3.2 Genes under Selection
The summary of synonymous and nonsynonymous polymorphisms and divergence
across species indicates that singleton removal increased the estimated
proportion of positively selected genes in all three species and reduced
indices of negative selection (Table 1), indicating the presence of
segregating weakly deleterious mutations. In G. calmariensis , we
detected mainly positive selection (α > 0) and a
higher proportion of positively selected genes. On the other hand, inG. tenella , negative selection was more common (α< 0) even after singleton removal and with a higher proportion
of negatively selected genes. In the following sections, we only discuss
inferences after removing singletons.
The HDMKPRF identified a similar number of genes under selection in the
three Galerucella species (Fig. 1). In G. pusilla , 451 and
562 genes were identified as being under positive and negative
selection, respectively. In G. calmariensis , 610 and 553 genes
were identified as being under positive and negative selection,
respectively. Finally, in G. tenella , 425 and 466 genes were
identified as being under positive and negative selection, respectively.
Because genes under positive selection are more commonly associated with
lineage-specific adaptive traits (e.g., immunity genes), we focus our
analyses on gene function connected to genes under positive selection.
The gene set enrichment analysis found several functions that were
enriched in genes under positive selection, some of which were common
among the three beetle species and some that differed (Table S2-S4).
First, enriched functions common among the beetle species included
functions involved in the formation of adult morphology, such as the
imaginal disc pattern formation (forming the adult cuticle and appendage
structures), the wing disc pattern formation (forming wing structures)
and the dorsal/ventral pattern formation. Second, unique gene categories
under positive selection in G. calmariensis included those coding
for metabolic processes (e.g., processes related to carbohydrate
derivatives, oligosaccharides, amino sugars, sulphur compounds and
catechol-containing compounds) and those coding for processes in the
nervous system (e.g., neuroblast proliferation, neuroblast
differentiation, nervous system process). Third, unique gene categories
under positive selection in G. pusilla included those coding for
positive regulation of the innate immune response (e.g., positive
regulation of small GTPase mediated signal transduction) and those
coding for axoneme assembly (e.g., cilium movement, cilium
organization). Finally, unique gene categories under positive selection
in G. tenella included genes coding for a range of biosynthetic
processes (e.g., nucleobase-containing compound biosynthetic processes,
heterocycle biosynthetic processes and aromatic compound biosynthetic
processes), genes coding for lipid metabolic processes (e.g., sterol
metabolism, membrane lipid biosynthesis, cellular lipid metabolism,
sphingolipid metabolism and lipoprotein metabolism), but also GO
pathways involving the activation of immune response, pigment metabolic
process involved in pigmentation, peripheral nervous system development
and response to oxidative stress.