Genomics-fueled approaches to current challenges in marine ecology

As a result of recent advances in genomic technology, a 'tool set' is emerging that can be used by marine ecologists to gain new perspectives on central questions in the field. Techniques such as gene expression profiling using DNA microarrays, when placed in an ecological context, stand to advance greatly our understanding of how organisms respond to abiotic and biotic stresses. Here, we target areas in which adding genomics to ecological and physiological investigations will significantly advance our understanding of crucial issues ranging from the general biological effects of environmental temperature changes on individuals and communities to the interactions between symbionts in coral bleaching. At a time when both short- and long-term perturbations of marine ecosystems are increasing in severity, this kind of integrative approach could generate new and exciting hypotheses about the functioning of marine organisms and communities.     

Reintroduction: challenges and lessons for basic ecology

Ecology is a subject where theoretical predictions are often difficult to test experimentally in the field. To address this challenge, the Ecological Society of America suggested exploiting large-scale environmental management decisions in a scientific way. This 'adaptive management' constitutes one of the purposes of the Sustainable Biosphere Initiative. Meanwhile, in the current context of the biodiversity crisis, translocations and particularly reintroductions of threatened species are becoming more numerous. It is time for ecologists and wildlife managers to collaborate on these unique opportunities for large-scale studies.     

Multimodel inference in ecology and evolution: challenges and solutions

Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.     

Pattern analysis in landscape ecology: progress, challenges and outlook

Landscape pattern indices or landscape metrics, an important means in landscape pattern analysis, has resulted in the prosperity of landscape ecology. However, landscape pattern analysis was criticized recently for its poor correlation with ecological processes. In this paper, the current situation and challenges in landscape pattern analysis was elaborated, and the future of landscape pattern analysis was discussed. We believe that the landscape metrics is still the main method in spatial pattern analysis, and is important for landscape ecology. However, there are 3 challenges in landscape pattern analysis: (1) how to develop new methods by integrating explicit ecological sense in landscape pattern analysis? (2) How to link landscape pattern and ecological processes? (3) How to apply the theory of “matrix-patch-corridor” to practice? In future, 5 issues are to be addressed: (1) to develop a methodology to describe landscape pattern in a dynamic manner; (2) to explore the ecological sense of landscape pattern using a series of landscape metrics; (3) to develop new methods for landscape pattern analysis related to ecological processes; (4) to conduct landscape pattern analysis at multi-dimensions; (5) to explain the relationship between landscape pattern and ecological processes by multi-scale pattern analysis.     

粪便DNA分析技术在分子生态学研究中的机遇与挑战

随着粪便DNA分析技术的不断发展与完善,其越来越多地被应用于分子生态学研究中,特别是野生动物的遗传状况评估研究。粪便DNA的获取可以在不干扰,甚至无需观察到动物本身的情况下展开,因此避免了取样活动可能给野生动物带来的干扰或伤害,极大地促进了野生动物分子生态学的研究。虽然粪便DNA分析技术在其建立伊始因DNA质量问题而受到了一定的挑战,但自其建立至今,研究者发展了多种技术来克服这一问题。现已能获得较高质量的粪便DNA,并将基因分型错误率控制在较低水平。本文将结合我们在粪便DNA分析技术上所积累的经验,从粪便样品采集、保存、DNA提取、PCR扩增以及等位基因分型等各个环节对该技术进行详细探讨,以期阐明该技术在野生动物分子生态学研究中所面临的机遇与挑战,进一步推动其在我国野生动物保护研究中的应用与发展。     

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.     

