Machine learning methods without tears: a primer for ecologists

Machine learning methods, a family of statistical techniques with origins in the field of artificial intelligence, are recognized as holding great promise for the advancement of understanding and prediction about ecological phenomena. These modeling techniques are flexible enough to handle complex problems with multiple interacting elements and typically outcompete traditional approaches (e.g., generalized linear models), making them ideal for modeling ecological systems. Despite their inherent advantages, a review of the literature reveals only a modest use of these approaches in ecology as compared to other disciplines. One potential explanation for this lack of interest is that machine learning techniques do not fall neatly into the class of statistical modeling approaches with which most ecologists are familiar. In this paper, we provide an introduction to three machine learning approaches that can be broadly used by ecologists: classification and regression trees, artificial neural networks, and evolutionary computation. For each approach, we provide a brief background to the methodology, give examples of its application in ecology, describe model development and implementation, discuss strengths and weaknesses, explore the availability of statistical software, and provide an illustrative example. Although the ecological application of machine learning approaches has increased, there remains considerable skepticism with respect to the role of these techniques in ecology. Our review encourages a greater understanding of machin learning approaches and promotes their future application and utilization, while also providing a basis from which ecologists can make informed decisions about whether to select or avoid these approaches in their future modeling endeavors.     

Sudden challenges in teaching ecology and aligned disciplines during a global pandemic: Reflections on the rapid move online and perspectives on moving forward

The challenges facing higher education in response to COVID‐19 are significant and possibly none more so than in ecology and aligned disciplines. Not only did most ecology lecturers have to rush lectures and tutorials online, but also laboratory and field classes. We reflect on our experience of this move and also consider those of 30 other ecology‐aligned teaching academics to summarize the challenges faced in the move online early in 2020 and the developing plans for adapting ecology teaching and learning going into the 2020/21 academic year. The move online had the most significant impact on field classes, with more of these canceled than lectures or laboratory classes. Most respondents to an online poll also highlighted that many respondents (~45%) felt that ecology was more impacted by COVID‐19 that even other STEM disciplines. The availability of technological solutions is key to moving forward and will hopefully enhance the teaching and learning experience for many beyond the current crisis.     

Hormones in the city: endocrine ecology of urban birds

Urbanization dramatically changes the landscape, presenting organisms with novel challenges and often leading to reduced species diversity. Urban ecologists have documented numerous biotic and abiotic consequences of urbanization, such as altered climate, species interactions, and community composition, but we lack an understanding of the mechanisms underlying organisms' responses to urbanization. Here, I review findings from the nascent field of study of the endocrine ecology of urban birds. Thus far, no clear or consistent patterns have been revealed, but we do have evidence that urban habitat can shape endocrine traits, and that those traits might contribute to adaptation to the urban environment. I suggest strong approaches for future work addressing exciting questions about the role of endocrine traits in mediating responses to urbanization within species across the globe.     

Ecology after 100 years: Progress and pseudo-progress

Has the science of ecology fulfilled the promises made by the originators of ecological science at the start of the last century? What should ecology achieve? Have good policies for environmental management flowed out of ecological science? These important questions are rarely discussed by ecologists working on detailed studies of individual systems. Until we decide what we wish to achieve as ecologists we cannot define progress toward those goals. Ecologists desire to achieve an understanding of how the natural world operates, how humans have modified the natural world, and how to alleviate problems arising from human actions. Ecologists have made impressive gains over the past century in achieving these goals, but this progress has been uneven. Some sub-disciplines of ecology are well developed empirically and theoretically, while others languish for reasons that are not always clear. Fundamental problems can be lost to view as ecologists fiddle with unimportant pseudo-problems. Bandwagons develop and disappear with limited success in addressing problems. The public demands progress from all the sciences, and as time moves along and problems get worse, more rapid progress is demanded. The result for ecology has too often been poor, short-term science and poor management decisions. But since the science is rarely repeated and the management results may be a generation or two down the line, it is difficult for the public or for scientists to decide how good or bad the scientific advice has been. In ecology over the past 100 years we have made solid achievements in behavioural ecology, population dynamics, and ecological methods, we have made some progress in understanding community and ecosystem dynamics, but we have made less useful progress in developing theoretical ecology, landscape ecology, and natural resource management. The key to increasing progress is to adopt a systems approach with explicit hypotheses, theoretical models, and field experiments on a scale defined by the problem. With continuous feedback between problems, possible solutions, relevant theory and experimental data we can achieve our scientific goals.     

