Research Article

Ancient hybridizations among the ancestral genomes of bread wheat

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Science  18 Jul 2014:
Vol. 345, Issue 6194, 1250092
DOI: 10.1126/science.1250092

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  1. Fig. 1 Analyses of gene tree topologies.

    (A) Superimposed ultrametric gene trees in a consensus DensiTree plot. The branch color changes for every 100 trees plotted. (B) Topology-based species phylogeny, assuming incomplete lineage sorting using a data set of 2269 gene trees inferred by PhyloNet. The results presented represent analyses of all gene trees (2269). The numbers on the branches represent estimates of parental contributions to the hybrid. Range estimates of parental contribution are extrapolated from results reported in Table 1. Species names are abbreviated as follows: Ash, Aegilops sharonensis; Asp, Ae. speltoides; At, Ae. tauschii; Tm, Triticum monococcum; Tu, T. urartu; Hv, Hordeum vulgare; TaA, T. aestivum A subgenome; TaB, T. aestivum B subgenome; TaD, T. aestivum D subgenome; Bd, Brachypodium distachyon; Os, Oryza sativa.

  2. Fig. 2 Coalescent-based genome divergence analyses.

    Coalescence times were estimated as the median of Bayesian MCMC sampling in BEAST. Genome divergence estimates were inferred with a Bayesian hierarchical model through WinBUGS and the R2OpenBUGS R package (35). (A) Divergence times (mean, 95% credibility interval) for the genome lineages A, B, and D for 2269 gene trees, excluding diploid species. A-B, blue; A-D, red; B-D, green. (B) Genome divergence network including diploid and hexaploid wheat genomes. Node age is given as mean genome divergence time, estimated independently for each pair of species representing that node. For nodes with more than two decendant tips, age is given as the mean for all relevant pairwise species comparisons, and bars span from the lowest minimal to the highest maximal 95% bound for their credibility intervals. Due to evidence of recent interlineage hybridizations (both in topology and coalescence analyses) in the Ae. sharonensis and Ae. speltoides genomes, these species are not considered in the estimation of the ancestral A, B, and D lineage divergence.

  3. Fig. 3 Model of the phylogenetic history of bread wheat (Triticum aestivum; AABBDD).

    Approximate dates for divergence and the three hybridization events are given in white circles in units of million years ago. Differentiation of the wheat lineage (Triticum and Aegilops) from a common ancestor into the A and B genome lineages began ~6.5 Ma. The first hybridization occurred ~5.5 Ma between the A and B genome lineages and led to the origin of the D genome lineage by homoploid hybrid speciation. The second hybridization, between a close relative (BB) of Ae. speltoides and T. urartu (AA), gave rise to the allotetraploid emmer wheat (T. turgidum; AABB) by polyploidization. Bread wheat originated by allopolyploidization from a third hybridization, between emmer wheat and Ae. tauschii (DD). The three diploid lineages are indicated with color and labels. Inflorescences (spikes) illustrate extant species closely related to those involved in the polyploidizations.