查理士 达尔文( Charles Darwin )( 1809 1882 )是英国博物学家和生物学家,进化论的奠基人。以关于生物进化的理论专著《物种起源》而闻名于世,达尔文的进化论与细胞学说和能量守恒与转化定律被恩格斯认为是 19 世纪自然科学的三大发现。 今年11月是达尔文发表《物种起源》150年,明年2月是达尔文诞辰200年。 探索进化足迹的巨人达尔文 达尔文是 19 世纪英国杰出的生物学家,也正是他找到了生物发展的规律,成为进化论的奠基人,他的《物种起源》对近代生物科学产生了巨大而深远的影响,具有划时代的意义。 1809 年 2 月 12 日 出生在英国的施鲁斯伯里。祖父和父亲都是当地的名医,家里希望他将来继承祖业, 16 岁时便被父亲送到爱丁堡大学学医。 因为达尔文无意学医,进到医学院后,他仍然经常到野外采集动植物标本。父亲认为他游手好闲、不务正业,一怒之下,于 1828 年又送他到剑桥大学,改学神学,希望他将来成为一个尊贵的牧师。 1831 年他毕业后就参加了测量考察舰贝格尔号历时 5 年的环球旅行。这对达尔文是有决定意义的 5 年。南美洲等地大量的物种变异的事实,使他对《圣经》产生了怀疑。通过对采集到的各种动物标本和化石进行比较和分析,他进而认识到物种是可变的。由此,他逐步摆脱了神创论的束缚,坚定地走上了相信科学和追求真理的道路。 1828 年的一天,在伦敦郊外的一片树林里,一位大学生围着一棵老树转悠。突然,他发现在将要脱落的树皮下,有虫子在里边蠕动,便急忙剥开树皮,发现两只奇特的甲虫,正急速地向前爬去。这位大学生马上左右开弓抓在手里,兴奋地观看起来。正在这时,树皮里又跳出一只甲虫,大学生措手不及,迅即把手里的甲虫藏到嘴里,伸手又把第三只甲虫抓到。看着这些奇怪的甲虫,大学生真有点爱不释手,只顾得意地欣赏手中的甲虫,早把嘴里的哪只给忘记了。嘴里的那只甲虫憋得受不了啦,便放出一股辛辣的毒汁,把这大学生的舌头蜇得又麻又痛。他这才想起口中的甲虫,张口把它吐到手里。然后,不顾口中的疼痛,得意洋洋地向市内的剑桥大学走去。这个大学生就是达尔文。后来,人们为了纪念他首先发现的这种甲虫,就把它命为达尔文。 1831 年,达尔文从剑桥大学毕业。他放弃了待遇丰厚的牧师职业,依然热衷于自己的自然科学研究。这年 12 月,英国政府组织了贝格尔号军舰的环球考察,达尔文经人推荐,以博物学家的身份,自费搭船,开始了漫长而又艰苦的环球考察活动。 达尔文每到一地总要进行认真的考察研究,采访当地的居民,有时请他们当向导,爬山涉水,采集矿物和动植物标本,挖掘生物化石,发现了许多没有记载的新物种。他白天收集谷类岩石标本、动物化石,晚上又忙着记录收集经过。 1832 年 1 月,贝格尔号停泊在大西洋中佛得角群岛的圣地亚哥岛。水兵们都去考察海水的流向。达尔文和他的助手背起背包,拿着地质锤,爬到山上去收集岩石标本。 在考察过程中,达尔文根据物种的变化,整日思考着一个问题:自然界的奇花异树,人类万物究意是怎么产生的?他们为什么会千变万化?彼此之间有什么联系?这些问题在脑海里越来越深刻,逐渐使他对神创论和物种不变论产生了怀疑。 1832 年 2 月底,贝格尔号到达巴西,达尔文上岸考察,向船长提出要攀登南美洲的安第斯山。当他们爬到海拔 4000 多米的高山上时,达尔文意外地在山顶上发现了贝壳化石。达尔文非常吃惊,他心中想到:海底的贝壳怎么会跑到高山上了呢?经过反复思索,他终于明白了地壳升降的道理。达尔文脑海中一阵翻腾,对自己的猜想有了更进一步的认识:物种不是一成不变的,而是随着客观条件的不同而相应变异! 后来,达尔文又随船横渡太平洋,经过澳大利亚,越过印度洋,绕过好望角,于 1836 年 10 月回到英国。在历时五年的环球考察中,达尔文积累了大量的资料。回国之后,他一面整理这些资料,一面又深入实践,同时,查阅大量书籍,为他的生物进化理论寻找根据。 1842 年,他第一次写出《物种起源》的简要提纲。 1859 年 11 月达尔文经过 20 多年研究而写成的科学巨著《物种起源》终于出版了。在这部书里,达尔文旗帜鲜明地提出了进化论的思想,说明物种是在不断的变化之中,是由低级到高级、由简单到复杂的演变过程。 这部著作的问世,第一次把生物学建立在完全科学的基础上,以全新的生物进化思想,推翻了神创论和物种不变的理论。《物种起源》是达尔文进化论的代表作,标志着进化论的正式确立。 《物种起源》的出版,在欧洲乃至整个世界都引起轰动。它沉重地打击了神权统治的根基,从反动教会到封建御用文人都狂怒了。他们群起攻之,诬蔑达尔文的学说亵渎圣灵,触犯君权神授天理有失人类尊严。与此相反,以赫胥黎为代表的进步学者,积极宣传和捍卫达尔文主义。指出:进化论轰开了人们的思想禁锢,启发和教育人们从宗教迷信的束缚下解放出来。 紧接着,达尔文又开始他的第二部巨著《动物和植物在家养下的变异》的写作,以不可争辩的事实和严谨的科学论断,进一步阐述他的进化论观点,提出物种的变异和遗传、生物的生存斗争和自然选择的重要论点,并很快出版这部巨著。晚年的达尔文,尽管体弱多病,但他以惊人的毅力,顽强地坚持进行科学研究和写作,连续出版了《人类的由来》等很多著作。 达尔文本人认为他一生中主要的乐趣和唯一的事业 , 是他的科学著作。还有一些在旅行中直接考察得到的最重要的科学成果,如:达尔文本人所写的著名的《考察日记》和《贝格尔号地质学》、《贝格尔号的动物学》等。在他的著作中,具有特别重大历史意义的是《物种起源》,表明达尔文的进化论思想和自然选择理论的逐步发展过程。《物种起源》的出版是一件具有世界意义的大事,因为《物种起源》的出版标志着十九世纪绝大多数有学问的人对生物界和人类在生物界中的地位的看法发生了深刻的变化。 《物种起源》的出版,引起造化论者和具有目的论情绪的科学家们(而这些人却是占绝大多数)对达尔文学说的猛烈攻击,也引起维护达尔文主义的相应斗争,积极参加这一斗争的除达尔文本人外还有进步的博物学家;他们到处都成为达尔文学说的热烈拥护者。 达尔文是一位不畏劳苦沿着陡峭山路攀登的人。在《物种起源》发表以后的 20 年里,他始终没有中断过科学工作。 1876 年,他写成的《植物界异花受精和自花受精的效果》一书,就是经过长期大量实验的结果。书中提出的异花受精一般是有利的结论,已在农业育种中广泛应用。到了晚年,达尔文心脏病严重,但他仍坚持科学工作。就在去世前两天,他还带着重病去记录实验情况。 1882 年 4 月 19 日 ,这位伟大的生物学家逝世了。由于达尔文一生对生物科学作出划时代的贡献,人们将他葬在伦敦威斯敏斯特寺院中堂的北廊,和杰出的科学家牛顿葬在同一个地方。 录自 http://news.xinhuanet.com/st/2005-04/19/content_2849168.htm ,略有改动 《 Nature 》 special issue Darwin 200: Beyond the origin February 2009 sees the 200th anniversary of the birth of Charles Robert Darwin and November 2009 the 150th anniversary of the publication of his great work, On the Origin of Species. In the intervening two centuries, no single scientist has matched Darwin s impact on the sciences, politics, religion, philosophy and art. This issue of Nature brings together news, research and analysis of Darwin , his life, his science and his legacy. Darwin saw the eye so complex and seemingly useless with any of its components part-formed as an obstacle to the acceptance of natural selection. Today we know it as one of evolution s crowning glories celebrated with a fold-out pictorial feature and current research that refers right back to the protoeyes hypothesized by Darwin. In later writings (Descent of Man ,1871), Darwin touched on a topic that still divides evolutionary biologists group selection. Does natural selection work for individuals against the interests of the group? Or is such thinking a historical mistake? We report on the debate and why it is important , and review a landmark book on the superorgansims of the insect world, where the group looms large . Extinction comes with the evolutionary territory. But is it for ever? With the publication of the genome sequence of the long-gone woolly mammoth , some researchers are even claiming that mammoths will one day be recreated . Biologists tend to see evolved living systems as finely tuned machines, prone to failure if one component is faulty. But, as Tanguy Chouard reveals, this is not what happens in the real world . Plenty for biologists to celebrate and plenty of places to do it: we have trawled the world for events commemorating Darwin s life and works and trawled the publishers lists for books doing the same . Not quite everybody will be in celebratory mood. The scientists we spoke to mostly are , but past celebrations have had to tread carefully . The Darwin-related content from this issue and extra online-only material can be accessed via: www.nature.com/darwin. Cover graphic: Jonathan Williams
