MBE Advance Access published online on May 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm091
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Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes
1 Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
2 Hayama Center for Advanced Studies, Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan
3 The Institute of Statistical Mathematics, Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan
4 Division of Life Science, Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 112-8610, Japan
5 Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193 Japan
+ Present address: School of Life Sciences, Fudan University, Shanghai 200433, China
++ Present address: Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya-shi, Aichi 464-8602, Japan
* E-mail: nozaki{at}biol.s.u-tokyo.ac.jp
Received for publication February 21, 2007. Revision received April 24, 2007. Accepted for publication May 2, 2007.
The biodiversity of photosynthetic eukaryotes, traditionally recognized as nine algal divisions or phyla, is attributed to two kinds of endosymbiotic events involving plastids: primary endosymbiosis and secondary endosymbiosis. Therefore, the phylogenetic positions of primary photosynthetic eukaryotes are fundamental for understanding the evolution of eukaryotic cells and establishing higher taxonomic concepts of eukaryotes. Recently, Rodriguez-Ezpeleta et al. [Curr. Biol. 15: 1325-1330, 2005] demonstrated the strong monophyly of the three groups of primary photosynthetic eukaryotes (green plants, glaucophytes, and red algae) based on 143 nuclear genes. However, they analyzed only two divisions of the secondary phototrophs belonging to the Stramenopiles–Alveolata (SA) lineage, and their 143 genes included rapidly evolving genes. Here, we reexamined the phylogeny of the primary phototrophs based on slowly evolving nuclear genes selected mainly from the data matrix of Rodriguez-Ezpeleta et al. [2005] using additional operational taxonomic units (OTUs) of free-living, secondary phototrophic group (Haptophyta) and Excavata (Heterolobosea and Reclinomonas) that do not belong to the SA lineage. Our phylogenetic results demonstrate the robust non-monophyly of the primary phototrophs and the basal position of red algae within the bikonts, suggesting the loss of plastids in certain eukaryotic lineages under the assumption of the single plastid primary endosymbiosis.
Key Words: eukaryote evolution • long branch attraction • phylogeny • plastid endosymbiosis • primary photosynthetic eukaryotes • taxon sampling
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