Direct measurement of spatial autocorrelation at the community level in four plant communities

Abstract. Four sites were sampled to determine spatial autocorrelation in vegetation at the community level. All were in western New Zealand, but on different substrates and of different physiognomy: a terrace forest, a floodplain forest, a mire and the middle of a logging road. In ‘dissimograms’the four communities all showed steady increases in dissimilarity with distance, but with shoulders in the curve for some sites, which could be related to plant morphology. Most of the increase in dissimilarity occurred over very short distances: less than 0.5 m in the forests, less than 1 m in the mire and less than 2 m in the road. Separate analyses of the woody and herbaceous guilds in the floodplain forest showed that herbaceous dissimilarities remained low at distances up to 20 m, probably because of clonal structure in some species. The mire showed low overall dissimilarity, which is attributed to the uniform substrate and the small species pool. Simulations showed that the approach is capable of indicating structure when it is present. Although the dissimogram was clearest when analysing a simulated grid of patches, other types of simulated patchiness showed dissimograms that were clearly distinguishable from those obtained from the vegetation studied. The almost continuous rise in dissimilarity with distance found in the four sites offers no support to the Hierarchy theory, fitting much more closely the alternative Continuum theory.     

Vervet monkeys use paths consistent with context‐specific spatial movement heuristics

Animal foraging routes are analogous to the computationally demanding “traveling salesman problem” (TSP), where individuals must find the shortest path among several locations before returning to the start. Humans approximate solutions to TSPs using simple heuristics or “rules of thumb,” but our knowledge of how other animals solve multidestination routing problems is incomplete. Most nonhuman primate species have shown limited ability to route plan. However, captive vervets were shown to solve a TSP for six sites. These results were consistent with either planning three steps ahead or a risk‐avoidance strategy. I investigated how wild vervet monkeys (Chlorocebus pygerythrus) solved a path problem with six, equally rewarding food sites; where site arrangement allowed assessment of whether vervets found the shortest route and/or used paths consistent with one of three simple heuristics to navigate. Single vervets took the shortest possible path in fewer than half of the trials, usually in ways consistent with the most efficient heuristic (the convex hull). When in competition, vervets' paths were consistent with different, more efficient heuristics dependent on their dominance rank (a cluster strategy for dominants and the nearest neighbor rule for subordinates). These results suggest that, like humans, vervets may solve multidestination routing problems by applying simple, adaptive, context‐specific “rules of thumb.” The heuristics that were consistent with vervet paths in this study are the same as some of those asserted to be used by humans. These spatial movement strategies may have common evolutionary roots and be part of a universal mental navigational toolkit. Alternatively, they may have emerged through convergent evolution as the optimal way to solve multidestination routing problems.     

Caught in the mesh: roads and their network‐scale impediment to animal movement

Roads have a pervasive multi‐faceted influence on ecosystems, including pronounced impacts on wildlife movements. In recognition of the scale‐transcending impacts of transportation infrastructure, ecologists have been encouraged to extend the study of barrier impacts from individual roads and animals to networks and populations. In this study, we adopt an analytical representation of road networks as mosaics of landscape tiles, separated by roads. We then adapt spatial capture–recapture analysis to estimate the propensity of wildlife to stay within the boundaries of the road network tiles (RNTs) that hold their activity centres. We fit the model to national non‐invasive genetic monitoring data for brown bears Ursus arctos in Sweden and show that bears had up to 73% lower odds of using areas outside the network tile of their home range centre, even after accounting for the effect of natural barriers (major rivers) and the decrease in utilization with increasing distance from a bear's activity centre. Our study highlights the pronounced landscape‐level barrier effect on wildlife mobility and, in doing so, introduces a novel and flexible approach for quantifying contemporary fragmentation from the scale of RNTs and individual animals to transportation networks and populations.     

Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19

On March 23 2020, the UK enacted an intensive, nationwide lockdown to mitigate transmission of COVID-19. As restrictions began to ease, more localized interventions were used to target resurgences in transmission. Understanding the spatial scale of networks of human interaction, and how these networks change over time, is critical to targeting interventions at the most at-risk areas without unnecessarily restricting areas at low risk of resurgence. We use detailed human mobility data aggregated from Facebook users to determine how the spatially-explicit network of movements changed before and during the lockdown period, in response to the easing of restrictions, and to the introduction of locally-targeted interventions. We also apply community detection techniques to the weighted, directed network of movements to identify geographically-explicit movement communities and measure the evolution of these community structures through time. We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown, a change that disproportionately affected long distance connections central to the mobility network. We also found that the community structure of areas in which locally-targeted interventions were implemented following epidemic resurgence did not show reorganization of community structure but did show small decreases in indicators of travel outside of local areas. We propose that communities detected using Facebook or other mobility data be used to assess the impact of spatially-targeted restrictions and may inform policymakers about the spatial extent of human movement patterns in the UK. These data are available in near real-time, allowing quantification of changes in the distribution of the population across the UK, as well as changes in travel patterns to inform our understanding of the impact of geographically-targeted interventions.     

Using fractal dimensions for characterizing tortuosity of animal trails

ABSTRACT. The tortuosity of mite trails was characterized by their fractal dimension, which is the non-Euclidean dimension varying between 1 (completely straight) and 2 (so tortuous that the complete two-dimensional space is used). This index was shown to be a good, discriminative index for mite trails, which is a completely new use of the fractal dimension. The value of this index is compared with other tortuosity indices.     

Variation in soil seed bank species composition of a dry coniferous forest: spatial scale and sampling considerations

In order to assess the effects of disturbance on soil seed bank spatial structure, variation in seed bank species composition was analyzed at two spatial scales in mature (undisturbed) and recently disturbed stands of Interior Douglas-fir forest in south-central British Columbia. Coarse-scale analysis among stands 10–100 km apart using Multi-Response Permutation Procedures showed that individual mature stands were mainly characterized by unique seed bank species compositions. Disturbance had an homogenizing effect on seed bank species composition at the coarse scale––there was less variability among stands following disturbance by both low and high severity fires, and by non-salvage logging. In contrast, finer scale analysis among sampling units c. 10 m apart showed that heterogeneity in seed bank species composition was greater on severely burned and logged sites, commensurate with greater levels of soil disturbance, than on lightly burned and undisturbed sites. Despite the high intensity of seed bank sampling (sixty 25 cm² soil samples from each of 16 sites), species-area curves leveled off only when infrequent species were removed from the dataset. The number of seed bank samples required to account for the common species ranged from 84 on severely burned sites, to 196 on undisturbed sites; more than the 240 samples collected per disturbance class in this study would have been required to account for the remaining infrequent species. Overall, this study highlights the importance of sampling intensively within multiple stands to capture the variation in species composition inherent to these dry coniferous forest soil seed banks.     

Roads as barriers to animal movement in fragmented landscapes

Roads can act as barriers to animal movement through mortality during crossing attempts or behavioral avoidance. This barrier effect has negative demographic and genetic consequences that can ultimately result in local or regional extinction. Here we use radio-telemetry data on three terrestrial vertebrates (eastern massasauga Sistrurus catenatus , eastern box turtle Terrapene carolina and ornate box turtle Terrapene ornata ) to test whether roads acted as barriers to movement. Specifically, we test whether individuals avoided crossing roads by comparing the number of observed crossings with the number of road crossings predicted by randomizations of individual movement paths. All species crossed roads significantly less often than predicted by chance, indicating strong road avoidance. Results of this study showing behavioral avoidance and previous studies on road mortality indicate that roads are strong barriers to these species. High mortality during crossing attempts would select for road avoidance, reducing the number of individuals killed on roads over time but leading to genetically partitioned subpopulations due to a lack of gene flow. In species that are long-lived and late-maturing, negative genetic effects might not be observable over short time-scales, thus placing populations at high risk of extinction because of a failure to detect an incrementally worsening problem. Formulating successful management strategies for many species in decline will require integrating data on road mortality, animal behavior and population genetics in order to understand more clearly the barrier effect of roads.     