The evolution of sex-biased genes and sex-biased gene expression Ellegren H, Parsch J. The evolution of sex-biased genes and sex-biased gene expression. Nat Rev Genet. 2007 Sep; 8 (9): 689-98. Epub 2007 Aug 7. Differences between males and females in the optimal phenotype that is favoured by selection can be resolved by the evolution of differential gene expression in the two sexes. Microarray experiments have shown that such sex-biased gene expression is widespread across organisms and genomes. Sex-biased genes show unusually rapid sequence evolution, are often labile in their pattern of expression, and are non-randomly distributed in the genome. Here we discuss the characteristics and expression of sex-biased genes, and the selective forces that shape this previously unappreciated source of phenotypic diversity. Sex-biased gene expression has implications beyond just evolutionary biology, including for medical genetics. The evolution of sex-biased genes and sex-biased gene expression Evolutionary complexity of MADS complexes Rijpkema AS , Gerats T, Vandenbussche M. Evolutionary complexity of MADS complexes. Curr Opin Plant Biol. 2007 Feb; 10 (1): 32-8. Epub 2006 Nov 30. Developmental programs rely on the timely and spatially correct expression of sets of interacting factors, many of which appear to be transcription factors. Examples of these can be found in the MADS-box gene family. This gene family has greatly expanded, particularly in plants, by a range of duplications that have enabled the genes to diversify in structure and function. MADS-box genes appear to have been instrumental in shaping one of the great evolutionary innovations, the true flower, which originated around 120-150 million years ago and led to the enormous radiation of the angiosperms. We propose a shift from analyzing individual gene functions towards studying MADS-box gene function at the subfamily level. This will enable us to distinguish subfunctionalization events from the evolutionary changes that defined floral morphology. Evolutionary complexity of MADS complexes Evolutionary genetics: fight or flinch? Brown JK, Handley RJ. Fight or flinch? Heredity. 2006 Jan; 96 (1): 3-4. Evolutionary genetics-fight or flinch Evolving disease resistance genes Meyers BC, Kaushik S, Nandety RS. Evolving disease resistance genes. Curr Opin Plant Biol. 2005 Apr; 8 (2): 129-34. Defenses against most specialized plant pathogens are often initiated by a plant disease resistance gene. Plant genomes encode several classes of genes that can function as resistance genes. Many of the mechanisms that drive the molecular evolution of these genes are now becoming clear. The processes that contribute to the diversity of R genes include tandem and segmental gene duplications, recombination, unequal crossing-over, point mutations, and diversifying selection. Diversity within populations is maintained by balancing selection. Analyses of whole-genome sequences have and will continue to provide new insight into the dynamics of resistance gene evolution. Evolving disease resistance genes
Chromosome evolution Schubert I. Chromosome evolution. Curr Opin Plant Biol. 2007 Apr; 10 (2): 109-15. Epub 2007 Feb 7. The idea of evolution as a principle for the origin of biodiversity fits all phenomena of life, including the carriers of nuclear inheritance, the chromosomes. Insights into the evolutionary mechanisms that contribute to the shape, size, composition, number and redundancy of chromosomes elucidate the high plasticity of nuclear genomes at the chromosomal level, and the potential for genome modification in the course of breeding processes. Aspects of chromosome fusion, as exemplified by karyotype evolution of relatives of Arabidopsis, have recently received special attention. Chromosome evolution Steps in the evolution of heteromorphic sex chromosomes Charlesworth D, Charlesworth B, Marais G. Steps in the evolution of heteromorphic sex chromosomes. Heredity. 