2.9 | Identification of positively selected genes
(PSGs)
Based on gene families retrieved from the TreeFam, we identify PSGs
between B. schroederi and other five species (A. suum ,T. canis , P. univalens , C. elegans and M.
hapla ). The branch-site model of CodeML in PAML (v4.8)(Bo & Yang,
2013) was used to detect potential PSGs. Using the null hypothesis and
the alternative hypothesis to estimate whether the dN/dS (ω) value of
the foreground branch (Marked as B. schroederi ) was larger than 1
or not. Then performing likelihood ratio test (LRT) using R
“chisq.test()” function to calculate chi-squared distributions with 1
degree of freedom. The PSG was identified by meeting the requirements of
a corrected P-value (< 0.05) and contained at least one
positively selected site with a posterior probability ≥1.