Phylogenetic Relationships and Gene Family Evolution
We estimated a coleopteran phylogeny with high support, with N.
riversi as the inferred outgroup (Figure 1 ). Fossil-based time
calibrations suggest a divergence time of ~300 million
years. The CAFÉ analysis of gene family turnover shows at least seven
large lineage-specific rapid gene expansion events in Polyphaga (Figure
1), but a very modest expansion in N. riversi . Most gene
contractions are quite small across the Coleoptera phylogeny. An
examination of the N. riversi orthogroup expansion events
(Table 3 ) shows expansions in zinc finger proteins, trehalose
transporters, protein kinases, troponins, multidrug
resistance-associated proteins, and synaptic vesile glycoproteins.
Contracting orthogroups in N. riversi (Table S10 )
include ligases, ion channel receptors, glutathione S-transferases,
nuclear receptor coactivators, aminophospholipid transporters,
regucalcin proteins, and dynein complex proteins.
Based on a conservative GSEA (p-value=0.001) of expanded gene families
in N. riversi , functionally enriched terms include pathways
involved in protein transport, protein phosphorylation, metabolic
processes, proteolysis (ubiquitination and proteasome), organismal and
brain development, response to heat and synaptic signaling
(Table S11; Figure 2 ).