Estimating divergence times in large phylogenetic trees. Export

@article{citeulike:1750283, abstract = {A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.}, address = {Department of Mathematics, Stockholm University, Stockholm, Sweden.}, author = {Britton, T. and Anderson, C. L. and Jacquet, D. and Lundqvist, S. and Bremer, K.}, citeulike-article-id = {1750283}, citeulike-linkout-0 = {http://dx.doi.org/10.1080/10635150701613783}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17886144}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17886144}, citeulike-linkout-3 = {http://dx.doi.org/http://dx.doi.org/10.1080/10635150701613783}, citeulike-linkout-4 = {http://dx.doi.org/10.1080/10635150701613783}, doi = {10.1080/10635150701613783}, issn = {1063-5157}, journal = {Syst Biol}, keywords = {phylogenetics, phylowidget}, month = {October}, number = {5}, pages = {741--752}, posted-at = {2008-12-08 12:02:04}, priority = {2}, title = {Estimating divergence times in large phylogenetic trees.}, url = {http://dx.doi.org/10.1080/10635150701613783}, volume = {56}, year = {2007} }

TY - JOUR ID - citeulike:1750283 L3 - citeulike-article-id:1750283 N2 - A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software. IS - 5 JF - Syst Biol SN - 1063-5157 AD - Department of Mathematics, Stockholm University, Stockholm, Sweden. EP - 752 TI - Estimating divergence times in large phylogenetic trees. VL - 56 SP - 741 KW - phylogenetics KW - phylowidget AU - Britton, T AU - Anderson, CL AU - Jacquet, D AU - Lundqvist, S AU - Bremer, K PY - 2007/October// UR - http://dx.doi.org/10.1080/10635150701613783 ER -