The American species of Hordeum form a monophyletic group of closely related species, in which a rapid radiation took place in South America during the last two million years. Species relationships within this group could up to now not be clarified because of the small sequence differences among the species or incomplete sorting of ancient alleles. To overcome these problems we analyzed 65 samples covering all 13 diploid New World species with amplified fragment length polymorphism analysis (AFLP). Six primer combinations yielded 858 fragments, 765 of which were potentially parsimony informative. Two samples of diploid Asian Hordeum species were included as outgroup taxa. AFLP analysis was able to resolve species relationships, showing Californian H. brachyantherum as sister to four major phylogenetic groups from South America. These are a central Argentine and northern Andean group (H. cordobense, H. muticum), a mainly central to northern Argentine group including two North American species (H. erectifolium, H. euclaston, H. intercedens, H. pusillum, H. stenostachys), a group occurring mainly in southern Patagonia (H. comosum, H. patagonicum, H. pubiflorum), and a group of two species, whose close relationship has not been inferred before (H. chilense, H. flexuosum). Within these groups, sister species can be resolved with high bootstrap support, while statistical support for the branches defining the relationships among these groups is relatively low. The AFLP results support the monophyly of the three annual New World species, as well as earlier findings regarding intercontinental long-distance dispersals from South to North America.
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