Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), olfactory receptor (OR), and antimicrobial peptide (AMP) subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the dete..., Raw alignment files for select Hymenoptera gene family phylogenies
For each gene family, a multi-species, amino acid phylogeny was constructed with manually curated annotations from N. lecontei, select Hymenoptera, and D. melanogaster. Intact sequences were size filtered (350³ for GR, OR, CYP; 100³ for histnavicin and OBP); pseudogenes and partial annotations were excluded. Select sequences were aligned with MAFFT (v7.305b) (Katoh et al. 2002) (parameters: --maxiterate 1000–localpair).
 Manual gene annotation sequences
The olfactory and gustatory receptor genes were annotated following Robertson et al. (2003, 2006). Briefly, manually curated chemoreceptor genes from select Hymenoptera were used as TBLASTN (v2.2.19) (Altschul et al. 1990) queries against the N. lecontei draft genome (parameters: -e 100000 -F F). Gene models were manually built in TextWrangler (v5.5) (Bare Bones Software) and new gene models were iteratively added to TBLASTN searches until new chemoreceptors were no longe...,