Abstract
BackgroundEstimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns (“broom” clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon – Australian grass trees (Xanthorrhoea) – whose substitution rate is slower than in its sister groups, as determined by relative rate tests.ResultsIn the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3–6 Ma versus 25–35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model.ConclusionsThe choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0263-3) contains supplementary material, which is available to authorized users.
Highlights
Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences
Simulations of strong among-clade substitution rate variation Our simulated datasets were designed to mirror our understanding of the evolution of the Xanthorrhoeaceae, i.e. a phylogenetic tree including a long-stemmed ? broom? clade, a slow molecular clock and a crown with no internal calibration, and a ? bush? sister clade with a short stem, faster clock and internal calibration (e.g., Figures 1? 2)
In the BEAST analyses, the random local clocks (RLC) clock model (Figure 3) outperformed uncorrelated lognormal (UCLN) (Figure 4) and accurately reconstructed the abrupt and sustained change in substitution rate occurring along the long internal branch of the broom clade
Summary
Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. A strict molecular clock has been rejected in analyses of most empirical datasets, and is inapplicable to data in which rate shifts occur, so relaxed molecular clock models are used widely (reviewed in [10]). The uncorrelated lognormal (UCLN) model draws its rates from a lognormal distribution and appears to be more robust to violation of assumptions about clock rate variation, and a better fit to simulated and empirical datasets, than are strict or autocorrelated clock models [11,12]. Having the means to detect if and when rates shift, and to correct branch lengths could be critically important to evolutionary analysis using molecular phylogenies
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