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.     

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.     

Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited

Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. Recently, it was shown that some CYP isoforms have been subject to positive selection. However, it is unknown whether the highly conserved phase I detoxification enzyme, FMO, has undergone similar positive Darwinian selection. We used maximum-likelihood models of codon substitution, evolutionary fingerprinting, and cross species comparison to investigate the occurrence of adaptive evolution in FMO sequences. We used recent genomic data from a range of species, including vertebrates and invertebrates. We present the evidence for the occurrence of adaptive evolution in mammalian FMO 3, 4, 5, and fugu FMOs but not in mammalian FMO 1, FMO 2, frog FMOs, other fish FMOs and invertebrate FMOs. The sites under adaptive evolution were significantly associated with the insertion domain in mammalian FMO 5. We identified specific amino acid sites in FMOs 3–5 that are likely targets for selection based on the patterns of parallel amino acid change. The most likely role of adaptive evolution is the repair of mutations that permitted optimal NADP+ binding and improved catalytic efficiency. The occurrence of positive selection during the evolution of phase I detoxification enzymes such as FMOs 3–5 and fugu FMO suggests the occurrence of both high selection pressure acting on species within their unique habitats and significant changes in intensity and direction (forms of xenobiotics and drugs) resulting from changes in microhabitat and food.     

语言变异的模因视角分析——从网络语言谈起

模因论将人类文化发展和传承类比于基因的复制、传播,甚至是变异。网络语言的发展和变化正体现了语言模因的自然选择过程。网络语言的传播和流行是语言模因适应信息时代语言交流的结果。     

Scanning for sisnatures of geosraphically restricted selection based on population genomics analysis

Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism （SNP） data from the International HapMap Project. Single locus FsTanalysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of FsT, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection.     

分子进化中性理论的进展

中性理论与达尔文的自然选择进化论有明显的差别。中性论认为在分子水平上覆盖着多数的进化改变，是在连续产生突变时，由于选择中性（即选择相等），使突变得到随机的固定（即小群体内，样本的随机漂变）。还认为在分子水平上，大多数的种内变异（如蛋白质和ＤＮＡ多态）是选择中性或近于中性，它们能够保持在种内是由于突变的产生和随机消失之间的平衡引起的。近年来，ＤＮＡ顺序的研究资料，都有力地支持中性论，如鼠的拟球蛋白基因、鼹鼠的αＡ－晶状体蛋白、流行性感冒Ａ病毒基因，果蝇的核和线粒体基因等。所以，从地球上生命的历史来看，中性进化的改变至少在数量上已超过达尔文自然选择进化的改变。     

Rapid evolution of male reproductive genes in the descent of man

A diverse body of morphological and genetic evidence has suggested that traits pertaining to male reproduction may have evolved much more rapidly than other types of character. Recently, DNA sequence comparisons have also shown a very high level of divergence in male reproductive proteins between closely related Drosophila species, among marine invertebrates and between mouse and rat. Here we show that rapid evolution of male reproductive genes is observable in primates and is quite notable in the lineages to human and chimpanzee. Nevertheless, rapid evolution by itself is not necessarily an indication of positive darwinian selection; relaxation of negative selection is often equally compatible with the DNA sequence data. By taking three statistical approaches, we show that positive darwinian selection is often the driving force behind this rapid evolution. These results open up opportunities to test the hypothesis that sexual selection plays some role in the molecular evolution of higher primates.     