生态位模型的理论基础、发展方向与挑战

生态位模型是一个以生态位理论为基础的新兴研究领域.它通过采集研究对象的已知分布点及其相关的环境数据组成训练样本,利用数理统计或机器学习理论分析数据,构建特征函数表示物种在生态位空间的实际生态位.以生态位模型预测物种潜在分布地或计算物种间的生态位重叠等研究,在生态学、生物地理学和进化生物学研究中显得越来越重要.本文从生态位概念出发,详细解析了生态位模型的理论基础、相关的焦点争论、使用时的注意点以及可能的发展方向与面临的挑战,指出模型中要考虑人类活动对物种生态位的影响.希望本文所探讨的本领域最新的争论焦点能引起相关学者的关注与深入思考.     

“环境污染的生物修复”课程教学改革探索与实践

“环境污染的生物修复(Bioremediation of Environmental Pollution)”是环境科学、环境工程、农业资源与环境等专业的专业选修课,在专业人才培养体系中具有重要地位。针对课程前期教学中存在的问题,任课教师结合高质量人才培养需求,从课程教学目标优化、课程教学内容重构与知识整合、教学方法改革与创新等环节对课程教学进行了改革探索。实践结果表明,改革后的课程教学不仅显著提升了课程教学目标的达成度,还有效提高了学生自主学习能力、思维能力和知识综合运用能力,取得了较好的教学效果。     

Estimating counterfactuals for evaluation of ecological and conservation impact: an introduction to matching methods

Matching methods encompass non-parametric approaches to estimating counterfactual states through a rigorous selection of control units with similar characteristics to units submitted to an intervention. These methods enable comparisons between treated and control units in a way that facilitates understanding of causal relationships between interventions and outcomes. Matching methods have been used only recently in ecology and conservation biology, where such applications changed the way the field investigates causal questions, for example, in impact-evaluation studies. However, the strengths and limitations of matching methods are not well understood by most ecologists and environmental scientists. Herein, we review state-of-the-art matching methods aiming to help fill this gap in understanding. First, we present relevant theoretical concepts related to matching methods and related subjects such as counterfactual states and causation. Next, we propose guidelines and strategies for the application of matching methods in ecology and conservation biology. Finally, we discuss the possibilities for future applications of matching methods in the environmental sciences.     

Introduction. Integration of ecology and endocrinology in avian reproduction: a new synthesis

Birds are some of the most familiar organisms of global ecosystems. Changes in the visibility and abundance of birds are therefore excellent indicators of population and physiological responses to habitat changes and are a major focus for public concern about detrimental environmental changes. In order to understand how birds respond to these challenges, it is essential to determine how the environment affects reproduction under natural conditions. The continuum from environmental variables (cues) to reproductive life-history traits depends upon a cascade of neural and physiological processes that determine the extent and rate at which birds will be able to adapt to changes in their environment. For a full understanding of this ability to adapt, ecologists and endocrinologists need to collaborate and build a common framework. The objective of this theme issue is to bring together a series of papers addressing how evolutionary ecologists and endocrinologists can collaborate directly using avian reproduction as a model system. First, we address the need to integrate ecology and endocrinology and what benefits to biological knowledge will be gained. The papers collected in this issue represent a new synthesis of ecology and endocrinology as discussed in three E-BIRD workshops. The three main foci are trade-offs and constraints, maternal effects and individual variation. Authors within each group present ecological and endocrinological aspects of their topics and many go on to outline testable hypotheses. Finally, we discuss where the major problems remain and how this issue points out where these need collaborative efforts of ecologists and endocrinologists. Specific challenges are raised to future researchers to break through intellectual barriers and explore new frontiers. This framework of topics will ultimately apply to all taxa because the principles involved are universal and hopefully will have direct application to programmes integrating organisms and genes throughout biological sciences.     

An evaluation of the state of spatial point pattern analysis in ecology

Over the last two decades spatial point pattern analysis (SPPA) has become increasingly popular in ecological research. To direct future work in this area we review studies using SPPA techniques in ecology and related disciplines. We first summarize the key elements of SPPA in ecology (i.e. data types, summary statistics and their estimation, null models, comparison of data and models, and consideration of heterogeneity); second, we review how ecologists have used these key elements; and finally, we identify practical difficulties that are still commonly encountered and point to new methods that allow current key questions in ecology to be effectively addressed. Our review of 308 articles published over the period 1992–2012 reveals that a standard canon of SPPA techniques in ecology has been largely identified and that most of the earlier technical issues that occupied ecologists, such as edge correction, have been solved. However, the majority of studies underused the methodological potential offered by modern SPPA. More advanced techniques of SPPA offer the potential to address a variety of highly relevant ecological questions. For example, inhomogeneous summary statistics can quantify the impact of heterogeneous environments, mark correlation functions can include trait and phylogenetic information in the analysis of multivariate spatial patterns, and more refined point process models can be used to realistically characterize the structure of a wide range of patterns. Additionally, recent advances in fitting spatially‐explicit simulation models of community dynamics to point pattern summary statistics hold the promise for solving the longstanding problem of linking pattern to process. All these newer developments allow ecologists to keep up with the increasing availability of spatial data sets provided by newer technologies, which allow point patterns and environmental variables to be mapped over large spatial extents at increasingly higher image resolutions.     

