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799 results for “abundance data”
Species abundances and functional traits data of frog assemblages in Amazonian forests (Tapajós FLONA and Alter do Chão village, Brazil)
<p>We sampled frogs along an edaphic and vegetation-structure gradient in the Brazilian Amazon. We sampled 33 plots organized in four modules (with 10, 6, 8 and 9 plots). Environmental data are composed of are litter depht(cm), distance to water bodies (m), temperature (ºC), vegetation structure (PCA axis), soil sand and silt content (g-kg), and proportion of the area deforested. Additionally, we measured snout-vent length (SVL) and leg length relative to SVL and evaluated the effects of environmental variables on thirteen binary traits used with presence or absence.</p>
Pacific Parasites Data - Life history mediates the association between parasite abundance and geographic features
<p>1. Though parasites are ubiquitous in marine ecosystems, predicting the abundance of parasites present within marine ecosystems has proven challenging due to the unknown effects of multiple interacting environmental gradients and stressors. Furthermore, parasites often are considered as a uniform group within ecosystems despite their significant diversity.</p> <p>2. We aim to determine the potential importance of multiple predictors of parasite abundance in coral reef ecosystems, including reef area, island area, human population density, chlorophyll-a, host diversity, coral cover, host abundance, and island isolation.</p> <p>3. Using a model selection approach within a database of more than 1200 individual fish hosts and their parasites from 11 islands within the Pacific Line Islands archipelago, we reveal that geographic gradients, including island area and island isolation, emerged as the best predictors of parasite abundance.</p> <p>4. Life history moderated the relationship; parasites with complex life cycles increased in abundance with increasing island isolation, while parasites with direct life cycles decreased with increasing isolation. Direct life cycle parasites increased in abundance with increasing island area, though complex life cycle parasite abundance was not associated with island area.</p> <p>5. This novel analysis of a unique dataset indicates that parasite abundance in marine systems cannot be predicted precisely without accounting for the independent and interactive effects of each parasite's life history and environmental conditions.</p>
Data from: A generalist nematode destabilizes plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobia abundance
<p><span>1. Difficulties quantifying pathogen load and mutualist abundance limit our ability to connect disease dynamics to host community ecology. For example, specific predictions about how differential pathogen load is hypothesized to drive host competitive outcomes are rarely tested. Additionally, although infection is known to affect mutualists, we rarely measure the magnitude of pathogen effects on mutualist abundance across host competitive contexts. <span>We </span>tested for both mechanisms <span>in </span>a plant-rhizobia-nematode system.</span></p> <p><span><span>2. We </span>paired the legume <i>Medicago lupulina </i>with intra- and interspecific plant <span>com</span>petitors, with and without a generalist nematode parasite <i>Meloidogyne </i>sp. <span>Relative </span>change in plant biomass was used to determine how nematode inoculation <span>affected </span>plant competitive outcomes. <span>We</span> counted nematode galls to test for direct effects of parasitism on plant competition, and rhizobia nodules to test for indirect effects <span>of </span>nematode presence on rhizobia abundance.</span></p> <p>3. Parasites were destabilizing despite similar nematode load across competition treatments. During inter- compared to intraspecific competition, nematode <span>inoculation </span>decreased nodulation on <i>M. lupulina</i>, increased nodulation on <i>Trifolium repens</i>, and had no effect on nodulation on <i>Chamaecrista fasciculata.</i></p> <p><span><span>4. We </span>found no support for hypothesized direct effects of nematode load on competitive outcomes, and strong but idiosyncratic indirect effects of nematode <span>inoculation </span>on rhizobia abundance.</span></p>
Data from: Landscape complementation is a driver of bumble bee (Bombus sp.) abundance in the Canadian Rocky Mountains
