Work

Phylogenetic Analysis Using Lévy Processes: Finding Jumps in the Evolution of Continuous Traits

Year: 2012

Type: article

Abstract: Gaussian processes, a class of stochastic processes including Brownian motion and the Ornstein-Uhlenbeck process, are widely used to model continuous trait evolution in statistical phylogenetics. Under such processes, observations at the tips of a phylogenetic tree have a multivariate Gaussian distribution, which may lead to suboptimal model specification under certain evolutionary conditions, as supposed in models of punctuated equilibrium or adaptive radiation. To consider non-normally distributed continuous trait evolution, we introduce a method to compute posterior probabilities when modeling continuous trait evolution as a Lévy process. Through data simulation and model testing, we establish that single-rate Brownian motion (BM) and Lévy processes with jumps generate distinct patterns in comparative data. We then analyzed body mass and endocranial volume measurements for 126 primates. We rejected single-rate BM in favor of a Lévy process with jumps for each trait, with the lineage leading to most recent common ancestor of great apes showing particularly strong evidence against single-rate BM.

Source: Systematic Biology

DOI: 10.1093/sysbio/sys086

Authors: Michael J. Landis, Joshua G. Schraiber, Mason Liang

Institution: University of California, Berkeley

Language: English

Topic: Evolution and Paleontology Studies

Subfield: Paleontology

Field: Earth and Planetary Sciences

Domain: Physical Sciences

Open Access status: green

Funders: National Institutes of Health, National Human Genome Research Institute, National Institute of General Medical Sciences

Awards: G173923842, Analysis of Admixture and Range Expansion in Humans and Extinct Hominims, Bayesian Joint Estimation of Alignment and Phylogeny, Extending Bayesian Phylogenetic Analysis, Berkeley Training Program in Genomics and Computational Biology