2.8 Phylogenetic analysis
1167 single-copy Orthologues shared by 10 insects were used to phylogenetic analysis. Supergenes formed by multiple alignment of single copy gene family were constructed for tree construction. The phylogenetic tree was constructed by maximum likelihood (ML) using IQ-tree with the best model (JTT+F+R5) and 1000 rapid bootstrap replicates. Another method to construct phylogenetic tree was used Astral-III to merge all gene trees obtained by OrthoFinder into one species tree. Two trees from above methods must be coincident. Divergence time was estimated by MCMCtree program in the PAML package v4.8 based on the multiple sequence alignment protein sequences. The calibration time points of P. xylostella (286 MYA), D. plexippus (179 MYA), S. frugiperd (140 MYA), B. mori (108MYA) and H. armigera (56 MYA) were obtained from TimeTree (http://timetree.org/). The gene family contraction and expansion were analyzed by CAFE v4.2 based on the results from orthofinder and phylogenetic tree with divergence time (Hanet al. , 2013). Finally, Evolview (http://evolgenius.info/#/) was used to beautify the phylogenetic tree.