Find research datasets worth reusing

Data from: The evolution of sex roles: The importance of ecology and social environment

Males and females often have different roles in reproduction, although the origin of these differences have remained controversial. Explaining the enigmatic reversed sex roles where males sacrifice their mating potential and provide full parental care is a particularly long-standing challenge in evolutionary biology. While most studies focused on ecological factors as the drivers of sex roles, recent research highlights the significance of social factors such as the adult sex ratio. To disentangle these propositions, here we investigate the additive and interactive effects of several ecological and social factors on sex role variation using shorebirds (sandpipers, plovers and allies) as model organisms that provide the full spectrum of sex role variation including some of the best known examples of sex role reversal. Our results consistently show that social factors play a prominent role in driving sex roles. Importantly, we show for the first time that reversed sex roles are associated with both male-skewed adult sex ratios and high breeding densities. Furthermore, phylogenetic path analyses provide the first general support for sex ratios driving sex role variations rather than being a consequence of sex roles. Together, these novel results open a new research direction by showing that different mating opportunities of males and females play a major role in generating the evolutionary diversity of sex roles, mating system and parental care.

Data from: The paleobiologic implications of modern nonmarine ecological gradients

In modern nonmarine settings, previous studies have demonstrated the importance of elevation-correlated ecological gradients, but such studies tend to focus on relatively small areas and only one higher taxon. Here, we analyze GBIF occurrence records from a wide variety of taxa across the southeastern United States coastal plain. Many taxa display ecological gradients (gradients in proportional or relative abundance) correlated with elevation, distance to the coast, and latitude. These gradients tend to be steepest within a few tens of kilometers near the coast and at elevations less than 25 m. Some taxa, notably terrestrial mammals, do not display gradients correlated with elevation and distance to the coast. The small sample sizes of these groups and their heterogeneous sampling raise concerns about whether sufficient data exists. Coupled with previous studies of these ecological gradients, their common presence over distances of tens to hundreds of kilometers and elevations of tens to hundreds of meters suggests they are likely important in the nonmarine fossil record. Because elevation and distance to the coast change predictably with cycles of accommodation and sediment flux, these ecological gradients are predicted to occur in the nonmarine stratigraphic record, especially through intervals that record transgression or regression. Such gradients will affect the local composition of species associations and occurrences, even in the absence of regional species origination, immigration, and extinction and in the absence of regional change in the structure of ecological gradients. The ordination of taxon counts in stratigraphically limited samples has great potential for establishing their existence.

Time series methods for cyclical ecological data

Biodiversity monitoring has entered an era of `big data', exemplified by a near-continuous collection of sounds, images, chemical, and other signals from organisms in diverse ecosystems. Such data streams have the potential to help identify new threats, assess the effectiveness of conservation interventions, as well as generate new ecological insights. However, appropriate analytical methods are often still missing, particularly with respect to characterizing cyclical temporal patterns. Here, we present a framework for characterizing and analyzing ecological responses that represent nonstationary, complex temporal patterns and demonstrate the value of using Fourier transforms to decorrelate continuous data points. In our example, we use a framework based on three approaches (spectral analysis, magnitude squared coherence, and principal component analysis) to characterize differences in tropical forest soundscapes within and across sites and seasons in Gabon. By reconstructing the underlying, cyclic behavior of the soundscape for each site, we show how one can identify circadian patterns in acoustic activity. Soundscapes in the dry season had a complex diel cycle, requiring multiple harmonics to represent daily variation, whilst in the wet season there was less variance attributable to the daily cyclic patterns. Our framework can be applied to most continuous, or near-continuous ecological data collected at a fine temporal resolution, allowing ecologists to explore patterns of temporal autocorrelation at multiple levels for biologically meaningful trends. Such methods will become indispensable as biological big data are used to understand the impact of anthropogenic pressures on biodiversity and to inform efforts to mitigate them.

opencc-by-4.0Apr 2024View details →

Data from: Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities

Data and code for the manuscript entitled "Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities" for Ecological Applications (2024).  The raw sequencing data was submitted to NCBI’s Sequence Read Archive (SRA) under BioProject number PRJNA1023717 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA1023717?reviewer=rciv7kme2qq5vpcnqqog4vjioo).

