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Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

Zhu T, Dos Reis M, Yang Z - Syst. Biol. (2014)

Bottom Line: Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis.Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment.Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation.

View Article: PubMed Central - PubMed

Affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

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Posterior distribution of divergence times in the primate tree of six species. In (a)-(b), the data consist of  independent loci, sampled at random from the 7947 genes ( upper panel of Table 3) The results are averages over 100 replicates. In (a′)-(b′), the 7947 genes are grouped into  partitions according to the relative rate of substitution. In (a) and (a′) the posterior mean and 95% CI for each node age  are plotted. In (b) and (b′), the 95% CI width () is plotted.
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Figure 5: Posterior distribution of divergence times in the primate tree of six species. In (a)-(b), the data consist of independent loci, sampled at random from the 7947 genes ( upper panel of Table 3) The results are averages over 100 replicates. In (a′)-(b′), the 7947 genes are grouped into partitions according to the relative rate of substitution. In (a) and (a′) the posterior mean and 95% CI for each node age are plotted. In (b) and (b′), the 95% CI width () is plotted.


Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

Zhu T, Dos Reis M, Yang Z - Syst. Biol. (2014)

Posterior distribution of divergence times in the primate tree of six species. In (a)-(b), the data consist of  independent loci, sampled at random from the 7947 genes ( upper panel of Table 3) The results are averages over 100 replicates. In (a′)-(b′), the 7947 genes are grouped into  partitions according to the relative rate of substitution. In (a) and (a′) the posterior mean and 95% CI for each node age  are plotted. In (b) and (b′), the 95% CI width () is plotted.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380039&req=5

Figure 5: Posterior distribution of divergence times in the primate tree of six species. In (a)-(b), the data consist of independent loci, sampled at random from the 7947 genes ( upper panel of Table 3) The results are averages over 100 replicates. In (a′)-(b′), the 7947 genes are grouped into partitions according to the relative rate of substitution. In (a) and (a′) the posterior mean and 95% CI for each node age are plotted. In (b) and (b′), the 95% CI width () is plotted.
Bottom Line: Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis.Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment.Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation.

View Article: PubMed Central - PubMed

Affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

Show MeSH