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.