Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.     

Dichotomy of major bacterial phyla inferred from gene arrangement comparisons

A computer search for gene arrangements that are present in Gram-positive bacteria but are absent from Proteobacteria and vice versa was carried out. Four such arrangements were detected, based on which major bacterial phyla were divided into two groups; Thermotoga, Deinococcus-Thermus, Chloroflexi (green non-sulfur bacteria), and Fusobacteria, represent Gram-positive bacterial gene arrangements, while Aquifex, Spirochetes, Planctomycetes, Chlorobi (green sulfur bacteria), Bacteroides show Proteobacterial arrangements. The division is almost consistent with another partition of the major phyla based on the comparison of domain architectures of RNA polymerase subunits and sigma factor, suggesting a fundamental split of the major bacterial phyla at an early stage of bacterial evolution.     

Phylogenetic reconstruction of Burmannia L. (Burmanniaceae): a preliminary study

Preliminary cladistic analyses of the genus Burmannia were performed using different outgroups. Although results from different analyses were inconsistent in some aspects, some clades were found in both analyses, suggesting the specific relationships among species in these clades are well-solved. Of the two sections recognized by Jonker, sect. Foliosa is probably a monophyletic group, while sect. Burmannia is not. If the loss of chlorophyll is considered to be an irreversibleprocess, holo-mycoheterotrophism has very likely emerged only once in the tribe Burmannieae.     

蒙古高原岩黄芪属植物的分支分类学研究

以蒙古高原岩黄芪属植物为对象, 应用徐克学的最大同步法, 探讨了蒙古高原岩黄芪属(豆科)植物的系统演化, 并根据分支分类结果对蒙古高原岩黄芪属进行了系统学处理。作者首次将蒙古高原岩黄芪属分为岩黄芪亚属、半灌木岩黄芪亚属(新拟)和无刺岩黄芪组、丛枝岩黄芪组、无茎岩黄芪组、半灌木岩黄芪组等4 个组。本文对蒙古高原岩黄芪组的划分符合苏联植物志(1945)中的观点。     

真正柑桔果树群植物的分支学研究

本文用相容性分析方法(Compatability snalysis)分析了真正柑桔果树群(芸香科Rutaceae-柑桔亚科Aurantioideae-柑桔族(Citreae)-柑桔亚族(Citrinae)植物内各属间的分支学关系。给出了建立在7个相容性性状组成的最大族所决定的分支图。性状极性的确定使用了外群法。结果表明,柑桔属(Citrus L.)和多蕊桔属(Clymenia Swing)构成一个单系类群,他们的姐妹群是金柑属(Fortunella Swing.)。被认为起源于中国的3个属,柑桔属(Citrus)、金柑属(Fortunella)和积属(Poncirus Raf.)并未构成一个单系类群。本文还利用分支关系分析和讨论了真正柑桔果树群的种系发生关系。     

PACT: an efficient and powerful algorithm for generating area cladograms

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.     

High diversity of Lauraceae from the Oligocene of Ningming,South China

Lauraceae is among the largest and floristically most important woody plant families in subtropical and tropical zones. However, the Cenozoic fossil records of Lauraceae are mostly from mid-latitude regions. Here we described eight lauraceous species from the Oligocene of Ningming, Guangxi, South China on the basis of leaf compressions with cuticular structure, providing new evidence for high diversity of Lauraceae in the low latitude region of the northern hemisphere during the late Paleogene. The extant genera to which the Ningming Oligocene fossils are possibly closely related include Cinnamomum, Neolitsea, Litsea, Alseodaphne, Laurus, and Beilschmiedia. All of these extant genera except Laurus still exist in Guangxi today, whereas Laurus is currently distributed in the Mediterranean and adjacent regions. A cladistic analysis based on leaf architectural and leaf cuticular characters for Paleogene Lauraceae species in the world indicated a possible relationship between European and East Asian Paleogene species.     

