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.