Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease

Reanalyzing previously published data on Daphnia magna susceptibility to infection by Pastueria ramosa, we identify genomic regions consistent with GxG interactions. We conclude by outlining possible avenues for designing more powerful and more repeatable association studies.

Usage notes

CoGWAS_Supplement Mathematica notebook deriving analytical models, numerical simulations, and for producing figures 1-4 and S1. CoGWAS_Supplement CDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1. CoGWAS_Supplement PDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1.

Fig. S1 - Matching-alleles model Row 1: Estimated allelic effects as a function of pathogen allele frequency (black: \beta_0, solid red: \beta_{Hi}, dashed red: \beta_{H1,H2}, blue \beta_{Pi}, blue dashed: \beta_{P1,P2}, purple dashed: \beta_{Hi,Pj}). Row 2: Variation explained by host additive effects only (solid red), host additive and epistatic effects (dashed red), host and pathogen additive and epistatic effects (dashed blue, overlaps with dashed red), and a full host pathogen model (dashed purple).

FigS1.gif Fig. S2 - GWAS of *Daphnia magna* susceptibility Genetic associations of each SNP with C1 (red circles), C19 (blue, squares), and "mixed'' susceptibility (green, triangles). Here, the mixed case was obtained by taking each host clone and randomly choosing the data upon exposure to C1 or C19 (not both, as incorporated in the overall analysis in figure 5). Hence each SNP is represented three times, once for each genome wide scan.

Note that closely linked SNPs often overlap with one another and are not all individually visible. Significant SNPs are shown in colour while those below the log-likelihood of 2 threshold or that are not clustered within a 10cM region of three other significant SNPs are shown in grey. The 10 linkage groups are delineated by vertical dashed lines.

FigS2.gif