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

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Abstract
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.
Keywords
Green algae, Phylogenomics, GC-heterogeneous sites, Heterogeneous models, Phylogenetic signals, NONCANONICAL GENETIC-CODE, COCCOID GREEN-ALGAE, LAND PLANTS, ORIGIN, TREBOUXIOPHYCEAE, GENUS, ROOT, NOV., TREE, 18S

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Chicago
Fang, Ling, Frédérik Leliaert, Phil M Novis, Zhenhua Zhang, Huan Zhu, Guoxiang Liu, David Penny, and Bojian Zhong. 2018. “Improving Phylogenetic Inference of Core Chlorophyta Using Chloroplast Sequences with Strong Phylogenetic Signals and Heterogeneous Models.” Molecular Phylogenetics and Evolution 127: 248–255.
APA
Fang, Ling, Leliaert, F., Novis, P. M., Zhang, Z., Zhu, H., Liu, G., Penny, D., et al. (2018). Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models. MOLECULAR PHYLOGENETICS AND EVOLUTION, 127, 248–255.
Vancouver
1.
Fang L, Leliaert F, Novis PM, Zhang Z, Zhu H, Liu G, et al. Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models. MOLECULAR PHYLOGENETICS AND EVOLUTION. 2018;127:248–55.
MLA
Fang, Ling et al. “Improving Phylogenetic Inference of Core Chlorophyta Using Chloroplast Sequences with Strong Phylogenetic Signals and Heterogeneous Models.” MOLECULAR PHYLOGENETICS AND EVOLUTION 127 (2018): 248–255. Print.
@article{8606344,
  abstract     = {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.},
  author       = {Fang, Ling and Leliaert, Frédérik and Novis, Phil M and Zhang, Zhenhua and Zhu, Huan and Liu, Guoxiang and Penny, David and Zhong, Bojian},
  issn         = {1055-7903},
  journal      = {MOLECULAR PHYLOGENETICS AND EVOLUTION},
  keywords     = {Green algae,Phylogenomics,GC-heterogeneous sites,Heterogeneous models,Phylogenetic signals,NONCANONICAL GENETIC-CODE,COCCOID GREEN-ALGAE,LAND PLANTS,ORIGIN,TREBOUXIOPHYCEAE,GENUS,ROOT,NOV.,TREE,18S},
  language     = {eng},
  pages        = {248--255},
  title        = {Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models},
  url          = {http://dx.doi.org/10.1016/j.ympev.2018.06.006},
  volume       = {127},
  year         = {2018},
}

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