乔治. 罗马尼斯（ George John Romanes），一位19世纪 英国 著名演化生物学家和生理学家。他的出名 可能并非仅仅因为他的职业或成就，可能也因为 他有一个挚友：查尔斯.达尔文。 乔治出身殷实的宗教家庭，受到过良好的教育，精通多国语言，热爱诗歌、音乐、科学。最为重要的是，他还承袭了父亲”随和平静的人格气质“。 当62岁的达尔文在剑桥大学第一次遇到了这位23岁的年轻人，他就交下了这个朋友，很快他们成为了莫逆之交。 作为达尔文的最年轻的朋友，乔治与达尔文的学术关系紧密。 达尔文生命最后的八年学术生涯是在乔治的帮助下度过的，乔治在此期间担任达尔文的研究助理工作。 虽然终身在捍卫达尔文的理论，但是乔治并没有被达尔文的光芒遮蔽。他的一系列贡献也引起了很多关注，其中包括： 第一次提出了”新达尔文主义（neo-Darwinism）“的概念（即自然选择是最主要的演化力量），并沿用至今。 第一次提出了”生理选择“的概念，并指出了自然选择并不是物种形成的直接原因，生理选择造成的生殖隔离才是第一起始原因。因此现在的课本中才有一种生物学物种的概念，即物种内没有生殖隔离。 His idea was that variation in reproductive ability, caused mainly by the prevention of inter-crossing with parental forms, was the primary driving force in the production of new species. The majority view then (and now) was that geographical separation is the primary force in species splitting (orallopatry) and secondarily was the increased sterility of crosses between incipient species. 1886年，乔治在nature发表了自己生理选择的学说（ Romanes, G. J. Physiological selection; an additional suggestion on the origin of species. Zool. J. Linn. Soc . 19 , 337–411 (1886). ），摘选如下： 1）But, in order to secure diversity, multiplication, or ramification of species, it appears to me obvious that the primary condition required is that of preventing intercrossing with parent forms at the origin of each branch-whether the prevention be from the first absolute, or only partial. 物种多样性、增殖、分化的前提是不育祖代杂交。生理选择造成的杂交抑制，是物种多样性的原因。 2）But when once this condition is supplied by physiological selection, I have no doubt that divergence of character may then be promoted by natural selection, in the way that is explained by Mr. Darwin. 先有生理的选择，导致了杂交不育（或不亲和），进而会出现自然选择导致的性状分化。 3) 作者提出生理的选择相对于自然选择有优势。因为生理选择可以解释达尔文提出的表型特征的分化，作者同时将这种分化称之为物种的衍生ramification of species. 达尔文的逻辑顺序，被他颠倒了。作者认为先有初级分化，然后才有自然选择。而不是达尔文认为的先有自然选择，然后有初级分化。该理论可以解释同域成种。同域成种现象似乎是达尔文自然选择原则无法解释的问题。 4) 该文章认为自然选择是属、科、目甚至纲级生物的起源原因；但是生理选择是物种水平的起源原因。 乔治的观点，于现代的生物学研究具有积极的意义，因为他提出了对于种内多样性或初始种（ incipient species ）、同域成种的一种生物学可检测的解释。 可能最难能可贵的是，乔治在达尔文的盛名之下，敢于发表自己独特的看法（尽管他自己认为是补充性的）；同时，达尔文对乔治科学观点的宽容，这或许也是英国学术得以昌盛的秘诀。
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Diversification Analysis: Lineage through time plots can be done in ape ; nLTT can estimate the normalized lineage through time statistic, which can be used as a summary statistic in ABC approaches . A simple birth-death model for when you have extant species only (sensu Nee et al. 1994) can be fitted in ape as can survival models and goodness-of-fit tests (as applied to testing of models of diversification). TESS can calculate the likelihood of a tree under a model with time-dependent diversification, including mass extinctions. Net rates of diversification (sensu Magellon and Sanderson) can be calculated in geiger . diversitree implements the BiSSE method (Maddison et al. 1997) and later improvements (FitzJohn et al. 2009). TreePar estimates speciation and extinction rates with models where rates can change as a function of time (i.e., at mass extinction events) or as a function of the number of species. caper can do the macrocaic test to evaluate the effect of a a trait on diversity. apTreeshape also has tests for differential diversification (see description ). iteRates can identify and visualize areas on a tree undergoing differential diversification. DDD can fit density dependent models as well as models with occasional escape from density-dependence. BAMMtools is an interface to the BAMM program to allow visualization of rate shifts, comparison of diversification models, and other functions. DDD implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, as well as identifies key innovations and simulate a density-dependent process. PBD can calculate the likelihood of a tree under a protracted speciation model. phyloTop has functions for investigating tree shape, with special functions and datasets relating to trees of infectious diseases. 