Heterozygosity and fitness in a threatened songbird: blood parasite infection is explained by single-locus but not genome-wide effects

This folder contains the R Code and input files used in the analysis for the paper "Heterozygosity and fitness in a threatened songbird: blood parasite infection is explained by single-locus but not genome-wide effects". Abstract: In non-pedigreed populations, insights into effects of inbreeding can be obtained by correlations between individual heterozygosity and fitness-related traits (HFCs). Using an information-theoretic approach, we explored whether heterozygosity of microsatellite markers, measured as internal relatedness (IR), is associated with infection by blood parasites (Plasmodium, Trypanosoma or Leucocytozoon) in the threatened Aquatic Warbler (Acrocephalus paludicola). We also explored whether any of the markers is more influential than others, or than IR, in explaining blood parasitism (single-locus effects). While we observed that IR was a relatively important predictor of Plasmodium parasitism, we did not find strong evidence for IR to correlate with infection by the identified blood parasites, accounting for sex and population effects. Therefore, our data did not support negative inbreeding effects on blood parasite infection in the Aquatic Warbler. However, we found single-locus effects such that individuals heterozygous at AW-03 and Ase19 had lower probability of infection by blood parasites pooled together and by Plasmodium, respectively. This indicates that these two markers are in linkage disequilibrium with unknown fitness loci which are related to resisting or clearing blood parasites, and which confer a heterozygote advantage in the Aquatic Warbler. Our results add to the growing evidence that single-locus effects contribute more to HFCs than formerly recognised and have implications for Aquatic Warbler conservation.