Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae

Area of Science:

• Phylogenetics and evolutionary biology
• Algal genomics
• Molecular evolution

Background:

• Chlorophyta (green algae) are ancient, diverse, and ecologically significant, but their deep phylogenetic structure remains poorly understood.
• Previous studies lacked sufficient taxon and gene sampling for robust phylogenetic reconstruction.
• Understanding Chlorophyta phylogeny is crucial for deciphering evolutionary patterns in eukaryotes.

Purpose of the Study:

• To reconstruct the deep phylogeny of core Chlorophyta using extensive transcriptomic data.
• To investigate the impact of different phylogenetic inference methods on tree topology.
• To elucidate evolutionary transitions in morphology, habitat, and genetic codes within Chlorophyta.

Main Methods:

• Phylogenetic analysis of 70 species representing 80% of extant Chlorophyta orders using transcriptomic data from up to 2,698 genes.
• Examination of phylogenetic inference parameters including outgroup choice, missing data, and model selection.
• Reconstruction of ancestral scenarios to infer evolutionary pathways.

Main Results:

• Highly congruent species tree topologies were recovered across different analyses, supporting key clades like Bryopsidales and Scotinosphaerales-Dasycladales.
• Monophyly of Chlorophyceae and Trebouxiophyceae confirmed; uncertain placements of Chlorodendrophyceae and Pedinophyceae corroborated previous findings.
• Evidence for independent origins of stop-to-sense codon reassignment in Ulvophyceae (at least three times) and noncanonical serine encoding in Scotinosphaerales.

Conclusions:

• A robust phylogenetic framework for core Chlorophyta was established, clarifying evolutionary history.
• Key evolutionary transitions, including habitat shifts (freshwater-sea) and morphological complexity (unicellular to multicellular), were illuminated.
• The study provides new insights into the evolution of noncanonical genetic codes and their relationship with morphological evolution in green algae.