分化分析： ape 可以谱系随时间变化的图形； nLTT 可以进行谱系的时间变化的标准化统计，从而汇总统计不同方法的结果。当你只有现存物种时（根据 Nee et al. 1994 ），一个简单的出生 - 死亡模型可以使用 ape 模拟 ，同时，可以用 ape 进行生存模型和拟合度测试（同多样化模型的测试）。 TESS 可以计算出一棵树在具有时间依赖的分化模型下的似然值，包括大规模灭绝。净分化速率（依据 Magellon and Sanderson ）可用 geiger 计算。 diversitree 可运行 BiSSE 方法（ Maddison et al. 1997 ）并进行后续优化（ FitzJohn et al. 2009 ）。 TreePar 通过模型估计物种形成和灭绝速率，模型中的速率可以随时间（即大规模灭绝事件）或物种数量的变化而变化。 caper 可以做 macrocaic 测试来评估一个性状对多样性的影响。 apTreeshape 也有趋异分化检验（见说明）。 iteRates 可以识别和可视化系统发育树上正在经历趋异分化的区域。 DDD 既能拟合密度依赖模型，也能拟合偶尔脱离密度依赖的模型。 BAMMtools 是 BAMM 程序的一个接口，用于可视化速率变化、多样化模型比较和其他功能。 DDD 实现了基于多样性依赖的出生 - 死亡过程的最大似然方法，以检验物种形成或灭绝是否依赖于多样性，识别关键创新并模拟密度依赖过程。 PBD 可以计算一棵树在长时间物种形成模型下的可能性。 phyloTop 具有研究树形的功能，具有与传染病树相关的特殊功能和数据集。 https://cran.r-project.org/web/views/Phylogenetics.html
新物种是怎样形成的？物种形成难以直接观测，因为它是一个漫长的过程。人们曾在理论上分为，当一个物种的种群相互分开、去适应不同环境时，它们在杂交方面就会变得不太成功，就可能形成新物种。在一个实验中，研究人员使用了两个菌种的 酵母 ，它们在能够加快物种形成的实验室条件下繁殖。该实验证实，适应于不同环境的种群的杂交与全部适应于同一环境的种群的杂交相比，前者的繁殖能力差一些（适应性差一些）。这是趋异适应与生殖隔离的发展之间的一个根本性联系的直接证据。 部分英文原文： Nature 447, 585-588 (31 May 2007) | doi:10.1038/nature05856 ; Received 2 November 2006; Accepted 12 April 2007 Incipient speciation by divergent adaptation and antagonistic epistasis in yeast Jeremy R. Dettman1, Caroline Sirjusingh1, Linda M. Kohn1 James B. Anderson1 Department of Ecology Evolutionary Biology, University of Toronto, Mississauga, Ontario, L5L 1C6, Canada Correspondence to: Jeremy R. Dettman1 Correspondence and requests for materials should be addressed to J.R.D. (Email:jdettman@utm.utoronto.ca). Abstract Establishing the conditions that promote the evolution of reproductive isolation and speciation has long been a goal in evolutionary biology1, 2, 3. In ecological speciation, reproductive isolation between populations evolves as a by-product of divergent selection and the resulting environment-specific adaptations4, 5, 6. The leading genetic model of reproductive isolation predicts that hybrid inferiority is caused by antagonistic epistasis between incompatible alleles at interacting loci1, 7. The fundamental link between divergent adaptation and reproductive isolation through genetic incompatibilities has been predicted1, 4, 5, but has not been directly demonstrated experimentally. Here we empirically tested key predictions of speciation theory by evolving the initial stages of speciation in experimental populations of the yeast Saccharomyces cerevisiae. After replicate populations adapted to two divergent environments, we consistently observed the evolution of two forms of postzygotic isolation in hybrids: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. This divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by the ecological speciation theory. Our experimental system allowed controlled comparison of the relative importance of ecological and genetic isolation, and we demonstrated that hybrid inferiority can be ecological and/or genetic in basis. Overall, our results show that adaptation to divergent environments promotes the evolution of reproductive isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature.
