Using ecological networks to answer questions in global biogeography and ecology

Ecological networks have classically been studied at site and landscape scales, yet recent efforts have been made to collate these data into global repositories. This offers an opportunity to integrate and upscale knowledge about ecological interactions from local to global scales to gain enhanced insights from the mechanistic information provided by these data. By drawing on existing research investigating patterns in ecological interactions at continental to global scales, we show how data on ecological networks, collected at appropriate scales, can be used to generate an improved understanding of many aspects of ecology and biogeography—for example, species distribution modelling, restoration ecology and conservation. We argue that by understanding the patterns in the structure and function of ecological networks across scales, it is possible to enhance our understanding of the natural world.     

To share or not to share: Incentivizing data sharing in life science communities

Most scientists recognize the importance of sharing data online in an open fashion. Nonetheless, many studies have documented the concerns that accompany data sharing activities, including loss of credit or IP, misuse and the time needed to curate interoperable data. To this end, discussions around data sharing often identify incentives that could potentially ameliorate these disincentivising concerns. Nonetheless, current Open Data discussions often rely on evidence‐based studies to identify the disincentives to overcome. This results in highly specific and directed interventions. In contrast, this paper offers a different interpretation of these concerns. To do so, it makes use of the Thomas Theorem which suggests that: “If men define situations as real, they are real in their consequences”. Using empirical evidence from sub‐Saharan African (bio)chemistry laboratories, this paper illustrates how individual perceptions of research environments – whether associated with evidence or not – are highly influential in shaping data sharing practices. It concludes with the suggestion that discussion on incentivising data sharing amongst scientific communities need to take a broader set of concerns into account and offer a more creative approach to ameliorating environmental disincentives.     

IRBAS: An online database to collate,analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide

Key questions dominating contemporary ecological research and management concern interactions between biodiversity, ecosystem processes, and ecosystem services provision in the face of global change. This is particularly salient for freshwater biodiversity and in the context of river drying and flow‐regime change. Rivers that stop flowing and dry, herein intermittent rivers, are globally prevalent and dynamic ecosystems on which the body of research is expanding rapidly, consistent with the era of big data. However, the data encapsulated by this work remain largely fragmented, limiting our ability to answer the key questions beyond a case‐by‐case basis. To this end, the Intermittent River Biodiversity Analysis and Synthesis (IRBAS; http://irbas.cesab.org ) project has collated, analyzed, and synthesized data from across the world on the biodiversity and environmental characteristics of intermittent rivers. The IRBAS database integrates and provides free access to these data, contributing to the growing, and global, knowledge base on these ubiquitous and important river systems, for both theoretical and applied advancement. The IRBAS database currently houses over 2000 data samples collected from six countries across three continents, primarily describing aquatic invertebrate taxa inhabiting intermittent rivers during flowing hydrological phases. As such, there is room to expand the biogeographic and taxonomic coverage, for example, through addition of data collected during nonflowing and dry hydrological phases. We encourage contributions and provide guidance on how to contribute and access data. Ultimately, the IRBAS database serves as a portal, storage, standardization, and discovery tool, enabling collation, synthesis, and analysis of data to elucidate patterns in river biodiversity and guide management. Contribution creates high visibility for datasets, facilitating collaboration. The IRBAS database will grow in content as the study of intermittent rivers continues and data retrieval will allow for networking, meta‐analyses, and testing of generalizations across multiple systems, regions, and taxa.     

多源数据融合技术在汶川地震生态环境影响应急评估中的应用

在实施汶川地震生态环境影响应急评估工作过程中,考虑到时间紧、范围大的现实情况,对空间数据处理技术与方法上进行了深入探索,成功地采用多源数据集成与融合技术,将不同传感器、不同空间分辨率、光谱分辨率、时间分辨率和不同格式的数据进行了集成与融合,大大提高了遥感影像的有效覆盖范围和灾害信息判读精度,快速、全面地实现了地震灾害对生态环境影响的初步评估,探索出应对巨灾后生态环境遥感监测与评估的基本方法与技术。最后,建议我国要加强生态环境本底数据库建设,完善部门间数据共享机制,促进多源数据集成与融合技术的推广与应用,为更好应对未来的生态灾难做准备。     

Ecobat: An online resource to facilitate transparent,evidence‐based interpretation of bat activity data

