Pavlinov I Ia
Zh Obshch Biol. 2004 Jul-Aug;65(4):334-66.
Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into phylistics (Rasnitsyn's term; close to Simpsonian evolutionary taxonomy) belonging rather to the classical realm, and Hennigian cladistics that pays attention to origin of monophyletic taxa exclusively. In early of the 20th century, microevolutionary doctrine became predominating in evolutionary studies. Its core is the population thinking accompanied by the phenetic one based on equation of kinship to overall similarity. They were connected to positivist philosophy and hence were characterized by reductionism at both ontological and epistemological levels. It led to fall of classical phylogenetics but created the prerequisites for the new phylogenetics which also appeared to be full of reductionism. The new rise of phylogenetic (rather than tree) thinking during the last third of the 20th century was caused by lost of explanatory power of population one and by development of the new worldview and new epistemological premises. That new worldview is based on the synergetic (Prigoginian) model of development of non-equilibrium systems: evolution of the biota, a part of which is phylogeny, is considered as such a development. At epistemological level, the principal premise appeared to be fall of positivism which was replaced by post-positivism argumentation schemes. Input of cladistics into new phylogenetics is twofold. On the one hand, it reduced phylogeny to cladistic history lacking any adaptivist interpretation and presuming minimal evolution model. From this it followed reduction of kinship relation to sister-group relation lacking any reference to real time scale and to ancestor-descendant relation. On the other hand, cladistics elaborated methodology of phylogenetic reconstructions based on the synapomorphy principle, the outgroup concept became its part. The both inputs served as premises of incorporation of both numerical techniques and molecular data into phylogenetic reconstruction. Numerical phyletics provided the new phylogenetics with easily manipulated algorithms of cladogram construing and thus made phylogenetic reconstructions operational and repetitive. The above phenetic formula "kinship = similarity" appeared to be a keystone for development of the genophyletics. Within numerical phyletics, a lot of computer programs were elaborated which allow to manipulate with evolutionary scenario during phylogenetic reconstructions. They make it possible to reconstruct both clado- and semogeneses based on the same formalized methods. Multiplicity of numerical approaches indicates that, just as in the case of numerical phenetics, choice of adequate method(s) should be based on biologically sound theory. The main input of genophyletics (= molecular phylogenetics) into the new phylogenetics was due to completely new factology which makes it possible to compare directly such far distant taxa as prokaryotes and higher eukaryotes. Genophyletics is based on the theory of neutral evolution borrowed from microevolutionary theory and on the molecular clock hypothesis which is now considered largely inadequate. The future developments of genophyletics will be aimed at clarification of such fundamental (and "classical" by origin) problems as application of character and homology concepts to molecular structures. The new phylogenetics itself is differentiated into several schools caused basically by diversity of various approaches existing within each of its "roots". Cladistics makes new phylogenetics splitted into evolutionary and parsimonious ontological viewpoints. Numerical phyletics divides it into statistical and (again) parsimonious methodologies. Molecular phylogenetics is opposite by its factological basis to morphological one. The new phylogenetics has significance impact onto the "newest" systematics. From one side, it gives ontological status back to macrotaxa they have lost due to "new" systematics based on population thinking. From another side, it rejects some basical principles of classical phylogenetic (originally Linnean) taxonomy such as recognitions of fixed taxonomic ranks designated by respective terms and definition of taxic names not by the diagnostic characters but by reference to the ancestor. The latter makes the PhyloCode overburdened ideologically and the "newest" systematics self-controversial, as concept of ancestor has been acknowledged non-operational from the very beginning of cladistics. Relation between classical and new phylogenetics is twofold. At the one hand, general phylogenetic hypothesis (in its classical sense) can be treated as a combination of cladogenetic and semogenetic reconstructions. Such a consideration is bound to pay close attention to the uncertainty relation principle which, in case of the phylogenetics, means that the general phylogenetic hypothesis cannot be more certain than any of initial cladogenetic or semogenetic hypotheses. From this standpoint, the new phylogenetics makes it possible to reconstruct phylogeny following epistemological principle "from simple to complex". It elaborates a kind of null hypotheses about evolutionary history which are more easy to test as compared to classical hypotheses. Afterward, such hypotheses are possible to be completed toward the classical, more content-wise ones by adding anagenetic information to the cladogenetic one. At another hand, reconstructions elaborated within the new phylogenetics could be considered as specific null hypotheses about both clado- and semogeneses. They are to be tested subsequently by mean of various models, including those borrowed from "classical" morphology. The future development of the new phylogenetics is supposed to be connected with getting out of plethora of reductionism inherited by it from population thinking and specification of object domain of the phylogenetics. As the latter is a part of an evolutionary theory, its future developments will be adjusted with the latter. Lately predominating neodarwinism is now being replaced by the epigenetic evolutionary theory to which phylistics (one of the modern versions of classical phylogenetics) seems to be more correspondent.
