自然选择和中性说

自然选择学说是达尔文进化论的核心理论,也是现代达尔文主义的主要依据。达尔文认为：自然选择即指适者生存,不适者被淘汰的现象。自然选择是通过积累微小的有利变异而促进生物进化。本世纪三、四十年代兴起的现代达尔文主义,将群体遗传学研究成果运用于进化理论,重申了达尔文自然选择学说在生物进化中的主导地位,并用选择的新概念解释了达尔文进化理论中的许多难点。他们认为,生物在进化过程中会产生许多有害的突变,自然选择淘汰对生存有害突变,而一些对生存有利的突变则在自然选择过程中得到扩散,增加了基因频率,促进了物种分化…     

点突变积累与分子进化

认为木村资生等人用分子进化的中性说向综合达尔文进化说提出了挑战，但在许多方面他们又未能摆脱综合进化说的概念框架和理论范式。进而从对分子进化有更深层意义的复制群体中的基因点突变特征入手，初步提出了一个分子进化的点突变积累模型，并以此解释了分子进化钟的成因，指出了现存物种高低分布与物种历史进化之间在分子水平上的渊源关系。     

试评“非达尔文主义进化”理论

日本遗传学家木村资生于1968年提出了分子进化的中性理论,它的中心思想是:“从分子水平上讲,绝大多数的演变和种内变异,都不是由选择引起的,而是由选择上等价的突变基因的随机漂移引起的”,由于木村否认达尔文的自然选择对分子进化的作用,所以,人们通常把他的“中性理论”称为“非达尔文主义进化”理论。     

生物进化论的由来和发展

本文讨论了生物进化论的发生及其随着细胞遗传学、群体遗传学和分子遗传学相继兴起而在细胞水平、群体的基因水平及分子水平上得到迅速发展的历程。并提及在分子水平上出现的“中性突变漂变学说”和化石真正应用于进化研究后提出的“间断平衡学说”对达尔文式进化所构成的挑战。     

点突变积累与分子地化

认为木村资生等人用分子进化的中性谱向综合达尔进化说提出了挑战，但在许多方面他们又未能摆脱综合进化谱的概念框架和理论范。革而从对分子进化有更深层意义的复制群体中的基因点突特征入手，实手提出了一个分子进化的点空变积累模型，并以解释了分子进化钟的成因，指出了现存物种高低分布与物种历史是化之间在分子水平上的渊源关系。     

试论“选择说”与“中性说”的辩证统一

“选择说”是达尔文在1859年创立的以自然选择为基础的进化学说。它的诞生曾对近代自然观的变革产生了重大的影响,成为马克思主义哲学的一大自然科学基石。1968年,日本的遗传学家木村资生提出了“中性突变漂移说”(简称“中性说”),认为进化的主导力量是中性突变,而这些中性突变不受自然选择的制约。由此产生了“选择说”与“中性说”的激烈论战。在这场争论中,一种观点认为非达尔文主义的出现标志着达尔文主义的终结,否认了自然选择在进化中的作用;另一种观点则认为非达尔文主义     

自然选择质疑

 当代对达尔文进化 论的争论几乎是全方位的,尽管当今达尔文主义者的立场和论调与原先的达尔文的进化论已有很大出入,比如：现代综合进化论对自然选择的创造性作用的突出强调、间断平衡论对达尔文随机渐变理论的重新解释,等等,但现代达尔文主义者对作为达尔文进化论核心的自然选择理论一般都是坚持的。本文试图立足于现代自然科学发展的前沿,对这一理论做出再反思。一、人工类比之误与“创造性”虚设达尔文的进化机制实质上可以概括为两个过程,第一步是随机的遗传变异。即进化根源于个体中随机的遗传性变异（突变）的积累。这些随机突变被看作是左右生物存在的生命的物理决定因素,也被看作是所有进化新特性的源泉。     

自然选择质疑

当代对达尔文进化 论的争论几乎是全方位的,尽管当今达尔文主义者的立场和论调与原先的达尔文的进化论已有很大出入,比如：现代综合进化论对自然选择的创造性作用的突出强调、间断平衡论对达尔文随机渐变理论的重新解释,等等,但现代达尔文主义者对作为达尔文进化论核心的自然选择理论一般都是坚持的。本文试图立足于现代自然科学发展的前沿,对这一理论做出再反思。一、人工类比之误与“创造性”虚设达尔文的进化机制实质上可以概括为两个过程,第一步是随机的遗传变异。即进化根源于个体中随机的遗传性变异（突变）的积累。这些随机突…     

基因表达式编程中性突变机理分析

针对基因表达式编程(GEP)的进化模型,其基因组存在不被表达的中性区,研究了GEP中性区在进化中的作用,指出GEP基因存在中性区域,进化进程中必存在中性突变,分析了GEP的基因表示的中性区域存在的特点;通过控制基因长度和基因数量技术,调控中性区的大小和数量,讨论了GEP的中性区域对进化的作用.实验表明,GEP中性区域保持50%～80%,能保证较高的挖掘成功率.     

