根瘤菌参比菌株23S rRNA基因数量和定位及其系统发育群

    为了明确23S rRNA基因数量和定位是否可更好地揭示根瘤菌参比菌株的系统发育关系,采用I-CeuI酶切和脉冲场凝胶电泳(PFGE)结合的方法,对根瘤菌株23S rRNA基因的数量和定位进行分析,并依据其相似性进行聚群.结果显示.根瘤菌参比菌株可聚为19个系统发育群.其中,在属的水平上,13个系统发育群与现行分类群(不包括依据16S rRNA基因序列分析结果)一致,6个不一致.在种的水平上,现行分类群中同种的根瘤菌可进一步细分为不同的系统发育群.这表明:I-CeuI酶切和PFGE结合的方法能从基因组特征角度对根瘤菌参比菌株进行更加细化的系统发育分类,并使其属种间的同质性更好.     

微卫星数据“01”化的研究

比较数据转化前后的遗传距离与聚类关系,发现“01”化后的数据因信息丢失引起遗传距离的减小,降低了聚类的分辨率与支持率。因此,建议不要将微卫星数据“01”化。     

The ediacarian period and syste: metazoa inherit the Earth

The Ediacarian, here defined as the initial period and system of the Phanerozoic Eon, is characterized by the oldest known multicellular animal life. The distinctive biotal assemblage comprises naked Metazoa, represented in the type region by 26 species in 18 genera and 4 or more phyla, plus simple metazoan surface tracks. Elements of this unique biota appeared worldwide at low paleolatitudes, following terminal Proterozoic glaciation. Ediacarian history lasted from about 670 million to 550 million years ago. This interval, plus Early Cambrian, was the time during which metazoan life diversified into nearly all of the major phyla and most of the invertebrate classes and orders subsequently known.     

Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists

Globular fossils showing palintomic cell cleavage in the Ediacaran Doushantuo Formation, China, are widely regarded as embryos of early metazoans, although metazoan synapomorphies, tissue differentiation, and associated juveniles or adults are lacking. We demonstrate using synchrotron-based x-ray tomographic microscopy that the fossils have features incompatible with multicellular metazoan embryos. The developmental pattern is comparable with nonmetazoan holozoans, including germination stages that preclude postcleavage embryology characteristic of metazoans. We conclude that these fossils are neither animals nor embryos. They belong outside crown-group Metazoa, within total-group Holozoa (the sister clade to Fungi that includes Metazoa, Choanoflagellata, and Mesomycetozoea) or perhaps on even more distant branches in the eukaryote tree. They represent an evolutionary grade in which palintomic cleavage served the function of producing propagules for dispersion.     

The premetazoan ancestry of cadherins

Cadherin-mediated cell adhesion and signaling is essential for metazoan development and yet is absent from all other multicellular organisms. We found cadherin genes at numbers similar to those observed in complex metazoans in one of the closest single-celled relatives of metazoans, the choanoflagellate Monosiga brevicollis. Because the evolution of metazoans from a single-celled ancestor required novel cell adhesion and signaling mechanisms, the discovery of diverse cadherins in choanoflagellates suggests that cadherins may have contributed to metazoan origins.     

Molecular and morphological supertrees for eutherian (placental) mammals

A large body of diverse comparative data now exists for a major phylogenetic synthesis of the higher-level relationships among eutherian (placental) mammals. We present such a phylogenetic synthesis using the composite trees or supertrees from the combined and separate analyses of their published molecular and morphological source phylogenies. Our combined and separate supertrees largely support the same suprafamilial taxa and orders, but different interordinal clades. These similarities and differences reinforce the continuing contributions of morphological studies, while highlighting the growing influence of molecular information on the field. As current summaries of past research, our supertrees emphasize opportunities for future work, while providing a step toward the eventual integration of the data and characters themselves.     

