Replicabilities against MAFs in the discovery study.

<p>For every SNP discovered in Europeans, all the replication attempts in East Asians were considered and classified by bins of OR found in Europeans. By means of windows with step 0.3, the average statistical power (empty black circles), average replication success (solid black circles) and effective replicability (the ratio between observed and expected replicability, the two former quantities, red circles) are shown (using only windows with ≥20 attempts). Top values of the graph represent the average date of publication and sample size of discovery GWAS, for each bin of MAF.</p

Replicabilities against ORs in the discovery study.

<p>For every SNP discovered in Europeans, all the replication attempts in East Asians were considered and classified by bins of OR found in Europeans. The OR of SNPs with risk alleles being major was transformed to ensure OR>1. By means of windows with step 0.3, the average statistical power (empty black circles), average replication success (solid black circles) and effective replicability (the ratio between observed and expected replicability, the two former quantities, red circles) are shown (using only windows with ≥20 attempts). Top values of the graph represent the average date of publication and sample size of discovery GWAS, for bins of 0.1 OR.</p

Similar correlation between European and East Asian log(OR), regardless of the discovery GWAS sample size.

<p>This figure is a redraw of the points shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003566#pgen-1003566-g001" target="_blank">Figure 1A</a> but colored according to the discovery GWAS sample size. The same correlations arose when using all replication attempts (as it is shown in Figure) or the filtered (n = 123) set of largest replication attempt per SNP (not shown).</p

Regions harboring non-replicated SNPs present larger differences in LD between Europeans and East Asians.

<p>Measures of difference in LD (varLD scores) are given for sliding windows of 50 SNPs with a 5-SNP step. Measures for replicated and non-replicated SNPs are given as blue and black lines, respectively. Shadowed areas represent the standard error of the mean. The vertical red band indicates that all windows with significant differences (P<0.01) locate in the vicinity of the associated SNPs.</p

East Asian GWAS find the same risk allele and similar log(OR) than European discovery GWAS.

<p><i>X</i> axis: log(OR) for the replication stage of the discovery European GWAS. <i>Y</i> axis: log(OR) for the initial stage of East Asian GWAS (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003566#s3" target="_blank">Materials and Methods</a>). Dots in blue indicate significant (<i>P</i><0.05) replication attempts in East Asia; dots in grey indicate non-significant replication attempts. (A) Using all replication attempts; (B) Using only the most-powered replication attempt per SNP; (C) Using the most-powered replication attempt per region. Attempts correspondent to SNPs with MAF<0.01 in East Asians are not shown.</p

Nucleotide diversity estimates among elements and species.

<p>(<b>A</b>) Conservation analysis of the six complete <i>HeT-A</i> elements from <i>D. </i><i>melanogaster</i>. Sliding windows of 25 ntds size and 1 ntd steps are represented. The significantly conserved regions (R) in the 3′UTR are marked with arrows. (<b>B</b>) Conservation analysis of the last 500 ntds of the 3′UTR among species (<i>D. melanogaster, D. sechellia, D. simulans, D. yakuba</i>). Graph constructed with an alignment of homologous sequences, longer than 350 ntds, obtained from the Blast analysis of the 3′ UTR sequence with a window size of 25 ntds and step size of 1 ntds (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037405#pone.0037405.s020" target="_blank">Methods and Results S1</a>). Number of aligned sequences: <i>D. melanogaster</i> 26, <i>D. sechellia</i> 26, <i>D. yakuba</i> 6 and <i>D. simulans</i> 12. The estimated average nucleotide diversity among all 72 sequences is 0.13571. For nucleotide diversity within each species see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037405#pone.0037405.s001" target="_blank">Figure S1</a>. (<b>C</b>) Alignment of the piRNA target sequence among <i>HeT-A</i> copies from four Drosophila species. Nucleotide diversities: all, 0.048; <i>D. sechellia</i>, 0.028, <i>D. yakuba</i>, 0.021; <i>D. simulans</i>, 0.058; and <i>D. melanogaster</i>, 0.0437 (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037405#pone.0037405.s001" target="_blank">Figure S1</a>).</p

Alignment of 3′UTR transcripts obtained from testes and ovaries of D. melanogaster Oregon R.

<p>Nucleotide polymorphisms are indicated. piRNA target HeT-A_pi1 is labelled with a red rectangle.</p

Number of piRNA reads, along the <i>HeT-A</i> copies and coordinates for piRNA targets HeT-A_pi1 and 2 in each described copy from <i>D. melanogaster.</i>

<p>Number of piRNA reads, along the <i>HeT-A</i> copies and coordinates for piRNA targets HeT-A_pi1 and 2 in each described copy from <i>D. melanogaster.</i></p

Most conserved target piRNAs from the seven analyzed TEs. The values presented are means and standard deviation across species (see Table S7 for individual species analyses).

<p>Most conserved target piRNAs from the seven analyzed TEs. The values presented are means and standard deviation across species (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037405#pone.0037405.s019" target="_blank">Table S7</a> for individual species analyses).</p

Coordinates of complete <i>gag</i> coding regions and HeT-A_pi1 targets in different Drosophila species. Nucleotide changes in the piRNA target sequence labeled in red, otherwise perfect identity.

<p>Coordinates of complete <i>gag</i> coding regions and HeT-A_pi1 targets in different Drosophila species. Nucleotide changes in the piRNA target sequence labeled in red, otherwise perfect identity.</p