为了理解物种形成（ speciation), 我们首先需要知道物种是什么，也就是物种的概念（ species concept) 。而关于物种概念的争论似乎从未休止，相比而言，有关物种形成的研究少得多。近年来，有关解决 所谓的 物中概念的争议取得了一些进展，越来越多地赞成基于谱系的进化物种概念（ Evolutionary Species Concept ）。这些新近取得成果要求我们重新考虑如何研究物种形成。传统的基于生物种概念（ Biological Species Concept ）的物种形成研究使得理解非异域物种形成 (non-allopatric spciation) 是如何发生，物种如何分化和物种间如何保持隔离等方面取得了重要的进展。然而，这些研究忽视了一个首要问题，即对于最普遍的物种形成的地理模式（异域式）下，新种是如何产生的，换句话说，一个物种怎样分裂成二个。这就需要采用一种新的和非常不同的研究方案来理解一个祖先种分裂出新的异域分布的谱系之生态和进化过程。这种研究方案将把物种形成和进化生物学、生态学和生物地理学及保护生物学中的许多其它基本问题联系在一起。（ Wiens JJ. What Is Speciation and How Should We Study It? Am Nat 163: 914-923, 2004. ) 评论：物种起源是进化生物学的基本问题之一，然而如果对物种形成没有比较统一的认识，这个问题似乎不可能解决。这篇关于物种概念的评论文章非常有趣，作者争论认为，当涉及到研究物种形成时，采用不同的物种概念会产生很大影响，他认为在众多的物种概念中，最适宜的物种概念是将有性生殖的物种定义为 : 通过基因流而相联系的最大的单个谱系（ lineage) 。采用这种定义的结果之一是将我们的注意力从探讨内部生殖隔离机制的演化转移到异域居群的演化上来，尤其是寻求异域性的生态和进化基础。尽管我们可以从此篇文章中诸多方面提出不同的看法，而作者列出的一些问题的确很新颖和富有说服力，必将给许多进化生物学家、生态学家、遗传学家和生理学家带来兴趣。
Speciation: A new role for reinforcement Smadja C, Butlin R. Speciation: A new role for reinforcement. Heredity. 2006 Jun; 96 (6): 422-3. Speciation-A new role for reinforcement Plant speciation Rieseberg LH, Willis JH. Plant speciation. Science. 2007 Aug 17; 317 (5840): 910-4. Like the formation of animal species, plant speciation is characterized by the evolution of barriers to genetic exchange between previously interbreeding populations. Prezygotic barriers, which impede mating or fertilization between species, typically contribute more to total reproductive isolation in plants than do postzygotic barriers, in which hybrid offspring are selected against. Adaptive divergence in response to ecological factors such as pollinators and habitat commonly drives the evolution of prezygotic barriers, but the evolutionary forces responsible for the development of intrinsic postzygotic barriers are virtually unknown and frequently result in polymorphism of incompatibility factors within species. Polyploid speciation, in which the entire genome is duplicated, is particularly frequent in plants, perhaps because polyploid plants often exhibit ecological differentiation, local dispersal, high fecundity, perennial life history, and self-fertilization or asexual reproduction. Finally, species richness in plants is correlated with many biological and geohistorical factors, most of which increase ecological opportunities. Plant speciation The nature of plant species Rieseberg LH, Wood TE, Baack EJ. The nature of plant species. Nature. 2006 Mar 23; 440 (7083): 524-7. Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera ( 80%), the correspondence of taxonomic species to these clusters is poor ( 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages. The nature of plant species There shall be order. The legacy of Linnaeus in the age of molecular biology Paterlini M. There shall be order. The legacy of Linnaeus in the age of molecular biology. EMBO Rep. 2007 Sep; 8 (9): 814-6. There shall be order DNA barcodes: recent successes and future prospects Dasmahapatra KK, Mallet J. DNA barcodes: recent successes and future prospects. Heredity. 2006 Oct; 97 (4): 254-5. Epub 2006 Jun 21. DNA barcodes-recent successes and future prospects The molecular genetics of crop domestication Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006 Dec 29; 127 (7): 1309-21. Ten thousand years ago human societies around the globe began to transition from hunting and gathering to agriculture. By 4000 years ago, ancient peoples had completed the domestication of all major crop species upon which human survival is dependent, including rice, wheat, and maize. Recent research has begun to reveal the genes responsible for this agricultural revolution. The list of genes to date tentatively suggests that diverse plant developmental pathways were the targets of Neolithic genetic tinkering, and we are now closer to understanding how plant development was redirected to meet the needs of a hungry world. The molecular genetics of crop domestication
标签: 物种形成
