Mapping of sample collection data: GIS tools for the natural product researcher

Scientists engaged in the research of natural products often either conduct field collections themselves or collaborate with partners who do, such as botanists, mycologists, or SCUBA divers. The information gleaned from such collecting trips (e.g. longitude/latitude coordinates, geography, elevation, and a multitude of other field observations) have provided valuable data to the scientific community (e.g., biodiversity), even if it is tangential to the direct aims of the natural products research, which are often focused on drug discovery and/or chemical ecology. Geographic Information Systems (GIS) have been used to display, manage, and analyze geographic data, including collection sites for natural products. However, to the uninitiated, these tools are often beyond the financial and/or computational means of the natural product scientist. With new, free, and easy-to-use geospatial visualization tools, such as Google Earth, mapping and geographic imaging of sampling data are now within the reach of natural products scientists. The goals of the present study were to develop simple tools that are tailored for the natural products setting, thereby presenting a means to map such information, particularly via open source software like Google Earth.     

Open data and open source for remote sensing training in ecology

Remote sensing is one of the most important tools in ecology and conservation for an effective monitoring of ecosystems in space and time. Hence, a proper training is crucial for developing effective conservation practices based on remote sensing data. In this paper we aim to highlight the potential of open access data and open source software and the importance of the inter-linkages between these and remote sensing training, with an interdisciplinary perspective. We will first deal with the importance of open access data and then we provide several examples of Free and Open Source Software (FOSS) for a deeper and more critical understanding of its application in remote sensing.     

3S技术及其在生态学研究中的应用

随着国民经济的迅速发展,人类对资源环境的需求越来越高,及时、准确、动态地获取资源现状及其变化信息对资源、生态环境的保护及可持续发展具有重要意义。本文综述了3S技术即遥感(RS)、地理信息系统(GIS)、全球定位系统(GPS)的概念、特点及其研究进展,探讨了3S技术在景观生态学及景观异质性研究、空间格局分析与模拟的应用;并对3S技术在群落生态学、植被调查、生物多样性研究、植被制图以及其它生态学领域中的应用作了展望。     

重庆市都市区绿地景观的连通性

城市绿地具有重要的生态功能和社会经济价值,是衡量城市生态可持续发展的重要标准.其中,连通性是维持景观功能的关键因素之一.以重庆市都市区为研究对象,结合TM遥感影像图,通过整体连通性指数(IIC)、可能连通性指数(PC)和景观中斑块对连通性的重要值对该区绿地景观的连通性进行了分析.研究结果表明,都市区绿地景观主要由少数巨型斑块和大量小型斑块组成.绿地景观整体连通性较差,这与绿地景观组成密切相关.对于绿地景观的连通性而言,巨型斑块的重要值最大,但小型斑块的重要性也不容忽视.对绿地景观连通性重要值最大的一些斑块主要分布于都市区的几大山脉上,这些斑块是城市绿地规划和保护的首要考虑的对象.基于研究结果,建议在重庆市都市区进行绿地规划时,优先考虑对重要斑块的保护,同时要考虑在巨型斑块之间构建小斑块,使其形成连通性廊道,提高绿地景观的连通性.     

Genetic Landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity

The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS^®, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo‐referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.     

Integration of landscape and structure indicators into a web-based geoinformation system for assessing wetlands status

Despite the important role of wetlands in our society, they are continuously threatened by human activity. In Canada, the critical loss of these habitats has fostered the application of preventive measures to at least reduce, if not avoid, their accelerated disappearance. In order to implement adequate environmental practices to protect these ecosystems, managers need to have a global knowledge of their situation. In this context, Web Geographic Information Systems (GIS) offer the possibility to visualize and share multiple integrated data as well as geoprocessings that can provide essential information to understand the relative risks wetlands are undergoing. In this work, we present the extension of an existing open source Web-GIS platform to manage wetlands in the province of Quebec, eastern Canada. The current platform offers new systematic and generalist spatial processing tools inspired on the metapopulation theory and on the concept of ecological integrity to evaluate changes in landscape that could affect wetlands systems. These new functionalities provides more compact and valuable information about wetlands' state that can inform decision-making in conservation of these habitats and biodiversity. The functions proposed can be used by different type of users without any particular or specific knowledge.     

