Absolute substitution rates during the evolutionary history of grasses.

<p>Values above each branch indicate absolute substitution rate (R) in substitutions per site per billion years (SSB) for that branch. Among them, 0.12±0.01 and 0.11±0.01 above and below the branch to <i>Oryza</i> are the mean values along the lineage from the common ancestor of <i>Oryza</i>/<i>Triticum</i> to <i>O. sativa</i> and <i>O. rufipogon</i>, respectively, while 0.21±0.02 above the branch to <i>Zea</i> is the average value of R along the lineage from the common ancestor of <i>Zea</i>/<i>Tripsacum</i> to three <i>Zea</i> species.</p

Main features of the assembled <i>F. rimosivaginus</i> mitochondrial genome.

<p>Main features of the assembled <i>F. rimosivaginus</i> mitochondrial genome.</p

Phylogenetic trees of 22 seed plants inferred from different datasets.

<p>The ML tree (A) and the MP tree (B) inferred from the concatenated 12 fast-evolving mitochondrial (mt) genes. The ML tree (C) and the MP tree (D) inferred from the concatenated 19 slow-evolving mt genes. Numbers associated with branches are bootstrap support (BS) values. <i>Oryza</i> and related BS values indicated in bold.</p

Rate change variation among genes in Poaceae.

<p>Each bar represents the ratio of absolute substitution rate (R) along the line leading to Poaceae to that on the line from the common ancestor of grasses to <i>O. sativa</i>.</p

Summary of the <i>F. rimosivaginus</i> mitochondrial genome sequencing and assembly.

<p>Summary of the <i>F. rimosivaginus</i> mitochondrial genome sequencing and assembly.</p

Mitochondrial genomes of the 22 seed plants included in phylogenetic analyses in this study.

<p>Mitochondrial genomes of the 22 seed plants included in phylogenetic analyses in this study.</p

Comparison of gene content among grass mitochondrial genomes.

<p>+, presence of the gene; −, absence of the gene; ψ, pseudogene;</p

Phylogenetic trees of 22 seed plants based on amino acid sequences of 31 mitochondrial genes.

<p>The ML tree (A) and the MP tree (B). Numbers associated with branches are bootstrap support (BS) values. <i>Oryza</i> and related BS values indicated in bold.</p

Phylogenetic trees of 22 seed plants as determined from mitochondrial and chloroplast genomes.

<p>The ML tree (A), the BI tree (B) and the MP tree (C) based on 31 mitochondrial (mt) genes. The topology of the chloroplast tree (D) is constrained by previous studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030297#pone.0030297-Zhang1" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030297#pone.0030297-Moore2" target="_blank">[25]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030297#pone.0030297-Kellogg1" target="_blank">[42]</a>. Numbers at nodes indicate bootstrap support (BS) values ≥50% or BI posterior probabilities. Branch lengths of the ML tree calculated through RAxML analysis, and correspond to scale bar (in units of substitutions/site).</p

Data matrices

This file contains 8 data matrices used in the study for phylogenetic analyses. The names of the data sets correspond to those in the main text