=42; AABBDD) improvement. In order to better understand the evolution of this species, the diversity of Ae. cylindrica was evaluated along with its progenitors, Ae. markgrafii (Greuter) Hammer (2n=2x=14; CC) and Ae. tauschii Coss. (2n=2x=14; DD), using chloroplast and nuclear microsatellite markers. Ae. cylindrica had lower levels of plastome and nuclear diversity than its progenitors. The plastome diversity of Ae. cylindrica was lower than its nuclear diversity. Ae. cylindrica was found to have either C-or D-type plastomes, derived from Ae. markgrafii or Ae. tauschii, respectively, where the C-type plastome was found to occur at a lower frequency than the D-type plastome. The nuclear genomes of Ae. cylindrica accessions with C-or D-type plastome were found to be very closely related, suggesting a monotypic origin. Furthermore, analyses suggests that Ae. tauschii ssp. tauschii contributed its D genome and D-type plastome to Ae. cylindrica. Ae. cylindrica accessions collected near Van Lake in southeastern Turkey, an area where Ae. tauschii ssp. tauschii and Ae. markgrafii overlap, showed high allelic diversity and may represent the site where Ae. cylindrica formed. Population structure analyses suggested a lack of regional genetic structure in Ae. cylindrica and evidence of migration of Ae. cylindrica among various regions. Finally, Ae. cylindrica accessions in the USA were found to be closely related to accessions from at least three regions of its native range central Anatolia, central East Turkey and western Armenia, and Caucasia. Wheat and jointed goatgrass are closely related and both have the D-genome. These two species can hybridize and produce backcross derivatives under natural conditions, a situation that may allow gene flow between these two species. In order to better understand mating patterns between these two species, a total of 413 first-generation backcross (BC₁) seeds obtained from 127 wheat-jointed goatgrass F₁ hybrids, produced under natural conditions, were evaluated for their parentage using chloroplast and nuclear microsatellite markers. Of the 127 F₁ hybrids evaluated, 109 had jointed goatgrass as the female parent, while the remaining 18 F₁ plants had wheat as the female parent. Of the 413 BC₁ plants analyzed, 358 had wheat and 24 had jointed goatgrass as the recurrent male parent. The male parentage of 31 BC₁ plants could not be determined. Although the majority of hybrids were pollinated by wheat, backcrossing of hybrids to jointed goatgrass would enable gene flow from wheat to jointed goatgrass. Though the observed frequency of jointed goatgrass-backcrossed hybrids (F₁ X jointed goatgrass) was low under field conditions, their absolute number is dependent on frequency of hybrids, which in turn, depends on the density of jointed goatgrass in wheat fields. Therefore, the recommendations to control jointed goatgrass in wheat fields and adjacent areas and to plant jointed goatgrass free wheat seed should be followed in order to avoid gene flow from wheat to jointed goatgrass. / Graduation date: 2006