真正柑橘果树类植物基于AFLP分子标记的分类与进化研究

用AFLP分子标记技术对芸香科Rutaceae柑橘亚科Aurantioideae真正柑橘果树类(the True Citrus Fruit Trees Group) 6属植物的59个生物类型以及九里香Murraya exotica L.、蚝壳刺Severinia buxifolia Tenore和酒饼簕Atalantia buxifolia Oliv.进行了分析。从64对引物组合中筛选出15对分辨率好的引物对全部材料进行了扩增, 共获得312条带, 其中多态型带305条, 多态位点达97.8%。利用PAUP软件构建了全部材料基于AFLP数据的UPGMA距离树。结果表明, AFLP证据支持基于形态特征建立的真正柑橘果树群以及群内各属的划分, 只是金柑属Fortunella Swingle作为一个独立的分支嵌于柑橘属Citrus L.内。对于柑橘属, 我们的分子证据支持Swingle关于亚属的划分以及Scora等关于C. medica、C. grandis和C. reticulata是真正柑橘亚属subgen. Eucitrus三个基本种的观点。AFLP分子证据显示宜昌橙C. ichangensis Swingle位于真正柑橘亚属中, 与香橙C. junos Sieb. ex Tanaka的亲缘关系最近, 而与大翼橙亚属subgen. Papeda中马蜂柑C. hystrix DC.相隔甚远。另外, 莽山野橘C. mangshanensis S. W. He &; G. F. Liu在系统树上居于宽皮柑橘类的基部。最后, 对真正柑橘果树群6属植物间以及柑橘属各主要类型(种)的进化关系进行了详细的讨论。     

AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies

The palaeotropic pioneer tree genus Macaranga Thouars (Euphorbiaceae) is characterized by various types of mutualistic interactions with specific ant partners (mainly Crematogaster spp.). About 30 species are obligate ant-plants (myrmecophytes). We used amplified fragment length polymorphism (AFLP) markers to assess phylogenetic relationships among 108 Macaranga specimens from 43 species, including all available taxa from the three sections known to contain myrmecophytes. Eight primer combinations produced 426 bands that were scored as presence/absence characters. Banding patterns were analyzed phenetically, cladistically and by principal coordinates analysis. Monophyly of section Pruinosae is clearly supported. There is also good evidence for a monophyletic section Pachystemon that includes the puncticulata group. The monophyly of section Winklerianae and relationships between the three sections remain ambiguous. Section Pachystemon is subdivided into four well-supported monophyletic subclades that presumably correspond to taxonomic entities.We acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG Fi606/4-1, DFG We1830/2-1, 4-1 and 4-2), which in part was granted in the frame of the DFG-SPP 1127 Radiations: origins of biological diversity. Part of the plant material was kindly supplied by Dr. H. Feldhaar (University of Würzburg), Dr. U. Moog (University of Kassel) and Dr. F. Slik (Leiden University Branch, Nationaal Herbarium Nederland). We thank the University of Malaysia (Dr. Rosli b. Hashim) and Taman Taman Sabah (Datuk Lamri Ali; Dr. J. Nais) for permits and logistic support, and EPU for permission to conduct research in Malaysia.     

Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis

 Relationships among 88 accessions representing 45 Citrus species, three man-made hybrids, and six related genera were examined for restriction fragment length polymorphisms (RFLP). Thirty-two Citrus and three Microcitrus accessions were also examined by random amplified polymorphic DNA (RAPD) analysis. A measure of relative heterozygosity was estimated based on the mean of the number of fragments per individual per probe-enzyme combination (PEC) divided by total number of fragments per PEC for all non-hybrid Citrus individuals. The presence in a Citrus species of a rare band found also in a related genus was taken as an indication of possible introgression, while the presence of several fragments unique to 1 species was used to indicate non-involvement of that species in hybridization events. Most species that have been described in the literature as hybrids had high heterozygosity indices and no unique fragments. Distance matrices and dendrograms were generated using simple matching coefficient and neighbor-joining cluster analysis. RFLP and RAPD data gave approximately the same results. These data showed C. maxima was affiliated with the papedas C. hongheensis and C. latipes. C. medica clustered with C. indica when only non-hybrid taxa were examined, or among limes, lemons, and relatives when all species were considered. Mandarins did not show strongly supported groupings among themselves, nor with other species. These data showed that several accessions were probably assigned to the wrong species. Received: 30 September 1997 / Accepted: 29 October 1997     