2005 Aug; 95 (2): 118-28. We review some recently published results on sex chromosomes in a diversity of species. We focus on several fish and some plants whose sex chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how sex chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process. Steps in the evolution of heteromorphic sex chromosomes Evolutionary genetics: when duplicated gene dont stick to the rules Van de Peer Y. Evolutionary genetics: when duplicated genes don't stick to the rules. Heredity. 2006 Mar; 96 (3): 204-5. when duplicated gene dont stick to the rules Junk DNA as an evolutionary force Bimont C, Vieira C. Genetics: junk DNA as an evolutionary force. Nature. 2006 Oct 5; 443 (7111): 521-4. Junk DNA as an evolutionary force The evolutionary dynamics of plant duplicate genes Moore RC, Purugganan MD. The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol. 2005 Apr; 8 (2): 122-8. Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution. The evolutionary dynamics of plant duplicate genes The rise and falls of introns Belshaw R, Bensasson D. The rise and falls of introns. Heredity. 2006 Mar; 96 (3): 208-13. There has been a lively debate over the evolution of eukaryote introns: at what point in the tree of life did they appear and from where, and what has been their subsequent pattern of loss and gain? A diverse range of recent research papers is relevant to this debate, and it is timely to bring them together. The absence of introns that are not self-splicing in prokaryotes and several other lines of evidence suggest an ancient eukaryotic origin for these introns, and the subsequent gain and loss of introns appears to be an ongoing process in many organisms. Some introns are now functionally important and there have been suggestions that invoke natural selection for the ancient and recent gain of introns, but it is also possible that fixation and loss of introns can occur in the absence of positive selection. The rise and falls of introns Retrotransposons: central players in the structure, evolution and function of plant geneomes Kumar A, Bennetzen JL. Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci. 2000 Dec;5 (12): 509-10. Retrotransposons-central players in the structure, evolution and function of plant geneomes
Eukaryotic evolution, changes and challenges Embley TM, Martin W. Eukaryotic evolution, changes and challenges. Nature. 2006 Mar 30; 440 (7084): 623-30. The idea that some eukaryotes primitively lacked mitochondria and were true intermediates in the prokaryote-to-eukaryote transition was an exciting prospect. It spawned major advances in understanding anaerobic and parasitic eukaryotes and those with previously overlooked mitochondria. But the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before. Eukaryotic evolution, changes and challenges Climbing the evolutionary tree- Andrews P Climbing the evolutionary tree- Andrews P Which evolutionar processes influence natural genetic variation for phenotypic traits Mitchell-Olds T, Willis JH, Goldstein DB. Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet. 2007 Nov; 8 (11): 845-56. Although many studies provide examples of evolutionary processes such as adaptive evolution, balancing selection, deleterious variation and genetic drift, the relative importance of these selective and stochastic processes for phenotypic variation within and among populations is unclear. Theoretical and empirical studies from humans as well as natural animal and plant populations have made progress in examining the role of these evolutionary forces within species. Tentative generalizations about evolutionary processes across species are beginning to emerge, as well as contrasting patterns that characterize different groups of organisms. Furthermore, recent technical advances now allow the combination of ecological measurements of selection in natural environments with population genetic analysis of cloned QTLs, promising advances in identifying the evolutionary processes that influence natural genetic variation. Which evolutionar processes influence natural genetic variation for phenotypic traits Phylogenomics and the reconstruction of the tree of life Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005 May; 6 (5): 361-75. As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence. Phylogenomics and the reconstruction of the tree of life Variation and constraint in plant evolution and development Kalisz S, Kramer EM. Variation and constraint in plant evolution and development. Heredity. 