Improving Aquatic Warbler Population Assessments by Accounting for Imperfect Detection

Monitoring programs designed to assess changes in population size over time need to account for imperfect detection and provide estimates of precision around annual abundance estimates. Especially for species dependent on conservation management, robust monitoring is essential to evaluate the effectiveness of management. Many bird species of temperate grasslands depend on specific conservation management to maintain suitable breeding habitat. One such species is the Aquatic Warbler (Acrocephalus paludicola), which breeds in open fen mires in Central Europe. Aquatic Warbler populations have so far been assessed using a complete survey that aims to enumerate all singing males over a large area. Because this approach provides no estimate of precision and does not account for observation error, detecting moderate population changes is challenging. From 2011 to 2013 we trialled a new line transect sampling monitoring design in the Biebrza valley, Poland, to estimate abundance of singing male Aquatic Warblers. We surveyed Aquatic Warblers repeatedly along 50 randomly placed 1-km transects, and used binomial mixture models to estimate abundances per transect. The repeated line transect sampling required 150 observer days, and thus less effort than the traditional ‘full count’ approach (175 observer days). Aquatic Warbler abundance was highest at intermediate water levels, and detection probability varied between years and was influenced by vegetation height. A power analysis indicated that our line transect sampling design had a power of 68% to detect a 20% population change over 10 years, whereas raw count data had a 9% power to detect the same trend. Thus, by accounting for imperfect detection we increased the power to detect population changes. We recommend to adopt the repeated line transect sampling approach for monitoring Aquatic Warblers in Poland and in other important breeding areas to monitor changes in population size and the effects of habitat management.     

Accounting for Imperfect Detection Is Critical for Inferring Marine Turtle Nesting Population Trends

Assessments of population trends based on time-series counts of individuals are complicated by imperfect detection, which can lead to serious misinterpretations of data. Population trends of threatened marine turtles worldwide are usually based on counts of nests or nesting females. We analyze 39 years of nest-count, female-count, and capture-mark-recapture (CMR) data for nesting loggerhead turtles (Caretta caretta) on Wassaw Island, Georgia, USA. Annual counts of nests and females, not corrected for imperfect detection, yield significant, positive trends in abundance. However, multistate open robust design modeling of CMR data that accounts for changes in imperfect detection reveals that the annual abundance of nesting females has remained essentially constant over the 39-year period. The dichotomy could result from improvements in surveys or increased within-season nest-site fidelity in females, either of which would increase detection probability. For the first time in a marine turtle population, we compare results of population trend analyses that do and do not account for imperfect detection and demonstrate the potential for erroneous conclusions. Past assessments of marine turtle population trends based exclusively on count data should be interpreted with caution and re-evaluated when possible. These concerns apply equally to population assessments of all species with imperfect detection.     

Spatially Explicit Modeling in Ecology: A Review

The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.     

数量生态学软件研发及应用

数量生态学是生物数学的重要组成部分,其数学基础是统计分析．由于数量生态学问题本身的复杂性以及研究中需要大量的数据处理,因此,大部分数量运算都要依赖于计算机完成．国际通用数学软件Matlab是一个具有强大数值计算能力、图形处理能力的交互式计算机代数系统,其强大的函数库和独特的内建程序设计语言为科学计算及程序设计提供了友好平台．本研究选择国际通用计算机代数系统Matlab作为程序设计平台,应用Matlab下强大的图形用户界面GUI软件包研发了植被数量生态学分析软件Quatitatlve Ecology中英文版,内容包括生物多样性,种间关联等简单的计算方法以及排序、分类、格局分析,生物一环境关系分析等复杂的分析方法．当进入应用状态时,只需要在相应的框中输入基本数据或者调用文本数据文件或Excel文件,即会得到具体的计算公式,计算结果,图形以及相应的分析或结论．特别是强大的帮助系统涵盖了所有数量分析方法并辅以应用实例供使用者参考．这将为数量生态学的发展注入新的活力．     

根系分泌物生态学研究

在植物生长过程中 ,由根系的不同部位分泌或溢泌一些无机离子及有机化合物 ,这些物质统称为根系分泌物。植物在其生长过程中不断地分泌无机离子及有机化合物 ,这是植物长期适应外界环境而形成的一种适应机制。早在 2 0世纪 5 0年代就有人对植物根系分泌物进行了研究 ,Ｒｏｖｉｒａ等[4 3] 和Ｖａｎｃｕｒａ等[4 7] 对根土界面根系分泌物进行了系统的研究 ,切尔诺布里维卡[2 6 ] 研究了植物根系分泌物的生物学作用 ,揭示了其在间作中的作用 ,直到 70年代对根系分泌物的研究才出现了蓬勃发展的趋势。近年来的研究表明 ,根系分泌物是保持根际微…     