家蚕高密度AFLP连锁图谱的构建

为了进行家蚕Bombyx mori数量性状的QTL定位研究,以白色茧系品种C₁₀₀ (♀)和近交系大造(P50)(♂)杂交得到F₁,用F₁(♂)与双隐性标记的C₁₀₀ (♀)回交,得到回交一代(BC₁),用改进的AFLP分子标记方法,经96组选择性扩增引物扩增,获得分离比为1∶1(P≤0.05)的1 744个AFLP位点。用Map Manager QTXb19（Version 0.29）连锁图谱构建软件,构建了具有814个标记,36个连锁群的家蚕高密度AFLP分子标记连锁图谱。该连锁图谱覆盖的家蚕基因组长度为13 005 cM,连锁群长度变化范围为109.0～1 573.7 cM,连锁群的平均长度为361.25 cM,其标记间平均图距15.98 cM,最小图距2.3 cM,最大图距47.7 cM,标记间大于30 cM的gap共有39个。该连锁图平均每个连锁群23个标记,最多一个连锁群有92个标记,最少8个标记。该连锁图谱确定了与经典实验遗传图谱第15连锁群和W染色体连锁群相对应的两个连锁群。     

Utility of AFLP markers for the assessment of molecular relationships in Ceratozamia Brongn. (Zamiaceae)

Abstract

The genus Ceratozamia has a distribution from Mexico to Central America. Molecular relationships were explored among Mexican Ceratozamia species using variable molecular markers, namely Amplified Fragment Length Polymorphisms (AFLP). Three AFLP primer-combinations generated 77 loci for a total of 1,684 fragments. Molecular variation was 75.72% among species and 24.28% within species, and a low correlation was present between genetic and geographical distances. Cluster analysis produced a phenogram in which two distinct clusters are clearly recognizable, one including C. alvarezii, C. sabatoi, C. zaragozae, C. kuesteriana, C. mexicana and C. robusta, and another one with C. zoquorum, C. miqueliana, C. latifolia, C. microstrobila, C. hildae and C. morettii. The AFLP proved to be suitable to study the relationships among species of Ceratozamia, and the results corroborated those from previous morphology-based studies.     

Tortula and some related genera (Pottiaceae, Musci): phylogenetic relationships based on chloroplast rps4 sequences

 According to chloroplast rps4 sequence data the genus Syntrichia forms a monophyletic clade clearly separated from Tortula, while Pottia is shown to be polyphyletic and the Rhynchostegiae species (with rostrate lid) are very similar to Tortula. Crossidium is probably polyphyletic. The close affinity of Desmatodon, Stegonia, Pterygoneurum and some of the species of Phascum with Tortula is confirmed by the molecular data. Received May 23, 2002; accepted August 23, 2002 Published online: November 22, 2002 Address of the authors: O. Werner, R. M. Ros, M. J. Cano, J. Guerra (E-mail: werner@um.es) Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, Campus de Espinardo, E-30100-Murcia, Spain.     

Molecular phylogenetic relationships of Melanthiaceae (Liliales) based on plastid DNA sequences

Melanthiaceae (Liliales) comprise 17 genera of rhizomatous or bulbous perennials and are distributed across the Northern Hemisphere. The relationships among the five tribes in this family have been evaluated in many molecular and morphological studies. In this study, we performed a phylogenetic analysis of the 17 genera, including 106 species of Melanthiaceae sensu APG III and nine related species as outgroups, based on sequences of five plastid regions (atpB, rbcL, matK, ndhF and trnL‐F). Support values for the monophyly of the family (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) and each tribe were improved in comparison with previous studies. Among the tribes, Melanthieae were sister to the remainder of the family and sister relationships between Xerophylleae and Parideae (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) and Chionographideae and Heloniadeae (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) were confirmed. Notably, the generic concept of Veratrum s.l. including Melanthium was not supported in the present study and these genera should be treated as distinct. In the case of Parideae, the relationship of Trillium govanianum to the other species remains uncertain and requires further studies. Finally, we mapped seven representative morphological characters onto the molecular phylogenetic tree for Melanthiaceae.     

