SUPPLEMENTARY ONLINE MATERIAL
Walter Jetz, Kyle G. Ashton & Frank A. La Sorte: Phenotypic population
divergence in terrestrial vertebrates at macro scales
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Appendix S1:
Phylogenetic analysis
Methods: To quantify and address potential phylogenetic signals in the data we compiled a
composite tetrapod phylogeny for the species in the study. Using several sources, our approach
was to begin with a tree for the major groups of tetrapods and successively attach trees for less
inclusive groups within this “backbone” tree. When studies gave conflicting relationships, we
chose the topology from the study that included more species for the group in question. For tree
topology and further details see Fig. S2. Branch length information varied across sources, and we
note that without knowing the phylogenetic placement of all terrestrial vertebrate species branch
lengths are not reliable. We therefore followed common practice and for analysis set all branch
lengths in the tree to equal. We acknowledge that this is an interim solution until a full
phylogenetic tree for vertebrates becomes available. We assessed the strength of the
phylogenetic signal in each model using the parameter λ (Pagel’s lambda). Lambda measures
and controls for the degree of phylogenetic dependence in the model residuals and is estimated
using a maximum-likelihood approach (Freckleton et al. 2002; Jetz et al. 2008) and has been
demonstrated to perform well with branch lengths set to equal (Freckleton et al. 2002; Freckleton
2009). Given that this phylogeny covers less than 1% of all terrestrial vertebrates and species are
missing non-uniformly across the tree, the results of the following analysis should be interpreted
with caution.
Results: We find a significant phylogenetic signal for the intraspecific variation in body mass
across species (λ = 0.73; test versus λ = 0: p < 0.001) that is weaker than the signal found for
body mass (λ = 1.00; test versus λ = 0: p < 0.0001). This phylogenetic effect is well explained at
the level of the five major clades in the dataset (accounting for Clade membership: λ = 0.00; test
versus λ = 0: n.s., Table S2). In the main results section we therefore continued with a crossspecies framework that includes Clade as predictor. The significant effects of Clade and Mass
that we found in the cross-species model remain in the phylogenetic analysis, with Area retaining
direction but losing significance (Table S2)
References: Freckleton R.P. (2009). The seven deadly sins of comparative analysis. J Evolution
Biol, 22, 1367-1375. Freckleton R.P., Harvey P.H. & Pagel M. (2002). Phylogenetic analysis and
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comparative data: a test and review of evidence. American Naturalist, 160, 712-726. Jetz W.,
Freckleton R.P. & McKechnie A.E. (2008). Environment, migratory tendency, phylogeny and
basal metabolic rate in birds. PLoS ONE, 3, e3261.
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