植物空间分布格局中邻体距离的概率分布模型及参数估计

最近邻体法是一类有效的植物空间分布格局分析方法,邻体距离的概率分布模型用于描述邻体距离的统计特征,属于常用的最近邻体法之一。然而,聚集分布格局中邻体距离(个体到个体)的概率分布模型表达式复杂,参数估计的计算量大。根据该模型期望和方差的特性,提出了一种简化的参数估计方法,并利用遗传算法来实现参数优化,结果表明遗传算法可以有效地估计的该模型的两个参数。同时,利用该模型拟合了加拿大南温哥华岛3个寒温带树种的空间分布数据,结果显示:该概率分布模型可以很好地拟合美国花旗松(P.menziesii)和西部铁杉(T.heterophylla)的邻体距离分布,但由于西北红柏(T.plicata)存在高度聚集的团簇分布,拟合结果不理想;美国花旗松在样地中近似随机分布,空间聚集参数对空间尺度的依赖性不强,但西北红柏和西部铁杉空间聚集参数具有尺度依赖性,随邻体距离阶数增加而变大。最后,讨论了该模型以及参数估计方法的优势和限制。     

Spatial arrangement and diet overlap between colonies of desert ants

Summary The spatial patterns and diets of three desert ant species were examined. The results indicate that food competition may account for the spatial arrangement of these species, and that only intraspecific interactions may be required. Each ant species was significantly overdispersed, and the average intraspecific nearest neighbor distances were greater than the interspecific nearest neighbor distances. A test of pairwise spatial arrangment showed that all three species pairs were aggregated interspecifically. The level of the interspecific aggregation was related to the diet similarity of the species. The two species pairs with the lowest diet overlaps were significantly aggregated, and the species pair with the most similar diets was not significantly aggregated. Pairwise dietary overlaps between colonies showed that average intraspecific overlaps were significantly greater than interspecific diet overlaps. Furthermore, the diet overlap was significantly positively correlated to the mean nearest neighbor distance for the three intraspecific and three interspecific comparisons. These data indicate competition for food, especially within species, may be regulating the intercolony distances of these ant species. A computer simulation tested whether only intraspecific territoriality is necessary to produce the observed nearest neighbor distances. A simulation that placed colonies randomly on a patch confirmed that these colonies are intraspecifically overdispersed. By adding intraspecific territoriality, the simulation nearest neighbor distances fit the empirical data reasonably well. Thus interspecific competitive interactions seem unnecessary to account for the spatial arrangement of these species.     

Detecting spatial aggregation from distance sampling: a probability distribution model of nearest neighbor distance

Spatial point pattern is an important tool for describing the spatial distribution of species in ecology. Negative binomial distribution (NBD) is widely used to model spatial aggregation. In this paper, we derive the probability distribution model of event-to-event nearest neighbor distance (distance from a focal individual to its n-th nearest individual). Compared with the probability distribution model of point-to-event nearest neighbor distance (distance from a randomly distributed sampling point to the n-th nearest individual), the new probability distribution model is more flexible. We propose that spatial aggregation can be detected by fitting this probability distribution model to event-to-event nearest neighbor distances. The performance is evaluated using both simulated and empirical spatial point patterns.     

Social Aggregation in Pea Aphids: Experiment and Random Walk Modeling

From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. The probabilities of motion state transitions, as well as the random walk parameters, depend strongly on distance to an aphid''s nearest neighbor. For large nearest neighbor distances, when an aphid is essentially isolated, its motion is ballistic with aphids moving faster, turning less, and being less likely to stop. In contrast, for short nearest neighbor distances, aphids move more slowly, turn more, and are more likely to become stationary; this behavior constitutes an aggregation mechanism. From the experimental data, we estimate the state transition probabilities and correlated random walk parameters as a function of nearest neighbor distance. With the individual-level model established, we assess whether it reproduces the macroscopic patterns of movement at the group level. To do so, we consider three distributions, namely distance to nearest neighbor, angle to nearest neighbor, and percentage of population moving at any given time. For each of these three distributions, we compare our experimental data to the output of numerical simulations of our nearest neighbor model, and of a control model in which aphids do not interact socially. Our stochastic, social nearest neighbor model reproduces salient features of the experimental data that are not captured by the control.     

