Ecological Archives Research Articles

The marriage between stable isotope ecology and plant metabolomics - new perspectives for metabolic flux analysis and the interpretation of ecological archives.

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.

Arctic bivalve dead-shell assemblages as high temporal- and spatial- resolution archives of ecological regime change in response to climate change

Abstract A 15-year time-series of data on benthic community response to rapid climate change at a biomass ‘hotspot’ in the northern Bering Sea, Alaska, provides an exceptional opportunity to evaluate naturally occurring molluscan dead-shell assemblages as ecological archives. We find that, at five middle-shelf stations censused annually from 2000 to 2014, dead-shell assemblages collected in 2014 are dominated by obligate deposit-feeding Nuculanidae bivalves as opposed to the other families in that guild or the facultative deposit-feeding Tellinidae that dominate the most recent living bivalve assemblages, thus correctly detecting the location and direction of known ecological changes. However, live–dead contrast is significant where the bivalve biomass and abundance has declined over time, and muted where bivalve abundances, and therefore shell input, increased, underscoring the general danger of assuming constant shell input. We also find that proportional abundance-based measures are best suited for detecting benthic response to climate change. Combined with preliminary results from shell age-dating, these results indicate that dead-shell assemblages provide a short-lived but compositionally faithful ecological memory well-suited for detecting recent site- and habitat-level ecological change under cold-water conditions. With marine regime change suspected to now be underway throughout the Arctic, molluscan dead-shell assemblages should become an integral part of efforts to detect transitioning regions.

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment.

Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes within diverse LMH guilds are difficult to pinpoint, and the magnitude and even direction of these effects often depends on environmental context. Since 2008, we have maintained the Ungulate Herbivory Under Rainfall Uncertainty (UHURU) experiment, a series of size-selective LMH exclosures replicated across a rainfall/productivity gradient in a semiarid Kenyan savanna. The goals of the UHURU experiment are to measure the effects of removing successively smaller size classes of LMH (mimicking the process of size-biased extirpation) and to establish how these effects are shaped by spatial and temporal variation in rainfall. The UHURU experiment comprises three LMH-exclusion treatments and an unfenced control, applied to nine randomized blocks of contiguous 1-ha plots (n=36). The fenced treatments are MEGA (exclusion of megaherbivores, elephant and giraffe), MESO (exclusion of herbivores ≥40 kg), and TOTAL (exclusion of herbivores ≥5kg). Each block is replicated three times at three sites across the 20-km rainfall gradient, which has fluctuated over the course of the experiment. The first 5 years of data were published previously (Ecological Archives E095-064) and have been used in numerous studies. Since that publication, we have (1) continued to collect data following the original protocols, (2) improved the taxonomic resolution and accuracy of plant and small-mammal identifications, and (3) begun collecting several new data sets. Here, we present updated and extended raw data from the first 12 years of the UHURU experiment (2008-2019). Data include daily rainfall data throughout the experiment; annual surveys of understory plant communities; annual censuses of woody-plant communities; annual measurements of individually tagged woody plants; monthly monitoring of flowering and fruiting phenology; every-other-month small-mammal mark-recapture data; and quarterly large-mammal dung surveys. There are no copyright restrictions; notification of when and how data are used is appreciated and users of UHURU data should cite this data paper when using the data.

Combined use of environmental and spectral variables with vegetation archives for large-scale modeling of grassland habitats

Grassland habitats provide many ecosystem services but are threatened by agricultural intensification and urbanization. While the lack of accurate and comprehensive inventories at the national scale makes them difficult to manage, advances in spatial modeling using open remote sensing data and open-source software, as well as the increasing use of ecological archives, provide new perspectives for mapping natural habitats. In this context, this study evaluated the contribution of spectral and environmental variables to discriminate and then map grassland habitats throughout France. To this end, 92 spectral variables derived from moderate-resolution imaging spectroradiometer data, 19 bioclimatic variables derived from WorldClim data, 4 topographic variables derived from the European Union Digital Elevation Model (DEM), and 8 soil variables derived from SoilGrids data were combined at a spatial resolution of 250 m. Reference plots that characterized 6 and 21 grassland ecosystems at European Nature Information System (EUNIS) levels 2 (broad habitats) and 3 (habitats), respectively, were collected from vegetation archives. We first performed descriptive analysis that included habitat description, ordination, and pairwise separability. We then performed predictive analysis of grassland habitats using a cross-validated random forest model that included a spatial constraint. While environmental and spectral variables characterized most grassland habitats well and consistently, some confusion occurred between habitats with similar abiotic conditions. The main grassland habitat types were correctly mapped at EUNIS level 2 ( F1 score = 0.68), but not at EUNIS level 3 ( F1 score = 0.52). In addition, the two variables that contributed most to the model were the near-infrared spectral band in spring and the minimum temperature of the coldest month. The model’s prediction at EUNIS level 2 for mainland France provides the map of grassland habitats at a new spatial scale.