公路路域动物生态学研究方法综述

从公路死亡效应、公路阻隔效应、公路回避效应和公路动物通道四个方面总结了国内外公路路域动物生态学研究的6种方法:样线法/样方法、痕迹法(主要是沙床/雪踪)、红外相机监控法、GPS项圈法、标记重捕法和遗传多样性分析法。通过比较分析各种方法优缺点并结合我国应用情况及国内外研究的发展趋势,提出了6种方法在四大研究领域应用对策:1)选择生态敏感区域的典型路段作为长期监测样线,采用样线法系统调查公路动物死亡效应,在部分路段试点与公路养护部门联合开展公路野生动物死亡的统计工作;2)选择生态敏感区域的典型路段作为长期监测样线,采用痕迹法进行公路阻隔与回避效应的监测,与野生动物保护部门合作,引入GPS项圈法提高监测精度;3)以痕迹法和红外相机监控法为主进行公路回避效应的监测研究,还可引入GPS项圈法从景观层面分析路网的道路影响域;4)以痕迹法和红外相机监控法为主进行野生动物通道的监测,逐步引入GPS项圈、遗传多样性分析法进行景观层面的种群稳定性分析,科学评价动物通道效率。     

Modeling Occupancy of Hosts by Mistletoe Seeds after Accounting for Imperfect Detectability

The detection of an organism in a given site is widely used as a state variable in many metapopulation and epidemiological studies. However, failure to detect the species does not necessarily mean that it is absent. Assessing detectability is important for occupancy (presence—absence) surveys; and identifying the factors reducing detectability may help improve survey precision and efficiency. A method was used to estimate the occupancy status of host trees colonized by mistletoe seeds of Psittacanthus plagiophyllus as a function of host covariates: host size and presence of mistletoe infections on the same or on the nearest neighboring host (the cashew tree Anacardium occidentale). The technique also evaluated the effect of taking detectability into account for estimating host occupancy by mistletoe seeds. Individual host trees were surveyed for presence of mistletoe seeds with the aid of two or three observers to estimate detectability and occupancy. Detectability was, on average, 17% higher in focal-host trees with infected neighbors, while decreased about 23 to 50% from smallest to largest hosts. The presence of mistletoe plants in the sample tree had negligible effect on detectability. Failure to detect hosts as occupied decreased occupancy by 2.5% on average, with maximum of 10% for large and isolated hosts. The method presented in this study has potential for use with metapopulation studies of mistletoes, especially those focusing on the seed stage, but also as improvement of accuracy in occupancy models estimates often used for metapopulation dynamics of tree-dwelling plants in general.     

扬子鳄(Alligator sinensis)生态学研究进展

简要介绍了半个多世纪以来,扬子鳄自然种群的变化、种群衰落的原因、生活史对策、栖息地选择、行为生态、生理生态等方面的主要研究成果,并对将来的研究进行了展望。     

Palm Uses in Northwestern South America: A Quantitative Review

A thorough review concerning palm uses in tropical rainforests of north-western South America was carried out to understand patterns of palm use throughout ecoregions (Amazonia, Andes, Chocó), countries (Colombia, Ecuador, Peru, Bolivia), and among the different human groups (indigenous, mestizos, afroamericans, colonos) that occur there. A total of 194 useful palm species, 2,395 different uses and 6,141 use-reports were recorded from 255 references. The Amazon had the highest palm use, whereas fewer, but similar uses were recorded for the Andes and Chocó. Ecuador was the most intensively studied country. Most palms were used for human food, utensils and tools, construction, and cultural purposes. Indigenous people knew more palm uses than mestizos, afroamericans and colonos. The use of palms was not random and the main uses were the same throughout the studied ecoregions and countries. Palms satisfy basic subsistence needs and have great importance in traditional cultures of rural indigenous and peasant populations in our study area. Arecaceae is probably the most important plant family in the Neotropics, in relation to use diversity and abundance.     

Occupancy Models for Monitoring Marine Fish: A Bayesian Hierarchical Approach to Model Imperfect Detection with a Novel Gear Combination

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics.     