进化思想是现代生物学的核心。因此,处理生物学历史重建的系统发育学在生物学科中占据优先地位。20世纪下半叶,人们对宏观分类水平上的系统发育重建产生了浓厚兴趣,这种兴趣取代了30年代至60年代占主导地位的微观进化研究。这意味着从群体思维向系统发育思维的转变,但这并非经典系统发育学的复兴;相反,一种新方法应运而生,并被称为“新系统发育学”。它是60年代至70年代独立发展的三门学科——分支系统学、数值系统学和分子系统学(现在基本上是基因系统学)——融合的结果。因此,新系统发育学可以被定义为进化生物学的一个分支,旨在通过数值方法,主要基于分子数据,构建“简约”的分支系统假设。经典系统发育学作为新系统发育学的历史前身,是在自然哲学世界观的基础上出现的,其中包括生物群落的超有机体概念。根据这种观点,历史发展(系统发育)被认为是个体发展(个体发育)的类比,因此其最基本的特征是“部分”(分类群)的渐进平行发展,并辅以达尔文的单系概念。根据对这些概念之间关系的特定解释,经典系统发育学中出现了两种主要传统。其中之一(科普、谢韦尔佐夫)轻视单系性,将大部分注意力放在形态特征的渐进平行发展上。这种态度使这种系统发育学更像是主要处理结构进化而非分类群进化的半遗传学。另一种传统(海克尔)同时考虑分类群起源的单系性和平行性:在20世纪中叶,它分为更属于经典领域的系统分类学(拉兹尼琴的术语;接近辛普森的进化分类学)和仅关注单系分类群起源的亨尼希分支系统学。在20世纪初,微观进化学说在进化研究中占据主导地位。其核心是群体思维,伴随着基于亲缘关系等同于总体相似性的表型分类思维。它们与实证主义哲学相关联,因此在本体论和认识论层面都具有还原论的特征。这导致了经典系统发育学的衰落,但为新系统发育学创造了前提条件,新系统发育学似乎也充满了还原论。20世纪最后三分之一时间里系统发育(而非树形)思维的新崛起,是由于群体思维解释力的丧失以及新世界观和新认识论前提的发展。这种新世界观基于非平衡系统发展的协同(普里戈金)模型:生物群落的进化,其中一部分是系统发育,被视为这样一种发展。在认识论层面,主要前提似乎是实证主义的衰落,它被后实证主义论证方案所取代。分支系统学对新系统发育学的贡献是双重的。一方面,它将系统发育简化为缺乏任何适应主义解释且假定最小进化模型的分支历史。由此得出,亲缘关系简化为姐妹群关系,而不涉及任何实际时间尺度和祖先 - 后代关系。另一方面,分支系统学基于共衍征原则阐述了系统发育重建的方法,外类群概念成为其一部分。这两个贡献都成为将数值技术和分子数据纳入系统发育重建的前提。数值系统学为新系统发育学提供了易于操作的分支图构建算法,从而使系统发育重建具有可操作性和重复性。上述表型公式“亲缘关系 = 相似性”似乎是基因系统学发展的关键。在数值系统学中,人们精心设计了许多计算机程序,这些程序允许在系统发育重建过程中处理进化场景。它们使得基于相同的形式化方法既可以重建分支发生,也可以重建半发生。多种数值方法表明,就像在数值表型分类学的情况一样,选择适当的方法应该基于生物学上合理的理论。基因系统学(=分子系统学)对新系统发育学的主要贡献在于全新的事实依据,这使得直接比较原核生物和高等真核生物等如此遥远的分类群成为可能。基因系统学基于从微观进化理论借鉴的中性进化理论和分子钟假设,而现在人们认为分子钟假设在很大程度上是不充分的。基因系统学未来的发展将旨在阐明一些基本(且起源上“经典”)的问题,比如特征和同源性概念在分子结构中的应用。新系统发育学本身由于其每个“根源”中存在的各种方法的多样性而分化为几个学派。分支系统学使新系统发育学分为进化和简约的本体论观点。数值系统学将其分为统计和(再次)简约的方法。分子系统学因其事实依据与形态学相反。新系统发育学对“最新”的分类学有重大影响。一方面,它将宏观分类群的本体论地位归还给它们,这些分类群由于基于群体思维的“新”分类学而失去了这种地位。另一方面,它摒弃了经典系统发育学(最初是林奈分类学)的一些基本原则,比如对由各自术语指定的固定分类等级的认可,以及分类名称不是由诊断特征而是通过参考祖先来定义。后者使得系统发育法规在思想上负担过重,并且“最新”的分类学自相矛盾,因为从分支系统学一开始,祖先概念就被认为是不可操作的。经典系统发育学和新系统发育学之间的关系是双重的。一方面,一般系统发育假设(在其经典意义上)可以被视为分支发生和半发生重建的组合。这样的考虑必然要密切关注不确定性关系原则,就系统发育学而言,这意味着一般系统发育假设不可能比任何初始的分支发生或半发生假设更确定。从这个角度来看,新系统发育学使得按照“从简单到复杂”的认识论原则重建系统发育成为可能。它阐述了一种关于进化历史的零假设,与经典假设相比,这些假设更容易检验。之后,可以通过向分支发生信息中添加前进演化信息,将这些假设完善为更具内容的经典假设。另一方面,在新系统发育学中构建的重建可以被视为关于分支发生和半发生的特定零假设。随后,它们将通过各种模型进行检验,包括那些从“经典”形态学借鉴的模型。新系统发育学未来的发展应该与摆脱它从群体思维继承的过多还原论以及明确系统发育学的对象领域相关联。由于后者是进化理论的一部分,其未来的发展将与进化理论相协调。最近占主导地位的新达尔文主义现在正被表观遗传进化理论所取代,而系统分类学(经典系统发育学的现代版本之一)似乎与表观遗传进化理论更相符。