[R-meta] phylogenetic information in both moderator and random part of rma.mv?

Sigurd Einum @|gurd@e|num @end|ng |rom ntnu@no
Wed Sep 28 21:03:43 CEST 2022

Dear list,
I want to test for evolutionary divergence (among ectothermic animals) in a single trait Y. My first approach to this was to test for divergence among taxonomic classes (specifically amphibians, reptiles, insects, fish, and crustaceans). I compiled data on several species per class, and multiple estimates of Y per species (from different experiments), and analysed the data using a traditional mixed effects model (lme), with species as a random effect and taxonomic class as fixed effect.

However, one reviewer suggested I should control for phylogeny (without being more specific). So I built a tree for these species (using package rotl), made it ultrametric (using compute.brlen in package ape), and computed the variance-covariance matrix A from this (using vcv from package ape). I then created a variable phylo to distinguish the phylogenetic component from the non-phlylogenetic species random effect, and used metafor to fit the model:

rma.mv(Y, sampvar,mods = ~ Class, random = list(~ 1 | species, ~ 1 | phylo),
               R = list(phylo = A), data = Final.data, sparse = TRUE, method = "ML")

(sampvar is the sampling variance associated with each estimate of Y)

However, now I have started doubting whether this model makes sense, i.e. to estimate an effect of taxonomic class (which in essence is a phylogenetic effect) while simultaneously modelling a random effect of phylogeny. Would an appropriate alternative be to not have class as a moderator, but rather compare fits of models with and without the phylogenetic variance-covariance matrix. If the model including phylogeny is better than one without it, can I conclude that there is evolutionary divergence in this trait?

Any advice anyone might have on this would be much appreciated!

Best wishes
Sigurd Einum

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