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Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate
Daniel G Mulcahy1, Brice P Noonan, Travis Moss
1Department of Biology, Brigham Young University, Provo, UT 84602, USA. MulcahyD@si.edu
Molecular Phylogenetics and Evolution
|September 18, 2012
Summary
Comparing phylogenetic dating methods, Bayesian estimation (BEAST) showed more consistent clade age estimates with fewer nuclear loci than penalized likelihood (r8s-PL). Mitochondrial DNA (ND2) data with r8s-PL produced significantly older estimates than nuclear loci.
Area of Science:
- Phylogenetics and evolutionary biology
- Molecular evolution and phylogenomics
- Computational biology and bioinformatics
Background:
- Phylogenetics routinely estimates clade ages alongside relationships.
- Various molecular dating methods exist, but their comparative performance is not well-understood.
- Squamate reptiles (lizards and snakes) provide a model system for evaluating these methods.
Purpose of the Study:
- To evaluate the performance of two widely used phylogenetic dating methods: penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates (BEAST).
- To assess the impact of data set size (number of nuclear loci) and data type (nuclear vs. mitochondrial DNA) on divergence time estimates.
- To compare the accuracy and consistency of r8s-PL and BEAST using a comprehensive phylogenomic dataset for squamate reptiles.
Main Methods:
- Assembled an extensive phylogenomic dataset from 25 nuclear loci (19,020 bp total) for 64 squamate species and nine outgroups.
- Estimated phylogeny and divergence dates using 14 fossil calibrations.
- Evaluated r8s-PL and BEAST performance using random subsets of nuclear loci (2-20 loci) and mitochondrial ND2 gene sequences.
Main Results:
- r8s-PL estimates using limited loci (2-10) differed considerably from 25-locus estimates (mean absolute difference: 9.0 Myr).
- BEAST estimates were more consistent with fewer loci (mean absolute difference: 5.0 Myr).
- ND2 data with r8s-PL yielded ages substantially older (mean: 73.1 Myr) than 25 nuclear loci with r8s-PL.
Conclusions:
- Divergence dates from r8s-PL with limited nuclear or mitochondrial data can deviate significantly from those using extensive nuclear loci.
- BEAST estimates showed greater consistency with reduced nuclear loci or mitochondrial data, but substantial deviations (>50 Myr) are still possible.
- Increasing nuclear loci improved accuracy but did not significantly alter confidence intervals in BEAST estimates, highlighting the importance of data quantity.
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