On the analysis of phylogenetically paired designs

Ecology and Evolution
Jennifer L FunkJ Michael Macpherson

Abstract

As phylogenetically controlled experimental designs become increasingly common in ecology, the need arises for a standardized statistical treatment of these datasets. Phylogenetically paired designs circumvent the need for resolved phylogenies and have been used to compare species groups, particularly in the areas of invasion biology and adaptation. Despite the widespread use of this approach, the statistical analysis of paired designs has not been critically evaluated. We propose a mixed model approach that includes random effects for pair and species. These random effects introduce a "two-layer" compound symmetry variance structure that captures both the correlations between observations on related species within a pair as well as the correlations between the repeated measurements within species. We conducted a simulation study to assess the effect of model misspecification on Type I and II error rates. We also provide an illustrative example with data containing taxonomically similar species and several outcome variables of interest. We found that a mixed model with species and pair as random effects performed better in these phylogenetically explicit simulations than two commonly used reference models (no or single random e...Continue Reading

References

Dec 10, 1997·Proceedings of the National Academy of Sciences of the United States of America·P B ReichD S Ellsworth
Feb 8, 2000·Journal of Theoretical Biology·W P Maddison
Dec 7, 2000·Evolution; International Journal of Organic Evolution·D D Ackerly
Aug 6, 2005·The Journal of Experimental Biology·Theodore GarlandEnrico L Rezende
Aug 18, 2006·Ecology Letters·Christina L RichardsMassimo Pigliucci
Aug 30, 2006·Ecological Applications : a Publication of the Ecological Society of America·Jean H Burns
Apr 27, 2007·Nature·Jennifer L Funk, Peter M Vitousek
May 26, 2012·Ecology·T Jonathan DaviesElizabeth M Wolkovich

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Citations

May 7, 2019·Frontiers in Plant Science·Reina L NielsenRebecca E Drenovsky
Apr 21, 2019·The New Phytologist·Justin M VallierePhilip W Rundel
Jul 9, 2020·The Science of the Total Environment·Zheng-Sheng He, Wei-Ming He

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Software Mentioned

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