Reconstructing and dating the early evolutionary history of eukaryotes have proven challenging questions due to the scarcity of the fossil record, especially for protists (1).In the Archean eon, biomarker compounds characteristic of possibly extinct stem eukaryotes are found ≈2,700 million years ago (Mya) (2).Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes.
Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating.
However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain.
Our results document a wide range of substitution rates across genes and bacterial taxa.
This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria.
Biologists have often attempted to estimate when key events on the Tree of Life (TOL) occurred.
This approach has experienced substantial success when used for dating events in the Phanerozoic [543–0 Mya], but when trying to date deep events on the TOL, such as endosymbiosis events in the Proterozoic (2,500–543 Mya), it becomes increasingly difficult to find reliable fossil calibrations.
Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude.
In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating.
It is sometimes called a gene clock or an evolutionary clock.