Xi Li, Xuan Shi, Hong Cheng, Shi‐Yu Zhang, Zhi‐Ping Yang, Xiao‐Ya Ma, and Bo‐Jian Zhong
Volvocales forms a species-rich clade with wide morphological variety and is regarded as an ideal model for tracing the evolutionary transitions in multicellularity. The phylogenetic relationships among the colonial volvocine algae and its relatives are important for investigating the origin of multicellularity in the clade Reinhardtinia. Therefore, a robust phylogenetic framework of the unicellular and colonial volvocine algae with broad taxon and gene sampling is essential for illuminating the evolution of multicellularity. Recent chloroplast phylogenomic studies have uncovered five major orders in the Chlorophyceae, but the family-level relationships within Sphaeropleales and Volvocales remain elusive due to the uncertain positions of some incertae sedis taxa. In this study, we contributed six newly sequenced chloroplast genomes in the Volvocales and analyzed a dataset with 91 chlorophycean taxa and 58 protein-coding genes. Conflicting phylogenetic signals were detected among chloroplast genes that resulted in discordant tree topologies among different analyses. We compared the phylogenetic trees inferred from original nucleotide, RY-coding, codon-degenerate, and amino acid datasets, and improved the robustness of phylogenetic inference in the Chlorophyceae by reducing base compositional bias. Our analyses indicate that the unicellular Chlamydomonas and Vitreochlamys are close to or nested within the colonial taxa, and all the incertae sedis taxa are nested within the monophyletic Sphaeropleales s.l. We propose that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity evolved once in the volvocine green algae and might be lost in Chlamydomonas and Vitreochlamys.
We assessed base compositional bias among 91 volvocine algae in the nt dataset and each of the three codon positions, and the percentage GC content of each species was plotted to visualize compositional heterogeneity. We compared the phylogenies inferred from different datasets with decreasing compositional biases (original nucleotide, RY-coding, codon-degenerate and amino acid datasets) and Robinson–Foulds (RF) algorithm was used for tree distance calculations. Conflicting phylogenetic signals among 58 plastid genes were detected and quantified through the calculation of genewise log-likelihood support, which resulted in discordant tree topologies at key nodes among different datasets. We hypothesize that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity has evolved once in the colonial clade, but was subsequently lost in Vitreochlamys and Chlamydomonas based on the phylogeny and ancestral state reconstruction analysis. We supplemented the chloroplast genomes and improved the robustness of phylogenetic inference in the Volvocales, which are crucial for studying the fundamental processes that shaped the initial advent of multicellularity.
