A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression

Richard Adams; Jenniffer Roa Lozano; Mataya Duncan; Jack Green; Raquel Assis; Michael DeGiorgio

doi:10.1093/molbev/msaf032

journal article Open Access Feb 11, 2025

A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression

Richard Adams

Jenniffer Roa Lozano Mataya Duncan Jack Green Raquel Assis

Michael DeGiorgio

Molecular Biology and Evolution Vol. 42 No. 3 · Oxford University Press (OUP)

View at Publisher Save 10.1093/molbev/msaf032

Abstract

Abstract
Just exactly which tree(s) should we assume when testing evolutionary hypotheses? This question has plagued comparative biologists for decades. Though all phylogenetic comparative methods require input trees, we seldom know with certainty whether even a perfectly estimated tree (if this is possible in practice) is appropriate for our studied traits. Yet, we also know that phylogenetic conflict is ubiquitous in modern comparative biology, and we are still learning about its dangers when testing evolutionary hypotheses. Here, we investigate the consequences of tree-trait mismatch for phylogenetic regression in the presence of gene tree–species tree conflict. Our simulation experiments reveal excessively high false positive rates for mismatched models with both small and large trees, simple and complex traits, and known and estimated phylogenies. In some cases, we find evidence of a directionality of error: assuming a species tree for traits that evolved according to a gene tree sometimes fares worse than the opposite. We also explored the impacts of tree choice using an expansive, cross-species gene expression dataset as an arguably “best-case” scenario in which one may have a better chance of matching tree with trait. Offering a potential path forward, we found promise in the application of a robust estimator as a potential, albeit imperfect, solution to some issues raised by tree mismatch. Collectively, our results emphasize the importance of careful study design for comparative methods, highlighting the need to fully appreciate the role of accurate and thoughtful phylogenetic modeling.

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Citations

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References

Details

Published: Feb 11, 2025
Vol/Issue: 42(3)
License: View

Authors

R

Richard Adams

Department of Entomology and Plant Pathology, University of Arkansas , Fayetteville, AR, USA; Center for Agricultural Data Analytics, University of Arkansas , Fayetteville, AR, USA

J

Jenniffer Roa Lozano

Department of Entomology and Plant Pathology, University of Arkansas , Fayetteville, AR, USA; Center for Agricultural Data Analytics, University of Arkansas , Fayetteville, AR, USA

M

Mataya Duncan

Department of Entomology and Plant Pathology, University of Arkansas , Fayetteville, AR, USA; Center for Agricultural Data Analytics, University of Arkansas , Fayetteville, AR, USA

J

Jack Green

Department of Entomology and Plant Pathology, University of Arkansas , Fayetteville, AR, USA; Center for Agricultural Data Analytics, University of Arkansas , Fayetteville, AR, USA

R

Raquel Assis

Department of Electrical Engineering and Computer Science, Florida Atlantic University , Boca Raton, FL, USA; Institute for Human Health and Disease Intervention, Florida Atlantic University , Boca Raton, FL, USA

M

Michael DeGiorgio

Department of Electrical Engineering and Computer Science, Florida Atlantic University , Boca Raton, FL, USA

Funding

National Science Foundation

Arkansas Economic Development Commission

Cite This Article

Richard Adams, Jenniffer Roa Lozano, Mataya Duncan, et al. (2025). A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression. Molecular Biology and Evolution, 42(3). https://doi.org/10.1093/molbev/msaf032

A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression

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