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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits.

Michael J Landis¹, Joshua G Schraiber, Mason Liang

¹Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.

Systematic Biology

|October 5, 2012

Summary

We introduce a new method for modeling continuous trait evolution using Lévy processes, which allows for non-normal distributions. This approach improves upon Brownian motion models in phylogenetic analysis, especially for primate traits.

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Area of Science:

Evolutionary biology
Phylogenetics
Statistical modeling

Background:

Gaussian processes, like Brownian motion, are standard for continuous trait evolution in phylogenetics.
These models assume multivariate Gaussian distributions, which may not fit evolutionary scenarios like punctuated equilibrium or adaptive radiation.
Non-normally distributed trait evolution requires alternative modeling approaches.

Purpose of the Study:

To introduce a computational method for modeling continuous trait evolution using Lévy processes.
To assess the distinct patterns generated by Brownian motion versus Lévy processes with jumps.
To analyze primate body mass and endocranial volume using these models.

Main Methods:

Developed a method to compute posterior probabilities for trait evolution modeled as a Lévy process.
Utilized data simulations and model testing to compare Brownian motion and Lévy processes.
Applied the Lévy process model to empirical data of primate body mass and endocranial volume.

Main Results:

Single-rate Brownian motion and Lévy processes with jumps produce distinguishable patterns in comparative data.
Analysis of primate traits (body mass, endocranial volume) rejected single-rate Brownian motion in favor of a Lévy process with jumps.
Strong evidence against single-rate Brownian motion was found in the lineage leading to the great apes' most recent common ancestor.

Conclusions:

Lévy processes offer a more flexible framework for modeling continuous trait evolution than standard Brownian motion.
The proposed method and findings highlight the importance of considering non-normal evolutionary models.
Empirical data from primates support the utility of Lévy processes with jumps in phylogenetic analyses.