Molecular phylogeny of the grass genus Brachypodium P. Beauv. based on RFLP and RAPD analysis

Nuclear genome analysis using RFLPs and RAPDs has been assessed within different species of the genus Brachypodium P. Beauv. and representatives of other grasses in order to determine the characteristics of the Brachypodium genome and to establish its evolutionary position in relation to other Pooideae. Distinctive features of the Brachypodium genome are its small size, the low amount of repetitive DNA, the lack of restriction fragment length polymorphisms within the genus for the assayed probe/enzyme combinations, and the genomic variability demonstrated at species level by random DNA amplification. These molecular studies confirm Brachypodium as an isolated ancient genus best placed in its own tribe (Brachypodieae). Its relationships to other tribes Bromeae, Triticeae, Poeae are resolved, Brachypodieae being the earliest tribe to diverge from this core of pooids. Within the genus two major Old World clades are distinguishable: an annual clade, represented only by B. distachyon; and a perennial clade, represented by all the other species studied (except B. mexicanum). The perennial American species B. mexicanum appears equally attached to these two clades. RFLP data were found to be useful in obtaining phylogenies at generic and higher rank levels, whereas the highly variable RAPD data were more suitable for resolving interspecific and intraspecific evolutionary pathways.     

A multidisciplinary approach to the fine-systematics within Tisbe - an evaluation of morphological and molecular methods

Six species from the species-rich taxon Tisbe (Copepoda, Harpacticoida) were selected that could be reared in the laboratory as mass cultures. Phylogenetic relationships among these species were assessed by morphological studies of adults and larvae, DNA restriction site polymorphisms, allozymic, immunological distance, and lipid composition. Limits of scope and practicability of these analyses became apparent, as well as their potential and importance for future work in zoological systematics.     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.

Zusammenfassung

Ein fundamentaler Unterschied zwischen der einzelnen Sequenzposition oder auch numerischen Merkmalen und komplexen morphologischen Merkmalen ist ihr Informationsgehalt. Merkmalsreihen komplexer Strukturen enthalten meist genügend Information, um a priori die Bestimmung der Lesrichtung zu ermöglichen. Die Feststellung des Ursprunges eines Dendrogramms ist somit ohne kladistischen Außengruppenvergleich möglich, während Bäume (Topologien), die auf wenig informativen Merkmalen beruhen, allgemein nur mit dem kladistischen Außengruppenvergleich 'gewurzelt' werden können. Die Qualität der insgesamt verwendeten Information ist entscheidend für die Wahl zwischen alternativen Verwandtschaftshypothesen. Numerische Methoden der Rekonstruktion der Phylogenese sind nützlich bei Verwendung einer gro β en Zahl informationsarmer Merkmale; das Hennigsche Verfahren ist für komplexe Merkmale vorzuziehen.     

功能性低分子量岩藻多糖的研究进展

低分子量岩藻多糖来源于褐藻,是一类含有硫酸基团的多糖,具有多种生物学功能,如抗凝血、抗病毒、抗血栓、抗肿瘤等功能,因此可被广泛地应用于医药、食品等领域。着重介绍了低分子量岩藻多糖的制备及其生物学功能的研究进展。     

On quality of evidence in phylogeny reconstruction: a reply to Zrzavý's defence of the 'Ecdysozoa' hypothesis

Zrzavý’s arguments against the critical analyses of data supporting the Ecdysozoa hypothesis (Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999) are discussed. Zrzavý does not understand that the same basic principle of a priori weighting can be applied to sequence data as well as to morphological characters. Quality of evidence is the same as probability of homology, which is estimated from the number of discernible identical details. In sequences it is the number of identical nucleotides. Spectral analyses, dismissed by Zrzavý, visualize patterns of putative homologies present in alignments and also the number of positions supporting splits by chance alone. In cases in which old phylogenetic signals for a given monophylum are eroded in a gene, plesiomorphies and chance patterns will have strong influence on tree topologies and spectra. If plesiomorphies are a cause of errors, the addition of taxa that shorten internal branches is a remedy, although, in many cases such taxa may be extinct. The place of a priori estimations of data quality in a sequence of steps necessary for a phylogenetic analysis is shown. Morphological complexity is used as a proxy for a complex genetic basis and is used as a major criterion to compare characters of the Ecdysozoa and the Articulata. The details associated with the character ‘complex cuticle’ are discussed. Neither moulting nor the known components of the cuticle are novelties occurring only in Ecdysozoa. A published total evidence analysis is used to show that the number of coded characters does not necessarily reflect the quality of the data set. Zrzavý’s misunderstanding of the role of evolutionary scenarios is clarified and the importance of the use of additional biological data for plausibility arguments is explained. Plausibility arguments in favour of the Articulata hypothesis rely on facts found in functional morphology and in the fossil record. Zrzavý’s critique follows the actual mainstream but does not uncover logical mistakes or erroneous data analyses in the work of 86 . It is concluded that the Articulata hypothesis is a well‐founded alternative to the Ecdysozoa; it is based on much better morphological evidence and supported by plausibility arguments that currently do not exist for the Ecdysozoa.     

