Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates

Jeremiah D. Hackett, Hwan Su Yoon, Shenglan Li, Adrian Reyes-Prieto, Susanne E. Rümmele, Debashish Bhattacharya

Research output: Contribution to journalArticle

179 Citations (Scopus)

Abstract

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 multigene 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.

Original languageEnglish (US)
Pages (from-to)1702-1713
Number of pages12
JournalMolecular biology and evolution
Volume24
Issue number8
DOIs
StatePublished - Aug 1 2007

Fingerprint

Rhizaria
Haptophyta
plastid
monophyly
plastids
Plastids
gene
algae
phylogeny
replacement
Stramenopiles
phylogenetics
Emiliania huxleyi
Plastid Genomes
protein
genes
Genes
gene transfer
Dinoflagellida
Horizontal Gene Transfer

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Keywords

  • Chromalveolates
  • Emiliania huxleyi
  • Endosymbiosis
  • Endosymbiotic gene transfer
  • Goniomonas cf. pacifica
  • Haptophyte

Cite this

Hackett, Jeremiah D. ; Yoon, Hwan Su ; Li, Shenglan ; Reyes-Prieto, Adrian ; Rümmele, Susanne E. ; Bhattacharya, Debashish. / Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. In: Molecular biology and evolution. 2007 ; Vol. 24, No. 8. pp. 1702-1713.
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Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. / Hackett, Jeremiah D.; Yoon, Hwan Su; Li, Shenglan; Reyes-Prieto, Adrian; Rümmele, Susanne E.; Bhattacharya, Debashish.

In: Molecular biology and evolution, Vol. 24, No. 8, 01.08.2007, p. 1702-1713.

Research output: Contribution to journalArticle

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