Properties of the nearest neighbor interchange metric for trees of small size

The crossover or nearest neighbor interchange metric has been proposed for use in numerical taxonomy to obtain a quantitative measure of distance between classifications that are modeled as unrooted binary trees with labeled leaves. This metric seems difficult to compute and its properties are poorly understood. A variant called the closest partition distance measure has also been proposed, but no efficient algorithm for its computation has yet appeared and its relationship to the nearest neighbor interchange metric is incompletely understood. I investigate four conjectures concerning the nearest neighbor interchange and closest partition distance measures and establish their validity for trees with as many as seven labeled vertices. For trees in this size range the two distance measures are identical. If a certain decomposition property holds for the nearest neighbor interchange metric, then the two distance measures are also identical at small distances for trees of any size.     

湖北九宫山成熟常绿落叶阔叶混交林3种优势种的邻域效应研究

以最近邻株距离统计研究了湖北九宫山成熟常绿落叶阔叶混交林3种优势种青冈栎(Cyclobalanopsis glauca)、甜槠(Castanopsis eyrei)和短柄枹栎(Quercus serrata var.brevipetiolata)的邻域效应,进而探讨了局域尺度上的竞争/帮促关系与物种共存格局.结果显示,青冈栎、甜槠和短柄枹栎的最近邻株距离不存在下限;青冈栎的胸径大小与其种内最近邻株距离存在正相关(p=0.029),甜槠的胸径大小与种内、种间最近邻株距离均无相关性(p≥0.360),而短柄枹栎的胸径大小与种间最近邻株距离为负相关(p=0.040);3树种中任意一个的种内与种间最近邻株距离都没有显著差异(p≥0.122).这些结果表明,九宫山成熟常绿落叶阔叶混交林内邻域尺度上的竞争排斥并未充分激化,但是青冈栎的种内竞争仍然在起作用,而甜槠的竞争效应不明显,短柄枹栎则依赖种间帮促甚于相互竞争.同种和异种之间的排斥效果没有差异表明局域尺度的物种共存格局可能出于随机过程而非负密度制约过程.     

EXAMINATION OF TWO DIMENSIONAL SPATIAL PATTERN OF PERIPHYTIC DIATOMS USING AN ADHESIVE SURFICIAL PEEL TECHNIQUE1

A simple surficial peel technique using adhesive tape was developed for quantitative removal of haptobenthic diatom communities from topographically simple substrata. The method combines high removal efficiency with low peel distortion, permitting the use of spatial statistics to test whether populations are distributed in the peel randomly or form aggregated or uniform patterns. Using this technique, the microdistribution of Cocconeis placentula Ehr. on a smooth acrylic rod was examined. Using conventional nearest neighbor analyses, a clonal population of C. placentula. characterized by an indentation of the value margin, was significantly aggregated, whereas the overall C. placentula population was uniform or aggregated depending on whether the method of analysis allowed for cell size. Using refined nearest neighbor analysis, the indented population was aggregated, and the overall population was random at distances greater than cell size. The results suggest that the indented clone was weakly motile following cell division and that its directional bearing was random.     

