CorrSieve: software for summarizing and evaluating Structure output

The clustering software Structure has been used extensively to infer population structure in natural populations from multilocus genotype data. Determining meaningful values of K, the assumed number of subpopulations is one of the primary challenges of making biological inferences from Structure data. The package CorrSieve summarizes Structure output and performs a number of tests, including both previously reported methods and novel ones, to help determine meaningful values of K.     

区域人群mtDNA序列聚类分析

人类mtDNA序列是遵循母系遗传的重要生物信息学资源,利用遗传算法和k-modes模型结合的聚类算法,对西安和长沙两个区域人群mtDNA序列进行聚类分析,在分子层次上阐明了西安和长沙两地区人口结构特点.发现西安地区人口是发散性分布,而长沙地区人口具有主导性类群.     

人类群体遗传空间结构对应分析中的“蹄型效应”及其遗传学解释

探讨了人类群体遗传结构对应分析中“蹄型效应”的产生机制及其遗传学解释。从分析基因频率矩阵的结构特点入手,以实例验证和比较了对应分析中散点图的结构特征。发现当基因频率矩阵的结构不同时,其对应分析中散点图的分布模式不同;当基因频率矩阵中存在稀有基因时,其对应分析的散点图则呈现明显的“蹄型效应”。“蹄型效应”经常会歪曲潜在遗传结构的真实形态,其产生主要是因为对应分析中的c2距离不相似测度高估了稀有基因的作用。在人类群体遗传结构对应分析中,当出现“蹄型效应”效应时,需认真分析基因频率矩阵的结构,寻找“蹄型效应”产生原因并给出合理的遗传学解释,以免做出错误结论。     

New Zealand Demersal Fish Assemblages

Demersal fish assemblages in the New Zealand Exclusive Economic Zone were identified using presence–absence data from 19215 bottom trawl tows made over a 37-year period. The dataset spanned latitudes 34–54°S and depths of 4–1500m. A total of 123 taxa occurred in more than 1% of the tows (121 fish and 2 squid). Multivariate ordination and classification (correspondence analysis and Ward's cluster analysis) identified four primary species assemblages that were associated with the inner continental shelf, mid–outer continental shelf and shelf edge, upper continental slope and mid continental slope. The most frequently occurring species (> 40% of tows) in each assemblage were (in descending order): inshore – Chelidonichthys kumu, Pagrus auratus and Zeus faber; shelf – Nototodarus spp., Squalus acanthias and Thyrsites atun; upper slope – Macruronus novaezelandiae, Lepidorhynchus denticulatus, Genypterus blacodes and Hydrolagus sp.; mid slope – Hoplostethus atlanticus, Etmopterus baxteri, Halargyreus johnsonii, Coryphaenoides subserrulatus, Deania calcea, Coryphaenoides serrulatus, Pseudocyttus maculatus, Mora moro, Diastobranchus capensis and Centroscymnus crepidater. Further species associations were also identified within each primary assemblage. Canonical correspondence analysis revealed that most of the explainable variation in species composition was associated with depth and latitude; longitude and season explained little extra variance. The usefulness of our results is limited by the use of presence–absence rather than abundance data, and by the uneven spatial distribution of trawl tows. However, the present study provides a large-scale framework within which to interpret the results of studies using abundance data over smaller spatial and temporal scales.     

中国特有植物——华南五针松群落的种间关系

采用连续样带取样法,在分析广东南岭华南五针松群落结构的基础上,测定了优势种群的种间协变系数,并将典范对应分析（Canonical Correspondence Analysis,CCA）和聚类分析（Cluster Analysis）相结合,探讨了华南五针松与群落中其它种群的种间相互关系.结果表明：（1）广东南岭华南五针松群落以A级频度占绝对优势,华南五针松在主林层占据显著地位,但在演替层和更新层中的优势远不及其他优势种群;（2）Spearman秩相关分析和相关分析的计算结果基本一致,华南五针松群落优势种群正协变种对数显著多于负协变的种对数,且Spearman秩相关比相关分析具有更高的灵敏度.华南五针松与长叶木姜存在显著负协变,与其它优势种群种对间协变关系不明显;（3）海拔高度、坡度、坡位、坡形、腐殖质层厚度以及枯枝落叶层厚度与3个排序轴都有较强的相关性,环境因子在第一和第二排序轴的位置明显反映其生态特点.105 个乔木种类沿第一排序轴的分类完全与物种的性状特征相符.海拔高度是影响华南五针松分布的主导因素;（4）华南五针松群落种间关系揭示了群落内不同乔木种类因受小生境因子影响而体现在空间分布上的差异.典范对应分析和聚类分析结果共同揭示环境因子影响物种的分布,并通过生态习性表达出来.     

Molecular characterization of toxigenic and atoxigenic Aspergillus flavus isolates,collected from peanut fields in China

Aims: The objectives of this study were to assess the genetic relationships between toxigenic and atoxigenic isolates of Aspergillus flavus collected from peanut fields in China, and to analyse deletions within the aflatoxin biosynthetic gene cluster for the atoxigenic isolates. Methods and Results: Analysis of random‐amplified polymorphic DNA and microsatellite‐primed PCR data showed that the toxigenic and atoxigenic isolates of A. flavus were not clustered based on their regions and their ability of aflatoxin and sclerotial production. These results were further supported by DNA sequence of ITS, pksA and omtA genes. PCR assays showed that 24 of 35 isolates containing no detectable aflatoxins had the entire aflatoxin gene cluster. Eleven atoxigenic isolates had five different deletion patterns in the cluster. Conclusions: Toxigenic and atoxigenic isolates of A. flavus are genetically similar, but some atoxigenic isolates having deletions within the aflatoxin gene cluster can be identified readily by PCR assays. Significance and Impact of the Study: Because the extensive deletions within the aflatoxin gene cluster are not rare in the atoxigenic isolates, analysis of deletion within the cluster would be an effective method for the rapid screening of atoxigenic isolates for developing biocontrol agents.     