<p><i>Context: </i>Land use change is a major factor influencing biodiversity, but the mechanisms that drive species losses require further examination. Habitat loss often reduces biodiversity, but habitat fragmentation can increase biodiversity when examined independently. Processes driving this pattern remain largely unclear.</p> <p><i>Objectives: </i>We aimed to determine the effects of habitat fragmentation on bumble bee populations after controlling for habitat amount, and to examine possible mechanisms behind observed effects.</p> <p><i>Methods: </i>We sampled 22 species of bumble bees (<i>Bombus</i> sp.) across 50 unique sites located throughout the Canadian Rockies using a sampling design that minimized correlations between amount and spatial arrangement of land covers that may represent important habitat for bees. We modeled bumble bee abundance, species richness and diversity as a function of land cover metrics.</p> <p><i>Results: </i>Effects of land cover fragmentation were dependent on both the measure of fragmentation used, and landscape scale. Bumble bee abundance was higher where nesting habitat (forest) and foraging habitat (grassland) were found adjacent to each other within 300 m, suggesting a landscape complementation effect where bees benefit from having access to both land cover types in proximity to one another. Having available habitat split into a greater number of patches was detrimental when considering the immediate area (0-300 m), but beneficial when quantified in more distant areas (300-600 m).</p> <p><i>Conclusions: </i>Landscape complementation may be an important component behind positive fragmentation effects. Estimates of multiple measures of fragmentation are important when testing the impacts of land cover and landscape changes on species abundance and biodiversity.</p>
Supplementary material for "Spatio-temporal modelling of abundance from multiple data sources in an integrated spatial distribution model"
<p><strong>Abstract</strong></p> <p><strong>Aim:</strong> In biodiversity monitoring, observational data are often collected in multiple, disparate schemes with greatly varying degrees of standardization and possibly at different spatial and temporal scales. Technical advances also change the type of data over time. The resulting heterogeneous data sets are often deemed to be incompatible. Consequently, many available data sets may be ignored in practical analyses. Here, we propose a more efficient use of disparate biodiversity data to assess species distributions and population trends.<br> <br> <strong>Location:</strong> Switzerland (Europe)<br> <br> <strong>Taxon:</strong> Birds</p> <p><strong>Methods: </strong>We developed an integrated, hierarchical species distribution model with a joint likelihood for all data sets using a shared state process (e.g., latent species abundance or occurrence), but distinct observation process for each data set. We show how the abundance submodel of a binomial N-mixture model can fuse four different data types (count, detection/non-detection, presence-only, and absence-only data) and enable improved inferences about spatio-temporal patterns in abundance. As case studies, we use data from multiple avian biodiversity monitoring schemes. In the first, the goal is estimating abundance-based species distribution maps. In the second, we infer trends in population abundance across time.</p> <p><strong>Results: </strong>Accuracy and precision of abundance estimates increased when combining data from different sources compared to using a single data source alone. This is particularly valuable when data from each single data source is too sparse for reliable parameter estimation.<br> Main conclusions: We show that exploiting the complementary nature of "cheap", but abundant, citizen-science data and less abundant, but more information-rich, data from structured monitoring programs might be ideal to estimate distribution and population trends more accurately, especially for rare species. Joint likelihoods allow to include a wide variety of different data sets to (1) combine all the available information and to (2) mitigate weaknesses of one by the strength of another.</p> <p> </p> <p> </p>
Submerged aquatic vegetation, water quality (pH, salinity, and turbidity) and waterfowl abundance data from 1991-2017 in Back Bay, Virginia
<p><span>Back Bay, Virginia, has been documented as an important foraging area for waterfowl since at least the mid-1800s. Expansive submerged plant beds historically supported diverse assemblages of non-breeding waterfowl, however coastal development and other anthropogenic influences have since led to fluctuations in submerged aquatic vegetation (SAV) and an associated decline in waterfowl abundance in the bay. To gain insight into the effects of environmental drivers on waterfowl foraging guilds, our study explores the effects of SAV frequency and water quality on the abundance of dabbling ducks, diving ducks, and swans and geese in Back Bay. We use 8 years of SAV, water quality, and waterfowl monitoring data collected by state and federal agencies to model the effects of salinity, turbidity, pH, and percent frequency of SAV on the relative abundance of waterfowl by foraging guild in Back Bay. The appropriateness of the data and reasonability of the preliminary results were then evaluated through semi-structured interviews with 11 local informants representing state, federal, and non-governmental organizations. Quantitative results indicated that dabbling ducks are affected differently than other guilds by water quality and percent frequency of SAV. Thematic analysis of the interview data revealed a number of potential explanations for the model results, as well as highlighted areas of uncertainty in need of further research. In a test of face validity, participants demonstrated a significant degree of belief in turbidity, salinity, and SAV as drivers of waterfowl abundance, but were not convinced by the potential effects of pH as demonstrated by the model. This mixed methods study provides insights that could potentially influence the management and conservation of non-breeding waterfowl populations by challenging the assumption that particular environmental conditions serve all foraging groups equally.</span></p>
