Stegall All glades All years

Microsatellite two-digit data in Genepop format from all samples collected between 1984 and 2006. Missing values are represented by zero. Data is partitioned such that each year represents a Genepop "population = 'Pop'". Each sample ID includes the year collected, the glade, and the unique ID (e.g. "1984-SM7-S030" is sample ID S030 collected on glade SM7 in 1984)

Plot of PCC edges for the 17 SNPs in the <i>ps_1</i> bloc.

<p>BlocBuster connected these 17 nodes into a single connected component, while PCC separated them into disconnected components. Overall, PCC identified 19 pair-wise correlations and CCC identified 39 correlations amongst these SNPs, as represented by edges in this plot and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003766#pcbi-1003766-g002" target="_blank">Figure 2</a>.</p

Comparison of SNP network construction methods.

<p>The network in (a) represents each SNP by a single node, as is done by previous approaches, and the network in (b) employs a node for each of the SNP alleles. Allele ‘A’ for SNP 1 is correlated with allele ‘b’ of SNP 2, and allele ‘B’ of SNP 2 is correlated with allele ‘C’ of SNP 3. Allelic information is lost in a standard network (a), resulting with an incorrect linking of allele 1A with 3C. The BlocBuster approach also enables allele-specific testing of bloc patterns.</p

Selection of previously identified risk alleles for psoriasis.

<p>Shown are the SNP IDs, chromosome, position, risk allele frequencies <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003766#pcbi.1003766-Tsoi1" target="_blank">[14]</a>, odds ratio (OR), and closest gene for all markers cited by Tsoi et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003766#pcbi.1003766-Tsoi1" target="_blank">[14]</a> with an OR of at least 1.4. Positions follow Genome Build 37.3, as given by NCBI's dbSNP website (<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target="_blank">http://www.ncbi.nlm.nih.gov/projects/SNP/</a>).</p><p>Selection of previously identified risk alleles for psoriasis.</p

Genotypes for ten individuals for a pair of SNPs.

<p>The first five individuals are perfectly correlated, but the others are not correlated at all. The absolute value of PCC is 0.3 and <i>r</i>² returns 0.0, due to the uncorrelated individuals. CCC supplies four correlation values, each of which corresponds to a specific type of correlation. These values are low for three of the possible combinations, but a high value of 0.7 for the T-G combination was returned.</p

Plot of 17-node bloc, <i>ps_1</i>.

<p>Each node represents a SNP allele and each edge represents a significant correlation between the SNP alleles representing its endpoints. The pattern corresponding to this bloc exhibited a risk association with psoriasis, with an odds ratio of 3.64 (CI: 2.75–4.80) and Bonferroni-corrected p-value of 5.01×10⁻¹⁶ in the discovery data and odds ratio of 3.86 (CI: 2.98–5.01) and Bonferroni-corrected p-value of 1.81×10⁻²⁵ in the validation data.</p

Description of SNP alleles corresponding to the nodes in <i>ps_1</i>.

<p>All SNPs are located on chromosome 6. The node numbers correspond to the numbers in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003766#pcbi-1003766-g002" target="_blank">Figures 2</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003766#pcbi-1003766-g004" target="_blank">4</a>. Shown are the frequencies of the risk alleles for psoriatic cases and controls, odds ratio (OR) for each individual SNP, SNP IDs, and chromosomal positions, where rsID is the dbSNP assigned reference SNP identification number and positions are for Genome Build 37.3, as given by NCBI's dbSNP website (<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target="_blank">http://www.ncbi.nlm.nih.gov/projects/SNP/</a>).</p><p>Description of SNP alleles corresponding to the nodes in <i>ps_1</i>.</p

Map of the <i>ps_1</i> bloc on chromosome 6.

<p>Genes are represented by: (A) <i>C6orf15</i>, (B) <i>PSORS1C1</i>, (C) <i>CDSN</i>, (D) <i>PSORS1C2</i>, (E) <i>CCHCR1</i>, (F) <i>TCF19</i>, (G) <i>POU5F1</i>, (H) <i>PSORS1C3</i>, (I) <i>HCG27</i>, (J) <i>HLA_C</i>, (K) <i>USP8P1</i>, (L) <i>RPL3P2</i>, and (M) <i>WASF5P</i>. Two SNPs are within known genes: rs3130573 in <i>PSORS1C1</i> and <i>PSORS1C2</i>, and rs1265078 in <i>CCHCR1</i>. Shown are chromosomal positions (in Mb) according to Genome Build 37.3, as given by NCBI's dbSNP website (<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target="_blank">http://www.ncbi.nlm.nih.gov/projects/SNP/</a>).</p

Proportion of allelic richness recovered by gene flow and cut-off frequencies (<i>Q_c</i>).

<p>Proportion of allelic richness recovered by gene flow and cut-off frequencies (<i>Q_c</i>).</p

Sampling localities for the 3N1 and 3N2 mitochondrial clones.

<p>Latitude/longitude data and sample sizes are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000760#pone-0000760-t005" target="_blank">Table 5</a>. Ranges of the CA6, EA6, and SM6 sexual chromosome races are shown in light gray. The inset in the upper right shows the extent of the arid zone in dark gray.</p