The maintenance of genetic diversity under host–parasite coevolution in finite,structured populations

As a corollary to the Red Queen hypothesis, host–parasite coevolution has been hypothesized to maintain genetic variation in both species. Recent theoretical work, however, suggests that reciprocal natural selection alone is insufficient to maintain variation at individual loci. As highlighted by our brief review of the theoretical literature, models of host–parasite coevolution often vary along multiple axes (e.g. inclusion of ecological feedbacks or abiotic selection mosaics), complicating a comprehensive understanding of the effects of interacting evolutionary processes on diversity. Here we develop a series of comparable models to explore the effect of interactions between spatial structures and antagonistic coevolution on genetic diversity. Using a matching alleles model in finite populations connected by migration, we find that, in contrast to panmictic populations, coevolution in a spatially structured environment can maintain genetic variation relative to neutral expectations with migration alone. These results demonstrate that geographic structure is essential for understanding the effect of coevolution on biological diversity.     

黄山松种群结构与动态研究

以“空间代替时间”的方法,以种群径级结构代替年龄结构,采用静态生命表和生存分析的方法,探讨了天柱山国家森林公园黄山松种群结构和动态规律。结果表明,随海拔升高,黄山松种群密度增大,径级分布范围减小,种群存活曲线由Deevey-Ⅱ型之间过渡到Deevey—Ⅰ型,种群由稳定型过渡为增长型。表明由低海拔向高海拔,黄山松种群处于不同的演替和发展阶段。     

南京市主城区苔藓植物多样性及其与环境的关系

苔藓植物是结构特殊的高等植物,种类数量仅次于被子植物,具有独特的观赏价值,应用前景广阔.为了更好地利用苔藓植物进行园林造景,本研究对南京市主城区10个绿地样点77个样地的苔藓植物进行了调查.结果表明: 共记录苔藓植物21科36属55种,其中丛藓科、羽藓科等苔藓种类在调查区域内分布广泛.苔藓种类丰富度由城中心向周围逐渐降低.根据苔藓植物多样性的聚类分析可将10个绿地样点分为3组,与园林生境、人为干扰频度、面积等因素有关.典范对应分析(CCA)表明,郁闭度、湿度和基质类型是影响苔藓植物分布的主要环境因子.南京市多数苔藓植物喜欢生长在湿度适中、较为开阔的区域.     

Photoaffinity labeling of platelet thrombin-binding proteins

The interaction of thrombin and platelets was studied with a heterobifunctional photoactivable crosslinking agent. Radiolabeled thrombin that was modified with ethyl-N-5-azido-2-nitrobenzoylaminoacetimidate formed two types of complex with platelet proteins; platelet-associated complexes and supernatant complexes. The platelet-associated complexes formed within 20 s. Autoradiography after electrophoresis with sodium dodecyl sulfate indicated that these complexes had apparent masses of 210, 185, 155 and 125 kDa. Formation of the complexes was blocked by hirudin; this is consistent with crosslinking that was a direct consequences of the binding of thrombin to a specific receptor, since hirudin blocks thrombin-induced platelet activation and the saturable binding of thrombin to platelets. The labeled supernatant complex had an apparent mass of about 490 kDa. It also formed in the supernatant solution of platelets after activation with a divalent cation ionophore, suggesting a complex of thrombin with a secreted protein. The supernatant complex did not involve fibrinogen or α₂-macroglobulin, but a similar complex was formed with partially purified secreted glycoprotein G (thrombin-sensitive protein, thrombospondin). Formation of the complex was blocked by hirudin. A similar complex was formed after prolonged (1 h) incubation without photoactivation. It is concluded that thrombin forms high-affinity, hirudin-sensitive complexes with secreted glycoprotein G, as well as with platelet surface proteins.     

Brightly fluorescent purple and blue labels for amines and proteins

Novel amino-reactive phenoxazines were obtained by reasonably simple synthetic protocols and characterized in terms of their use as fluorescent labels for amines, amino acids and proteins in general. Purple labels (alternatives to Texas Red) and blue labels (alternatives to Cy-1) were obtained by this strategy. The absorption/emission maxima, in aqueous solution, are at around 589/630 nm and 648/670 nm, respectively, thus indicating larger Stokes' shifts than those of common cyanine-type of labels. The new labels are compatible with commercial diode laser light sources.     

GeneticStudio: a suite of programs for spatial analysis of genetic-marker data

The analysis of genetic marker data is increasingly being conducted in the context of the spatial arrangement of strata (e.g. populations) necessitating a more flexible set of analysis tools. GeneticStudio consists of four interacting programs: (i) Geno a spreadsheet-like interface for the analysis of spatially explicit marker-based genetic variation; (ii) Graph software for the analysis of Population Graph and network topologies, (iii) Manteller, a general purpose for matrix analysis program; and (iv) SNPFinder, a program for identifying single nucleotide polymorphisms. The GeneticStudio suite is available as source code as well as binaries for OSX and Windows and is distributed under the GNU General Public License.