人博卡病毒基因克隆及衣壳编码基因序列变异分析

为了解人博卡病毒(Human Bocavirus,HBoV)VP1基因进化关系;阐明HBoV目前具体的变化规律,用PCR的方法扩增了1株HBoV的全基因和9株HBoV的VP1基因,克隆并测序,在此基础上,将HBoV的全基因序列和衣壳序列分别与细小病毒亚科其他14个有代表性的病毒进行遗传分析,构建进化树,对目前所有可得到的HBoV的17个衣壳蛋白进行二级结构分析和抗原性分析。结果显示:HBoV全基因序列与B19关系较远,但衣壳序列遗传关系较近。以有典型性的猫瘟细小病毒(Feline parvovirus,FPV)衣壳蛋白为参照,分析多个HBoV衣壳序列之间的变异情况,显示HBoV衣壳的二级结构基础表现出较高的保守性,序列之间的变化主要发生在高抗原区域和感染活性区域。衣壳病毒变异情况显示HBoV在稳定自身的情况下表现出一定的活跃性以逃避免疫反应,也表现出一定的感染适应力。     

Leaf epidermal features of Rhododendron (Ericaceae)from China and their systematic significance

Rhododendron is the largest genus within the subfamily Rhododendroideae, which has about 1000 known species in the world and more than 500 species in China. Since the genus was established by Linnaeus, its infrageneric relationships have been well studied by many taxonomists on the basis of morphological characters and molecular data. In 1996, Chamberlain et al. proposed a new system of Rhododendron with eight subgenera, i.e., Azaleastrum, Candidastrum, Hymenanthes, Mumeazalea, Pentanthera, Rhododendron, Therorhodion, and Tsutsusi. In this paper, micromorphological characters of leaf epidermis in 4 varieties, 48 species, 6 subgenera of Rhododendron from China were examined using light microscopy (LM) and scanning electron microscopy (SEM). Leaf epidermal features are described and micromorphological types are distinguished here according to morphological characters such as scale, gland, foliar trichome and stomatal apparatus of leaf epidermis. It is shown that the leaf epidermal cells are usually irregular or polygonal in shape. The patterns of anticlinal walls are straight, arched or undulate. The stomatal apparatuses are anomocytic and are usually found on abaxial, not adaxial, epidermis. The results also show that: (1) the lepidote rhododendron (i.e., subgen. Rhododendron), which has both scales and papillae on leaf epidermis, differs distinctly from the elepidote rhododendron; (2) three types of leaf epidermis are identified in subgen. Hymenanthes (i.e., R. fortunei-type, R. chihsinianum-type and R. simiarum-type), whereas four in subgen. Tsutsusi (i.e., R. mariesii-type, R. simsii-type, R. mariae-type and R. flosculum-type); (3) except for R. westlandii and R. henryi, the species of subgen. Azaleastrum show similar morphological characters, i.e., dense stomatal apparatuses surrounded by ringed or discontinuous striates; (4) R. molle of subgen. Pentanthera differs from the species of other subgenera on morphological characters such as foliar trichomes, dense stomatal apparatuses with asymmetrical outer stomatal rims surrounded by undulate-striates, and no gland; (5) only R. redowskianum is found with distinct T-pieces at the polar region of guard cells in Rhododendron. The results support the conclusion inferred from molecular systematic studies that subgen. Therorhodion is the basal clade of Rhododendron. Finally, the relationships between the closely related species are also discussed on the basis of leaf epidermal features.     

ALLOZYME DIVERSITY AND GENETIC IDENTITY IN SCHIEDEA AND ALSINIDENDRON (CARYOPHYLLACEAE: ALSINOIDEAE) IN THE HAWAIIAN ISLANDS