Simulation data for "A new convective parameterization applied to Jupiter: implications for water abundance near the 24deg N region"
<p>Simulation outputs and initialization for the journal article titled "A new convective parameterization applied to Jupiter: implications for water abundance near the 24º N region" by Sankar & Palotai.</p>
Data from: Tree species with conservative foliar nutrient status and strong phosphorus homeostasis are regionally abundant in subtropical forests
<p><span>Foliar </span><span>nitrogen (N) or phosphorus <em>(P)</em> </span><span>status and their </span><span>stoichiometric homeostasis </span><span>are integral parts of the plant nutrient economy </span><span>that determines the success of plant species</span><span> in environments where N or P limits plant growth. </span><span>Despite growing evidence </span><span>for higher predictability of </span><span>stoichiometric </span><span>homeostasis </span><span>of N</span><span> (</span><em><span>H</span></em><sub><span>N</span></sub><span>) than that of P (</span><em><span>H</span></em><sub><span>P</span></sub><span>) on plant species abundance</span><span> in temperate grasslands</span><span>, no previous studies e</span><span>xplicitly examined how foliar N and P status modulate the relationships between </span><span>stoichiometric </span><span>homeostasis and</span><span> species distribution (regional species abundance)</span><span> of woody plants, especially in P-limited (sub)-tropical ecosystems. W</span><span>e hypothesized that species with a conservative foliar nutrient status but a higher </span><em><span>H</span></em><sub><span>P</span></sub><span> (but not</span><span> <em>H</em><sub>N</sub></span><span>) would be regional abundant in </span><span>P-limited</span><span> forest.</span></p> <p><span>We measured foliar N (LNC) and P (LPC) contents of 54 woody species, community composition and soil N and P </span><span>contents across</span><span> 94 forest plots in Chinese subtropical forests. Then we evaluated the species' levels of N and P </span><span>stoichiometric homeostasis</span><span> and their regional abundance to test our hypotheses.</span></p> <p><span><em><span>H</span></em><sub><span>N</span></sub><span> and <em>H</em><sub>P</sub> significantly increased with decreasing LNC and LPC. Foliar nutrient status positively correlated </span><span>with the minimum values of both soil N and P contents, but only negatively associated with the maximum value </span><span>of soil P content, </span><span>indicating that conservative species can occupy a wider range of soil P- than N-based nutrient niche.</span><span> Meanwhile, species abundance negatively correlated with LNC and LPC, and positively correlated with <em><span>H</span></em><sub><span>N</span></sub><span> and <em>H</em><sub>P</sub></span>. However, the structure equation model analysis showed that species abundance increased with decline of LNC but not yet with increased HN. In contrast, species abundance enhanced with increased <span><em>H</em><sub>P</sub> </span>and decreased LPC via <em><span>H</span></em><sub><span>N</span></sub>, rather than directly with a decline of LPC.</span></span></p> <p><span><strong>Synthesis</strong>.</span><span> This study provides empirical evidence that species with conservative foliar nutrient status are more stable in terms of N and P stoichiometric homeostasis, and foliar N and P economy modulate species abundance distribution in different ways. Our results suggest that maintaining strong stoichiometric homeostasis of leaf P, while maintaining conservative economy of N, is a key physiochemical mechanism for shaping species abundance distribution in P-limited forests.</span></p>
Data from: Forest hoverfly community collapse: abundance and species richness drop over four decades
<p>To study abundance trends in hoverflies (Diptera: Syrphidae) in a Dutch forest, we monitored hoverflies over the course of 4 decades. Within the ‘Boeschoten’ forest the same permanent route of approximately 3 kilometres was inspected for the presence of hoverflies in the second half of the morning (10:00-13:00), for a duration of approximately 2 hours. The forest was included up to 30 meters from the route to obtain a complete inventory of the ecosystem; a complete list of all present hoverflies was aimed for each time. Monitoring was done only on sunny days, independent from temperature. All observed specimens have been counted and collected with an insect net, species and sex identified in the field, or preserved for identification later on (with e.g. Barendregt 1978; van der Goot 1981; Bot & van de Meutter 2019; Speight et al. 2020). While monitoring started in 1974, it was only from 1979 onwards that complete species lists were kept, and from 1982 onwards that the number of observed