2008 Feb; 100 (2): 171-7. Epub 2007 Jan 31. The goal of this short review is to consider the interrelated phenomena of phenotypic variation and genetic constraint with respect to plant diversity. The unique aspects of plants, including sessile habit, modular growth and diverse developmental programs expressed at the phytomer level, merit a specific examination of the genetic basis of their phenotypic variation, and how they experience and escape genetic constraint. Numerous QTL studies with wild and domesticated plants reveal that most phenotypic traits are polygenic but vary in the number and effect of the loci contributing, from a few loci of large effects to many with small effects. Further, somatic mutations, developmental plasticity and epigenetic variation, especially gene methylation, can contribute to increases in phenotypic variation. The flip side of these processes, genetic constraint, can similarly be the result of many factors, including pleiotropy, canalization and genetic redundancy. Genetic constraint is not only a mechanism to prevent change, however, it can also serve to direct evolution along certain paths. Ultimately, genetic constraint often comes full circle and is released through events such as hybridization, genome duplication and epigenetic remodeling. We are just beginning to understand how these processes can operate simultaneously during the evolution of ecologically important traits in plants. Variation and constraint in plant evolution and development
见这里: http://blog.lib.umn.edu/denis036/thisweekinevolution/ 由University of Minnesota的R. Ford Denison教授做的,题目是: This Week in Evolution Each week I discuss one of the hundreds of papers with new data on evolution, published in the past month. 他的相关资料见这下: R. Ford Denison Adjunct Professor, Dept. of Ecology, Evolution, and Behavior Ph.D., Cornell University, 1983 Contact Information Phone: 612-626-6462 Fax: 612-624-6777 E-mail: denis036@umn.edu Graduate Faculty Memberships Ecology, Evolution and Behavior, Plant Biological Sciences Research Interests Evolution of mutualism (especially legumes and rhizobia); implications of past and ongoing evolution for agriculture. Statement How does evolution based on selfish genes maintain cooperation? We are trying to answer this question for rhizobia, symbiotic bacteria that infect legume plants like alfalfa or soybean and (to varying extents) supply them with nitrogen. Fixing nitrogen is costly for rhizobia, so why haven't rhizobia that supply their plant hosts with nitrogen (indirectly benefiting competing rhizobia infecting the same plant) been completely displaced by ineffective rhizobia? Why are ineffective rhizobia common enough to be a problem in some soils but not others? This research may lead to practical applications, such as legume crops that selectively enrich the soil with the most-beneficial local strains of rhizobia. This research may also be relevant to other cases where symbiosis breaks down, as in coral bleaching. As time allows, I also hope to explore other applications of modern evolutionary theory, pursuing some of the ideas in our paper on Darwinian Agriculture. To pursue my research objectives, I have often had to develop new tools, including mechanistic computer models and noninvasive scientific instruments, such as the nodule oximeter or a laser-scanner measure green leaf area index in the field. Selected Publications Kiers, E.T., R.A. Rousseau, and R.F. Denison. 2006. Measured sanctions: legume hosts detect quantitative variation in rhizobium cooperation and punish accordingly. Evolutionary Ecology Research 8:1077-1086. R.F. Denison and E.T. Kiers. 2004. Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis. FEMS Microbiology Letters 237:187-193. Martini, E.A., J.S. Buyer, D.C. Bryant, T.K. Hartz, and R.F. Denison. 2004. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research 86:255-266. Kiers, E.T., R.A. Rousseau, S.A. West, and R.F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81. Kinraide, T.B., and R.F. Denison. 