基于AFLP的菊属、亚菊属及其近缘属的属间关系

【目的】由于研究材料、地理分布等条件的限制,菊属(Dendranthema)、亚菊属(Ajania)及其近缘属的属间关系未得到很好解决。核糖体ITS区和叶绿体trnL/trnF间区等相关分子序列解析用于研究植物系统进化具有较大优势,但在菊属及其近缘属等相关类群间存在信息位点低的问题,而AFLP标记以其高多态性的优点在亲缘关系很近类群的系统演化研究中表现出一定的优势,因此本研究利用AFLP技术对菊属、亚菊属及其近缘属的属间关系进行研究,旨在分析和探讨菊属、亚菊属及其近缘属的系统关系,同时为菊花(D.×grandiflorum)等材料的遗传育种提供参考。【方法】利用9对荧光标记引物对东亚蒿亚族菊属、亚菊属及其近缘类群共50个分类单元进行AFLP分析,同时分别利用SPSS11.0软件采用非加权平均数UPGMA方法和PAUP*4.0b10软件采用最大简约法进行聚类分析。【结果】AFLP分析共获得1695个多态性条带。根据相似性系数,无论是整个蒿亚族及其近缘类群内部,还是菊属、亚菊属内部,均表现出较高的遗传多样性,种间分化明显。【结论】无论是UPGMA聚类分析结果还是构建的最大简约树,AFLP结果均将菊属和Arctanthemum先聚为一亚分支,各自形成两个种群,各自种群包含亚菊属的个别类群;亚菊属的大部分类群和太行菊属(Opisthopappus)形成另一亚分支,与菊属亚分支互为姐妹群形成菊属-亚菊属大分支。这说明菊属和亚菊属可能是由共同的祖先类群平行演化而来,其中亚菊属的多花亚菊(A.myriantha)、铺散亚菊(A.khartensis)等与菊属亲缘关系较近,而原产日本的矶菊(A.pacifica)、盐菊(A.shiwogiku)等是亚菊属中较进化类型;太行菊属的系统地位可能更接近于蒿亚族;短舌菊属(Brachanthemum)则被排除于菊属群之外。柳叶亚菊(A.salicifolia)、异叶亚菊(A.variifolia)等应从亚菊属中分离出来,支持单列成栎叶菊属(Phaeostigma)。     

Tempo and mode of evolutionary radiation in iguanian lizards

Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.     

广西环江喀斯特常绿落叶阔叶林土壤微生物类群的空间格局

运用地理统计学和Illumina 16S rRNA基因测序等手段,研究广西环江木论国家自然保护区25 hm~2喀斯特常绿落叶阔叶林土壤主要门级微生物类群的空间分布。结果表明:广西环江木论国家自然保护区喀斯特森林土壤中优势菌门为变形菌门(Protebacteria,34.5%)、放线菌门(Actinobacteria,30.7%)和酸杆菌门(Acidobacteria,12.2%);土壤细菌类群显示空间相关性的自相关范围为44.4～841.4m,其中大部分细菌类群的变程在研究区域范围(500 m)内;在研究区内,变形菌门的相对丰度从北到南逐渐升高,而放线菌门和厚壁菌门(Firmicutes)的相对丰度则从北到南逐渐降低,绿弯菌门(Chloroflexi)、酸杆菌门、奇古菌门(Thaumarchaeota)、拟杆菌门(Bacteroidetes)、芽单胞菌门(Gemmatimonadetes)、疣微菌门(Verrucomicrobia)的相对丰度呈斑片状分布,硝化螺旋菌门(Nitrospirae)的相对丰度呈单峰型分布,WS3(Latescibacteria)的相对丰度则呈间歇性的低值条带和高值条带状分布。可见,喀斯特土壤主要微生物类群相对丰度呈现不同的空间分布格局。     

Morphological disparity in the cambrian

An analysis of the range of morphology among arthropods demonstrates that disparity among living arthropods is similar to that in Cambrian arthropods. The range of morphological design resulting from the Cambrian "explosion" has been overestimated, reflecting a tendency to separate as "problematic" taxa that cannot be accommodated in the classification on the basis of the living biota. Problematic taxa are largely an artifact of an inadequate taxonomy. Special evolutionary processes may not be necessary to explain the early radiation of the metazoans.     

