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.     

蚂蚁分子系统学研究进展

蚂蚁是分布广泛、种类和数量丰富的社会性昆虫.蚂蚁的传统分类学研究存在一定局限性,而分子生物学为蚂蚁的系统学研究提供了新途径.概述了蚂蚁分子系统学在研究内容和技术方法上的研究进展,并对今后的研究做了展望.     

核糖体DNA在黏菌分子系统学研究中的应用与发展

文中综述了核糖体基因在黏菌分子系统学研究中应用现状,并就目前黏菌分子系统中存在的问题及发展方向提出了看法。     

Systematics,conservation and sustainable development

The contribution of systematics to conservation and sustainable use of species is discussed. An adequate inventory of species is required for both areas and recent field work shows that the inventory is far from complete. This supports the first mission of Agenda 2000 which is to discover described and inventory global species diversity. The importance of making these data available in data base format is stressed. Sound systematics is a necessity for conservation legislation where control depends on the ability to identify organisms correctly. The establishment of reserves is also dependent upon data from systematics about centres of diversity and endemism and examples of this are given. Molecular systematics has made new tools available to conservation such as genetic fingerprinting which is useful both to breeding programmes of rare species and for identification for legal proceedings.Systematics is also one of the foundations for programmes of sustainable development especially in the search for new crops, non-timber forest plants from extraction forests and the identification of wild relatives of crop species. Examples of the role of systematics in a fuelwood programme in Zimbabwe, a sustainable development programme in northeast Brazil and in the search for a chemical component with medicinal properties for curing AIDS are given. The more predictive a classification we can develop using modern cladistic and molecular techniques the more useful systematics will be for both conservation and sustainable development. The goal of Agenda 2000 to organize the information derived from the programme in an efficiently retrievable form that best meets the needs of science and society is a laudable target that is crucial for conservation and the sustainable use of the plant resources of the world.     

The progress of DNA analyzing techniques and its impact on plant molecular systematics

Recent advances in manipulating nucleic acids have opened a new research field called plant molecular systematics. This short review provides an overview of molecular techniques which have been used in the analysis of DNA molecules for the study of plant systematics, with a special emphasis on PCR. The early application of DNA analysis, DNA/DNA hybridization, has not become popular with plant systematists, because of several disadvantages inherent in the method. The survey of restriction fragment length polymorphisms (RFLPs), on the contrary, has become one of the preferred methods used by plant molecular systematists, since the method is relatively easy to perform. Although unambiguous data can be obtained by both long-range restriction mapping and nucleotide sequencing, these approaches may have limited use in plant molecular systematics because of their laborious experimental procedures relying on conventional molecular cloning techniques. To date, PCR based analyses of the DNA molecule seem to be the most suitable experimental approach for plant molecular systematics. Several advantages of the method have changed both the quality and quantity of the DNA data. Further application of PCR to plant molecular systematics will open up a new era in the field. The present paper is based on the contribution which was read in a symposium entitled “Organellar DNA Variations in Higher Plants and their Taxonomic Significance”, at the 50th Annual Meeting of the Botanical Society of Japan in Shizuoka on October 2, 1990, under the auspices of the Japan Society of Plant Taxonomists.     

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.     

From birth to christening

A brief history of comparative studies of nucleic acids for systematic purposes is given. These studies were initiated by a group of Moscow State University scientists headed by A. N. Belozersky. Based mostly on comparative DNA studies, some main dogmas of a new branch of systematics were gradually developed. In Russia, this new branch of systematics is called "genosystematics". Some of the main results obtained by genosystematics since its birth (1957) and up to its "christening" (1974) are described.     

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.     

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.     

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

The advent and maturation of algorithms for estimating species trees—phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes—represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long‐standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.     

On the difference between mono-, holo-, and paraphyletic groups: a consistent distinction of process and pattern

About 50 years ago, the German entomologist Willi Hennig presented a new approach in biological systematics that he called a phylogenetic systematics. The main difference between his approach and traditional Linnean systematics was that he distinguished two new kinds of groups that he called mono- and paraphyletic groups, and whereof he considered only monophyletic groups to be natural groups. However, almost immediately after publication of his approach in English, some biological systematists commented that his monophyletic groups rather ought to be called holophyletic groups. The comment sparked a heated debate about the definition of the concept 'monophyletic groups', but the debate never reached consensus. In this paper, I claim that the controversy does not concern the definition of the concept monophyletic groups per se , but instead conceptualization of phylogenies (i.e. dichotomously branching processes) in a general sense. I discuss the relation between mono-, holo- and paraphyletic groups, and conclude that Hennig's conceptualization of phylogenies is both inconsistent and empirically wrong, whereas Linné's instead is consistent and correct.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 217–220.     