2003. Strong inference, the way of science. American Biology Teacher 65:419-424. Denison, R.F., E.T. Kiers, and S.A. West. 2003. Darwinian Agriculture: When can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78:145-168. Denison, R.F., C. Bledsoe, M. Kahn, F. O'Gara, E.L. Simms,and L.S. Thomashow. 2003. Cooperation in the rhizosphere and the free rider problem. Ecology 84:838-845. Denison, R.F. 2000. Legume sanctions and the evolution of symbiotic cooperation by rhizobia. American Naturalist 156:567-576. 另外他以前在UCDavis的网站也对他自己做了很详细的介绍: R. Ford Denison, Professor Emeritus, UC Davis New Address Darwinian Agriculture Teaching Research and Grants Publications Education and Employment Mathematical Models Lectures, Essays, and Rants From 1993 through 2002, R. FORD DENISON taught crop ecology and conducted research at the University of California, Davis, on topics ranging from agricultural sustainability to the evolution of cooperation between microbes and plants. For most of this time, he directed the world's youngest 100-year experiment (LTRAS.ucdavis.edu) , tracking the long-term trends that determine agricultural sustainability. His work on symbiotic nitrogen fixation, a possible alternative to nitrogen fertilizers, has led to a patent and publications in journals from Nature to Field Crops Research . One recent paper, Darwinian Agriculture : When Can Humans Find Solutions Beyond the Reach of Natural Selection? points out some limitations both of agricultural biotechnology and of agriculture that mimics natural ecosystems. He has been interviewed on National Public Radio, Science Update (AAAS), and DeutschlandRadio and has been an invited speaker at international meetings and at institutions from Japan's National Agricultural Research Center to the Scripps Institute of Oceanography. He was educated at Harvard, Evergreen , and Cornell, where he earned a Ph.D. in Crop Science, with postdoctoral and sabbatical research at UC Davis, UCLA, Queen's University (Ontario), Welsh Plant Breeding Station (Aberystwyth), and University of Minnesota. His research has been supported by NSF, USDA, and California's Agricultural Experiment Station. This web page was last updated May 2005, when he moved to the University of Minnesota. Teaching PLB 142. Ecology of Crop Systems (4) II. Denison. Lecture, 3 hours; discussion, 1 hour. Prerequisite: Agricultural Systems and Environment 2 or Biological Sciences 1C; Math 16A or Physics 1A, or consent of instructor. Ecological processes governing the structure and behavior of managed ecosystems. Emphasis on mechanistic and systems views of the physical environment, photosynthetic productivity, competition, adaptation, nutrient cycling, energy relations and contemporary issues such as climate change. PBI 225. Methods and Instrumentation for Crop and Soil Science (3) III. Denison, Hsiao, Hartz, Mitchell, Pettygrove, Scow van Kessel. Lecture, 1 hour; discussion, 1 hour; laboratory, 3 hours. Prerequisite: Basic knowledge of plant physiology, soil science, chemistry and physics. Theory and practice of in situ sampling and instrumentation methods for crop science and related aspects of soil science (e.g. moisture and fertility) and laboratory analysis. Not offered every year. The challenge of cooperation: from bacteria to humans (Spring 2004) Defense Against Dark Information (freshman seminar, Fall 2003) Featured speaker at workshop Education for Sustainable Agriculture, California State University, Chico, March 26, 1999. Agroecology Seminar Series (Winter 1999 and 2000) and student participatory seminars. Research How does evolution based on selfish genes maintain cooperation? We are trying to answer this question for rhizobia, symbiotic bacteria that infect legume plants like alfalfa or soybean and (to varying extents) supply them with nitrogen. Fixing nitrogen is costly for rhizobia, so why haven't rhizobia that supply their plant hosts with nitrogen (indirectly benefiting competing rhizobia infecting the same plant) been completely displaced by ineffective rhizobia? Why are ineffective rhizobia common enough to be a problem in some soils but not others? This research may lead to practical applications, such as legume crops that selectively enrich the soil with the most-beneficial local strains of rhizobia. This research may also be relevant to other cases where symbiosis breaks