有瓣蝇类分类、系统发育及演化

有瓣蝇类(Calyptratae)隶属于昆虫纲(Insecta)四大超适应辐射类群之一的双翅目(Diptera),占双翅目已知物种多样性的近20%。有瓣蝇类分布广泛,生物学习性极为多样,在维系生态系统稳定中发挥着重要作用,是媒介、法医、传粉和天敌昆虫学研究领域的热点类群,也是探究双翅目系统演化及其成功适应辐射的关键类群。为了还原有瓣蝇类的演化历史,许多著名昆虫学者先后对该类昆虫开展过不同层面的研究。有瓣蝇类的单系性得到了普遍支持,并被分为3个总科——虱蝇总科(Hippoboscoidea)、蝇总科(Muscoidea)和狂蝇总科(Oestroidea),其中单系的狂蝇总科与多系的蝇总科聚为一支,再与虱蝇总科成为姐妹群。在科级阶元水平,蝠蝇科(Streblidae)(虱蝇总科)、花蝇科(Anthomyiidae)(蝇总科)、丽蝇科(Calliphoridae)(狂蝇总科)、邻寄蝇科(Rhinophoridae)(狂蝇总科)等类群的单系性仍有待验证,且新的科仍在不断被建立［如粉蝇科(Polleniidae)、乌鲁鲁蝇科(Ulurumyiidae)］,因此,有瓣蝇类科级系统发育关系仍不十分明晰。已有研究对虱蝇总科虱蝇科(Hippoboscidae)、蝠蝇科、蛛蝇科(Nycteribiidae),蝇总科蝇科(Muscidae)、粪蝇科(Scathophagidae),狂蝇总科麻蝇科(Sarcophagidae)、狂蝇科(Oestridae)胃蝇亚科(Gasterophilinae)的演化历史进行研究,明确了起源与扩散、寄主转移、取食策略等关键生物学习性的演化历史。但由于部分关键类群生活史信息的缺失,以及尚未有效解决的系统发育关系,有瓣蝇类演化历史仍有许多待解之谜。本文综述了有瓣蝇类分类、系统发育及演化研究进展,是在系统学研究进入系统发育基因组学时代后对该类群相关研究进展的首次全面总结。     

介形类系统分类与起源演化的形态、分子和化石证据

介形类(Ostracoda)因其丰富的化石记录和广布的海陆现生代表类群,而被认为是进化生物学中研究生物多样性产生机制和演变历程的颇具潜力的重要模式生物。介形类在甲壳亚门中的谱系发生位置、起源及其内部各类群间的系统关系还存在诸多争议。基于其体制构造的形态学特征,介形类被归入甲壳亚门下的颚足纲(Maxillopoda),但来自18S rDNA序列数据分析却显示Maxillopoda不是单系群。基于化石记录和壳体形态特征,高肌虫(Bradoriida)长期以来被认为是介形类的一个祖先类群,但保存有软躯体的早寒武世化石的研究表明,Bradoriida不是介形类甚至可能也不属于甲壳类。不同的研究者所强调的壳体和肢体形态特征各异,导致介形类最大的现生类群速足目(Podocopida)的四个超科之间的关系也存在诸多推测。壳体和肢体特征在系统演化意义上的不兼容,需要分子生物学等证据的介入。分子、形态和化石证据的积累及各种信息整合是系统演化研究的必然趋势。     

广西百色和永乐盆地的始新世猪类化石—兼论早期猪类的分类的演化

描述了广西百色及永乐盆地发现的中始新世最晚期－晚始新世的猪类化石,这批已知最早的猪超科化石,大大丰富了亚洲地区的早期猪类,对了解全球猪类的早期演化有着重要价值。广西的材料被确定为两个新属新种：萨氏始新猪Eocenchoerus savagei和广西华夏猪Huaxiachoerus guangxiensis,一个新种：粗壮暹罗猪Siamochoerus viriosus和一个未定属种：Tayassuidae gen.et sp.indet.加上已发表的单尖旅游Odiochoerus uniconus。百色,永乐盆地共计发现了5种始新世猪粉化石。新属Eocenchoerus虽然臼齿结构简单,与原始的古猪类（Palaeochoerid)接近,但因其M3具有一个明显的跟座而被归人猪科,早期猪科动物非常原始的臼齿形式证明,猪科动物 起源并不晚于古猪科（Palaeochoeridae)和西瑞科（Tayassuidae)。旧大陆的古猪类长期以来被认为与新大陆的西瑞类（tayassuid)更为接近,多数学者钭其归入西瑞科。笔者认为两者共有的近祖特征,并不能支持它们更摈 亲缘关系,而且古猪类缺乏典型西瑞类的近裔特征。因而支持将Palaeochoerinae亚科作为一个独立的Palaeochoeridae科,并将发现的两个新属种Huaxiachoerus guangxiensis和Siamochoerus viriosus归入该科,西瑞类材料的发现,再次肯定了东南亚地区确实存在与新大陆典型西湍类如Perchoerus,相似的古老猪类,另外新属Huaxiachoerus在臼齿结构上也显得比其他古猪类更接近新大陆的Cynorca,如果Perchoerus和Cynorca确属新大陆西湍类两个演化支系的祖选类型,那么新大陆的猪类动物很可能源于旧大陆,鉴于百色,永乐盆地的猪类已发生了较大分异,猪类动物的分化似应不晚于中始新世。     

