Assessing progress in systematics with continuous jackknife function analysis

Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted against the accumulating number of characters. Continuous jackknife function (CJF) analysis is a new graphical method that portrays the extent to which available data converge on a specified phylogenetic hypothesis, the reference tree. The method removes characters with increasing probability, analyzes the rarefied data matrices phylogenetically, and scores the clades shared between each of the resulting trees and the reference tree. As more characters are removed, the number of shared clades must decrease, but the rate of decrease will depend on how decisively the data support the reference tree. Curves for stable phylogenies are clearly asymptotic with nearly 100% congruence for a substantial part of the curve. Less stable phylogenies lose congruent nodes quickly as characters are excluded, resulting in a more linear or even a sigmoidal relationship. Curves can be interpreted as predictors of whether the addition of new data of the same type is likely to alter the hypothesis under test. Continuous jackknife function analysis makes statistical assumptions about the collection of character data. To the extent that CJF curves are sensitive to violations of unbiased character collection, they will be misleading as predictors. Convergence of data on a reference tree does not guarantee historical accuracy, but it does predict that the accumulation of further data under the sampling model will not lead to rapid changes in the hypothesis.     

分子系统学在真菌分类命名中的应用与进展

真菌分子系统学以分子生物学、遗传学和生物信息学为手段,以分子水平对真菌进行种属识别,与传统的表型分类系统相比,更为可靠、高效,极大地推动了真菌分类学的发展。因此,真菌分类学正处于一个划时代的转变时期,即由表型分类向基因型分类的转变,以形态学为基础的种属概念向以分子系统学为基础的种属概念转变。综合论述了分子系统学在真菌分类和命名中的应用,并介绍近年来真菌分类和命名方面的变化和进展,供国内科研和临床工作者参考。     

块菌属分子系统学及菌根共生机制研究进展

块菌属Tuber是一类珍贵的地下生外生菌根食药用真菌,具有重要的经济和生态价值。分子生物学技术的快速发展尤其是高通量测序技术在块菌属研究领域的应用,极大地推动了块菌属分类、系统学、生态、生化、菌根共生机制及人工种植等研究。本文重点从块菌的分子系统学、群体遗传学及菌根共生机制3个方面对近5年的研究成果进行综述,并对其研究和应用前景进行了展望。     

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.     

From the phylogeny of the Satyrinae butterflies to the systematics of Euptychiina (lepidoptera: nymphalidae): history, progress and prospects

We review the various proposals of evolutionary and classification schemes for Satyrinae and particularly Euptychiina butterflies, assessing progress and prospects of research for the group. Among the highlights is the proposal to include Morphini, Brassolini and Amathusiini as part of Satyrinae. Although it is clear that this hypothesis requires further investigation, phylogenetic studies recently conducted recover this clade as part of Satyrinae with high support. The phylogenetic analyses for Euptychiina carried out to date recover the monophyly of the group and have identified a variety of genera as non-monophyletic. Further work is necessary to resolve the position of the subtribe and the evolutionary relationships of several genera.     

Characters: the central mystery of taxonomy and systematics

Taxonomic and systematic theory is hopelessly confused because the term character has nine different, previously confused, meanings. After a historical analysis, it is shown that some form pairs, one used in taxonomy (= operational identification of phenetic patterns of character x individual spread) and the other in systematics (= theoretical analysis of patterns of taxonomy). On the basis of a stratigramy model, names are given to each usage and are defined for taxonomy, then systematics, as necessary: component : (tax.) a defined bit-or-piece of one individual (no syst. meaning); homology : (tax.) conceptual identity of components of several individuals, attributable (syst.) to common ancestry; homology avatar : (tax.) case of recognized homology which (syst.) shows broad phylogenetic continuity (e.g. eye) (= character sensu Sokal and Sneath); homolostratum/homology state : (tax.) specified condition of a homology avatar whose distribution (syst.) enables cladogenetic happenings to be identified (e.g. colour:red/green/blue/etc.) (= character state of Sokal and Sneath); character sensu stricto : (tax.) homolostratum limited to a taxon which (syst.), with hierarchy, identifies chronological sequences of most cladogenetic happenings; taxonomoids : (tax.) mixed group of homolostrata, including yet unknown characters, that identifies a taxon and so (syst.) has same role as characters (= roughly symplesiomorphies); Ante- (Ah) and Post-(Ph) happening characters : (tax.) the hierarchy levels immediately above and below an empty level which (syst.) reveal a cladistic happening (= roughly one usage of synapomorphies and apomorphies).     

