DNA水平上检测正选择方法的研究进展

达尔文的自然选择学说指出, 自然选择作用是物种进化的主要因素。而1968年Kimura提出的中性进化学说认为中性突变和随机漂变才是进化的主要动力。在接下来的30多年时间中, 人们尝试从各种角度来检测自然选择是否存在。随着DNA测序技术的发展, 大量的DNA序列信息为检验自然选择提供了丰富的数据。因为自然选择会影响DNA变异模式, 所以可以通过分析现有的DNA样本来推断过去是否发生了自然选择。另一方面, 种群历史等因素也会影响到DNA变异模式, 因此会对自然选择的检测产生干扰。文章主要介绍了中性检验基本的概念, 全面回顾了一些经典的检验方法, 并着重介绍了近几年新发展出的研究方向。     

脊椎动物线粒体DNA的进化遗传学

近年来,在分子进化遗传学研究中又产生出一个新的生长点,这就是线粒体DNA(mtDNA)的进化遗传学研究。因为mtDNA结构简单,与拥有4×10~8到4×10~(11)个碱基对的多细胞动物的核基因组相比,比其最小者小25000倍;在不同物种间,mtDNA上的基因成分相对稳定,很少受到序列重排的影响;另一方面,mtDNA又具有广泛的种内和种间多态性,且为母性遗传,在亲缘关系相近的物种间其进化速度比核基因快,因而它为从分子水平上研究种群遗传学和进化遗传学提供了理想的研究对象。     

人类胎儿的性别选择属自然选择

现代人类的祖先在数百万年的演化史中,不断为适应自然,逐渐地向现代人进化。     

一种在核苷酸水平检测自然选择的新方法

非编码区序列在基因表达调控中起着重要作用,但其在进化过程中是否受到选择作用一直较难检测。最近有一些研究使用平均的核苷酸替换速率与中性序列的核苷酸替换速率的比值(ω)作为检测非编码区总体受选择作用的指标;但是对于非编码区而言,了解具体哪些核苷酸受到选择作用更具有意义。我们借鉴Nielsen&Yang(1998)检测单个氨基酸位点是否受选择作用的思路,在最大似然法的模型下,提出一种在核苷酸位点水平上对自然选择作用检测的方法。本方法能够检测在进化过程中对功能分化有重要贡献的核苷酸位点,包括编码和非编码区。将此方法应用于熟知的受到正选择作用的蛋白编码基因序列(HIV-1包装蛋白基因编码区),均能够检测到那些已知的受到正选择的核苷酸(密码子)位点,说明此方法可以有效地在核苷酸位点水平检测选择作用;又将此方法应用于非编码区(CTGF基因5′UTR),也得到了良好的结果。     

植物种群分子进化中对生境的适应——对荒漠植物遗传多样性研究结果的初步分析

长期以来,自然选择理论与中性理论对生物分子进化中的环境适应机理存在着激烈争论。目前,在植物种群分子进化中对生境适应的研究中正面临着一些难题：中性突变是分子水平进化的唯一原因,自然选择发挥主要作用的适应性进化是否存在于分子水平,选择与中性两种学说两种机制完全不同,如何才能将两者联系和统一起来,部分学者利用建立各种模型来描述自然选择对分子标记位点以及连锁序列的直接作用,如生态位宽度变异假设等。本研究小组以新疆阜康荒漠植物为研究对象,通过对两种重要荒漠植物遗传多样性的研究,分析两种植物各亚种群不同生境的生态因子与其遗传变异的关系,讨论生态位宽度变异假设,揭示遗传变异的产生与维持。中性论者与选择论者都试图解释生物环境适应与分子变异之间的关系。中性论和选择论是反映进化的两个侧面,它们不是绝对的,可以相互转化。     

“中性说”是非达尔文主义的吗？

“中性说”是非达尔文主义的吗？马刚（第四军医大学生物教研室,西安７１００３２）木村资生等人提出的“中性说”因直接违反了达尔文主义的核心一“自然选择说”,而被认为是作达尔文主义的．并由此引起了一场反对和维护达尔文主义的长时期的论战。迄今,论战仍在继续。...     

