A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

Severe Acute Respiratory Syndrome (SARS) is a newly identified infectious disease[1—5]. The global outbreak of SARS has been threatening the health of people worldwide and has killed 353 people and infected more than 5462 in 27 countries, as reported by WHO on April 29, 2003 (http://www.who.int/csr/sarscountry/en). Although it has been recognized that a variant of virus from the family of coronavirus might be the candidate pathogen of SARS[1—5], its identity as the unique pathogen sti…     

似然比检验和贝叶斯推论在雉科分子系统学中的应用

应用似然比检验和贝叶斯推论进行雉科分子系统学研究．所用的56条纫胞色素b基因全序列代表了雉科24属50种以及作为外类群的6个相关属．等级制似然比检验表明该数据集的最佳进化模型为GTR I——G。建立在坚实的统计学基础上的贝叶斯系统树表明雉科可以分为3个分支．特别是包括角雉、松鸡、火鸡和gallopheasant等在内的第3分支的单系群性质得到了充分的支持．深层分支格局的高分辨率和高支持率说明将雉科划分为雉族和鹑族是人为的．结果表明，似然比检验和贝叶斯推论是分子系统学研究的强有力工具．     

山茶科系统发育诠释：Ⅸ.山茶属的原始特征及其演化趋向

讨论和比较了关于山茶属演化趋向的两种观点，认为根据现存种类及目前发现的化石资料，花无梗，苞被不分化为苞片和萼片，代表了山茶属的原始特征；而花梗伸长，引起了苞萼分化，苞片在花梗上疏离，宿存，脱落或减少，演化出更加进步的类群；而苞被保持不分化，多数状态下也可能在花和果等方面得到演化，体现了系统发育和个体发育在山茶属内次级分类群中并不一致     

盲蝽科(半翅目异翅亚目)部分昆虫酯酶同工酶比较研究

运用酯酶同工酶电泳技术获得盲蝽亚科Mirinae、合垫盲蝽亚科Orthotylinae、叶盲蝽亚科Phylinae和齿爪盲蝽亚科Deraeocorinae 4个亚科12个属的23种盲蝽的酯酶同工酶(EST)酶谱．将所获得的酶谱数据(酶带和相对迁移率Rf)转化为二态特征数据，建立矩阵，用系统发育分析软件包WinClada 1．00．04对数据矩阵进行分析运算，分别获得各个亚科内和亚科间的系统发育树．分析结果表明：①酯酶同工酶酶谱特征在不同属级单元之间以及同属的不同种类之间都存在着明显的差异；②不同属种之间酯酶同工酶特征的相似程度与外部形态特征之间的相似程度不一致，以外部形态为主要依据的传统分类的一些属不是真正的单系群；③酯酶同工酶酶谱特征所反映出的盲蝽科4个亚科间的相互关系与Sehuh 1974年所做的盲蝽科内系统发育部分一致，但合垫盲蝽亚科与叶盲蝽亚科之间不是直接的姐妹群关系．4个亚科的关系为(((盲蝽亚科Mirinae，齿爪盲蝽亚科Deraeocorinae)叶盲蝽亚科Phylinae)合垫盲蝽亚科Orthotylinae)；④盲蝽亚科内存在着明显的异质性，需要进一步分类修订．     

基于trn L-F序列数据利用贝叶斯法推测罗汉松科的系统发育

以黑松和Agathis australis为外类群,基于罗汉松科42种植物的叶绿体trnL-F序列数据通过贝叶斯法对该科的系统发育进行了推测.结果显示:①Phyllocladus为单系分支,位于罗汉松科的基部,是罗汉松科所有其余成员的姊妹群;②Nageia嵌套在罗汉松科内,同罗汉松属、Afrocarpus及Retrophyllum的关系较为密切;③Dacrycarpus为单系群且处于姊妹分支Falcatifolium-陆均松属的基部;④Lagarostrobs franklinii和Manoao colensoi应置于同一属Lagarostrobs内;⑤支持成立Halocarpus和Lepidothamnus属;⑥赞同Microstrobos和Microcachrys两属亲缘密切的观点.     

Histories of molecules: Reconciling the past

Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of ‘simple-to-complex’ modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.     