湖北九宫山成熟常绿落叶阔叶混交林 3种优势种的邻域效应研究

以最近邻株距离统计研究了湖北九宫山成熟常绿落叶阔叶混交林3种优势种青冈栎(Cyclobalanopsis glauca)、甜槠(Castanopsis eyrei)和短柄枹栎(Quercus serrata var.brevipetiolata)的邻域效应,进而探讨了局域尺度上的竞争/帮促关系与物种共存格局。结果显示,青冈栎、甜槠和短柄枹栎的最近邻株距离不存在下限;青冈栎的胸径大小与其种内最近邻株距离存在正相关(p= 0.029),甜槠的胸径大小与种内、种间最近邻株距离均无相关性(p≥ 0.360),而短柄枹栎的胸径大小与种间最近邻株距离为负相关(p= 0.040);3树种中任意一个的种内与种间最近邻株距离都没有显著差异(p≥ 0.122)。这些结果表明,九宫山成熟常绿落叶阔叶混交林内邻域尺度上的竞争排斥并未充分激化,但是青冈栎的种内竞争仍然在起作用,而甜槠的竞争效应不明显,短柄枹栎则依赖种间帮促甚于相互竞争。同种和异种之间的排斥效果没有差异表明局域尺度的物种共存格局可能出于随机过程而非负密度制约过程。     

从空间分布特征认识珍稀植物领春木的种群动态

领春木(Euptelea pleiosperrnum)系第三纪孑遗植物和东亚特有种,目前已被列为国家Ⅲ级重点保护植物.基于空间定位数据以最近邻体距离统计研究了神农架地区领春木的空间分布特征,比较幼苗(DBH≤2.5cm)、幼树(2.5～7.5cm)和成树(＞7.5cm)各径级(代表各生活史阶段)形成的时间序列上的空间格局差异,进而探讨空间格局与立苗、补员、种内竞争等种群动态过程的相互关系.结果显示,在邻域尺度上,领春木的空间格局呈聚集态;幼苗(或幼树)的大小与其距离最近幼树(或成树)的远近没有相关性,幼树(或成树)周围一定距离以内出现同等大小个体的概率约等于幼苗(或幼树)出现的概率,且幼树与最近幼苗(或成树与最近幼树)的平均距离与幼树之间(或成树之间)的平均最近邻体距离没有显著差异;任意个体的大小、任意个体与相应最近邻体的大小之和与相应的最近邻体距离均为显著的正相关关系,但幼树间的最近邻体距离并不大于幼苗随机死亡产生的最近邻体距离,成树间最近邻体距离也不大于幼苗+幼树随机死亡产生的最近邻体距离.这些结果表明,领春木的聚集分布可能与种子散布、生境异质性对立苗格局的作用有关;已定植的大个体可能不限制其邻域内小个体的布局与生长,但是长期的补员过程与邻体间的相互作用不无关系;邻体间存在一定程度的竞争作用,但是竞争强度并未充分激化至发生距离依赖的死亡.     

种群分布格局的多尺度分析

种群分布格局的分析对于了解种群空间分布规律以及种内与种间关系具有重要的意义。最近邻体分析方法 (Nearestneighboranalysis, NNA) 作为种群空间分布格局的重要分析方法, 仅局限于种群格局的单尺度分析。改进NNA方法以应用于种群格局的多尺度分析, 将有助于解决种群格局的尺度依赖性。该文在前人研究的基础上提出扩展最近邻体分析方法 (Extendednearestneighboranalysis, ENNA), 也即在传统Clark_Evans指数公式的基础上增加一个距离尺度参数d (m), 并定义其所对应的Clark_Evans 指数CE (d) 的计算公式及其相应的显著性检验计算公式 (u (d) ) 分别为 :CE (d) =rdA/rdE= (1Nd∑Ndi=1 rdi) / (0.5Ad/Nd+0.0 5 14Pd/Nd+0.0 4 1Pd/Nd3 /2 ) 和u (d) = (rdA-rdE) /σd, 在距离尺度d (m) 范围内, 参数rdA指样地内各个体与其最近邻体间距离的平均值 (m) 、rdE指相同环境中个体呈随机状态时最近邻体距离的平均值 (m) 、Nd 为样地内个体总数、rdi为第i个个体与其最近邻体间的距离 (m) 、Ad 为样地面积 (m2 ) 、Pd 为样地周长 (m) 和σd 代表标准差。ENNA尺度变换采用与分形理论中计算沙盒维数相类似的过程, 而格局类型判断的标准与传统最近邻体分析方法相同。传统最近邻体分析结果是EN NA中距离尺度d取最大值dmax时的一个特例。以广东省黑石顶自然保护区针阔叶混交林中的马尾松 (Pinusmas soniana) 、黄牛奶树 (Symplocoslaurina) 、水栗 (Castanopsisnigrescens) 、鼠刺 (Iteachinensis) 和桃金娘 (Rhodomyrtustomentosa) 等 5个代表性种群为例, 在地理信息系统软件ArcViewGIS技术平台上进行的实例研究显示, 5个种群均表现出不同程度的尺度相关性。由此表明, 该文提出的新方法ENNA能够检测出种群空间分布格局的尺度依赖性, 获得关于种群空间分布格局的多尺度信息, 是进行种群空间格局多尺度分析的有效方法。     