A polytene chromosome analysis of the Anopheles gambiae species complex

Field-collected specimens of all known taxa in the Anopheles gambiae complex were analyzed on the basis of chromosome inversions with reference to a standard polytene chromosome map. The phylogenetic relationships among the seven described species in the complex could be inferred from the distribution of fixed inversions. Nonrandom patterns of inversion distribution were observed and, particularly on chromosome arm 2R, provided evidence for genetically distinct populations in A. gambiae, A. arabiensis, and A. melas. In A. gambiae from Mali, stable genetic differentiation was observed even in populations living in the same region, suggesting a process of incipient speciation which is being confirmed by studies with molecular markers. The possible role of chromosome differentiation in speciation of the A. gambiae complex and in the emergence of distinct chromosomal forms within the nominal species is discussed in relation to human malaria.     

弯翅蠊亚科Panesthiinae（蜚蠊目:硕蠊总科）分子研究进展

弯翅蠊亚科Panesthiinae (蜚蠊目:硕蠊总科)为一类钻蛀朽木生活的木食性蜚蠊(wood-feeding cockroaches),是森林生态系统中重要的分解者,主要分布在澳洲、马来-印尼群岛以及东南亚等热带亚热带地区.该亚科分类学研究多数为早期的形态学研究,近年有少数新种利用现代分子技术进行研究.NCBI网站共提交了弯翅蠊亚科59个分类单元,194条核苷酸序列.该亚科分子系统发育学方面已有较丰富的研究,主要用于推断属间和种间进化关系和亲缘关系,同时根据这些分子证据进行谱系地理学研究,推断弯翅蠊亚科昆虫的种群扩散和生物入侵时间和方式,侧面猜测地理历史事件.另外,分子研究报道了一些弯翅蠊亚科体内的内共生物,并深入进行了协同进化等方面的研究.展望了新技术方法在弯翅蠊亚科分子研究中的应用.     

青藏高原仲彬草属植物叶绿体rbcL序列的谱系分析

对9个青藏高原植被区的仲彬草属(StYP基因组组成)植物及2个拟鹅观草属(St基因组)物种和2个冰草属(P基因组)植物共13个类群的叶绿体rbcL序列进行遗传和基因谱系分析,探讨青藏高原仲彬草属植物的系统关系及其物种形成的母本供体来源。结果表明:①Kengyilia stenachyra、Kengyilia kokonorica、Kengyilia hirsuta、Kengyilia rigidula和Kengyilia grandiglumis的种间关系较近;②Kengyilia stenachyra和Kengyilia geminata在rbcL序列上发生了一定程度的分化;③拟鹅观草属和冰草属植物均可能作为母本供体参与青藏高原植被区不同仲彬草属植物的物种形成。     

Lower Cambrian vendobionts from China and early diploblast evolution

Ediacaran assemblages immediately predate the Cambrian explosion of metazoans and should have played a crucial role in this radiation. Their wider relationships, however, have remained refractory and difficult to integrate with early metazoan phylogeny. Here, we describe a frondlike fossil, Stromatoveris (S. psygmoglena sp. nov.), from the Lower Cambrian Chengjiang Lagerst?tte (Yunnan, China) that is strikingly similar to Ediacaran vendobionts. The exquisite preservation reveals closely spaced branches, probably ciliated, that appear to represent precursors of the diagnostic comb rows of ctenophores. Therefore, this finding has important implications for the early evolution of this phylum and related diploblasts, some of which independently evolved a frondose habit.     

利用ITS序列探讨锦鸡儿属(Caragana Fabr.)植物系统关系(英文)

