基因进化的同义与非同义替代计算及统计检验的比较分析

基因氨基酸编码区的核苷酸具有不同替代速率.同义替代不引起氨基酸改变,它们基本是中性替代速率;非同义替代引起氨基酸变化,替代速率常常比同义替代速率低. 非同义(或同义)替代速率定义为单位时间(如1年)内或者一个世代内1个非同义(或同义)位点上发生替代的数目,用符号dN(或dS)来表示. 生物体内发生的非同义突变大多数属于有害突变,只有少数是中性突变或有利突变. 对有害的非同义突变来说,dN-dS＜1;而对于有利的非同义突变来说,dN-dS＞1. 仅仅通过比较dN和dS还不能确定是否就一定受到选择作用,还必须用统计学的方法来检验它们的真实性和可靠性. 计算dN和dS的方法有多种,常见的是4种:N-G模型、改进的N-G模型、Li-Wu-Luo模型和P-B-Li模型.4种方法从不同的角度计算编码区核苷酸的dN,dS值,它们各有特点,适合不同基因的计算.对dN,dS值进行统计检验的方法也有多种,常见的方法有5种:Z检验、Tajima‘s D 检验、Fu and Li检验、HKA检验和MK检验.这5种检验方法也各有特点,适合不同基因dN,dS值的检验.

Comparing and Analysing on Models of Calculation and Statistical Testing of Nosynonymous Substitution Rate and Synonymous Substitution Rate during Gene Evolution

Substitution rate of nucleotide acids varies in amino acid encoding region of gene.Synonymous substitution rate nearly is neutral,which not chang amino acids of protein;Nosynonymous substitution rate is lower than that of synonymous substitution,which lead to changing of amino acids in protein.nosynonymous(or synonymous) substitution rate is defined as substitution number of nucleotide acids in nosynonymous(or synonymous) positions during a constant period(such as one year) or a period of generation.Symbol nosynonymous(or synonymous) substitution rate is d_N(or d_S).Major of nosynonymous substitution in organism is deleterious mutation and only minority is neutral or advantageous mutation.When nosynonymous substitution is deleterious mutation,d_N-d_S<1;If nosynonymous substitution become neutral or advantageous mutation,d_N-d_S>1.However,we,only by comparing value of d_N and d_S,are not able to determine whether the nosynonymous substitution get selective pressure.We must use statistical methods to test the selective pressure being true or false.There are many methods caculating d_N and d_S,but only four kinds of method are carried out by most people.These methods are respectly N-G model,improved N-G model,Li-Wu-Luo model and P-B-Li model,which calculate d_N and d_S with various parameters.Every kind of models has particular advantage which is favour of corresponding genes.There are also some methods testing value of d_N and d_S,five kinds of which are often used. The five kinds of methods testing value of d_N and d_S are respectly Z-test,Tajima's D-test,Fu and Li-test,HKA-test and MK-test.Every tests own itself advantage which is favour of corresponding genes.