2.11 Phylogenetic analyses and divergence time
A total of 619 single-copy orthologous gene clusters were extracted from the OrthoMCL clustering results. Protein sequences from each cluster were aligned using Mafft (Katoh & Standley 2013) with default parameters. Protein-aligned sequences were translated into coding sequence (CDS), and the CDS regions were filtered using Gblocks (Castresana 2000). Thereafter, ghost shark was used as an outgroup to construct the phylogenetic tree using RaxML (Stamatakis 2006) with Gtrgamma model and bootstrap of 100. With the calibration divergence times deposited in the Timetree database (Hedges et al. 2006), we selected calibration times at four sites, 471.34, 239.84, 98.25, and 28.46 million years ago (Mya), and MCMCTREE in PAML packages (Yang 1997) was used to confirm the estimated divergence time.