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

Abstract

Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossilcalibrated molecular clock-based methods. 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. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655 -2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together

“…These factors, combined with the variability in estimates and credible intervals yielded by different molecular clock model assumptions, have led to the wide ranges of estimated ages for LECA and the eukaryote supergroups that have been published in the last decade. The most recent analyses provide estimates for the age of LECA in the range of 1000 to 1600 Ma (Eme et al, 2014). Despite the uncertainty about the precise ages, these analyses define a relatively short time interval of ∼300 million years between the age of LECA and the emergence of all eukaryotic supergroups, which is consistent with rapid diversification events.…”

Biosilicification Drives a Decline of Dissolved Si in the Oceans through Geologic Time

“…During the past few decades significant efforts have been made to infer the age of major evolutionary events along the tree of life using fossil-calibrated molecular clock-based methods (Eme et al, 2014). Molecular clocks use the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged.…”

Contrasting microfossil preservation and lake chemistries within the 1200–1000 Ma Torridonian Supergroup of NW Scotland

“…The patchy fossil record between c. 2000 and 1000 Ma, plus the inability to assign many such fossils to crown groups, markedly influences the extent to which the Proterozoic fossil record may yet be used to calibrate molecular trees (Eme et al 2014). There is a pressing need to identify the controls on fossil preservation and to learn what inferences we might make when the preservation is less good, so that we are not forced to interpret the lack of evidence as biological absence.…”