Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.     

动物系统发育和大规模测序:进展和问题

Phylogenomics, the inference of phylogenetic trees using genome-scale data, is becoming the rule for resolving difficult parts of the tree of life. Its promise resides in the large amount of information available, which should eliminate stochastic error. However, systematic error, which is due to limitations of reconstruction methods, is becoming more apparent. We will illustrate, using animal phylogeny as a case study, the three most efficient approaches to avoid the pitfalls of phylogenomics (1) using a dense taxon sampling, (2) using probabilistic methods with complex models of sequence evolution that more accurately detect multiple substitutions, and (3) removing the fastest evolving part of the data (e.g., species and positions). The analysis of a dataset of 55 animal species and 102 proteins (25712 amino acid positions) shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so. The latter model correctly locates three very fast evolving species, the appendicularian tunicate Oikopleura, the acoel Convoluta and the myxozoan Buddenbrockia. Overall, the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence. This further emphasizes the importance of secondary simplification in animals, and for organismal evolution in general.     

基因组尺度分析和代谢工程策略

代谢工程是近年来发展起来的新技术,随着各种组学技术的发展,高通量数据整合方法用于分析细胞的代谢网络,改造代谢途径,以提高目标产物的产量。本文就代谢工程的发展状况,基因组尺度的分析技术,以及代谢工程策略进行了综述。分析了生物信息学和系统生物学方法在代谢途径构建和代谢网络分析中的作用,并就存在的问题和可能的解决途径进行了阐述。     

全基因组范围代谢网络的构建和最小基因组研究

全基因组范围代谢网络（genome-scale metabolic network,GSMN）的构建是合成生物学研究的一个重要研究手段。通过整合各种组学数据和借助计算机进行模拟分析,将基因型与表型的关系进行定量关联,从而为从全局的角度探索和揭示生物代谢机制,进而对生物进行合理的重新设计和工程改造提供了有效的框架。该方法在最小基因组研究中也有着突出的优势,通过计算机辅助的基因组最小化模拟与分析,能够系统鉴定微生物基因组基因的必需性。迄今为止,已有近百个基因组范围的代谢网络发表,覆盖的生物包括原核生物、真核生物和古生生物,并广泛应用于医药、能源、环境、工业和农业等多个领域,展现出了广阔的应用前景。将对全基因组范围代谢网络构建的方法、应用,特别是其在最小基因组研究中的应用作简要的综述。     

Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses

Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not clearly resolved. Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually reproducing genera were therefore selected, and their phylogenetic relationships were investigated using nuclear sequences of the largest subunit and second largest subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the recognition of six major phylogenetic groups (A-F). Group A contains six facultative pathogenic Candida species, which seem to have derived from nonpathogenic species, while Group B contains species of Clavispora, Metschnikowia, and Pichia guilliermondii. Species of Debaryomyces form an independent group C that is related to groups A and B. Pichia fermentans and other environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex.     

Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.     

Genome-scale phylogeny of the alphavirus genus suggests a marine origin

The genus Alphavirus comprises a diverse group of viruses, including some that cause severe disease. Using full-length sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the Alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences. Our phylogeny suggests the origin of the alphaviruses occurred in the southern oceans and spread equally through the Old and New World. Since lice appear to be involved in aquatic alphavirus transmission, it is possible that we are missing a louse-borne branch of the alphaviruses. Complete genome sequencing of all members of the genus also revealed conserved residues forming the structural basis of the E1 and E2 protein dimers.     

华南地区柑橘木虱与柑橘粉虱内共生菌检测及其Wolbachia共生菌的系统发育关系分析

【目的】探明不同地理种群的柑橘木虱Diaphorina citri Kuwayama和柑橘粉虱Dialeurodes citri Ashmead体内昆虫内共生菌的种类及其感染率,并以Wolbachia共生菌为代表,对其系统发育关系进行分析,为今后自共生菌角度研发柑橘木虱和柑橘粉虱的新型防控技术奠定基础。【方法】以16S r DNA、23S r DNA以及wsp为目标基因,利用PCR技术检测采自于广州、湛江、南宁、桂林、厦门的柑橘木虱以及采自广州的柑橘粉虱体内共生菌的种类及其感染率;利用多位点序列分型(MLST)技术和MEGA 5.0软件对不同昆虫样本中的Wolbachia进行系统发育关系分析。【结果】本研究采集的柑橘木虱和柑橘粉虱均含有原生共生菌Portiera和次生共生菌Wolbachia、Cardinium、Rickettsia,但该3种次生共生菌在不同木虱与粉虱种群的感染率有所不同;Arsenophonus只在广州和湛江种群的柑橘木虱中检出。基于wsp基因及MLST基因序列的Wolbachia系统发育分析表明,华南地区柑橘木虱和柑橘粉虱体内的Wolbachia均属于Wolbachia的B大组Con亚组。【结论】不同地理种群的柑橘木虱与柑橘粉虱体内感染的共生菌种类及其感染率不同;Wolabchia共生菌与柑橘木虱寄主不存在协同进化关系,在同一采集点存在Wolbachia通过柑橘寄主在柑橘木虱之间、柑橘木虱与柑橘粉虱之间水平传播的可能性。     

