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.
primates.eastman.isler_pruned.tree.txt
126 tip tree resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Branches are measured in units of Ma.
primates.eastman.isler_pruned.ecv.data
126 row data matrix of endocranial volume (ECV) measurements resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.
primates.eastman.isler_pruned.mass.data
126 row data matrix of body mass measurements resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.
primates.eastman.isler_pruned.massecvratio.data
126 row data matrix of ratios of body mass to endocranial volume (ECV) ratios resulting from intersecting the Redding et al. (2010) primate phylogeny in auteur with the primate data reported Isler et al. (2008). Data has been log-transformed.
Levy_processes_supplementary_materials
Supplementary materials contains tables of results from simulation study and empirical inference upon primate data. See manuscript for table references. In addition, the supplementary materials contains the signal-to-noise ratio color-coded phylogenies with fully named tips, whereas the manuscript phylogeny only provides family names (Platyrrhini, Catarrhini, and Strepsirrhini).
suppmat.pdf
