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The Streptophyta/Chlorophyta divergence correlates with a remarkably conservative preference for freshwater/marine habitats, and the early freshwater adaptation of streptophyte algae was a major advantage for the earliest land plants, even before the origin of the embryo and the sporophyte generation. The complete genomes of a few key streptophyte algae taxa will be required for a better understanding of the colonization of terrestrial habitats by streptophytes.

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The great majority of metazoans belong to bilaterian phyla. They diversified during a short interval in Earth's history known as the Cambrian explosion, ∼540 million years ago. However, the genetic basis of these events is poorly understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor) played an important role for the evolution of bilaterian animals. We provide evidence that the CTCF protein and a genome-wide abundance of CTCF-specific binding motifs are unique to bilaterian phyla, but absent in other eukaryotes. We demonstrate that CTCF-binding sites within vertebrate and Drosophila Hox gene clusters have been maintained for several hundred million years, suggesting an ancient origin of the previously known interaction between Hox gene regulation and CTCF. In addition, a close correlation between the presence of CTCF and Hox gene clusters throughout the animal kingdom suggests conservation of the Hox-CTCF link across the Bilateria. On the basis of these findings, we propose the existence of a Hox-CTCF kernel as principal organizer of bilaterian body plans. Such a kernel could explain (i) the formation of Hox clusters in Bilateria, (ii) the diversity of bilaterian body plans, and (iii) the uniqueness and time of onset of the Cambrian explosion.

Although the combination of different genes in phylogenetic analyses is a promising approach, the methodology is not well established and analyses often suffer from inadequate, noncongruent taxon sampling, long-branch attraction, or conflicting evolutionary models of the genes analyzed. Conflicts or congruence between multigene and single-gene phylogenies, as well as the assumed superiority of the multigene approach, are often difficult to assess solely because of incongruent taxon sampling. In the present study, a data set of 43 nuclear-encoded SSU rDNA and plastid-encoded rbcL gene sequences was generated from the same strains of conjugating green algae (Zygnematophyceae, Streptophyta). Phylogenetic analyses used the genes individually and in combination, either as concatenated sequences or with the log-likelihood summation method. Single-gene analyses, although mostly congruent, revealed some conflicting nodes and showed different patterns of statistical support. Combined analyses confidently resolved the conflicts between the single-gene analyses, enhanced phylogenetic resolution, and were better supported by morphological information. Long-branch taxa were not the same for the two genes analyzed, and, thus, their effect on phylogenetic resolution was minimized in the combined analyses.