基于无人机航测的漯河市土地利用景观格局尺度效应

景观格局的尺度效应一直是景观生态学研究的核心内容,对于揭示景观空间格局变化规律及其生态过程具有重要意义。以漯河市中心城区为研究对象,基于景观生态学原理,采用无人机航测技术获取空间分辨率为0.09 m的无人机影像,结合GIS空间分析法,量化分析了漯河市土地利用景观格局的尺度效应。结果表明:(1)漯河市中心城区土地利用景观格局具有明显的粒度和幅度效应。(2)粒度越小,景观格局指数随空间粒度的变化趋势越稳定,其表达的生态过程越真实;景观水平上景观格局的粒度效应是由建筑、道路和绿地景观在景观优势度、破碎度和聚集度等方面的变化导致的;35 m和3 m分别为研究粒度效应的临界阈值和最佳粒度。(3)景观优势度、破碎度和蔓延度随空间幅度的增加而降低,景观复杂程度和聚集度随空间幅度的增加而增加;景观格局具有明显的空间梯度分布特征——从市中心往外由不透水地面向透水地面过渡;建筑和道路在城市中心区聚集度较高,而绿地景观在城市内部破碎度较高,进而主导了整体景观格局的梯度变化;景观组分的稳定与城市规模有关。(4)无人机航测技术可以更快速、准确地获取城市尺度上的景观生态信息,揭示景观格局对尺度效应的响应特征,可为景观格局优化和城乡景观规划提供科学依据。     

GIS和遥感技术在生态安全评价与生物多样性保护中的应用

综合近年来国内外生态安全评价和生物多样性保护领域的研究成果:简要总结了地理信息系统(GIS)和遥感(RS)技术在生态学热点领域的应用研究现状和特点;归纳论述了GIS和RS在生态安全评价和生物多样性保护研究中存在的不足;在此基础上,尝试性地提出了可扩展的集成研究框架——"生产线"框架;最后探讨了GIS和RS技术与生态学集成研究的未来发展趋势。     

地理信息系统及其在动物空间行为研究中的应用

空间属性是动物行为的重要特征,也是行为生态学研究中必须要面对的难题之一。地理信息系统(Geographic Information System,GIS)具有强大的空间分析功能,它在动物行为生态学研究中得到了越来越广泛的应用,如生境选择、领域分析、迁徙路线、活动节律等。本文较系统地阐述了GIS的原理以及在行为生态学研究中所涉及的基本概念和原理,对近年来利用GIS进行的行为生态学研究做了回顾和总结,并对其未来的发展进行了展望。     

Integrating statistical genetic and geospatial methods brings new power to phylogeography

The field of phylogeography continues to grow in terms of power and accessibility. Initially uniting population genetics and phylogenetics, it now spans disciplines as diverse as geology, statistics, climatology, ecology, physiology, and bioinformatics to name a few. One major and recent integration driving the field forward is between "statistical phylogeography" and Geographic Information Systems (GIS) (Knowles, 2009). Merging genetic and geospatial data, and their associated methodological toolkits, is helping to bring explicit hypothesis testing to the field of phylogeography. Hypotheses derived from one approach can be reciprocally tested with data derived from the other field and the synthesis of these data can help place demographic events in an historical and spatial context, guide genetic sampling, and point to areas for further investigation. Here, we present three practical examples of empirical analysis that integrate statistical genetic and GIS tools to construct and test phylogeographic hypotheses. Insights into the evolutionary mechanisms underlying recent divergences can benefit from simultaneously considering diverse types of information to iteratively test and reformulate hypotheses. Our goal is to provide the reader with an introduction to the variety of available tools and their potential application to typical questions in phylogeography with the hope that integrative methods will be more broadly and commonly applied to other biological systems and data sets.     

中国园林生态学发展综述

运用文献计量等方法对已有科研成果进行统计分析,结果表明:中国近50年园林生态学科领域科研发展经过了起步探索(1962-1981)、缓慢发展(1982-2001)、快速发展(2002-2011)3个时期,园林生态学作为生态学一个新的分支学科,于20世纪90年代末初见端倪,作为一门新兴独立的应用生态学分支学科于21世纪初已基本形成.中国园林生态学领域的研究包括园林生态系统中生物与环境相互作用关系问题、人与环境相互作用关系问题以及园林生态系统与其他生态系统之间相互作用关系问题.当代园林生态研究主要有生态效益研究、生物与环境研究、人的需求与行为研究、生态规划与生态管理研究4个方面,目前园林生态学研究主要侧重生物与环境研究和生态效益研究,两方面的研究成果占总体研究成果的76.3％.不同研究方面也有各自的侧重点,如生物与环境研究侧重对植物的研究,生态效益研究侧重净化环境、水土保持和防灾减灾,生态规划与生态管理研究则侧重生态规划与设计.对四个研究方面的论文主题词检索和高频主题关键词的分布进行统计,结果显示,研究的热点有多样性、群落、水土保持、防灾避险、净化环境、生态规划与设计等.对CNKI中4个研究方面成果中获基金资助项目论文进行统计(不排重),总体成果中基金项目论文所占比重为10.8％,国家和地方基金是园林生态学科研基金资助的主要来源,基金论文比例之和达到85.4％,且国家和地方基金资助论文较多的是“生态与环境研究”和“生态效益研究”,合计占基金论文79.1％.SCI-E中收录的文献基金论文率为47.1％,是CNKI数据库收录的文献基金论文率的4.3倍,且国际基金是基金论文的主要资助来源之一,说明中国园林生态学领域部分科研成果得到国际学界关注.基于CNKI相关主题词统计,“园林生态学”的研究成果只有“景观生态学”的1％,“城市生态学”的8.3％,“园林生态学”学科系统理论研究在相关生态学科研究中所占比重很低,其理论和方法研究还较薄弱.今后在进一步完善学科理论体系、持续开展生态效益和园林植物研究的同时,为更好地研究和解决人-自然复合生态系统问题,提供更多的科学理论支撑,还需拓展交叉生态心理学或环境心理学等其他相关理论,更多地关注人与环境互相作用关系以及生态规划与生态管理等方面的研究,既使环境更好地满足人的行为需求,也使人认识到改变一些行为能更好地保护环境.     

