Structural and evolutionary constraints shape adaptive landscapes of immune-related genes across mammalian phylogeny

The evolutionary dynamics of immune-related genes GBP5, GZMB, IFNG, IRF7, KLRD1, RTP4, TNFSF4, and TRAT1 were investigated through comprehensive phylogenetic and selection analyses across mammalian species. Using concatenated gene sequences, we applied advanced methods including PAML (a software tool that analyzes evolutionary selection pressures by comparing rates of genetic changes), MEME (a method to identify patterns in protein sequences that may indicate functional sites), and structural modeling (a technique to predict 3D protein shapes) to assess co-evolution and adaptation. Site- and branch-specific selection tests revealed widespread positive selection (ω > 1), with 15-26 branches showing statistically significant adaptive evolution (p < 0.05), particularly in functional domains critical for pathogen recognition and immune regulation. Recombination analysis identified gene-specific patterns, with GBP5, GZMB, and IRF7 exhibiting significant recombination breakpoints, while IFNG and TNFSF4 remained conserved. Functional annotation highlighted the biological relevance of selected sites, linking them to inflammasome activation (GBP5), apoptotic pathways (GZMB), interferon signaling (IFNG, IRF7), and lymphocyte regulation (KLRD1, TNFSF4). Tissue-specific expression analysis confirmed these genes' roles in immune-active tissues, with enriched pathways including Th1/Th2 differentiation (KEGG hsa04658) and cytokine regulation. These findings underscore the persistent evolutionary arms race between hosts and pathogens, with immune genes adapting to maintain effective defense mechanisms. The study provides a framework for understanding mammalian immune gene evolution, offering insights into conserved functional domains that may inform therapeutic targeting and vaccine design. By integrating phylogenetics, selection analysis, and functional genomics, we elucidate the molecular signatures of adaptation in key immune regulators, advancing our knowledge of host-pathogen coevolution.