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opencc-zeroDec 2017View details →

Data from: Linking species abundance and overyielding from experimental communities with niche and fitness characteristics

1) So far, the principal force shaping local plant abundance patterns remains unclear. Rarity can result from poor competitive ability or from small vegetative or generative reproduction, but also from strong self-limitation. The same mechanisms can drive species-specific overyielding, i.e. increased species productivity at high community diversity. Rare species can then benefit more (i.e. overyield to a larger extent) from growing in species-rich communities because of altered competitive hierarchies or smaller conspecific frequencies. Here we test which mechanism is the most important determinant of species rarity and of species-specific productivity across a diversity gradient ranging from one- to 60-species plots. 2) For that we measured vegetative growth, competitive ability (competitive effect), and negative frequency dependence for 49 perennial grassland species from Central Europe. We then linked these characteristics with species abundance (measured as species biomass from 60-species plots) and with species-specific overyielding in The Jena Experiment. 3) Species with higher rates of vegetative growth (when grown without neighbors) were also more abundant in the Jena Experiment. Larger species-specific overyielding was then associated with a stronger negative frequency dependence. As species with greater vegetative growth were also more self-limited, larger overyielding in species-rich communities was characteristic for common rather than for rare species, refuting our initial hypothesis. Finally, path analysis indicated that species with poor capacity to suppress neighbors also profited more from growing in diverse communities. 4) Synthesis. Our results identify key mechanisms driving abundance and productivity of species in synthetic communities differing in species richness. While vegetative reproduction was closely associated with abundance, intraspecific interactions (strength of negative frequency dependence) shaped species productivity across a richness gradient. Our study sheds light on the abundance patterns of species and their influence on community functions, such as biomass production, of species-rich and -poor vegetation.

opencc-zeroDec 2013View details →

Data from: Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community

To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change.

opencc-zeroDec 2017View details →

Data from: Experimental small-scale flower patches increase species density but not abundance of small urban bees

1. Large flower plantings are often used to combat negative effects of habitat loss on pollinators, but whether these floral additions are effective at smaller scales remains unclear, particularly in urban settings. 2. To test the effectiveness of small-scale floral additions on enhancing urban bee populations, as well as their impact from one year to the next, different quantities of potted sweet alyssum (Lobularia maritima) flowers were placed across sites in Ann Arbor, Michigan for two consecutive years and the resulting Halictid bee visitors were monitored. 3. Overall we found the number of flowers added at the local level was significantly and positively correlated with small Halictid bee abundance and species density in an urban landscape. At smaller flower quantities dynamics were clearly linear, where incremental increases in number of flowers showed significant increases in bee abundance and species density. At larger quantities of floral additions, however, dynamics were nonlinear in that incremental increases in flower quantity had no effect on bee abundance and highly variable effects on bee species density. 4. When comparing the change in small Halictid bee abundance and species density from one year to the next, we found a significant increase in bee species density in the second year of small-scale floral additions, but no significant difference in bee abundance. 5. Synthesis and applications. Our results show that small flower plantings can have positive effects on small bee communities in urban systems even over a short period of time, and therefore confirm that encouraging citizens to plant flowers can be an effective conservation strategy for certain urban pollinator populations. In addition, our finding that smaller flower plantings may have higher impacts on small pollinators than larger plantings suggests resource managers interested in pollinator conservation should consider spreading multiple, smaller floral plantings across the urban landscape, rather than pooling all resources into one large flower patch.29-Nov-2017

opencc-zeroNov 2021View details →

Species abundances and functional traits data of frog assemblages in Amazonian forests (Tapajós FLONA and Alter do Chão village, Brazil)

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.

opencc-by-4.0Feb 2023View details →

Using species distribution modeling to generate relative abundance information in unstable territories: conservation of Felidae in Mexico

Raw data used in the abovementioned manuscript

opencc-zeroJan 2022View details →

Relative species abundance successfully predicts nestedness and interaction frequency of monthly pollination networks in an alpine meadow

Plant-pollinator networks have been repeatedly reported as cumulative ones that are described with >1 years observations. However, such cumulative networks are composed of pairwise interactions recorded at different periods, and thus may not be able to reflect the reality of species interactions in nature (e.g., early-flowering plants typically do not compete for shared pollinators with late-flowering plants, but they are assumed to do so in accumulated networks). Here, we examine the monthly sampling structure of an alpine plant-pollinator bipartite network over a two-year period to determine whether relative species abundance and species traits better explain the network structure of monthly networks than yearly ones. Although community composition and species abundance varied from one month to another, the monthly networks (as well as the yearly networks described with annual pooled data) had a highly nested structure, in which specialists directly interact with generalist partners. Moreover, relative species abundance predicted the nestedness in both the monthly and yearly networks and accounted for a statistically significant percentage of the variation (i.e., 20%-44%) in the pairwise interactions of monthly networks, but not yearly networks. The combination of relative species abundance and species traits (but not species traits only) showed a similar prediction power in terms of both network nestedness and pairwise interaction frequencies. Considering the previously recognized structural pattern and associated mechanisms of plant-pollinator networks, we propose that relative species abundance may be an important factor influencing both nestedness and interaction frequency of pollination networks.