Nonlinear relationships between phytoplankton nutrient utilization traits and environmental factors

Relationships between the functional traits of phytoplankton and environmental factors remain insufficiently explored. However, these dependencies could be very useful for trait-based ecological modelling of phytoplankton communities. The purpose of this study is to estimate possible connections between nutrient utilization traits of marine phytoplankton, cell volume, temperature of the experiment, irradiance and taxonomic category of the species collected in Ecological Archives E096–202 (Edwards et al., 2015).The search for patterns was made using the author's technique of polynomial multilayered neural network (NN) building. The optimal set of neurons' connections with the preceding layer of the network was obtained by means of a genetic algorithm run for each neuron. This approach gave good results given the sparse data sets and small samples. Categorical predictor “taxonomic group” was parameterized by an integer.We found approximations for maximal uptake and growth rates, half-saturation constants, maximum and minimum nutrients quotas as nonlinear functions of cell volume, taxon number, temperature and irradiance. Mean-square errors were lower than the errors in respective relationships to the cell volume only. These functions were used to fill in the gaps in the ecological archive. Verification of the obtained relationships was performed using an energy balance model and new data on nutrient utilization traits not used for their estimation.

Environmental Status of a City Based on Heavy Metal Content of the Tree-Rings of Urban Trees: Case Study at Szeged, Hungary

Abstract Urban vegetation, especially urban trees could act as ecological archives, as they reflect various elements of their environment. The main aim of the study is to evaluate the spatial and temporal variations of environmental conditions in the city of Szeged (Hungary) based on long-term monitoring of the heavy metal content of tree-rings (soft wood). In general, the living conditions of the urban trees (and other organisms as well) at Szeged was the worst in 2001/05, when the heavy metal pollution was the greatest, therefore the biomass production of the sampled trees decreased. Fortunately, the environmental conditions became better, only there are some points in the industrial area, where the heavy metal pollution of the environment is gradually increases. The temporal change in lead pollution (considerable decline in 2013/17) could be explained by the obligatory usage of lead-free petrol since 1999 and the diversion of through-traffic from the town (2011). The introduction of unleaded petrol had delayed favourable results, as the dust particles containing lead probably circulated in the air for a while before they were gradually become fixed in the soil or they were washed out from the town during heavy rains. The cadmium pollution also declined after the traffic diversion, as it is connected to the usage of brake-linings. Whilst the lead and cadmium content of the tree-rings decreased during the studied decades, the trees accumulated increasing amount of zinc throughout the studied periods, as this element could be up-taken from the ground-water, as the larger the canopy of a tree the denser and deeper its root system is.

Historic log structures as ecological archives: A case study from eastern North America

Forests of eastern North America have undergone abrupt transformations over the last several centuries due to changing land use and climate. Researchers look to pre-settlement forests as a guide for forest restoration, though much of our understanding of composition and dynamics in pre-settlement forests is based on spatially restricted sediment records, few and fragmented old-growth stands in a narrow range of site types, and potentially biased historical documentation. Logs from historic structures hold information that may be useful to forest ecology in eastern North America, but before these records can be used, we must first establish where the logs originated, why they were selected over other trees, and what they can and cannot tell us about past forest ecology. Using a case study approach, I collected data from fifteen log structures in the central Appalachian region to compare construction site locations, species used, and mean diameter of logs through time to determine the ecological biases associated with human behavior in log structure construction. Construction site locations changed from valleys to mountains through time and the species used in construction shifted from Quercus alba to a mix of Quercus alba, Liriodendron tulipifera, Pinus strobus, and Castanea dentata over time. The diameter of logs used in construction were generally consistent through time, with an average basal diameter of 31.3cm (±4.7). Mean age of logs increased through time for Quercus species, regardless of log diameter. These results suggest the species used for structural logs were selected by their abundance at the location of construction but that as construction site locations and resource availability changed through time, the species used in construction changed as well. While there are biases and limitations of dendroecological data from historic structures, the results presented here demonstrate that structural log data provide greater replication during the early European immigration period, representation of upland (valley) forest sites, and establishment of chronologies for species that are not well represented in current tree-ring chronologies (e.g. Castanea dentata, Liriodendron tulipifera). These results suggest structural logs can benefit ecological research by filling the temporal, spatial, and species gaps in tree-ring chronologies not only for the central Appalachian region, but also for other areas in eastern North America.