Functional spatial scale of community composition change in response to windthrow disturbance in a deciduous temperate forest

Community dynamics in local habitats are affected by landscape characteristics such as the area and connectivity of surrounding habitats at a functional spatial scale where the community responds to landscape structure. However, the functional spatial scale at which community composition is affected by landscape structure has never been explored. We assessed the functional spatial scales of composition change in birds and in three types of arthropod communities (canopy, forest-floor and flying ones) with regard to landscape heterogeneity resulting from a large typhoon in a temperate forest of Japan. We examined the effects of tree-fall disturbance on the communities at various spatial scales, with special attention to compositional evenness. The spatial scale of the best-fitting model, which was selected from models fitted to the disturbance area at stepwise spatial scales, was interpreted as the community-specific functional spatial scale. The composition of all communities studied was all significantly dependent on gap area. The functional spatial scale was highest in birds (370 m in radius), intermediate in flying arthropods (90 m) and lowest in canopy and forest-floor arthropods (10 m). This result may reflect typical dispersal ability and the spatial range of resource use in the community. Compositional changes in each community were consistent with theory regarding traits and responses of component taxa, although the enhancement of evenness was observed only in the arthropod communities. These results imply that management and reserve selection based on functional spatial scales can be effective in the conservation of biodiversity and ecosystem services at the community level.     

Using reaction mechanism to measure enzyme similarity

The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.     

动物移动网络研究对景观生态学的贡献

景观生态学在其发展之初的20世纪80年代, 提出了关于景观网络研究(包括景观网络概念、网络结构指数和景观连接度)的基本构想, 这些构想需要在景观过程的研究中逐渐被落实和发展。动物移动过程因动物在斑块或廊道上有着独特丰富的属性特征、与周围资源环境之间存在复杂反馈而区别于无机物运移的景观过程, 则动物移动网络研究在实现关于景观网络研究的基本构想、推动景观生态学发展中贡献独特。因此, 总结动物移动网络研究的来源脉络及其对景观生态学的理论贡献对于景观网络领域和景观生态学学科的发展都具有重要意义。本文抓住景观生态学发展之初提出的关于景观网络研究的基本构想, 寻找和剖析其中所蕴含的景观生态学思想, 追踪这些思想如何被落实、发展、并形成目前的三个热点方向: 动物移动网络模拟、重要值评价和景观连接度分析; 总结这三个方向的研究进展, 指出整合动物的空间行为特征是必然发展趋势; 揭示出动物移动网络研究始终都以发掘斑块或廊道的动物有机体的属性特征(如种群数量)、以及描述这种属性在不同斑块或廊道之间的差异和联系为方向, 正是这种属性的发掘有效地落实、发展和丰富了关于景观网络研究的最初构想, 对景观生态学的贡献比其他过程更为独特。文章还总结了我国动物移动网络研究与国际研究相比较为滞后的现状, 指出其暂时尚未显示出对我国景观生态学的独特贡献; 强调发展源于跟踪定位数据的动物空间行为生态学研究是减小差距的重要、必要前提。期望本文能引发关于景观网络乃至景观生态学理论发展的方向性思考, 为研究者提供参考。     

A behavioural scale to measure ease of farrowing in sows

Farrowing is one of the most critical phases in pig production, as it has an impact on neonatal pig survival. Assessing the ease of farrowing can improve the management of sows and thus increase litter survival. The aims of this study were: 1) to develop an ease of farrowing score (EFS) in sows based on the behaviour of the sows and their piglets, and 2) to determine the relationship between the EFS and productive, physiological, and subjective parameters. Eighty hybrid (Large White × Landrace) sows from first to seventh parity housed in individual crates were used. An EFS was constructed using the total duration of farrowing, the birth interval, the total time standing or sitting, the number of position changes during the day before and the day of farrowing, the sow posture at birth, the viability and the position of the piglets at birth (head or back born). Moreover, rectal temperature at 90 min after farrowing, a four categorical subjective visual assessment (VA) of farrowing and litter size (piglets born alive, stillborn and mummified foetus) were recorded. A common factor analysis model yielded five factors with an eigenvalue higher than 0.95 that accounted for 75.05% of the total variation between individuals. The three main factors were “farrowing duration”, “sow posture”, and “sow activity” of sows and explained 23.44%, 15.67%, and 14.23% of the variance, respectively. Primiparous sows had higher values for factor 3 (sow activity) than multiparous sows (P = 0.02). Sows without stillborn or mummification foetus showed higher values of EFS than sows with at least one stillborn or mummification foetus (P = 0.06 and 0.01, respectively). Sows that received a visual assessment of 3 and 4 showed higher values of EFS than sows that received a VA of 1 and 2 (P = 0.0017). The EFS appears to be a good behavioural scale to measure ease of farrowing in sows kept in individual farrowing crates. Duration of farrowing, sow position, and presence of stillborn piglets and mummified foetuses appear to be important ease of farrowing indicators.     

