Line transect methods for plant surveys

Interest in surveys for monitoring plant abundance is increasing, due in part to the need to quantify the rate of loss of biodiversity. Line transect sampling offers an efficient way to monitor many species. However, the method does not work well in some circumstances, for example on small survey plots, when the plant species has a strongly aggregated distribution, or when plants that are on the line are not easily detected. We develop a crossed design, together with methods that exploit the additional information from such a design, to address these problems. The methods are illustrated using data on a colony of cowslips.     

The decay of similarity over geographical distance in parasite communities of marine fishes

Aim We evaluate, for the first time, the decay of similarity over distance in four species of marine fishes with different vagility: Trachurus murphyi (pelagic, highly vagile), Merluccius gayi (demersal, highly vagile), Sebastes capensis (demersal, low vagility) and Hippoglossina macrops (benthic, non‐vagile). Location We use our own data of the species composition of parasite communities in four host species: T. murphyi (Perciformes), M. gayi (Gadiformes), H. macrops (Pleuronectiformes) and S. capensis (Scorpaeniformes), from the coast of Chile and southern Argentina. Trachurus murphyi, M. gayi and H. macrops in the area studied live closely associated with the cold waters of the Humboldt Current System, while S. capensis in southern Chile is associated with the fjord areas south of c. 43° S, and in Argentina this species lives in close association with the cold water of the Malvinas Current, which mixes with the warm water of the Brazilian Current in the sampled area. Thus, for all four host species there are no known geographical (oceanographic) barriers that interrupt their continuous distributions. Methods Fish were collected and frozen (?18 °C) until examination in the laboratory. After thawing, each visceral organ was dissected separately, washed in running water, filtered using a mesh of 0.25 mm, and examined under a stereomicroscope (20×). For S. capensis, only ectoparasites were included in this study because data on endoparasites for some locations are not available. The approach of Poulin [Journal of Biogeography 30 (2003) 1609] was used. For each host species, we computed similarity in parasite composition using the Bray–Curtis distance on a presence/absence matrix. Similarity between each pair of localities was correlated (linear regression on raw and transformed data) with the distance (in nautical miles) among those sites. Results Among conspecific populations of host fish, there was no correlation between sample size and parasite species richness. The same pattern was evident when all host populations were pooled and treated as a single sample. Except for H. macrops, an important proportion of the geographical ranges of the host species was covered. The decay in similarity of parasite communities over distance was recorded in three of the four hosts analysed. For H. macrops, no relationship between distances and decay of similarity was evident. A linear regression on non‐transformed data provided a good fit, and the regression on log(n + 1) does not change significantly for both r² and probability, but slopes are smaller for log‐transformed than for non‐transformed data. Main conclusions Three of the four fish parasite systems studied fit well with the expected decay of similarity over distance. The slopes of the relationship between distance and similarity in the marine fishes studied are lower, but significant (three orders of magnitude) than those recorded in freshwater fishes by Poulin (2003) . In our case, Hippoglossina macrops (benthic, non‐vagile host) does not show any relationship, suggesting homogeneity over the geographical area studied for this species.     

Distance decay of community dynamics in rocky intertidal sessile assemblages evaluated by transition matrix models

It is well known that the similarity in species composition between two communities decays with the geographic distance that separates them. It is thus likely that the similarity in the dynamics of two communities also decays with distance, because the distance–decay relationship is fundamental in nature. However, the distance–decay relationships of community dynamics have not yet been revealed. We used transition matrix models to evaluate distance–decay relationships of seasonal community dynamics (from spring to summer) in rocky intertidal sessile assemblages along the Pacific coast of Japan between 31°N and 43°N. We evaluated the distance–decay relationships of whole-community dynamics and of three dynamics-related components—recruitment, disturbance, and species interaction (competition and facilitation)—for communities separated by distances ranging from several meters to thousands of kilometers. The similarity of the recruitment dynamics among communities declined rapidly with distance within the fine spatial scale, but only moderately within larger scales. The similarity of the disturbance dynamics was independent of distance, and the similarity of species interaction declined slightly with increasing distance. The similarity of whole-community dynamics declined rapidly with distance at a fine spatial scale and moderately at larger scales. The fact that the distance–decay relationship of whole-community dynamics was similar to that of recruitment may suggest that recruitment processes are the most important determinant of spatial variability of community dynamics at our study sites during the study period.     