Data sharing and reuse: What are the issues?

Data sharing and reuse: What are the issues?

Editorial

Close to 1400 manuscripts were submitted to Ecology in 2013. A group of editors looks over each submission to determine whether to send the manuscript out to review. Generally within a week authors are notified if their manuscripts will not go out for peer review, so they can recast their manuscripts for resubmission elsewhere. Occasionally we offer authors the option to transfer their manuscript as is to one of our sister journals (Ecosphere, Ecological Applications, or Ecological Monographs) when the editors judge it may find a niche there. Approximately 50% of the submissions were assigned in the past year to one of our 138 subject-matter editors, or to one of 57 guest editors. Potential reviewers are selected, and with the assistance of the Publications Office staff, about four people are contacted per manuscript in order to find two who are willing and able to review. In the past year 1643 people reviewed at least one manuscript for Ecology, and we are very grateful for their service. Authors of manuscripts sent out for review generally receive a decision in less than three months from submission. Thanks to our editors, authors, reviewers, and staff, (but most of all our authors), 300 manuscripts were published in the past year. Ecology's 2012 Journal Citation Impact Factor was 5.175 and the journal was ranked 15th out of 136 journals in the “Ecology” category. This places the journal among those at the forefront of influential journals in the field. Reports made up 15% of those published. Although the acceptance rate for Reports is somewhat lower than for regular articles (18% vs. 22%), we continue to encourage authors to submit short concise papers of exceptional impact and broad interest as Reports. From submission to publication, these papers are put on a fast track. They are prominently placed at the beginning of each issue and, more importantly, are all published on an Open Access platform to further enhance their visibility. Reports in general have twice as many full-text views as regular articles. Over 70% of articles published in Ecology in 2013 were submitted less than a year prior. For fast-tracked Reports, over 90% were published in an issue within one year of submission. Authors who opt to post their accepted manuscripts as a preprint (and 72% did in the past year) generally see their manuscripts posted within six months of original submission. With this option, manuscripts can be posted within a few days of acceptance. Subsequent publication in an issue brings with it the added value of careful copyediting of both text and graphics by our staff, but no longer do authors need to wait to get the word out about their research. We now ask our authors to provide full disclosure on statistical methods and any novel computer code used. It is essential to display the utmost transparency and replicability. Although Ecology is not requiring authors to archive all their raw data at this time, we are closely examining this issue as two of our sister journals (Ecological Monographs and now Ecological Applications) have made this a requirement and the NSF is contemplating making data archiving a requirement. We strongly encourage authors to utilize the capabilities of Ecological Archives, Dryad, and other data depositories to make their data publicly accessible.

Minutes of the ESA Governing Board, December 18‐19, 2012 Washington, DC

Minutes of the ESA Governing Board, December 18‐19, 2012 Washington, DC

ESA and Scientific Publishing—Past, Present, and Pathways to the Future

The leadership of the Society recognizes the potential of new trends toward open access (OA) publishing and the value of having the papers published in ESA journals freely accessible to the widest possible audience. However, because fully OA journals do not charge for subscriptions, applying such a model to the ESA journals would require major changes in the financial basis and the operations both of the ESA journals and of the Society’s activities more broadly. For most of our history, library subscriptions have paid for copyediting, typesetting, archiving, distribution, and other publication services, allowing us to keep charges to authors at a relatively low level. Subscription fees have also partially defrayed the costs of outreach, education, and scientific meetings, providing stable core funding to complement membership fees, the annual meeting, donations, and grants.

