July 15, 2005 | David F. Coppedge

More Evidence the Molecular Clock is Broken

“We live in interesting times,” grinned David Penny in Nature,1 reporting on how estimates of evolutionary past based on comparative genomics (the molecular clock) is producing confusing results.  Apparently, evolutionary geneticists are going to have to make use of the theory of relativity – i.e., that how fast the clock ticks depends on the viewpoint of the observer.  “An analysis of genetic data sets from primates and birds provides firm evidence that molecular evolution is faster on shorter than on longer timescales,” his subtitle explained.  “The estimated times of various evolutionary events require a rethink” (emphasis added in all quotes).  It’s hard to give up a pet theory, he continued:

The relative constancy of the rate at which DNA sequences evolve has been a treasured icon of molecular evolution for nearly 40 years.  The occurrence of such a stochastic ‘molecular clock’ was initially quite unexpected, and was explained by Motoo Kimura by assuming that most changes to amino-acid and nucleotide sequences were neutral – “neither beneficial nor injurious”, in Charles Darwin’s prescient phrase.
    However, there have been several inklings that the rate of molecular evolution accelerates when measured over evolutionarily short timescales.  As they report in Molecular Biology and Evolution, Ho and colleagues have now put the evidence together.  Their analyses of primate and bird data sets reveal that there is indeed a decided acceleration of molecular evolution on short timescales.  This is an effect that demands explanation; moreover, estimates for the timing of recent events in population biology will need to be reconsidered.

Penny discussed whether the phenomenon is real, whether it can be explained, and why it was not picked up earlier.  Part of the reason is no one was looking:

For some reason, the continuum between population heterozygosity and long-term evolution has not been adequately studied.  Although it is a continuum, the techniques required may change as the timescale decreases.  For example, some concepts from long-term evolution (binary evolutionary trees with sequences studied only at the tips) have been extended into populations where trees are no longer binary, and ancestral sequences (at internal nodes) are still present in the population.  There are hints that a formal multiscale study is necessary, because even though the same underlying process is occurring, different features of trees are observed as the timescale changes.

Lastly, he asked what are the consequences of this revelation.  Many time estimates will require recalculation – that’s one practical aspect.  “In some cases the constraints are from recent events, and it is the long-term events that require re-analysis,” he explained; “Much more remains to be done.”  The assumption of a single mutation rate is gone; “Even for nucleotides there are many ‘mutation rates’,” he pointed out.  Penny feels the solution is tractable, but the implication is that many former assumptions have been invalidated by the new data – hence his last sentence, “we live in interesting times.”


1David Penny, “Evolutionary biology: Relativity for molecular clocks,” Nature 436, 183-184 (14 July 2005) | doi: 10.1038/436183a.

Another evolutionary assumption has been overturned by more careful analysis; keep up the good work.  Next time, though, remove the assumption of evolution before making the observations.  Relativity applies to physics, not biology.  An evolutionary tale that requires relativity to keep its plot together has left the science department for the theater class (see 11/29/2004 entry).

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Categories: Genetics

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