景观生态学中的格局分析：现状、困境与未来

作为景观格局分析的重要手段,景观格局指数的提出与发展极大地推动了景观生态学的发展,但是由于众多景观格局指数在指示生态学过程方面的不足,近年来景观格局分析已经走入困境。在总结近年来国内外相关研究的基础上,对景观格局分析的现状、困境及未来发展方向进行了综述。景观格局分析仍然是景观生态学的重要方面,景观格局指数仍然是景观格局分析的主要手段。但是如何建立具有生态学意义的景观格局指数和分析方法,如何将景观格局与生态过程联系起来,以及如何将＂基质—斑块—廊道＂的景观生态学理论应用到实际中是目前景观格局分析面临的主要困境。基于对景观格局分析现状及困境的认识,提出了景观格局分析未来的5个发展方向：（1）景观格局分析应该从目前的静态格局描述发展到对动态格局的刻画,只有找到刻画动态格局的方法,才能将格局和过程有机地联系在一起;（2）通过对多种景观格局指数的联合应用,发掘景观格局指数集合体对生态过程的解释能力;（3）发展基于生态过程的景观格局指数和分析方法;（4）通过多维景观格局分析,定量研究景观格局演变与生态过程之间的关系;（5）多尺度景观格局分析,将为解决格局与过程的关系提出有效手段。     

UAVs as remote sensing platforms in plant ecology: review of applications and challenges

无人机遥感在植物生态学中的应用与挑战 无人机为获取高时空分辨率的遥感数据提供了经济灵活的工具,为植物生态学家开展从个体到区域尺度的生态学研究提供了新的机遇和手段。但作为一种新兴的技术手段,当前无人机遥感在植物生态学中的应用仍充满了挑战,植物生态学的科研需求与无人机遥感的生态应用需要更为深入的融合。本文综述了无人机遥感技术在植物生态学中的应用,展望了无人机在植物生态学研究中的应用前景。在所综述的400篇文献中,59%的文章发表于非植物生态学领域的遥感类期刊,遥感学者与生态学者的关注点存在较大差异。当前的研究集中在无人机遥感的技术层面,如数据处理和遥感反演方法等,对生态学问题本身的关注较少。综述的文献中,61%的研究案例集中在群落尺度,可见光(RGB)相机和多光谱相机是最常用的传感器类型(75%)。无人机遥感数据中蕴藏着诸多待挖掘的、有重要意义的生态参数,这些参数有助于我们识别林窗的几何特征,构建林冠的化学组合,更好地了解林冠表面的不规则性和群落的异质性。无人机遥感技术在植物生态学研究中的深入应用,需要集植物生态学家和遥感专家之合 力共同推进。     

The challenges that spatial context present for synthesizing community ecology across scales

Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro‐ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub‐divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta‐analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.     

The grand challenges of migration ecology that radar aeroecology can help answer

Many migratory species have experienced substantial declines that resulted from rapid and massive expansions of human structures and activities, habitat alterations and climate change. Migrants are also recognized as an integral component of biodiversity and provide a multitude of services and disservices that are relevant to human agriculture, economy and health. The plethora of recently published studies reflects the need for better fundamental knowledge on migrations and for better management of their ecological and human‐relevant effects. Yet, where are we in providing answers to fundamental questions and societal challenges? Engaging a broad network of researchers worldwide, we used a horizon‐scan approach to identify the most important challenges which need to be overcome in order to gain a fuller understanding of migration ecology, and which could be addressed using radar aeroecological and macroecological approaches. The top challenges include both long‐standing and novel topics, ranging from fundamental information on migration routes and phenology, orientation and navigation strategies, and the multitude of effects migrants may have on resident communities, to societal challenges, such as protecting or preventing migrant services and disservices, and the conservation of migrants in the face of environmental changes. We outline these challenges, identify the urgency of addressing them and the primary stakeholders – researchers, policy makers and practitioners, or funders of research.     

Teaching and learning in ecology: a horizon scan of emerging challenges and solutions

