阿米巴-细菌互作：进化、生态与环境效应

阿米巴是原生动物的主要类群,是陆地和水生生态系统的关键组成部分。阿米巴与细菌之间有着密切而复杂的相互作用。一方面,阿米巴通过捕食直接影响细菌群落与多样性,增强细菌活性。另一方面,细菌也进化出抵抗捕食的机制来抵抗甚至感染阿米巴,反向影响阿米巴的生长和多样性。近年来,阿米巴-细菌互作的研究开始受到了广泛关注。本文总结了阿米巴-细菌互作的进化历史、生态关系(捕食、偏利共生、寄生和互利共生)以及其对环境的潜在影响,旨在更好地理解阿米巴-细菌互作这一研究领域,为其他原生动物-微生物之间的研究提供新的思路,也为探究宿主-微生物互作的机制提供参考。     

细菌比较基因组学和进化基因组学

通过比较不同细菌基因组间差异性与相似性,进而深入研究其分子机理,最终与其表型特征联系起来,是为比较基因组学;不同细菌经过长期进化,其基因组在结构与功能上存在着明显的分化,并构成表型进化的遗传基础,大量细菌全基因组测序的完成,细菌进化基因组学应运而生;以比较基因组学为研究手段,细菌进化基因组学可从基因组水平深入认识物种分化、生境适应、毒力进化、耐药性产生蔓延等表型进化过程。     

一株含有5个原噬菌体的单增李斯特菌比较基因组分析

单增李斯特菌是一种重要的人畜共患病原菌,对食品安全和人类健康造成了严重威胁,但现阶段对其进化规律的研究仍相对较少。本研究运用Illumina测序技术对一株中国单增李斯特菌WaX12的基因组进行了测定,并通过比较基因组学分析了该菌的微进化规律。结果表明:WaX12的基因组与Finland 1998相似度最高,但两者基因组间存在135个基因的差异,主要集中在WaX12的原噬菌体上。进一步分析可知,WaX12的基因组携带5个原噬菌体,除原噬菌体1外,其余4个原噬菌体均未存在于Finland 1998中。原噬菌体3和原噬菌体5来源于其他单增李斯特菌的基因组,而原噬菌体2和原噬菌体4则分别来自于大肠杆菌和粪球菌。由此可见,原噬菌体是该单增李斯特菌微进化的主要原因,而这种微进化的发生不仅限于同一种属的细菌之间,还可能源于不同种属细菌间的基因转移。     

细菌-噬菌体对抗性共进化研究进展 *

共进化现象在自然界中普遍存在。细菌和细菌的天敌噬菌体之间的对抗是一场持久战,细菌-噬菌体系统是研究共进化的模式材料。目前关于细菌-噬菌体对抗性共进化的机制有两种公认的模型,即GFG模型和MA模型,对应于两种模式,即ARD模式和FSD模式;主要采用Time-Shift Assays方法测定细菌-噬菌体的对抗性共进化动力学模式。长尾噬菌体是有尾噬菌体中最大的家族。目前关于细菌-噬菌体系统共进化的研究主要集中在短尾和肌尾噬菌体与其宿主之间,而细菌-长尾噬菌体共进化的研究报道较少。     

细菌-噬菌体对抗性共进化研究进展

共进化现象在自然界中普遍存在。细菌和细菌的天敌噬菌体之间的对抗是一场持久战,细菌-噬菌体系统是研究共进化的模式材料。目前关于细菌-噬菌体对抗性共进化的机制有两种公认的模型,即GFG模型和MA模型,对应于两种模式,即ARD模式和FSD模式;主要采用TimeShift Assays方法测定细菌-噬菌体的对抗性共进化动力学模式。长尾噬菌体是有尾噬菌体中最大的家族。目前关于细菌-噬菌体系统共进化的研究主要集中在短尾和肌尾噬菌体与其宿主之间,而细菌-长尾噬菌体共进化的研究报道较少。     

CRISPR-Cas系统与细菌和噬菌体的共进化

细菌在适应噬菌体攻击的过程中,进化了多种防御系统,噬菌体在细菌的选择压力下,也在不断进化反防御策略,双方的这种进化关系与发生机制一直尚不完全清楚。近年在细菌和古细菌中发现一种新的免疫防御系统,即CRISPR-Cas(clustered regularly interspaced short palindromic repeats-CRISPR-associated system)系统。在对其功能和作用机制深入研究的同时,也不断地揭示了细菌和噬菌体之间的共进化关系。为此,文章在介绍原核细胞中CRISPR-Cas系统介导的免疫机制基础上,重点综述了CRISPR系统在细菌和噬菌体进化中的作用。     