Common Errors in Ecological Data Sharing

<strong>Objectives:</strong> (1) to identify common errors in data organization and metadata completeness that would preclude a “reader” from being able to interpret and re-use the data for a new purpose; and (2) to develop a set of best practices derived from these common errors that would guide researchers in creating more usable data products that could be readily shared, interpreted, and used. <strong>Methods:</strong> We used directed qualitative content analysis to assess and categorize data and metadata errors identified by peer reviewers of data papers published in the Ecological Society of America’s (ESA) Ecological Archives. Descriptive statistics provided the relative frequency of the errors identified during the peer review process. <strong>Results:</strong> There were seven overarching error categories: Collection & Organization, Assure, Description, Preserve, Discover, Integrate, and Analyze/Visualize. These categories represent errors researchers regularly make at each stage of the Data Life Cycle. Collection & Organization and Description errors were some of the most common errors, both of which occurred in over 90% of the papers. <strong> Conclusions:</strong> Publishing data for sharing and reuse is error prone, and each stage of the Data Life Cycle presents opportunities for mistakes. The most common errors occurred when the researcher did not provide adequate metadata to enable others to interpret and potentially re-use the data. Fortunately, there are ways to minimize these mistakes through carefully recording all details about study context, data collection, QA/ QC, and analytical procedures from the beginning of a research project and then including this descriptive information in the metadata.

Food web including infectious agents for a California freshwater pond

This data set presents a comprehensive food web for Quick Pond, a northern California pond ecosystem. The web includes organisms from all regions of the pond (i.e., littoral, limnetic, profundal, and benthic zones) as well as terrestrial organisms that interact with the aquatic community or have aquatic life‐stages. The food web has three attributes that are often omitted from freshwater food webs: inclusion of (1) parasites and other infectious agents, (2) ontogenetic stages of most animals with complex life cycles, and (3) biomass information for many animals. Data on species presence was obtained over three years using field sampling techniques (i.e., seine‐ and D‐nets, stove‐pipe samplers, and visual encounter surveys) and laboratory examinations of free‐living organisms for infectious agents (primarily metazoan parasites, but also some microbes). We collected body size and biomass data for abundant aquatic animals &gt;1 mm and for trematode parasites, which were the most abundant parasitic group. Information on trophic interactions was obtained from direct observations and published literature sources. Within the food‐web data we include supporting information for each node on taxonomy, lifestyle, and residency; and for each link we include information on type of interaction and the source of evidence (e.g., direct observation, literature, or inferred). The food web contains 113 nodes, 1905 links, and 63 species. To facilitate comparisons between food webs from different ecosystems we present the data in a system‐neutral format.The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)

Matrix population models from 20 studies of perennial plant populations

Demographic transition matrices are among the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long‐term demographic monitoring. These data were assembled as part of the “Testing Matrix Models” working group through the National Center for Ecological Analysis and Synthesis (NCEAS). The data represent 82 populations with &gt;460 total population‐years of observations. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)

A rediscovered treasure: mycorrhizal intensity database for 3000 vascular plant species across the former Soviet Union

The symbiosis between vascular plants and mycorrhizal fungi is paramount for carbon and nutrient cycling in most of the world's ecosystems. Most vascular plant species are associated with mycorrhizal fungal partners, and the association is essential for the carbon and nutrition economies of both partners. However, despite its clear importance, data on this symbiosis are lacking: for most vascular plant species, mycorrhizal type is unknown. Very rarely is there data on the levels of mycorrhizal infection intensity in multiple habitats.We translated and digitized a huge data set on vascular plant mycorrhizal intensity throughout the former Soviet Union, previously available only as a hard copy appendix of the doctoral thesis of Ivan A. Selivanov published in Russian in 1976 and not accessible to the international research community. We updated the taxonomic plant nomenclature to the International Plant Name Index and adjusted mycorrhizal and ecological terminology according to the modern international literature.The database contains 7445 records on mycorrhizal infection type and intensity of 2970 plant species from 155 families, in 154 sites, situated across the former Soviet Union (mostly on the territory of the current Russia, Ukraine, and Kazakhstan), comprising together extensive geological, topographic, and climatic gradients. The data set includes percentage infection for each species–site combination for arbuscular, ericoid, arbutoid, endo‐mycorrhizal, dark septate, orchid‐ and ecto‐mycorrhizal fungi. Each record has a detailed description of geography. For many records, soils and host plant community are described. Most of the sites are natural; 10 sites are situated in botanical gardens. For 1291 species the intensity of mycorrhizal infection is quantified in multiple plant communities (2–57). The remaining species are described at single sites.Selivanov developed his own methods for quantifying mycorrhizal infection intensity. These methods are comparable, but not identical to, the methodology commonly used today. Based on our own sampling of 99 plant species collected in two distant sites (Caucasus [Russia] and Abisko [Sweden]), we provide a simple equation for data conversion between the two methods.The availability of this database will help to provide answers to important questions concerning biogeochemical cycling, climate change impacts, and co‐evolution of plants and fungi. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)

