Phylogenetic analyses
We inferred the phylogenetic relationships among the members of the
chemoreceptor gene families identified in the genome of D.
silvatica by the maximum likelihood method implemented in IQ-TREE. We
also included Drosophila melanogaster chemoreceptors in the
analysis as evolutionary references (D. melanogaster is the best
annotated genome so far for these families in Arthropods), and only
complete proteins from both species (i.e., using MSAp; see above). For
the analysis we used the best-fit amino acid substitution model found by
IQ-TREE, and estimated node support from 1000 ultrafast bootstrap
replicates. To test whether amino acid variation in the ligand-binding
domain (LBD: PF00060; Mistry et al., 2021) can be used to distinguish
between iGluR and Ir subfamilies, we built an additional
MSA (MSAp2) including only the sequences encoding this domain inD. silvatica and in D. melanogaster . We used HMMSEARCH
(Eddy, 2011) and in-house Perl scripts to identify and cut the
sequences encoding this domain in all complete Ir/iGluR genes. We
used the iTOL web server to visualize and manipulate the trees (Letunic
& Bork, 2007).