细菌基因组进化的分子策略

论述了细菌基因组进化的 4个分子策略 :点突变 ,基因组内重排 ,基因水平转移 ,基因缺失。从经典的达尔文进化论角度探讨了细菌基因组进化与表型进化的关系。     

乳酸菌微进化的研究进展

摘要:乳酸菌是食品工业中重要的微生物,乳酸菌微进化研究有助于深入解析其生物学功能与机制。随着分子生物学的发展,多位点序列分型(Multi-locus Sequence Typing,MLST)及基因组重测序(Whole-genome resequencing)等技术手段应运而生,使得从分子水平上阐述乳酸菌的系统发育和种群进化关系成为可能。MLST已被广泛用于乳酸菌遗传多样性和种群结构等微进化研究中,近期,测序成本的锐减使全基因组测序技术在乳酸菌微进化研究中的优势日益突显。本文对乳酸菌微进化的理论基础、研究方法和意义进行了阐述,并介绍了全基因组测序技术在乳酸菌微进化方面的应用,旨在为乳酸菌微进化分析研究提供新思路。     

5_S rRNA分子进化的研究

截至目前为止,人们已测出了300余种5SrRNA分子的一级结构。本文在其中选择了具有代表性的脊椎动物、无脊椎动物、原生动物以及植物和细菌等共130个种的5SrRNA一级结构,通过运用分子进化研究中的“今祖法”,在TRS—80型微机上,进行了比较和计算,作出了相应的系统树,并得到了与其它一些研究结果基本一致的结论。同时,讨论了分子进化的研究本身以及“今祖法”在分子进化研究中的问题和局限性。     

重金属胁迫下的细菌适应性进化研究进展

细菌进化的本质是碱基突变、基因重排或水平基因转移,在适应性进化过程中,主要受生物和非生物因素的影响,其中重金属胁迫也是细菌适应性进化的主要因素之一.重金属胁迫促使细菌适应性地强化与金属输入和转化有关的代谢途径,而过量的金属则诱导金属积累和外排过程.在重金属胁迫下,基于重金属抗性(HMR)基因和酶蛋白的适应,细菌抗性机制...     

Towards a postmodern synthesis of evolutionary biology

In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin constructed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology—and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin’s legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas.     

邮票图说达尔文和他的昆虫情缘

今年是伟大的进化论创建者达尔文诞生200周年,本文通过邮票介绍达尔文的昆虫情缘。其中主要内容有:(1)有关纪念达尔文的邮票;(2)他青少年时代是个甲虫迷;(3)在南美和昆虫打交道;(4)昆虫成为进化论的重要元素;(5)他睿智预测马达加斯加存在长喙天蛾,足以为花冠长300mm的兰花授粉。     

Darwin’s Galapagos gourd: providing new insights 175 years after his visit

The year 2010 marks the 175th anniversary of Charles Darwin’s visit to the Galapagos Islands. A recent paper by J. C. Briggs, ‘Darwin’s biogeography’ (Journal of Biogeography, 2009, 36 , 1011–1017), summarizes Darwin’s contributions to the field of biogeography, stressing the importance of his natural history specimens. Here, we illustrate how a plant collected by Darwin during his visit to Floreana and not collected since can provide insights into dispersal to oceanic islands as well as extinction of island plants, based on ancient DNA from Darwin’s herbarium specimen.     

Monkeys into Men and Men into Monkeys: Chance and Contingency in the Evolution of Man, Mind and Morals in Charles Kingsley’s Water Babies

The nineteenth century theologian, author and poet Charles Kingsley was a notable populariser of Darwinian evolution. He championed Darwin’s cause and that of honesty in science for more than a decade from 1859 to 1871. Kingsley’s interpretation of evolution shaped his theology, his politics and his views on race. The relationship between men and apes set the context for Kingsley’s consideration of these issues. Having defended Darwin for a decade in 1871 Kingsley was dismayed to read Darwin’s account of the evolution of morals in Descent of Man. He subsequently distanced himself from Darwin’s conclusions even though he remained an ardent evolutionist until his death in 1875.     

