Phylogenetic systematics of the nymphaeales

A cladistic analysis was applied to reveal the phylogenetic relationships among the Nymphaeales. Seventeen out of twenty three characters in gross morphology, anatomy and palynology were analyzed, for their evolutionary polarities. From the results of the present analysis, the phylogenetic status of each genus and their relationships were clarified: 1)Nelumbo is a distinct taxon and is presumed to have originated from an ancestral stock of the Nymphaeales; 2)Ceratophyllum has a close phylogenetic relationship withCabomba; and 3) in the Nymphaeaceaesensu stricto, Nuphar and the remaining genral constitute a monophyletic group. A conclusion obtained from the present analysis was that the following three families should be recognized in the Nymphaeales; Nelumbonaceae Nymphaeaceae, and Ceratophyllaceae. The generaBrasenia andCabomba are traditionally classified in the Nymphaeaceae or in the independent family Cabombaceae. However, they should be included in the family Ceratophyllaceae.     

Introducing systematics Agenda 2000

Systematics Agenda 2000 is an ambitious initiative emanating from biological systematists in the USA. It proposes an intensive international programme over a 25 year period;-(i) to discover, describe and inventory global species diversity, (ii) to synthesize the resulting data into a predictive classification, and (iii) to develop an appropriate information system to handle the resulting information.     

Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self‐organizing map (SOM)

Aims: To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self‐organizing map (SOM). Methods and Results: DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. [2000, Self‐Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27–34]. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro‐organisms. Although the results obtained by SOM were similar to those obtained by the neighbour‐joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro‐organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium. Conclusions: As the SOM method defined phylotypes of unreported rumen micro‐organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro‐organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases. Significance and Impact of Study: Through SOM analysis, a better means of identifying rumen micro‐organisms and estimating their roles in rumen function was provided.     

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0–10 cm) could be discriminated from those of the intermediate (11–27 cm) and deep (28–40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.     

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.     

Phylogenetic systematics of leaffishes (Teleostei: Polycentridae,Nandidae)

The Asian (nandid) and Afro‐Neotropical (polycentrid) leaffishes represent two superficially similar, but historically poorly diagnosed families – a situation resulting in a convoluted systematic history. Here, and including for the first time in a molecular study all leaffish genera, we generate a hypothesis of the phylogenetic history of both groups. We analyse a multilocus molecular data set encompassing 257 acanthomorph taxa, carry out a survey and assessment of selected osteological characters for the polycentrid leaffishes and also provide a reanalysis of previously published morphological data. Our results confirm: (1) that the Polycentridae and Nandidae are only remotely related, and hence, the classic leaffishes are diphyletic; (2) that the Polycentridae is monophyletic, with new skeletal synapomorphies being congruent with molecular data in placing the enigmatic Afronandus – a taxon that thus far has never been included in any molecular study – as sistergroup to the remaining genera; (3) the monophyly of the Nandidae + Badidae and their inclusion into a larger monophyletic group – along with the Pristolepididae, Anabantoidei and Channoidei – comprising the Labyrinthici sensu Rosen & Patterson. We also review the morphological and molecular evidence for both the conflicting placement of Pristolepis and the putative sistergroup relationship between the labyrinth fishes (Anabantoidei) and snakeheads (Channoidei).     

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.     

黑胸散白蚁（Reticulitermes chinensis Snyder）肠道共生古菌的系统发育分析

摘要：【目的】利用非培养法对黑胸散白蚁（Reticulitermes chinensis Snyder）肠道共生古菌进行系统发育分析。【方法】采用古菌16S rDNA通用引物以黑胸散白蚁全肠DNA为模板扩增共生菌的16S rDNA并建立基因文库,对得到的基因序列进行系统发育分析。【结果】从黑胸散白蚁肠道得到5个不同的16S rDNA序列,它们之间的相似性为93.2%～99.2%,系统发育分析表明这5个16S rDNA序列代表的克隆分别与来源于黑胸散白蚁近缘种,栖北散白蚁和北美散白蚁肠道中的甲烷短杆菌克隆或     

Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus

The tribe Cercosaurini is one of the most poorly studied groups of the lizard family Gymnophthalmidae. Recent studies have suggested that two cercosauriine genera, Neusticurus and Proctoporus , are polyphyletic. The aim of the current study was to rectify the polyphyletic relationships and construct a phylogenetic taxonomy of the Cercosaurini that is congruent with evolutionary history. Neusticurus is divided into two genera, one of them new ( Potamites ), based on the clades recovered by molecular studies and previously discussed morphological data. Proctoporus is divided into three genera, one of which is new ( Petracola ), while an older name ( Riama ) is resurrected for another. All five genera are described and defined and taxonomic keys are presented. This study represents an important advance in rectifying the taxonomy of the Cercosaurini. Many other para- and polyphyletic genera remain in the Gymnophthalmidae and much future work on this group is warranted.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 405–416.     

长期施肥对土壤氨氧化微生物的影响

长期施肥可改变土壤碳氮等养分供应,进而影响微生物数量与群落组成。本研究基于棕壤长期定位实验站,分析不同施肥方式下(不施肥,CK;低量无机氮肥,N₂;高量无机氮肥,N₄;有机无机氮肥配施,M₂N₂)土壤氨氧化古菌(AOA)和细菌(AOB)的变化,为土壤氮素转化的微生物学机制和培肥土壤提供依据。结果表明:不同施肥方式下,土壤AOA与AOB的数量比值为2.28～61.95。与CK相比,施肥后土壤AOA数量降低了1.6%～13.6%。N₄处理AOB数量随土壤深度增加呈先降低后升高的趋势,其他处理则相反。土壤AOB群落Shannon多样性指数、均匀度指数和Simpson指数均高于AOA。M₂N₂处理0～20 cm土层土壤AOB多样性增加,但AOA多样性降低。土壤AOB主要因土壤深度发生聚类,AOB和AOA均未因施肥方式发生聚类。综上,长期施肥改变了土壤AOA和AOB的构成状况,AOA对环境变化较为敏感,AOB较为丰富和稳定。     

Circularity,evolution, systematics … and circularity

Many have argued strongly that incorporation of evolutionary theory into systematics is dangerously circular, while others have maintained that such an integrated approach increases the accuracy of phylogenetic inference. Here, it is demonstrated that such blanket statements regarding exclusion or inclusion of evolutionary principles in systematics fail to distinguish between two very different types of principles. ‘Phylogeny-neutral’ evolutionary principles are those inferred without any recourse to specific phylogenetic hypotheses (e.g. via developmental genetics, biomechanics). In contrast, ‘phylogeny-dependent’ principles are those which can only be inferred on the basis of specific phylogenetic hypotheses (e.g. character associations detected via ‘comparative methods’). Inclusion of phylogeny-neutral principles in systematic studies as a priori assumptions can be justified, since these principles have (often strong) external empirical support from other spheres of investigation. However, inclusion of phylogeny-dependent principles in systematic studies is circular, since such principles have no external empirical support but are themselves derived from systematic studies. Advocating inclusion or exclusion of all (or as many as possible) evolutionary principles from phylogenetic analysis is therefore misguided. Rather, phylogeny-neutral principles are independently supported and can be included, while phylogeny-dependent principles are unjustified assumptions and should be excluded to avoid circularity. However, integration of complex phylogeny-neutral principles in systematics can create operational problems, even though there are no methodological reasons against their inclusion.     

Molecular phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): systematics and biogeography

