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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
Miguel Navascués1, Brent C Emerson
1Equipe Eco-évolution Mathématique, CNRS UMR 7625 Ecologie et Evolution, Université Pierre et Marie Curie & Ecole Normale Supérieure, Paris, France.
Molecular Ecology
|September 9, 2009
Summary
Bayesian inference using ancient and modern DNA can estimate evolutionary rates. However, complex population histories can bias substitution rate estimates, though mild misspecification still allows for accurate rate coverage.
Area of Science:
- Evolutionary Biology
- Genetics
- Bioinformatics
Background:
- Advancements in ancient DNA (aDNA) and modern DNA (mDNA) sequencing enable analysis of extinct species, evolutionary origins, and phylogeography.
- Coalescence-based Bayesian inference offers a novel approach to estimate molecular substitution rates and divergence dates using temporal DNA data, bypassing traditional fossil or geological calibrations.
Purpose of the Study:
- To critically assess the accuracy of Bayesian Markov chain Monte Carlo (MCMC) analysis for estimating molecular substitution rates using simulated ancient and modern DNA datasets.
- To investigate the impact of demographic complexities, such as population bottlenecks and structure, on the reliability of Bayesian inference for molecular rate estimation.
Main Methods:
- Utilized simulated ancient DNA (aDNA) and modern DNA (mDNA) samples to test Bayesian MCMC methods.
- Focused on heterochronous (time-separated) mtDNA data to evaluate substitution rate estimation.
- Assessed the influence of model misspecification arising from complex population histories.
Main Results:
- Current Bayesian MCMC models and priors show an upward bias in substitution rate estimation when applied to populations with non-simple demographic histories (e.g., bottlenecks, structure).
- This bias is attributed to model misspecification inherent in analyzing complex population dynamics.
- In cases of mild model misspecification, the 95% highest posterior density intervals demonstrated adequate frequentist coverage of true evolutionary rates.
Conclusions:
- Bayesian MCMC analysis of heterochronous DNA is susceptible to biased substitution rate estimates due to model misspecification in populations with complex demographic histories.
- Researchers must carefully consider potential demographic complexities when applying these methods to avoid upward bias in rate estimations.
- Despite limitations, Bayesian methods can provide reliable rate estimates when model misspecification is minimal.
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