New gammaroid family, genera and species from subterranean waters of Japan, and their phylogenetic relationships (Crustacea: Amphipoda)

Luciobliviidae, a new family in the superfamily Gammaroidea (Amphipoda: Crustacea), is described on the basis of species in the genus Lucioblivio gen. nov. from subterranean waters of Japan. Mesogammaridae Bousfield, 1977 is rediagnosed; Octopupilla gen. nov. from subterranean waters of Japan is described and Eoniphargus (Uéno, 1955) from subterranean waters of Japan and Korea is included. The members of Lucioblivio , Octopupilla and Eoniphargus share several characters, including reduced eyes, a setose body, reduced coxae, feeble appendages and pedunculate coxal gills. To elucidate the phylogeny of the three genera among others, a sequence analysis of the 28S rRNA gene was conducted for 14 species in six families, including the three genera, from the superfamilies, Gammaroidea, Crangonyctoidea and Hadzioidea. The tree from a neighbour-joining analysis and the strict consensus tree from a maximum-parsimony analysis indicate monophyly of Mesogammaridae. Luciobliviidae is embedded within a clade of taxa belonging to the superfamily Gammaroidea. These results and the occurrence of gammarid-type calceoli in species of the new family indicate that Luciobliviidae should be placed within the superfamily Gammaroidea. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 643–670.     

Rapidly evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida)

The phylogenetic relationships of the Clitellata were investigated using a data set with published and new complete or partial 18S rRNA and mtCOI gene sequences of 13 and 49 taxa representing 8 and 14 families, respectively. Three different alignments were considered for 18S, and the possible influence of departures from rate constancy among sites was evaluated by analyses using a Gamma model of rate heterogeneity. Maximum-likelihood estimates of the shape parameter alpha of the Gamma distribution were very low, whatever the alignment or the gene considered, suggesting that phylogenetic reconstructions taking into account the rate heterogeneity among sites are likely to be the most reliable. Analyzed separately, the two genes did not resolve the relationships among the Clitellata, but the consensus tree was congruent with the morphology-based relationships. Our data suggest the inclusion of the Euhirudinea, Acanthobdellida, and Branchiobdellida in the Oligochaeta and suggest the Lumbriculidae as the link between both assemblages. Although separate analyses of both genes, as well as different alignments for the 18S rRNA sequences, yielded conflicting results concerning the phylogenetic position of leeches and leech-like worms vis-à-vis the Oligochaeta, subsequent analyses using the Gamma model greatly reduced the observed inconsistencies. Our analyses show that among the Clitellata, the leeches and the leech-like and gutless worms represent significantly faster evolving lineages. It is suggested that the observed higher mutation rates may be explained by the fact that these lineages contain almost exclusively commensal and/or parasitic taxa.     

Tertiary plotopterids (Aves, Plotopteridae) and a novel hypothesis on the phylogenetic relationships of penguins (Spheniscidae)

Plotopterids (Aves: Plotopteridae) are extinct wing-propelled diving birds which exhibit a strikingly similar wing morphology to penguins (Spheniscidae), but also share derived characters with 'pelecaniform' birds that are absent in penguins. The similarities between Plotopteridae and Spheniscidae have hitherto been attributed to convergence, and plotopterids were considered to be most closely related to the 'pelecaniform' Phalacrocoracidae (cormorants) and Anhingidae (anhingas). However, here I show that assignment of plotopterids to 'pelecaniform' birds does not necessarily preclude them from being the sister taxon of penguins. Cladistic analysis of 68 morphological characters resulted in sister group relationship between Plotopteridae and Spheniscidae, and the clade (Plotopteridae + Spheniscidae) was shown to be the sister taxon of the Suloidea, i.e. a clade including Sulidae (boobies and gannets), Phalacrocoracidae, and Anhingidae. Derived characters are discussed which support this novel hypothesis. Paedomorphosis probably accounts for the absence of derived characters in penguins that are shared by Plotopteridae and members of the Steganopodes. Plotopterids exemplify the importance of fossil birds for analyzing the phylogenetic relationships of modern taxa that exhibit a highly apomorphic morphology.     

