Abstract: Branch-Site and Site-Specific Models are statistical simulation methods for detecting molecular adaptive evolution at individual among specific lineages. The models not only indicate whether genes of phylogeny are under positive selection or not but also can identify the codon sites which are under the positive selection promoting gene divergence and polymorphism. For protein-coding gene, detecting the positive selection sites is important to understand the structure and function of proteins. Interferon is a very important cytokine in innate immune system. Interferon genes present evolutional polymorphism when the innate immune factors are under high selective pressure. Using the computer models to simulate and analyze the molecular adaptive evolution of interferon genes, it is found that interferon genes are under the positive selection and the positive selection sites existing in the interferon gene sequences are also located. These results show that Branch-Site Models and Site-Specific Models can detect molecular adaptive evolution of innate immune genes which are highly divergent.
Lihua Fan, Min Tao, Shujun Wang and Chengyu Hu, 2012. Codon-Substitution Simulation Models for Detecting Molecular Adaptive Evolution. Journal of Animal and Veterinary Advances, 11: 1622-1626.