DOI: 10.5061/dryad.n8pk0p320
title: Data from: Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)

description: 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 detection of
 bitter compounds. In contrast, these gene families had little evidence of
 recent contraction via pseudogenization. Overall, our results are
 consistent with the hypothesis that in response to novel selection
 pressures, gene families that mediate ecological interactions may expand
 and contract predictably. Testing this hypothesis will require the
 comparative analysis of high-quality annotation data from phylogenetically
 and ecologically diverse insect species and functionally diverse gene
 families. To this end, increasing sampling in under-sampled hymenopteran
 lineages and environmentally responsive gene families and standardizing
 manual annotation methods should be prioritized.
description: 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 <em>N. lecontei</em>, select Hymenoptera, and
 <em>D. melanogaster</em>. 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 <em>olfactory</em> and
 <em>gustatory receptor</em> 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
 <em>N. lecontei</em> 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 longer found. <em>Odorant binding protein</em>
 genes were annotated with custom scripts that identified
 automated Maker gene annotations with the classic/6C, Plus-C, Minus-C, or
 atypical odorant binding protein motif (Xu et al. 2009).
 <em>Cytochrome P450</em> genes were annotated with a
 search of 52 insect CYP genes against the <em>N. lecontei</em>
 genome assembly (E-value cutoff 1e3). Scaffolds with hits were then
 searched against 8782 known insect CYPs. Based on these searches,
 candidate <em>N. lecontei</em> CYP sequences were manually
 curated based on comparison to the best BLAST hits.
 <em>Antimicrobial protein</em> genes (including
 <em>Hisnavicin</em>) were annotated with BLAST queries from
 three representative hymenopterans. BLASTP searches were performed against
 the annotated proteins and TBLASTN searches were performed against the
 assembled genome.