基于遥感数据源的景观分析系统的设计与实现

在Ｖｉｓｕａｌ Ｃ＋＋环境下,设计并实现了一个景观分析系统。该系统采用提取斑块边界象素集的方法,提高了斑块搜索的速度,而且提供了斑块间距离计算、相邻斑块间边界长度计算等景观分析功能。该系统被应用到北京西北郊同分析中。通过分析表明,该系统不仅能计算面积、周长、中心坐标和最近同类型斑块的距离等单个斑块指数,而且能在此基础上计算景观类型和整个景观层次上的各种指数,从而弥补了目前多数地理信息系统在分析应用     

Landscape ecology development supported by geospatial technologies: A review

Numerous technologies have contributed to the recent development of landscape ecology, especially the geospatial technological advances constitute a revolution in landscape ecology. Extensive applications of geospatial technologies, such as fractal theory, geographic information systems (GIS) and remote sensing (RS) in landscape ecology research, suggest the necessity of such a review of research progress in this field. In this study, a brief introduction to fractal theory, GIS and RS and how they were applied in landscape ecology were provided first. Then, the current state-of-the-art was summarized and analyzed as reference for further promoting the development of landscape ecology science and its applications. Finally, opportunities and challenges of landscape ecology applications using these new technologies were discussed and concluded for future research. It was contended that a combination and integration of these technologies can substantially advance the study of landscape ecology for data acquisition, process modeling, scale transformation, result analysis and visualization. However, as no theoretical framework and application cases of applying an integration of fractal theory, GIS and RS techniques to landscape ecology research have been established, further studies are still much needed.     

山水林田湖草沙一体化保护和修复工程与景观生态学

我国山水林田湖草沙生命共同体及其保护和修复工程的理论研究和实践正逐渐开展,需要系统的学科理论支撑,景观生态学作为地理学和生态学的交叉科学,能够以其宏观空间理论和技术体系满足这一需求。本文将景观生态学作为山水林田湖草沙一体化保护和修复工程的支撑学科,首先,明确了山水林田湖草沙生命共同体是镶嵌的异质景观、具有景观的所有特征并遵循景观生态学原理;其次,阐述了景观生态建设理论如何应用于山水林田湖草沙一体化保护和修复工程的规划和评价;最后,总结景观生态建设研究的新趋势,提出待解决的理论和实践问题,并论述山水林田湖草沙一体化保护和修复工程如何为解决这些问题提供广阔的研究空间。景观生态学和山水林田湖草沙一体化保护和修复工程实践相结合,将为实现我国乃至全球生态、经济、社会可持续发展提供极为有效的途径。     

PhyloGeoViz: a web-based program that visualizes genetic data on maps

The first step of many population genetic studies is the simple visualization of allele frequencies on a landscape. This basic data exploration can be challenging without proprietary software, and the manual plotting of data is cumbersome and unfeasible at large sample sizes. I present an open source, web-based program that plots any kind of frequency or count data as pie charts in Google Maps (Google Inc., Mountain View, CA). Pie polygons are then exportable to Google Earth (Google Inc.), a free Geographic Information Systems platform. Import of genetic data into Google Earth allows phylogeographers access to a wealth of spatial information layers integral to forming hypotheses and understanding patterns in the data.     