We currently face significant, anthropogenic, global environmental challenges and the role of ecologists in mitigating these challenges is arguably more important than ever. Consequently there is an urgent need to recruit and train future generations of ecologists, both those whose main area is ecology, but also those involved in the geological, biological and environmental sciences. Here we present the results of a horizon scanning exercise that identified current and future challenges facing the teaching of ecology, through surveys of teachers, students and employers of ecologists. Key challenges identified were grouped in terms of the perspectives of three groups: students, for example the increasing disconnect between people and nature; teachers, for example the challenges associated with teaching the quantitative skills that are inherent to the study of ecology; and society, for example poor societal perceptions of the field of ecology. In addition to the challenges identified, we propose a number of solutions developed at a workshop by a team of ecology teaching experts, with supporting evidence of their potential to address many of the problems raised. These proposed solutions include developing living labs, teaching students to be ecological entrepreneurs and influencers, embedding skills-based learning and coding in the curriculum, an increased role for learned societies in teaching and learning, and using new technology to enhance fieldwork studies including virtual reality, artificial intelligence and real-time spoken language translation. Our findings are focused towards UK higher education, but they should be informative for students and teachers of a wide range of educational levels, policy makers and professional ecologists worldwide.     

Undaria pinnatifida: A case study to highlight challenges in marine invasion ecology and management

Marine invasion ecology and management have progressed significantly over the last 30 years although many knowledge gaps and challenges remain. The kelp Undaria pinnatifida, or “Wakame,” has a global non‐native range and is considered one of the world's “worst” invasive species. Since its first recorded introduction in 1971, numerous studies have been conducted on its ecology, invasive characteristics, and impacts, yet a general consensus on the best approach to its management has not yet been reached. Here, we synthesize current understanding of this highly invasive species and adopt Undaria as a case study to highlight challenges in wider marine invasion ecology and management. Invasive species such as Undaria are likely to continue to spread and become conspicuous, prominent components of coastal marine communities. While in many cases, marine invasive species have detectable deleterious impacts on recipient communities, in many others their influence is often limited and location specific. Although not yet conclusive, Undaria may cause some ecological impact, but it does not appear to drive ecosystem change in most invaded regions. Targeted management actions have also had minimal success. Further research is needed before well‐considered, evidence‐based management decisions can be made. However, if Undaria was to become officially unmanaged in parts of its non‐native range, the presence of a highly productive, habitat former with commercial value and a broad ecological niche, could have significant economic and even environmental benefit. How science and policy reacts to the continued invasion of Undaria may influence how similar marine invasive species are handled in the future.     

生物入侵: 中国学者面临的转化生态学机遇与挑战

今天,乘坐飞机长途旅行已是一件太普通不过的事情了,我们可以在不到一天的时间内到达世界的任何大城市.在我们的孩提时代,世界大城市是‘那么的遥不可及,而今只不过是邻近的"小村落"而已,世界变得越来越小.近代技术革新所带来的空间上的相对变小不仅给我们人类的各种交往和商业活动带来了便捷,而且也有助于生物物种越过自然的物理屏障,进行快速和低风险的长距离扩散,从而重塑物种的分布区.从这种意义上来说.全球化就像地质事件一样,对物种的分布区产生着深刻的影响.就全球范围来看,由人类有意或无意"嫁到"新的地理分布区的物种总数可能已达到50万种之多(Pimentel et a1..2001).     

Animal ecology meets GPS-based radiotelemetry: a perfect storm of opportunities and challenges

Global positioning system (GPS) telemetry technology allows us to monitor and to map the details of animal movement, securing vast quantities of such data even for highly cryptic organisms. We envision an exciting synergy between animal ecology and GPS-based radiotelemetry, as for other examples of new technologies stimulating rapid conceptual advances, where research opportunities have been paralleled by technical and analytical challenges. Animal positions provide the elemental unit of movement paths and show where individuals interact with the ecosystems around them. We discuss how knowing where animals go can help scientists in their search for a mechanistic understanding of key concepts of animal ecology, including resource use, home range and dispersal, and population dynamics. It is probable that in the not-so-distant future, intense sampling of movements coupled with detailed information on habitat features at a variety of scales will allow us to represent an animal''s cognitive map of its environment, and the intimate relationship between behaviour and fitness. An extended use of these data over long periods of time and over large spatial scales can provide robust inferences for complex, multi-factorial phenomena, such as meta-analyses of the effects of climate change on animal behaviour and distribution.     

Molecular ecology studies of species radiations: current research gaps,opportunities and challenges

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro‐ and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high‐profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species‐rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site‐associated DNA sequencing (RAD‐seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole‐genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted (‘capture’) resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.