Appendix B. Summary data on the effects of Phryganoporus candidus colonies on seed damage by heteropterans, weevils, and wasps.

Summary data on the effects of Phryganoporus candidus colonies on seed damage by heteropterans, weevils, and wasps

Phylogeny for the species in the Lynch & Conery dataset [<b>7</b>], with a reconstruction of genome sizes.

<p>(See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s4" target="_blank">Materials and Methods</a>).</p

Relationship between <i>N_eu</i> and genome size across 22 eukaryotic and 7 prokaryotic species from the dataset of Lynch & Conery [<b>7</b>].

<p>(A) Ordinary least squares regression (OLS); <i>r²</i> = 0.64, <i>P</i><0.0001. (B) Standardized phylogenetically independent contrasts (equivalent to PGLS) using branch lengths of 1.0; <i>r²</i> = 0.08, <i>P</i> = 0.138. Values have been “positivized” on the x-axis <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland4" target="_blank">[35]</a>.</p

Ignoring phylogenetic history can lead to incorrect conclusions about the nature of evolutionary associations between traits.

<p>In this hypothetical example, eight species have been measured for two traits, x and y, as indicated by pairs of values at the tips of the phylogenetic tree (A). Ordinary least-squares linear regression (OLS) indicates a statistically significant positive relationship (B; <i>r²</i> = 0.62, <i>P</i> = 0.02), potentially leading to an inference of a positive evolutionary association between x and y. However, inspection of the scatterplot (B) in relation to the phylogenetic relationships of the species (A) indicates that the association between x and y is <i>negative</i> for the four species within each of the two major lineages. Regression through the origin with phylogenetically independent contrasts (computed using <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Midford1" target="_blank">[34]</a> and setting all branches to length 1.0), which is equivalent to phylogenetic generalized least squares (PGLS) analysis, accounts for the nonindependence of species and indicates no overall evolutionary relationship between the traits (C, standardized contrasts, <i>r²</i> = 0.01, <i>P</i> = 0.82; basal contrast indicated in red). The apparent pattern across species was driven by positively correlated trait change only at the basal split of the phylogeny; throughout the rest of the phylogeny, the traits mostly changed in <i>opposite</i> directions (A; basal contrast in red). Notes: In A, the estimated nodal values for both traits are shown in parentheses. These are intermediate steps in the independent contrasts algorithm and are not to be taken as optimal estimates of the states at internal nodes; rather, they are a type of “local parsimony” estimate (except the estimate at the basal node, which is equivalent to the estimate under squared-change parsimony). Contrasts are taken between sister nodes on a phylogeny, not along each branch segment <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Felsenstein1" target="_blank">[15]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland1" target="_blank">[16]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland2" target="_blank">[18]</a>.</p

Relationships between <i>N_eu</i> and genomic attributes in nonphylogenetic (OLS) and phylogenetic (PGLS, RegOU) models.

<p>Log₁₀-transformed dependent variables were regressed on log₁₀(<i>N_eu</i>). Phylogenetic models used arbitrary branch lengths of 1.0 (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s4" target="_blank">Materials and Methods</a>). Note that <i>r²</i> values are not comparable across OLS, PGLS, and RegOU models. Asterisks indicate RegOU models with significantly better fit than OLS models, based on ln likelihood ratio tests (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s2" target="_blank">Results</a>); <i>b</i> = regression slope; significant <i>P</i>-values are in bold.</p>†<p>Lynch & Conery <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Lynch3" target="_blank">[7]</a> reported <i>r²</i> = 0.659; the discrepancy apparently arises because their analysis used 30 species, only 29 of which were reported in their online supplement.</p

Radish DATA_IND

Radish DATA_IN

Radish DATA_PLOT

Radish DATA_PLO

Univariate measures of phylogenetic signal for log₁₀-transformed traits in the dataset.

<p>K varies from 0 to 1 to >1, indicating, respectively, no phylogenetic signal, that relatives resemble each other as much as expected under Brownian motion–like evolution, and that relatives are more similar to each other than expected under Brownian motion <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002092#pgen.1002092-Blomberg1" target="_blank">[7]</a>. <i>P</i>-values indicate significant phylogenetic signal based on randomization tests of the mean squared error. Results are from the Picante package in R <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002092#pgen.1002092-Kembel1" target="_blank">[34]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002092#pgen.1002092-R1" target="_blank">[35]</a> utilizing the phylogeny presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002092#pgen.1002092-Whitney1" target="_blank">[1]</a> with all = 1 branch lengths.</p

Linkage Map

This Excel file contains the estimated linkage map for the H. a. annuus x H. debilis backcross1 mapping populations. The position of each marker on the linkage group is given in centiMorgans (cM)

Phenotype and SNP Genotype Data

This Excel file contains information on 906 field-grown backcross1 sunflower plants. Field site is identified in column Z. Plants are identified by the number in column AA. Columns A-Y contain field-measured trait data. Trait names correspond to the abbreviations in Table 1 of the associated manuscript. Columns AH - HO contain SNP genotype data; A = H. a. annuus allele; D = H. debilis allele