Estimating the Deviation from a Molecular Clock [chapter]

Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy Warnow
2002 Lecture Notes in Computer Science  
We address the problem of estimating the degree to which the evolutionary history of a set of molecular sequences violates the strong molecular clock hypothesis. We quantify this deviation formally, by defining the "stretch" of a model tree, with respect to the underlying ultrametric tree (indicated by time). We then define the "minimum stretch" of a dataset on a tree, and show how this can be computed optimally in polynomial time. We also present a polynomial time algorithm for computing a
more » ... r bound on the stretch of a given dataset on any tree. We then explore the performance of standard techniques in systematics for estimating the deviation of a dataset from a molecular clock. We show that standard methods, whether based upon maximum parsimony or maximum likelihood, can return infeasible values (i.e. values for the stretch which cannot be realized on any model tree), and often under-estimate the true stretch. This suggests that current estimations of the degree to which datasets deviate from a molecular clock may significantly underestimate these deviations. We conclude with some suggestions for further research. § © ¡ § © ¡ time. Simulation Study.
doi:10.1007/3-540-45784-4_22 fatcat:mkj74tyc7bfabbkocnijdisl3m