The Implications of Lineage-Specific Rates for Divergence Time Estimation

Area of Science:

• Molecular Phylogenetics
• Evolutionary Biology
• Genomics

Background:

• Estimating divergence times in molecular phylogenetics is complicated by rate variation among lineages.
• Understanding different types of rate variation, including lineage-specific, residual, and gene-specific rates, is crucial for accurate phylogenetic inference.

Purpose of the Study:

• To evaluate the impact of lineage-specific rates on the accuracy of divergence time estimation.
• To compare the effects of lineage-specific rates with residual and gene-specific rates.
• To assess the influence of genomic-scale multilocus data and Bayesian inference frameworks on these rate variations.

Main Methods:

• Simulations were used to model different types of rate variation (lineage-specific, residual, gene-specific).
• The impact of these rate variations on divergence time estimates was analyzed, particularly within a Bayesian inference framework.
• The scale of simulated lineage-specific rates was compared to empirical data from the angiosperm genus Ipomoea.

Main Results:

• Lineage-specific rates consistently lead to erroneous divergence time estimates, irrespective of the number of loci sampled.
• Stronger lineage-specific rates result in greater estimation errors.
• In Bayesian analyses, lineage-specific rates reduce the accuracy of highest posterior density intervals and increase sensitivity to prior specifications.
• Increased data (genomic scale multilocus data) and complex rate priors do not overcome the errors caused by lineage-specific rates.

Conclusions:

• Lineage-specific rates are a significant source of error in molecular divergence time estimation.
• This error cannot be resolved by analyzing large, multilocus genomic datasets.
• Accurate divergence time estimation requires careful consideration and modeling of lineage-specific rate variation.