The phylogeny of the Rosaceae

KALKMAN, C., 1988. The phylogemy of the Rosaceae. A phylogenetic (cladistic) analysis of Rosaceae (excluding Chrysobalanaceae and Neuradaceae) is presented, based on the postulated direction of evolution in 14 morphological characters. Tribes or smaller groups, considered to be holophyletic, are taken as operational units. Three possible cladograms, made by hand, are presented and discussed. One of them is, within the limits of the method, selected as the most plausible image of real history, but this cladogram is not fully resolved and contains much homoplasy. Also presented is a fourth cladogram, produced by computer (CAFCA program); it is of about the same quality.
It is not justified to base drastic alterations in current classification on the weak phylogenetic hypothesis. For the time being it seems better not to recognize any subfamilies, but only a number of tribes.
It is hypothesized that the family originated in West Gondwana. A diagram is presented in which the most plausible cladogram is combined with the present distribution, clarifying the postulated routes of migration.
The sistergroup of Rosaceae is far from evident. The Cunoniaceae are considered to be the most plausible choice.     

跳虫系统进化的研究进展

跳虫是弹尾纲（Collembola）的俗称,在所有六足动物中化石年代最早,因此跳虫是六足动物起源及进化研究中非常重要的类群。跳虫的起源、分类地位和系统关系等问题,对于阐明六足动物甚至节肢动物各大类群的系统关系非常关键,日益成为相关学者关注和争论的焦点。本文就跳虫形态学和分子系统学方面的研究工作进行了综述。     

Molecular detection,community structure and phylogeny of ericoid mycorrhizal fungi

Through traditional culturing and molecular characterization, we have determined that five putative species and 2 polyphyletic assemblages of fungi produce ericoid mycorrhizae in Gaultheria shallon, other Ericaceae and Epacridaceae. Using phylogenetic analysis of ITS2 sequences in GenBank, we have confirmed that most of these fungi occur in North America, Europe, and Australia. The low recovery rate of culturable ericoid mycorrhizal fungi from Gaultheria shallon may partly be explained by the fact that most mycorrhizal root segments contain an unculturable basidiomycete, revealed by direct amplification, cloning, and sequencing of LSU fungal DNA from root. Molecular characterization and phylogenetic analysis are powerful tools in revealing the geographic distribution and identity of ericoid mycorrhizal fungi.     

Aspects of the phylogeny of the marine Tubificidae

A tentative phylogeny of the oligochaete family Tubificidae, with emphasis on the marine representatives, is presented. The scheme is based on the morphology and arrangements of prostate glands and the setal patterns. The rhyacodriline, more or less diffuse prostates are regarded as a primitive stage in prostate evolution, preceded only by the aprostate condition assumed for the ancestor of the family. An early split of the subfamily Rhyacodrilinae supposedly led to (1) a marine branch, from which evolved the highly diverse, exclusively marine subfamilies Phallodrilinae and Limnodriloidinae, and (2) a freshwater branch, which later divided into the Telmatodrilinae, Tubificinae and Aulodrilinae. The marine subfamilies invariably lack hair setae, whereas about half of the species within the other, freshwater subfamilies possess such setae in their dorsal bundles. Some marine genera, such as Monopylephorus (Rhyacodrilinae), Tubificoides and Clitellio (both Tubificinae) are regarded as recent off-shoots from the main freshwater stock.The families Naididae and Opistocystidae are considered likely to have evolved from rhyacodriline Tubificidae, whereas Phreodrilidae, the fourth family within the suborder Tubificina, is regarded as a sister group to the Tubificidae.     

Myzostomida: A review of the phylogeny and ultrastructure

Myzostomids are minute, soft-bodied, marine worms associated with echinoderms since the Carboniferous. Due to their long history as host-specific symbionts, they have acquired a highly derived body plan that obscures their phylogenetic affinities to other metazoans. Because certain organs are serially arranged a closer relationship between polychaetes and myzostomids has repeatedly been discussion. We presented here a review on the ultrastructure of myzostomids with the most recent analyses that concern their phylogenetic position. The ultrastructure of the integument, digestive system, excretory system and nervous system are summarized. Unpublished information on the gametogenesis and reproductive systems of myzostomids are also exposed with a view on their reproductive process.     

