Appendix A. Descriptions of species, data, and study systems.

Descriptions of species, data, and study systems

Appendix C. References for Appendices A and B.

References for Appendices A and B

Appendix B. Explanation of the density dependence calculations.

Explanation of the density dependence calculations

Map and location of the experimental trap.

<p>1.A. Map of the Île-de-France region and locations of the study plots and B. Experimental trap used in the study.</p

Models tested using the GLM procedure and the associated Akaike Information Criterion (AIC) obtained by backward stepwise selection procedure.

<p>Models tested using the GLM procedure and the associated Akaike Information Criterion (AIC) obtained by backward stepwise selection procedure.</p

Uncoupled responses of butterfly density and parasitism rate to urbanization.

<p>Relationship between the proportion of artificial urban landscape and A. <i>Pieris brassicae</i> density (number of individuals/m²) and B. the parasitism rate. Black squares figure the relation between parasitism rate and proportion of artificial urban landscape and full black and bold line represents linear regression these two variables (R = −0.85). Pale grey triangles figure the relation between the proportion of artificial urban landscape and <i>Pieris brassicae</i> density and dotted grey line represents linear regression these two variables (R = −0.18).</p

Appendix B. Report on the whole simulations.

Report on the whole simulations

Supplement 1. Source code and directions for computing, displaying, and testing the decomposition of trait diversity along a phylogenetic tree, with example data sets provided.

<h2>File List</h2><blockquote> <p><a href="supfileA.R">supfileA.R</a></p> <p><a href="supfileB.pdf">supfileB.pdf</a></p> </blockquote><h2>Description</h2><blockquote> <p>The file subfileA.R provides the source code for three functions in the R environment. The functions depend on the ade4 package of R. The function decdiv decomposes trait diversity across the nodes of a phylogenetic tree. It depends on the phylogenetic tree, a data frame (or alternatively a vector) containing the abundances of the species in communities, and trait distances between species. The trait distances might have been computed in R, for instance with the ade4 package where several functions are available (e.g., ‘dist.ktab’, ‘dist.binary’, ‘dist.quant’, ‘dist.prop’). The function plot.decdiv opens a graphics device and displays the phylogeny. It includes an argument that allows the display of circles at nodes whose diameter reflects the contributions of nodes to trait diversity. The function rtest.decdiv computes the “single-node skewness test”, “few-nodes skewness test” and “tips/root node skewness test” (or alternatively tips skewness test and root skewness tests separately by specifying options).</p> <p>The file subfileB.pdf contains directions for using the functions. It also provides examples with data sets contained in the package ade4 of the R environment.</p> </blockquote

Partitioning of the diversity in dispersal along the phylogeny of European butterflies: permutation tests (N = 1000 permutations).

a<p>Replicates of a dispersal measurement for a given species are treated as if they were from virtual sister-taxa descending from an artificial terminal node in enlarged trees (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011123#s4" target="_blank">methods</a>). Metrics are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011123#pone-0011123-t001" target="_blank">Table 1</a>.</p>b<p>Test S₃ from Pavoine et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011123#pone.0011123-Pavoine1" target="_blank">[13]</a>. S_c is the proportion of dispersal diversity attributed to within-species variability.</p>c<p>P: P-values corrected for multiple comparisons.</p>d<p>The diversity is significantly skewed towards nodes that were the most distant from tips in the original phylogeny (with 369 butterfly species considered).</p

Theoretical distribution for <i>S</i>_c obtained from 1000 permutations.

<p>Diamonds show the observed values of <i>S</i>_c. A: <i>dispersal fraction</i>: proportion of recaptures with inter-patch movement in multisite mark-recapture. B, C: respectively <i>Alpha1</i> and <i>alpha2</i> that describe the shape of a negative exponential dispersal kernel measured in small (<1.9 km) or large (>1.9 km) study sites. D: <i>P5km</i>, the probability of dispersal movement ≥5 km, estimated from the shape of inverse power dispersal kernels. E: <i>Daily moves</i>, the mean daily displacements in mark-release-recapture surveys. F, G, H: <i>FstL</i>, <i>FstR</i> and <i>FstC</i>, measures of the genetic structuring (<i>F</i>_ST) from allozyme surveys respectively at the landscape scale (<100 km), the regional scale (100-600 km), or the continental scale (>600 km).</p