The evolution of Queensland spiny mountain crayfish of the genus Euastacus. I. Testing vicariance and dispersal with interspecific mitochondrial DNA

The upland mesic rainforests of eastern Australia have been described as a "mesothermal archipelago" where a chain of cool mountain "islands" arise from a warm "sea" of tropical and subtropical lowlands. An endemic freshwater crayfish belonging to the genus Euastacus is found on each of these mountain "islands." The Euastacus are particularly suitable for the study of evolution because each mountain harbors a unique species, there are many taxa present providing replication within the group and, most importantly, their distribution is linear, extending along a south-north axis. This group could have evolved by "simultaneous vicariance" where there was one vicariant separation event of a widespread ancestor, or by "south to north stepping stone dispersal" where there were long distance dispersal events from neighboring mountain islands, starting in the south and proceeding north in a dispersal-colonization wave. We used pairwise genetic distances between nearest geographic neighbors as a novel way to test the two hypotheses. If diversification was due to "south to north stepping stone dispersal," then pairwise genetic distances between nearest geographic neighbors should decrease progressively the farther north the taxon pairs are found, reflecting the decreasing periods of isolation. In this case there should be a negative correlation between the south to north rank order of nearest neighbors and pairwise genetic distances. A Spearman's correlation on 16S mtDNA pairwise genetic distances and geographic rank order was not significant, indicating there was no support for the south to north stepping stone dispersal hypothesis. If simultaneous vicariance was responsible for diversification then all nearest geographic neighbor taxon pairs should have similar genetic distances and, therefore, the variance in nearest neighbor distances should be zero, or close to it. To test if the observed variance was tending towards zero we developed a randomization test where nearest neighbor taxon pairs were assigned random genetic distances and the variances calculated. The observed variance lay in the < 0.05 range of the simulated variances, providing support for the simultaneous vicariance hypothesis. The data also suggest there was simultaneous vicariance of at least two ancestral Queensland lineages. The timing of this vicariant event was probably in the Pliocene, which is consistent with the divergence times reported for other Australian mesic rainforest restricted taxa.     

Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method

Amphiphilic pseudo-amino acid composition (Am-Pse-AAC) with extra sequence-order information is a useful feature for representing enzymes. This study first utilizes the k-nearest neighbor (k-NN) rule to analyze the distribution of enzymes in the Am-Pse-AAC feature space. This analysis indicates the distributions of multiple classes of enzymes are highly overlapped. To cope with the overlap problem, this study proposes an efficient non-parametric classifier for predicting enzyme subfamily class using an adaptive fuzzy r-nearest neighbor (AFK-NN) method, where k and a fuzzy strength parameter m are adaptively specified. The fuzzy membership values of a query sample Q are dynamically determined according to the position of Q and its weighted distances to the k nearest neighbors. Using the same enzymes of the oxidoreductases family for comparisons, the prediction accuracy of AFK-NN is 76.6%, which is better than those of Support Vector Machine (73.6%), the decision tree method C5.0 (75.4%) and the existing covariant-discriminate algorithm (70.6%) using a jackknife test. To evaluate the generalization ability of AFK-NN, the datasets for all six families of entirely sequenced enzymes are established from the newly updated SWISS-PROT and ENZYME database. The accuracy of AFK-NN on the new large-scale dataset of oxidoreductases family is 83.3%, and the mean accuracy of the six families is 92.1%.     