Data from: Reproductive ecology of the critically endangered pancake tortoise (Malacochersus tornieri) in the wild

Reproduction of the pancake tortoise in the wild has remained poorly known over the decades. This study fills the knowledge gap by investigating the reproductive ecology of the species in its natural habitats in Kenya. Data were collected using the time-constrained search-and-seize method, group-level scan sampling, radio tracking, and camera-trapping. Our observations revealed a total of 19 mating events that occurred between December and April, predominantly during the rainy seasons. Mating duration averaged 15.2±2.4 minutes. Male-male aggression was observed during the mating season, with the dominant male keeping off all other males and mating with the resident females. Nest preparation events occurred between April and June. Nine nesting events were recorded, but in only five of them was an egg deposited. The nests were dug in loose soil, appeared almost circular, and measured 8.4±0.9 cm wide and 7.0±0.1 cm deep (n=7). The average clutch size was one egg. The eggs were white, hard-shelled, oval, and elongated measuring 4.4±0.4 cm long, 2.7±0.04 cm wide and weighed 17±0.6 g (n=3). Incubation period lasted 177± 5.7 days (n=2), and hatching coincided with the onset of the short rainy season in November, aligned with the availability of abundant food for the tortoises. The hatchlings were minimally wider than long, having an average straight carapace length of 4.5±0.6 cm, an average width of 4.5±0.4 cm, and on average weighed 14.7±3.7g, (N=9). They remained near the nest site for 4-5 days before relocating to tiny rock crevices away from the adult tortoise crevices. Egg and hatchling predation was high, with four of the total of six eggs, observed after they were laid, being destroyed. Three juveniles, out of nine, were also eaten by predators. These findings contribute useful information for the formulation of effective conservation and management strategies for this critically endangered species.

Data from: Ecological release and insular shifts in avian morphological traits in the Caribbean

We compared support for 3 hypotheses that might explain observed morphological variation among islands of 4 1.70 species of Caribbean land birds: ecological release from competition and predation pressure, predation pressure from 1 novel predator species (small Indian mongoose, Herpestes auropunctatus), and climate. We measured wing chord, tarsus length, bill length, and mass of Bananaquits (Coereba flaveola), Black-faced Grassquits (Tiaris bicolor), Lesser Antillean Bullfinches (Loxigilla noctis), and Common Ground Doves (Columbina passerina) in Grenada, 2015–2017, and combined these measures with data from 23 other Caribbean islands collated from academic papers and researchers, for a total sample size of 6,518 individuals. We found the strongest support for the ecological release hypothesis, but each of our hypotheses received some support, suggesting that ecological release from competition, predation pressure from mongoose, and climate may all interact to influence morphological adaptations of birds to local conditions in the Caribbean.

opencc-by-4.0Dec 2020View details →

Data from: Socio-ecological drivers of long-term ecosystem carbon stock trend: An assessment with the LUCCA model of the French case

Open the record for dataset details and reuse information.

Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models

Ecological niche models (ENMs) are a powerful tool in ecological research and conservation planning. Since ENMs provide probability maps of suitable areas under environmental change, they may assist in designing conservation actions and addressing conservation priorities. However, ENMs are usually implemented by learning the species climatic preferences from their current geographic distribution, which leaves them vulnerable to the issue of niche truncation issues, as if comes with non-climatic limits to the current species distribution posed by e.g. anthropic activities and settlements, and is bound to assume that species are at equilibrium with their environments. These problems might be alleviated by the inclusion of fossil occurrences, which refer to moments during species evolution when such limits were absent, and a larger fraction of the species fundamental niche was probably explored. Here, we combined current and fossil occurrence data for 38 medium-large mammal species of conservation concern to assess the influence of the fossil record on ENM predictions under future climate change scenarios. We found that ignoring or including fossil data yields consistent trends in terms of predicted range increase/decrease. Yet, although adding fossil data invariably results in increased niche width, estimates of range change magnitude improved for just one half only of the species. These results suggest that most species might be in non-equilibrium with their environment, and that the inclusion of fossil data may be crucial to the better understanding of species climatic requirements, hence for designing effective conservation strategies.

