Genosystematics: from E. Chargaff and A. N. Belozersky up to date

A review of history of genosystematics (macromolecular systematics) from E. Chargaff and A. N. Belozersky up to date. The role of A.N. Belozersky and his collaborators in the development of this new branch of systematics is analyzed. Genosystematics was the source of valuable information clarifying some aspects of biological evolution. Its methods were successfully employed in microorganisms--(e.g., discovery of archaebacteria) and in eucaryote systematics (origin of plastids, falcification of "molecular clock" hypothesis, substantial changes in higher plants phylogenetics, etc.). However, attempts to employ some fragmentary and unreliable data obtained by genosystematics for modifying the existing phylogenetic schemes and systems of organisms failed. Nowadays genosystematics is like a newborn child suffering from children's diseases well-known to "classical" systematics. It is rather far from final conclusions describing the evolution of genotypes. Some of its recent achievments, e.g., elaboration of the concept of PhyloCode, allow to believe that this science is able to suggest revolutionary changes in Linnean systematics.     

Genosystematics: From E. Chargaff and A.N. Belozersky To the Present

This review considers the history of genosystematics (macromolecular systematics) from early studies of E. Chargaff and A.N. Belozersky up to the present, with emphasis on the most important discoveries in the field. The potential and limitations of genosystematics and possible ways of further development are analyzed using plants as an example. The future of genosystematics depends to a great extent on adequate employment of its methods in studying the problems of phylogeny and taxonomy. Analysis of recent publications shows that this requirement is not always met. It is no less important to design and improve the methods of genosystematics, especially those for comparing complete genomes.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 581–589.Original Russian Text Copyright © 2005 by Antonov.     

On interrelation between genetic systematics and genomics

Review papers describing recent achievements of genomics usually do not pay attention to direct interrelation between genomics and genosystematics (DNA-systematics). Genomics on general is based in complete DNA sequencing of genomes. Initial aim of genosystematics was the same. Absence of historical perspective in review papers devoted to genomics decreases its value. In case it is done deliberately it becomes the problem of scientific ethics. It is postulated that genomics is a natural stage of genosystematics (DNA-systematics) development. Russian scientists were among the founders of these branches of biology.     

TRENDS IN AVIAN SYSTEMATICS

The classical "new systematics" with its replacement of the monotypic by the polytypic species, and of the morphological by the biological species concept, is now so universally accepted in ornithology that it can hardly be considered any longer as "new". Present trends indicate two areas of avian systematics favourable for active expansion, population systematics and phylogenetic systematics. Instead of describing the population structure of species in terms of subspecies, the trend will be to describe it in terms of "geographical isolates", "population continuats", and "zones of secondary intergradation" of former geographic isolates. Such an analysis can shed much light on the ecological requirements of species and on their former history. The other area of new avian systematics is a re-activated study of the higher categories of birds, with new methods and interpreted by a re-evaluated set of phylogenetic and evolutionary concepts.     

哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

Foundations of the new phylogenetics

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.     

Gene trees and species trees – mutual influences and interdependences of population genetics and systematics

Both population genetics and systematics are core disciplines of evolutionary biology. While systematics deals with genealogical relationships among taxa, population genetics has mainly been based on allele frequencies and the distribution of genetic variants whose genealogical relations could for a long time, due mainly to methodological constraints, not be inferred. The advent of mitochondrial DNA analyses and modern sequencing techniques in the 1970s revolutionized evolutionary genetic studies and gave rise to molecular phylogenetics. In the wake of this new development systematic approaches and principles were incorporated into intraspecific studies at the population level, e.g. the concept of monophyly which is used to delineate evolutionarily significant units in conservation biology. A new discipline combining phylogenetic analyses of genetic lineages with their geographic distribution ('phylogeography') was introduced as an explicit synthesis of population genetics and systematics. On the other hand, it has increasingly become obvious that discordances between gene trees and species trees not only result from spurious data sets or methodological flaws in phylogenetic analyses, but that they often reflect real population genetic processes such as lineage sorting or hybridization. These processes have to be taken into account when evaluating the reliability of gene trees to avoid wrong phylogenetic conclusions. The present review focuses on the phenomenon of non-phylogenetic sorting of ancestral polymorphisms, its probability and its consequences for molecular systematics.     

