Relaxed phylogenetics and dating with confidence drummond

Posted by / 13-Jan-2017 02:42

Relaxed phylogenetics and dating with confidence drummond

Nevertheless, a well-known problem that has persistently troubled phylogenetic inference is that of substitution rate variation among lineages.In order to infer divergence dates, it is convenient to assume a constant rate of evolution throughout the tree [ 1, 2].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.Under such an assumption, it is possible to infer phylogenies (e.g., [ 9, 10]), but not to estimate molecular rates or divergence times, because the individual contributions of rate and time to molecular evolution cannot be separated.If the rate and time along each branch can only be estimated as their product, then the position of the root of the tree cannot be estimated without additional assumptions such as an outgroup or a non-reversible substitution process.

Recently, it has been realized that less drastic alternatives to the unrooted model of phylogeny may exist.Relaxed-clock models present a potentially useful method for removing the assumption of a strict molecular clock, but a major shortcoming of the methods that have been proposed thus far is that they require the user to specify the tree topology.This is a problem because in many cases, important parts of the tree may be uncertain or unresolved, resulting in a number of plausible tree topologies.However, assigning branches to different groups can be a difficult exercise if the number of sequences is large or if there is considerable uncertainty about the phylogenetic relationships among the taxa.Essentially, such models are only useful in cases in which there is a strong prior hypothesis that the rate of specific taxa will differ from the rest of the tree [ 6].

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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.