Orthology identification and phylogenetic inference
Protein-coding genes from another 11 species of Lepidoptera as well as
two species of Coleoptera and two species of Diptera were obtained from
the NCBI genomes database for comparative analysis (Table 1 ).
Orthologs were identified using OrthoFinder version 2.2.7 (Emms &
Kelly, 2015) under default parameters. The phylogenetic tree was
inferred in the OrthoFinder pipeline with an
approximately-maximum-likelihood method implemented in FastTree v2.1.10
(Price, Dehal, & Arkin, 2009) based on a concatenated multiple sequence
alignment (MSA) of single-copy genes. The most likely category for each
site was set using a Bayesian approach with a gamma prior. Amino acid
sequences were aligned in MAFFT
v7.450 (Katoh & Standley, 2013) with the G-INS-I algorithm.