Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae)

The phylogenetic position of hexaploid Elymus repens within the tribe Triticeae (Poaceae) was examined using cloned sequences from the low-copy nuclear genes encoding phosphoenolpyruvate carboxylase (pepC) and beta-amylase. A previous analysis of E. repens using data from the nuclear granule-bound starch synthase I (GBSSI) gene had yielded five phylogenetically distinct gene copies, two more than expected from hexaploidy alone. The three gene trees share three distinct E. repens clades, suggesting that E. repens contains three phylogenetically divergent genomes, contributed by Hordeum, Pseudoroegneria, and an unknown donor. The two additional GBSSI sequences, including one that was apparently derived from outside of the tribe, appear to reflect past introgression of GBSSI sequences into the E. repens genome. On all three trees, the Hordeum-like E. repens sequences are polyphyletic within Hordeum, and the trees are in conflict with regard to the placement of these sequences within Hordeum, highlighting multiple contributions from Hordeum to E. repens.