P48L和D74N突变影响P16基因功能

应用ＰＣＲ技术，对Ｐ１６抑癌基因进行体外定突变。在Ｐ１６ｃＤＮＡ中引入第４８位密码子ＣＣＧ（Ｐｒｏ）→ＣＴＧ（Ｌｅｕ）和第７４位密码子ＧＡＣ（Ａｓｐ）→ＡＡＣ（Ａｓｎ）突变，构建了ｐ１６－Ｐ４８Ｌ和ｐ１６－Ｄ７４Ｎ突变体，并把它们导入纯合缺失Ｐ１６基因的人肺癌细胞株Ｈ４６０。     

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.     

Adaptive protein evolution at the Adh locus in Drosophila

Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.     

The molecular clock runs more slowly in man than in apes and monkeys

The molecular clock hypothesis postulates that the rate of molecular evolution is approximately constant over time. Although this hypothesis has been highly controversial in the past, it is now widely accepted. The assumption of rate constancy has often been taken as a basis for reconstructing the phylogenetic relationships among organisms or genes and for dating evolutionary events. Further, it has been taken as strong support for the neutral mutation hypothesis, which postulates that the majority of molecular changes in evolution are due to neutral or nearly neutral mutations. For these reasons, the validity of the rate constancy assumption is a vital issue in molecular evolution. Recent studies using DNA sequence data have raised serious doubts about the hypothesis. These studies provided support for the suggestion made from immunological distance and protein sequence data that a rate slowdown has occurred in hominoid evolution, and showed, in agreement with DNA hybridization studies, that rates of nucleotide substitution are significantly higher in rodents than in man. Here, rates of nucleotide substitution in rodents are estimated to be 4-10 times higher than those in higher primates and 2-4 times higher than those in artiodactyls. Further, this study provides strong evidence for the hominoid slowdown hypothesis and suggests a further rate-slowdown in hominoid evolution. Our results suggest that the variation in rate among mammals is primarily due to differences in generation time rather than changes in DNA repair mechanisms. We also propose a method for estimating the divergence times between species when the rate constancy assumption is violated.     

DNA中性标记反映的非随机亲缘地理格局——以东亚植物物种为例

基于DNA中性分子标记的亲缘地理学研究却多获得非随机的空间遗传格局,与气候、环境因子或者表型性状具有很好的一致性,这种非随机格局是如何形成和维持的.本文以东亚植物物种为例,分析了其空间遗传格局的非随机性及其一般特点,讨论了其可能的成因.冰期避难所隔离、物种分布区变化等中性过程是目前大多研究采用的解释,然而仍有部分线索暗示可能存在自然选择导致的适应性进化.我们认为这种基于"中性"分子标记的亲缘地理研究对未来适应性进化研究具有重要的启发作用,提出可能的一般研究框架,并展望了二代测序技术在未来适应性进化研究中的作用.     

Positive Darwinian selection in human population: A review

This paper reviews a large number of genes under positive Darwinian selection in modern human populations, such as brain development genes, immunity genes, reproductive related genes, percep- tion receptors. The research on the evolutionary property of these genes will provide important insight into human evolution and disease mechanisms. With the increase of population genetics and com- parative genomics data, more and more evidences indicate that positive Darwinian selection plays an indispensable role in the origin and evolution of human beings. This paper will also summarize the methods to detect positive selection, analyze the interference factors faced and make suggestions for further research on positive selection.     

Investigation of genetic linkage between myosin and actin genes using an interspecific mouse back-cross

The introduction of cloned probes to follow the segregation of DNA restriction fragment length polymorphisms (RFLPs) has led to a revival of mendelian genetics in attempts to map the human genome. In the mouse, however, it has often proved difficult to detect an RFLP with a DNA probe between different inbred strains of the laboratory mouse. To circumvent this problem, we have used two species, Mus musculus domesticus and Mus spretus which interact as sympatric species but can be interbred under laboratory conditions. Because of the relative evolutionary distance between these species, they exhibit polymorphism at many more loci than do different strains of the usual M. m. domesticus laboratory mouse. This is also observed at the DNA level when the sizes of restriction fragments encoding a specific gene are compared. We have used these RFLPs between M. m. domesticus and M. spretus to follow the segregation of genes encoding different isoforms of myosin alkali light chains in the backcross progeny between these species and to compare this with that of other contractile protein genes. No linkage between these genes was observed.     

