Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes

Abstract

The phylogeny and evolutionary history of the rice tribe (Oryzeae) were explored using sequences of five DNA fragments (matK, trnL, nad1, Adh2, and GPA1) from chloroplast, mitochondrial, and nuclear genomes. Results indicate that (1) Oryzeae is monophyletic and falls into two main clades corresponding to the traditionally recognized subtribes; (2) previous recognition of three monotypic genera (Hydrochloa, Porteresia, and Prosphytochloa) is not justified; and (3) close affinities of the monoecious genera are not supported, suggesting the possibility of multiple origins of unisexual florets. Based on the magnitude of matK and GPA1 sequence divergence, we suggest that Oryza and Leersia branched off from the remaining genera of Oryzeae ∼20 million years ago (mya), and separated from each other ∼14 mya. A divergence time of ∼9 mya is obtained for the most basal split within Oryza. These estimates suggest that Oryzeae diverged during the Miocene, and thus imply that long-distance dispersal appears to be one of the important factors in the diversification of the tribe.

The Evolutionary History of Ehrhartoideae, Oryzeae, and Oryza

“…The two tribes are estimated to have diverged 34.5±6.8 million years ago (Vicentini et al 2008), in the late Eocene or early Oligocene when the earth as a whole was becoming cooler and global CO 2 concentration was dropping to near its pre-industrial levels. Guo and Ge (2005) cite a fossil member of Oryzeae from this time period (Litke 1968), consistent with the molecular date, but Thomasson (1987) referred this fossil simply to an unidentified grass, not specifically oryzoid. Figure 3 shows the phylogeny of the 13 genera of Ehrhartoideae, created by grafting the phylogeny of Ehrharta from Verboom et al (2003) to that of Oryzeae (Ge et al 2002;Guo and Ge 2005).…”

“…Guo and Ge (2005) cite a fossil member of Oryzeae from this time period (Litke 1968), consistent with the molecular date, but Thomasson (1987) referred this fossil simply to an unidentified grass, not specifically oryzoid. Figure 3 shows the phylogeny of the 13 genera of Ehrhartoideae, created by grafting the phylogeny of Ehrharta from Verboom et al (2003) to that of Oryzeae (Ge et al 2002;Guo and Ge 2005). No one has undertaken a single comprehensive phylogenetic analysis for the entire subfamily, although this would be straightforward given the appropriate plant material.…”

“…Oryzeae includes nine or ten genera and 60 to 70 species, and is very likely monophyletic (Ge et al 2002;Guo and Ge 2005;Kellogg and Watson 1993). In all studies to date, the number of outgroup taxa included is not large enough to rule out completely the possibility of paraphyly, but available morphological and molecular data suggest that this is unlikely.…”

“…However, this could be an analytical artifact. The tree presented here is a grafted tree, created by simply pasting the phylogeny of Verboom et al (2003) on to that of Guo and Ge (2005). If the Ehrharteae subclade were in fact rooted along the internode leading to the Cape Province Ehrharta species, then the ambiguity of the ancestral node would be removed and an African origin would be inferred.…”

“…In addition, large open cells in the Fig. 3 Phylogeny of Ehrhartoideae, created by grafting the phylogeny of Ehrharteae (unshaded box) from Verboom et al (2003) onto that of Oryzeae (gray box) from Ge et al (1999) and Guo and Ge (2005). Polyploid members of Oryzeae are placed to the right of the diploid species according to their genomic constitution.…”