individuals per species was recorded. Boeschoten is an (extensively used) agricultural enclave within large mixed deciduous-coniferous forests in the center of The Netherlands, 40-50 m a.m.s., west of the village of Garderen (52º13'24"N, 5º40'31"E). The sandy soil is very dry and open water is only available in some small pools. The selected forest sections (ca. 20 ha) are partly dominated by <em>Quercus</em> for hundreds of years, partly former heathlands planted with <em>Pinus </em>and <em>Pseudotsuga </em>in the period 1900-1950. Locally, other tree species (<em>Fagus, Larix</em>) dominate; in the shrub layer <em>Sorbus, Amelanchier,</em> and <em>Rhamnus</em> are important. In the ground layer <em>Vaccinium myrtillus </em>dominates at many locations, next to some <em>Rubus </em>along paths. The forest did not change for at least 60 years in land use or management: only the trees matured further (no new planting) and in the ground layer the vegetation changed in some species after the period of intense acid rain around 1985, when <em>Galium saxatile </em>and <em>Deschampsia flexuosa </em>decreased and <em>Rubus </em>increased in abundance. In the surroundings of Boeschoten there are some smaller arable fields; 5 km to the south and west there is intensive livestock farming. </p> <p>The file ‘counts.csv’ contains the counts per species per monitoring day. The file contains the following variables:</p> <p>date: date of monitoring (in the second half of the morning)</p> <p>Baccha.elongata and next 104 variables:</p> <p> number of observed individuals of a particular species per day of monitoring. Species lists were not complete in 1974-1978, hence the NAs when a species was not recorded in that period. Systematic counting started in 1982. Presence before 1982 is indicated with a ‘1’, meaning ‘at least 1’.</p> <p>observer: initials of the person responsible for a day of monitoring. AB = Aat Barendregt, TZ = Theo Zeegers, WS = Wouter van Steenis.</p> <p>temp: mean temperature in degrees Celsius between 10:00 and 13:00 (i.e. during the general time of monitoring) on the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>sun: mean proportion of time with direct sunlight between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>precip: total amount of precipitation in millimeters between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>relhumid: mean relative humidity (percentage) between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>T30d: mean temperature in degrees Celsius in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>S30d: mean proportion of time with direct sunlight in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>P30d: mean amount of precipitation (in millimeters) per day in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Tapr: mean temperature in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Sapr: mean proportion of time with direct sunlight in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Papr: mean amount of precipitation (in millimeters) per day in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>seasonScore: day-of-the-year-specific GAM prediction of the total abundance of hoverflies, rescaled between 0 and 1</p>
Data for: Abundance and accessibility of forage for reindeer in forests of Northern Sweden: impacts of landscape and winter climate regime
<p>The survival of reindeer during winter, their period of greatest food stress, is largely dependent upon the abundance and accessibility of food in their pastures. In Northern Sweden this realised availability of forage is notably affected by snow conditions and the impacts of forestry on understorey in these pastures. Whilst these factors have been examined to some extent in isolation, their combined effect on overall forage availability has, to the best of our knowledge to date, not been studied.</p> <p>In this study, vegetation surveys and analysis of snow conditions were undertaken in 16 forest stands at various stages of recovery from clear-cutting. The variation in abundance and growth of understorey species edible by reindeer, such as lichen, were noted as forest age increased. The barrier effect of ice lenses in snow during winter was also noted. Lichen biomass was significantly affected by a combination of stand age, understorey vegetation height, and lichen height. Soil disturbance from the processes of felling, and competition in the vegetation communities recovering from this disturbance were identified as key drivers of change in lichen biomass. Overall, clear-cut forests had some of the greatest prevalence of ice lenses in the snow column, and forage availability at these sites was up to 61 % less than in stands over 58 years in age.</p>
Data from: A new composite abundance metric detects stream fish declines and community homogenization during six decades of invasions
