Molecular evolutionary genetics analysis of major histocompatibility complex class I, II and III genes in ruminants and monogastrics.
The steady accumulation of mutations over long periods gives rise to MHC polymorphisms and this impacts how each species responds to the host organisms. The nucleotide sequences of MHC class I, II and III genes were retrieved from six selected mammalian livestock species from GenBank, NCBI. ClustalX 2.1 and MUSCLE in the MEGA 7 software were used for the multiple sequences alignment of the nucleotide and amino acids sequences. DnaSP 6.0 software was used to calculate the population genetics parameters. The evolutionary relationship of the MHC I to III proteins of the livestock species was determined by Phylogenetic trees which were constructed using the Neighbour-joining method in the MEGA 7. The DNA polymorphisms of MHC I to III genes among the ruminants and monogastrics revealed high and similar haplotypes diversity. However, the ruminants and monogastrics MHC I gene had low nucleotide diversity in contrary to the MHC II and III genes with high nucleotide diversity. MHC Ito III genes had high guanine-cytosine, GC content except the MHC II monogastrics with low guanine-cytosine content. The evolutionary change observed on the livestock MHC I to III genes population deviated from Hardy-Weinberg Equilibrium. Phylogenetic and evolutionary analyses of mammalian livestock species MHC I to III molecules revealed they are slow-evolving at 5, 20 and 2% rates respectively. Similarly, the orthologous relationship existence among the ruminants and monogastrics MHC I to III molecules showed amino acids substitutions of 6 - 18, 5 - 29 and 1- 12% respectively since they diverged from the common ancestor. Likewise the optimal trees' sum of branch length (8 × 10-8, 2 × 108, and 4 × 10-8) indicated that the MHC protein I, II, III molecules of ruminants and monogastrics might have undergone birth-and-death evolution respectively. Since gene duplication and deletion seem to be prevalent among the MHC I, II and III genes and the primary function of MHC is to defend the host from various invaders and great diversity is required; therefore the evolutionary force is mandatory for the diversification. The above information can be utilized to assess the immunogenetic status of livestock population, which will help to increase knowledge on the importance of adaptive genetic polymorphisms in both free ranging and domesticated livestock populations.