Evolution and systematic relationships in theTriticeae (Poaceae)

The evolution and taxonomic relationships in theTriticeae are discussed with the view to highlight aspects of this agronomically important group of plants, which may be of interest to molecular biology. Some of these aspects are addressed in more detail in adjoining papers in which specific genomic loci have been examined at the DNA sequence or isozyme level. Aspects discussed include the systematics and geographic distribution of theTriticeae species, isozyme and chromosome pairing studies on some of the species as well as more recent developments in DNA analyses. A survey of the systematics of theTriticeae indicated that the genomic system ofLöve is probably the most useful starting point for interpreting molecular data even though the system has many problems from a taxonomic point of view. The geographical distribution ofTriticeae species, using both published and unpublished data, suggested that information of this type taken together with the theory of continental drift provides a broad time-span for considering data from DNA sequence studies. The significance, and modes of analyses, of isozyme studies were assessed because they often provide valuable characters in determining relationships between species. The main character underlyingLöve's andDewey's analyses of theTriticeae, namely chromosome pairing, is discussed with particular reference to isozyme studies to show that in some cases, such as species ofHordeum sensu lato, consistent relationships are obtained. Finally, new developments in understanding chromosome structure are considered in relation to the above variables in the taxonomy and evolution of theTriticeae.     

《中国植物志》和《中国被子植物科属综论》所涉及"科"界定之比较

对采用A .Engler (1936 )被子植物分类系统的《中国植物志》和根据吴征镒等(2 0 0 2 )被子植物分类系统的《中国被子植物科属综论》中科的界定进行了比较。这不仅有助于掌握吴征镒等系统的观点 ,也有益于理解被子植物系统学中当前划分“科”的新趋向。     

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.     

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.     

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     

齿蟾属的系统学研究进展

齿蟾属(Oreolalax)为中国特有属,主要分布在我国西南地区。本文对该属的系统学研究进行了综述,包括属的建立与物种组成、地理分布特征、细胞分类学、系统发育研究历史,以及尚需研究或进一步研究的问题。     

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.     

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.     

Influence of the Latency Fluctuations and the Quantal Process of Transmitter Release on the End-Plate Potentials' Amplitude Distribution

Spontaneous synaptic potentials and their relation to the end-plate potential (e.p.p.) are studied. It has been suggested earlier that the e.p.p. at a single nerve-muscle junction is built up statistically of small all-or-none units which are identical in size with the spontaneous miniature end-plate potentials (m.e.p.p.'s). In this paper, a more general theory is developed which takes into account latency fluctuations of the unit components. A general equation for e.p.p. amplitude probability distribution is derived. This probability distribution is a function of the latency distribution, m.e.p.p.'s pulse shape, m.e.p.p.'s amplitude distribution, and the mean quantal content. The time course of transmitter release, or latency distribution, is derived from a histogram of synaptic delays in a frog muscle, but obtained equations can be used for other distribution functions as well.     

1068. Amorphophallus ongsakulii Hett. & A.Galloway: Araceae

Amorphophallus ongsakulii Hett. & A.Galloway is illustrated from plants cultivated by the authors. Its ecology, distribution, and systematics are described, along with notes on cultivation.     

DNA profiling of complex bacterial populations: toxic cyanobacterial blooms

Cyanobacteria are prokaryotic photosynthetic living organisms that inhabit our planet for over three billion years. With a worldwide distribution, they can be found in all types of environments: fresh, brackish and saltwater as well as terrestrial. Though beneficial in the development of life on earth, they also constitute a serious risk to our ecosystems since they can biologically produce harmful secondary metabolites named cyanotoxins. When studying cyanobacteria and their cyanotoxins, several methodologies have been applied with an increasing relevance to molecular methods. Therefore, the aim of this review is to describe alternative molecular methods that can be used as alternative methods for the identification of cyanobacteria. More traditional chemotaxonomic methods are discussed briefly as are the standard and somewhat dated techniques for assessing genome content for taxonomic classification schemes. The use of DNA amplification technology has been applied to the systematics and phylogeny of many bacterial groups, and the optimisation of methods for rapid identification and classification of cyanobacteria are presented. Together with novel methods developed for these photosynthetic microorganisms, the generated DNA profiles have been utilised to study cyanobacterial bloom population diversity and prediction of strain toxigenicity. Finally, the genotypes found were applied to a variety of phylogenetic analyses; trees were reconstructed and compared to the current morphological system of classification. The ecology and diversity of the cyanobacteria is discussed with respect to the derived molecular phylogenies and systematics.     

Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus.