Ecological data in the Information Age

Ecological data in the Information Age

Editorial

Editorial

Species composition and abundance of mammalian communities

Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, compiling existing information from the literature provides the best avenue for acquiring the necessary data. Here, we provide a data set that includes species lists for 1000 mammal communities, excluding bats, with species-level abundances available for 940 of these communities. All communities found in the literature that included complete, site-specific sampling data, composed of species lists with or without associated abundances, were included in the data set. Most, but not all, sites are limited to species groups that are sampled using a single technique (e.g., small mammals sampled with Sherman traps). The data set consists of 7977 records from 1000 georeferenced sites encompassing a variety of habitats throughout the world, and it includes data on 660 mammal species with sizes ranging from 2 g to >500 kg. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)

Fourteen years of mapped, permanent quadrats in a northern mixed prairie, USA

This historical data set consists of 44 permanent 1-m2 quadrats located on northern mixed prairie in Miles City, Montana, USA. Individual plants in these quadrats were identified and mapped annually from 1932 through 1945. Quadrats were located in six pastures assigned to cattle grazing treatments with light, moderate, and heavy stocking rates of 1.24, 0.92, and 0.76 ha/animal-unit-month (two pastures in each). These data provide unique opportunities to test the interactive effects of grazing and climate variables on demographic rates, plant–plant interactions, and population and community dynamics. We provide the following data and data formats: (1) the digitized maps in shapefile format; (2) a tabular version of the entire data set [a table that replaces the full spatial data with one (x, y) coordinate for each individual perennial plant record]; (3) grazing treatment information; (4) an inventory of the years each quadrat was sampled; (5) a species list, containing information on plant growth forms and shapefile geometry type (e.g., points or polygons); (6) a record of changes in species names; (7) daily precipitation and temperature records; and (8) counts of annual plants in the quadrats (annuals were counted, not mapped, by the original mappers). The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈http://esapubs.org/archive〉. (The accession number for each Data Paper is given directly beneath the title.)

ERRATA

While these two equations were coded correctly, there was an important transposition error in the execution of the calculation of the transition matrices. Upon correcting this error, we obtain significantly different results for both the baseline and gypsy moth specific scenarios (see revised Fig. 2). Our original results suggested that reducing large patches to medium patches, eradicating medium patches, and reducing colonization from the front are the dominant strategies for the baseline management scenario, with the first two strategies remaining optimal when specifying parameters for gypsy moth management. These points remain the same with the new results. However, reducing colonization from the front is only selected as optimal for a few states with no or few medium or large patches, and eradicating large patches also becomes optimal, especially for the case of gypsy moth specific management for states with no more than a few medium patches and few to moderate large patches. Reducing large patches to medium patches becomes the overwhelmingly dominant strategy across states in the baseline scenario and for the final year of a gypsy moth management program. One final clarification is of how the calculation of the extinction transitions are described in the text versus how they are executed in the model. We treat each part of extinction as a separate step, with a binomial probability, which requires the assumption that just as colonization, growth, and extinction happen in a given order, the three types of extinction (extinction of large, extinction of medium, or decline of large to medium) must happen in a specified order as well. An alternative execution would be to calculate extinction as a single step. Our implementation is the simplest to execute and sufficient for the purposes of the current study. Our revised Fig. 2 is available online (Ecological Archives A021-084-A1). It shows the clearest differences arising from our corrections. We thank P. Fackler for queries that motivated us to re-examine our model. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.