A new superfamily classification of the Caridea (Crustacea: Pleocyemata) based on phylogenetic pattern

Present groupings of Caridea are notoriously unsatisfactory at the superfamily level. Principles of phylogenetic systematics are used to reconstruct 14 monophyletic subgroups of Caridea, based on 19 synaomorphies of adults. The following sequenced phylogenetic classification is provided (main diagnostic character for each superfamily within brackets): 1. Atyoidea (distal lash of Mxp, reduced); Oplophoridae; Atyidae; Pasiphaidae; Agostocarididae; Alvinocarididae; Bresiliidae; Psalidopodidae; Disciadidae; 2. Stylodactyloidea (mandibular palp with 2 segments or absent); Stylodactylidea; Campylonotidae; 3. Eugonatonotoidea (abdominal somite III with dorsal carina bifurcate); Eugonatonotidae; 4. Palaemonoidea (basal segment of antennular peduncle with distolateral tooth); Rhynchocinetidae; Palaemonidae; 5. Nematocarcinoidea (ventral lobe of scaphognathite narrowly triangular); Nematocarcinidae; 6. Pandaloidea (P₁ with chela microscoic or absent); Pandalidae; “Plesionikidae”; Heterocarpidae; Heterocarpoididae; Dorodoteidae; Thalassocarididae; Physetocarididae; 7. Crangonoidea (incisor process of mandible absent); Barbouriidae; Lysmatidae; Merguiidae, fam. n.; Processidae; Glyphocrangonidae; Crangonidae; 8. Alpheoidea (carpus of P₂ with less than 17 segments); Merhippolytidae, fam. n.; Nauticarididae; Alopidae; Bythocarididae; Thoridae; Hippolytidae; Pterocarididae, fam. n.; Ogyrididae; Alpheidae. The monotypic hippolytid taxon Thorellinae, subfam. n., has been formally diagnosed. A survey of the lower Caridea has furnished 276 enera and 2418 species and subspecies. The new superfamily system is simpler, genealogically informative and more precisely diagnosed than previous schemes. These have failed as general reference systems because they were based on the wrong premises that similarities indicate phylogenetic relationships or can be used to construct a single acceptable hierarchy.     

Panbiogeographical study of hagfishes: an anachronistic analysis

In a recent paper by M. J. Cavalcanti and V. Gallo, 'Panbiogeographical analysis of distribution patterns in hagfishes (Craniata: Myxinidae)' ( Journal of Biogeography , 2008, 35 , 1258–1268), the authors studied the biogeography of an ancient fish family (Myxinidae) in the hope that the contemporary distributions of the species would reveal their past history and that of the ocean basins where they reside. In order to accomplish this task, there are several criteria that should have been met: (1) the ages of the taxa utilized (species) would have to be old enough to reflect the history of the areas where they are found, (2) the identification of the species as listed in the databases would have to be accurate, (3) the geographical locations indicated on the figures would have to be consistent with the statements in the text, and (4) the significance of the vicariant patterns would have to depend on evidence pertaining to the ages of such patterns. Unfortunately, it appears that none of these conditions has been met. It seems apparent that faith in an antiquated method of analysis led to neglect of the necessary steps in the analysis. This leaves little justification for publication of the paper, except to show that hagfishes are very widely distributed.     

中国小蜂科属间系统发育关系分析(膜翅目:小蜂科)

利用Hennig86程序的nelsen合意和Phylip程序的多数规则合意2种支序分析方法,探讨了中国小蜂科的系统发育关系。基于中国21属的30个性状,计算得到2个合意树,其分类系统与传统分类系统基本保持一致。在进化关系和亲缘关系上表现为:小蜂属(Chalcis)、卡诺小蜂属(Conura)、大腿小蜂属(Brachymeria)和脊柄小蜂属(Epitranus)相对最为原始,而泰内小蜂属(Tainaniella)和背突小蜂属(Oxycoryphe)相对最为进化,前者和后者之间的亲缘关系最远;亲缘关系最近的有:泰内小蜂属(Tainaniella)和背突小蜂属(Oxycoryphe),泊卡小蜂属(Proconura)和日本小蜂属(Nipponochalcidia),小蜂属(Chalcis)和卡诺小蜂属(Conura)以及细尾小蜂属(Megalocolus)和三角小蜂属(Trigonura),它们分别构成姊妹群关系。