金丝猴属的DNA序列变异及进化与保护遗传学研究

金丝猴的分类及系统发育存在许多争议。本文测定了２只川金丝猴、８只滇金丝猴、１只越南金丝猴和１只灰叶猴的２５３ｂｐ的线粒体细胞色素ｂ基因的序列。其中４７个位点（１９％）检出变异。我们采用简约法、最大似然法和距离法构建了一系列的分子系统树,得到相同的拓扑结构,从而可能在分子水平澄清了金丝猴属的系统发育。结果表明,云南金丝猴与越南金丝猴间的关系较与川金丝猴的为近。金丝猴属的分化大约发生在２～６百万年以前。这３种金丝猴均是独立的种,且都应归入金丝猴属。对８只来自野外的滇金丝猴（其中包括了昆明动物研究所圈养群体的所有６只创立者）的非损伤性遗传分析提示,编号为ＹＫ２的母猴是维持该圈养群体遗传多样性的关键猴。我们建立的这种非损伤性遗传分析方法广泛适用于珍稀濒危动物的遗传多样性及遗传管理研究。     

真核生物DNA的进化

真核生物ＤＮＡ的进化刘振山（河北省张家口市教委科学研究室０７５０３１）生物在进化过程中的演变都是由ＤＮＡ的自发改变开始的,当生物从简单形式进化到较复杂的形式后,基因组无论是在遗传物质ＤＮＡ的含量上,还是在基因的数目上都有所扩大,遗传物质的这种量和质的...     

鱼类线粒体DNA及其在分子群体遗传研究中的应用

鱼类是脊椎动物亚门中种属数量最多的类群,分布广泛,起源复杂,拥有丰富的遗传多样性.多种自然和人为因素对鱼类遗传资源存在不同程度的作用,对鱼类生存和进化有重要影响.采用分子手段探讨鱼类遗传资源现状,可为遗传育种、鱼类进化研究和遗传资源保护等提供一定科学依据.以鱼类线粒体DNA(mtDNA)为代表的分子标记技术已被用于研究鱼类群体遗传结构及其与影响因素间的关系.本文综述了鱼类mtDNA的结构特征及其在鱼类分子群体遗传研究中的应用,对了解和运用mtDNA等分子标记研究鱼类群体遗传具有一定参考价值.     

动物线粒体DNA在进化遗传学研究中的应用

介绍了进化遗传学研究的主要内容、基本的研究方法以及线粒体的结构和遗传特点;综述了近年来线粒体DNA在进化遗传研究上的主要应用情况。     

Population Level Causation and a Unified Theory of Natural Selection

Sober (1984) presents an account of selection motivated by the view that one property can causally explain the occurrence of another only if the first plays a unique role in the causal production of the second. Sober holds that a causal property will play such a unique role if it is a population level cause of its effect, and on this basis argues that there is selection for a trait T only if T is a population level cause of survival and reproductive success. Sterelny and Kitcher (1988) claim against Sober that some traits directly subject to selection will not satisfy the probabilistic condition on population level causation. In this paper I show that Sober has the resources to resist the Sterelny-Kitcher complaint, but I argue that not all traits that satisfy the probabilistic condition play the required unique role in the production of their effects.     

Addressing Undergraduate Student Misconceptions about Natural Selection with an Interactive Simulated Laboratory

Although evolutionary theory is considered to be a unifying foundation for biological education, misconceptions about basic evolutionary processes such as natural selection inhibit student understanding. Even after instruction, students harbor misconceptions about natural selection, suggesting that traditional teaching methods are insufficient for correcting these confusions. This has spurred an effort to develop new teaching methods and tools that effectively confront student misconceptions. In this study, we designed an interactive computer-based simulated laboratory to teach the principles of evolution through natural selection and to correct common student misconceptions about this process. We quantified undergraduate student misconceptions and understanding of natural selection before and after instruction with multiple-choice and open-response test questions and compared student performance across gender and academic levels. While our lab appeared to be effective at dispelling some common misconceptions about natural selection, we did not find evidence that it was as successful at increasing student mastery of the major principles of natural selection. Student performance varied across student academic level and question type, but students performed equally across gender. Beginner students were more likely to use misconceptions before instruction. Advanced students showed greater improvement than beginners on multiple-choice questions, while beginner students reduced their use of misconceptions in the open-response questions to a greater extent. These results suggest that misconceptions can be effectively addressed through computer-based simulated laboratories. Given the level of misconception use by beginner and advanced undergraduates and the gains in performance recorded after instruction at both academic levels, natural selection should continue to be reviewed through upper-level biology courses.     

