The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

Abstract

The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large data set containing 123 genes for representatives of three phenotypically highly divergent major amoeboid lineages: Pelobionta, Entamoebidae, and Mycetozoa. Phylogenetic reconstruction was performed on approximately 25,000 aa positions for 30 species by using maximum-likelihood approaches. All well-established eukaryotic groups were recovered with high statistical support, validating our approach. Interestingly, the three amoeboid lineages strongly clustered together in agreement with the Conosa hypothesis [as defined by T. Cavalier-Smith (1998) Biol. Rev. Cambridge Philos. Soc. 73, 203-266]. Two amitochondriate amoebae, the free-living Mastigamoeba and the human parasite Entamoeba, formed a significant sister group to the exclusion of the mycetozoan Dictyostelium. This result suggested that a part of the reductive process in the evolution of Entamoeba (e.g., loss of typical mitochondria) occurred in its free-living ancestors. Applying this inexpensive expressed sequence tag approach to many other lineages will surely improve our understanding of eukaryotic evolution.

Figure 1

ML tree based on 25,032 aa positions. * indicates a constrained node. We used the JTT model, without taking into account among-sites rate variation. The branch lengths have been computed on the concatenated sequences. BVs were obtained by bootstrapping the 123 genes.

Figure 2

ML tree based on 25,032 aa positions, taking into account among-sites rate variation (JTT + Γ model). See Fig. 1 for details.

Figure 3

Effect of the number of genes studied on the evolution of BVs for the grouping of Entamoeba/Mastigamoeba (a), for the monophyly of Conosa (b), for the monophyly of chromalveolates (c), and for the sister group of Conosa and Opisthokonta (d). ● indicate the mean BVs without Γ law correction, and ▴ indicate the mean BVs with Γ law correction. Vertical bars correspond to 1 SD computed from 1,000 jackknife replicates.