On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta)

Friedemann K., Wipfler B., Bradler S. and Beutel R.G. 2011 . On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta). —Acta Zoologica (Stockholm) 00 : 1–16. External and internal head structures of Phyllium siccifolium are described in detail. The findings are compared with conditions found in other phasmatodeans and members of other neopteran lineages. The compiled 125 characters were analysed cladistically. A clade Eukinolabia (Phasmatodea + Embioptera) was confirmed. Synapomorphies of these two taxa are the shift of the origin of M. tentorioparaglossalis to the hind margin of the prementum, the presence of M. tentorioscapalis medialis, and antennal muscles that originate exclusively on the anterior tentorial arms. Within Eukinolabia, the position of Timema remains somewhat ambiguous because of missing anatomical data. However, it was confirmed as sister group of Euphasmatodea in a monophyletic Phasmatodea. Apomorphic groundplan features of Euphasmatodea are salivary ducts with separate external openings, apically rounded glossae, the presence of the galealobulus, and the reduction of the antennifer. The monophyly of Neophasmatidae was confirmed. Autapomorphies are the loss of M. frontobuccalis posterior, the anteriorly or dorsally directed maxillary palps, and the reduction of the mandibular incisivi. The analysis of characters of the head yielded three new autapomorphies of Phylliinae, the presence of a protuberance on the attachment site of the dorsal tentorial arms, dorsoventrally flattened maxillary‐ and labial palps, and possibly the narrow and U‐shaped field of trichomes on the apical part of the galea.     

Convergent evolution and paraphyly of the hawk-eagles of the genus Spizaetus (Aves, Accipitridae) – phylogenetic analyses based on mitochondrial markers

The phylogenetic relationships within the New and Old World hawk-eagle assemblage (genus Spizaetus ; Aves: Accipitridae) were studied using mitochondrial DNA sequences ( cytochrome b , control region). Eighty-four specimens representing all Spizaetus species and almost all currently distinguished subspecies as well as 11 other booted and non-booted 'eagle' genera from the Neotropics, Africa, Eurasia, South Asia and Australasia ( Oroaetus , Harpia , Morphnus , Lophaetus , Stephanoaetus , Hieraaetus , Aquila , Ictinaetus , Spilornis , Pithecophaga , Harpyopsis ) were investigated. Although the basal branching could not be resolved, our investigations clearly indicate that hawk-eagles represent a paraphyletic assemblage and thus their external similarities have to be ascribed to convergent evolution. The New World taxa of Spizaetus cluster together, but the South American species Oroaetus isidori appears embedded within this clade. The taxa from Southeast to East Asia form a clearly separated monophyletic group. It is further divided into two subgroups, which are also characterized by distinct juvenile plumage patterns. Spizaetus africanus , the only African representative of the genus, is found in a mixed cluster consisting of members of the genera Aquila and Hieraaetus . These findings are in accordance with previous studies of other authors based on various molecular markers and different sets of taxa, but disagree with current taxonomy. Therefore, we suggest assigning the species of the genus Spizaetus to three different genera: (1) Spizaetus (including Oroaetus isidori ) in Central and South America and (2) Nisaetus for the Southeast to East Asian group. (3) The African taxon ( Spizaetus africanus ) is discussed to be included into the genus Aquila. Furthermore, we propose to use the former genus name Lophotriorchis Sharpe, 1874, for the monotypic species Hieraaetus kienerii , which has an isolated phylogenetic position.     

