[R-sig-ME] MCMCglmm: correctly estimating phylogenetic heritability

Jarrod Hadfield j.hadfield at ed.ac.uk
Wed Oct 3 13:07:32 CEST 2012

Hi Iain,

var(phylo)/(var(phylo)+var(residual)+var(random effects)) ?

is probably what you want to use. Presumably, you have multiple  
observations per species/population combination. In this case may want  
to interpret the residual variance as measurement error variance and  
exclude it from the denominator. Alternatively, you may interpret it  
as biological variation and include it. It depends on how you chose to  
interpret the residual variance and what you want the phylogentic  
heritability to refer to.  Note, that the fixed effects are also  
'removing' variance which may be phylogentic or not depending on the  
phylogenetic distribution of the predictors.



Quoting "Stott, Iain" <ims203 at exeter.ac.uk> on Fri, 28 Sep 2012  
15:31:49 +0000:

> Dear all,
> I am working with MCMCglmm models that include a phylogenetic  
> component. The aim of the study is to estimate the influence of  
> phylogeny on certain aspects of demography in plant populations.
> The models are constructed as follows:
> Univariate response
> One fixed factor (categorical, four levels)
> Two nested random grouping factors (Population nested within Species)
> Phylogenetic scaling of random effects (using a 'phylo' object and  
> the 'animal' argument)
> Default uninformative priors for fixed effects (mu=0, sigma^2=10^10)
> Uninformative priors for random effects and residuals (V=1, nu=0.001)
> Parameter expansion for random effects priors (I had some problems  
> with chains sticking at 0)
> DIC from models with phylogeny vs. without phylogeny are very  
> similar, hence there are two separate sets of rival models. The only  
> discernable effect that phylogeny has is to increase the credible  
> intervals on the fixed effect posteriors.
> Estimating a heritability factor (i.e. something akin to Pagel's  
> lambda) could clear up how important phylogeny actually is. Hadfield  
> & Nakagawa (2010) in J. Evol. Biol. state that this can be found  
> using:
> var(phylo)/(var(phylo)+var(residual)) .
> Fitted variance for phylogeny is very small compared to species,  
> population and residuals which could explain some of the strange  
> results we're getting: phylogeny may be statistically important, but  
> have a very small effect. BUT, the variance attributed to phylogeny  
> seems to be partitioned primarily into Species in non-phylogenetic  
> models (which makes sense). SO, is the above correct or should we  
> actually be using something like:
> var(phylo)/(var(phylo)+var(residual)+var(random effects)) ?
> Hope someone can shed some light,
> Iain
> - - - - - - - - - - - -
> Dr. Iain Stott
> Centre for Ecology and Conservation
> University of Exeter, Cornwall Campus
> Tremough, Treliever Road
> Penryn, Cornwall, TR10 9EZ, UK.
> Tel (office): 01326 371852
> http://biosciences.exeter.ac.uk/staff/postgradresearch/iainstott/
> - - - - - - - - - - - -
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

More information about the R-sig-mixed-models mailing list