3.4. Genome wide test of selection
While we were able to detect signatures of selective sweeps in all three
species, the patterns were strikingly different between G.
calmariensis and the other two species (Fig. 2). In G.calmariensis , the outlier loci were concentrated in a handful of
locations, which had strong signatures of selection large and were large
(Fig. 3). In contrast, both G. tenella and G. pusillaexhibited signatures of selection that were generally weaker, with
identified genomic regions that were more evenly distributed across
their genomes (Fig. 2) and narrower in G. tenella and G.
pusilla than in G. calmariensis (Fig. 3). To make a direct
comparison with the HDMKPFR test that is focused upon the coding region
of genes, we identified genes having a direct overlap of the sweep
region with any part of a gene body, from the start to stop, and in
between. This intersection of the outlier haplotypes with annotated
genes revealed a total of 192, 115, and 154 genes in G.calmariensis, G. pusilla and G. tenella, respectively.
When we included 10 kb on either side of each gene when detecting
overlap with outlier haplotypes, a total of 216, 305, and 430 genes were
intersected, suggesting that in the latter two species, there was more
overlap with potential regulatory regions. We next sought to assess to
what extent the identified candidate targets of positive selection from
the genome wide analysis overlapped with our candidate immune genes.
Unlike our results for the HDPRFMK test, the distribution of these
outlier genes (with 10kb on either side) were roughly equally
distributed among the three species (7, 6, and 6 genes in G.calmariensis, G. pusilla and G. tenella, respectively).