Quartered neighbor method: A new distance method for density estimation

Quantitative data are essential to an appro-priate characterization of vegetation. In the past few years, considerable attention has been paid to vegetation sampling techniques. A number of methods have been developed for plant density estimations that utilize spacing distances instead of fixed-area quadrats. In this paper, we review the main distance methods for estimating density and propose a new distance method denominated the quartered neighbor method. In this method, the sampling point is considered the center, and the area around it is divided into four quadrants. The distance from the closest individual in each quadrant to its closest neighbor in the same quadrant is measured, and the average of them is the distance we need. It is actually an integration of two old distance methods, the nearest neighbor method, and the point-centered quarter method. With our new method and an old distance method (the point-centered quarter method), we calculated the average spacing distances of the Larix principis-rupprechtii population in the larch forests of the Donglingshan Mountain. Comparing the two methods with the quadrat method, we found they were almost the same in accuracy, but the precision of the new one was better. Meanwhile, it is adequate in sampling intensity and adaptable for general use in rapid ecological survey work.     

Quartered neighbor method: A new distance method for density estimation

Quantitative data are essential to an appropriate characterization of vegetation. In the past few years, considerable attention has been paid to vegetation sampling techniques. A number of methods have been developed for plant density estimations that utilize spacing distances instead of fixed-area quadrats. In this paper, we review the main distance methods for estimating density and propose a new distance method denominated the quartered neighbor method. In this method, the sampling point is considered the center, and the area around it is divided into four quadrants. The distance from the closest individual in each quadrant to its closest neighbor in the same quadrant is measured, and the average of them is the distance we need. It is actually an integration of two old distance methods, the nearest neighbor method, and the point-centered quarter method. With our new method and an old distance method (the point-centered quarter method), we calculated the average spacing distances of the Larix principis-rupprechtii population in the larch forests of the Donglingshan Mountain. Comparing the two methods with the quadrat method, we found they were almost the same in accuracy, but the precision of the new one was better. Meanwhile, it is adequate in sampling intensity and adaptable for general use in rapid ecological survey work.     

X-ray absorption fine-structure spectroscopy studies of Fe sites in natural human neuromelanin and synthetic analogues.

X-ray absorption fine-structure spectroscopy is used to study the local environment of the iron site in natural (human) neuromelanin extracted from substantia nigra tissue and in various synthetic neuromelanins. All the materials show Fe centered in a nearest neighbor sixfold (distorted) oxygen octahedron; the Fe-O distances, while slightly different in the natural and synthetic neuromelanin, are both approximately 2.0 A. Appreciable differences arise, however, in the second (and higher) coordination shells. In this case the synthetic melanin has the four planar oxygens bound to carbon rings with Fe-C distances of approximately 2.82 and 4.13 A; the human sample does not show the 2.82 A link but instead indicates a double shell at approximately 3.45 and 3.78 A.     

On the computation of the tertiary structure of globular proteins

A method is presented to compute the approximate locations of α carbon atoms of proteins using experimentally obtainable information. This information consists of distances between nearest neighbor α carbon atoms, locations of SS bonds, primary sequence of amino acids as reflected by hydrophobic and hydrophylic residues and the assumption of globularity. The method permits the reconstruction of structure similar to the real ones, and is readily extendable to compute structures more accurately by incorporating additional information.     