鬼灯檠属的系统发育、分类和地理分布

本文对鬼灯檠属Rodgersia Gray的染色体数、花粉体积和纹饰、萼片数目、萼片脉序和脉型、萼片腹面毛被、花梗和花序轴毛被、叶的类型等关键性状进行了分析,确定了其进化顺序,依据性状的系统发生,绘制了鬼灯檠属的瓦格勒尔系统树;确认本属有5种和3变种,其中以R.podophylla为最原始,R.nepalensis为最进化,而R.aesculifolia,R.sambucifolia．和R.pinnata则居于两者之间。本属分两组Sect．Rodgersia,仅含R．podophylla Sect．Sambucifolia J．T．Pan,含R．aesculifolia,R.sambucifolia,R.pinnata,R.nepalensis。依据种的主要分布区,划本属植物为4个分布类型,即：日本—朝鲜间断分布,秦岭—大巴山分布,横断山分布和东喜马拉雅分布。笔者认为,本属的起源地在日本-朝鲜一带,横断山地区是其现代分布中心和分化中心;本属的散布路线是自日本—朝鲜,经秦岭—大巴山,通过横断山地区而进入东喜马拉雅,本属的起源时间,当在晚第三纪以前(晚白垩世至早第三纪)。此外,还报道了鬼灯檠属植物的花粉形态。     

利用18S和ITS序列揭示8种鲇形目鱼类的系统发育

为了探讨鲇形目(Siluriformes)鱼类系统发育关系,本研究克隆了黄颡鱼(Pelteobagrus fulvidraco)、长吻(Leiocassis longirostris)、斑鳠(Mystus guttatus)、革胡子鲇(Clarias gariepinus)、鲇鱼(Silurus asotus)和斑点叉尾(Ictalurus punctatus)6种鱼类的18S和两个内转录间隔区(包括全长ITS1-5.8S-ITS2)基因,结合GenBank中双须缺鳍鲇(Kryptopterus bicirrhis)和脂鳍胡鲇(Dinotopterus cunningtoni)的同源序列进行比较分析,结果表明,(1)8种鱼18S的长度为1814～1842bp,同源性达97%以上,5.8S均为157bp,同源性也高达99.36%～100%;(2)8种鱼ITS1长度为335～620bp,其中,黄颡鱼的最长,为618～620bp,斑点叉尾的最短,为335～336bp;ITS2长度为265～459bp,其中,脂鳍胡鲇最长,为459bp,斑点叉尾的最短,约为270bp。ITS1序列的同源性为29.45%～88.21%,其中,革胡子鲇和脂鳍胡鲇同源性最高,鲇鱼和革胡子鲇同源性最低。ITS2序列的同源性为41.59%～94.07%,其中,革胡子鲇和脂鳍胡鲇同源性最高,鲇鱼和革胡子鲇同源性最低;(3)分别以鲤鱼(Cyprinus carpio)18S和ITS为外群,采用NJ法构建18S、ITS系统发育树,结果显示,鲇科与胡鲇科的关系最近,鲿科与这两科关系较远,科与另外3科关系最远。鲿科中属和黄颡鱼属的关系较鳠属更近;胡鲇科的胡鲇属和脂鳍胡鲇属是关系很近的两个属;鲇科的鲇属和缺鳍鲇属是关系较远的两属。     

我国中生代的Margaritiferidae和它的演化

对我国中生代珍珠蚌科内的属、种进行了较系统的修订，归并了１科、１亚属、１０种，并据这些属、种纵向、横向的分布情况及其壳形、壳饰、内部构造等特征，进一步探讨了它们的起源和演化规律。     