<p><b>Aim</b>:<b> </b>We developed a new technique, utilizing species-specific counts of individuals from historical fish community samples, to examine landscape-level, spatiotemporal trends in relative abundance distributions. Abundance-based historical distribution analyses are often plagued by data comparability issues, but provide critical information about community composition trends inaccessible to those using analyses based only on species presence-absence. We established trends in native and non-native fish abundance and community homogenization, uniqueness, and diversity to help local conservation managers prioritize targets and motivate similar studies globally to support fish conservation.</p> <p><b>Location</b>: Upper and middle New River (UMNR) basin, Appalachian Mountains, USA.</p> <p><b>Methods</b>: We compiled catch data from 61 years of fish community surveys (1958-2019) and tested for community homogenization by comparing data from repeatedly sampled sites (1900s versus 2000s samples) using dispersion analyses. We measured community uniqueness (site contributions to beta diversity) and species diversity (Shannon index) at sampled streams to identify potential conservation hotspots. We then used regression analyses and Wilcoxon signed-rank tests to examine species-specific basin-wide and local abundance trends and identify species of potential conservation concern.</p> <p><b>Results</b>: Dispersion of sites in species-abundance space was significantly greater in the 1900s compared to the 2000s, indicating homogenization had occurred. Of 36 native species analyzed, 44.4% (16) showed basin-wide declines. Non-native species exhibited mixed patterns; site-level abundance increased in 2 of 15 species analyzed (13%).</p> <p><b>Main conclusions</b>: Our results indicate basin-wide community homogenization has occurred within the UMNR, but many unique and diverse communities persist. If conserved, these could help maintain regional fish diversity. We found basin-wide declines in four endemic species, as well as spread patterns of non-native and native species that were not detected by a presence-absence analysis applied within the same study area. This finding illustrates the importance of considering both species' abundance and occurrence patterns as separate dimensions of biodiversity to inform conservation planning.</p>
Bioclimatic, soil, terrain, distance to Native American settlement, and historical tree taxon relative abundance data at 8-km resolution for the northeastern United States
<p><span>Researchers have debated impacts of past Native American land use on forests including upon tree species composition in northeastern United States (US), with estimates of impacts ranging from local to regional extent. This study examines tree relative abundances in the </span><span>northeastern US </span><span>(approx. 420,000 km2) </span><span>to assess whether Native Americans influenced geographic distributions of 18 tree taxa prior to Euro-American settlement. </span><span>We used boosted regression trees to model abundance patterns and to assess the importance of distance-based proxies of Native American land use versus environmental variables. We trained models that included and excluded distance-based proxies. Abundance estimates from original land survey records (1650-1850 CE) were acquired for taxa at 8 km spatial resolution, and related to Native American settlement locations (1500-1800 CE) and 27 environmental variables. </span><span>When evaluated upon test data, regional-scale models of relative abundance that included distance-based proxies performed only slightly better than models that excluded them, with mean improvements in RMSE of 0.1 percentage points. Models suggest that Native American land use modestly altered the relative abundance of taxa locally, extending no more than 50 km from settlement. Models also suggest slight increases near settlement of a few percentage points in relative abundance for fire-tolerant and/or dietary taxa (e.g. oak, hickory, and pine), and for early-successional taxa (e.g. ash). </span><span>Past</span><span> Native American land use had no detectable effect on forest composition across a regional extent, but increased the abundance of fire-tolerant, shade-intolerant, and nut-producing trees locally.</span></p> <p><span>The Excel-format (.xlsx) dataset here provides the training and testing data for the BRT models in this publication. It contains relative abundances of the 18 tree taxa expressed as a fraction of total number of trees. It also provides bioclimatic (e.g. annual temperature, annual preciptation), soil (e.g. pH, percent sand), terrain (e.g. slope), and Native American (e.g. distance to settlement) variables developed from multiple sources. A column also indicates whether an observation was part of the training data or the test data. See the publication and its Supporting Information for full details on the acquisition and processing of these data, as well as the original providers of the data. If using these data, please </span><span>cite both this dataset's corresponding article, as well as the original providers of the data.</span></p> <p>Also provided are ascii-format (.asc) gridded data layers that were used for making spatial predictions of taxon relative abundances from BRT models.