Ant-mediated seed dispersal contributes to the local spatial pattern and genetic structure of Globba lancangensis (Zingiberaceae)

Globba lancangensis is a typical myrmecochorous perennial herb found in southwest China. In 2002 and 2003, seed dispersal by ants was examined. Twelve ant species were recorded and found to move seeds 0.01-3.35 m. This removal promoted seed dispersal. In 2003, ant exclusion was made in 4 of 8 study plots for 1 year to practically detect the effects of ant dispersal. As a result, nearest neighbor analyses indicated that although ant dispersal could not significantly change the mean nearest neighbor distance, it obviously reduced the clustering degree of seedlings. Spatial genetic structure (SGS) of mature plants in 2003 and sequent seedlings in 2004 were investigated with intersimple sequence repeats. The whole correlagram of all individuals from 2003 showed significant positive autocorrelations between genetic and geographical distances within 4 m, suggesting a patchy structure at such short distances in the studied population. This pattern is likely associated with limited seed dispersal. The comparative analysis of fine-scale correlograms (<4 m) for ant-excluded treatment indicated lacking ants as the primary dispersers could have a similar pattern to ant dispersal presence, which is likely due to the restriction of ant dispersal distance. In conclusion, ant-mediated dispersal contributes to reduce seedling clustering degree and plays a minor role in developing and maintaining the local SGS in G. lancangensis.     

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures.     

Tree dispersion in oak-dominated forests along an environmental gradient

Summary Spatial pattern was analyzed in seventeen stands of oak-dominated forest to address the hypothesis that species tended to be aggregated under favorable conditions and widely spaced in xeric, nutrient poor conditions. Trees were sampled at 80–100 points in each stand with the distance-to-nearest neighbor method. Soil samples were collected in each stand for analysis of total nitrogen, total phosphorus, total potassium, soil pH, soil texture, and soil organic matter. Growing season precipitation was also recorded from climate stations near each stand. Quercus stellata (Wang.) dominated 10 stands, Q. marilandica (Muenchh.) dominated three stands and these species were codominant in four stands. Principal components analysis identified a soil texture/fertility gradient across the study area. Quercus stellata and all species combined were aggregated in most stands, whereas Q. marilandica was mostly randomly distributed within a stand. Small trees of all species combined tended to be aggregated and large trees were randomly dispersed in all but two stands, suggesting competition. Mean distance between large-large pairs was always greater than mean distance between small-small pairs in all stands, but this difference was only significant in one stand. Correlations between nearest neighbor distance and combined size of nearest neighbors were significant and positive in 12 of 17 stands. In all cases, however, slopes were shallow suggesting that competition is weak in these communities and has a limited effect on spacing of neighboring trees. Contrary to our hypothesis, trees were more aggregated on coarse-textured soils with low organic matter content. For all species combined, degree of aggregation was unrelated to growing season precipitation. Aggregation appears to be common in these forests because environmental stress in many stands reduces growth rates. Trees have not yet reached a size at which competition or other interactions can greatly increase interplant distances and reduce the degree of aggregation. A simple graphical model is developed to describe the relationship between patterns, stress and competition in plant communities.     

A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history

Microbial genomes are thought to be mosaic, making it difficult to decipher how these genomes have evolved. Whole-genome nearest-neighbor analysis was applied to the Sinorhizobium meliloti pSymB replicon to determine its origin, the degree of horizontal transfer, and the conservation of gene order. Prediction of the nearest neighbor based on contextual information, i.e., the nearest phylogenetic neighbor of adjacent genes, provided useful information for genes for which phylogenetic relationships could not be established. A large portion of pSymB genes are most closely related to genes in the Agrobacterium tumefaciens linear chromosome, including the rep and min genes. This suggests a common origin for these replicons. Genes with the nearest neighbor from the same species tend to be grouped in "patches". Gene order within these patches is conserved, but the content of the patches is not limited to operons. These data show that 13% of pSymB genes have nearest neighbors in species that are not members of the Rhizobiaceae family (including two archaea), and that these likely represent genes that have been involved in horizontal transfer.