2.4 Candidate gene analysis
To analyse immune genes specifically, we first used BLASTP to detect the set of candidate genes identified in a previous RNA-seq study (Yang et al., 2020) in the G. calmariensis proteome. This gene set contains 166 genes suggested to be important in immune response against parasitoid wasp attack in Drosophila (Table S2), subdivided into seven functional immune gene categories: recognition (N =17), signalling (N =35), effector (N =21), proteases (N =35), haematopoiesis (N =31), melanisation (N =18), and wound healing (N =9). The threshold used in BLASTP was an E-value≤1×10−6 and a bitscore>60, which identified a set of 96 immune genes in our genomic dataset. When multiple hits were recovered during BLAST, we always used the one with the highest bit-score. When working to include these into our SCO gene analysis, only 40 of these genes passed this conservative threshold (they are part of the 4154 SCOs gene set). In order to more fully focus upon the 96 immune genes themselves, we performed a second HDMKPRF analysis. Because this second analysis is run on a smaller gene set, HDMKPRF has less power. We therefore compared the estimated selection intensities for the 40 SCOs between the two analyses, and confirmed that these were almost identical, suggesting this set size was sufficient for model parameter estimates.