Spatial Representations Are Specific to Different Domains of Knowledge

There is evidence that many abstract concepts are represented cognitively in a spatial format. However, it is unknown whether similar spatial processes are employed in different knowledge domains, or whether individuals exhibit similar spatial profiles within and across domains. This research investigated similarities in spatial representation in two knowledge domains – mathematics and music. Sixty-one adults completed analogous number magnitude and pitch discrimination tasks: the Spatial-Numerical Association of Response Codes and Spatial-Musical Association of Response Codes tasks. Subgroups of individuals with different response patterns were identified through cluster analyses. For both the mathematical and musical tasks, approximately half of the participants showed the expected spatial judgment effect when explicitly cued to focus on the spatial properties of the stimuli. Despite this, performances on the two tasks were largely independent. Consistent with previous research, the study provides evidence for the spatial representation of number and pitch in the majority of individuals. However, there was little evidence to support the claim that the same spatial representation processes underpin mathematical and musical judgments.     

北京东灵山地区辽东栎林种群空间分布分形分析

通过植物个体的坐标点与模拟冠幅的分形维数的分析,对辽东栎林内不同种群沿海拔梯度变化的空间分布格局和种群动态进行了比较和讨论。结果表明:模拟冠幅分形分析方法更适于分析具有大小不等、复杂多样的冠幅的植物个体空间分布格局。随着海拔的升高,不同种群的空间占据能力也随之变化。辽东栎种群的空间分布占绝对优势地位,分形维数可达1.9811;五角枫种群则逐步下降,分形维数最低为0.1170。低海拔山坡六道木种群空间占据能力较强,高海拔山坡照山白种群有较大的空间占据能力。在一定的环境条件下,不同的种群可能具有相近的空间占据能力,但对乔木层与灌木层来说,相同的分形维数的内涵是不同的。冠幅的分形维数作为表征植物种群空间占据能力的工具,是种群动态分析和种群分布格局研究的的重要指标之一。     

皖南山区南方红豆杉种群不同龄级立木的点格局分析

采用点格局分析方法O-ring统计,利用Programita软件对皖南山区霞乡村和仙寓山的南方红豆杉种群不同龄级个体的分布格局及其相互关系进行了分析.结果表明：霞乡村南方红豆杉种群各尺度下均表现为随机分布,而仙寓山南方红豆杉种群在2～25 m的空间尺度上呈随机分布,＜2 m尺度上为集群分布;仙寓山种群Ⅰ龄级在＜5 m尺度上呈集群分布,而高龄级个体在较多尺度上有偏离随机分布的倾向.随着龄级差距的加大,南方红豆杉幼龄个体与其他个体的空间负关联逐渐显现,而相邻龄级在空间分布上相互独立,关联性很小.南方红豆杉种群的这种空间关系有利于其对资源环境的有效利用,随着个体的生长,南方红豆杉种群的空间分布有一个从聚集到随机的过渡.     

Variation in foraging behavior facilitates resource partitioning in a polymorphic cichlid, Herichthys minckleyi

We examined foraging behavior (microhabitat use and feeding behavior) in a trophically polymorphic cichlid fish, Herichthys minckleyi, to address several questions regarding resource partitioning in this threatened species. These include: (1) do morphotypes demonstrate different foraging behaviors? (2) do individuals within a morphotype vary in their foraging behavior (e.g. are some individuals specialists, only using a subset of available resources, while other are generalists)? (3) do foraging behaviors vary between isolated pools? (4) do foraging behaviors vary across seasons? We quantified microhabitat use and feeding behavior for over 100 individuals (of two morphotypes) feeding freely in two isolated pools (populations) and across two seasons (winter and summer). We found differences in foraging behavior between morphotypes and individual specializations within morphotypes; i.e. some individuals specialize on certain food resources by using a few feeding behaviors within a subset of microhabitats, whereas others employ a range feeding behaviors across many microhabitats. Foraging behavior also varied between pools and across seasons. This spatial and temporal variation in foraging behavior and resource use may serve to maintain this polymorphism, as the relative fitness of the each morph may vary over space and time.     

