Topological variation in single-gene phylogenetic trees

Abstract

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.

Figure 1

A phylogenetic tree depicting all nodes (branchpoints) on the evolutionary line leading to humans. The species groupings (clades) given here along the top are those used in [8]. The 'basal eukaryotes' are a diverse polyphyletic group (not a single clade) of mainly unicellular organisms such as excavates and chromalveolates, and this grouping is thus labelled 'uncertain'. The nodes studied by Huerta-Cepas et al. [3] are indicated by the black bars. The clades in which at least one complete genome sequence is available are marked with an asterisk. All eukaryotic clades with a genome sequence were included in the phylogenetic analysis of Huerta-Cepas et al., except for the Ambulacraria, for which a genome sequence (of the echinoderm Strongylocentrotus purpuratus) has only recently become available.