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Mol Phylogenet Evol. 2018 Oct;127:248-255. doi: 10.1016/j.ympev.2018.06.006. Epub 2018 Jun 8.

Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models.

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College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
Botanic Garden Meise, 1860 Meise, Belgium; Phycology Research Group, Biology Department, Ghent University, 9000 Ghent, Belgium.
Allan Herbarium, Manaaki Whenua-Landcare Research, Lincoln 7640, New Zealand.
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
College of Life Sciences, Nanjing Normal University, Nanjing 210023, China. Electronic address:


Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.


GC-heterogeneous sites; Green algae; Heterogeneous models; Phylogenetic signals; Phylogenomics

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