A mixed relaxed clock model | JoVE Visualize

Area of Science:

Evolutionary biology
Phylogenetics
Computational biology

Background:

Bayesian phylogenetic dating commonly uses relaxed clock models to account for rate variation across evolutionary lineages.
Existing models are categorized as uncorrelated (white noise) or autocorrelated (Brownian motion) across branches, with the choice between them being a persistent challenge.
Neither uncorrelated nor autocorrelated models fully capture the complex patterns of rate variation, which may involve both long-term trends and short-term fluctuations.

Purpose of the Study:

To introduce and evaluate a novel mixed relaxed clock model for Bayesian phylogenetic dating.
To provide a statistically robust alternative to choosing between uncorrelated and autocorrelated clock models by integrating their strengths.
To assess the impact of different relaxed clock models on divergence time estimation, particularly using tip-dating.

Main Methods:

A mixed relaxed clock model was developed, mechanistically representing rate variation as short-term fluctuations superimposed on long-term Brownian trends.
The model was fitted to a dataset of 105 placental mammals using both node-dating and tip-dating approaches.
Statistical comparisons were made against traditional uncorrelated (white noise) and autocorrelated (Brownian motion) relaxed clock models.

Main Results:

The mixed relaxed clock model was favored over pure uncorrelated or autocorrelated models, with roughly equal contributions from both components.
Tip-dating analyses were highly sensitive to the choice of clock model, with the classical Brownian clock showing rigidity and potential biases.
The mixed clock model yielded more recent and biologically plausible crown age estimates for placental mammal orders and superorders.

Conclusions:

The proposed mixed relaxed clock model offers a more empirically adequate approach to modeling rate variation in phylogenetic trees.
This model provides a valuable alternative for resolving the dichotomy between uncorrelated and autocorrelated relaxed clocks.
The findings highlight the importance of selecting appropriate relaxed clock models for accurate divergence time estimation, especially with tip-dating methods.