Molecular phylogenetic position of the genera Stephanonympha and Caduceia (Parabasalia) inferred from nuclear small subunit rRNA gene sequences

Nuclear small subunit (SSU) rRNA gene sequences were obtained by polymerase chain reaction from trichomonad symbionts of termites that belong to the Devescovinidae (Caduceia versatilis) and polymastigont Calonymphidae (Stephanonympha nelumbium). The unidentified SSU rRNA sequence Nk3, previously obtained from the termite Neotermes koshunensis, has also been shown to derive from a Stephanonympha sp. by in situ hybridization. These sequences were analysed in a broad phylogeny including nearly all identified parabasalid sequences available in the databases, and some as yet unidentified sequences likely deriving from the new order Cristamonadida (Devescovinidae, Calonymphidae, and hypermastigids Lophomonadida). A global phylogeny of parabasalids reveals a partial agreement between the clades identified in this work and the last classification of this phylum into four orders. However, this classification is still incongruent with our data and new taxonomic considerations are proposed. The analysis confirms the monophyly of the Cristamonadida and separates this order into two groups: the first unites nearly all the Devescovinidae including Caduceia and the Calonymphidae Coronympha and Metacoronympha, whereas the second group is composed of a few Devescovinidae, Lophomonadida, and Calonymphidae such as Stephanonympha. Caduceia is closely related to Devescovina, corroborating the marked morphological similarity between these two genera whereas Stephanonympha groups together with the Calonymphidae Snyderella and Calonympha. These data also confirm the polyphyly of the families Devescovinidae and Calonymphidae and support the arrangement of the axostyle-pelta complexes as a valuable character for taxonomic considerations within the Calonymphidae.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

The phylogenetic relationships of the physaloid genera (Solanaceae) based on morphological data

A group of genera, e.g., Chamaesaracha, Leucophysalis, Physaliastrum, Margaranthus, and Withania, in the subfamily Solanoideae (Solanaceae) is centered around the genus Physalis and has been named the physaloid group. It comprises a number of small and often poorly known genera, sometimes seen as united with Physalis and/or each other. A hypothesis of the phylogenetic relationships within this group, based on parsimony analyses of morphological data, is here presented for the first time. The result is discussed in relation to prevailing generic circumsciptions and taxonomic consequences. It is also compared with hypotheses of relationships based on cpDNA data.     

基于线粒体ND2基因的中国斑翅蝗科部分种类分子系统学研究（直翅目：蝗总科）

本文的目的是通过对斑翅蝗科部分种类的线粒体ND2基因进行分析,重建斑翅蝗科昆虫的系统发育关系,并探讨分子系统发育关系和传统分类结果的异同。扩增并测定了我国斑翅蝗科10属16种蝗虫的线粒体ND2全基因1 023 bp的序列,对序列的碱基组成、转换颠换、系统发育信号等进行了分析。并基于ND2全基因序列数据,分别采用邻接法（NJ）、最简约法（MP）、最大似然法（ML）和贝叶斯法重建了10属16种蝗虫的系统发育关系。结果表明：斑翅蝗科蝗虫ND2全基因A+T含量平均为74.6%;痂蝗亚科和异痂蝗亚科没能得到区分,建议合并为一个亚科;而斑翅蝗亚科和飞蝗亚科的分类地位还存在争议。     

Genetic differentiation of Helicoverpa armigera (Hübner) and H. assulta (Guenée) (Lepidoptera: Noctuidae) based on AFLP markers

Abstract Here we use amplified fragment length polymorphism (AFLP) to assess genetic differentiation of Helicoverpa armigera and H. assulta . The results indicated that both species-specific fingerprints and cluster analysis showed the ability of AFLP technique to discriminate the two sibling species; among a total 1963 AFLP markers amplified from nine primer combinations: 777 (39.6%) were H. armigera -specific, 602 (30.7%) were H. assulta -specific, and 584 (29.7%) were common bands. The mean number of H. armigera -specific bands was significantly more than that of H. assulta -specific bands for nine primer combinations ( P < 0.05); the intraspecific distance of H. armigera and H. assulta was 0.123 0 and 0.110 7 respectively, and the interspecific distance was 0.178 3. In addition, the percentage of polymorphic loci and estimated average heterozygosity were used to estimate genetic diversity of the two species. This study therefore demonstrates that AFLP analysis is a sensitive and reliable technique to study genetic differentiation and genetic relationships between species and provides sufficient molecular markers for future linkage map construction, location and eventual cloning of genes involved in traits differentiation.