Long-Term Ecological Research in a Human-Dominated World

Spatial and temporal non-stationarity in long-term population dynamics of over-wintering birds of North America

Understanding population changes across long time scales and at fine spatiotemporal resolutions is important for confronting a broad suite of conservation challenges. However, this task is hampered by a lack of quality long-term census data for multiple species collected across large geographic regions. Here, we used century-long (1919-2018) data from the Audubon Christmas Bird Count (CBC) survey to assess population changes in over 300 avian species in North America and evaluate their temporal non-stationarity. To estimate population sizes across the entire century, we employed a Bayesian hierarchical model that accounts for species detection probabilities, variable sampling effort, and missing data. We evaluated population trends using generalized additive models (GAMs) and assessed temporal non-stationarity in the rate of population change by extracting the first derivatives from the fitted GAM functions. We then summarized the population dynamics across species, space, and time using a non-parametric clustering algorithm that categorized individual population trends into four distinct trend clusters. We found that species varied widely in their population trajectories, with over 90% of species showing a considerable degree of spatial and/or temporal non-stationarity, and many showing strong shifts in the direction and magnitude of population trends throughout the past century. Species were roughly equally distributed across the four clusters of population trajectories, although grassland, forest, and desert specialists more commonly showed declining trends. Interestingly, for many species, region-wide population trends often differed from those observed at individual sites, suggesting that conservation decisions need to be tailored to fine spatial scales. Together, our results highlight the importance of considering spatial and temporal non-stationarity when assessing long-term population changes. More generally, we demonstrate the promise of novel statistical techniques for improving the utility and extending the temporal scope of existing citizen science datasets.

A comprehensive but practical methodology for selecting biological indicators for long-term monitoring

The selection of the many biological indicators described in scientific literature is rarely based on systematic or clear-cut processes, and often takes into account only a single or very few taxa, or even disregards the complex interactions that exist between the components of biodiversity. In certain cases, the particular context of a site–for example in the Mediterranean Basin–makes it difficult to apply the choice of indicators to other regions proposed in the literature. Therefore, the selection of appropriate methodologies for generating relevant indicators for a particular site is of crucial importance. Here, we present a simple quantitative methodology capable of incorporating multidisciplinary information for assessing and selecting appropriate methods and indicators for monitoring local biodiversity. The methodology combines several ecological levels (species, habitats, processes, and ecosystem disturbances), and embraces biological interactions and common functional guilds (detritivores, producers, herbivores, and carnivores). We followed an iterative selection procedure consisting of five phases: 1) collection focal area useful information; 2) classification of this information into interrelated datasets; 3) assessment and selection of the relevant components using a quantitative relevance index; 4) the adding of taxonomic, physiognomic and functional similarities to the relevant components; and 5) the quantitative selection of the priority indicators in the study area. To demonstrate the potential of this methodology, we took as a case study the biodiversity components and their ecological interactions present in a protected area. We show that our methodology can help select appropriate local and long-term indicators, reduce the number of components required for thorough biodiversity monitoring, and underline the importance of ecological processes.

OUP accepted manuscript

In this article marking the 40th anniversary of the US National Science Foundation's Long Term Ecological Research (LTER) Network, we describe how a long-term ecological research perspective facilitates insights into an ecosystem's response to climate change. At all 28 LTER sites, from the Arctic to Antarctica, air temperature and moisture variability have increased since 1930, with increased disturbance frequency and severity and unprecedented disturbance types. LTER research documents the responses to these changes, including altered primary production, enhanced cycling of organic and inorganic matter, and changes in populations and communities. Although some responses are shared among diverse ecosystems, most are unique, involving region-specific drivers of change, interactions among multiple climate change drivers, and interactions with other human activities. Ecosystem responses to climate change are just beginning to emerge, and as climate change accelerates, long-term ecological research is crucial to understand, mitigate, and adapt to ecosystem responses to climate change.

Discrimination of Spatial Distribution of Aquatic Organisms in a Coastal Ecosystem Using eDNA

The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.

