The evolution of Zea and, especially, the domestication of maize have undergone multifaceted assessment for many decades. New analyses have often demonstrated inconsistencies that prompted new thinking. Reexamination of chloroplast microsatellite data from a broad sampling of Zea reveals clear phenetic patterns, notably: 1) The various teosinte taxa are related to each other as expected; 2) Chloroplasts of the tested maize landraces form two very different groups; 3) Mexican annual teosintes are closely linked to only one maize group. These and other results are supported by a wide range of older studies. The latter two patterns deserve careful consideration because they contradict the model that a Mexican annual teosinte was domesticated, then evolved to all present maizes. They do not contradict the model that a small, domesticated maize was greatly changed by introgression, probably by a teosinte in section Luxuriantes of Zea. The introgression probably also led to great evolutionary acceleration, several important bottlenecks and the enormous diversity of modern maize. These chloroplast microsatellite relationships have various implications and deserve careful attention in designing future studies (see discussion)
