Diversity (<i>θ</i>_<i>π</i>) as a function of distance from new mutations in <i>D. yakuba</i> for putatively neutral intronic SNPs (black) and for tandem duplications (red) by chromosome with lowess smoothing.

<p>Duplicates show a reduction in diversity approaching duplications on chromosome 3L, whereas neutral SNPs show no reduction in diversity. Plots exclude centromeric regions and the 4th chromosome which have atypical nucleotide diversity. <i>D. yakuba</i> chromosome 2 displays an atypical pattern of increased diversity and was handled separately from chromosome 3 due to segregating inversions in populations.</p

SFS for tandem duplications in <i>D. yakuba</i> and <i>D. simulans</i>, corrected for ascertainment bias.

<p>A. Site frequency spectra on the autosomes (black) and on the X (grey) in <i>D. yakuba</i>. B. SFS on the autosomes (black) and on the X (grey) in <i>D. simulans</i>. C. SFS for X-linked intronic SNPs (black) and duplicates (white) in <i>D. simulans</i>. The excess of high frequency variants on the X in <i>D. simulans</i> suggests widespread selection for tandem duplicates on the <i>D. simulans</i> X.</p

Genomewide population mutation rates for all duplications (<i>θ</i>), population sizes (<i>N</i>_<i>e</i>), and per gene mutation rates (<i>μ</i>) for gene structures produced by whole gene duplication, recruitment of non-coding sequence, and chimeric genes by species.

<p>Low mutation rates and mutation limited evolution leads to low levels of parallel recruitment of tandem duplications.</p

Observed and predicted scaled diversity levels around amino acid substitutions.

<p>(<b>A</b>) Comparison of scaled diversity levels around non-synonymous (NS) and synonymous (SYN) substitutions. (<b>B</b>) Comparison of predicted, scaled diversity levels based on our method and that of Sattath et al. (2011) [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006130#pgen.1006130.ref048" target="_blank">48</a>].</p

The contribution of background selection and classic sweeps to scaled diversity levels around non-synonymous and synonymous substitutions.

<p>(<b>A</b>) Observed and predicted scaled diversity levels around non-synonymous (left) and synonymous (right) substitutions. The predictions are based on the joint model for background selection and classic sweeps. (<b>B</b>) The contribution of background selection (blue) and classic sweeps (red) measured in terms of the coalescent rates that they induce. The rates are measured in units of 1/2<i>N</i>_<i>e</i>, where <i>N</i>_<i>e</i> is our estimate of the effective population size in the absence of linked selection. To make these graphs comparable to the scaled diversity levels in (A), with lower rates corresponding to higher scaled diversity levels, the direction of the y-axis is reversed. (<b>C</b>) The density of exonic sites (blue) and non-synonymous substitutions (red) as a function of distance from non-synonymous and synonymous substitutions. Densities are normalized by the average densities at distance >0.06cM; the shaded areas correspond to the use of a different linear scale.</p

A comparison of observed and predicted scaled diversity levels along the major autosomes of <i>Drosophila melangaster</i>.

<p>Throughout, we refer to “scaled diversity” as synonymous heterozygosity divided by synonymous divergence, to control for variation in the mutation rate (as detailed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006130#pgen.1006130.s001" target="_blank">S1C Text</a>); scaled diversity is shown relative to the genome average. (<b>A</b>) Observed and predicted scaled diversity over non-overlapping 1 Mb windows across chromosomal arms. (<b>B</b>) Summaries of the goodness of fit for models including background selection (BS), classic sweeps (CS) and both (BS & CS). <i>R</i>² is calculated for autosomes using non-overlapping windows of different sizes. Selection parameters are inferred using synonymous sites with recombination rate >0.75cM/Mb, while the predictions and corresponding summaries are calculated for sites with recombination rate >0.1cM/Mb.</p

Comparing alternative models around substitutions in proteins and UTRs.

<p>(<b>A</b>) Comparison of predicted scaled diversity levels around non-synonymous substitutions based on models including background selection (BS), classic sweeps (CS) and both (BS & CS). (<b>B</b>) Comparison of predicted scaled diversity levels around substitutions in UTRs based on models with and without sweeps in UTRs.</p