Adaptive Evolution Of Mammalian Innate Immune Pattern Recognition Receptor PRRs

Mammals are widely adapt to different habitats, including terrestrial, aerial,aquatic and underground habitats. Herein, they evolved specific immune mechanism challenged with diverse pathogens. Innate immunity, the first line of immune defense,sensing pathogens through pattern recognition receptors (PRRs). However, this adaptive molecular mechanism remain poorly explored. Here, we choosed 17 PRRs genes as candidate genes. Aim to explore positive selection in mammals and what is the major driving force exert on PRRs.A total of 20 genes for analysis, including ten numbers of TLRs family (TLR1-10),whole of RLRs family (LGP2, MDA5, RIGI), four numbers of NLRs family (NLRP3,NLRX1, NOD1, NOD2) and three numbers of CLRs family (Dectin1, Dectin2,MINCLE). PAML selection pressure analysis showed that strong purifying selection played a vital role in the evolution of PRRs. Overall, selection constraint relaxed in TLRs when compared with non-TLRs. Strong positive selection was detected in some amino acid sites or taxa though purify selection exert on PRRs. Of which, TLR4, TLR8,TLR9,MNOD2 found strong positive selection signal. Through the branch model analysis,we found that habitat prominently drives population divergent evolution other than diet or population size, especially for aquatic mammals with co value elevated significantly.Moreover, 164 SNPs of TLRs identified from 48 finless porpoises (Neophocaena phocaenoides) in China. Population genetic analysis showed that "bacterial-sensing"TLRs more abundant genetic polymorphisms than "viral-sensing" TLRs. For each gene,TLR4 show the highest polymorphisms but TLR7 is the lowest. For each population,NAS (N. a. sunameri) genetic polymorphism level is higher than the NAA (N. a.asiaeorientalis) and NPP (N. p. phocaenoides), suggesting that the NAS is the oldest population. Although there is a certain degree of differentiation between freshwater and seawater groups (NAA-NAS: FST = 0.023), clustering results couldn't be separated completely, which conssistent with finless porpoise' s recent differentiation event.Outlier analysis added for detection of positive selected sites, in order to verify the differentiation between different groups result from adaptation to the specific environment. Several outliers (TLR2: 52N513K; TLR5: 10998D, 110I232V, 113M300T,116I673N; TLR7: 130R634V) were identified not only by two methods but also detected by at least two comparisons. In which TLR5 signal was the strongest,significantly deviate from neutral evolution (Tajima's D = -2.10288, p = 0.00000). Furthermore, these outliers also located in vital function domain of TLRs proteins, such as pathogen-binding site or leucine-rich repeat region (LRR).In this study, we conducted a complete evolution analysis of PRRs in mammals,and revealed the evolutionary pattern of PRRs. Furthermore, population genetics analysis of TLRs in cetacean (finless porpoise) found some specific adaptive changes in fresh water groups of finless porpoise. This study was the first to investigate genetic evolutionary through different time scales in whole PRRs, from mammals's level to populations's level. The results of this study provide a comprehensive comprehension of PRRs adaptive evolution.