Polychaete systematics: Past and present

In this paper, we first demonstrate the historical background for the current unsatisfactory state of systematics of the polychaetes. We then briefly discuss our knowledge of internal and external structures. A review of the polychaete families makes up the third section; 81 families are treated in detail. Five families have been recently synonymized with others, and six families are too poorly known to be sufficiently characterized. Fossil polychaetes are briefly mentioned, with specific attention to problems associated with incorporating them in recent systematics.
The traditional separation in 'errant' and 'sedentary' polychaetes has increasingly become recognized as being unsatisfactory; however, the current trend towards grouping the polychaetes in many orders without specifying the relationships among the orders, is no more satisfactory. The lack of consistent morphological information is a major source of uncertainty. Intensive morphological studies should remove terminological ambiguities and alleviate some of the problems.     

Rhodococcal systematics: problems and developments

Various approaches that have been used in the development of a system of classification for the genus Rhodococcus are discussed. The application of chemotaxonomic, molecular systematic and numerical phenetic methods have greatly contributed to improvements in the systematics of rhodococci and related mycolic- acid containing actinomycetes. The genus currently encompasses twelve validly described species but improved diagnostic methods are needed to distinguish between them. In addition, evidence from 16S ribosomal RNA sequencing suggests that the genus is still heterogeneous.     

Parasite systematics in the 21st century: opportunities and obstacles

Thanks to the phylogenetic systematics revolution, systematic parasitology is poised to make significant contributions in tropical medicine and public health, biodiversity science, and evolutionary biology. At the same time, the taxonomic impediment is acute within parasitology. Both systematists and non-systematists must be interested in working towards common goals and establishing collaborative efforts in order to re-vitalize and re-populate systematic parasitology.     

Morphology and systematics of the Scytopetalaceae

The present study is based on a re-investigation of the vegetative and reproductive structures of the West African family Scytopetalaceae. Special emphasis is paid to inflorescence morphology and seed anatomy. The inflorescences of all genera of Scytopetalaceae can be interpreted as derived from panicles through reductions and structural changes. Thyrsoids prevail, but panicles, botryoids and racemes occur as well. Within the family cauliflory appears as the derived condition. Seed coat structure is extremely simplified and very stable in the Scytopetalaceae. The horny endosperm contains amyloid as the main storage compound. The presence of two obviously different forms of ruminate endosperm indicates that rumination arose twice within the family. The neotropical genus Asteranthos (Lecythidaceae) agrees in almost all relevant characters with the Scytopetalaceae. Therefore the proposed inclusion of Asteranthos in the latter family is fully confirmed. Scytopetalaceae, Lecythidaceae, Foetidiaceae and Napoleonaeaceae apparently form a natural alliance. Two new subfamilies (Scytopetaloideae, comprising Scytopetalum, Oubanguia , and Asteranthos; Rhaptopetaloideae comprising Rhaptopetalum, Pierrina and Brazzeia ) are proposed and fully described.     

跳甲亚科系统分类学研究进展

跳甲作为叶甲科Chrysomelidae中最大的一个类群具有重要的经济意义。该文简述了跳甲亚科Alticinae的分类研究历史 ,回顾了世界及中国的研究概况 ,从分类地位、族级阶元的划分、支序系统学及分子系统学等方面综述了跳甲亚科的最新研究进展 ,并简要讨论了存在的问题及研究前景     

Kluyveromyces: systematics since 1970

The taxonomy ofKluyveromyces has been the object of intense study since van der Walt's (1970) monograph. This is an account of the major developments and the classification to be adopted in the 4th edition ofThe Yeasts, a Taxonomic Study. The guiding principles that will be followed in eventual revisions of the genus are presented.     

Three-Dimensional Puzzles: Southern African and Upper Palaeolithic Rock Art

The history of anthropology is a growing field of study within the discipline itself. Our series 'Key Informants on the History of Anthropology' contributes to the discussion of how anthropology, as it is understood and practised today, evolved and took shape. In the following invited contribution, David Lewis-Williams reflects on the major reinterpretation of southern African rock art and Upper Palaeolithic art that took place in the 1970s and 1980s. An earlier interpretation of the rock art as representing hunters' impressions of their prey was replaced by sophisticated interpretations of the cosmology of the first inhabitants of South Africa. Lewis-Williams's work was crucial in bringing about this shift. David Lewis-Williams is Professor Emeritus of Archaeology and founder of the Rock Art Research Institute of the University of the Witwatersrand, South Africa, which promotes studies of the more than 15,000 sites within the country.