down, as in coral bleaching. As time allows, I also hope to explore other applications of modern evolutionary theory, pursuing some of the ideas in our paper on Darwinian Agriculture. Steve Kaffka has replaced me as Director of LTRAS , but I remain interested in scientific approaches to the problem of long-term sustainability, especially that of agriculture. To pursue my research objectives, I have often had to develop new tools, including mechanistic computer models and noninvasive scientific instruments, such as the nodule oximeter or a laser-scanner (at right) to measure green leaf area index in the field. Grants Explaining variation in legume-rhizobium mutualism. 8/04-7/07. NSF, Ecological and Evolutionary Physiology program. Other recent grants on which I was principal investigator or co-PI include: Legume-rhizobium interactions that maintain mutualism. 8/02-7/04. NSF. Cooperation and conflict in the legume-rhizobium symbiosis . 9/00-8/02. NSF. Can soil quality trends explain the organic transition effect? 7/98-6/01. Kearney Foundation. Physical changes associated with stress-induced changes in nodule oxygen permeability. 12/99-12/01. USDA/NRI. Long-Term Sustainability of Irrigated Agriculture. 9/96-9/98. USDA/NRI. Developing Site-Specific Farming Information for Cropping Systems in California. Calif. Fertilizer Research Education Program. Real-time Educational Monitoring Of The Environment ( REMOTE ). UC Instructional Use of Computers program. Patent Method and Apparatus for Measuring Oxygen Concentration and its Subsequent Use in Estimating Nitrogen Fixation in Plants. D.B. Layzell, S. Hunt, G. Palmer, R.F. Denison. #5,096,294 . Publications E.T. Kiers, S.A. West, and R.F. Denison. 2005? Maintaining cooperation in the legume-rhizobia symbiosis: identifying selection pressures and mechanisms. In: J. Sprent and E. James (eds.) Leguminous Symbioses. Kluwer Academic Publishers (in press). Kong, A.Y., J. Six, D.C. Bryant, R.F. Denison, and C. van Kessel. 2005. The relationship between carbon input, aggregation, and soil organic carbon stabilization in sustainable cropping systems. Soil Science Society of America Journal (in press). R.F. Denison and E.T. Kiers. 2005. Sustainable crop nutrition: constraints and opportunities. In : M. Broadley (ed.) Plant Nutritional Genomics. Blackwell. Hasegawa, H., and R.F. Denison. 2005. Model predictions of winter rainfall effects on N dynamics of winter wheat rotation following legume cover crop or fallow. Field Crops Research 91:251-261. R.F. Denison and E.T. Kiers. 2004. Why are most rhizobia beneficial to their plant hosts, rather than parasitic? (Invited review.) Microbes and Infection 6:1235-1239. R.F. Denison and E.T. Kiers. 2004. Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis. (Invited review.) FEMS Microbiology Letters 237:187-193. Denison, R.F., D.C. Bryant, and T.E. Kearney. 2004. Crop yields over the first nine years of LTRAS, a long-term comparison of field crop systems in a Mediterranean climate. Field Crops Research 86:267-277 . Martini, E.A., J.S. Buyer, D.C. Bryant, T.K. Hartz, and R.F. Denison. 2004. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research 86:255-266 . Okano, Y., K.R. Hristova, C. Leutenegger, L. Jackson, R.F. Denison, B. Gebreyesus, D. LeBauer, and K.M. Scow. 2004. Effects of ammonium on the population size of ammonia-oxidizing bacteria in soil -- Application of real-time PCR. Applied and Environmental Microbiology 70:1008-1016. Kiers, E.T., R.A. Rousseau, S.A. West, and R.F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81 . Widely covered in scientific and popular press . Kinraide, T.B., and R.F. Denison. 2003. Strong inference, the way of science. American Biology Teacher 65:419-424. Denison, R.F., E.T. Kiers, and S.A. West. 2003. Darwinian Agriculture: When can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78:145-168. See updates and commentary . Denison, R.F., C. Bledsoe, M. Kahn, F. O'Gara, E.L. Simms,and L.S. Thomashow. 2003. Cooperation in the rhizosphere and the free rider problem. Ecology 84:838-845 . Denison, R.F., and Y. Okano. 2003. Leghemoglobin oxygenation gradients in alfalfa and yellow sweetclover nodules. Journal of Experimental Botany 54:1085-1091 . Kiers, E.T., S.A. West R.F. Denison. 