Harnessing synthetic biology for kelp forest conservation1

Environmental and climatic change is outpacing the ability of organisms to adapt, at an unprecedented level, resulting in range contractions and global ecosystem shifts to novel states. At the same time, scientific advances continue to accelerate, providing never‐before imagined solutions to current and emerging environmental problems. Synthetic biology, the creation of novel and engineered genetic variation, is perhaps the fastest developing and transformative scientific field. Its application to solve extant and emerging environmental problems is vast, at times controversial, and technological advances have outpaced the social, ethical, and practical considerations of its use. Here, we discuss the potential direct and indirect applications of synthetic biology to kelp forest conservation. Rather than advocate or oppose its use, we identify where and when it may play a role in halting or reversing global kelp loss and discuss challenges and identify pathways of research needed to bridge the gap between technological advances and organismal biology and ecology. There is a pressing need for prompt collaboration and dialogue among synthetic biologists, ecologists, and conservationists to identify opportunities for use and ensure that extant research directions are set on trajectories to allow these currently disparate fields to converge toward practical environmental solutions.     

Back to the future: natural history and the way forward in modern fungal ecology

The growing power and increasing availability of molecular tools for identifying fungi in environmental samples has revolutionized the way that fungal ecologists work. As a result, more people from around the globe have jumped into the fungal community sequencing endeavor. Paradoxically, as these extensive datasets accumulate we are often at a loss for interpretation due to the lack of basic autecology and natural history information for most fungi. As a result we are in danger of learning less and about more and more. I suggest that one way forward in fungal ecology is through a modern version of fungal natural history, with a focus on holistic understanding of individual species and ecosystems, but driven by modern genomic and molecular tools. By combining the extensive data generated through environmental sequencing with an intensive, molecular-based natural history we can create a synergy that will propel fungal ecology forward.     

Natural and human impact in Mediterranean landscapes: An intriguing puzzle or only a question of time?

Time is a key factor to understand the effects of disturbance on natural communities or ecosystems. In Mediterranean landscapes, where nature and humans have been strongly intermingling since mid-Holocene, the relationships between plant ecology and palaeoecology and their role for the interpretation of natural and anthropogenic changes still needs to be clearly understood. Ecology and palaeoecology are both investigating such problems, but each of them cannot disentangle the specific role played by nature and by humans in shaping the present plant communities and landscapes. A new age of cooperation among researchers in ecology and palaeoecology is needed, and the integration of these closely related but separated research fields is necessary to explain the resulting dynamic puzzle. Plant ecologists should avoid the oversimplification of the actual causes as the exclusive drivers of plant communities and landscapes and force the exploitation of the available data to generate and test new hypotheses for past, present and future environmental reconstructions and management. Even when planning for the future biodiversity conservation, we need to properly use the existing information about millennia of human effects on the natural biotas, to properly set landscape management and conservation priorities.     

Endangered species and a threatened discipline: behavioural ecology

Behavioural ecologists often see little connection between the current conservation crisis and the future of their discipline. This view is myopic because our abilities to investigate and interpret the adaptive significance and evolutionary histories of behaviours are increasingly being compromised in human-dominated landscapes because of species extinctions, habitat destruction, invasive species, pollution, and climate change. In this review, we argue that many central issues in behavioural ecology will soon become prohibitively difficult to investigate and interpret, thus impeding the rapid progress that characterizes the field. To address these challenges, behavioural ecologists should design studies not only to answer basic scientific questions but also to provide ancillary information for protection and management of their study organisms and habitats, and then share their biological insights with the applied conservation community.     

