TY - JOUR
T1 - Phylogenetic analysis using Lévy processes
T2 - Finding jumps in the evolution of continuous traits
AU - Landis, Michael J.
AU - Schraiber, Joshua G.
AU - Liang, Mason
N1 - Funding Information:
FUNDING M.J.L. was supported by the National Institutes of Health (NIH; RO1-GM069801) and the University of California, Los Angeles (R01 GM086887), J.G.S. was supported by a NIH Human Resources and Services Administration trainee appointment (NIHRSA; T32-HG00047) and by the NIH (R01-GM40282), and M.L. was supported by a NIHRSA trainee appointment (T32-HG00047) and by Rasmus Nielsen.
PY - 2013/3
Y1 - 2013/3
N2 - 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. Continuous traits; saltational evolution; Lévy processes; Bayesian inference.
AB - 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. Continuous traits; saltational evolution; Lévy processes; Bayesian inference.
UR - http://www.scopus.com/inward/record.url?scp=84873604684&partnerID=8YFLogxK
U2 - 10.1093/sysbio/sys086
DO - 10.1093/sysbio/sys086
M3 - Article
C2 - 23034385
AN - SCOPUS:84873604684
SN - 1063-5157
VL - 62
SP - 193
EP - 204
JO - Systematic Biology
JF - Systematic Biology
IS - 2
ER -