A re‐evaluation of the homoploid hybrid origin of A egilops tauschii , the donor of the wheat D‐subgenome

Hybridization is a prominent evolutionary force promoting plant diversification, either with or without subsequent genome doubling (Abbott et al., 2013; Soltis et al., 2014; Yakimowski & Rieseberg, 2014). The Aegilops–Triticum complex is an ideal system to investigate how natural hybridization and allopolyploidization have caused species diversification (Matsuoka, 2011). Recently,Marcussen et al. (2014) proposed the tantalizing scenario that the ancestralD lineage originated via homoploid hybridization between ancient A and B lineages some 5 million years ago (Mya) (the definition of A, B andD lineages shown inFig. 1). Evidence for this mode of origin was derived from phylogenomic and population genetic analyses of nuclear genes, but without taking into account the evolutionary history and chloroplast topology of this species complex. Meanwhile, in a recent issue of New Phytologist, Gornicki et al. (2014) reported the chloroplast phylogeny of the Triticum–Aegilops complex based on 25 chloroplast genomes of eight modern A, S and D genome diploid species and four polyploidwheat species, but they did not address the origin of theD genome. Here, by re-analyzing critical data used by both studies and additional data, we present evidence for amore complex hybrid origin of the D genome of A. tauschii.