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Background    Elymus  (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of  Elymus  species with a tetraploid genome complement derived from  Pseudoroegneria  (genome  St ) and  Hordeum  ( H ). We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting.    Methodology/Principal Findings  We sequenced portions of three unlinked nuclear genes—phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I—from 27 individuals, representing 14 Eurasian and North American  StStHH   Elymus  species.  Elymus  sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the  StStHH  genome configuration of the  Elymus  species. They suggest that the  StStHH  group originated in North America, and do not support separate North American and European origins. Our results point to North American  Pseudoroegneria  and  Hordeum  species as potential genome donors to  Elymus . Diploid  P. spicata  is a prospective  St- genome donor, though conflict among trees involving  P. spicata  and the Eurasian  P. strigosa  suggests either introgression of GBSSI sequences from  P. strigosa  into North American  Elymus  and  Pseudoroegneria , or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid  H. californicum  and/or allotetraploid  H. jubatum  are possible  H -genome donors; direct involvement of an allotetraploid  Hordeum  species would simultaneously introduce two distinct  H  genomes to  Elymus , consistent with some of the relationships among  H -genome sequences in  Hordeum  and  Elymus .    Conclusions/Significance  Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees—identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.

Reticulate Evolutionary History of a Complex Group of Grasses: Phylogeny of Elymus StStHH Allotetraploids Based on Three Nuclear Genes