一种基于免疫机理的入侵检测系统模型

在比较了生物免疫系统和入侵检测系统的相似性后,在入侵检测系统中引入了免疫相关机理,建立了一种基于免疫机理的入侵检测系统模型,并对系统模型中涉及的关键技术进行了详细阐述。在模型检测器的生成规则中首次提出并运用了n-r规则,在检测器的生成算法中将克隆选择、否定选择和思维进化相结合,提出了一种全新的算法。理论分析表明该系统模型能有效检测已知和未知的攻击活动,也为解决入侵检测系统的高误报率和缺乏自适应性的难题提供了思路。     

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。     

人类未来的进化问题

人类过去几百万年的进化史,已经充分说明人类作为生物的一分子,同样遵循达尔文的进化理论:物竞天择、适者生存。这种适应环境的自然选择进化在未来的人类进化中还会起作用吗?达尔文的进化理论是否适用于未来的人类?本文将通过详细的分析试图回答这个问题。现在的人类已经知晓设计人类自身生命的蓝图:DNA,并必然会在未来的几百万年中充分利用基因技术服务和改造人类自身,所以适应环境的自然选择进化还会在多大程度上影响人类的进化是一个值得研究的问题。本文中分析了自然进化和人为进化的区别,以及它们各自在人类未来进化中的作用,同时给出了一种未来文明分类标准,提出了智慧文明的局域同步发展说,用这样的学说可以解释为什么人类至今还没有发现外星人。     

Sequence analysis of the Microcystis aeruginosa FACHB-912 phytochrome gene supports positive selection in cyanobacteria

The phytochrome gene from Microcystis aeruginosa FACHB-912,isolated from algal blooms in Taihu Lake in China,was sequenced and found to code for a wavelength transition light receptor protein.The gene was composed of five distinct domains:a PAS fold domain,a GAF domain,a phytochrome domain,a His Kinase A(phosphoacceptor) domain,and a histidine kinase domain.Red-absorbing phytochrome,far-red-absorbing phytochrome,and photoconversion kinetics were monitored via the spectral characteristics of the protein.To detect positive selection,homologous sequences from cyanobacterium phytochrome genes were obtained from GenBank.Potential selective pressure was identified by phylogenetic analysis with maximum likelihood analyses.The frequency of the phytochrome gene being subjected to selective constraints suggests that positive selection is a potentially important mechanism that promotes the evolution of the cyanobacteria phytochrome gene.The sites identified in this study provide targets for further research on the structural-functional role of these residues,and on the correlation with the mechanism of algal blooms.     

浅谈大进化,分子进化与自然选择的关系

本文阐明了自然选择在大进化与分子进化的层次上也起作用.     

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.     

Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes

Recent years have seen rapid growth in amino acid sequence data on globins and nucleotide sequence data on haemoglobin genes and pseudogenes, and cladistic analysis of these data continues to reveal new facets of globin evolution. Our present findings demonstrate: (1) avian and mammalian embryonic alpha genes (pi and xi, respectively) had a monophyletic origin involving an alpha locus duplication about 400 Myr ago soon after the duplication which separated alpha and beta genes; (2) much later in phylogeny, independent beta-gene duplications produced the embryonic rho locus of birds and embryonic epsilon and fetal gamma loci of mammals. This parallels the earlier finding that myoglobins evolved more than once from generalized globin ancestors. Here we support the view that such globin evolution resulted from natural selection acting on mutations in duplicated genes. Thus, our evidence contradicts the neutralist view in which almost all amino acid substitutions in descent to extant globins evaded positive selection.     

基于角色—业绩矩阵的素质模型在跨职能团队成员选拔与配置中的应用

随着市场竞争环境的加剧 ,全球越来越多的企业都在借助跨职能团队这种灵活的组织形式来解决企业所面临的新问题。企业在实践中发现 ,有效地对团队成员进行选拔和配置是团队取得高绩效的关键 ,而应用素质模型进行团队成员的选拔与配置是一个有效的方法 ,同时也是一个新的研究领域。本文首先概述了国内外有关团队绩效与跨职能团队成员配置方面的研究 ,论证了素质模型的意义及其在团队成员选拔与配置中的重要性。并在实践的基础上 ,总结了运用基于角色—业绩矩阵的素质模型进行跨职能团队成员选拔与配置的技术与方法 ,以作为组合团队成员的参考模式     

