Relaxed phylogenies and dating with confidence grounds for invalidating a contract
These models open the gate to a new field of ''relaxed phylogenetics.'' Here we introduce a new approach to performing relaxed phylogenetic analysis.
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.
However, it is difficult to predict where the boundaries between these effects are and thus to specify what the degree of autocorrelation will be.
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.
In order to infer divergence dates, it is convenient to assume a constant rate of evolution throughout the tree [1,2].
This practice has been regularly challenged by results from datasets showing considerable departures from clocklike evolution , and rate variation among lineages can seriously mislead not only divergence date estimation  but also phylogenetic inference (e.g., [7,8]).
Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments.
Instead of dispensing with the molecular clock entirely, attempts have been made to relax the molecular clock assumption by allowing the rate to vary across the tree .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.At the other extreme, over very long timescales, we might expect so much variation in the inherited determinants of rate that the autocorrelation from lineage to lineage begins to break down, especially with sparse taxon sampling.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.
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.
 and Aris-Brosou and Yang , present an enticing alternative to local clock models.