3.3 Candidate gene analysis
The 96 candidate immune genes (out of 166) that remained in our second
HDMKPRF analysis include 13/17 recognition genes, 21/35 signalling
genes, 4/21 effectors, 16/35 protease coding genes, 24/31 haematopoiesis
genes, 13/18 melanisation genes and 5/9 wound healing genes (Table S2).
Seven of these immune genes were found to be under positive selection inG. pusilla , which was significantly more than the single gene
identified under positive selection in G. calmariensis (Fisher’s
Exact test: Odds ratio = 0.10, p<0.02), but not significantly
greater than the four genes under positive selection in G.
tenella (Odds ratio = 0.61, p>0.3), when related to all
genes under positive selection in respective species. However, while the
number of genes under positive selection in G. tenella was
marginally higher than the genes under positive selection in G.
calmariensis , this was not significant (Odds ratio = 0.17,
p<0.09). Positively selected immune genes in G. pusillainclude genes involved in parasitoid recognition (santa-maria andCorin ), Toll and JNK pathways (grass and Tak1 ), a
protease with serine-type carboxypeptidase activity and genes involved
in lamellocyte differentiation (cher and zfh1 ) (Table 2,
Table S6). The four immune genes under positive selection in G.
tenella included two recognition genes (Corin andPGRP-LE ) and two genes with important roles in haematopoiesis
through regulation of lamellocyte differentiation (cher andCyt-b5 ) (Table 2, Table S6). Finally, the single gene under
positive selection in G. calmariensis was Cyp9f2 , which is
involved in melanization.