生态位构建的进化意义及其生态与行为响应

生态位构建是指有机体对局部环境中重要组成成分的建造、修复以及选择的一种能力.重点讨论了生态位构建的进化意义以及由生态位构建引起的生态和行为响应,主要结果包括:(1)生态继承作为与基因继承并行的遗传途径,扩展了对有机体适应性的机理解释;(2)环境变化与有机体对该变化导致的选择压的响应之间存在的时滞能够产生进化惯量与动量;(3)生态位构建与生态系统工程之间存在三个层面的差异;(4)Baldwin效应、自然选择和生态位构建分别体现了有机体对环境变化的中性、被动和主动等三种不同响应;(5)由于生态位构建可取决于学习的过程,因此它可以解释动物行为对策的进化.通过对生态位构建中这些热点问题以及其理论研究不足的讨论,提出了该领域中三个潜在的研究方向.     

Testing the neutral theory of molecular evolution with genomic data from Drosophila

Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/S ratio of polymorphism in Drosophila melanogaster with that of divergence from Drosophila simulans shows that the A/S ratio of divergence is twice as high---a difference that is often attributed to positive selection. But an increase in selective constraint owing to an increase in effective population size could also explain this observation, and, if so, all genes should be affected similarly. Here we show that the difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible. A higher A/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution.     

禾本科植物β-淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析

 β-淀粉酶(beta-amylase,BAM)是一类关键的淀粉水解酶,在禾谷类作物生长发育过程中起着重要作用,与植物多种非生物胁迫响应相关.本研究通过系统发育分析,将水稻、玉米、高粱、谷子、二穗短柄草5 种禾本科植物中共54 个BAM 基因分为10 个同源基因簇,每个同源基因簇都涵盖了这5 个物种,因此推测在禾本科祖先物种中至少含有10 个BAM 基因,并且在禾本科植物分化后没有发生明显的基因丢失事件.基于对编码蛋白质序列的功能分化分析,表明同源基因簇间存在明显的进化速率的差异.对10 个同源基因簇进行了适应性进化检测,发现有3 个同源簇在禾本科植物的进化过程中经历了适应性进化.此外,对水稻β-淀粉酶的表达分析发现,一些β-淀粉酶具有组织特异性表达特征,并且至少有5 个水稻的β-淀粉酶基因具有受到非生物逆境的胁迫而表现出不同的表达模式.本研究结果为进一步探讨禾本科BAM 基因的生物学功能提供了一定的理论基础.     

改进的mRmR特征选择方法在人体行为识别中的应用

在基于惯性传感器人体行为识别的研究中,特征选择的作用是挑选相关特征,以提高分类性能,去除冗余特征以降低计算复杂度。针对传统的过滤式特征选择方法仅使用一种相关度量系数筛选特征效果不佳的问题,提出一种改进的基于最大相关与最小冗余(mRmR)准则的特征选择方法。该方法在基于mRmR准则下,采用多种相关度量系数融合的方式,在考虑分类类别的条件下,分析待挑选特征与已选特征间的相关性对特征筛选可能产生的积极影响,以去除部分冗余、不相关特征,进而得到初选特征子集;然后利用二进制数对筛选后的特征编码,通过遗传算法搜索最优或次优特征子集。分别使用SVM和KNN分类器对7种日常行为进行分类。实验结果表明,与其他几种方法相比,该方法对实验分类的7种行为有最高的总体平均识别精度,通过SVM和KNN分类的各行为总体平均识别精度分别达到了97.02%和95.73%,与传统的mRmR方法相比,分别提高了13.72%和9.92%。     

探寻语言模因对英汉语符的解构

宣扬主体的消散、意义的延异、能指的自由、强调语言与思想的自由嬉戏是解构主义的基本特征。而语言模因理论是建立在达尔文进化理论基础上的新理论,也被广泛应用于语言学研究的各个领域。本文试图用语言模因的基本理论来解构英汉语符转换的主要途径与策略,尝试重新构建基于语言模因理论的英汉语符转换体系。