Anopheles (Cellia) epiroticus (Diptera: Culicidae), a new malaria vector species in the Southeast Asian Sundaicus Complex

Anopheles sundaicus species A of the Southeast Asian A. sundaicus complex is formally named Anopheles epiroticus Linton & Harbach based on DNA sequence differentiation of the whole nuclear ITS2 region and a portion of both the cytochrome b and cytochrome c oxidase I mitochondrial genes. Detailed comparative morphological studies of the adult, larval and pupal stages did not reveal any differential or diagnostic differences that reliably distinguish A. epiroticus from A. sundaicus s.s. Information is provided on the bionomics and systematics of the new species.     

A problem of truth in biological systematics

A possibility to put a question of truth of knowledge in biological systematics is studied. It is shown that the problem of truth in reference to systematics is wider than a question of classified information reliability. Prerequisites needed for logically accurate formulation of a definition and criteria of truth are considered. It is shown that such prerequisites are present in taxonomic practice, namely in a process of diagnosis compiling. Philosophical analysis of this work has been carried out. Interpretation of an essence of systematics as classification is connected with use of classical concept of truth (which defines truth as correspondence between knowledge and object) in its undeveloped form. Carried analysis allows supposing that a theory of systematics based on diagnostics rather than on classification would be more prospective. Use of imperfect concept of truth can be seen also in notions that system of taxa must reflect its evolutionary history. Development and modernization of Aristotle's orientation to discovery of the object form can become an alternative to such opinions. An aspiration to achieve the truth is the main motive of systematic work. An influence of this aspiration on a selection of purposes of taxonomic work and theoretical comprehension of its bases is shown. Such features of modern biological systematics as its accessibility for new results, criticism in respect of external morphological characters, and interest in intraspecific variability are connected with this aspiration. This motive comes into contradiction with a tendency to withdraw the problem of truth as such, which takes place in some brunches of theoretic systematics.     

中国昆虫分类学研究进展

<正> 中国自然条件复杂,昆虫种类繁多,特别是横断山区、青藏高原和云南西双版纳等热带雨林地区昆虫区系丰富多彩,受到国内、外昆虫分类学家的青睐。根据保守估计,中国应有15万种昆虫。中华人民共和国成立前夕我国仅记载20069种昆虫,其中中国人命名的仅204种,绝大多数模式标本及文献资料均散落于国外;分     

PARTIAL CHARACTERIZATION OF THE CHLOROPLAST GENOME FROM THE CHROMOPHYTIC ALGA SYNURA PETERSENII (SYNUROPHYCEAE)1

Hoechst dye 33258-CsCl density gradients were used to isolate two satellite DNA species from Synura petersenii Korsh. sensu lato, a member of the Synurophyceae. One satellite DNA was identified as the chloroplast genome. The chloroplast genome is the smallest (91.5 kb) published for any chromophyte and approximates the size of the smallest functional chlorophyte chloroplast genome (Codium fragile, 89 kb). The second satellite DNA was small (34.5 kb), and its origin is undetermined. The potential of using the S. petersenii chloroplast genome in comparative studies for evaluating organellar evolution and algal systematics is discussed.     

Zoo behaviour science in the Research Centre for Vertebrate Studies of the Academy of Sciences of the German Democratic Republic (in the Animal Park of Berlin)

This is a report of the results of behaviour science studies in the Animal Park of Berlin and the Academy of Sciences in the German Democratic Republic (G.D.R.). The major goal of this research is to investigate the behaviour of rare animals as a basis for zoological research, systematics and comparative studies in evolution. In addition, further research provided information directly applicable to behavioural management in zoos, farms and wild animal collections. Three main comparative studies dealt with urination and defecation in mammals, allelomimetic behaviour in vertebrates, and audio-visual orientation responses in several species of birds and mammals. Ethograms were created for the Red Woolly Opossum, Maned Wolf, Takin and Giant Eland Antelope. Social and reproductive behaviour studies were conducted on the Wolf, Golden Lion Marmoset, Père David's Deer, Mouflon and Wild Boar. Reports are included on the circadian activity of Pigmy Armadillo and Wild Boar. New information was revealed regarding communication in Mouflon and Père David's Deer, in addition to the new finding that some social behaviour patterns in Wild Boar are dependent on circadian rhythms. Three wolf packs studied consecutively in the same enclosure revealed that each pack differed in its social behaviour and that the dominant female (alpha female) determined the social structure. The problem of animal-human interactions is discussed. Zoos are seen as a medial stage between wilderness and farm management. It is suggested that an important task of zoo behaviour science is to study the ability of wild animals to adapt to purposes such as animal farms, animal husbandry institutes and domestic animal productivity, and to study the behaviour of the original forms of domestic animals in order to better understand and manage them.     