Interval-based distance function for identifying RNA structure candidates

Many clustering approaches have been developed for biological data analysis, however, the application of traditional clustering algorithms for RNA structure data analysis is still a challenging issue. This arises from the existence of complex secondary structures while clustering. One of the most critical issues of cluster analysis is the development of appropriate distance measures in high dimensional space. The traditional distance measures focus on scale issues, but ignores the correlation between two values. This article develops a novel interval-based distance (Hausdorff) measure for computing the similarity between characterized structures. Three relationships including perfect match, partially overlapped and non-overlapped are considered. Finally, we demonstrate the methods by analyzing a data set of RNA secondary structures from the Rfam database.     

塔里木板块西南依格孜牙剖面上泥盆统—下石炭统地层学

塔里木板块西南英吉莎县依格孜牙出露上泥盆统—下石炭统序列。克里塔格组下段以法门阶牙行刺Icriodus alternatus alternatus为特征,中段的Spathognathodus aciedentatus和Polygnathus inornatus属杜内阶上部,上段的Scaphignathus sp.大致相当于维宪阶,可能还包括部分谢尔普霍夫阶。岩相序列表明,从奇自拉夫组紫红色石英砂岩、含砾石英砂岩相变为克里塔格组台地浅海相碳酸盐岩指示一次海进过程,克里塔格组礁灰岩可视为大灭绝事件之后全球最早的珊瑚礁群落复苏代表实例之一。     

蓝舌病毒HbC株与不同种系细胞相互作用及群特异性抗原特征

BTV-HbC株和蓝舌病毒标准株BTV-10分别接种在不同种系细胞如猴肾传代细胞(Vero)、人宫颈癌细胞(Hela)和小鼠神经胶质瘤细胞(C6)等细胞株上,比较研究了BTV-HbC在不同种系细胞上的增殖特征,BTV-HbC与BTV-10在相同细胞上的复制增殖特征,病毒与细胞相互作用的显微和超微结构特征.用免疫交叉反应研究了BTV-HbC株与BTV-10型标准株之间的血清学关系.本研究结合本室对BTV-HbC株基因组图谱分析和蓝舌病毒群特异性抗原编码基因S7的RT-PCR分析,进一步证实了BTV-HbC株可能是一个新的血清型蓝舌病毒.     

北京市水果消费的生态足迹距离研究

采用生态足迹距离指标方法体系,对2009年至2012年间北京市水果消费的生态足迹距离进行研究。结果表明4年间:跨区转移的生态承载力质量距离,由2009年的11.5×10~8t km逐年增加到了2012年的17.01×10~8t km,共增加了47.91%;生态足迹距离则相对稳定在886.66 km至1073.55 km之间;人均生态足迹距离,总体上由2009年的4.39×10~4km增加到2012年的5.55×104km,共增加了26.42%。从类别的视角,年均生态足迹距离最大的是香蕉(2072 km),最小的是苹果(476 km);年均跨区转移的生物承载力质量距离,最大的是西瓜(4978×10~8kg km),最小的是香蕉(518×10~8kg km);而4年平均人均生态足迹距离,最大的是西瓜(17.7×10~4km),最小的是香蕉(1.92×10~4km)。快速城市化阶段的北京,对外生态依赖范围也迅速扩大,并高于人口增加的速率。     

恒河猴外周血及肾组织SV40病毒基因分析

SV40即猿猴病毒40(simian virus 40),是DNA肿瘤病毒的原型代表,其基因结构为共价闭合环状双股DNA分子,标准参考株SV40-776含5243个核甘酸,不同分离株bp数略有差异.     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。     

Pollen and gene flow in fragmented habitats

Abstract. Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and the quantity and quality of pollinations. Seed set in small populations is often reduced and genetic variation is expected but not always found to be low. The majority of studies show that low flower densities have reduced pollination success and higher inbreeding. Density effects are stronger than size effects. Most studies concluded that species richness in flower-visiting insects is directly related to richness in plant species. However, the consequences of low insect species richness for pollination are not always clear, depending on the studied pollinator-plant relationship. The effects of the presence of simultaneously flowering species are highly dependent on the circumstances and may range from competition to facilitation. Other flowering plant species may play a role as stepping stones or corridor in the connection between populations. In the absence of stepping stones even short distances between populations act as strong barriers for gene flow. We illustrate the present review paper with own data collected for three plant species, rare in The Netherlands: Phyteuma spicatum ssp. nigrum (Campanulaceae), Salvia pratensis (Labiatae) and Scabiosa columbaria (Dipsacaceae). The species differ in their breeding systems and in the assemblage of visitor species. Data are shown on the effects of population size on species richness with consequences for seed set. Effects of flower density and isolation on pollen exchange are given. Since plant reproduction depends on the behaviour of individual insects and not on the overall behaviour of the species, the examples all point to individual insects and extrapolate to effects at the species level.