Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

Crisp, Michael D., Hardy, Nate B. and Cook, Lyn G. (2014) Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees. BMC Evolutionary Biology, 14 1-17. doi:10.1186/s12862-014-0263-3


Author Crisp, Michael D.
Hardy, Nate B.
Cook, Lyn G.
Title Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees
Journal name BMC Evolutionary Biology   Check publisher's open access policy
ISSN 1471-2148
Publication date 2014-12-19
Year available 2014
Sub-type Article (original research)
DOI 10.1186/s12862-014-0263-3
Open Access Status DOI
Volume 14
Start page 1
End page 17
Total pages 17
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2015
Language eng
Formatted abstract
Background

Estimating 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.

Results

In 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.

Conclusions

The 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.
Keyword Divergence times
Substitution rate heterogeneity
Uncorrelated lognormal clock
Random local clocks
Relative rates
Life history
Xanthorrhoea
Nucleotide substitution rates
Molecular clock
Relaxed phylogenetics
Divergence times
Evolution
Angiosperms
Asparagales
Sequences
Patterns
Chloroplast
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Biological Sciences Publications
 
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Created: Tue, 10 Mar 2015, 20:54:49 EST by Gail Walter on behalf of School of Biological Sciences