Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

<div><p>Rate of substitution of genomic regions is among the most debated intrinsic features that impact phylogenetic informativeness. However, this variable is also coupled with rates of nonsynonymous substitutions that underscore the nature and degree of selection on the selected genes. To empirically address these variables, we constructed four completely overlapping data sets of plastid <i>matK</i>, <i>atpB</i>, <i>rbcL</i>, and mitochondrial <i>matR</i> genes and used the rosid lineage (angiosperms) as a working platform. The genes differ in combinations of overall rates of nucleotide and amino acid substitutions. Tree robustness, homoplasy, accuracy in contrast to a reference tree, and phylogenetic informativeness are evaluated. The rapidly evolving/unconstrained <i>matK</i> faired best, whereas remaining genes varied in degrees of contribution to rosid phylogenetics across the lineage's 108 million years evolutionary history. Phylogenetic accuracy was low with the slowly evolving/unconstrained <i>matR</i> despite least amount of homoplasy. Third codon positions contributed the highest amount of parsimony informative sites, resolution and informativeness, but magnitude varied with gene mode of evolution. These findings are in clear contrast with the views that rapidly evolving regions and the 3^rd codon position have inevitable negative impact on phylogenetic reconstruction at deep historic level due to accumulation of multiple hits and subsequent elevation in homoplasy and saturation. Relaxed evolutionary constraint in rapidly evolving genes distributes substitutions across codon positions, an evolutionary mode expected to reduce the frequency of multiple hits. These findings should be tested at deeper evolutionary histories.</p></div

Variation in bootstrap support for the major rosids lineages derived from gene partition analyses.

<p>Illustration of the differential bootstrap support for the rosids orders and the major clades calculated from the RAxML analyses based on partitioned gene data sets of <i>matK</i> (red), <i>matR</i> (yellow), <i>rbcL</i> (blue), and <i>atpB</i> (green).</p

A summarized backbone relationships among the rosids lineages based on Wang et al. [19] phylogenetic study.

<p>A total evidence maximum likelihood rosid tree redrawn from Wang et al. (2009) with percent bootstrap support values ≥50% noted on branches. COM: Celastrales, Malpighiales, and Oxalidales. NFC (Nitrogen Fixing Clade): Rosales, Fabales, Cucurbitales, and Fagales. The malvids clade includes the basal three orders Myrtales+Geranials/Crossosomatales as sister to the core group.</p

Diagrammatic representation of information on molecular characters from the four gene data sets.

<p>The number of total, variable and parsimony informative (PI) characters calculated from the maximum parsimony analyses of <i>matK</i>, <i>matR</i>, <i>rbcL</i>, and <i>atpB</i>. (A) gene partitions, (B) the three codon positions partitions (B).</p

Informativeness profiles for codon positions measured in PhyDesign.

<p>Net informativeness profiles for 1^st (green), 2^nd (blue) and 3^rd (red) codon positions of <i>matK</i>, <i>matR</i>, <i>rbcL</i>, and <i>atpB</i> computed in PhyDesign. Note the informativeness values for <i>matK</i> codon positions starting at 0.5, highlighted by double lines on the y-axis. Both <i>matK</i> and <i>matR</i> exhibit spikes in their informativeness profiles at very recent times.</p

Summaries of the rosids RAxML trees based on the four gene partitions.

<p>The backbone relationships among the rosids lineages based on partitioned data sets of <i>matK</i>, <i>matR</i>, <i>rbcL</i>, and <i>atpB</i>. Percent bootstrap support values ≥50% are noted. COM: Celastrales, Malpighiales, and Oxalidales. NFC (Nitrogen Fixing Clade): Rosales, Fabales, Cucurbitales, and Fagales. The core malvids group and the Zygophyllales were not recovered as monophyletic lineages in the <i>rbcL</i> partition analysis.</p

Rosids ultrametric reconstructed in PATHd8 and the informativeness profiles estimated in PhyDesign along with their variability at different epochs of rosids history.

<p>(A) Ultrametric tree for the rosids calculated in PATHd8 based on the concatenated four-gene data set. (B) Net informativeness profiles for <i>matK</i> (red), <i>matR</i> (yellow), <i>rbcL</i> (blue), and <i>atpB</i> (green) gene partitions; (C) Per-site informativeness profiles for the same genes; (D) The mean (gray) and standard deviation (black) for gene informativeness at four equally divided epochs in the evolutionary history of the rosids. COM: Celastrales, Malpighiales, and Oxalidales. NFC: Nitrogen Fixing Clade, Rosales, Fabales, Cucurbitales, and Fagales. Both <i>matK</i> and <i>matR</i> display spikes in their informativeness profiles at very recent times.</p