Allelematch: an R package for identifying unique multilocus genotypes where genotyping error and missing data may be present

We present allelematch, an R package, to automate the identification of unique multilocus genotypes in data sets where the number of individuals is unknown, and where genotyping error and missing data may be present. Such conditions commonly occur in noninvasive sampling protocols. Output from the software enables a comparison of unique genotypes and their matches, and facilitates the review of differences between profiles. The software has a variety of applications in molecular ecology, and may be valuable where a large number of samples must be processed, unique genotypes identified, and repeated observations made over space and time. We used simulations to assess the performance of allelematch and found that it can reliably and accurately determine the correct number of unique genotypes (± 3%) across a broad range of data set properties. We found that the software performs with highest accuracy when genotyping error is below 4%. The R package is available from the Comprehensive R Archive Network (http://cran.r-project.org/). Supplementary documentation and tutorials are provided.     

Roadside revegetation with native plants: Experimental seeding and transplanting of stem cuttings

Questions: Can we use local native plants for roadside revegetation? What cultural methods help enhance the process? Location: Trans Canada Highway, Terra Nova National Park, Newfoundland. Objectives: To (1) test stratification requirements for seed ger‐mination, (2) determine if germination, survival and growth of seedlings and stem cuttings of selected plants can be increased by mulching treatments and (3) identify native plants and cultural treatments useful for revegetation. Methods: We tested seed germination of Kalmia angustifoliaIris versicolorJuncus effususEriophorum vaginatum, Clintonia borealis and Cornus canadensis in a greenhouse experiment. We conducted field experiments of roadside revegetation using seeds of K. angustifolia, I. versicolorJ. effusus and E. vaginatum, as well as seedlings of I. versicolor and rooted stem cuttings of Emptrum nigrum and Juniperus communis after hay‐mat mulch and organic matter mulch application. Results: Stratified seeds of K. angustifoliaI. versicolor, J. effusus and E. vaginatum germinated successfully in the greenhouse, whereas C. borealis and C. canadensis seeds did not. Along roadsides, only I. versicolor seeds germinated. Iris versicolor cover increased significantly in organic matter mulch compared to hay‐mat mulch and control. Transplanted I. versicolor seedlings had high survival in all treatments but growth was reduced in organic matter mulch. Survival and growth of stem cuttings of E. nigrum and J. communis were significantly increased on hay‐mat mulch. Application: Rooted stem cuttings of E. nigrum and J. communis planted on hay‐mat mulch can be used as a practical method of roadside revegetation. These shrubs have low structure, are evergreen, and exhibit stress‐tolerance properties, which make them ideal species for roadside revegetation. They are also non‐palatable to wildlife. Roadside ditches can be revegetated by seeds or seedlings of I. versicolor. Robust roots and rhizomes of this plant may provide soil stability and dark green leaves and attractive flowers create aesthetically pleasing vegetation cover.     

楸树嫩枝扦插生根的主要影响因子分析

研究了插条的不同取材部位、不同激素组合以及不同扦插时间对4个类型（品种）楸树（Catalpa bungei C．A．Mey．）嫩枝插条生根的影响。结果显示,取楸树嫩枝的梢部与中部作为插条,扦插生根效果较好;用1．0g·L^-1 IBA和0．5g·L^-1 NAA混合溶液处理的插条生根效果最好,生根率可达45．43％;6月中旬是楸树嫩枝扦插的最适时期。4个楸树类型（品种）中,‘圆基长果楸’和‘豫楸1号’插条的生根能力较高,而‘金丝楸’的生根能力较差。     

河北地区熊蜂物种多样性与蜂群繁育特性

基于2005-2009年从河北地区（包括河北省、北京市和天津市）所采集的1893号熊蜂标本资料,结合中国科学院动物研究所馆藏记录,分析了河北地区熊蜂物种多样性和蜂群繁育特性. 结果表明：河北地区共有熊蜂属昆虫8亚属32种,其中河北省32种,北京市18种,天津市5种;西部太行山区、北部燕山山区和坝上高原地区熊蜂种类丰富度和多度较高;河北地区熊蜂的访花植物涉及到21科80种,其中,菊科、豆科和唇形科植物是大多数熊蜂种类访问的主要对象;小峰熊蜂、红光熊蜂、密林熊蜂、火红熊蜂和重黄熊蜂5种熊蜂群势强大,平均单群蜂的工蜂数量在110只以上,雄蜂数量在160只以上,子代蜂王数在30只以上;这5种熊蜂的繁育成群率均在50%以上,易于人工驯养,具有重要的传粉利用价值.     

Using scissors to quantify hardness of insects: do bats select for size or hardness?

Scissors are used to determine the hardness of fresh insects of different size and taxa. Our results indicate a strong relationship between the size of an insect and its hardness, which can be expressed as log( F _max)=0.65 × log( V )+ α . F _max is the maximal force needed to cut the insect and is our measure of insect hardness. V is the volume of the insect and α is a constant that can be derived for different insect taxa. The value of 0.65 was found as an average of beetle and moth samples, and this number appears consistent across insect taxa. We found that beetles averaged about 3.2 times harder than moths of the same size. Beetles were also more variable in hardness than moths, with the softest beetles about equal in hardness to an average moth of the same size. Using our data on insect hardness coupled with data on the diets of bats and their bite forces from the literature, we attempt to determine whether the upper size limit of insects taken by a bat is limited by the insect's dimensions or its hardness. Our results indicate that both these factors may be important.     