根瘤菌多样性和系统发育研究的多相分类体系及其进展

近年来对新的根瘤菌资源的不断发掘及现代分子生物学技术的发展和应用使根瘤菌分类研究有了突破性进展。多相分类通过综合获取信息,多种方法相互印证、互为补充,推进了根瘤菌的表型、遗传型和系统发育三方面的发展,从而较全面地反映根瘤菌的生物多样性特征,是根瘤菌多样性研究工作中常常采用的技术手段。文中主要阐述了根瘤菌多相分类体系中的主要方法及现代根瘤菌系统发育地位的研究和进展。     

古生代轮藻类的演化和分类

本文通过对古生代轮藻类群形态结构的比较研究,认为Ｔｒｏｃｈｉｌｉｓｃｕｓ和Ｍｏｅｌｌｅｒｉｎａ具有不同的起源。前者藏卵器包围细胞右旋具横脊,底部结构两侧对称,起源于Ｓｙｃｉｄｉｕｍ;后者的左旋轮藻类包围细胞简单,底部结构辐射对称源于具简单直立包围细胞的Ｘｉｎｊｉａｎｇｏｃｈａｒａ。根据底部结构的对称性,将轮藻门划分为Ｓｙｃｉｄｉｐｈｙｃｅａｅ和Ｃｈａｒｏｐｈｙｃｄｅａｅ两个纲,Ｓｙｃｉｄｉｐｈｙｃ     

Phylogeny and Evolution in Cariceae (Cyperaceae): Current Knowledge and Future Directions

The goal of this study was to review the impact of DNA sequence analyses on our understanding of Cariceae phylogeny, classification and evolution. To explore character evolution, 105 taxa from four different studies were included in an nrDNA ITS + ETS 1f analysis of all recognized genera (Carex, Cymophyllus, Kobresia, Schoenoxiphium, Uncinia) and Carex subgenera (Carex, Psyllophora, Vignea, Vigneastra). As in previous analyses, four major Cariceae clades were recovered: (1) a “Core Carex Clade” (subg. Carex, Vigneastra, Psyllophora p.p); (2) A “Vignea Clade” (subg. Vignea, Psyllophora p.p.); (3) a “Schoenoxiphium Clade” (Schoenoxiphium, subg. Psyllophora p.p.), and (4) a “Core Unispicate Clade” (Uncinia, Kobresia, subg. Psyllophora p.p.). All studies provide strong support (86–100% BS) for the Core Carex and Vignea Clades, but only weak to moderate support (<50%–78% BS) for the Core Unispicate and Schoenoxiphium Clades. The relationships of these groups are unresolved. Studies suggest that Carex is either paraphyletic with respect to all Cariceae genera or to all genera except Schoenoxiphium. Kobresia is a grade, but Uncinia and possibly Schoenoxiphium are monophyletic. The monotypic Cymophyllus is indistinct from Carex subg. Psyllophora species. Character analyses indicate that inflorescence proliferation and reduction have occurred in all major clades, and that the Cariceae’s unisexual flowers have evolved from perfect flowers. The ancestor to Cariceae possessed a multispicate inflorescence with cladoprophylls and female spikelets with tristigmatic gynoecia and closed utricles. This morphology is most similar to extant Carex subg. Carex species, which contradicts the nearly unanimous assumption that the highly compound inflorescences of Schoenoxiphium are primitive. Since taxonomic sampling and statistical support for phylogenies have generally been poor, we advocate the temporary maintenance of the four traditional Carex subgenera with androgynous unispicate species placed within subg. Psyllophora and dioecious and gynaecandrous unispicate species distributed amongst subgenera Carex and Vignea. A collective effort focused on developing new nuclear markers, on increasing taxonomic and geographic sampling, and on studying development within the context of phylogeny, is needed to develop a phylogenetic classification of Cariceae.     

Classification and evolution of metazoan traces at a topological level

Topological fidelity of metazoan traces formed by metazoan behaviour is little influenced by compaction, diagenesis, continuous soft-sediment deformation and biostratinomy, substrate consistency, etc., whereas all of these can greatly alter the Euclidean geometric attributes of metazoan traces. Morphological characteristics of trace fossils can be distinguished and described objectively by both topological and Euclidean geometric parameters. The former constitute the basis of ichnoorder and ichnofamily. On the basis of topological criteria, metazoan traces can be classified as 4 ichnoorders and 22 ichnofamilies, consisting of 9 basic and 3 combined topological configurations. At a topological level, the behavioural diversity and complexity indicated by metazoan topoichnotaxa remain fairly stable in the Phanerozoic. All ichnoorders, 75% of ichnofamilies and all 9 basic topological configurations of metazoan traces are formed in the late Neoproterozoic, and all ichnofamilies, a combination of topological configurations and the most complex and highest level of topological configurations of metazoan traces, occurred in the early Cambrian. The evolution of metazoan traces can be expressed in three ranks. Changes at ichnoorder level constitute the first evolution, which is associated with the advent of kingdoms (animalia and plantae, etc.) and phyla (Ediacara and bilaterian, etc.), and the first level of palaeoecological and palaeoenvironmental changes, such as the appearance or disappearance of an ecosystem (Precambrian biomat). The first evolution terminated in the late Neoproterozoic. Changes at the ichnofamily level constitute the second evolution, which is associated with the advent of important phyla such as coelomate animal explosion and the second level of palaeoecological and palaeoenvironmental changes, such as structural changes within an ecosystem. The second evolution terminated in the early Cambrian. Changes at the ichnogeneric and ichnospecific levels constitute the third evolution, which is associated with the appearance or disappearance of the organic taxa lower than phylum, such as dinosaurs and birds, etc., and the third and fourth levels of palaeoecological and palaeoenvironmental changes, such as community-type level changes, within an established ecological structure and community level. The third evolution has been taking place since the Proterozoic.     

