Reticulate evolutionary history of a complex group of grasses: phylogeny of Elymus StStHH allotetraploids based on three nuclear genes.

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, beta-amylase, and granule-bound starch synthase I-from 27 individuals, representing 14 Eurasian and North American StStHHElymus 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.

Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: analyses of three nuclear gene trees.

This phylogenetic study focuses on a subset of the species in Elymus-specifically, the endemic Asian tetraploids presumed to combine the St genome from Pseudoroegneria with the Y genome from an unknown donor. The primary goals were to (1) determine whether the St and Y genomes are derived from phylogenetically distinct donors; (2) identify the closest relative, and potentially the likely donor, of the Y genome; and (3) interpret variation among StStYY species in terms of multiple origins and/or introgression. The goals were addressed using phylogenetic analyses of sequences from three low-copy nuclear genes: phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I. Data sets include 16 StStYY individuals representing nine species, along with a broad sample of representatives from most of the monogenomic (i.e., non-allopolyploid) genera in the tribe. To briefly summarize the results: (1) the data clearly support an allopolyploid origin for the Asian tetraploids, involving two distinct donors; (2) the Y genome was contributed by a single donor, or multiple closely-related donors; (3) the phylogenetic position of the ElymusY genome varies among the three trees and its position is not strongly supported, so the identity of the donor remains a mystery; and (4) conflicts among the gene trees with regard to the St-genome sequences suggest introgression involving both Elymus and Pseudoroegneria.

Single origin of Malagasy Carnivora from an African ancestor.

The Carnivora are one of only four orders of terrestrial mammals living in Madagascar today. All four (carnivorans, primates, rodents and lipotyphlan insectivores) are placental mammals with limited means for dispersal, yet they occur on a large island that has been surrounded by a formidable oceanic barrier for at least 88 million years, predating the age of origin for any of these groups. Even so, as many as four colonizations of Madagascar have been proposed for the Carnivora alone. The mystery of the island's mammalian origins is confounded by its poor Tertiary fossil record, which leaves us with no direct means for estimating dates of initial diversification. Here we use a multi-gene phylogenetic analysis to show that Malagasy carnivorans are monophyletic and thus the product of a single colonization of Madagascar by an African ancestor. Furthermore, a bayesian analysis of divergence ages for Malagasy carnivorans and lemuriforms indicates that their respective colonizations were temporally separated by tens of millions of years. We therefore conclude that a single event, such as vicariance or common dispersal, cannot explain the presence of both groups in Madagascar.