A Review on Reservoir System and Its Ecology in Indian Perspective

Rural populations often depend on small reservoirs for their water supply. These are not natural aquatic system but are designed to serve specific purposes and provide the means to utilize water in a variety of useful and efficient ways. Water from these sources is not only utilized for drinking purposes, but also for commercial and industrial use. Though reservoirs are constructed, they are considered as an intermediate between a river and a lake. Thus limnological characteristics of this hybrid system have been of great interest to ecologists and researchers. Several limnological attributes regarding water quality, plankton abundance, fish population are been discussed in this review article. Ecological studies on global and Indian perspective are the major highlight of this review. A few modeling approaches are also discussed which are commonly used globally to preserve and manage the pristine aquatic nature of this hybrid ecosystem.     

A Review of the Chemical Ecology of Antarctic Marine Invertebrates

The interdisciplinary field of marine invertebrate chemicalecology is relatively young, and particularly so in polar marineenvironments. In this review we present evidence that the incidenceof chemical defense in antarctic benthic marine invertebratephyla is widespread. Mechanisms of chemical defense have beendetected in antarctic representatives of the Porifera, Cnidaria,Brachiopoda, Tunicata, Nemertea, Mollusca and Echinodermata.This argues against earlier bio-geographic theories that predicteda low incidence of chemical defense in polar waters where levelsof fish predation are low. Selection for chemical defense inbenthic sessile and sluggish marine invertebrates is likelya response to an environmentally stable community shown to bestructured primarily by biotic factors such as predation andcompetition. Holoplankton and the eggs, embryos and larvae ofboth benthic and planktonic antarctic macroinvertebrates mayalso employ chemical defense to offset mortality during characteristicallyslow development and long life span where susceptibility topredation is seemingly high. While most research to date hasfocused on the role of secondary metabolites in mediating predation,it is likely that bioactive compounds in antarctic marine invertebratesalso serve roles as antifoulants and allelochemics. The diversityof bioactive metabolites detected to date in antarctic marineinvertebrates sets the stage both for continuing and for broadeningefforts to evaluate their functional and ecological significance.     

A Lateral Flow Assay for Quantitative Detection of Amplified HIV-1 RNA

Although the accessibility of HIV treatment in developing nations has increased dramatically over the past decade, viral load testing to monitor the response of patients receiving therapy is often unavailable. Existing viral load technologies are often too expensive or resource-intensive for poor settings, and there is no appropriate HIV viral load test currently available at the point-of-care in low resource settings. Here, we present a lateral flow assay that employs gold nanoparticle probes and gold enhancement solution to detect amplified HIV RNA quantitatively. Preliminary results show that, when coupled with nucleic acid sequence based amplification (NASBA), this assay can detect concentrations of HIV RNA that match the clinically relevant range of viral loads found in HIV patients. The lateral flow test is inexpensive, simple and rapid to perform, and requires few resources. Our results suggest that the lateral flow assay may be integrated with amplification and sample preparation technologies to serve as an HIV viral load test for low-resource settings.     

水生低等脊椎动物病毒生态学研究

初次系统介绍两栖类、爬行类和鱼类病毒学的专著<低等脊椎动物病毒学>于1989年问世[1],是目前尚处在萌芽期的水生低等脊椎动物病毒生态学的基础文献之一.可将生态学分为以个体和群体为中心同其环境关系的宏观生态学、以(单)细胞为中心同其环境关系的微生态学、及以细胞内的生物活性分子为中心同其分子环境关系的分子生态学[2]等3个层次.水生低等脊椎动物病毒生态学旨在阐明病毒与宿主及水环境之间的各种作用及其机理,探讨病毒与宿主在水体环境中相互作用而产生的生理平衡态与病理失调的机制,以因势利导,寻求维持宿主生理平衡、防止病理失调及保护水体环境的措施.     

Generalizations in Ecology: A Philosophical Taxonomy

There has been a significant amount of uncertainty and controversy over the prospects for general knowledge in ecology. Environmental decision makers have begun to despair of ecology's capacity to provide anything more than case by case guidance for the shaping of environmental policy. Ecologists themselves have become suspicious of the pursuit of the kind of genuine nomothetic knowledge that appears to be the hallmark of other scientific domains. Finally, philosophers of biology have contributed to this retreat from generality by suggesting that there really are no laws in biology. This paper addresses these issues by providing a framework for thinking about general knowledge claims in ecology. It introduces a philosophical taxonomy that classifies generalizations into three broad categories – phenomenological, causal and theoretical. It then turns to the difficult problem of laws, arguing that, while there are probably no laws as that term has been understood in philosophy of science, it doesn't follow that everything in ecology is equally contingent. A mechanism for recognizing degrees of contingency in ecological generalizations is developed. The paper concludes by examining the implications of the analysis for the controversies noted at the outset.