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Article (Published Version) Article Phylogenomics Reshuffles the Eukaryotic Supergroups BURKI, Fabien, et al. Abstract Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Reference BURKI, Fabien, et al. Phylogenomics Reshuffles the Eukaryotic Supergroups. PLOS ONE, 2007, vol. 2, no. 8, p. e790 DOI : 10.1371/journal.pone.0000790 Available at: http://archive-ouverte.unige.ch/unige:77963 Disclaimer: layout of this document may differ from the published version. 1 / 1 Phylogenomics Reshuffles the Eukaryotic Supergroups Fabien Burki1*, Kamran Shalchian-Tabrizi3, Marianne Minge3,A˚smund Skjæveland3, Sergey I. Nikolaev2, Kjetill S. Jakobsen3, Jan Pawlowski1 1 Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland, 2 Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland, 3 Department of Biology, University of Oslo, Oslo, Norway Background. Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings. Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions. This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes. Citation: Burki F, Shalchian-Tabrizi K, Minge M, Skjæveland A˚, Nikolaev SI, et al (2007) Phylogenomics Reshuffles the Eukaryotic Supergroups. PLoS ONE 2(8): e790. doi:10.1371/journal.pone.0000790 INTRODUCTION protein sequences led to two potential affiliations with other A well resolved phylogenetic tree describing the relationships eukaryotes. According to the first hypothesis, Rhizaria was sister among all organisms is one of the most important challenges of group to an excavate clade defined by G. lamblia, T. vaginalis, and modern evolutionary biology. A current hypothesis for the tree of Euglenozoa. The second hypothesis suggested that Rhizaria are eukaryotes proposes that all diversity can be classified into five or closely related to stramenopiles, which form together with six putative very large assemblages, the so-called ‘supergroups’ alveolates, haptophytes, and cryptophytes the supergroup of (reviewed in [1] and [2]). These comprise the ‘Opisthokonta’ and chromalveolates. Besides our study, the branching pattern between ‘Amoeboza’ (often united in the ‘Unikonts’), ‘Archaeplastida’ or Rhizaria and other supergroups has been specifically evaluated ‘Plantae’, ‘Excavata’, Chromalveolata’, and ‘Rhizaria’. The super- only by Hackett et al. (2007), who reported a robust relationship group concept as a whole, however, has been shown to be only between Rhizaria and members of the chromalveolates. moderately supported [3] and the evolutionary links among these Here, we further address the phylogenetic position of Rhizaria groups are yet to be confirmed. These uncertainties may be due to within the eukaryotic tree using an extensive multigene approach. the limited amounts of available data for the most parts of the For this purpose, we have carried out two expressed sequence tag eukaryotic diversity. In particular, only a small fraction of the (EST) surveys of rhizarian species: an undetermined foraminiferan unicellular eukaryote diversity [4] has been subject to molecular species belonging to the genus Quinqueloculina (574 unique studies, leading to important imbalances in phylogenies sequences, Accession Numbers: EV435154-EV435825) and Gym- and preventing researchers to reliably infer deep evolutionary nophrys cometa (628 unique sequences, Accession Numbers: relationships. EV434532-EV435153) (Cienkowski, 1876), a freshwater protist The supergroup Rhizaria [5] is particularly interesting for testing that has been shown to be part of core Cercozoa [20]. Using novel different possible scenarios of eukaryote evolution. This assemblage EST datasets for two rhizarians [21,22] and data from publicly has only recently been described and is based exclusively on available protists (TBestDB; http://tbestdb.bcm.umontreal.ca/ searches/login.php), we constructed a taxonomically broad dataset molecular data; nevertheless it is very well supported in most of 123 protein alignments amounting to nearly 30000 unambig- phylogenies [3]. It includes very diverse organisms such as filose testate amoeba, cercomonads, chlorarachniophytes (together, core Cercozoa), foraminifers, plasmodiophorids, haplosporidians, gro- Academic Editor: Geraldine Butler, University College Dublin, Ireland miids, and radiolarians (see [2] for an overview or [6–11]). In opposition to Rhizaria, the monophyly of Chromalveolata is far from Received June 17, 2007; Accepted July 26, 2007; Published August 29, 2007 being undisputed (see [12], or [3,13–15]). Chromalveolates were Copyright: ß 2007 Burki et al. This is an open-access article distributed under originally defined by their plastid of red algal origin that (when the terms of the Creative Commons Attribution License, which permits present) is believed to have arisen from a single secondary endo- unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. symbiosis [16]. This supergroup encompasses many ecologically important photosynthetic protists, including coccolithophorids Funding: This research was supported by the Swiss National Science Foundation (belonging to the haptophytes), cryptophytes, diatoms, brown grant 3100A0-100415 and 3100A0-112645 (JP); and by research grant (grant no 118894/431) from the Norwegian Research Council (KSJ). seaweeds (together, the chromists) and dinoflagellates (which form together with ciliates and apicomplexans the alveolates) [17,18]. Competing Interests: The authors have declared that no competing interests Using a phylogenomic approach we recently confirmed the exist. monophyly of Rhizaria and addressed the question of its * To whom correspondence should be addressed. E-mail: Fabien.Burki@zoo. evolutionary history [19]. The analyses of 85 concatenated nuclear unige.ch PLoS ONE | www.plosone.org 1 August 2007 | Issue 8 | e790 Reshuffling the Supergroups uously aligned amino acid positions. Our superalignment includes in the ML inference (68% and 61% BP, respectively) but 1.0 BiPP. several representatives for all described eukaryotic supergroups. Finally, alveolates, stramenopiles, and Rhizaria all formed mono- Our results show an unambiguous relationship between Rhizaria phyletic groups with 100% BP and 1.0 BiPP. Although most of the and stramenopiles, confirming the hypothesis we had previously recognized eukaryotic supergroups are recovered in our analyses, proposed and suggesting the emergence of a new super assemblage the relationships among them are generally not well resolved. This of eukaryotes that we propose to name ‘SAR’ (stramenopiles+al- is with two notable exceptions: the union of the unikonts and, veolates+Rhizaria). much more interestingly, the strongly supported (BP = 100%; BiPP = 1.0) assemblage of stramenopiles, Rhizaria, and alveolates RESULTS (clade SAR), with these last two groups being robustly clustered together (BP = 88%; BiPP = 1.0) (clade SR). Comparisons of Single-gene analyses and concatenation substitution rates between the different lineages were highly non 49 eukaryotic species representatives of all five current super- significant at 1.25%, indicating that all species evolve at very groups for which large amounts of data are available were selected. similar rates, thus rendering unlikely a possible artefact caused by We identified 123 genes (see Table S1) that fulfilled the following long branches (data not shown). criteria: 1) at least one of the four rhizarian species as well as at To further test this unexpected nested position of Rhizaria least one member of unikonts, plants, excavates, alveolates, and between alveolates and stramenopiles, we compared different stramenopiles were present in every single-gene alignment; 2) the topologies by performing the approximately unbiased (AU) test, orthology in every gene was unambiguous on the base of single- which is considered as the least-biased and most rigorous test genes bootstrapped
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