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 Ϸ25,000 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.

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

“…This is the largest ''ciliate-based'' phylogenetic dataset assembled to date in terms of number of bases included. All previous studies were based either on single or a couple of genes or contained extremely limited sampling of ciliates (Bapteste et al, 2002;Brown et al, 2012;Budin and Philippe, 1998;Burki et al, 2009Burki et al, , 2013Greenwood et al, 1991;Hampl et al, 2009;Hammerschmidt et al, 1996;Katz et al, 2004;Lynn and Sogin, 1988;Sogin and Elwood, 1986).…”

Origin and Distribution of Calvin Cycle Fructose and Sedoheptulose Bisphosphatases in Plantae and Complex Algae: A Single Secondary Origin of Complex Red Plastids and Subsequent Propagation via Tertiary Endosymbioses

“…In contrast, more than 5000 aa positions were required to achieve significant support (95% BP) for the common origin of alveolates and stramenopiles (Rodriguez-Ezpeleta et al 2005). However, a closer look at the ingroup topologies of these five "lucky genes" (Bapteste et al 2002) reveals discrepancies with the accepted relationships of the host cells. The SBP phylogeny (Fig.…”

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

“…More recently, a better understanding of protistan ultrastructural diversity and the development of phylogenomic approaches have refined this picture and further delineated these groups (see also Fig. 1) (Bapteste et al 2002;Burki et al 2007;Hampl et al 2009;Brown et al 2012;Zhao et al 2012).…”