opencc-zeroDec 2021View details →

Species-level tree crown maps improve predictions of tree recruit abundance in a tropical landscape

Predicting forest recovery at landscape scales will aid forest restoration efforts. The first step in successful forest recovery is tree recruitment. Forecasts of tree recruit abundance, derived from the landscape-scale distribution of seed sources (i.e. adult trees), could assist efforts to identify sites with high potential for natural regeneration. However, previous work has revealed wide variation in the effect of seed sources on seedling abundance, from positive to no effect. We quantified the relationship between adult tree seed sources and tree recruits, and predicted where natural recruitment would occur in a fragmented tropical agricultural landscape. We integrated species-specific tree crown maps generated from hyperspectral imagery and property boundaries data on individual property ownership with field data on the spatial distribution of tree recruits from five species. We then developed hierarchical Bayesian models to predict landscape-scale recruit abundance. Our models revealed that species-specific maps of tree crowns improved recruit abundance predictions. Conspecific crown area had a much stronger impact on recruitment abundance (8.00% increase in recruit abundance when conspecific tree density increases from zero to one tree; 95% CI: 0.80 to 11.57%) than heterospecific crown area (0.03% increase with the addition of a single heterospecific tree, 95% CI: -0.60 to 0.68%).Individual property ownership was also an important predictor of recruit abundance: the best performing model had varying effects of conspecific and heterospecific crown area on recruit abundance, depending on individual property ownership. We demonstrate how novel remote sensing approaches and cadastral data can be used to generate high-resolution and landscape-level maps of tree recruit abundance. Spatial models parameterized with field, cadastral, and remote sensing data are poised to assist decision support for forest landscape restoration.

opencc-zeroFeb 2022View details →

Removing understory vegetation in oil palm agroforestry reduces ground-foraging ant abundance but not species richness

Ants are known to provide valuable ecosystem services in agricultural landscapes, including oil palm plantations. Their communities are less diverse and more uneven in oil palm compared with forest, and this may increase their vulnerability to disturbance. This study quantifies ant communities in oil palm agroforestry and experimentally tests their robustness to a common-practice high-disturbance management intervention: removing understory vegetation. Fieldwork was based at the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Understory Vegetation Project in Sumatra, Indonesia, where three treatments varying in their degree of understory vegetation management were established in 2014: (1) widespread herbicide was applied removing all understory vegetation (Reduced); (2) herbicide was applied to the harvesting paths and circles, and other vegetation was allowed to grow (Normal – control); (3) no herbicide was applied (Enhanced). We measured ground-foraging ant communities before and after the treatments were implemented, using pitfall traps over 324 trap-nights (a trap-night is one trap set for one night). We investigated how ant abundance, species richness, species evenness, beta diversity, and community composition differed between the treatments. We found 3507 ants across 68 species or morphospecies. Seven of these were highly abundant and accounted for 78% of individuals. Post-treatment ant abundance was lower in the reduced treatment (mean per plot: 84) than in the normal (159) and enhanced (131) treatments, which did not differ from each other. Species richness, species evenness, beta diversity and community composition were not affected by the vegetation treatments. We recommend that oil palm growers maintain understory vegetation in oil palm plantations to support ground-foraging ants. Though not tested here, this may also improve ant-mediated ecosystem services, such as pest control, seed dispersal, nutrient redistribution, and the maintenance of soil health. This study demonstrates that enhancing habitat complexity through management practices can support biodiversity in monocrop landscapes.

opencc-zeroMar 2022View details →

Data from: Tree species with conservative foliar nutrient status and strong phosphorus homeostasis are regionally abundant in subtropical forests

Foliar nitrogen (N) or phosphorus (P) status and their stoichiometric homeostasis are integral parts of the plant nutrient economy that determines the success of plant species in environments where N or P limits plant growth. Despite growing evidence for higher predictability of stoichiometric homeostasis of N (HN) than that of P (HP) on plant species abundance in temperate grasslands, no previous studies explicitly examined how foliar N and P status modulate the relationships between stoichiometric homeostasis and species distribution (regional species abundance) of woody plants, especially in P-limited (sub)-tropical ecosystems. We hypothesized that species with a conservative foliar nutrient status but a higher HP (but not HN) would be regional abundant in P-limited forest. We measured foliar N (LNC) and P (LPC) contents of 54 woody species, community composition and soil N and P contents across 94 forest plots in Chinese subtropical forests. Then we evaluated the species' levels of N and P stoichiometric homeostasis and their regional abundance to test our hypotheses. HN and HP significantly increased with decreasing LNC and LPC. Foliar nutrient status positively correlated with the minimum values of both soil N and P contents, but only negatively associated with the maximum value of soil P content, indicating that conservative species can occupy a wider range of soil P- than N-based nutrient niche. Meanwhile, species abundance negatively correlated with LNC and LPC, and positively correlated with HN and HP. 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 HP and decreased LPC via HN, rather than directly with a decline of LPC. Synthesis. 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.

openMar 2022View details →

Data from: Forest hoverfly community collapse: abundance and species richness drop over four decades