THE EVOLVING GENETIC HISTORY OF A POPULATION OF LATHYRUS SYLVESTRIS: EVIDENCE FROM TEMPORAL AND SPATIAL GENETIC STRUCTURE

We analyze patterns of genetic microdifferentiation within a natural population of Lathyrus sylvestris, a perennial herb with both sexual reproduction and clonal growth. In a population from the northern foothills of the Pyrénées in southwestern France, a combined demographic and genetic investigation enabled the study not only of spatial genetic structure of the population, but also of the history of the population's spatial genetic structure over time. Excavation of all individuals allowed identification of clonemates. Age of each individual was determined by counting annual growth rings in the taproot, a method tested with individuals of known age planted in experimental gardens. Each individual was mapped, and genotypes of all individuals were determined using allozyme markers for a number of polymorphic loci. Distribution patterns and spatial genetic structure, both for all individuals and for different age classes, were analyzed using spatial autocorrelation statistics (Geary's Index, Moran's Index). Patterns of gene flow within the population were also studied using F-statistics and tests for random associations of alleles. Because age, allele frequencies, and location were known for each individual, it was possible to study how spatial genetic structure changed over time. Results from all these diverse approaches are consistent with one another, and clearly show the following: (1) founder effects, with the study transect being first colonized by individuals at either end of the transect that were homozygous for different alleles at one marker locus; (2) a difference in spatial distribution of individuals originated from sexual reproduction (seedlings) and from clonal growth (connected individuals); (3) restricted gene flow, due to inbreeding among related, clumped individuals; and (4) increase in heterozygote deficit within the youngest cohort of individuals. The results indicate that genetic differentiation in time was much less marked than differentiation in space. Nevertheless, the results revealed that the studied population is experiencing demographic and genetic variation in time, suggesting that it is not at equilibrium. On the one hand, spatial structuring is becoming less marked due to the recombination of founder genotypes; on the other hand, as establishment of new individuals increases, a new spatial structure emerges due to mating between relatives.     

Genetic groups in the common plant species Castanopsis chinensis and their associations with topographic habitats

In general, even within a local area, many common plant species are found in different types of environment. We propose that if the association of a common plant species with different types of environment is investigated, by analysing all individuals in a given population as a single entity, the results might be misleading or incomplete owing to intraspecific variation. To test this hypothesis, we used molecular markers to classify mature Castanopsis chinensis individuals with a diameter at breast height ≥ 40 cm into different genetic groups and analysed the associations of these groups with topographic features and habitats within a 20‐ha Dinghushan forest plot, South China. Our results indicated that the different groups had different topographical associations, and that the spatial distributions and genetic structures of individuals varied among the groups. Therefore, if significant genetic structure exists in the population of a common species within a community, to understand the relationship between the spatial distributions of individuals in the population and the environment, it is necessary to classify the individuals into genetic groups and analyse the data for these groups, rather than for a combined group of all individuals.     

Too close for comfort: spatial patterns in acorn barnacle populations

Spatial patterns in aggregations form as a result of the interplay between costs and benefits experienced by individuals. Such self-organisation of aggregations can be explained using a zonal model in which a short-range zone of repulsion and longer-range zone of attraction surrounding individuals leads to emergent pattern properties. The signal of these processes can be detected using spatial pattern analyses. Furthermore, in sessile organisms, post-settlement mortality reveals the relative costs and benefits of positions within the aggregation. Acorn barnacles are known to require contact with conspecifics for reproduction and are therefore believed to aggregate for this purpose; isolated individuals may also be more susceptible to abiotic stress and predation. At short distances, however, competition for space and resources is likely to occur. In this study spatial patterns of barnacles (Semibalanus balanoides L.) were analysed using pair-correlation functions. Individuals were dispersed at distances below 0.30 cm, but peak relative density occurred at a distance of 0.36 cm from conspecifics. This is much closer than required for reproductive access, implying a strong aggregative drive, up to the point of physical contact with neighbours. Nevertheless, analysis of dead barnacles illustrated that such proximity carries a cost as barnacles with many neighbours were more likely to have died. The inferences obtained from these patterns are that barnacles aggregate as closely as they can, and that local neighbourhood competition is a powerful determinant of mortality. These processes give rise to the observed pattern properties.     

Quantitative comparison of freeware software for bone mesh from DICOM files

Musculo-skeletal modelling, 3D printing of bone models and also custom design of relevant prostheses starts from accurate STL files. These are obtained from medical imaging after careful segmentation and 3D reconstruction using specialized software, but most of these are very expensive. The aim of the present study is to assess and compare alternative software available for free. Three freeware software were selected from the most popular, and one standard platform was made available at the institute of the authors. Using each of these four software and starting from available DICOM files obtained previously by a CT scanner, three different bone models were reconstructed from each of five different human anatomical areas for a total of 60 bone model reconstructions. A young radiographer performed the bone reconstruction without specific technical training. 3D spatial matching of corresponding anatomical models was also performed to determine distance-maps for the assessment of final surface quality. In all four software many valuable features were available, with minimum differences, and bone models of good quality were obtained. Large differences in file sizes (mean range over the five anatomical models 66-338) and in the number of triangles (870-1350 thousands) were found, with triangles for MByte ratio ranging from about 4 to 20 thousands. The distance-map analysis revealed that root mean square deviation averaged over the five anatomical models ranged from 0.13 to 2.21 mm for the six spatial matches between the four software. These software are suitable for 3D bone model reconstruction, and do not require special training, and as such these can open up opportunities for biomechanical modelling and medical education.     

