Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

The basic process of adaptive evolution by natural selection is the replacement of one allele gene by an- other with a higher fitness in a population. Detecting the adaptive evolution would be helpful for better un- derstanding of bio-evolutionary mechani…     

Detecting positive darwinian selection in brain-expressed genes during human evolution

To understand the genetic basis that underlies the phenotypic divergence between human and non- human primates, we screened a total of 7176 protein-coding genes expressed in the human brain and compared them with the chimpanzee orthologs to identify genes that show evidence of rapid evolution in the human lineage. Our results showed that the nonsynonymous/synonymous substitution (Ka/Ks) ratio for genes expressed in the brain of human and chimpanzee is 0.3854, suggesting that the brain-expressed genes are under functional constraint. The X-linked human brain-expressed genes evolved more rapidly than autosomal ones. We further dissected the molecular evolutionary patterns of 34 candidate genes by sequencing representative primate species to identify lineage-specific adaptive evolution. Fifteen out of the 34 candidate genes showed evidence of positive Darwinian selection in human and/or chimpanzee lineages. These genes are predicted to play diverse functional roles in em- bryonic development, spermatogenesis and male fertility, signal transduction, sensory nociception, and neural function. This study together with others demonstrated the usefulness and power of phy- logenetic comparison of multiple closely related species in detecting lineage-specific adaptive evolu- tion, and the identification of the positively selected brain-expressed genes may add new knowledge to the understanding of molecular mechanism of human origin.     

Statistical analysis on adaptive evolution of SQUA genes in angiosperms

SQUAMOSA (SQUA) subfamily includes important perianth identity genes of MADS-box gene family. SQUA genes of Dendrocalamus latiflorus were sequenced, and phylogenetic form on SQUA genes in angiosperms was analyzed. Relative rate and adaptive evolution after SQUA gene duplication in recent common ancestor of monocots and eudicots were analyzed using the methods of relative rate test, statistic on synonymous and non-synonymous coden substitution sites and likelihood rate test. The results show that both of relative rate and synonymous and non-synonymous coden substitution in eudicot clade are significantly higher than those in monocot clade, and the value of dN/ds uncovered possible positive selective pressure in eudicot clade.     

Selection pressure drives the co-evolution of several lipid metabolism genes in mammals

Adipose tissue is an important endocrine organ and energy supplier.Its physiological effect on the regulation of the energy balance is considered an important factor underlying the evolution of mammals.To test whether the genes controlling lipid metabolism have undergone adaptive molecular change in the evolution of mammals,in this study,we used the orthologous gene sequences of 12 important lipid metabolism proteins (leptin,OB-RL,RXRA,RXRB,RXRG,PPARA,PPARB/D,PPARG,PNLIP,ADIPOQ,LPL and UCP1) from NCBI’s databases.We found evidence that 4 of the corresponding genes (leptin,ADIPOQ,PNLIP and PPARA) have undergone positive selection in their evolutionary history and that most adaptive changes occurred during the evolution of the super-clades Laurasiatheria (placentals) and suborders within Euarchontoglires (primates and rodents).Comparisons across sets of genes showed that in a third of cases,bursts of positive selection,more than would be expected by chance,occurred on corresponding branches.We propose that the positive selection drives adaptive changes in some lipid metabolism genes in or within Laurasiatheria and Euarchontoglires clades.Along with evidence from earlier studies,our results show that co-evolution among interacting lipid metabolism proteins has taken place.     

哺乳动物Gpx 基因家族进化选择和功能分歧研究 (动物科学)

研究哺乳动物谷胱甘肽过氧化物酶基因家族(Gpx)的亲缘关系和进化选择压力性质。从NCBI等网站获取哺乳动物Gpx基因编码区核酸序列和GPX蛋白氨基酸序列,并用MEGA、Clustal构建亲缘关系树,用SignalP和TargetP分析信号肽和亚细胞定位信息;用K estimator和PAML分析其Gpx基因家族进化先后顺序和选择压力;用Diverge分析GPX蛋白家族功能分歧。结果表明,GPX蛋白家族进化中形成两个亚类,其一包括GPX1和GPX2,其二包括GPX3、GPX5和GPX6;各GPX蛋白成员均有高度保守的GPX蛋白家族基序和高度保守的硒代半胱氨酸或半胱氨酸残基,氨基端信号肽分析显示,GPX1蛋白为胞浆线粒体型,其余家族成员均为胞外分泌型;哺乳动物Gpx1基因进化上受到严格的负选择作用,Gpx基因家族成员保守区也受到负选择作用,但用枝位点模型却检出了正选择作用,GPX蛋白家族内存在轻微的功能分歧。哺乳动物GPX蛋白家族的进化上的负选择作用表明其在哺乳动物清除自由基抗氧化方面的关键作用。     

同域培养下大肠杆菌氮、磷含量的进化趋异研究

利用9株具有不同进化背景的大肠杆菌构成5个短期可竞争共存的祖先配对,在限制氮、磷资源的环境下,对5个进化组下6个重复家系进行了约1 100世代的选择实验,考察了这些细菌在进化前后菌体氮、磷质量分数w的变化,并评估了这些性状的趋异程度.研究发现:后代细菌w(氮)的变动范围在13.1%~14.2%,而w(磷)为1.70%~1.95%;不同进化组内,细菌氮、磷含量改变的模式不同;同域后代细菌的趋异模式也并不相同.推测细菌进化本身可能会产生许多独特的性状,连同生态相互作用一起,增加了结果的复杂性,需要在更精细的水平上寻找产生这种结果的原因.     

Adaptation to salinity in mangroves: Implication on the evolution of salt-tolerance

A plant＇s adaptation to its environment is one of the most important issues in evolutionary biology. Mangroves are trees that inhabit the intertidal zones with high salinity, while salt tolerance competence of different species varies. Even congeneric species usually occupy distinct positions of intertidal zones due to differential ability of salt tolerance. Some species have different ecotypes that adapt well to littoral and terrestrial environments, respectively. These characteristics of mangroves make them ideal ecological models to study adaptation of mangroves to salinity. Here, we briefly depict adaptive traits of salt tolerance in mangroves with respect to anatomy, physiology and biochemistry, and review the major advances recently made on both the genetic and genomic levels. Results from studies on individual genes or whole genomes of mangroves have confirmed conclusions drawn from studies on anatomy, physiology and biochemistry, and have further indicated that specific patterns of gene ex- pression might contribute to adaptive evolution of mangroves under high salinity. By integrating all information from mangroves and performing comparisons among species of mangroves and non-mangroves, we could give a general picture of adaptation of mangroves to salinity, thus providing a new avenue for further studies on a molecular basis of adaptive evolution of mangroves.