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.