Revealing cryptic spatial patterns in genetic variability by a new multivariate method

Increasing attention is being devoted to taking landscape information into account in genetic studies. Among landscape variables, space is often considered as one of the most important. To reveal spatial patterns, a statistical method should be spatially explicit, that is, it should directly take spatial information into account as a component of the adjusted model or of the optimized criterion. In this paper we propose a new spatially explicit multivariate method, spatial principal component analysis (sPCA), to investigate the spatial pattern of genetic variability using allelic frequency data of individuals or populations. This analysis does not require data to meet Hardy-Weinberg expectations or linkage equilibrium to exist between loci. The sPCA yields scores summarizing both the genetic variability and the spatial structure among individuals (or populations). Global structures (patches, clines and intermediates) are disentangled from local ones (strong genetic differences between neighbors) and from random noise. Two statistical tests are proposed to detect the existence of both types of patterns. As an illustration, the results of principal component analysis (PCA) and sPCA are compared using simulated datasets and real georeferenced microsatellite data of Scandinavian brown bear individuals (Ursus arctos). sPCA performed better than PCA to reveal spatial genetic patterns. The proposed methodology is implemented in the adegenet package of the free software R.     

浙江天台山甜槠种群遗传结构的空间自相关分析

采用空间自相关分析方法对浙江天台山亚热带常绿阔叶林优势种甜槠种群全部个体及不同年龄级个体的小尺度空间遗传结构进行了分析,以探讨甜槠种群内遗传变异的分布特征及其形成机制。根据11个ISSR引物所提供的多态位点,经GenAlEx 6软件计算地理坐标和遗传距离矩阵在10个距离等级下的空间自相关系数。在样地内,甜槠种群内个体在空间距离小于10 m时存在显著的正空间遗传结构,其X-轴截矩为9.945。甜槠种群的空间遗传结构与其种子短距离传播和广泛的花粉传播有关。Ⅰ年龄级、Ⅱ年龄级和III年龄级个体在空间距离小于10 m时存在显著的正空间遗传结构,其X-轴截矩分别为11.820、9.746和9.792。当距离等级为5 m时,其空间自相关系数r分别为0.068、0.054和0.070。Ⅳ年龄级个体在所有空间距离等级中均不存在显著的空间遗传结构。甜槠是多年生、长寿命植物,自疏作用是导致IV年龄级个体空间遗传结构消失的主要原因。     

The environmental impact of engineering education in Australia

Background, aim, and scope  The process of producing a graduate is a complex one involving major effort usually by large institutions such as universities. The Faculty of Engineering and Surveying at the University of Southern Queensland, Australia produces several hundred engineering and spatial science graduates each year using both on-campus and external modes of study. The purpose of this study is to determine the major causes of environmental impact in this process with a view to targeting areas where improvements may be made. Materials and methods  An inventory of all major inputs to and outputs from the faculty was compiled from a mixture of measurements, real data, and financial data for the calendar year 2006. Data for graduate output were also compiled. These data were then assessed using SimaPro software, mainly Australian data and predominantly the Eco-indicator 99 (E) method of impact assessment. Results  The analysis shows that environmental impacts are many and varied as might be expected from a complex operation like a university. However, energy inputs in the form of electricity from black coal, staff and student travel and the embodied impact of buildings were dominant. Discussion  The results obtained may point the way towards future consideration of areas where environmental impact might be reduced by changes in institution strategies such as the way external students are taught and the way the electricity usage in our buildings is managed. Conclusions  The environmental impact of undergraduate education is complex and involves many different areas of activity. However, the use of energy in various forms is of major significance in this impact. Recommendations and perspectives  It is recommended that university managers consider the results presented in this paper and use them as a starting point in developing strategies to reduce the impact of their institutions.     

A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS

Abstract Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software package from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope-based methods that are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation. We have also created export ability to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardization process. The software is provided to users with a simple graphical user interface for accessing the different features. The underlying programming interface may also be used by Java developers to develop other routines for analyzing data produced by Progenesis.     

