title: Chloroplast Phylogenomic Inference of Green Algae Relationships.
abstract: The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences.
authors: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
authors: Linhua
authors: L
authors: Sun
authors: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
authors: Ling
authors: L
authors: Fang
authors: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
authors: Zhenhua
authors: Z
authors: Zhang
authors: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
authors: Xin
authors: X
authors: Chang
authors: Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors: David
authors: D
authors: Penny
authors: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
authors: Bojian
authors: B
authors: Zhong
mesh_terms: D000460:Chlorophyta / Q000145:classification* / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D061125:Genes, Chloroplast; D023281:Genomics; D010802:Phylogeny