Margin feeding damage on the leaves of conifers and ginkgoales from the Mesozoic of Transbaikalia

A new approach to the formal classification of arthropod margin feeding plant damage is proposed. Several types of margin feeding traces on the leaves of Pityophyllum sp. and Ginkgoites sp. from the Upper Jurassic-Lower Cretaceous Chernovskie Kopi locality, Transbaikalia, are described as five new species in the genus Pinovulnus gen. nov.     

Phylogeny vs genome reshuffling: horizontal gene transfer

The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.     

Taxonomy,phylogenetics and biogeography of Chesneya (Fabaceae), evidenced from data of three sequences,ITS, trnS-trnG,and rbcL

Plants of Central Asia have played a significant role in the origin of floras of Eurasia and the Northern Hemisphere. Chesneya, a small leguminous genus occurring in Central Asia, western Asia, and Tibet, is used to establish phylogenetic relationships and discuss the evolutionary and biogeographical history based on sequence data of ITS and trnS-trnG and rbcL. We employed BEAST Bayesian inference for dating, and S-DIVA, Lagrange and BBM for ancestral area reconstruction. Our results indicate that Chesniella should be a separate genus, while Spongiocarpella should be included in Chesneya. A classification system within Chesneya comprising five sections is presented. The diversification of Chesneya (crown age ca. 16.56 Ma) is speculated to have been associated with Qinghai-Tibetan Plateau (QTP) uplift. The following aridification process resulted in the Pliocene diversification of four sections of Chesneya during 4.8–2.06 Ma. Ancestral area reconstruction indicates the Himalayas is the ancestral area of Chesneya and Chesniella, but within Central Asia, the western lowlands, can be inferred as the cradle of most dispersals.     

Downsized Dinosaurs: The Evolutionary Transition to Modern Birds

Living birds are the most diverse land vertebrates and the heirs of a rich chapter in the evolution of life. The origin of modern birds from animals similar to Tyrannosaurus rex is among the most remarkable examples of an evolutionary transition. A wealth of recently discovered fossils has finally settled the century-old controversy about the origin of birds and it has made the evolutionary saga toward modern birds one of the best documented transitions in the history of life. This paper reviews the evidence in support of the origin of birds from meat-eating dinosaurs, and it highlights the array of fossils that connect these fearsome animals with those that fly all around us.     

Phylogeny and classification of the Asteroidea (Echinodermata)

Post-Palaeozoic asteroids share a large number of derived characters of the ambulacral column and the mouth frame, and constitute the crown group of the monophyletic group Asteroidea. This crown group is here called the Neoasteroidea (new subclass). The stem species of the crown group lived in the Permian or early Triassic and so the evolution of the asteroids parallels that of the echinoids. Character distribution within the Neoasteroidea, especially morphology of the skeleton, digestive system, larvae and tube feet, allows subdivision into four orders (Paxillosida, Notomyotida, Valvatida, Forcipulatida). The latter three orders possess the synapomorphy of suckered tube feet and are united as the Surculifera (new superorder); the Paxillosida are their primitive sister group. Palaeozoic asteroids represent the stem group of the class, and may be divided into plesions according to the order of appearance of synapomorphies with the crown group. Classification of Palaeozoic asteroids requires much further study. The appearance of new characters within the crown group asteroids, such as suckered tube feet, implies that these were absent in the stem group. The range of life-habits possible in Palaeozoic asteroids can thus be partly deduced from evidence provided by living asteroids. Palaeozoic asteroids are deduced to have lacked suckered tube feet and were presumably unable to evert the stomach; hence they were precluded from life on hard substrates and extraoral feeding on epifaunal organisms. It is suggested that they lived on soft substrates by deposit feeding, scavenging and predation on small benthos.     

