Phylogeny of Eukaryotes recovered with molecular data: highlights and pitfalls

Abstract

Molecular data gained increased importance in phylogenetic analyses of protists when automated techniques of DNA amplification and sequencing became available. A new picture of eukaryote phylogeny rapidly emerged from small subunit ribosomal RNA (ssu rRNA) sequence comparisons. This tree splits off basal branching amitochondriate taxa such as microsporidians, parabasaleans, and diplomonads. Euglenozoans, heteroloboseans, and dictyostelids branch in the middle part of the tree. Subsequently, a rapid ramification occurs which is often referred to the “crown” group, including red algae, chlorobionts (green algae, mosses, and vascular plants), fungi, metazoans, and choanoflagellates. Also included in this radiation are the stramenopiles (oomycetes, hyphochitridiomycetes, and heterokont algae), the alveolates (dinoflagellates, apicomplexa, and ciliates), cryptomonads, and some amoeboid lineages. However, the ssu rRNA tree was challenged by refined methods of sequence analysis and by alternative molecular markers, such as protein coding genes. Considerable progress in the reconstruction of the “tree of life” comes from multi-gene sequence comparisons, and from structural data (e.g. insertions, deletions, and gene fusions). Nevertheless, many of the groupings suggested by the ssu rRNA tree were readily confirmed, such as the close relationship of fungi and metazoans, the alveolates, and their sister group relationship with the stramenopiles. However, others, such as the amitochondriate microsporidians, were radically misplaced in these trees.