3.5. Comparison of results from molecular tests of selection
In order to compare results from our two tests of positive selection, via the HDMKPRF and LASSI Plus analyses, we necessarily must focus uponG. calmariensis . In order to ensure locus orthology in our HDMKPRF analyses, we both identified 1:1:1 orthologs among the three species and mapped all of our population data to this reference and used a single annotation (i.e. all gene information in with reference to theG. calmariensis genome). However, for our LASSI Plus analysis, we mapped reads to each species genome, in order to be able to accurately assess the haplotype frequency spectrum outside of coding regions. Thus, we are only able to accurately compare results from both analyses for G. calmariensis . While 595 genes were identified as having experienced positive selection via the first HDMKPRF, that included all 4151 genes, only 10 of these overlapped with the set of 216 genes found to be overlapping with haplotype sweep regions (with genes having a 10kb flaking region for overlap assessment) and none of these immune genes. However, the comparison with the second HDMKPRF that included all 96 candidate immune genes identified a larger overlap, with 7,6 and 6 genes identified respectively.