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 Quercus for hundreds of years, partly former heathlands planted with Pinus and Pseudotsuga in the period 1900-1950. Locally, other tree species (Fagus, Larix) dominate; in the shrub layer Sorbus, Amelanchier, and Rhamnus are important. In the ground layer Vaccinium myrtillus dominates at many locations, next to some Rubus 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 Galium saxatile and Deschampsia flexuosa decreased and Rubus 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.  The file ‘counts.csv’ contains the counts per species per monitoring day. The file contains the following variables: date:                      date of monitoring (in the second half of the morning) Baccha.elongata and next 104 variables:                               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’. observer:               initials of the person responsible for a day of monitoring. AB = Aat Barendregt, TZ = Theo Zeegers, WS = Wouter van Steenis. 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. 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. 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. 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. T30d:                     mean temperature in degrees Celsius in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen. 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. 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. Tapr:                     mean temperature in April of the year of monitoring, based on daily data from KNMI weather station Deelen. Sapr:                     mean proportion of time with direct sunlight in April of the year of monitoring, based on daily data from KNMI weather station Deelen. 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. seasonScore:        day-of-the-year-specific GAM prediction of the total abundance of hoverflies, rescaled between 0 and 1

opennotspecifiedOct 2019View details →

Distribution. Lowland forests of W Brazil, E Peru, and N Bolivia, S of the Amazon River. Because of abundance of individuals in the C. castanea complex, hampering precise species identification in the field and in collections, a detailed assessment ofits distribution is still needed. in Phyllostomidae

Distribution. Lowland forests of W Brazil, E Peru, and N Bolivia, S of the Amazon River. Because of abundance of individuals in the C. castanea complex, hampering precise species identification in the field and in collections, a detailed assessment ofits distribution is still needed.

opencc-zeroDec 2022View details →

Data from: Synergistic use of UAV surveys, satellite tracking data and mark-recapture to estimate abundance of elusive species

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.

opencc-zeroJul 2022View details →

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e. more-individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual-based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two datasets spanning latitudinal diversity gradients in trees and marine reef fish, and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more-individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS-curve has the potential to quantify the underlying factors influencing most aspects of diversity change. --

opencc-zeroJul 2022View details →

Population abundance data and species range maps

Aim – 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. Location – Americas. Time Period – 1800-2017. Major taxa studied – mammal, bird, fish and tree seedlings. Methods – 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. Results – 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. Main conclusions – 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.

opencc-zeroAug 2022View details →

Abundance of fungal species in slug feces collected in a temperate forest

In the DNA barcoding study, a total of 288,630 OTU sequences were recovered from feces of eight field-captured slugs. Major taxa were Ascomycota (52.5%), Basidiomycota (46.1%), Mortierellomycota (0.2%), Chytridiomycota (0.1%) and Mucoromycota (0.1%) (Table 2). In Basidiomycota, 17 orders were detected (Table 2). The dominant order was Agaricales (66.1%), followed by Trichosporonales (29.7%) and Hymenochaetales (2.9%). In Agaricales, the dominant genera were Armillaria (35.7%) and Gymnopilus (29.8%). The dominance of Agaricales spores may be due to that the slugs used in this study were collected in September and October when fruiting bodies of Agaricales were abundant.

opencc-by-4.0Oct 2022View details →

Increasing landscape complexity enhances species richness of farmland arthropods, agri-environment schemes also abundance–A meta-analysis

Article dataset

Figures 10–13 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution

Figures 10–13. Photographs of specimens in vivo after squeeze preparation (10, 12) and diagrammatic reconstructions (11, 13) in dorsal view of species of Dalytyphloplanida recorded for the Coastal Plain of southern Brazil. 10, 11. Baicalellia evelinae. 12, 13. Gieysztoria chiqchi. Details of the penis stylet are shown in 11B and 13B.

Figures 8, 9 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution

Figures 8, 9. Photograph of specimen in vivo after squeeze preparation (8) and diagrammatic reconstruction (9) in dorsal view of Stenostomum hemisphericum recorded for the Coastal Plain of southern Brazil.

Figures 2–7 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution

Figures 2–7. Photographs of specimens in vivo after squeeze preparation (2, 4, 6) and diagrammatic reconstructions in dorsal view (3, 5, 7) of species of Catenula recorded in the Coastal Plain of southern Brazil. 2, 3. Catenula evelinae. 4, 5. C. leuca. 6, 7. C. turgida. Scale bars = 100 µm.

Figure 1 in Six freshwater microturbellarian species (Platyhelminthes) in permanent wetlands of the Coastal Plain of southern Brazil: new records, abundance, and distribution

Figure 1. Study areas in the Coastal Plain of the southern Brazilian state of Rio Grande do Sul (white area): Terra de Areia (1 = 29°29'05" S, 049°52'21" W), Osório (2 = 29°53'20" S, 050°08'09" W, and 3 = 29°52'02" S, 050°05'16" W), Tramandaí (4 = 30°05'09" S, 050°10'24" W), and Capivari do Sul (5 = 30°10'22" S, 050°23'10" W).