Biodiversity responds to increasing climatic extremes in a biome-specific manner

An unprecedented rate of global environmental change is predicted for the next century. The response to this change by ecosystems around the world is highly uncertain. To address this uncertainty, it is critical to understand the potential drivers and mechanisms of change in order to develop more reliable predictions. Australia's Long Term Ecological Research Network (LTERN) has brought together some of the longest running (10-60years) continuous environmental monitoring programs in the southern hemisphere. Here, we compare climatic variables recorded at five LTERN plot network sites during their period of operation and place them into the context of long-term climatic trends. Then, using our unique Australian long-term datasets (total 117 survey years across four biomes), we synthesize results from a series of case studies to test two hypotheses: 1) extreme weather events for each plot network have increased over the last decade, and; 2) trends in biodiversity will be associated with recent climate change, either directly or indirectly through climate-mediated disturbance (wildfire) responses. We examined the biodiversity responses to environmental change for evidence of non-linear behavior. In line with hypothesis 1), an increase in extreme climate events occurred within the last decade for each plot network. For hypothesis 2), climate, wildfire, or both were correlated with biodiversity responses at each plot network, but there was no evidence of non-linear change. However, the influence of climate or fire was context-specific. Biodiversity responded to recent climate change either directly or indirectly as a consequence of changes in fire regimes or climate-mediated fire responses. A national long-term monitoring framework allowed us to find contrasting species abundance or community responses to climate and disturbance across four of the major biomes of Australia, highlighting the need to establish and resource long-term monitoring programs across representative ecosystem types, which are likely to show context-specific responses.

Decadal phytoplankton dynamics in response to episodic climatic disturbances in a subtropical deep freshwater ecosystem

Information of the decadal timescale effects of episodic climatic disturbances (i.e., typhoons) on phytoplankton in freshwater ecosystems have received less attention and fewer seasonal evaluations partly due to the lack of long-term time-series monitoring data in typhoon prevailing areas. Through field observations of a total 36 typhoon cases in a subtropical deep freshwater ecosystem in the period of 2005-2014, we quantified phytoplankton biomass, production and growth rate in response to meteorological and hydrological changes in the weeks before, during and after typhoons between summer and autumn, and also investigated the effects of typhoon characteristics on the aforementioned phytoplankton responses. The results showed that phytoplankton exposed to typhoon disturbances generally exhibited an increasing trend over the weeks before, during and after typhoons in summer but varied in autumn. The correlations and multivariate regressions showed different contributions of meteorological and hydrological variables to individual phytoplankton responses before, during and after typhoons between seasons. The post-typhoon weeks (i.e., within two weeks after a typhoon had passed) were especially important for the timeline of phytoplankton increases and with a detectable seasonal variation that the chlorophyll a concentration significantly increased in autumn whereas both primary production and growth rate were associated with significant changes in summer. Additionally, phytoplankton responses during the post-typhoon weeks were significantly different between discrete or continuous types of typhoon events. Our work illustrated the fact that typhoons did influence phytoplankton responses in the subtropical deep freshwater ecosystem and typhoon passages in summer and autumn affected the phytoplankton dynamics differently. Nevertheless, sustained and systematic monitoring in order to advance our understanding of the role of typhoons between seasons in the modulation of phytoplankton productivity and functioning is required because such episodic climatic disturbances are projected to have intense magnitude and inconsistent frequency under 21st century climate change.

Discovering hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems

Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft‐bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4‐fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.

The promise and peril of intensive-site-based ecological research: insights from the Hubbard Brook ecosystem study

Ecological research is increasingly concentrated at particular locations or sites. This trend reflects a variety of advantages of intensive, site-based research, but also raises important questions about the nature of such spatially delimited research: how well does site based research represent broader areas, and does it constrain scientific discovery? We provide an overview of these issues with a particular focus on one prominent intensive research site: the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA. Among the key features of intensive sites are: long-term, archived data sets that provide a context for new discoveries and the elucidation of ecological mechanisms; the capacity to constrain inputs and parameters, and to validate models of complex ecological processes; and the intellectual cross-fertilization among disciplines in ecological and environmental sciences. The feasibility of scaling up ecological observations from intensive sites depends upon both the phenomenon of interest and the characteristics of the site. An evaluation of deviation metrics for the HBEF illustrates that, in some respects, including sensitivity and recovery of streams and trees from acid deposition, this site is representative of the Northern Forest region, of which HBEF is a part. However, the mountainous terrain and lack of significant agricultural legacy make the HBEF among the least disturbed sites in the Northern Forest region. Its relatively cool, wet climate contributes to high stream flow compared to other sites. These similarities and differences between the HBEF and the region can profoundly influence ecological patterns and processes and potentially limit the generality of observations at this and other intensive sites. Indeed, the difficulty of scaling up may be greatest for ecological phenomena that are sensitive to historical disturbance and that exhibit the greatest spatiotemporal variation, such as denitrification in soils and the dynamics of bird communities. Our research shows that end member sites for some processes often provide important insights into the behavior of inherently heterogeneous ecological processes. In the current era of rapid environmental and biological change, key ecological responses at intensive sites will reflect both specific local drivers and regional trends.

