Relative evolutionary rates
The evolutionary rate of these 11 species was calculated using the
coding sequences (CDS) of all single-copy genes. Initially, all of these
single-copy genes were connected into one super sequence and aligned
using MUSCLE (v3.8.31) (Edgar 2004a,
b). L. oculatus was used as the
outgroup species; both LINTRE software
(Takezaki et al. 1995) and MEGA
(Tajima’s relative rate test) (Kumaret al. 2016) were used for this analysis. In Tajima’s test, the
higher number of lineage-specific substitutions corresponds to a faster
evolutionary rate. In the LINTRE method, the evolutionary rate of each
species was checked using Z-statistics and the tpcv module.