</p> <p>The original creators/providers of the relative abundance, bioclimatic, soil, terrain, and Native American data or layers used for creating the gridded data in this study are:</p> <p><span>Abel, T. (2016). The Iroquoian occupations of Northern New York: A summary of current research. Ontario Archaeology, 96, 65–75. </span></p> <p><span>CIFAS. (2017). Map Of First Nations in New Brunswick. Comitas Institute for Anthropological Study. <a href="http://cifas.us/first-nations-maps/">http://cifas.us/first-nations-maps/</a> </span></p> <p><span>Grumet, R. S. (1995). Historic Contact: Indian People and Colonists in Today's Northeastern United States in the Sixteenth through Eighteenth Centuries. University of Oklahoma Press.</span></p> <p><span>Jordan, K. A. (2013). Incorporation and colonization: Postcolumbian Iroquois satellite communities and processes of indigenous autonomy. American Anthropologist, 115(1), 29–43.</span></p> <p><span>Milner, G. R., & Chaplin, G. (2010). Eastern North American population at ca. A.D. 1500. American Antiquity, 75(4), 707–726.</span></p> <p><span>NASA. (2000). SRTM 90m Digital Elevation Database v4.1. <a href="https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/">https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/</a> </span></p> <p><span>O'Donnell, M. S., & Ignizio, D. A. (2012). Bioclimatic Predictors for Supporting Ecological Applications in the Conterminous United States (Data Series 691; p. 10). U.S. Geological Survey. <a href="https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392">https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392</a> </span></p> <p><span>Paciorek, C. J., Goring, S. J., Thurman, A. L., Cogbill, C. V., Williams, J. W., Mladenoff, D. J., Peters, J. A., Zhu, J., & McLachlan, J. S. (2016). Statistically-estimated tree composition for the northeastern United States at the time of Euro-American settlement. PLoS ONE, 11(2), e0150087. <a href="https://doi.org/10.1371/journal.pone.0150087">https://doi.org/10.1371/journal.pone.0150087</a> </span></p> <p><span>Peters, M. P., Iverson, L. R., Prasad, A. M., & Matthews, S. N. (2013). Integrating Fine-scale Soil Data into Species Distribution Models: Preparing Soil Survey Geographic (SSURGO) Data from Multiple Counties (General Technical Report NRS-122; p. 70). U.S. Forest Service. <a href="https://www.fs.usda.gov/treesearch/pubs/45308">https://www.fs.usda.gov/treesearch/pubs/45308</a> </span></p>
Data from: Synergistic use of UAV surveys, satellite tracking data and mark-recapture to estimate abundance of elusive species
<p>Estimating population abundance is central to many ecological studies and important in conservation planning. Yet the elusive nature of many species makes estimating their abundance challenging. Abundance estimates of sea turtles, marine birds and seals are usually made when breeding adults are ashore, while life-stages spent at sea, including as juveniles, are often poorly sampled. We used a combination of high-resolution satellite tracking (Fastloc-GPS), Unmanned Aerial Vehicle (UAV) surveys and catch-mark-recapture approaches to assess abundance of immature hawksbills (Eretmochelys imbricata) and green turtles (Chelonia mydas) in a tidal lagoon of the Chagos Archipelago (Indian Ocean). We captured, marked, and released 50 turtles (48 hawksbill and 2 green turtles) prior to UAV surveys and used satellite tracking data from 27 immature turtles (25 hawksbill and 2 green turtles) to refine the estimated numbers of marked turtles available for resighting and those likely to have emigrated from the study area. We estimated a total of 339 turtles in the lagoon with a density between 265 turtles km-2 at high water and 499 turtles km-2 at low water. Of these 84% were hawksbills and 16% were green turtles. These hawksbill densities are the highest reported amongst 17 foraging sites recorded around the world, likely reflecting successful long-term protection of turtles in the Chagos Archipelago. </p>
Data from: Predation probabilities and functional responses: How piscivorous waterbirds respond to pulses in fish abundance
<p>How predators respond to changes in prey abundance (i.e. functional responses) is foundational to consumer-resource interactions, predator-prey dynamics, and the stability of predator-prey systems. Predation by piscivorous waterbirds on out-migrating juvenile steelhead trout (<em>Oncorhynchus mykiss</em>) is considered a factor affecting the recovery of multiple Endangered Species Act-listed steelhead populations in the Columbia River basin. Waterbird functional responses, however, may vary by predator species and location, with important implications to predator management strategies. We used a 13-year dataset on waterbird abundance across seven breeding colonies (three Caspian tern [<em>Hydroprogne caspia</em>], two double-crested cormorant [<em>Nannopterum auritum</em>], and two California and ring-billed gull [<em>Larus californicus</em> and <em>L. delawarensis</em>] colonies) and steelhead tag-recovery data (>645,000 tagged and >32,000 recovered steelhead) to quantify weekly predation probabilities and functional responses across waterbird species, colonies, and years. Weekly predation probabilities were highly variable, ranging from 0.01–0.30 at tern colonies, 0.01–0.20 at cormorant colonies, and 0.03–0.13 at gull colonies. Per