Consequence of altered nitrogen cycles in the coupled human and ecological system under changing climate: The need for long-term and site-based research

Anthropogenically derived nitrogen (N) has a central role in global environmental changes, including climate change, biodiversity loss, air pollution, greenhouse gas emission, water pollution, as well as food production and human health. Current understanding of the biogeochemical processes that govern the N cycle in coupled human-ecological systems around the globe is drawn largely from the long-term ecological monitoring and experimental studies. Here, we review spatial and temporal patterns and trends in reactive N emissions, and the interactions between N and other important elements that dictate their delivery from terrestrial to aquatic ecosystems, and the impacts of N on biodiversity and human society. Integrated international and long-term collaborative studies covering research gaps will reduce uncertainties and promote further understanding of the nitrogen cycle in various ecosystems.

Integrative invasion science: model systems, multi-site studies, focused meta-analysis and invasion syndromes

Invasion science is a very active subdiscipline of ecology. However, some scientists contend that theoretical integration has been limited and that predictive power remains weak. This paper, focusing on plants, proposes a new multi-pronged research strategy that builds on recent advances in invasion science. More intensive studies on particular model organisms and ecosystems are needed to improve our understanding of the full suite of interacting factors that influence invasions ('model system research'). At the same time, comparative studies across many study systems are essential for unravelling the context-dependencies of insights that emerge from particular studies ('multi-site studies'); and quantitative synthesis based on large datasets should be constrained to well-defined theoretical domains ('focused meta-analysis'). We also suggest ways for better integration of information about species biology and ecosystem characteristics ('invasion syndromes'). We expect that a resulting theory of invasions will need to be conceived as a somewhat heterogeneous conglomerate of elements of varying generality and predictive power: laws that apply to well-specified domains, general concepts and theoretical frameworks that can guide thinking in research and management, and in-depth knowledge about the drivers of particular invasions.

Techniques for optimising long-term, large-scale capture–mark–resighting raptor studies: climb hard, band fast

Context Efficiency of large-scale capture–mark–recapture (CMR) studies can be improved by developing accurate methods for predicting the window of opportunity in which banding can occur. Aims This research aimed to investigate potential efficiency improvements in a long-term CMR raptor study. The research focussed on: (1) developing selection processes for adopting CMR protocols; (2) testing methods for increasing the number of nestlings successfully banded; and (3) assessing the efficacy of visual identification (VID) bands for collecting re-sight data. Methods Ten selection criteria were developed into a robust CMR-technique selection process and used to assess marking techniques commonly applied to birds. Optimising banding effort by predicting banding dates using two different techniques a priori and a posteriori were tested against a traditional approach to the timing of banding. The cost (in time) to collect resight data at an active nest site was also measured. Key results The CMR selection criteria and parameters provided a transparent selection process and scored metal VID bands the highest for the study design. This provided individual recognition of marked birds up to the expected life-span of 14 years. Both techniques for predicting banding dates improved the proportion of whole clutches banded by 40%. The average time to identify both peregrine falcon adults of a breeding pair wearing VID bands was 30 min. Conclusions The two methods described here for predicting preferred banding dates are of particular value as efficient approaches to banding large numbers of nestlings are key to the success of CMR studies. All of the methods developed in this research can be applied to CMR studies of almost any bird species with a predictable seasonal breeding system. Implications Optimisation and cost effectiveness of CMR studies for seasonal breeding birds can be significantly improved by accurately predicting the window of opportunity in which banding of nestlings can be carried out, and also utilising VID colour bands for rapid collection of recapture data.