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A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts) - PubMed

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

Romain Derelle et al. Mol Biol Evol. 2016 Nov.

Abstract

Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large data set of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.

Keywords: Bigyra; Chrysista; Diatomista; Gyrista; phylogenomics.

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Figures

Figure 1
Figure 1. Bayesian phylogenomic tree of stramenopiles.

Bayesian consensus tree obtained from the full data set under the CAT-GTR + Γ4 model. The tree is arbitrary rooted on Rhizaria and Alveolata. Branch supports correspond to Bayesian posterior probabilities obtained under the CAT-GTR + Γ4 (left) and CAT-Poisson + Γ4 (right; inferred from the two converging chains) models. Branches with posterior probabilities equal to 1 in both Bayesian analyses are marked with a bullet.

Figure 2
Figure 2. The root of stramenopiles in maximum likelihood (ML) analyses.

A, Schematic representation of the two alternative positions of the root of stramenopiles observed in ML analyses. B, Evolution of bootstrap supports for the two topologies shown in Figure 2A along the removal of fast evolving sites and divergent species.

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