Using path analysis to measure natural selection

We expand current methods for calculating selection coefficients using path analysis and demonstrate how to analyse nonlinear selection. While this incorporation is a straightforward extension of current procedures, the rules for combining these traits to calculate selection coefficients can be complex. We demonstrate our method with an analysis of selection in an experimental population of Arabidopsis thaliana consisting of 289 individuals. Multiple regression analyses found positive directional selection and positive nonlinear selection only for inflorescence height. In contrast, the path analyses also revealed positive directional selection for number of rosette leaves and positive nonlinear selection for leaf number and time of inflorescence initiation. These changes in conclusions came about because indirect selection was converted into direct selection with the change in causal structure. Path analysis has great promise for improving our understanding of natural selection but must be used with caution since coefficient estimates depend on the assumed causal structure.     

天目山物种多样性尺度依赖及其与空间格局关系的多重分形

以浙江省天目山国家级自然保护区为例,采用多尺度分析思想,利用多重分形分析方法,研究了不同尺度下物种多样性的变化、空间分布格局以及多样性与空间格局之间的关系。研究主要得到3方面的结论：（1）物种多样性具有尺度依赖性,随着空间尺度的增大,Shannon-Wiener多样性指数Ⅳ增大,Margalef多样性指数足和均匀度指数E减小;（2）多重分形参数αmin。多重分形谱的变化范围SR等能够定量反映物种的空间分布特征,空间大尺度越大,物种越聚集,空间分布越不均匀;（3）物种多样性与空间格局存在线性或幂函数关系。研究表明多重分形分析定量描述物种空间格局是有效性的,多重分形参数与生物多样性之间的定量关系为研究物种空间格局、生态属性与尺度之间的关系奠定了基础。因此,分形结合传统方法,在生物多样性方面的研究将有很大的潜在价值。     

基于多光谱影像的森林树种识别及其空间尺度响应

当前,不同空间分辨率卫星影像对森林类型识别结果中普遍存在的尺度效应,而且纹理参量对不同尺度下树种识别精度的影响仍缺乏广泛认知.本研究以中国东北旺业甸林场为研究区,采用观测时相同步、地理坐标匹配的GF-1 PMS、GF-2 PMS、GF-1 WFV,以及Landsat-8 OLI卫星传感器数据组成空间尺度观测序列(1、2、4、8、16、30 m),并结合支持向量机(SVM)模型,探讨了区域内5种优势树种遥感识别结果的尺度变化规律及其纹理特征参数的影响,同时检验了基于尺度上推转换影像的树种识别结果差异.结果表明: 影像空间分辨率对区域树种识别结果具有显著影响,其中,研究区森林树种识别的最佳影像分辨率为4 m,当分辨率降低至30 m时,树种识别结果最差.在1～8 m影像分辨率范围内,增加纹理信息能够显著提高不同优势树种的识别精度,使总分类精度提升了2.0%～3.6%,但纹理信息对16～30 m影像的识别结果没有显著影响.与真实尺度卫星影像相比,基于升尺度转换影像的树种识别结果及其尺度响应特征存在显著差异,表明在面向多个空间尺度的遥感观测和应用研究中,需要采用真实分辨率影像以确保结果的准确性.     

Human cerebral response to animal affective vocalizations

It is presently unknown whether our response to affective vocalizations is specific to those generated by humans or more universal, triggered by emotionally matched vocalizations generated by other species. Here, we used functional magnetic resonance imaging in normal participants to measure cerebral activity during auditory stimulation with affectively valenced animal vocalizations, some familiar (cats) and others not (rhesus monkeys). Positively versus negatively valenced vocalizations from cats and monkeys elicited different cerebral responses despite the participants' inability to differentiate the valence of these animal vocalizations by overt behavioural responses. Moreover, the comparison with human non-speech affective vocalizations revealed a common response to the valence in orbitofrontal cortex, a key component on the limbic system. These findings suggest that the neural mechanisms involved in processing human affective vocalizations may be recruited by heterospecific affective vocalizations at an unconscious level, supporting claims of shared emotional systems across species.     