2002. Mediating mutualisms: the influence of farm management practices on the evolutionary maintenance of symbiont cooperation. Journal of Applied Ecology 39:745-754 . West, S.A., E.T. Kiers, I. Pen R.F. Denison. 2002. Sanctions and mutualism stability: when should less beneficial mutualists be tolerated? Journal of Evolutionary Biology 15:830-837 . West, S.A., E.T. Kiers, E.L. Simms R.F. Denison. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proceedings of the Royal Society, London 269:685-694 . Denison, R.F. 2001. Meeting report: ecologists and molecular biologists find common ground in the rhizosphere. Trends in Ecology and Evolution 16:535-536 . Denison, R.F. 2000. Legume sanctions and the evolution of symbiotic cooperation by rhizobia. American Naturalist 156:567-576. Hasegawa, H. , D.C. Bryant, and R.F. Denison. 2000. Testing CERES model predictions of crop growth and N dynamics, in cropping systems with leguminous green manures in a Mediterranean climate. Field Crops Res. 67:239-255 . Hasegawa, H.,J.M. Labavitch, A.M. McGuire, D.C. Bryant, and R.F. Denison. 1999. Testing CERES model predictions of N release from legume cover crop residue. Field Crops Res. 63:255-267 . Plant, R.E., A. Mermer, G.S. Pettygrove, M.P. Vayssieres, J.A. Young, R.O. Miller, L.F. Jackson, R.F. Denison, and K. Phelps. 1999. Factors underlying grain yield spatial variability in three irrigated wheat fields. ASAE Transactions 42:1187-1202. Serraj, R., V. Vadez, R.F. Denison, and T.R. Sinclair. 1999. Involvement of ureides in nitrogen fixation inhibition in soybean. Pla nt Physiol. 119:289-296. McGuire, A.M., D.C. Bryant, and R.F. Denison. 1998. Wheat yields, nitrogen uptake, and soil moisture following winter legume cover crop vs. fallow. Agron. J. 90:404-410. Denison, R.F. 1998. Decreased oxygen permeability: a universal stress response in legume root nodules. Bot. Acta 111:191-192. Jacobsen, K.R., R.A. Rousseau, and R.F. Denison. 1998. Tracing the path of oxygen into birdsfoot trefoil and alfalfa nodules using iodine vapor. Bot. Acta. 111:193-203. (cover article) Pettygrove,G.S., S.K. Upadhyaya, M.G. Pelletier, T.K. Hartz, R.E. Plant, and R.F. Denison. 1998. Tomato yield - color infrared photograph relationships. Proc. 4th Intl. Conf. Precision Agric., St. Paul, MN. Arrese-Igor,C., A.J. Gordon, F.R. Minchin, and R.F. Denison. 1998. Nitrate entry and nitrite formation in the infected region of soybean nodules. J. Exp. Bot. 9:41-48. Miller, R.O., G.S. Pettygrove, R.F. Denison, L. Jackson, M. Cahn, R. Plant, T. Kearney. 1998. Site specific relationships between flag leaf nitrogen, SPAD meter values and grain protein in irrigated wheat. Commun. Soil Sci. Plant Anal. 9:1381-1382. Denison, R.F., and R. Russotti. 1997. Field estimates of green leaf area index using laser-induced chlorophyll fluorescence. Field Crops Res. 52:143-150 . Denison, R.F. 1997. Minimizing errors in LAI estimates from laser-probe inclined-point quadrats. Field Crops Res. 51:231-240. Denison, R.F. 1997. Review of Long-Term Experiments in Agricultural and Ecological Sciences. Field Crops Res. 54:74-75. Shimada, S., R. Rousseau, and R.F. Denison. 1997. Wavelength options for monitoring leghemoglobin oxygenation gradients in intact legume root nodules. J. Exp. Bot. 48:1251-1258. (cover article) Denison, R.F., R.O. Miller, D. Bryant, A. Abshahi, and W.E. Wildman. 1996. Image processing extracts more information from color infrared aerial photos.Calif. Agric. 50(3):9-13 (cover article) Denison, R.F., and B.L. Harter. 1995. Nitrate effects on nodule oxygen permeability and leghemoglobin Nodule oximetry and computer modeling. Plant Physiol. 107:1355-1364 . Denison, R.F., and T.B. Kinraide. 1995. Oxygen-induced membrane depolarizations in legume root nodules: possible evidence for an osmoelectrical mechanism controlling nodule gas permeability. Plant Physiol. 108:235-240 Denison, R.F. 1995. Agricultural soil and crop practices. McGraw-Hill Yearbook of Science and Technology, pp. 6-9. Denison, R.F., J.F. Witty, and F.R. Minchin. 1992. Reversible O 2 -inhibition of nitrogenase activity in attached soybean nodules. Plant Physiol. 100:1863-1868 . Denison, R.F., S. Hunt, and D.B. Layzell. 1992. Nitrogenase activity, nodule respiration, and O 2 permeability following detopping of alfalfa and birdsfoot trefoil. Plant Physiol. 98:894-900 . Denison, R.F. 1992. Mathematical modeling of oxygen diffusion and respiration in legume root nodules. Plant Physiol. 