分子系统学研究进展

分子系统学 ( molecular systematics)是近 30年发展起来的一门综合性前沿学科 ,它在分子水平上对生物进行遗传多样性、分类、系统发育和进化等方面的研究 ,其研究结果对于保护生物多样性 (尤其是遗传多样性 ) ,揭示生物进化历程及机理具有十分重要的意义。1　分子系统学的定义及发展简史分子系统学是通过检测生物大分子包含的遗传信息 ,定量描述、分析这些信息在分类、系统发育和进化上的意义 ,从而在分子水平上解释生物的多样性、系统发育及进化规律的一门学科。它以分子生物学、系统学、遗传学、分类学和进化论为理论基础 ,以分子生物学…     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

分子生物学手段在植物系统与进化研究中的应用

在植物系统与进化研究中,为了揭示真实本质,必须从分子水平进行研究。植物分子系统学的研究包括两大方面,一是蛋白质与酶,二是核酸。酶电泳是分子水平上研究植物分子遗传学最经济有效的方法,可以有效地揭示自然居群中遗传结构、基因流动、变化系统、选择作用和系统发育等问题。植物核酸系统学的研究倍受青睐,因为核酸分子是最基本的进化单元,几乎不受主观因素影响。相关的核酸分析技术主要有：DNA杂交、DNA限制酶谱分析、RFLP分析、DNA指纹图技术、RAPD分析和核酸序列分析。在植物系统学和进化研究中,结合各方面的生物学证据,才能显示植物分子系统学的独特优势。     

分子生物学技术在昆虫系统学研究中的应用

分子生物学技术应用于昆虫系统学研究,是８０年代末新兴起来的,近几年来发展相当迅速。为了把握这个研究方向,并促进这个研究领域的发展,作者从研究方法、研究内容、研究对象等方面着手,对近１０年来分子生物学技术应用于昆虫系统学中的研究进展进行了概括和总结。介绍了ＤＮＡ序列测定、ＲＦＬＰ,分子杂交技术、ＲＦＰＬ、分子杂交技术、ＲＡＰＤ、ＳＳＣＰ及ＤＳＣＰ等几种主要方法及其应用情况,并从种及种下阶元的分类鉴定     

Morphobiological aspects of Rhodnius brethesi Matta, 1919 (Hemiptera:Reduviidae) from the Upper and Middle Negro River, Amazon region of Brazil: I - scanning electron microscopy

The occurrence of autochthonous cases of Chagas disease in the Amazon region of Brazil over recent decades has motivated an intensification of studies in this area. Different species of triatomines have been identified, and ten of these have be proven to be carriers of the parasite Trypanosoma cruzi or " cruzi-like " parasites. Studies conducted in the municipalities of Santa Isabel do Rio Negro and Barcelos, located on the Upper and Middle of the Negro River, microregion of Negro River, state of Amazonas have confirmed not only that Rhodnius brethesi is present in the palm tree Leopoldinia piassaba, but also that this insect was recognized by palm fiber collectors. A morphological study of eyes, inter-ocular and inter-ocellar regions, antennae, buccula, labrum, rostrum, stridulatory sulcus and feet, including the apex of the tibia, spongy fossette and ctenidium was conducted by scanning electron microscopy. The buccula and the stridulatory sulcus presented notable differences in specimens of different genera and also of different species. These data make it possible to suggest that the details presented in these structures can be included as diagnostic characteristics to be used in new dichotomous keys, thereby contributing towards studies of taxonomy and systematics and furnishing backing for comparative analysis of specimens collected from different localities.     

Middle ear morphology of Lemur variegatus. Some implications for primate paleontology.

The middle ear morphology of Lemur variegatus, a strepsirhine primate, is described. Although no promontory branch of the internal carotid artery appears, there is a well-developed "promontory canal" containing a nerve trunk. This structure, which is previously undescribed in strepsirhines, is made up of the tympanic nerve and the internal carotid nerve. The implications of this discovery for paleontology, systematics, and future research are discussed.