Effects of plot vegetation diversity and spatial scale on Coccinella septempunctata movement in the absence of prey

The influence that vegetation diversity and the spatial scale of that diversity exert on insect behavior has increasingly been explored in the ecological literature, but relatively few experiments have explicitly incorporated both factors in experimental treatments. We conducted a field study designed to explore the effect of both of these factors on insect movement behavior in a broccoli agroecosystem. We caught and released seven‐spotted ladybird beetles (Coccinella septempunctata L.) in plots containing different degrees of vegetation diversity at two different spatial scales in which prey had been removed. Beetle movement was recorded at timed intervals, and move lengths and turning angles were used to generate discrete path maps for each beetle. Observed mean beetle net squared displacements were compared with predicted net squared displacements, and 95% confidence intervals were generated using a bootstrap method described by Turchin (1998 ) [Quantitative Analysis of Movement: Measuring and Modeling Population Redistribution in Animals and Plants. Sinauer Associates Inc., Sunderland, MA.]. Predicted net squared displacements underestimated beetle movement in smaller plots with both low and higher vegetation diversity for the first five move lengths, whereas no significant difference between observed and predicted net squared displacement for beetles in larger plots of either level of vegetation diversity were detected. These findings highlight the need for a better understanding of how natural enemies are influenced by vegetation diversity and the spatial scale of that vegetation in agroecosystems. The implications of these results for biological control are discussed.     

Using digital photography to study animal coloration

In understanding how visual signals function, quantifying the components of those patterns is vital. With the ever-increasing power and availability of digital photography, many studies are utilizing this technique to study the content of animal colour signals. Digital photography has many advantages over other techniques, such as spectrometry, for measuring chromatic information, particularly in terms of the speed of data acquisition and its relatively cheap cost. Not only do digital photographs provide a method of quantifying the chromatic and achromatic content of spatially complex markings, but also they can be incorporated into powerful models of animal vision. Unfortunately, many studies utilizing digital photography appear to be unaware of several crucial issues involved in the acquisition of images, notably the nonlinearity of many cameras' responses to light intensity, and biases in a camera's processing of the images towards particular wavebands. In the present study, we set out step-by-step guidelines for the use of digital photography to obtain accurate data, either independent of any particular visual system (such as reflection values), or for particular models of nonhuman visual processing (such as that of a passerine bird). These guidelines include how to: (1) linearize the camera's response to changes in light intensity; (2) equalize the different colour channels to obtain reflectance information; and (3) produce a mapping from camera colour space to that of another colour space (such as photon catches for the cone types of a specific animal species).  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 211–237.     

Using Mixtures to Model Heterogeneity in Ecological Capture‐Recapture Studies

Modelling heterogeneity of capture is an important problem in estimating animal abundance from capturerecapture data, with underestimation of abundance occurring if different animals have intrinsically high or low capture probabilities. Mixture models are useful in many cases to model the heterogeneity. We summarise mixture model results for closed populations, using a skink data set for illustration. New mixture models for heterogeneous open populations are discussed, and a closed population model is shown to have new and potentially effective applications in community analysis. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Habitat structure and animal movement: the behaviour of bumble bees in uniform and random spatial resource distributions

Foraging organisms (like bumble bees) move between resource points (like flowers) whose natural distributions vary enormously: from hyperdispersed to random to clumped. These differences in habitat structure may significantly influence the fitness of both plant and pollinator. To examine the effect of habitat structure on pollinator movement and fitness, we observed captive worker bumble bees collecting nectar from artificial flowers containing equal volumes of reward and arranged in two spatial configurations: a hexagonal array with constant distances between flowers (“constant”), and an “exploded hexagonal” array, with variable distances between flowers (“variable”). The mean nearest-neighbour distance was the same in both arrays, as was the general hexagonal appearance. The experiment therefore compares how resource dispersion, independent of nearest-neighbour distance, influences bee behaviour. Bees in the variable array showed decreased directionality, higher revisitation frequencies, and greater inter-flower flight distances than shown in the constant array. As a consequence, bees in the variable array had a 19% lower gross rate of nectar collection. Our results suggest that wild-foraging bees should prefer regularly spaced flowers (when all else, including mean nearest-neighbour distance, is equal), and that plants can decrease self-pollination by regular spacing between flowers, inflorescences, or individuals. Received: 16 January 1996 / Accepted: 30 June 1997