Data from: Severity of topsoil compaction controls the impact of skid trails on soil ecological processes

Skid trails are a major management-induced disturbance in temperate forest ecosystems with considerable impact on soil ecological processes that are so far poorly understood. In German forests, skid trails comprise 10 – 20 % of the forest area that is potentially affected by soil compaction through heavy machinery. We systematically investigated the influence of skid trails on physical, chemical, and microbiological soil parameters at 84 paired plots across four Central European forest types. In low mountain forests with steeper topography, skid trails had more drastic effects than in lowland forests. Skid trails in low mountain areas showed a decrease in the C to N ratio of microbial biomass (MBC/MBN), as well as increased microbial (MBC/SOC) and enzyme activities leading to faster carbon turnover (lower C/N, EOC/EN) and increased CO2 losses (CO2/SOC) from the soil. The overall effects of the skid trails in lowland forests were small. On base-poor soils, we found an increase in the MBC/MBN ratio, while skid trails in base-rich lowland soils showed a reduction in CO2/SOC, suggesting a proportional increase in soil carbon storage. Regardless of region-specific effects, the relative increase in the bulk density of the fine soil was identified as a 'golden trait' that determined the effects of skid trails on many soil parameters, as shown by negative correlations with SOC, N, MBC, MBN, MBP, MBC/SOC and CO2/SOC and positive ones with the activities of certain hydrolytic enzymes. Synthesis and Applications: Our data clearly showed that carbon conversion processes and soil respiration leading to significant carbon and nutrient losses increased significantly on skid trails in low mountain regions with relatively steep slopes, which was in sharp contrast to lowland sites. The strong context dependence of our findings suggests that the mapping of soil conditions in terms of slope, substrate and moisture with high spatial resolution is mandatory to assess the vulnerability of sites to soil compaction by heavy machinery. Based on such vulnerability analysis, negative impacts can be minimized through the designation of permanently fixed skid trails, the technical adaptation of vehicles (e.g., wide base tyres) as well as careful planning and timing of management operations that should be restricted to dry weather and soil moisture conditions or periods of frost.

opencc-by-4.0Jun 2024View details →

Statistical Decision Trees for Marine Ecological Data

Both decision trees can be used to choose an appropriate statistical analysis when dealing with ecological (marine) data. For each analysis, an example publication using/explaining the method, some of the R commands required and a tutorial are listed. Please note that (1) these statistical analyses should be seen as suggestions and other approaches are available, (2) papers listed are only provided as examples but appropriate referencing of the method is expected and (3) some analyses have specific assumptions that the users should check before analysing their data.

Data from: Among-species variation in six decades of changing migration timings explained through ecology, life-history and abundance

Species utilising seasonal environments must now alter timings of key life-history events in response to large-scale climatic changes, thereby maintaining trophic synchronies. Yet substantial among-species variation in cross-decadal phenological changes is observed. Transitioning from basic description of such variation towards prediction of future phenological responses now requires standardised studies that rigorously quantify and explain variation in the direction, magnitude and form of changing timings across diverse species in relation to key ecological and life-history variables. Accordingly, we fitted multi-quantile regressions to 59 years of high-quality multi-species data on spring and autumn bird migration timings through northern Scotland. We demonstrate substantial variation in cross-decadal changes in timings among 72 species, and quantify the degree to which variation can be explained through differences in species ecology, life-history and population trajectories. Consistent with predictions, species with seasonal diets, narrower breeding habitat breadths, shorter generation lengths and capability to produce multiple offspring broods per year advanced their migration timing in one or both seasons. In contrast, species with less seasonal diets, and that produce single annual offspring broods, showed no change. Meanwhile, contrary to prediction, long-distance migrants advanced their migration timings as much as short-distance migrants. Changes in migration timing also varied with changes in local migratory abundance, such that species with increasing seasonal abundance apparently altered their migration timing, whilst species with decreasing abundance did not. These patterns concur with expectation if changing migration timing is adaptive. However, we demonstrate that similar patterns can be generated through numerical sampling processes given changing abundances, implying that apparent phenology-abundance relationships should be carefully validated and interpreted. Overall, our results show that migrant bird species with differing ecologies and life-histories have shown systematically differing phenological changes over six decades contextualised by large-scale environmental changes, potentially facilitating future predictions and altering temporal dynamics of seasonal species co-occurrences.

Data from: Occurrence, ecology and management of Fascioloides magna in Bavaria, Southern Germany

