<p>Experimental quantification of the Dl gradient (solid line) and model simulations (dotted lines). Shadowed area indicates mean±SD A–D) <i>D. melanogaster</i> (A, adjusted parameters shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003807#pcbi-1003807-t001" target="_blank">Table 1</a>); and species gradient simulations according to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003807#pcbi-1003807-t002" target="_blank">Table 2</a> (B, <i>busckii;</i> C, <i>simulans</i>; D, <i>sechellia</i>). Experimental data was obtained from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003807#pcbi.1003807-Chahda1" target="_blank">[8]</a>. <b>V</b> indicates v...
FIGURE S6. The effects of selection on species tree estimates for the deep species tree simulations....
Individual points are for each replicate (change in viral load between day 0 and day 2 post infectio...
<p>A–C) Increasing nuclear size and decreasing nuclei density from haploids (<i>ssm,</i> B) to diplo...
<p>Bold numbers indicate modified values in relation to <i>D. melanogaster</i>. Abbreviations: <b>bu...
<p>A–D) Contours represent a drop of 0.01 in fit (square root of the sum of square differences betwe...
<p>Bold numbers indicate modified values in relation to <i>D. melanogaster</i>. Simulations 3 and 4 ...
(a) Phylogenetic definition of the strata used in the analyses for A. thaliana (top) and D. melanoga...
<p>Revised parameter values discussed in the text are indicated in bold. For abbreviations of model ...
<p>Site-specific codon Model 8 (M8) in PAML was used to identify codons under selection. This model,...
<p>Those cases for which both models agree are shown in white. Families with at least one fixed inse...
<p>A) The embryo is modeled as a single string of <i>n</i> cuboid cellular compartments. B) Chemical...
<p>We used BLASTZ alignments as well as our own MAUVE alignments to infer the evolution of six <i>D....
<p>(A) Layout of the seven C2H2-ZF domains in <i>D. melanogaster</i> protein FBpp0072605. All domain...
FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulati...
FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulati...
FIGURE S6. The effects of selection on species tree estimates for the deep species tree simulations....
Individual points are for each replicate (change in viral load between day 0 and day 2 post infectio...
<p>A–C) Increasing nuclear size and decreasing nuclei density from haploids (<i>ssm,</i> B) to diplo...
<p>Bold numbers indicate modified values in relation to <i>D. melanogaster</i>. Abbreviations: <b>bu...
<p>A–D) Contours represent a drop of 0.01 in fit (square root of the sum of square differences betwe...
<p>Bold numbers indicate modified values in relation to <i>D. melanogaster</i>. Simulations 3 and 4 ...
(a) Phylogenetic definition of the strata used in the analyses for A. thaliana (top) and D. melanoga...
<p>Revised parameter values discussed in the text are indicated in bold. For abbreviations of model ...
<p>Site-specific codon Model 8 (M8) in PAML was used to identify codons under selection. This model,...
<p>Those cases for which both models agree are shown in white. Families with at least one fixed inse...
<p>A) The embryo is modeled as a single string of <i>n</i> cuboid cellular compartments. B) Chemical...
<p>We used BLASTZ alignments as well as our own MAUVE alignments to infer the evolution of six <i>D....
<p>(A) Layout of the seven C2H2-ZF domains in <i>D. melanogaster</i> protein FBpp0072605. All domain...
FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulati...
FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulati...
FIGURE S6. The effects of selection on species tree estimates for the deep species tree simulations....
Individual points are for each replicate (change in viral load between day 0 and day 2 post infectio...
<p>A–C) Increasing nuclear size and decreasing nuclei density from haploids (<i>ssm,</i> B) to diplo...