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Principled, practical, flexible, fast: A new approach to phylogenetic factor analysis

Gabriel W. Hassler Orcid Logo, Brigida Gallone, Leandro Aristide, William Allen Orcid Logo, Max R. Tolkoff, Andrew J. Holbrook, Guy Baele, Philippe Lemey, Marc A. Suchard

Methods in Ecology and Evolution, Volume: 13, Issue: 10, Pages: 2181 - 2197

Swansea University Author: William Allen Orcid Logo

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DOI (Published version): 10.1111/2041-210x.13920

Abstract

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic comparative methods seek to disentangle these relationships across the evolutionary history of a group of organisms. Unfortuna...

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Published in: Methods in Ecology and Evolution
ISSN: 2041-210X 2041-210X
Published: Wiley 2022
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URI: https://cronfa.swan.ac.uk/Record/cronfa60450
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Abstract: Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic comparative methods seek to disentangle these relationships across the evolutionary history of a group of organisms. Unfortunately, most existing methods fail to accommodate high-dimensional data with dozens or even thousands of observations per taxon. Phylogenetic factor analysis offers a solution to the challenge of dimensionality. However, scientists seeking to employ this modeling framework confront numerous modeling and implementation decisions, the details of which pose computational and replicability challenges.We develop new inference techniques that increase both the computational efficiency and modeling flexibility of phylogenetic factor analysis. To facilitate adoption of these new methods, we present a practical analysis plan that guides researchers through the web of complex modeling decisions. We codify this analysis plan in an automated pipeline that distills the potentially overwhelming array of decisions into a small handful of (typically binary) choices.We demonstrate the utility of these methods and analysis plan in four real-world problems of varying scales. Specifically, we study floral phenotype and pollination in columbines, domestication in industrial yeast, life history in mammals, and brain morphology in New World monkeys.General and impactful community employment of these methods requires a data scientific analysis plan that balances flexibility, speed and ease of use, while minimizing model and algorithm tuning. Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning. These efforts coalesce to create an accessible Bayesian approach to high-dimensional phylogenetic comparative methods on large trees.
Keywords: Bayesian inference, BEAST, latent factor model, Geodesic Hamiltonian MonteCarlo, phylogenetic comparative methods, Stiefel manifold
College: Faculty of Science and Engineering
Funders: Research Foundation - Flanders. Grant Numbers: G098321N, G0E1420N, G051322N; H2020 European Research Council. Grant Number: 725422-ReservoirDOCS; Internal Funds KU Leuven. Grant Number: C14/18/094; National Human Genome Research Institute. Grant Number: T32HG002536; National Institute of Allergy and Infectious Diseases. Grant Numbers: F31AI154824, K25AI153816, R01AI153044; National Science Foundation. Grant Number: DMS 2152774; Wellcome Trust. Grant Number: 206298/Z/17/Z; MCIN/AEI/10.13039/501100011033. Grant Number: FJC2019-042184-I
Issue: 10
Start Page: 2181
End Page: 2197

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