Survival of Salmonella on refrigerated chicken carcasses and subsequent transfer to cutting board

Objective:  To determine the effect of refrigeration time and temperature on Salmonella cell numbers on inoculated chicken carcasses and their transfer to a plastic cutting board.
Methods and Results:  The survival of Salmonella on chicken skin and the transfer to a plastic cutting board when exposed to different refrigeration temperatures (2, 6 or 8°C) for 9 days were the two main issues on which this work focused. Two scenarios were carried out to ascertain these effects: carcasses treated with a decontaminating acetic acid solution and untreated carcasses. All of the contaminated carcasses remained contaminated after 9 days of refrigeration. However, on untreated samples, while Salmonella numbers increased almost 1·5 log at 8°C, the pathogen numbers decreased about 1 log at 2 and 6°C. On acid-treated samples, cell numbers slightly decreased at all of the temperatures studied. Temperature did not affect salmonellae transfer to the cutting board, but time did. Acid decontamination increased cell numbers transferred to the cutting board compared with untreated samples.
Conclusion:  Proper refrigeration at low temperatures did not allow Salmonella numbers to rise, regardless of which carcasses had been, or had not been, acid treated. Despite the fact that the rate of transfer was not affected by temperature, the acid treatment detached Salmonella cells from the chicken skin and, therefore, the probability of greater cross-contamination should be studied further.
Significance and Impact of the Study:  The results of this study may provide better information about the refrigeration conditions for fresh chicken storage and also determine if these, along with acetic acid decontamination of broiler chicken, would affect the pathogen transfer to a cutting board.     

采伐干扰对东北温带次生林土壤CH4通量的影响

2007年6月至2009年10月,采用静态箱/气相色谱法测定了不同采伐干扰(皆伐后农作、皆伐后造林、50%强度采伐、25%强度采伐和对照)条件下,东北地区典型次生林的土壤CH₄通量. 结果表明: 研究样地的土壤均为CH₄的吸收汇.采伐干扰降低了土壤的CH₄吸收能力,不同处理样地土壤的CH₄吸收通量大小依次为:对照(-85.03 μg CH₄·m^-2·h^-1)>50%强度采伐(-80.31 μg CH₄·m^-2·h^-1)>25%强度采伐(-70.97 μg CH₄·m^-2·h^-1)>皆伐后农作(-65.57μg CH₄·m^-2·h^-1)>皆伐后造林(-62.02μg CH₄·m^-2·h^-1).各处理样地土壤CH₄吸收通量的季节动态相似,均表现为生长季吸收值较高,冬季较低.采伐干扰后各处理的土壤温度、土壤湿度、土壤硝态氮和铵态氮含量均增加,而土壤CH₄吸收通量与土壤温度呈显著二次相关,与土壤含水量呈线性负相关.次生林采伐后土壤含水量、土壤铵态氮和硝态氮含量的增加是土壤CH₄吸收通量降低的重要控制因子.     

矩阵模型在森林择伐经营中的应用

采用矩阵模型预测未干扰下长白山阔叶红松林不同初期密度和直径分布林分300年的动态生长过程,比较12种不同采伐方案(最小采伐直径分别为70、60、50、40cm,采伐周期分别为10、20、30年)经过300年采伐保留林分的密度、断面积和林分收获量。结果表明,无论初始状态如何,未干扰林分经过约200多年后变化趋于平稳,径阶结构、断面积均能达到近似相等的稳定状态;采伐以最小采伐直径60cm、采伐周期20年较适宜。得出了不同采伐方案的收获量及保留林分各因子变化规律。     

不同基质和处理对6种山茶花扦插成活率的影响

研究不同基质和处理对6个拟作为年宵花的山茶花新品种扦插成活率的影响。采用3种不同的基质配比和3种不同的处理对6个品种的山茶花进行了扦插试验。结果表明,泥炭与黄土或珍珠岩的混合基质最适合该6个品种的扦插生根,生根粉对6个山茶花品种的成活率影响不大,但插口加裹黄土后能有效提高其成活率。6个品种在最佳的扦插条件下的成活率在85%-92%之间。研究结果为快速大量地生产这些品种提供技术支持。     

抚育择伐对马尾松林主要树种空间分布格局及其关联性的短期影响

探讨不同抚育择伐方式下森林群落物种空间分布格局和关联性,对科学优化森林结构和促进森林稳定发展具有重要意义。以三峡库区马尾松飞播林为研究对象,采用未择伐、伐除优势马尾松、伐除非马尾松、除灌等处理方式建立固定监测样地,利用Ripley′s L函数的空间点格局方法,分析抚育择伐3年后马尾松林的群落组成、空间分布格局、种间关联性的变化特征。结果表明:1)不同抚育择伐措施均在一定程度上改变了物种组成以及部分树种的优势程度,降低了各样地乔木层物种多样性。2)未择伐主要树种空间分布格局以随机分布为主,伐除优势马尾松样地优势树种主要呈现聚集分布,伐除非马尾松改变了香椿和盐肤木等树种的分布格局,呈聚集分布,其他优势树种空间分布格局与对照样地相似;除灌进一步加剧林下更新树种的随机分布。3)未择伐样地主要树种空间关联性表现为正相关或不相关,伐除优势马尾松增加了主要树种间的负相关性,伐除非马尾松和除灌措施则增加了种间的不相关性。短期人为择伐干扰明显改变了林分空间结构和稳定性,择伐对象不同对林分结构产生的影响也不同。单纯调整某个树种或单个层次的结构来开展森林经营,不利于林分空间结构的整体优化,必须要综合考虑择伐强度和择伐对象的选择,将有助于实现森林结构优化和功能提升。