98:901-907 . Denison, R.F., and D.B. Layzel l . 1991. Measurement of legume nodule respiration and O 2 permeability by noninvasive spectrophotometry of leghemoglobin. Plant Physiol. 96:137-143 . Denison, R.F., D.L. Smith, T. Legros, and D.B. Layzell. 1991. Noninvasive measurement of internal oxygen concentration in field-grown soybean nodules. Agron. J. 83:166-169 . Denison, R.F., and H.D. Perry. 1990. Seasonal growth rate patterns for orchardgrass and tall fescue on the Appalachian Plateau. Agron. J. 82:869-873 . Denison, R.F., J.M. Fedders, and C.B.S. Tong . 1990. Amyloglucosidase digestion can overestimate starch content of plants. Agron. J. 82:361-364 . Denison, R.F. 1989. Implications of competitive inhibition in the acetylene reduction assay for dinitrogen fixation. Ann. Bot. 64:167-169. Denison, R.F., and R.S. Loomis. 1989. An Integrative Physiological Model of Alfalfa Growth and Development . Univ. Calif. Div. Agric. Natural Resources, Publ. 1926, 73 pp. Denison, R.F., and P.S. Nobel. 1988. Growth of Agave deserti without current photosynthesis. Photosynthetica 22:51-57. Denison, R.F., P.R. Weisz, and T.R. Sinclair. 1988. Oxygen supply to nodules as a limiting factor for symbiotic nitrogen fixation. p. 767-776. In: R.J. Summerfield (ed.) World Crops: Cool Season Food Legumes. Kluwer Academic Publishers, Dordrecht. Weisz, P.R., R.F. Denison, and T.R. Sinclair. 1985. Response to drought stress of nitrogen fixation (acetylene reduction) rates by field-grown soybeans. Plant Physiol. 78:525-530. Sinclair, T.R., P.R. Weisz, and R.F. Denison. 1985. Oxygen limitation to nitrogen fixation in soybean nodules. p. 797-806. In: R. Shibles (ed.) Proceedings, World Soybean Conf. III. Westview Press, Boulder. Denison, R.F., and T.R. Sinclair. 1985. Diurnal and seasonal variation in dinitrogen fixation (acetylene reduction) rates by field-grown soybeans. Agron. J. 77:679-684. Denison, R.F., P.R. Weisz, and T.R. Sinclair. 1985. Variability among plants in dinitrogen fixation Agron. J.77:947-950. Denison, R.F., P.R. Weisz, and T.R. Sinclair. 1983. Analysis of acetylene reduction rates of soybean nodules at low acetylene concentrations. Plant Physiol. 73:648-651. Denison, R.F., T.R. Sinclair, R.W. Zobel, M.N. Johnson, and G.M. Drake. 1983. A nondestructive field assay for soybean nitrogen fixation by acetylene reduction. Plant Soil 70:173-182. Denison, R.F. 1979. A 2K Symbolic Assembler for the 6502. Self-published manual recently reincarnated on the web. Denison, R., B. Caldwell, B. Bormann, L. Eldred, C. Swanberg, and S. Anderson. 1976. The effects of acid rain on nitrogen fixation in western Washington coniferous forests. Water Air Soil Pollut. 8:21-34. Computer Models Available to Download ALFALFA model (Denison Loomis, 1989). Mathematical model of light interception by a row crop (Denison, 1997). Download a Model Education and Employment History Professor and Agronomist, Department of Agronomy and Range Science, 1993 to present (Assoc. Prof. 5/93-6/99). Plant Physiologist, USDA/ARS, Beckley WV. 1986 to 1993. Postgraduate Researcher, with P.S. Nobel, UCLA. 1985. Postdoctoral Research Agronomist, with R.S. Loomis, UC Davis. 1982 to 1984. Ph.D., crop science, with T.R. Sinclair, Cornell University, 1983. (M.S., 1980). B.A., with ecology emphasis, The Evergreen State College, 1975. Another Harvard dropout. Professional Activities Member of the Editorial Board, Field Crops Research , 1994-present Invited talks: Intl. Cong. N 2 Fixation, European N 2 Fixation Congress, Amer. Soc. Agron. national meeting, Nat. Agric. Res. Center (Japan), Scripps Inst. Oceanography, Bodega Marine Lab., UC Berkeley Grad School Journalism, UCD Law School, Calif. Dept. Food Agric., UCD Center Pop. Biol., Calif. Plant Soil Conf., etc. Annual guest lectures at UC Davis in graduate ecology and upper division crop evolution classes; departmental seminars at UC Davis and elsewhere. Chair of Agroecology Curriculum Review Committee, member College Committee on Sustainable Agriculture . Grant reviews for USDA, NSF, NSERC, Swiss and Russian National Science Foundations, IPM program, etc. Webmaster for Environmental Plant Biology and Small Farm Technology websites. New address Ecology, Evolution and Behavior University of Minnesota 1987 Upper Buford Circle St. Paul, MN 55108 E-mail: First five letters of my last name + 036 + umn.edu (you know where to put the @)