Relaxed phylogenetics and dating with
Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments.
From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.
We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.
In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme.
We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.
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Alternatively, the use of an exponential distribution would imply that changes occurred at the nodes, with the size of the change being independent of the branch length.
From obscure beginnings, phylogenetics has become an essential tool for understanding molecular sequence variation.
As one looks over smaller and smaller timescales, the differences in such inherited factors become smaller relative to the variance caused by stochastic and uninherited factors (such as environmental or chance events).
An alternative way of considering this is that the autocorrelation is so strong that very little of the variation in rate can be attributed to inherited factors.
This practice has been regularly challenged by results from datasets showing considerable departures from clocklike evolution [ 3– 5], and rate variation among lineages can seriously mislead not only divergence date estimation [ 6] but also phylogenetic inference (e.g., [ 7, 8]).
Such problems with the molecular clock hypothesis have resulted in it being abandoned almost entirely for phylogenetic inference in favor of a model that assumes that every branch has an independent rate of molecular evolution.