[目的]利用ITS序列探讨锦鸡儿属(Caragana Fabr.)植物系统关系。[方法]以锦鸡儿属11个系29种为代表材料,选择性扩增nrITS序列并双向测序,结合黄耆亚族Astralinae(Adens)Benth其他6属7个代表种的nrITS序列进行最大简约性(MP)和最小进化(ME)的系统发育分析。[结果]锦鸡儿植物ITS序列长度在611-614bp之间,与外类群排序后长度为655bp,共有170个可变位点,其中107个简约信息位点,简约信息位点在总排序序列中达16.3%,可以为属内及属间系统关系提供有力的分子证据;锦鸡儿属在系统发育上不是一个单系类群,与丽豆属(Calophaca Fish.exDC.)植物具有极为相近的亲缘关系;Sect.tragacanthoides的种在MP和ME进化树中位置分散,其组的分类有待进一步研究。卷叶锦鸡儿(C.ordosica,新种)虽然形态上与垫状锦鸡儿(C.tibetica)相似,但它与荒漠锦鸡儿(C.roborovskyi)遗传学关系紧密;C.davazamcii是一个独立的种。[结论]ITS序列在锦鸡儿属内及属间的系统学研究中具有重要的参考价值。     

Evolutionary exploitation of design options by the first animals with hard skeletons

The set of viable design elements available for animals to use in building skeletons has been fully exploited. Analysis of animal skeletons in relation to the multivariate, theoretical "Skeleton Space" has shown that a large proportion of these options are used in each phylum. Here, we show that structural elements deployed in the skeletons of Burgess Shale animals (Middle Cambrian) incorporate 146 of 182 character pairs defined in this morphospace. Within 15 million years of the appearance of crown groups of phyla with substantial hard parts, at least 80 percent of skeletal design elements recognized among living and extinct marine metazoans were exploited.     

江西猕猴桃属植物POD同工酶研究

采用垂直平板聚丙烯酰胺凝胶电泳技术，分析了江西野生猕猴桃20种或变种的叶片POD同工酶，并运用相似关系R-链连接法进行了模糊聚类分析。结果表明：(1)不同种间POD同工酶谱存在很大的差异；(2)POD同工酶有阶段性和相对稳定性，可运用于猕猴桃属植物的亲缘关系鉴定和初步分类；(3)模糊聚类反映了各分类群的亲缘关系，与传统依据形态分类提及的亲缘关系大体一致。本研究将江西猕猴桃属植物聚为4类，这与传统的分类方式并不一致，只有净果组的几个种成为单一类群，其余种或变种相互混杂。因此，认为现有的分类方法有待于进一步修订。     

基因组时代的植物系统发育研究进展

系统发育研究是进化生物中的基本问题,也是其他众多生物学分支学科的基础问题,其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降,系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果,总结了植物不同基因组的特征及其在系统发育研究中的优势与局限,探讨了系统发育树构建的主要方法,并对未来研究进行了展望。目前,植物体内的3套基因组适用于不同阶元和类群的系统发育研究,不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用：(1)叶绿体基因组结构相对简单,序列保守,不易重组,单亲遗传,是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源;(2)植物线粒体基因组序列进化速率较慢,目前仅适用于早期植物和大尺度水平的系统发育研究;(3)核基因组为双亲遗传,可综合揭示双亲谱系及系统网状进化关系,在系统发育研究中具有巨...     

Comment on "Positive selection of tyrosine loss in metazoan evolution"

Tan et al. (Reports, 25 September 2009, p. 1686) argued that loss of tyrosine residues from proteins in metazoans was driven by positive selection to remove potentially deleterious phosphorylation sites. We challenge this hypothesis, providing evidence that the high guanine-cytosine (GC) content of metazoan genomes was the primary driver in the loss of tyrosine residues.     

基于线粒体COX1基因的蚕蛾类系统发育分析

基于生物信息学的方法,以16种蚕蛾类昆虫作为研究对象,利用线粒体基因COX1的碱基序列作为分子标记对其系统发育信息进行分析。结果表明,COX1基因序列具有明显的AT偏倚性,编码氨基酸的密码子有26个具有明显的使用偏好性,种群间的校正遗传距离在0.003～0.177之间,表明蚕蛾类昆虫的亲缘关系近。利用MEGA6软件,分别采用邻接法（NJ）和最大似然法( ML)构建系统发育树,其发育树的分支明显,大部分的节点支持率都很高,进一步说明了蚕蛾类昆虫的亲缘关系较近。本研究补充了对蚕蛾类传统分类的认识,也为蚕蛾类昆虫的分类提供依据。