A sort of revolution: Systematics and physical anthropology in the 20th century

During the first four decades of the 20th century, a system of ideas about the evolution and systematics of humans and other primates coalesced around the work of George Gaylord Simpson and W. E. Le Gros Clark. Buttressed by the “new physical anthropology” of the 1950s, that system provided an authoritative model—a disciplinary matrix or paradigm—for the practice of that aspect of biological anthropology. The Simpson-Le Gros Clark synthesis began to unravel in the 1960s and collapsed in the 1970s under the onslaught of cladistic systematics. The cladistic “revolution” resembles a paradigm shift of the sort proposed by Thomas Kuhn because it was driven, not by new biological discoveries or theories, but by a change in aesthetics.     

State of the art and perspectives on neotropical fern and lycophyte systematics

For ferns and lycophytes, the Neotropics is a hotspot of diversity (3000–4500 species), and second only to Southeastern Asia in richness and endemism. This paper presents the current state of knowledge on fern and lycophyte systematics in the Neotropics, and emphasizes sampling sufficiency and current taxonomic and phylogenetic knowledge. Plant systematics plays an important role in documenting diversity and geographic distribution patterns that are needed to understand relationships and evolutionary patterns, and a vital role in species conservation. Although in recent decades this field of science has undergone a revolution because of new approaches and techniques, data presented in this work shows that large gaps remain and there is still a long path towards fully understanding fern and lycophyte systematics in Neotropics. Approaches and how to choose areas that should be targeted in order to try to fulfill these knowledge gaps are discussed.     

Population thinking and tree thinking in systematics

Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead inter-connected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology.     

Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes

To fully understand the evolutionary history of parasitic kinetoplastids and to understand the context within which the evolution of each parasite group has developed, an understanding not just of the parasites, but of all kinetoplastids is required. Accordingly, this paper provides an overview of kinetoplastid evolution and systematics, including coverage of the proposal by Moreira et al. (2004) to divide kinetoplasts into Prokinetoplastina (Ichthyobodo and Perkinsiella) and Metakinetoplastina (other bodonids and trypanosomatids). The implications of such a revision, with regard to correctly identifying outgroup taxa for studies of evolution within taxa of medical importance, are addressed, together with a more detailed review of the evolution and origins of the trypanosomes in the light of new phylogenies, new approaches and revisions in kinetoplastid systematics.     

A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa

Prokaryotic systematics is a fundamentally important discipline that provides a framework for the activities of all microbiologists. Here we propose that the field has become mired in a sea of perceived rules and regulations, many of which stipulate what is considered ‘sufficient’ for the phenotypic characterisation of novel prokaryotic taxa. Importantly, we argue also that the principles and practise of prokaryotic systematics have not yet fully embraced the revolution in biological understanding that has occurred through the availability of huge numbers of whole genome sequences. We therefore propose that a significant reappraisal of the procedures used to describe novel prokaryotic taxa is needed, including the likely introduction of new publication formats. Urgent action is needed to revitalise the practise of prokaryotic systematics in order to maintain this discipline as an attractive career choice for twenty first century life scientists.     

The current status of chemical systematics

Chemical systematics sets out to interpret the phylogenetic implications of the occurrence and distribution of secondary metabolites. In this review, a number of the major contributions from the 1960's and 1970's are identified and re-assessed in the light of recent evidence gained from DNA studies. It is shown that for the most part conclusions drawn on the basis of secondary metabolite distribution have been confirmed by the new techniques and it is concluded that chemical systematics can continue to provide useful insights into plant phylogeny.     

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     

Ontogeny, systematics, and phylogenetics: Perspectives of future synthesis and a new model of the evolution of bilateria

Ontogeny is considered as a process that allows linking two key components of biological systematics in an objective way: historically independent character attribution and phylogeny. It is proposed to designate the general theory that unifies the ??static?? traditional taxonomy and the dynamic evolutionary process on the basis of ontogenetic transformation of shapes of organisms as the ontogenetic systematics. One of the important practical applications is a new model of the evolution of bilaterian animals, which supposes an ancestral status of clonal asexual reproduction and its multiple reduction in different lines of Bilatera.