土壤细菌和真菌群落的物种续存模式对扰动的响应

通过研究物种存活概率和局域多度间的关系, 对微生物群落动态是否符合中性假说进行检验. 使用野外采集的土壤进行土壤微宇宙实验,微宇宙经受了稀释扰动,剔除一些非常稀有的物种. 微宇宙经过恢复培养后, 用454高通量焦磷酸测序方法分别对土壤细菌16SrRNA 基因和真菌18SrRNA 基因进行测序, 检测多度≥1的物种, 从而探究细菌和真菌物种组成相对于源土壤发生的变化. 结果发现: 恢复生长过程中细菌和真菌物种丰富度都显著降低(>50%); 受到扰动的微宇宙恢复生长以后, 土壤细菌和真菌物种存活概率与其在源土壤中的初始相对多度之间呈正相关, 这个结果符合中性假说的预测,即最初多度较高的物种平均灭绝概率较低.      

Dynamic response of Permian brachiopod communities to long-term environmental change

The fossil record preserves numerous natural experiments that can shed light on the response of ecological communities to environmental change. However, directly observing the community dynamics of extinct organisms is not possible. As an alternative, neutral ecological models suggest that species abundance distributions reflect dynamical processes like migration, competition, recruitment, and extinction. Live-dead comparisons suggest that such distributions can be faithfully preserved in the rock record. Here we use a maximum-likelihood approach to show that brachiopod (lamp shell) abundance distributions from four temporally distinct ecological landscapes from the Glass Mountains, Texas (of the Permian period), exhibit significant differences. Further, all four are better fitted by zero-sum multinomial distributions, characteristic of Hubbell's neutral model, than by log-normal distributions, as predicted by the traditional ecological null hypothesis. Using the neutral model as a guide, we suggest that sea level fluctuations spanning about 10 Myr altered the degrees of isolation and exchange among local communities within these ecological landscapes. Neither these long-term environmental changes nor higher-frequency sea level fluctuations resulted in wholesale extinction or major innovation within evolutionary lineages.     

The gene encoding the T-cell receptor alpha-chain maps close to the Np-2 locus on mouse chromosome 14

Serological and molecular genetic analyses of T-cell clones have shown that the T-cell antigen receptor apparently comprises two glycosylated, disulphide-linked polypeptide chains (alpha and beta), both of which span the cell membrane. Cloning of the genes encoding the two chains from mouse and human DNA has shown that the alpha- and beta-chains are composed of variable (V) and conserved (C) regions in agreement with peptide mapping data. Gene segments encoding variable and conserved domains of the beta-chain have been identified and undergo rearrangements during T-cell differentiation. The genes encoding the alpha-chain, so far described at the level of complementary DNA clones, also identify DNA rearrangements. Thus, the genes encoding the T-cell receptor show the same structure and dynamic behaviour as immunoglobulin genes, indicating that the two gene families belong to the same supergene family; this evolutionary relationship is supported by the fact that the genes encoding the beta-chain of the T-cell receptor are closely linked to immunoglobulin kappa light-chain genes on chromosome 6 in mouse. In man, however, the beta genes map to chromosome 7 (ref. 14) whereas the kappa-chain genes are located on chromosome 2, indicating that linkage between the two gene families is not needed for proper expression. Here we describe genomic clones encoding the constant portion of the T-cell receptor alpha-chain and map the gene to chromosome 14 in mouse, close to the gene for purine nucleoside phosphorylase (Np-2) which, in man, has been associated with T-cell immunodeficiencies.     

一种有效的基于4D图形表示法的DNA序列相似性比较方法

研究了一种有效地DNA序列相似性比较方法,在将每条DNA序列平均分成两个片段的基础上,采用4D图形表示法构建了每个片段的中心几何点重现模型,以此为基点,建立了DNA序列间的相似性与不相似性的欧氏距离比较法.最后,11个物种球蛋白基因的第一个外显子的DNA序列比较的结果验证表明:欧氏距离越小,其相似性越大,在进化上越趋于同源性;反之,欧氏距离越大,则物种差异性越大.实验结果表明,通过这样的方式可以有效避免信息的丢失,结果更具有统计显著性,并更有效地反映位置信息,可以对DNA序列的研究提供良好的支撑作用.