Squamate phylogeny and the relationships of snakes and mosasauroids

Cladistic analysis of extant and fossil squamates (95 characters, 26 taxa) finds the fossil squamate, Coniasaurus Owen, 1850, to be the sister-group of the Mosasauroidea (mosasaurs and aigialosaurs). This clade is supported in all 18 shortest cladograms (464 steps; CI 0.677; HI 0.772) by nine characters of the dermatocranium, maxilla, and mandible. A Strict Consensus Tree of the 18 shortest trees collapses to a basal polytomy for most major squamate clades including the clade (Coniasaurus, Mosasauroidea). A Majority Rule Consensus Tree shows that, in 12 of 18 shortest cladograms, the clade Coniasaurus- Mosasauroidea is the sister-group to snakes (Scolecophidia (Alethinophidia, Dinilysia); this entire clade, referred to as the Pythonomorpha ([[Scolecophidia [Alethinophidia, Dinilysia]], [Coniasaurus, Mosasauroidea]]) is the sister-group to all other scleroglossans. Pythonomorpha is supported in these 12 cladograms by nine characters related to the lower jaw and cranial kinesis. In 6 of 18 shortest cladograms, snakes are the sister-group to the clade (Amphisbaenia (Dibamidae (Gekkonoidea, Eublepharidae))). None of the cladograms support the hypothesis that coniasaurs and mosasauroids are derived varanoid anguimorphs. Two additional analyses were conducted: (1) manipulation and movement of problematic squamate clades while constraining ‘accepted’ relationships; (2) additional cladistic analyses beginning with extant taxa, and sequentially adding fossil taxa. From Test I, at 467 steps, Pythonomorpha can be the sister-group to the Anguimorpha, Scincomorpha, ‘scinco-gekkonomorpha’ [scincomorphs, gekkotans, and amphibaenids-dibamids]. At 471 steps Pythonomorpha can be placed within Varanoidea. Treating only mosasauroids and coniasaurs as a monophyletic group: 469 steps, mosasauroids and coniasaurs as sister-group to Anguimorpha; 479 steps, mosasauroids and coniasaurs nested within Varanoidea. Test II finds snakes to nest within Anguimorpha in a data set of only Mosasauroidea + Extant Squamates; the sistergroup to snakes + anugimorphs is (Amphisbaenia (Dibarnidae (Gekkonoidea, Eublepharidae))). No one particular taxon is identified as a keystone taxon in this analysis, though it appears truc that fossil taxa significantly alter the structure of squamate phylogenetic trees.     

Molecular phylogeny of French Guiana Hylinae: implications for the systematic and biodiversity of the Neotropical frogs

In this study we used nucleotide sequences from a segment of mitochondrial 16S ribosomal DNA gene to investigate the evolutionary relationships of some French Guiana Hylinae. New sequences, representing the members of different French Guiana frogs-five specimens of the Scinax genus, two Hyla, one Osteocephalus, one Hyalinobatrachium and two Rana as out-group-were examined. In addition, 26 sequences available from GenBank database representing the other subfamilies of the Hylidae were added to our study. This work allowed us to clarify relationships within the four hylids subfamilies (Pelodryadinae, Phyllomedusinae, Hemiphractinae and Hylinae) and the phylogenetic placement of the enigmatic Scinax genus within the Hylidae. We found that: (1) the Scinax genus displays a high level of differentiation in comparison to two other genera (Litoria and Hyla) belonging to 'Hylidae' family; (2) the Hylinae are paraphyletic given the position of the Litoria, which was the sister-group of the Hyla and the Osteocephalus genera; (3) the anterior works and our results (based on two different data sets) showed the paraphyly of the Hylidae questioning the validity of this family; (4) the reassessment of these different taxonomic groups will induce a huge implication on the estimation (past, present and future) of the biodiversity (in Neotropical frogs).     

果蝇Drosophila nasuta亚群系统发育问题的探讨

果蝇Ｄｒｏｓｏｐｈｉｌａｎａｓｕｔａ亚群由在１４个处于不同物种分化阶段的种,亚种和分类元组成,这个亚群的物种有许多进化上的独特之处,使得它在物种分化研究方面倍受关注,然而,在形态学,生殖隔离,染色体和同工酶多态,线粒体ＤＮＡＲＦＬＰ,求偶歌特征惟及线粒体和核基因序列分析等方面的研究都未能清楚地阐明这一亚群的系统进化关系,本文综合分析了关于这一亚群的进化遗传学的研究结果,并提出了有待进一步的一些问题     

The phylogeny and ontogeny of humeral torsion

In a series of specimens extending from fossil material through recent vertebrates including man there occurs a gradual phylogenetic increase in the degree of humeral torsion. A further (ontogenetic) torsion is superimposed upon the phylogenetic one in man which increases from birth until the proximal epiphysial cartilage of the humerus disappears and bony fusion occurs. There is a distinct correlation between the calculated strength of humeral rotator muscles inserting above and below the proximal epiphysis; this suggests that they provide the forces involved in the production of humeral torsion. It is shown that ontogenetic or secondary torsion occurs proximally and not along the shaft of the bone. Differences in the degree of humeral torsion in either sex of adult Whites and Negroes are given and discussed.