capita predation probabilities were an order of magnitude higher at inland tern and cormorant colonies relative to estuary colonies of the same species. Terns displayed Type II functional responses across colonies and years, where predation probabilities peaked at low steelhead abundances and declined as steelhead abundance increased (i.e., predator swamping). Cormorants nesting at the large estuary colony (several thousand birds) displayed a Type III functional response, but cormorants nesting at the smaller inland colony (several hundred birds) displayed a Type II response. Consumption probabilities of steelhead by gulls remained consistent across a large range of steelhead availability, suggesting a Type I or a Type III functional response, but a lack of colony abundance data prevented quantifying functional responses. The level of tern predation combined with Type II functional responses indicate possible population-level impacts that could destabilize small or declining prey populations. Conversely, the apparent Type III functional responses of gulls and estuary nesting cormorants are indicative of prey switching behaviors targeted at periods of high steelhead abundance. Our results illustrate the complexity of predator-prey interactions and the importance of quantifying predator- and location-specific functional responses when predicting the efficacy of management strategies to enhance prey populations.</p>
Microarthropod abundance data of a drought experiment comparing organic and conventional farming
<p>In Central Europe summer droughts are increasing in frequency which threatens production and biodiversity in agroecosystems. The potential of different farming systems to mitigate detrimental drought effects on soil animals is largely unknown. We investigated the effects of simulated drought on the abundance and community composition of soil microarthropods (Collembola, Oribatida, Meso‑, Pro‑ and Astigmata) in winter wheat fields under long-term conventional and organic farming in the DOK trial, Switzerland. We simulated drought by excluding 65% of the ambient precipitation during the wheat growing season from March to June 2017. The abundance of Collembola and Oribatida declined more consistently in conventionally compared to organically managed fields under simulated drought. The abundance of Collembola as well as Meso‑, Pro‑ and Astigmata, but not the abundance of Oribatida, increased in deeper soil layers due to simulated drought, suggesting vertical migration as drought avoidance strategy. The species composition of Oribatida communities, but not of Collembola communities, differed significantly between drought treatments as well as between farming systems. Soil carbon content was a major factor structuring Oribatida communities. Our results suggest that organic farming buffers negative effects of drought on soil microarthropods, presumably due to higher soil carbon content, and associated higher soil moisture and improved soil structure. This potential of organic farming systems to mitigate consequences of future droughts on soil biodiversity is promising and needs further exploration across larger climatic and spatial scales and should be extended to other groups of soil biota.</p>
Data from: Tracking trends in monarch abundance over the 20th century is currently impossible using museum records
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Data from: Wolbachia infection alters the relative abundance of resident bacteria in adult Aedes aegypti mosquitoes, but not larvae
Insect-symbiont interactions are known to play key roles in host functions and fitness. The common insect endosymbiont Wolbachia can reduce the ability of several human pathogens, including arboviruses and the malaria parasite, to replicate in insect hosts. Wolbachia does not naturally infect Aedes aegypti, the primary vector of dengue virus, but transinfected Ae. aegypti have anti-dengue virus properties and are currently being trialled as a dengue biocontrol strategy. Here, we assess the impact of Wolbachia infection of Ae. aegypti on the microbiome of wild mosquito populations (adults and larvae) collected from release sites in Cairns, Australia, by profiling 16S rRNA gene using next generation sequencing. Our data indicate that Wolbachia reduces the relative abundance of a large proportion of bacterial taxa in Ae. aegypti adults, that is in accordance with the known pathogen-blocking effects of Wolbachia on a variety of bacteria and viruses. In adults, several of the most abundant bacterial genera were found to undergo significant shifts in relative abundance. However, the genera showing the greatest changes in relative abundance in Wolbachia-infected adults represented a low proportion of the total microbiome. In addition, there was little effect of Wolbachia infection on the relative abundance of bacterial taxa in larvae, or on species diversity (accounting for species richness and evenness together) detected in adults or larvae. These results offer insight into the effects of Wolbachia on the Ae. aegypti microbiome in a native setting, an important consideration for field releases of Wolbachia into the population.