Identification of apomorphies and the role of groundpatterns in molecular systematics

Putative apomorphic character states are the only relevant phylogenetic signal contained in sets of sequence data. Using the sequence position as a character, a way to identify putative apomorphies prior to phylogenetic analysis is proposed. It is shown that distance-matrix methods use trivial characters. The concept of the asymmetrical split is presented for determination of character polarity. It is furthermore argued that groundpatterns (node sequences) should be reconstructed prior to the study of relationships between taxa of high phylogenetic age. The 'evolutionary noise'contained in groundpatterns can be illustrated with a network of distances using a split-decomposition analysis.     

Four new Candida species from geographically diverse locations

Four new species of Candida are described based on their unique nucleotide sequences in the D1/D2 domain of large subunit (26S) ribosomal DNA. Candida peoriaensis (type strain NRRL YB-1497, CBS 8800) and C. ponderosae (type strain NRRL YB-2307, CBS 8801) are members of the Pichia anomala clade and were isolated in the U.S. from, respectively, the stump of an elm tree (Ulmus sp.) and from insect frass of a Ponderosa pine (Pinus ponderosa). Candida ghanaensis (type strain NRRL YB-1486, CBS 8798) is a phylogenetically divergent species from soil in Ghana and appears related to the Dipodascus/Geotrichum clade. Candida litsaeae (type strain NRRL YB-3246, CBS 8799) was isolated from the frass of an insect-infested Litsaea polyantha tree from India, and is a divergent species that is most closely related to Candida ontarioensis.     

DNA水平上的植物系统学研究进展

分子钟假说为在分子水平上研究生物进化提供了理论基础,分子系统学已成为当前生物学领域中的热门课题,并取得了许多引人注目的进展。本方要以高等植物为对象,从核ＤＮＡ,叶绿体ＤＮＡ和线粒体ＤＮＡ三方面对植物分子系统学进行了综述。     

中国燕山地区地星属2个新种

地星属Geastrum隶属于担子菌门Basidiomycota、伞菌纲Agaricomycetes、地星目Geastrales、地星科Geastraceae,因奇特的外观、生态和医药用价值吸引了国内外真菌工作者的关注.本研究对燕山地区地星种类进行了详细调查,通过形态学观察结合ITS-LSU-rpb1-atp6四基因系统...     

线粒体DNA序列在半翅目异翅亚目昆虫分子系统学上的应用

随着PCR技术的发展以及大量DNA序列的累积,昆虫分子系统学近年来快速发展。线粒体DNA(mtDNA)序列相对于核内DNA序列进化速率较快,常被用于昆虫的系统发育研究。本文综述了国内外学者利用各种线粒体DNA序列来研究半翅目异翅亚目昆虫系统发育的研究概况。总结发现,COⅠ、COⅡ、12S rDNA、16S rDNA、Cytb、ND1、ND2和ND5等线粒体区段被用于半翅目异翅亚目系统发育的研究,其中以COI、COⅡ、16S rDNA和Cytb应用最广泛,但目前尚缺乏不同分子标记间的联合分析。进一步的研究最好在选定半翅目异翅亚目昆虫的分类阶元(如科间、亚科间、科内属间、种间或种内)后,集中测定线粒体某几个区段的DNA序列,然后进行单一分析和联合分析,并与传统形态学研究结果进行比较,可望全面分析半翅目异翅亚目昆虫的系统发育关系。     

Metaves,Mirandornithes, Strisores and other novelties – a critical review of the higher‐level phylogeny of neornithine birds

Recent hypotheses on the higher‐level phylogeny of modern birds are reviewed, and areas of agreement and major conflict are detailed, with emphasis being put on congruence among independent molecular and morphological data sets. Although molecular data significantly contributed to a better understanding of avian phylogeny, they do not seem to be free of homoplasy and caution is warranted in the interpretation of some results. The recently proposed ‘Metaves’ clade is likely to be an artefact of the β‐fibrinogen gene, and current molecular data do not yield well‐supported phylogenies for some groups whose interrelationships can be resolved with morphological evidence. There exists, however, congruent and strong molecular evidence for several novel clades that were not recognized by morphologists before, and to ease future discussions the terms Picocoraciae (non‐leptosomid ‘Coraciiformes’ and Piciformes) and Aequornithes (‘waterbird assemblage’) are introduced. Molecular studies further congruently recover some clades, which have not yet been adequately appreciated and are outlined in the present review.