2.7 | Identification of positively selected genes (PSGs)
Based on gene families retrieved from TreeFam, we identify PSGs betweenB. schroederi and the 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. The null hypothesis and the alternative hypothesis was used to estimate whether the dN/dS (ω) value of the foreground branch (Marked as B. schroederi ) was larger than 1 or not followed by likelihood ratio test (LRT) using R “chisq.test()” function to calculate chi-squared distributions with 1 degree of freedom. A PSG was identified by meeting the requirements of a corrected P-value (< 0.05) and containing at least one positively selected site with a posterior probability ≥1.
2.8 | The change of effective population size