Constructing species tree
Extracted amino acid sequences of Single Copy Ortholog, one of the
outputs of OrthoFinder, were aligned by MAFFT (Katoh, Misawa, Kuma, &
Miyata, 2002). To remove regions where sequence alignments were
incomplete, trimAl (Capella-Gutiérrez, Silla-Martínez, & Gabaldón,
2009) was used. Finally, trimmed alignments were submitted to IQ-TREE
ver. 1.6.11 (Nguyen, Schmidt, Haeseler, & Minh, 2015; Hoang, Chernomor,
Haeseler, Minh, & Vinh, 2018) for maximum likelihood tree
reconstruction, with ‘-sp’ option (Chernomor, Haeseler, & Minh, 2016)
to allow different substitution model and branch lengths for each
alignment. The model of each partition was determined by ModelFinder (S.
Kalyaanamoorthy, Minh, Wong, Haeseler, & Jermiin, 2017). Branch
supports were evaluated based on 1,000 bootstrap replicates.