MBE Advance Access published online on May 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm089
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Research Article |
Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of ‘Rhizaria’ with Chromalveolates
Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
1 Woods Hole Oceanographic Institution, MS#32, Woods Hole, MA 02543, USA
2 Present address: Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
* Corresponding author: University of Iowa, Department of Biological Sciences and the Roy J. Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, Iowa 52242-1324, USA, Telephone: (319) 335-1977, Fax: (319) 335-1069, Email: debashi-bhattacharya{at}uiowa.edu
Received for publication February 15, 2007. Revision received April 6, 2007. Accepted for publication April 25, 2007.
Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup ‘Chromalveolata’ (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multi-gene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and surprisingly, two members of the ‘Rhizaria’, Reticulomyxa filosa and Bigelowiella natans. The association of the two ‘Rhizaria’ with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.
Key Words: chromalveolates • endosymbiosis • Emiliania huxleyi • endosymbiotic gene transfer • Goniomonas cf. pacifica • haptophyte
3 These authors contributed equally to the manuscript.
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