Acoustic surveys of bats are one of the techniques most commonly used by ecological practitioners. The results are used in Ecological Impact Assessments to assess the likely impacts of future developments on species that are widely protected in law, and to monitor developments’ postconstruction. However, there is no standardized methodology for analyzing or interpreting these data, which can make the assessment of the ecological value of a site very subjective. Comparisons of sites and projects are therefore difficult for ecologists and decision‐makers, for example, when trying to identify the best location for a new road based on relative bat activity levels along alternative routes. Here, we present a new web‐based, data‐driven tool, Ecobat, which addresses the need for a more robust way of interpreting ecological data. Ecobat offers users an easy, standardized, and objective method for analyzing bat activity data. It allows ecological practitioners to compare bat activity data at regional and national scales and to generate a numerical indicator of the relative importance of a night's worth of bat activity. The tool is free and open‐source; because the underlying algorithms are already developed, it could easily be expanded to new geographical regions and species. Data donation is required to ensure the robustness of the analyses; we use a positive feedback mechanism to encourage ecological practitioners to share data by providing in return high quality, contextualized data analysis, and graphical visualizations for direct use in ecological reports.     

Tackling unresolved questions in forest ecology: The past and future role of simulation models

1. Understanding the processes that shape forest functioning, structure, and diversity remains challenging, although data on forest systems are being collected at a rapid pace and across scales. Forest models have a long history in bridging data with ecological knowledge and can simulate forest dynamics over spatio‐temporal scales unreachable by most empirical investigations.
2. We describe the development that different forest modelling communities have followed to underpin the leverage that simulation models offer for advancing our understanding of forest ecosystems.
3. Using three widely applied but contrasting approaches – species distribution models, individual‐based forest models, and dynamic global vegetation models – as examples, we show how scientific and technical advances have led models to transgress their initial objectives and limitations. We provide an overview of recent model applications on current important ecological topics and pinpoint ten key questions that could, and should, be tackled with forest models in the next decade.
4. Synthesis. This overview shows that forest models, due to their complementarity and mutual enrichment, represent an invaluable toolkit to address a wide range of fundamental and applied ecological questions, hence fostering a deeper understanding of forest dynamics in the context of global change.

Forest models can help understanding the processes that shape forest functioning, structure and diversity, since they can can simulate forest dynamics over spatio‐temporal scales unreachable by most empirical investigations. Here we describe the development of three widely applied but contrasting forest mo−delling approaches — species distribution models, individual‐based models and dynamic global vegetation models. We provide an overview of recent model applications and pinpoint ten key questions that could, and should, be tackled with forest models in the next decade.     

Beyond trophic morphology: stable isotopes reveal ubiquitous versatility in marine turtle trophic ecology

The idea that interspecific variation in trophic morphology among closely related species effectively permits resource partitioning has driven research on ecological radiation since Darwin first described variation in beak morphology among Geospiza. Marine turtles comprise an ecological radiation in which interspecific differences in trophic morphology have similarly been implicated as a pathway to ecopartition the marine realm, in both extant and extinct species. Because marine turtles are charismatic flagship species of conservation concern, their trophic ecology has been studied intensively using stable isotope analyses to gain insights into habitat use and diet, principally to inform conservation management. This legion of studies provides an unparalleled opportunity to examine ecological partitioning across numerous hierarchical levels that heretofore has not been applied to any other ecological radiation. Our contribution aims to provide a quantitative analysis of interspecific variation and a comprehensive review of intraspecific variation in trophic ecology across different hierarchical levels marshalling insights about realised trophic ecology derived from stable isotopes. We reviewed 113 stable isotope studies, mostly involving single species, and conducted a meta‐analysis of data from adults to elucidate differences in trophic ecology among species. Our study reveals a more intricate hierarchy of ecopartitioning by marine turtles than previously recognised based on trophic morphology and dietary analyses. We found strong statistical support for interspecific partitioning, as well as a continuum of intraspecific trophic sub‐specialisation in most species across several hierarchical levels. This ubiquity of trophic specialisation across many hierarchical levels exposes a far more complex view of trophic ecology and resource‐axis exploitation than suggested by species diversity alone. Not only do species segregate along many widely understood axes such as body size, macrohabitat, and trophic morphology but the general pattern revealed by isotopic studies is one of microhabitat segregation and variation in foraging behaviour within species, within populations, and among individuals. These findings are highly relevant to conservation management because they imply ecological non‐exchangeability, which introduces a new dimension beyond that of genetic stocks which drives current conservation planning. Perhaps the most remarkable finding from our data synthesis is that four of six marine turtle species forage across several trophic levels. This pattern is unlike that seen in other large marine predators, which forage at a single trophic level according to stable isotopes. This finding affirms suggestions that marine turtles are robust sentinels of ocean health and likely stabilise marine food webs. This insight has broader significance for studies of marine food webs and trophic ecology of large marine predators. Beyond insights concerning marine turtle ecology and conservation, our findings also have broader implications for the study of ecological radiations. Particularly, the unrecognised complexity of ecopartitioning beyond that predicted by trophic morphology suggests that this dominant approach in adaptive radiation research likely underestimates the degree of resource overlap and that interspecific disparities in trophic morphology may often over‐predict the degree of realised ecopartitioning. Hence, our findings suggest that stable isotopes can profitably be applied to study other ecological radiations and may reveal trophic variation beyond that reflected by trophic morphology.     