Genetic diversity of allozymes, genetic identity based on allozyme variability, and phylogenetic relationships were studied with respect to breeding system diversity, population size, and island age in 20 of the 29 species of Schiedea and Alsinidendron (Caryophyllaceae: Alsinoideae), a monophyletic lineage endemic to the Hawaiian Islands. Average levels of genetic variability in Schiedea and Alsinidendron were comparable to or higher than those found in other Hawaiian lineages for which equivalent data are available [Bidens, Tetramolopium, and the silversword alliance (Asteraceae: Madiinae)] and similar to average values for species of dicots. Allozyme variability was strongly dependent on breeding system, which varies widely in the Hawaiian Alsinoideae. Species with autogamous breeding systems showed very low variability, measured as the number of alleles per locus, percent polymorphic loci, and mean heterozygosity per locus. Outcrossing hermaphroditic and dimorphic species (those with gynodioecious, subdioecious, and dioecious breeding systems) showed significantly higher genetic variability. Small population size was associated with lower values for all measures of genetic variability. Nearly half of the species occurring in small populations are also autogamous; thus, both factors may have influenced levels of genetic variability in these species. Founder effect was apparent in one species (Schiedea adamantis), which occurs in a single large population, has a gynodioecious breeding system but a very low genetic variability. Island age appeared to have little effect on genetic variability. Slightly lower values of genetic variability for species occurring on Kaua'i and O'ahu result primarily from the occurrence of autogamous Alsinidendron species on those islands. Values for Nei's genetic identity for different species pairs were 0.201–0.942, a far greater range than in Bidens, the silversword alliance, and Tetramolopium. Using UPGMA clustering, there was only moderate support for relationships detected through cladistic analysis. Nei's unbiased genetic identity (I) was greatest among species with outcrossing breeding systems, which for the most part clustered together. Nei's genetic identities for self-fertilizing species were low, indicating that these species are less similar to one another and to outcrossing species, regardless of their affinities based on cladistic analysis. Parsimony analysis of allele frequency data supported two clades also found in phylogenetic analyses using morphological and molecular data. Clades recognized in parsimony analysis of allele frequencies were those lineages containing selfing species, indicating that conditions favoring fixation of alleles occurred in ancestral species. In contrast, maintenance of high genetic diversity in outcrossing species interferes with recognition of phylogenetic relationships using allozyme variability.     

油樟内生芽孢细菌的系统发育多样性

摘要：【目的】为了解油樟产芽孢内生细菌的多样性。【方法】采用改良的牛肉膏琼脂培养基分离、去除冗余及芽孢染色,测定所得产芽孢内生细菌的16S rRNA基因,进行系统发育分析。【结果】40株产芽孢内生细菌数量占分离得到的内生细菌总数的38.1％,其中根、茎、叶中分别分离得到24株、7株和9株。16S rRNA基因序列系统发育分析结果表明,35株菌可能分属于Bacillus、Lysinibacillus、Paenibacillus属的16个种,还有5株菌的序列与数据库中典型菌株序列相似性低于97％,代表着潜在新类群的存在。【结论】从油樟3个部位分离出的产芽孢内生细菌存在明显的系统发育多样性,而且3个部位分离出的产芽孢内生细菌区系既呈现出一定程度的细菌区系相似性,又表现出器官细菌区系的特异性。     

在系统发育分析中编码空位

空位包含了可用于系统发育分析的进化信息.为了准确地计算系统发育关系,空位包含的信息应该予以考虑.本文讨论了7种最常用的空位编码方法,并举例说明这些方法的编码原理.另外,本文还介绍了一些经验用以帮助研究者在使用现有的系统发育软件时选择空位编码方法.但是,所有的空位编码方法都有其优点和缺点,需要提出新的空位编码方法才能使空位信息在系统发育分析中得以充分地应用.     

Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

We present five case studies among articulate (rhynchonelliform) brachiopods, i.e. of Rhynchonellida, Cancellothyridoidea, Terebratuloidea, Dyscolioidea, Laqueoidea, and various terebratulids with modified long‐loops, in an attempt to illustrate and better understand congruence and conflict between morpho‐classification and rDNA‐based molecular clade structure, having been prompted to address these issues by difficulties encountered when describing the newly collected brachiopod, E biscothyris bellonensis gen. et sp. nov. The five studies reveal dramatic conflict in the Rhynchonellida and Terebratuloidea/Dyscolioidea, good congruence in the Cancellothyridoidea and Laqueoidea, and fair congruence (albeit with weak phylogenetic signal) in the long‐looped terebratulids. We suggest that the leading cause of the observed conflict lies in the use of inadequately specific morphological characters and morpho‐classification. Phylogenetic systematic (cladistic) analyses of Rhynchonellida also conflict markedly with the rDNA gene tree, leading us to recognize that such analyses are not only conceptually circular (using morphological characters to assess a morphological classification) but also to propose that they are biased by the act of classification that necessarily precedes the identification of putatively homologous characters; when the prior classification does not reflect evolutionary history, phylogenetic analysis will do likewise. In addition, we propose that the brachiopod community has overlooked the significance of two sources of morphological homoplasy affecting brachiopod systematics: (1) the loss of co‐adapted genomic complexes caused by mass extinctions at the end of the Permian; and (2) the pervasive consequences of developmental integration and constraint resulting from the integrated roles of the outer mantle epithelium in shell deposition and growth that underly the determination of form and the shell‐based classification. © 2015 The Linnean Society of London     

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86±6.36. The overall expected heterozygosity of all population was 0.6708±0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds→primitive breeds (Chahua chicken and Tibetan)→red jungle fowl in China (G. gallus spadiceus)→red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.