达尔文-科学进化论的奠基者

2009年, 时逢英国博物学家查尔斯·罗伯特·达尔文(Charles Robert Darwin,1809-1882)诞辰200周年, 进化论光辉著作《物种起源》发表150周年。历史的发展不断认证达尔文的《物种起源》一书是生物学史上不朽的经典著作, 如今《物种起源》所提及的许多观点已成为人尽皆知的常识, 并且还在不断地发展、完善, 为人类认识自然和自身发展指点方向。文章追忆了先贤的卓越科学贡献和科学探索精神, 并对百年来科学进步和进化论的发展重要成果进行了简要的评述, 指出了进化论未来研究的重点问题。     

Charles Darwin,embryology, evolution and skeletal plasticity

Darwin provided us with the theory of evolutionary change through natural selection. Just as important to the science of biology was Darwin’s recognition that all organisms could be classified and were related to one another because they arose from a single common universal ancestor – what we know as the universal tree of life (UtoL). All the features of the skeletal biology of fish therefore can be explained, both in an evolutionary framework (ultimate causation) and in the framework of development, growth and physiology (proximate causation). Neither approach is complete without the other. I will outline the elements of Darwin’s theories on evolution and classification and, as importantly, discuss what was missing from Darwin’s theories. An important class of evidence for evolution used by Darwin came from embryology, both comparative embryology and the existence of vestiges and atavisms. After discussing this evidence I examine some fundamental features of skeletal development and evolution These include: the presence of four skeletal systems in all vertebrates; the existence of two skeletons, one based on cartilage, the other on bone and dentine; the modular nature of skeletal development and evolution; and the plasticity of the skeleton in response to either genetic or environmental changes.     

An introduction to microevolution: rate,pattern, process

This special issue of Genetica brings together a diverse collection of contributions that examine evolution within and among populations (i.e., microevolution), and the role that microevolution plays in the formation of new species and morphological forms (i.e., macroevolution). Many of the papers present evidence of microevolution occuring over contemporary time frames, further validating the near ubiquity of ongoing evolution in the world around us. Several synthetic reviews of empirical work help to define the conditions under which microevolution is or is not likely to occur. Some of the studies speak directly to current controversies in evolutionary biology, such as the relative roles of determinism and contigency, and the nature of the relationship between microevolution and macroevolution. In general, microevolution seems driven largely by deterministic mechanisms, particularly natural selection, but contingency plays a role in (1) determining whether or not suitable conditions are present for evolution to proceed, and (2) guiding the precise manner by which evolution proceeds. Several theoretical treatments and empirical reviews confirm previous research in showing that microevolutionary processes are at least capable of generating macroevolutionary trends. Macroevolution may indeed reflect microevolution writ large but the pattern by which it arises is perhaps best charcaterized as microevolution writ in fits and starts.     

Cultural Evolution: A Review of Theory,Findings and Controversies

The last two decades have seen an explosion in research analysing cultural change as a Darwinian evolutionary process. Here I provide an overview of the theory of cultural evolution, including its intellectual history, major theoretical tenets and methods, key findings, and prominent criticisms and controversies. ‘Culture’ is defined as socially transmitted information. Cultural evolution is the theory that this socially transmitted information evolves in the manner laid out by Darwin in The Origin of Species, i.e. it comprises a system of variation, differential fitness and inheritance. Cultural evolution is not, however, neo-Darwinian, in that many of the details of genetic evolution may not apply, such as particulate inheritance and random mutation. Following a brief history of this idea, I review theoretical and empirical studies of cultural microevolution, which entails both selection-like processes wherein some cultural variants are more likely to be acquired and transmitted than others, plus transformative processes that alter cultural information during transmission. I also review how phylogenetic methods have been used to reconstruct cultural macroevolution, including the evolution of languages, technology and social organisation. Finally, I discuss recent controversies and debates, including the extent to which culture is proximate or ultimate, the relative role of selective and transformative processes in cultural evolution, the basis of cumulative cultural evolution, the evolution of large-scale human cooperation, and whether social learning is learned or innate. I conclude by highlighting the value of using evolutionary methods to study culture for both the social and biological sciences.     

Alfred Russel Wallace deserves better

During 2009, while we were celebrating Charles Darwin and his The origin of species, sadly, little was said about the critical contribution of Alfred Russel Wallace (1823–1913) to the development of the theory of evolution. Like Darwin, he was a truly remarkable nineteenth century intellect and polymath and, according to a recent book by Roy Davies (The Darwin conspiracy: origins of a scientific crime), he has a stronger claim to the Theory of Evolution by Natural Selection than has Darwin. Here we present a critical comparison between the contributions of the two scientists. Sometimes referred to as ‘The other beetle-hunter’ and largely neglected for many decades, Wallace had a far greater experience of collecting and investigating animals and plants from their native habitats than had Darwin. He was furthermore much more than a pioneer biogeographer and evolutionary theorist, and also made contributions to anthropology, ethnography, geology, land reform and social issues. However, being a more modest, self-deprecating man than Darwin, and lacking the latter’s establishment connections, Wallace’s contribution to the theory of evolution was not given the recognition it deserved and he was undoubtedly shabbily treated at the time. It is time that Wallace’s relationship with Darwin is reconsidered in preparation for 2013, the centenary of Wallace’s death, and he should be recognized as at least an equal in the Wallace-Darwin theory of evolution.