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However, recovering deep phylogenetic relationships among eukaryotes has proven to be an extremely challenging task. Consequently, various alternative methods have been used in the last decade, yielding different results regarding the placement of the root; between Amorphea (or “unikonts”) and all other eukaryotes (i.e., “bikonts”) (Richards and Cavalier-Smith 2005; Roger and Simpson 2009; Cavalier-Smith 2010), which, despite being the current leading working hypothesis, is challenged by several lines of evidence (Arisue et al.

The most recent conceptions of the eukaryotic tree of life feature five or six “supergroups” (Keeling et al. 2005; Roger and Simpson 2009): at the base of an Excavata lineage, Euglenozoa (Cavalier-Smith 2010); between Archaeplastida and other eukaryotes (Rogozin et al.

Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages.

After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations.

However, attempts to estimate the age of deep divisions within eukaryotes using these methods have yielded vastly different estimates (e.g., see Douzery et al. We first discuss recent progress in our understanding of eukaryotic phylogeny and the ancient eukaryotic fossil record, and then we review the development of molecular clock-based methods and how fossil constraints are treated.