Antagonistic pleiotropy can maintain fitness variation in annual plants

Antagonistic pleiotropy (AP) is a genetic trade‐off between different fitness components. In annual plants, a trade‐off between days to flower (DTF) and reproductive capacity often determines how many individuals survive to flower in a short growing season, and also influences the seed set of survivors. We develop a model of viability and fecundity selection informed by many experiments on the yellow monkeyflower, Mimulus guttatus, but applicable to many annual species. A viability/fecundity trade‐off maintains stable polymorphism under surprisingly general conditions. We also introduce both spatial heterogeneity and temporal stochasticity in environmental parameters. Neither is necessary for polymorphism, but spatial heterogeneity allows polymorphism while also generating the often observed non‐negative correlations in fitness components.     

Spatio-temporal Processes in a Calcareous Grassland

Abstract The herbaceous plant communities occurring on nutrient-poor calcareous soils of north-western Europe are typically rich in species, with as many as 30–40 species m^-2. It is an open question as to what dynamic properties allow this diversity. We review evidence that we have collected on the spatial and temporal processes operating in a calcareous grassland community in England to address this issue. Our data indicate spatial aggregation of individuals within species consistent with the modular growth of the species concerned, but there is little evidence to suggest spatial structure generated by interactions between species, and we have been unable to separate most species tested into different niches. The development of spatial structure of the community through time is also consistent with dynamics that depend principally on the modular growth patterns of the different species. We suggest that there is a nonlinearity in the per capita rate of increase with the property that the community is no more than weakly dependent on densities of the species under natural conditions. The dynamic of the community is then driven more by forces external to the community than by density-dependent effects within the community.     

How does starvation affect spatial organization within nests in <Emphasis Type="Italic">Lasius niger</Emphasis>?

Spatial distribution of ant workers within the nest is a key element of the colony social organization contributing to the efficiency of task performance and division of labour. Spatial distribution must be efficiently organized when ants are highly starved and have to get food rapidly. By studying ants’ behaviour within the nest during the beginning of food recruitment, this study demonstrates how the spatial organization is affected by starvation and improves the efficiency and the speed of recruitment as well as the allocation of food. (1) In starved nests, nestmates left the deep part of the nest and crowded near the nest entrance. This modification of the spatial distribution is a local phenomenon concerning only the individuals situated in the first chamber near the nest entrance. These starved individuals have a higher probability of leaving the nest after a contact with recruiters than nestmates situated deeper in the nest. This strongly suggests that nestmates situated near the nest entrance have a low response threshold to the signals emitted by recruiters. Their higher responsiveness speeds up their exit to the foraging area and hence may increase the efficiency of highly starved colonies in exploiting new food opportunities. (2) In starved nests, the trajectory covered by recruiters between contacts with nestmates was nearly twice as small. For recruiters, this represented a gain of time in the allocation of food. As the recruitment process follows snowball dynamics, this gain of time by starved recruiters might also speed up the exploitation of food. This study evidences how the spatial distribution of individuals as a function of their motivational state might have a regulatory function in the recruitment process, which should be generic for many social species.     

Finding essential scales of spatial variation in ecological data: a multivariate approach

The identification of spatial structures is a key step in understanding the ecological processes structuring the distribution of organisms. Spatial patterns in species distributions result from a combination of several processes occuring at different scales: identifying these scales is thus a crucial issue. Recent studies have proposed a new family of spatial predictors (PCNM: principal coordinates of neighbours matrices; MEMs: Moran's eigenvectors maps) that allow for modelling of spatial variation on different scales. To assess the multi-scale spatial patterns in multivariate data, these variables are often used as predictors in constrained ordination methods. However, the selection of the appropriate spatial predictors is still troublesome, and the identification of the main scales of spatial variation remains an open question. This paper presents a new statistical tool to tackle this issue: the multi-scale pattern analysis (MSPA). This ordination method uses MEMs to decompose ecological variability into several spatial scales and then summarizes this decomposition using graphical representations. A canonical form of MSPA can also be used to assess the spatial scales of the species-environment relationships. MSPA is compared to constrained ordination using simulated data, and illustrated using the famous oribatid mites dataset. The method is implemented in the free software R.     