The length of the small subunit ribosomal DNA (SSU rDNA) differs significantly among individuals from natural populations of the ascomycetous lichen complex Cladonia chlorophaea. The sequence of the 3' region of the SSU rDNA from two individuals, chosen to represent the shortest and longest sequences, revealed multiple insertions within a region that otherwise aligned with a 520-nucleotide sequence of the SSU rDNA in Saccharomyces cerevisiae. The high degree of variability in SSU rDNA size can be accounted for by different numbers of insertions; one individual had two group I introns and the second had five introns, two of which were clearly related to introns at identical positions in the other individual. Yet, introns in different positions, whether within an individual or between individuals, were not similar in sequence. The distribution of introns at three of the positions is consistent with either intron loss or acquisition, and clearly indicates the dynamic variability in this region of the nuclear genome. All seven insertions, which ranged in size from 210 to 228 nucleotides, had the conserved sequence and secondary structural elements of group I introns. The variation in distribution and sequence of group I introns within a short highly conserved region of rDNA presents a unique opportunity for examining the molecular evolution and mobility of group I introns within a systematics framework.     

中国鼩鼱亚科的系统分类和分布的评论(英文)

中国动物区系中的鼩(鼠青)类,或称赤齿鼩类,包括31个种;除此之外,东北省份还可能存在另外2个种。生物地理类群包括:1)东北寒温带针叶林(泰加)-Neomys fodiens,Sorex caecutiens,S.daphaenodon,S.gracillimus,S.isodon,S.mirabilis,S.roboratus,S.tundrensis以及S.unguiculatus;2)在山区针叶林中具有孤立居群的东北寒温带针叶林-Sorex minutissimus;3)中国喜马拉雅地区-Chimarrogale himalayica,Nectogale elegans,Sorex bedfordiae,s.thibetanus,Soriculus caudatus,S.leucops,S.macrurus,及S.nigrescens;4)中国特有种,或接近于特有种-Anourosorex squamipes,Blarinella quadraticauda,Chimarrogale styani,So-rex asper,S.cansulus,S.cylindricauda,S.excelsus,S.sinalis,Soriculus fumidus,S.hypsibius,S.lamula,S.parca,S.salenskii,及S.smithii。Sorex minutus的生物地理位置(仅见于天山)目前尚不清楚。     

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.     

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.     

Ronald Brady and the cladists

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre-Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.     

Genomewide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba

DINE-1 (Drosophila interspersed element) is the most abundant repetitive sequence in the Drosophila genome derived from transposable elements. It comprises >1% of the Drosophila melanogaster genome (DMG) and is believed to be a relic from an ancient transpositional burst that occurred approximately 5-10 MYA. We performed a genomewide comparison of the abundance, sequence variation, and chromosomal distribution of DINE-1 in D. melanogaster and D. yakuba. Unlike the highly diverged copies in the DMG (pairwise distance approximately 15%), DINE-1's in the Drosophila yakuba genome (DYG) have diverged by only 3.4%. Moreover, the chromosomal distribution of DINE-1 in the two species is very different, with a significant number of euchromatic insertions found only in D. yakuba. We propose that these different patterns are caused by a second transpositional burst of DINE-1's in the D. yakuba genome approximately 1.5 MYA. On the basis of the sequence of these recently transposed copies, we conclude that DINE-1 is likely to be a family of nonautomomous DNA transposons. Analysis of the chromosomal distribution of two age groups of DINE-1's in D. yakuba indicates that (1) there is a negative correlation between recombination rates and the density of DINE-1's and (2) younger copies are more evenly distributed in the chromosome arms, while older copies are mostly located near the centromere regions. Our results fit the predictions of a selection-transposition balance model. Our data on whole-genome comparison of a highly abundant TE among Drosophila sibling species demonstrate the unexpectedly dynamic nature of TE activity in different host genomes.     

A phylogenetic investigation of the Neotropical genus Alphamenes van der Vecht, 1977 (Hymenoptera,Vespidae, Eumeninae)

Advances in potter wasp systematics have been achieved recently, with classificatory changes resulting from analyses based upon large scale molecular datasets. For the Neotropics, recent hypotheses point to the occurrence of an exclusive clade recognized within the tribe Eumenini. In this group, several contributions regarding taxonomy and systematics have been proposed in the last five years, including the genus Alphamenes. This taxon contains seven described species whose distribution is exclusively Neotropical. Females are morphologically homogeneous, and characters related to copulatory organs are useful in male diagnosis. This contribution forms the first phylogenetic approach to include all species of Alphamenes, hence the first to strongly test for group monophyly. Our cladistic results recovered Alphamenes as a monophyletic group supported by male genital features. Relationships among included species also rely upon genitalic characters, highlighting the importance of these attributes for eumenine systematics. Recent phylogenetic investigations applied to the Neotropical fauna of potter wasps represent desirable advancements towards a natural classification for the group.     

Combined support for wholesale taxic atavism in gavialine crocodylians

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.