Integrating models with data in ecology and palaeoecology: advances towards a model-data fusion approach

It is increasingly being recognized that global ecological research requires novel methods and strategies in which to combine process-based ecological models and data in cohesive, systematic ways. Model-data fusion (MDF) is an emerging area of research in ecology and palaeoecology. It provides a new quantitative approach that offers a high level of empirical constraint over model predictions based on observations using inverse modelling and data assimilation (DA) techniques. Increasing demands to integrate model and data methods in the past decade has led to MDF utilization in palaeoecology, ecology and earth system sciences. This paper reviews key features and principles of MDF and highlights different approaches with regards to DA. After providing a critical evaluation of the numerous benefits of MDF and its current applications in palaeoecology (i.e., palaeoclimatic reconstruction, palaeovegetation and palaeocarbon storage) and ecology (i.e. parameter and uncertainty estimation, model error identification, remote sensing and ecological forecasting), the paper discusses method limitations, current challenges and future research direction. In the ongoing data-rich era of today's world, MDF could become an important diagnostic and prognostic tool in which to improve our understanding of ecological processes while testing ecological theory and hypotheses and forecasting changes in ecosystem structure, function and services.     

From information to understanding: the role of model organism databases in comparative and functional genomics

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.     

Cooperative breeding in birds: the role of ecology

Theory predicts that cooperative breeding should only occurin species in which certain individuals are constrained frombreeding independently by some peculiarity of the species' ecology.Here, we use comparative methods to examine the role of variationin ecology in explaining differences between taxa in the frequencyof cooperative breeding. We address three questions. First,does the frequency of cooperative breeding vary at just one phylogeneticlevel, or across several levels? Second, are differences inthe frequency of cooperative breeding among closely-relatedspecies correlated with ecology? Last, are ecological differencesbetween ancient lineages important in predisposing certain lineagesto cooperative breeding? We find that variation in the frequencyof cooperative breeding occurs across all phylogenetic levels,with 40% among families and 60% within families. Also, variationin the frequency of cooperative breeding between closely related speciesis associated with ecological differences. However, differencesin the frequency of cooperative breeding among more ancientlineages are not correlated with differences in ecology. Together,our results suggest that cooperative breeding is not due toany single factor, but is a two step-process: life-history predispositionand ecological facilitation. Low annual mortality predisposescertain lineages to cooperative breeding. Subsequently, changesin ecology facilitate the evolution of cooperative breedingwithin these predisposed lineages. The key ecological changesappear to be sedentariness and living in a relatively invariableand warm climate. Thus, although ecological variation is notthe most important factor in predisposing lineages to cooperativebreeding, it is important in determining exactly which speciesor populations in a predisposed lineage will adopt cooperativebreeding.     