Testing whether ensemble modelling is advantageous for maximising predictive performance of species distribution models

Predictive performance is important to many applications of species distribution models (SDMs). The SDM ‘ensemble’ approach, which combines predictions across different modelling methods, is believed to improve predictive performance, and is used in many recent SDM studies. Here, we aim to compare the predictive performance of ensemble species distribution models to that of individual models, using a large presence–absence dataset of eucalypt tree species. To test model performance, we divided our dataset into calibration and evaluation folds using two spatial blocking strategies (checkerboard-pattern and latitudinal slicing). We calibrated and cross-validated all models within the calibration folds, using both repeated random division of data (a common approach) and spatial blocking. Ensembles were built using the software package ‘biomod2’, with standard (‘untuned’) settings. Boosted regression tree (BRT) models were also fitted to the same data, tuned according to published procedures. We then used evaluation folds to compare ensembles against both their component untuned individual models, and against the BRTs. We used area under the receiver-operating characteristic curve (AUC) and log-likelihood for assessing model performance. In all our tests, ensemble models performed well, but not consistently better than their component untuned individual models or tuned BRTs across all tests. Moreover, choosing untuned individual models with best cross-validation performance also yielded good external performance, with blocked cross-validation proving better suited for this choice, in this study, than repeated random cross-validation. The latitudinal slice test was only possible for four species; this showed some individual models, and particularly the tuned one, performing better than ensembles. This study shows no particular benefit to using ensembles over individual tuned models. It also suggests that further robust testing of performance is required for situations where models are used to predict to distant places or environments.     

Genetic and molecular analysis of nonrandom dimer assembly of the creatine kinase isozymes of fishes

Species within many families of actinopterygian bony fishes (class Osteichthyes) have a two-banded allelic isozyme phenotype in individuals heterozygous at the creatine kinase A locus. This two-banded pattern is formed by the presence of the two homodimeric isozymes and the absence of the expected heterodimer. Sharks and amphibians have retained the ability to form all three allelic isozymes in individuals which are heterozygous. Reversible denaturation procedures were able to assemble the different allelic CK-A subunits within a species to form CK-A₂ heterodimers. Furthermore, heterodimers were formed from different CK-A subunits from highly divergent species after this in vitro molecular hybridization process. It is concluded from these studies that the polypeptidebinding sites of creatine kinase are structurally conservative in most fishes and that the absence of a heterodimer in heterozygous individuals is not due to a structural incompatibility between the different A subunit types or to an instability of the heterodimer during electrophoresis. A temporal and/or spatial isolation of allelic CK-A subunit synthesis and assembly, within differentiated skeletal muscle, appears to have evolved in the actinopterygian bony fishes.This research was supported by NSF Grant PCM76-08383 to G. S. W. and by a NIH Cell and Molecular Biology Traineeship to S. D. F.     

Performance of individual vs. group sampling for inferring dispersal under isolation‐by‐distance

Models of isolation‐by‐distance formalize the effects of genetic drift and gene flow in a spatial context where gene dispersal is spatially limited. These models have been used to show that, at an appropriate spatial scale, dispersal parameters can be inferred from the regression of genetic differentiation against geographic distance between sampling locations. This approach is compelling because it is relatively simple and robust and has rather low sampling requirements. In continuous populations, dispersal can be inferred from isolation‐by‐distance patterns using either individuals or groups as sampling units. Intrigued by empirical findings where individual samples seemed to provide more power, we used simulations to compare the performances of the two methods in a range of situations with different dispersal distributions. We found that sampling individuals provide more power in a range of dispersal conditions that is narrow but fits many realistic situations. These situations were characterized not only by the general steepness of isolation‐by‐distance but also by the intrinsic shape of the dispersal kernel. The performances of the two approaches are otherwise similar, suggesting that the choice of a sampling unit is globally less important than other settings such as a study's spatial scale.     

大兴安岭次生林区优势种落叶松分布格局及竞争作用

竞争是形成特定群落结构、构成分布格局的基本驱动力之一,树种的空间分布和大小并不是相互独立的,而是广泛受到竞争过程影响。在大兴安岭设置一块具有代表性的天然次生林恢复样地,采用点格局分析中的最近邻体距离G（r）函数、双关联函数g（r）和基于个体胸径标记的点格局分析方法同时结合4种点格局零模型（完全随机模型、均值托马斯模型、随机标签模型、先决条件零模型）研究分析大兴安岭次生林区优势种落叶松不同生活史阶段的分布格局、关联性及竞争作用。研究结果显示：落叶松不同发育阶段分布格局不同、同一发育阶段不同研究尺度分布格局也不同;落叶松种群内存在潜在的竞争、且竞争作用与龄级和研究尺度有关;落叶松幼龄个体在小尺度（r<5m）下的聚集分布是由扩散限制作用和竞争作用所导致;落叶松种群内成龄与幼龄个体间有较强的正关联性、成龄个体对幼龄个体在小尺度下有明显的庇护作用;标记点格局分析方法在检测植物群落中的竞争作用时敏感性较高。