Data on bird abundance in urban woodlands in 32 Swedish cities
<p>The expansion of urban areas is increasingly contributing to biodiversity declines. Several studies have analyzed the effect of increasing urbanization on bird diversity, but few have differentiated effects of urban landscapes (matrix) from changes in focal habitat quality at multiple spatial scales. In this study we analyzed the effect of urbanization on bird communities in individual (local scale) and across multiple (regional scale) cities while controlling for the quality of sampled natural habitats. We conducted bird point counts and habitat quality mapping of trees, dead wood and shrubs in 459 forest remnants along an urbanization gradient in 32 cities in Sweden. We then analyzed how the degree of urbanization affected species richness of woodland-breeding bird and red-listed bird species at a regional and local scale. We also analyzed how urbanization affected beta-diversity and dissimilarity between communities at the different spatial scales, and if dissimilarities in species communities along the urbanization gradient were driven by species nestedness or turnover. We found that urbanization decreased species richness, and the number of red-listed species, at both the regional and local scale. Dissimilarities in woodland-breeding bird communities among urban, semi-urban and peri-urban areas at the local scale were particularly due to turnover, and at the regional scale to nestedness. Since there was no difference in habitat quality among woodlands across the urbanization gradient, we conclude that landscape urbanization systematically causes poorer and more homogeneous bird communities. However, despite that natural habitats in cities contribute less to the regional diversity, they are critical to maintain the local bird communities of individual cities and their surroundings.</p>
Population abundance data and species range maps
<p><b>Aim </b>–<b> </b>The abundant-center hypothesis (ACH) predicts a negative relationship between species abundance and the distance to geographic range center. Since its formulation, empirical tests of the ACH have involved different settings (e.g. the distance to the ecological niche or to the geographic range center), but studies found contrasting support for this hypothesis. Here, we evaluate whether these discrepancies might stem from differences regarding the context in which the ACH is tested (geographical or environmental), how distances are measured, how species envelopes are delineated, how the relationship is evaluated and which data are used.</p> <p><b>Location</b> – Americas.</p> <p><b>Time Period </b>– 1800-2017.</p> <p><b>Major taxa studied</b> – mammal, bird, fish and tree seedlings.</p> <p><b>Methods</b> – Using published abundance data for 801 species, together with species range maps, we tested the ACH using three distance metrics in both environmental and geographical spaces with range and niche envelopes delineated using two different algorithms, totaling 12 different settings. We then evaluated the distance-abundance relationship using correlation coefficients (traditional approach) and mixed-effect models to reduce the effect of sampling noise on parameter estimates.</p> <p><b>Results</b> – Similar to previous studies, correlation coefficients indicated an absence of effect of distance on abundance for all taxonomic groups and settings. In contrast, mixed-effect models highlighted relationships of various strengths and shapes, with a tendency for more theoretically-supported settings to provide stronger support for the ACH. The relationships were however not consistent across taxonomic groups and settings, and were sometimes even opposite to ACH expectations.</p> <p><b>Main conclusions</b> – We found mixed and inconclusive results regarding the ACH. These results corroborate recent findings, and suggest either that our ability to predict abundances from the location of populations within geographical or environmental spaces is low, or that the data used here have a poor signal-to-noise-ratio. The latter calls for further testing on other datasets using the same range of settings and methodological framework.</p>
Data and code for "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management"
<p>## Secondary data and code to accompany the research entitled "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management" by Padullés Cubino et al. (2024).</p> <p># There are four folders with (1) "raw data", (2) "processed data", (3) "results", and (4) "scripts".</p> <p># The raw and processed data folders contain the CSV and XLSX files with all the data used for analysis and produced from them</p> <p># The "results" folder contains the figures and table presented in the manuscript.</p> <p># The "scripts" folder contains four scripts for the analyses described in the manuscript:</p> <p> 01_preparation_ClimEdge.R -> data cleaning and processing</p> <p> 02_script_Fig1.R -> code to produce Fig1</p> <p> 03_script_Fig2.R -> code to produce Fig2</p> <p> 04_script_Table1_Fig3.R -> code to produce Table 1 and Fig3</p> <p># If anything is unclear, please contact the corresponding author for clarification (padullesj@gmail.com).</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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