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Rate variation and estimation of divergence times using strict and relaxed clocks.

ABSTRACT: Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models.Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, ?, was low (? 0.1), but were inappropriate when ?>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when ? = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for ? = 0.01-0.1, but high power for ? = 0.5-2.0. Posterior means of ?2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher ?2 for one or more partitions, supporting the simulation results.The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on ?2.

SUBMITTER: Brown RP

PROVIDER: S-EPMC3205074 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Rate variation and estimation of divergence times using strict and relaxed clocks.

Brown Richard P RP Yang Ziheng Z

BMC evolutionary biology 20110926

<h4>Background</h4>Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models wer ...[more]

PMID: 21943087

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Project description:The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into different partitions, and then use different models or different values of model parameters for different partitions to account for the among-partition heterogeneity. However, how to partition data in practical phylogenetic analysis, and in particular in relaxed-clock dating analysis, is more art than science. Here, we use computer simulation and real data analysis to study the impact of the partition scheme on divergence time estimation. The partition schemes had relatively minor effects on the accuracy of posterior time estimates when the prior assumptions were correct and the clock was not seriously violated, but showed large differences when the clock was seriously violated, when the fossil calibrations were in conflict or incorrect, or when the rate prior was mis-specified. Concatenation produced the widest posterior intervals with the least precision. Use of many partitions increased the precision, as predicted by the infinite-sites theory, but the posterior intervals might fail to include the true ages because of the conflicting fossil calibrations or mis-specified rate priors. We analyzed a data set of 78 plastid genes from 15 plant species with serious clock violation and showed that time estimates differed significantly among partition schemes, irrespective of the rate drift model used. Multiple and precise fossil calibrations reduced the differences among partition schemes and were important to improving the precision of divergence time estimates. While the use of many partitions is an important approach to reducing the uncertainty in posterior time estimates, we do not recommend its general use for the present, given the limitations of current models of rate drift for partitioned data and the challenges of interpreting the fossil evidence to construct accurate and informative calibrations.

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Rate variation and estimation of divergence times using strict and relaxed clocks.

Publications

Rate variation and estimation of divergence times using strict and relaxed clocks.

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