New Methods for Detecting Positive Selection at Single Amino Acid Sites

Inferring positive selection at single amino acid sites is of particular importance for studying evolutionary mechanisms of a protein. For this purpose, Suzuki and Gojobori (1999) developed a method (SG method) for comparing the rates of synonymous and nonsynonymous substitutions at each codon site in a protein-coding nucleotide sequence, using ancestral codons at interior nodes of the phylogenetic tree as inferred by the maximum parsimony method. In the SG method, however, selective neutrality of nucleotide substitutions cannot be tested at codon sites, where only termination codons are inferred at any interior node or the number of equally parsimonious inferences of ancestral codons at all interior nodes exceeds 10,000. Here I present a modified SG method which is free from these problems. Specifically, I use the distance-based Bayesian method for inferring the single most likely ancestral codon from 61 sense codons at each interior node. In the computer simulation and real data analysis, the modified SG method showed a higher overall efficiency of detecting positive selection than the original SG method, particularly at highly polymorphic codon sites. These results indicate that the modified SG method is useful for inferring positive selection at codon sites where neutrality cannot be tested by the original SG method. I also discuss that the p-distance is preferable to the number of synonymous substitutions for inferring the phylogenetic tree in the SG method, and present a maximum likelihood method for detecting positive selection at single amino acid sites, which produced reasonable results in the real data analysis.     

Natural hierarchy emerges from energy dispersal

Hierarchical organization of ‘systems within systems’ is an apparent characteristic of nature. For many biotic and abiotic systems it is known how the nested structural and functional order builds up, yet the general principle why matter evolves to hierarchies has remained unfamiliar to many. We clarify that increasingly larger integrated systems result from the quest to decrease free energy according to the 2nd law of thermodynamics. The argumentation is based on the recently derived equation of motion for natural processes. Hierarchically organized energy transduction machinery emerges naturally when it provides increased rates of energy dispersal. Likewise, a hierarchical system will dismantle into its constituents when they as independent systems will provide higher rates of entropy increase. Since energy flows via interactions, decreasing strengths of interactions over increasingly larges lengths scales mark natural boundaries for nested integrated systems.     

悬钩子属DNA条形码通用序列的初步筛选

为了建立悬钩子属（Rubus）植物的DNA条形码分子鉴定技术,筛选获得适用于悬钩子属植物的通用条形码序列。该研究基于GenBank数据对ITS、ITS2、matK、rbcL、trnH-psbA、trnL-trnF 6个DNA条形码序列进行了遗传变异、barcoding gap、建树等评估分析。结果显示,trnH-psbA、matK、rbcL、rtnL-trnF的种内变异与种间变异差异较大,变异分辨率分别为97.32%、83.33%、79.07%、64.95%,存在较大的barcoding gap;NJ一致树分析显示,matK的单系性比例最高（67%）,其次为trnH-psbA（64%）,rtnL-trnF（43%）,rbcL（30%）。结果表明,悬钩子属植物的matK与trnH-psbA序列种内变异与种间变异差异较大,能较好地区分不同物种,具有较大的鉴定潜力。建议将matK和trnH-psbA作为悬钩子属植物鉴定的核心条形码序列,rtnL-trnF、rbcL作为辅助条形码序列。     

An Evolutionary Footprint of Age-Related Natural Selection in Mitochondrial DNA

By comparing mtDNA sequences between different orders of mammals, we show that both longevity and generation time are significantly correlated with the nucleotide content of the mtDNA. Specifically, there is a positive correlation between generation time and mt GC content. This correlation is repeated, at a finer evolutionary scale, within the primates. Moreover, a comparison of human and chimpanzee mtDNAs shows that the effect has been very pronounced during the short evolutionary period since the divergence of these two species, with human mtDNA showing a GC-biased pattern of substitution at the variable sites. In addition to these DNA sequence patterns, comparisons between the human and the chimp mt protein sequences also revealed a surprisingly high substitution rate for threonine residues, resulting in a reduction of threonine in the human mt proteome. These patterns of both DNA and protein evolution can be explained by a balance between AT-biased mutational pressure and age-related purifying selection.     

