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. 2004 Oct 26;101(43):15386-91.
doi: 10.1073/pnas.0403984101. Epub 2004 Oct 19.

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

Emmanuel J P Douzery  1 , Elizabeth A Snell, Eric Bapteste, Frédéric Delsuc, Hervé Philippe
Affiliations

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

Emmanuel J P Douzery et al. Proc Natl Acad Sci U S A. .

Abstract

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be approximately 100 million years more ancient than the Cambrian boundary.

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Figures

Fig. 1.
Fig. 1.
Divergence time estimates (Mya) among eukaryotes, based on a Bayesian relaxed molecular clock applied to 30,399 amino acid positions. The topology is the highest-likelihood one, with branch lengths proportional to the absolute ages of the subtending nodes. Dictyostelium rooted the tree but was pruned from dating analyses. White rectangles delimit 95% credibility intervals on node ages. Stars indicate the six nodes under prior paleontological calibration (lower bound only for the white star; lower and upper bounds for black stars). Gray areas encompass the bounds between which calibration nodes stand a posteriori during the Bayesian search. Primary and secondary plastid endosymbioses are indicated, respectively, by the circled 1 and 2. Double horizontal arrows and dotted lines indicate the displacement of 95% credibility intervals for eight selected nodes after rerooting the tree along the kinetoplastid branch. Paleozoic, Mesozoic, and Cenozoic are indicated by I, II, and III, respectively. Transitions between Meso-/Neo-Proterozoic and Cambrian are indicated by vertical dashed lines.
Fig. 2.
Fig. 2.
Relationship between node rates and node times. For each node of the chronogram, the amino acid replacement rate has been plotted against the estimated divergence times. The Cambrian boundary is indicated by the vertical line. The mean and ± 2 SDs of the rates are indicated by the continuous and dashed horizontal lines, respectively.
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