Supporting Information Notes S1 and Fig. S1
Notes S1 Methods for phylogenetic independent contrasts
Comparisons across species risk pseudoreplication if phylogeny is ignored (Felsenstein, 1985),
so we obtained phylogenetically independent contrasts for habitat type and our three measures of
endophyte frequency. For each analysis, we assembled trees for host plants in Mesquite version
2.71 (Maddison & Maddison, 2009) using phylogenetic data from published trees constructed
using molecular data sets (Vergara & Bughrara, 2003; Catalan et al. 2004; Torrecilla et al., 2004;
Blattner, 2004; Strauss et al., 2006). Because branch length information was not available, we
chose the best branch length estimator for each variable following published recommendations
(PDAP PDTREE; Midford et al., 2005). To examine the relationship between endophyte status
and habitat type, we performed phylogenetic logistic regression (PlogReg.m; Ives & Garland,
2010) using MATLAB (version 5.0 MathWorks, 1996). PlogReg.m requires a phylogenetic
variance-covariance matrix and a tip (variables) data file which were generated using the
programs PDIST (Garland et al., 1993) and PDTREE (Midford et al., 2005), respectively. We
report means and bootstrapped 95% confidence intervals for the regression coefficient and the
parameter α (a measure of the strength of the phylogenetic signal). To examine relationships
between habitat type and our two measures of endophyte frequency, we performed regression
through the origin (SAS Institute 2004) using the phylogenetically independent trait values (i.e.,
standardized contrast values), and we report adjusted correlation coefficients (Garland et al.,
1992). For a phylogenetic tree with some polytomous nodes, the degress of freedom range from
a minimum of the number of nodes minus one to a maximum of the number of species minus
two (Midford et al., 2005). Because it remains unclear whether polytomies in our trees are hard
or soft, we present the full range of P- values for the correlations.
Fig. S1 Phylogenetic trees used for examining relationships between endophyte frequency and
habitat type.
(a) Phylogenetic tree used for examining the relationship between mean endophyte frequency per
population and habitat type (shaded or not). For the calculation of independent contrasts, the
best branch length estimator for the mean frequency per population was Nee’s arbitrary branch
length, in which the depths of the nodes equal the log of the number of extant (tip) species
descendent in the tree (Midford et al., 2005) For habitat type the best branch length estimator
was all branch lengths = 1.
(b) Phylogenetic tree used for examining the relationship between percentage of populations
with the endophyte and habitat type (shaded or not). For the calculation of independent
contrasts, the best branch length estimator for the percentage of populations was Nee’s arbitrary
branch length. For habitat type the best branch length estimator was all branch lengths = 1.
(c) Tree used for examining the relationship between the endophyte status of potential grass
hosts and habitat type (shaded or not). The best branch length estimator for both variables was
Nee’s arbitrary branch length (Midford et al., 2005).
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