Study On The Evolutionary Mechanism Of Gene Expression During Embryonic Development Of Drosophila

Speciation occurs as species adapt to the surrounding ecological environment.The underlying mechanism is that variations in the sequences and their expression of genes cause phenotypic differences within a species,when these variations accumulate to a certain extent,a new species will be formed.The variations in the sequences and their expression of genes can be caused by randomly genetic mutations.Currently,there are two different theories about the mechanisms determines the genetic mutations that should be retained for the variations in the seqences and their expression of genes:one is the Natural Selection Theory proposed by Darwin,and the other is the Neutral Theory--Random Genetic Drift Hypothesis proposed by Motoo Kimura.The former is derived from phenotypic study and the latter is an accumulative appreciation of molecular evolution.The question is then why there is such a contradiction?One possibility is that the complexity of biological traits hinders establishment of a good correlation between phenotype and genetic variations.Then,whether there is an existence of a simple and quantifiable biological trait may become a bottleneck in such an evolutionary analysis.Unfortunately,almost all of the biological traits are complex.Since the gene expression is a link between stable genotypes and complex phenotypes,changes in gene expression can relatively reflect phenotypic changes,so as to that the gene expression divergences correlate with traditional divergence of species.For example,phylogenetic trees constructed based on gene expression divergences resemble those based on traditional phylogenetics,which suggests that gene expression can be used as an indicator for evolutionary study.It has been shown that neutral selection is a determinant factor of the gene expression divergence during the evolution.On the other hand,it has also been shown that Darwin's natural selection plays an important role in this process.Thus,how gene expression divergence impacts evolution still requires further study.This study chose Drosophila as experiment materials to study the evolutionary mechanisms of gene expression.It was done by establishing a relationship between gene expression divergence(GEA:gene expression abundance,GEB:gene expression breadth)and gene evolution rate(Ka,Ks,Ka/Ks(?))during Drosophila embryo development.Ka is non-synonymous nucleotide substitution rate that equals to the ratio of the number of non-synonymous nucleotide substitutions actually occurred between homologous gene pairs to all the non-synonymous nucleotide site.Ks is synonymous nucleotide substitution rate that equals to the ratio of the number of synonymous nucleotide substitutions actually occurred between homologous gene pairs to all the synonymous nucleotide sites.Since synonymous nucleotide substitutions did not cause functional changes in the genes,Ks can be an indicator of neutral selection while Ka/Ks(?)can be used as an indicator of the selective pressure(selective constraint)of the protein coding genes during the evolution.Based on the selection constrain,there are three different selections:when Ka/Ks(?)<1,genes are subjected to negative selection,when Ka/Ks(?)= 1,genes are subjected to neutral selection and when Ka/Ks(?)>1,genes are subjected to positive selection.We calculate Ka,Ks and Ka/Ks(?)of Drosophila homologous gene pairs by YN algorithm,and then study the frequency distribution of Ks and Ka/Ks(?),followed by establishing the relationship of GEA and GEB with Ks and Ka/Ks(?).The main findings are as follows:1.Ks between Drosophila homologs approximately obeys a normal distribution or a mixed normal distribution,so it can be considered as a marker for neutral selection.2.By linear regression analysis,gene expression abundance(GEA)was strongly anti-correlated with selective constraint(Ka/Ks(?)),but weakly correlated with Ks obtained from Drosophila homologous gene pairs between species.GEA was divided into low,medium and high groups and then analyzed with Ks and Ka/Ks(?).GEA(low,medium and high)are also anti-correlated with Ka/Ks(?)but weakly correlated with neutral selection(Ks).3.Gene expression breadth(GEB)was strongly anti-correlated with selective constraint(Ka/Ks(?))and with the incidence of Ka/Ks(co)>1 loci(positive selection markers)obtained from Drosophila homologous gene pairs between species.But GEB was only minimally anti-correlated with neutral selection(Ks).4.Genes with specific expression had much higher ? but not much higher Ks.Therefore,gene expression divergences were strongly anti-correlated with Ka/Ks(?)and positive selection(Ka/Ks(?)>1),but weakly correlated with neutral selection(Ks)during Drosophila embryo development.Thus,the sequence divergences of coding genes are selectively fixed by natural selection instead of neutral selection.Since expression divergences of coding genes are the main reason of the species diversification,the main driving force for regulation of gene evolution for Drosophila embryo development is natural selection rather than neutral selection,supporting Darwin's theory.