We present a comprehensively sampled three‐gene phylogeny of the monophyletic Forcipulatacea, one of three major lineages within the crown‐group Asteroidea. We present substantially more Southern Hemisphere and deep‐sea taxa than were sampled in previous molecular studies of this group. Morphologically distinct groups, such as the Brisingida and the Zoroasteridae, are upheld as monophyletic. Brisingida is supported as the derived sister group to the Asteriidae (restricted), rather than as a basal taxon. The Asteriidae is paraphyletic, and is broken up into the Stichasteridae and four primary asteriid clades: (1) a highly diverse boreal clade, containing members from the Arctic and sub‐Arctic in the Northern Hemisphere; (2) the genus Sclerasterias; (3) and (4) two sister clades that contain asteriids from the Antarctic and pantropical regions. The Stichasteridae, which was regarded as a synonym of the Asteriidae, is resurrected by our results, and represents the most diverse Southern Hemisphere forcipulatacean clade (although two deep‐sea stichasterid genera occur in the Northern Hemisphere). The Labidiasteridae is artificial, and should be synonymized into the Heliasteridae. The Pedicellasteridae is paraphyletic, with three separate clades containing pedicellasterid taxa emerging among the basal Forcipulatacea. Fossils and timing estimates from species‐level phylogeographic studies are consistent with prior phylogenetic hypotheses for the Forcipulatacea, suggesting diversification of basal taxa in the early Mesozoic, with some evidence for more widely distributed ranges from Cretacous taxa. Our analysis suggests a hypothesis of an older fauna present in the Antarctic during the Eocene, which was succeeded by a modern Antarctic fauna that is represented by the recently derived Antarctic Asteriidae and other forcipulatacean lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 646–660.     

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).     

Molecular systematics of the genus Allodontichthys (Cyprinodontiformes: Goodeidae)

Phylogenetic analyses of cytochrome c oxidasesubunit I (627bp) and mitochondrial controlregion (338bp aligned) sequences for all knownspecies of Allodontichthys wereperformed. Allodontichthys was recoveredas monophyletic, and A. hubbsi wassupported as the most primitive member of thegenus in all analyses. Combined-data analysessuggest that A. polylepis is sister to aclade comprising A. tamazulae and A. zonistius; however, a strict consensus of COIand control region cladograms results in acollapse of this node. The two species thatare broadly sympatric, A. hubbsi and A. tamazulae, are not sister taxa.Allodontichthys was found the sistergroup of a clade including Ilyodon andXenotaenia. These three genera are theonly goodeids to occupy high-gradient riversystems. Ilyodon and Allodontichthys share similar distributions;however, Allodontichthys exhibits greaterthan an order of magnitude more geneticvariation in COI than Ilyodon incomparisons of individuals from the samelocalities in the Ameca and Armeria drainagesystems. This is interpreted to mean Allodontichthys arrived in some westerndrainages significantly before Ilyodon.The Rio Coahuayana appears to be the center oforigin of the genus Allodontichthys. This river basin contains the most primitivemember of the genus, and appears to haveconnected with the Mesa Central, the center of endemism of the Goodeidae. A calibrated rateof molecular change in COI reveals Allodontichthys began diverging approximately6.2 million years ago (mya). Remainingspeciation in the group appears to haveoccurred about 2.7 to 3.3 mya. The hypothesisthat a hard polytomy comprising A. zonistius, A. polylepis, and A. tamazulae could be explained by speciation ofA. polylepis and A. tamazulae fromdifferent A. zonistius ancestors ispresented. Stream capture is evident but notfrequent in the history of Allodontichthys, and speciation does notclearly correlate with documented geologicactivity of the Mexican Transvolcanic Belt.     

好氧氨氧化微生物系统发育及生理生态学差异

作为好氧氨氧化的驱动者,氨氧化古菌(Ammonia-oxidizing archaea,AOA)和细菌(Ammonia-oxidizing bacteria,AOB)一直是氮的生物地球化学循环的研究热点之一。由于它们的相对丰度、群落结构和活性因环境而异,目前二者对全球氮循环的相对贡献仍存在争议。对培养物和环境样品的动力学、基因组学等研究结果表明,这种差异主要是由AOA和AOB的生理生态学差异导致的。氨浓度、pH、溶氧、温度等环境因素以及代谢途径等生理因素导致AOA和AOB的生态位分化。通过比较AOA和AOB在系统发育、对环境因子的响应以及代谢途径等方面的差异,对好氧氨氧化微生物相关研究成果进行概括和总结,以便深入了解它们在不同环境中对氮循环的相对贡献;同时对好氧氨氧化微生物今后的研究重点进行了展望。     

蝗虫分子系统学研究进展

本文从遗传多样性、近缘种鉴别以及分子进化和系统发育重建 3个方面综述了蝗虫分子系统学的研究进展。     

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐vs.‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.