Classification,reconstructed phylogeny and geographic history of the Neotropical phorid flies of the genus Gymnophora (Diptera: Phoridae)

The Neotropical species of Gymnophora are revised to include 28 species, 17 of which are new. Two subgenera, Cerocratia (in a revised sense) and Gymnophora s.s. are recognized. Cerocratia includes Gymnophora triangularis sp. nov., G. acutangula Schmitz, G. latibrachia sp. nov., G. lacertosa sp. nov., G. chilensis Borgmeier, G. parachilensis sp. nov., G. aemula Borgmeier, G. forticornis Schmitz, and doubtfully G. colona Brues. G. adumbrata Borgmeier is considered as a junior synonym of G. aemula (syn. nov.). Within Gymnophora s.s. there are four major lineages, the G. commotria-group, the G. carina-group, the G. cymatoneura-group and the G. quartomollis-group. Of these, the G. carina-group and the G. quartomollis-group are known only from the Holarctic Region. The G. commotria-group consists of the G. forcipis-series, containing G. forcipis sp. nov., subuncata sp. nov. and uncata sp. nov., and G. damula-series, whose species are further organized into the G. strigula-subseries, containing G. strigula sp. nov. and G. unidentata sp. nov., plus the G. falciformis-subseries, containing G. alces sp. nov., damula sp. nov. and falciformis sp. nov. Also included in the G. commotria-group are eight residual species whose relationships cannot be deduced at this time. Three of these species, G. commotria Schmitz, penai sp. nov. and quadrata sp. nov. are more closely related to each other than to G. auricula sp. nov., brasiliensis Borgmeier, heteroneura Schmitz, inusitata sp. nov. and trispina sp. nov. The G. cymatoneura-group contains G. cymatoneura Enderlein and G. spiracularis Borgmeier, and the male of G. spiracularis is described for the first time. A key is given that permits identification of males of most species, but females cannot be identified with certainty. A partially sequenced classification of the genus indicates the relationships of most of the included species. The genus may have originated in the Neotropical Region, although the evidence is tenuous, and shows some similarity of distribution to Andean-centered plant groups.     

Phylogenetic relationships of millipedes in the subclass Penicillata (Diplopoda) with a key to the genera

Bristly millipedes (subclass Penicillata, order Polyxenida) are minute diplopods characterised by uncalcified cuticle and a body covered with unique tufts of bristles. The order is found worldwide and comprises less than 200 described species divided into three families, with many of the species and genera being poorly known. The first evolutionary analysis of the order presented here utilises both molecular (COI, 18S rRNA and 16S rRNA) and morphological data to examine monophyly of the families and subfamilies and the evolutionary relationships between them. Maximum likelihood analysis was based on molecular data only, whereas parsimony analyses were based on molecular data as well as combined morphological and molecular data. The results of these analyses with two different optimality criteria were incongruent in many aspects. Unlike parsimony, the likelihood result found strong support for a basal position of the family Synxenidae and separation of the order into two monophyletic clades corresponding to the two superfamilies Synxenoidea, containing the family Synxenidae, and Polyxenoidea, containing the families Polyxenidae and Lophoproctidae. Parsimony results did not support the existence of the two superfamilies. Both analyses resolved the family Synxenidae as monophyletic and Polyxenidae as polyphyletic, whereas the family Lophoproctidae was shown to be paraphyletic in likelihood and monophyletic in parsimony analysis. The subfamilies Monographinae and Polyxeninae were found to be monophyletic in the likelihood tree but parsimony suggested paraphyly of both. The results suggest that further revision of the systematics of the Polyxenida may be necessary. However, a much larger molecular data set will be necessary to clarify and provide stronger nodal support for phylogenetic trees and to confirm the relationships, particularly of the families Polyxenidae and Lophoproctidae. Molecular identification is likely to be an important tool for this taxonomically challenging order in future. A simplified key to the genera is provided.     

Taxonomy and genetic variation in the Australian lizards of the genus Pseudemoia (Scincidae: Lygosominae)

This study reviews the taxonomy of the southern Australian scincid lizards previously referred to Leiolopisma entrecasteauxii (Duméril and Bibron, 1839) and L. baudini Greer, 1982; here placed along with L. spenceri and the recently described L. rawlinsoni in the genus Pseudemoia. Electrophoretic, karyotypic and morphological data show that populations assigned to P. entrecasteauxii belong to three species. The name Pseudemoia entrecasteauxii is restricted here to a morphologically variable species which occurs in woodlands, forests and heathlands from the Blue Mountains, NSW, through the southeastern mainland, Bass Strait islands and Tasmania, to the islands of Spencer Gulf, SA. Populations designated as L. entrecasteauxii Form B by recent authors are mostly referrable to P. entrecasteauxii (s.s.). Pseudemoia pagenstecheri (Lindholm, 1901) is resurrected to apply to strongly striped populations disjunctly distributed in open grassland habitats from Tasmania, south-central Victoria, the southeast Australian highlands, Blue Mountains and New England Tableland. This species largely encompasses those populations referred to by several workers as L. entrecasteauxii Form A. A neotype for Lygosoma (Liolepisma) pagenstecheri is designated. A new species, P. cryodroma, is restricted to alpine and subalpine habitats on the high plains of Victoria. Pseudemoia cryodroma may have had a hybrid origin from P. entrecasteauxii and P. pagenstecheri. Pseudemoia baudini, hitherto known only from the unique holotype, is redescribed. This species extends eastward along the coast of the Great Australian Bight as far as the Eyre Peninsula, South Australia. A key to the species of Pseudemoia is provided.