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.
Highlights
Chloroplast phylogenomics has become a useful approach to elucidate the enigmatic evolutionary relationships of different taxonomic levels of plants[1,2,3,4]
By estimating the relative evolutionary rate and among-site compositional heterogeneity, we demonstrate that fastest-evolving sites show strong compositional heterogeneity, and have a much poorer fit to the evolutionary model
By assessing the impact from compositional heterogeneity, fast-evolving sites, and the model fit in the green algal chloroplast genomic data, the correlation analyses show that the sites with fastest evolutionary rates significantly correlate with strong among-site compositional heterogeneity, and have much poorer fit to the evolutionary model
Summary
Chloroplast phylogenomics has become a useful approach to elucidate the enigmatic evolutionary relationships of different taxonomic levels of plants[1,2,3,4]. Resolving the ancient phylogenetic history remains difficult because of non-phylogenetic signal[5], or use of simplistic substitution models[6] in the large-scale molecular data. Resolving the Charophytes phylogeny has received attention because of their close evolutionary relationship to the land plants[12,18,19,20], but a reliable phylogeny of Chlorophyta is important to understanding ancient evolution and diversification of morphological and cytological characters of green algae. We attempt to reconstruct a more reliable phylogenetic tree of Chlorophyta both by using a site-heterogeneous substitution model, and by removing non-phylogenetic signal. These fastest-evolving sites and using a site-heterogeneous model, we produced a congruent phylogenetic tree of Chlorophyta supporting the following: (1) The class Chlorophyceae is a monophyletic group. These fastest-evolving sites and using a site-heterogeneous model, we produced a congruent phylogenetic tree of Chlorophyta supporting the following: (1) The class Chlorophyceae is a monophyletic group. (2) The class Ulvophyceae is a polyphyletic group. (3) The class Trebouxiophyceae is a paraphyletic group. (4) The class Chlorophyceae is likely close to a group uniting Chlorodendrophyceae and one clade of Ulvophyceae
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