Phylogeny and diversification of the green algae inferred from nuclear and chloroplast genes

Green algae exhibit a remarkable cytological diversity ranging from unicellular microscopic algae with a single nucleus, over multicellular filaments and foliose blades, to coenocytic and siphonous life forms. Accurate reconstruction of the phylogenetic relationships of this diverse group is paramount to understanding the evolution of multicellularity and cytological layouts. Because ribosomal RNA and plastid genes have failed to resolve relationships among the major groups with confidence, we have generated data for 7 nuclear housekeeping genes. We present a phylogeny based on analyses (ML and BI) of these seven genes, SSU nrDNA and two plastid markers with carefully chosen partitioning strategies and models of sequence evolution. We obtained high support across the topology of the Chlorophyta, show the monophyly of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) classes and reveal a sister relationship between Chlorophyceae and Ulvophyceae. The inferred relationships provide novel insights into the evolution of multicellularity and multinucleate cells in the Ulvophyceae. Guided by this improved green algal phylogenetic tree, we address various topics relating to molecular evolution of the Chlorophyta. The distribution of elongation factor genes EFL and EF1-alpha, reassignment of stop codons to glutamine, a relatively even use of synonymous codons and high rates of molecular evolution of the ribosomal RNA indicate that profound changes occurred to the translational system of the Ulvophyceae