Evolutionary Analysis Of TLR1,2 And 4 In Order Carnivora

A long-term and open question is whether the selective pressure underwent by vertebrates and invertebrates are similar. One may think that the acquisition of adaptive immune system may alter the evolutionary pressure on innate immune genes. Previous studies have shown that the pattern recognition receptors (PRR) in Drosophila exhibited more obvious of adaptive evolution across species than other innate immune genes. Animals with different diet can habit vastly different intestinal microorganisms. Evidence that intestinal microorganisms can regulate the immune system of host have been established early. In the view of genetic, whether the intestinal microorganisms will influence the selection pressure of innate immune genes increased our attention. In addition, with the mathematic models introduced and improved, molecular methods have been developed as a powerful tool to detect adaptive evolution. Great panda and red panda are special organisms in Carnivora, because of their diet shift. Therefore, it is an advantage and convenient to explore the two questions above that studying the evolutionary dynamics of innate immune genes in Carnivora. With the simple and mature molecular biology technology, this research has been carried out to test the evolutionary dynamics of TLR1,2 and 4 in Carnivora and diet influence on the three genes with an emphasize on typical different diet, and the main results and conclusions of this thesis are as follows: 1) In our study, we have obtained TLR1 sequences from 4 species, including two complete coding sequences (CDS) of hog badger and Siberian tiger with the full-length 2370bp, and partial CDS from Asiatic black bear and Siberian weasel with the length 2229bp; Complete TLR2 CDS from 7 species, including Siberian tiger, Asiatic black bear, leopard cat, civet cat, Siberian weasel, Chinese ferret-badger, and hog badger, with full-length 2358bp; Complete TLR4 CDS from 9 species, including Siberian tiger, Asiatic black bear, leopard cat, civet cat, Siberian weasel, Chinese ferret-badger, hog badger, red panda, and spotted linsang, with full-length 2502bp; The homology analysis of three genes showed that they were extremely conserved, and the similarity between nucleotide and amino acid sequences were above 80%.2) Selective pressure of TLR1,2 and 4 detected by Branch model have shown that target genes have been through purifying selection in Carnivora; 4,2, and 14 sites have been detected under selection in TLR1,2, and 4 datasets, respectively. Some of these sites are located adjacent to the important sites involved with binding the ligands or dimerization with homology or heterogeneity counterparts. In summary, adaptive evolution have been detected in innate immune genes TLR1,2 and 4, supporting the "Red-queen hypothesis" between the host and pathogens;3) Considering the diet specificity of giant panda and red panda in Carnivora, we used the branch-site model to detect whether the adaptive evolution have been occurred in these two branches. The results showed that 608V in TLR4 from red panda and 203R and 3511 in TLR1 from panda have been detected under selection, with an insignificant support, demonstrating that diet shift exerts barely influences on evolutionary dynamics of TLR1,2 and 4.4) To understand the influence of diet on evolutionary dynamics of innate immune genes, firstly, we choose two different groups with an emphasize on typical diet to estimate the evolution rates of TLR1,2 and 4 using maximum likelihood methods. The results showed that all three genes were underwent purifying selection and experienced functional constraint. The comparison between model that inhabiting two evolution rates (co) for different diet groups and model that with one ω between them showed that diet difference did not cause the significant variation of evolutionary dynamics. Secondly, classifying panda and red panda to carnivores and herbivores, respectively, revealed that the genetic background of ancestral carnivores of panda and red panda have no influence on evolutionary dynamics analysis of diet on TLR1,2, and 4 in Carnivora.Collectively, our study demonstrated the evidence of adaptive evolution of innate immune genes in Carnivora by means of molecular evolution, and provided the clue on studying the impact of diet on evolutionary dynamics of innate immune genes.