Assessing Phylogenetic Signal
Because of shared evolutionary history, closely related host species may
have similar effect sizes. We use Pagel’s lambda
(Pagel 1999) to
estimate phylogenetic signal in the distribution of effect sizes across
taxa. We obtained a phylogeny of relevant prey/host species from the
Open Tree of Life using the ROTL package
(Hinchliff et
al. 2015; Michonneau et al. 2016); then we used the apepackage to prune the tree to our host species, to resolve polytomies,
and to generate branch lengths
(Paradis & Schliep
2018). For host species with multiple effect sizes, we calculated the
average effect size for each species weighted by the sample size of each
component study. We then used the pgls function of thecaper package to estimate Pagel’s lambda by maximum likelihood
for each of our datasets
(Orme et al.2018). We statistically tested the difference between this estimate and
two alternative hypotheses: phylogenetic independence (lambda = 0) and
phylogenetic dependence as characterized by Brownian motion (lambda =
1). We failed to detect evidence of phylogenetic dependence in any
dataset using this method.
RESULTS