全英文“环境工程微生物学”的国家线下一流本科课程成长之路

国家一流本科课程的评审认定是教育部全面深化教育教学改革的重要举措,也是提升本科教学质量的重要一环,极大地促进了任课教师对标评价量规进行教研教改。为促进环境工程专业核心基础课的教改,“环境工程微生物学”全英课程组在先进的教育思想、方法和教育心理学的指导下,对教学理念、课程内容、教学组织和实施等多方面进行了大胆的改革和创新,注重课程思政和因材施教,增加课堂教学的师生互动和生生互动;针对工科类学生的培养目标,引入实际工程的应用案例,在课内外补充环境微生物工程领域研究的最新进展和教师的科研成果,注重提升课程的高阶性、创新性和挑战度,从多方面强化知识、能力、素质的有机融合,学生学习效果明显提高。申报并获认定为首批国家线下一流本科课程和广东省一流本科课程。     

Developing a flexible learning activity on biodiversity and spatial scale concepts using open‐access vegetation datasets from the National Ecological Observatory Network

Biodiversity is a complex, yet essential, concept for undergraduate students in ecology and other natural sciences to grasp. As beginner scientists, students must learn to recognize, describe, and interpret patterns of biodiversity across various spatial scales and understand their relationships with ecological processes and human influences. It is also increasingly important for undergraduate programs in ecology and related disciplines to provide students with experiences working with large ecological datasets to develop students’ data science skills and their ability to consider how ecological processes that operate at broader spatial scales (macroscale) affect local ecosystems. To support the goals of improving student understanding of macroscale ecology and biodiversity at multiple spatial scales, we formed an interdisciplinary team that included grant personnel, scientists, and faculty from ecology and spatial sciences to design a flexible learning activity to teach macroscale biodiversity concepts using large datasets from the National Ecological Observatory Network (NEON). We piloted this learning activity in six courses enrolling a total of 109 students, ranging from midlevel ecology and GIS/remote sensing courses, to upper‐level conservation biology. Using our classroom experiences and a pre/postassessment framework, we evaluated whether our learning activity resulted in increased student understanding of macroscale ecology and biodiversity concepts and increased familiarity with analysis techniques, software programs, and large spatio‐ecological datasets. Overall, results suggest that our learning activity improved student understanding of biological diversity, biodiversity metrics, and patterns of biodiversity across several spatial scales. Participating faculty reflected on what went well and what would benefit from changes, and we offer suggestions for implementation of the learning activity based on this feedback. This learning activity introduced students to macroscale ecology and built student skills in working with big data (i.e., large datasets) and performing basic quantitative analyses, skills that are essential for the next generation of ecologists.     

地方院校《环境工程微生物学》课程改革与实践

《环境工程微生物学》是环境工程专业的核心课程之一,为提高教学质量,以湖南文理学院环境工程专业为例,从明确课程定位、提升教师教学水平、提高学生兴趣以及加强实践教学几个方面进行了探讨。首先需明确该课程不同于普通的微生物学,教师在授课中应将微生物学相关理论知识与环境科学、环境工程领域实践相结合。其次,教师应通过多种方式提高自身教学水平。在授课中应注意通过合理使用教具、引入热点问题以及善于使用多媒体设备、提高学生课堂参与力度等方式来培养学生的学习兴趣。同时,在实践教学中也应注意促进学生对于环境工程微生物理论知识的理解和运用,提高动手能力和实验独操能力,以期达到更好的教学效果。     

微生物学全英文教学的意义、问题以及促研促教的实践探索北大核心CSCD

微生物涉及人类生活的方方面面,微生物学是各类高校为生命科学、医学、药学、农业、林业、食品等有关专业开设的本科生必修专业基础课。在国际化和一流学科发展趋势下,全英文授课具有重要意义并越来越受到重视。本文旨在探讨在如今面向人类生命健康、强调学科交叉的时代,如何结合本学校专业优势,开展微生物学英文教学的课程改革,将微生物学与医药、农业、环境、健康等充分结合,力争做到以学促研、以学促教,打造出具有本学校特色的微生物学全英文课程,将有关实践探索与微生物学教学工作者进行交流。     

Connecting ecology to daily life: how students and teachers relate food webs to the food they eat

This study used sociocultural learning theory to better understand how middle and high school environmental science and biology students and pre- and in-service science teachers connect the daily life activity of eating to the food web model learned in school. We sought to understand how student and teacher perceptions of the environment and their experiences influenced their responses to interview questions regarding this topic. Findings, based on transcribed interviews with 54 study participants, indicate that three quarters of teachers and students were unable to connect the food they eat with ecosystem food webs. Even so, many respondents particularly those from elite public schools, did not demonstrate common food web misconceptions identified by other researchers, instead showing a sophisticated understanding of food web interactions. These findings indicate that even though participants were proficient in their school science understanding of food web interactions, they did not readily think about how their everyday out of school activities, like eating, relate to those interactions. This may be representative of a more general disconnect between formal ecology instruction and daily life activities. We provide several recommendations for how this disconnect can be remedied in our classrooms.