大肠杆菌DNA聚合酶Ⅰ的“碱基选择”作用

用双脱氧核苷酸研究了大肠杆菌ＤＮＡ聚合酶Ⅰ的Ｋｌｅｎｏｗ片段的“碱基选择”作用．当引物末端为３’ＯＨ时,Ｍｎ２＋代替Ｍｇ２＋对ｄＮＴＰ的Ｋｍ影响不大,而使ｄｄＮＴＰ的Ｋｉ大大降低,非配对的ｄｄＮＴＰ仍无抑制作用。当引物末端为ｄｄＮＭＰ且与模板配对时是ＤＮＡ合成的抑制剂,与模板配对的下一个ｄＮＴＰ可增强这一抑制作用,Ｍｎ２＋代替Ｍｇ２＋使ｄＮＴＰ的诱导作用大大增强而ｄｄＮＴＰ无诱导作用。这些结果表明引物末端对于酶选择核苷酸起着重要作用,ＤＮＡ聚合酶Ⅰ选择核苷酸的过程应是个有序的构象变化的过程。下一互补核苷酸的结合抑制３＇→５＇外切活性对引物末端ｄｄＮＭＰ的水解作用为此提供了又一证据。     

Polite DNA: Functional density and functional compatibility in genomes

Summary Certain as yet poorly defined functions of DNA appear to involve collectively domain-sized sequences. It is proposed that most sequence segments within a domain may be either functionally superfluous or instrumental, depending on how many related sequences are present in the domain. When redundant and functionally dispensable, such DNA segments presumably still have to conform to compositional or sequence-motif patterns that characterize the domain. In its relations with neighboring sequences, such DNA is required to be polite. Polite DNA is DNA that, without being crucially involved in function, is subject to constraints of conformity and, through its base composition, respects a function for which it is not required. This concept is developed by contrasting the distribution of specific and general functions over DNA with this distribution as found in proteins and by distinguishing functional compatibility from pivotal functionality. The sequence constraints to which heterochromatin as well as, apparently, long interspersed repetitive sequences are known to be subject seem to imply that DNA, even when it does not carry out a pivotal function, is indeed, at the very least, required to be polite.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

白山原麝国家级自然保护区獐春夏生境选择

生境与动物个体密切相关,生境中元素的不同影响着动物个体对不同生境的选择。2018年5-7月和2019年3-4月在吉林省白山原麝国家级自然保护区对獐（Hydropotes inermis）的春夏季生境选择进行了研究,共记录利用样方104个（春季53个,夏季51个）,对照样方85个（春季46个,夏季39个）。利用卡方检验对植被类型、优势植物、坡位、坡向4种非数值型环境因子进行分析,结果表明春季和夏季獐对这4种环境因子的选择均具有显著性差异,偏好选择以青蒿（Artemisia carvifolia）为优势植物,位于中坡位,坡向为阳坡的草地生境活动。利用独立样本T检验和Mann-Whitney U检验对海拔、人为干扰距离、水源距离、草本覆盖度、优势草本高度、隐蔽级、坡度7种数值型环境因子进行分析,结果表明春季和夏季獐均偏好选择隐蔽级较高（春季30.189±14.609,夏季62.745±29.737）、优势草本高度较高（春季87.359±16.190,84.510±29.618）、坡度较缓的生境（春季14.245±3.721,13.333±5.260）活动。此外,资源选择函数模型对獐的春季和夏季的生境选择预测正确率均大于90%,表明该模型可以较好地预测獐的生境选择。白山原麝国家级自然保护区獐种群数量较小,适宜性栖息地面积较少,应加强对其种群及适宜性生境的保护。