国家微生物科学数据中心数据资源服务与应用

作为解决生命领域复杂科学问题的关键要素以及驱动科学发现与决策的基础资源,微生物科学数据资源已成为国家的重要战略资源。国家微生物科学数据中心(https://nmdc.cn/)的建设使得海量微生物数据资源可以得到有效的整理整合和开放共享,这对于微生物资源的研究、利用和可持续发展都起着至关重要的作用。本文从核心资源、服务内容、功能特色等多方面总结了国家微生物科学数据中心平台的建设进展,并提出了面向微生物领域科研及产业用户的应用实践。     

Managing biodiversity data within the context of climate change: towards best practice

Decision makers, planners and researchers have identified the need to assess the effects of climate change on biodiversity, resulting in extensive research across a number of fields. The availability of comprehensive, accurate and relevant data is central to undertaking effective research. However, the quality and availability of biodiversity information is substantially determined by current and historical data collection strategies. If researchers and planners are to make effective use of existing and future investments in biodiversity information, a strategic approach should be taken in identifying and implementing best practice information management. This paper discusses ways to improve institutional support for information management and increase the availability of quality information. The paper reviews the most common areas of climate change and biodiversity research, and identifies best practices in information management, focusing on data used within biodiversity and climate change analyses.     

Contemplating the future: Acting now on long‐term monitoring to answer 2050's questions

In 2050, which aspects of ecosystem change will we regret not having measured? Long‐term monitoring plays a crucial part in managing Australia's natural environment because time is a key factor underpinning changes in ecosystems. It is critical to start measuring key attributes of ecosystems – and the human and natural process affecting them – now, so that we can track the trajectory of change over time. This will facilitate informed choices about how to manage ecological changes (including interventions where they are required) and promote better understanding by 2050 of how particular ecosystems have been shaped over time. There will be considerable value in building on existing long‐term monitoring programmes because this can add significantly to the temporal depth of information. The economic and social processes driving change in ecosystems are not identical in all ecosystems, so much of what is monitored (and the means by which it is monitored) will most likely target specific ecosystems or groups of ecosystems. To best understand the effects of ecosystem‐specific threats and drivers, monitoring also will need to address the economic and social factors underpinning ecosystem‐specific change. Therefore, robust assessments of the state of Australia's environment will be best achieved by reporting on the ecological performance of a representative sample of ecosystems over time. Political, policy and financial support to implement appropriate ecosystem‐specific monitoring is a perennial problem. We suggest that the value of ecological monitoring will be demonstrable, when plot‐based monitoring data make a unique and crucial contribution to Australia's ability to produce environmental accounts, environmental reports (e.g. the State of the Environment, State of the Forests) and to fulfilling reporting obligations under international agreements, such as the Convention on Biological Diversity. This paper suggests what must be done to meet Australia's ecological information needs by 2050.     

Think globally,measure locally: The MIREN standardized protocol for monitoring plant species distributions along elevation gradients

Climate change and other global change drivers threaten plant diversity in mountains worldwide. A widely documented response to such environmental modifications is for plant species to change their elevational ranges. Range shifts are often idiosyncratic and difficult to generalize, partly due to variation in sampling methods. There is thus a need for a standardized monitoring strategy that can be applied across mountain regions to assess distribution changes and community turnover of native and non‐native plant species over space and time. Here, we present a conceptually intuitive and standardized protocol developed by the Mountain Invasion Research Network (MIREN) to systematically quantify global patterns of native and non‐native species distributions along elevation gradients and shifts arising from interactive effects of climate change and human disturbance. Usually repeated every five years, surveys consist of 20 sample sites located at equal elevation increments along three replicate roads per sampling region. At each site, three plots extend from the side of a mountain road into surrounding natural vegetation. The protocol has been successfully used in 18 regions worldwide from 2007 to present. Analyses of one point in time already generated some salient results, and revealed region‐specific elevational patterns of native plant species richness, but a globally consistent elevational decline in non‐native species richness. Non‐native plants were also more abundant directly adjacent to road edges, suggesting that disturbed roadsides serve as a vector for invasions into mountains. From the upcoming analyses of time series, even more exciting results can be expected, especially about range shifts. Implementing the protocol in more mountain regions globally would help to generate a more complete picture of how global change alters species distributions. This would inform conservation policy in mountain ecosystems, where some conservation policies remain poorly implemented.     

宏观生态系统科学整合研究的多学科知识融合及其技术途径

综合认识大尺度的宏观生态系统结构功能、空间变异和动态演变的过程机理和模式机制,实现对生态系统变化及其对人类福祉影响的定量模拟、科学评估和预测预警,服务生态系统的利用保护及调控管理,是当代宏观生态系统科学的重要发展方向,正在孕育并形成大尺度的宏观生态系统科学整合生态学(IEMES)研究新领域.本研究通过对宏观生态系统科学...