Table 1.
Primary sequence data and summary of clustering results.
Figure 1.
Ortholog identification method.
This diagram outlines the steps used for identifying orthologous genes for phylogenetic analysis. A) Unresolved phylogenetic scheme relating chlorophytes, charophytes, and embryophytes with a list of the six taxa with fully sequenced genomes used for the core ortholog determination. B) Core ortholog prediction from the previous six taxa. C) Charophyte orthog prediction. The core orthologs were then used to search for proteins in each of the eight charophyte transcriptomes. We filtered for good taxon sampling and removed orthologs with significant amino acid bias, resulting in 160 aligned proteins. These were concatenated onto one large multigene data matrix for phylogenetic analysis.
Figure 2.
Phylogenetic relationships of 14 Viridiplantae taxa determined by 160 concatenated proteins.
Phylogenetic analyses are summarized by a BI (CAT-Poisson model) consensus tree with branch support values from both BI and ML analyses (ML bootstrap/Bayesian posterior probabilities).
Table 2.
Summary of missing data.
Figure 3.
Hypothesis of character evolution in the Charophytes.
The earliest branching streptophytes (Mesostigma and Chlorokybus) were unicellular, flagellate, and isogamous. Multicellularity in the form of unbranched filaments evolved in the common ancestor of the remaining streptophytes and is represented in the Klebsormidiales. The most recent common ancestor of Charales+Coleochaetales+Zygnematales+LP most likely was an alga with plant-like cell division (phragmoplast), branched filaments, and oogamous sexual reproduction. The Charales went on to independently evolve a complex macrophytic form. The Coleochaetales independently acquired parenchymatous tissue and maternally retained zygotes. However, the Zygnematales went the route of reduction: loss of flagellate cells (reproduction via conjugation), loss of multicelluarity (Desmids), and loss of the phragmoplast.