GIS支持下的青石山小流域农业生态信息系统(QWAEIS)及其应用研究

应用地理信息系统（ＧＩＳ）,建立了青石山小流域农业生态信息系统（ＱＷＡＥＩＳ）,该系统综合了土壤、土地利用、水资源及地形地貌等空间信息和气候、人口、农业生产等基本信息。该系统能对小流域农业生态信息进行有效地分析和管理,应用此系统,进行了小流域的土地适宜性评价,获得土地适宜性评价结果,为小流域规划提供了空间定位信息。     

景观组成、结构和梯度格局对植物多样性的影响

植物多样性作为生物多样性研究的主要内容,一直以来受到广泛关注。近20年来,随着景观生态学的兴起和地理信息技术的发展,景观生态学与岛屿生物地理学、异质种群理论相结合,在植物多样性的保护和利用研究中得到运用。本文就在这3个理论的基础上,简述了景观组成(斑块、廊道、基质)、景观结构(斑块面积、边缘、隔离程度)和梯度格局(海拔、演替、土壤养分、干扰)对植物多样性的影响,强调了地理信息技术应用的重要性和景观层次上进行植物多样性研究的必要性。因此,在多个尺度上共同研究多个影响因子对植物多样性的复合作用,利于进一步揭示植物多样性的变化过程及其机制,有利于植物多样性的保护和利用。     

Greater Sage-Grouse Nesting Habitat: The Importance of Managing at Multiple Scales

Abstract: Considering habitat selection at multiple scales is essential to fully understand habitat requirements and management needs for wildlife species of concern. We used a hierarchical information-theoretic approach and variance decomposition techniques to analyze habitat selection using local-scale habitat variables measured in the field and landscape-scale variables derived with a Geographic Information System (GIS) for nesting greater sage-grouse (Centrocercus urophasianus) in the Powder River Basin (PRB), Montana and Wyoming, USA, 2003–2007. We investigated relationships between habitat features that can and cannot be mapped in a GIS to provide insights into interpretation of landscape-scale—only GIS models. We produced models of habitat selection at both local and landscape scales and across scales, yet multiscale models had overwhelming statistical and biological support. Variance decomposition showed that local-scale measures explained the most pure variation (50%) in sage-grouse nesting-habitat selection. Landscape-scale features explained 20% of pure variation and shared 30% with local-scale features. Both local- and landscape-scale habitat features are important in sage-grouse nesting-habitat selection because each scale explained both pure and shared variation. Our landscape-scale model was accurate in predicting priority landscapes where sage-grouse nests would occur and is, therefore, useful in providing landscape context for management decisions. It accurately predicted locations of independent sage-grouse nests (validation R² = 0.99) and showed good discriminatory ability with >90% of nests located within only 40% of the study area. Our landscape-scale model also accurately predicted independent lek locations. We estimated twice the amount of predicted nesting habitat within 3 km of leks compared to random locations in the PRB. Likewise we estimated 1.8 times more predicted nesting habitat within 10 km of leks compared to random locations. These results support predictions of the hotspot theory of lek placement. Local-scale habitat variables that cannot currently be mapped in a GIS strongly influence sage-grouse nest-site selection, but only within priority nesting habitats defined at the landscape scale. Our results indicate that habitat treatments for nesting sage-grouse applied in areas with an unsuitable landscape context are unlikely to achieve desired conservation results.     

Using Viewsheds to Determine Area Sampled by Ground-Based Radiotelemetry

Abstract: Geographic Information System (GIS) viewsheds have been suggested as a possible way to determine area sampled by ground telemetry. Although this would be useful information to have, there has been little use of the technique. To investigate if viewsheds could be of use, we produced a telemetry viewshed and compared the results to previously collected radiotelemetry data. Given positive initial results and potential applications, we think GIS viewsheds could be useful for radiotelemetry studies and we encourage further research in this area.     

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

Background

Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). Here we describe an application ontology that we developed de novo, and a specially designed database that, based on this ontology, can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit.

Methodology/Principal Findings

The ontology, named MIRO for Mosquito Insecticide Resistance Ontology, developed using the OBO-Edit software, describes all pertinent aspects of insecticide resistance, including specific methodology and mode of action. MIRO, then, forms the basis for the design and development of a dedicated database, IRbase, constructed using open source software, which can be used to retrieve data on mosquito populations in a temporally and spatially separate way, as well as to map the output using a Google Earth interface. The dependency of the database on the MIRO allows for a rational and efficient hierarchical search possibility.

Conclusions/Significance

The fact that the MIRO complies with the rules set forward by the OBO (Open Biomedical Ontologies) Foundry introduces cross-referencing with other biomedical ontologies and, thus, both MIRO and IRbase are suitable as parts of future comprehensive surveillance tools and decision support systems that will be used for the control of vector-borne diseases. MIRO is downloadable from and IRbase is accessible at VectorBase, the NIAID-sponsored open access database for arthropod vectors of disease.