Phylogeny and genus-level classification of mantellid frogs (Amphibia, Anura)

We propose a novel classification of frogs in the family Mantellidae, based on published phylogenetic information and on a new analysis of molecular data. Our molecular tree for 53 mantellid species is based on 2419 base pairs of the mitochondrial 12S rRNA, 16S rRNA, tRNAVal and cytochrome b genes, and of the nuclear rhodopsin gene. Because the genus Mantidactylus Boulenger sensu lato is confirmed to be paraphyletic with respect to Mantella Boulenger, and is highly diverse in morphology and reproductive biology, we propose to partition Mantidactylus into seven genera by elevating four subgenera to genus rank (Blommersia Dubois, Guibemantis Dubois, Spinomantis Dubois, and Gephyromantis Methuen) and creating two new genera (Boehmantis gen. n. and Wakea gen. n.). In addition, we create the new subgenera Boophis (Sahona) subgen. n., Gephyromantis (Duboimantis) subgen. n., G. (Vatomantis) subgen. n., and Mantidactylus (Maitsomantis) subgen. n. The following species are transferred to Spinomantis, based on their phylogenetic relationships: S. elegans (Guibé) comb. n. (formerly in Mantidactylus subgenus Guibemantis); S. bertini (Guibé) comb. n. and S. guibei (Blommers-Schlösser) comb. n. (both formerly in Mantidactylus subgenus Blommersia); S. microtis (Guibé) comb. n. (formerly in Boophis Tschudi). Within Boophis, the new B. mandraka species group and B. albipunctatus species group are established. Boophis rhodoscelis (Boulenger) is transferred to the B. microtympanum group. The following five species are revalidated: Mantidactylus bellyi Mocquard and M. bourgati Guibé (not junior synonyms of M. curtus (Boulenger)); M. cowanii (Boulenger) (not syn. M. lugubris (Duméril)); M. delormei Angel (not syn. M. brevipalmatus Ahl); Mantella ebenaui (Boettger) (not syn. M. betsileo (Grandidier)). The new classification accounts for recent progress in the understanding of the phylogeny and natural history of these frogs, but it is still tentative for a number of species. Future modifications may be necessary, especially as concerns species now included in Gephyromantis and Spinomantis.Full article published online at: http://www.senckenberg.de/odes/06-11.htm     

Phylogeny and physiology of Drosophila opsins

Phylogenetic and physiological methods were used to study the evolution of the opsin gene family in Drosophila. A phylogeny based on DNA sequences from 13 opsin genes including representatives from the two major subgenera of Drosophila shows six major, well-supported clades: The blue opsin clade includes all of the Rhl and Rh2 genes and is separated into two distinct subclades of Rhl sequences and Rh2 sequences; the ultraviolet opsin clade includes all Rh3 and Rh4 genes and bifurcates into separate Rh3 and Rh4 clades. The duplications that generated this gene family most likely took place before the evolution of the subgenera Drosophila and Sophophora and their component species groups. Numerous changes have occurred in these genes since the duplications, including the loss and/or gain of introns in the different genes and even within the Rhl and Rh4 clades. Despite these changes, the spectral sensitivity of each of the opsins has remained remarkably fixed in a sample of four species representing two species groups in each of the two subgenera. All of the strains that were investigated had R1-6 (Rhl) spectral sensitivity curves that peaked at or near 480 nm, R7 (Rh3 and Rh4) peaks in the ultraviolet range, and ocellar (Rh2) peaks near 420 nm. Each of the four gene clades on the phylogeny exhibits very conservative patterns of amino acid replacement in domains of the protein thought to influence spectral sen sitivity, reflecting strong constraints on the spectrum of light visible to Drosophila.     

Nudivirus Genomics： Diversity and Classification

Nudiviruses represent a diverse group of arthropod specific, rod-shaped and dsDNA viruses. Due to similarities in pathology and morphology to members of the family Baculoviridae, they have been previously classified as the so-called “non-occluded” baculoviruses. However, presently they are taxonomically orphaned and are not assigned to any virus family because of the lack of genetic relatedness to Baculoviridae,. Here, we report on recent progress in the genomic analysis of Heliothis zea nudivirus 1 (HzNV-1), Oryctes rhinoceros nudivirus (OrNV), Gryllus bimaculatus nudivirus (GbNV) and Heliotis zea nudivirus 2 (HzNV-2). Gene content comparison and phylogenetic analyses indicated that the viruses share 15 core genes with baculoviruses and form a monophyletic sister group to them. Consequences of the genetic relationship are discussed for the classification of nudiviruses.