Efficient Bayesian inference of general Gaussian models on large phylogenetic trees

DOI10.1214/20-AOAS1419zbMATH Open1477.62308arXiv2003.10336OpenAlexW3181640967MaRDI QIDQ2245176FDOQ2245176

Authors: Paul Bastide, Lam Si Tung Ho, Guy Baele, Philippe Lemey, Marc A. Suchard 

Publication date: 15 November 2021

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To incorporate such uncertainty, we present a scalable Bayesian inference framework under a general Gaussian trait evolution model that exploits Hamiltonian Monte Carlo (HMC). HMC enables efficient sampling of the constrained model parameters and takes advantage of the tree structure for fast likelihood and gradient computations, yielding algorithmic complexity linear in the number of observations. This approach encompasses a wide family of stochastic processes, including the general Ornstein-Uhlenbeck (OU) process, with possible missing data and measurement errors. We implement inference tools for a biologically relevant subset of all these models into the BEAST phylogenetic software package and develop model comparison through marginal likelihood estimation. We apply our approach to study the morphological evolution in the superfamilly of Musteloidea (including weasels and allies) as well as the heritability of HIV virulence. This second problem furnishes a new measure of evolutionary heritability that demonstrates its utility through a targeted simulation study.

Full work available at URL: https://arxiv.org/abs/2003.10336

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zbMATH Keywords

heritabilitymodel selectionBayesian inferenceHamiltonian Monte CarloOrnstein-Uhlenbeck processHIVstatistical phylogeneticsphylodynamicsBEASTMusteloideatotal evidence

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Probabilistic graphical models (62H22) Problems related to evolution (92D15)

Cites Work

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Cited In (10)

• Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach
• Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees
• Phylogenetic Gaussian processes for bat echolocation
• Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference
• Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO
• Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
• Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements
• When can we reconstruct the ancestral state? Beyond Brownian motion
• Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts
• A phylogenetic Gaussian process model for the evolution of curves embedded in \(d\)-dimensions

Uses Software

• R
• BEAST
• mvMORPH
• Tracer
• diversitree
• Rphylopars
• logKDE
• ggtree
• NUTS
• treeio

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