ANCOVA results for genome size range compared to λ p-values across taxa numbers.

<p>ANCOVA results for genome size range compared to λ p-values across taxa numbers.</p

Comparative phylogenetic output for <i>Sophophora</i> phylogeny.

<p>Comparative phylogenetic output for <i>Sophophora</i> phylogeny.</p

Boxplots for each phylogenetic analysis.

<p>Raw values from comparative phylogenetic tests are plotted for each group of taxa. There is no clear pattern with increasing taxa number for Pagel’s parameters of evolution or Blomberg’s K; however, there is an increase in values for both Moran’s I and Abouheif’s C_mean. These differences are tested statistically in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173505#pone.0173505.s002" target="_blank">S2 Table</a>.</p

Genome size estimates for 87 species of Drosophilidae.

<p>Genome size estimates for 87 species of Drosophilidae.</p

Bayesian phylogeny of <i>Sophophora</i>.

<p>Phylogeny of 87 Drosophilidae reconstructed using MrBayes 3.2.3 with a focus on <i>Sophophora</i>. Nodes with posterior probabilities lower than 80 are indicated with ‘*’. Genome size is visualized in color: smaller sizes in red, larger in blue, and intermediate in green.</p

The mode and tempo of genome size evolution in the subgenus <i>Sophophora</i>

<div><p>Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 <i>Sophophora</i> species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s C_mean and Moran’s I. In addition to testing the mode and rate of genome size evolution in <i>Sophophora</i> species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. <i>Sophophora</i> genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that <i>Sophophora</i> genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s C_mean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.</p></div

Boxplots of significance values for λ and Blomberg’s K analyses.

<p>Plotted significance values from phylogenetic signal tests of λ and Blomberg’s K decrease as the number of taxa in the analyses increase, most notably above 15 taxa. These are tested for significance in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173505#pone.0173505.s003" target="_blank">S3 Table</a>.</p

Phylogenetic generalized least squares results for genome size and climatic variables.

<p>Phylogenetic generalized least squares results for genome size and climatic variables.</p

Least square estimates of mean ploidy levels post-emergence (intercept), and change of ploidy over time (slope) for five different worker honey bee (<i>Apis mellifera</i>) tissues: Brain, thoracic (flight) muscle, leg muscle, Malpighian tubules, and stinger.

<p>Adult honey bee workers were collected at different days post emergence (See <i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122208#sec002" target="_blank">Methods</a></i>for details).</p

Least squares estimates of endopolyploid levels in newly emerged honey bee workers (i.e., "Intercept") and rate of change of endopolyploidy per day (i.e., "Slope") for the five tissues studied.

<p>* <i>P</i> < 0.05</p><p>*** <i>P</i> < 0.001</p><p>Least squares estimates of endopolyploid levels in newly emerged honey bee workers (i.e., "Intercept") and rate of change of endopolyploidy per day (i.e., "Slope") for the five tissues studied.</p