Research And Application Of Nucleotide Substitution Model In The Process Of Genetic Evolution

The process of biological evolution is complex and long,and its foundation and intrinsic motivation are the evolution of genes,and the theory of neutral evolution is laid the foundation for the evolution of gene from molecular level.Since the Darwinian era,many researchers have tried to use phylogenetic trees to reproduce the evolutionary relationships between the various organisms.Beginning in the 1980 s,the relevant researchers mainly through the bioinformatics means to carry out the reconstruction of phylogenetic trees.The selection of the evolutionary distance model is the basis for constructing the phylogenetic tree,and the mathematical statistical method for calculating the evolution distance between genes is to estimate the number of nucleotides in the DNA sequence.Selecting the different nucleotide substitution model,the final construction of the phylogenetic tree is also different.Therefore,the choice of nucleotide substitution model will directly affect the tree results and the rationality of phylogenetic tree.Based on this,this paper explores the nature of the nucleotide substitution model in gene evolution and tries to apply it to the development of phylogenetic tree by MEGA software.On the basis of the previous research results,this paper summarizes the existing conclusions and makes some new explorations.Mainly include the following:1.Starting from the existing nucleotide substitution models,several typical and widely accepted nucleotide substitution models have been introduced.2.Based on the previous studies,the entropy properties of DNA sequence point mutations under different nucleotide substitution models were studied by establishing differential equations.Including entropy properties of point mutations in infinite DNA sequences,the maximum entropy of point mutation in finite DNA sequence under one-parameter model and the Tamura model,especially the maximum entropy of point mutation in DNA sequence under the equal-input model was investigated.By solving the differential equations,combined with the idea of extreme values,the maximum entropy of DNA sequences under the equal-input model is explored.It is found that the entropy of the finite length DNA sequence fluctuates with the generation and tends to the maximum entropy for the finite length of the DNA sequence.However,since the static distribution of the nucleotides is assumed by the equal-input model,The equilibrium frequencies of nucleotides in the equal-input model are not all 1/4.And the Mathematica is used to simulate the change of DNA sequence entropy with the generation in the equal-input model.In the process of computer simulation,in order to observe the simulation effect more clearly,the mutation rate is appropriately amplified.In order to be closer to the actual mutation process,The use of computers to produce several longer DNA sequences,showing the DNA sequence entropy with the generation of random fluctuations,and gradually tend to the maximum entropy of the process.3.Classifying the nucleotide substitution models according to the different characteristics of them,that is,the difference in the limit distribution..And two new models are proposed,and the transition/transversion dynamic equations are established under the new models,and the limit distribution of nucleotides under the new models are given.4.By reviewing the different literatures,the classification of phylogenetic trees is described in detail,including rootless trees and rooted trees,species trees and gene trees,expectation trees and realistic trees.There are several commonly used classical tree methods,including distance-based methods,including unweighted pair group method with arithmetic mean(UPGMA),Neighbor-joining method(NJ),Including the maximum parsimony method(MP),the maximum likelihood method(ML).In addition,the phylogenetic tree was constructed by molecular evolutionary genetic analysis software MEGA.