In 2015, red deer infected with American liver fluke were discovered in the Veldenstein Forest area for the first time. This was the first detection of the fluke in a wild deer population in Bavaria. The aim of the study was to determine the American liver fluke prevalence rates in red deer, roe deer and wild boar in the Veldenstein Forest, as well as factors influencing these rates. Since 2018, the livers of 83% of the red deer culled in the study area have been examined, as well as those of the occasional roe deer and wild boar. The livers are classified by adspection and dissection into four levels of infection. The age of the animals was estimated on the basis of dentition and tooth cementum annuli in the first molar (M1). The livers of 520 red deer, 226 roe deer and 75 wild boar were dissected. All wild boar livers tested negative. 3% of roe deer and 36% of red deer livers were positive. To lower the prevalence, the red deer population was reduced, beginning in 2018. In the following years, it fell significantly. Medium and high levels of infection were initially detected in 61% of adult red deer. Since 2018, the median number of flukes per infected liver has decreased significantly from 17.51 flukes/liver to 10.0 flukes/liver. On driven hunts, significantly more diseased deer were found than during hunting from raised hides. Furthermore, there are close correlations between infectations and the age of the red deer, and infections and the distance from the Pegnitz floodplains. The American liver fluke leads to the extinction of roe deer locally and to a massive infectation and decimation of the red deer population. Without a drastic reduction of the numbers in infected red deer populations, there is a risk of large-scale infection of native deer species across large areas in Bavaria.

opencc-by-4.0Jun 2024View details →

Data for "Citizen science as a valuable tool for environmental review" - Frontiers in Ecology and the Environment - Callaghan et al.

This dataset is the dataset used in Callaghan et al. Citizen science as a valuable tool for environmental review. Frontiers in Ecology and the Environment. The data are Environmental Impact Statement titles, and our coding of those documents. See paper for details.

opencc-zeroJul 2024View details →

Data from: Community ecology in a bottle: Leveraging eDNA metabarcoding data to predict occupancy of co-occurring species

Detecting environmental DNA (eDNA) of numerous organisms from the same samples has been revolutionized by metabarcoding. However, utilizing the vast amounts of data generated from metabarcoding to predict occupancy probabilities for co-occurring species is currently rare. Here, we demonstrate how metabarcoding data can be used to advance community ecology research through a case study using replicate stream water samples and Bayesian occupancy models to test hypotheses of eDNA occurrence for a native fish (brook trout, Salvelinus fontinalis), its major ectoparasite (gill lice, Salmincola edwardsii), and an introduced potential competitor (brown trout, Salmo trutta). Gill lice DNA occupancy was positively associated with brook trout biomass determined via electrofishing conducted near eDNA sampling sites, suggesting gill lice occupancy is dependent on host density. Leveraging site-specific molecular operational taxonomic units identified from metabarcoding, DNA occupancy of trout and gill lice was often positively predicted by species richness of aquatic insect orders trout commonly feed on, which are also environmental quality indicators. Thus, high-quality habitat that environmentally sensitive salmonids and their primary prey rely on may promote higher fish occupancy rates, further facilitating the spread of fish parasites. An increasing amount of community-level data is being generated from global metabarcoding efforts, and we suggest our framework could be broadly implemented to enhance understanding of factors impacting distributions of co-occurring species, reveal new ecological phenomena, and support management and conservation efforts.

opencc-by-4.0Jul 2024View details →

Polyandry in Lepidoptera, ecological and evolutionary implications – preliminary review - RAW data

RAW data of manuscript, entitled "Polyandry in Lepidoptera, ecological and evolutionary implications – preliminary review".

opencc-zeroJul 2024View details →

Modeling data and R code for Chrysodeixis chalcites ecological niche

The golden twin-spot moth, Chrysodeixis chalcites Esper (Lepidoptera: Noctuidae), is a polyphagous, polyvoltine crop pest occurring natively from northern Europe to Mediterranean Africa and the Canary Islands. Larvae feed on a wide variety of naturally occurring plants as well as soybean and other legume crops, short staple cotton, tomato, potato, peppers, tobacco, and banana. Chrysodeixis chalcites has been recorded in agricultural lands in the Ontario peninsula in eastern Canada and in northern counties of Indiana, USA. Given the strong potential for C. chalcites to invade USA crop lands, it is important to identify environments most likely to sustain growing populations of this pest. Though C. chalcites is native to Europe and North Africa, it has invaded sub-Saharan Africa. Using occurrence data form the native and invaded ranges, and environmental predictors including bioclimatic conditions and human disturbance, we trained three ecological niche models to estimate an ensemble prediction of environmental suitability in the contiguous US. Because human impact is potentially a confounding predictor, models were trained both with and without it. High environmental suitability was projected for the Atlantic coast from New England to Florida, the Gulf coast, the lower Midwest, and the Pacific coast and Central Valley of California.

opencc-by-4.0Dec 2006View details →

Figure 8 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 8: E. sicanus collecting sites. Eastern Sardinia (Italy): 1. Genna Silana Pass; 2. Baunei.

opencc-by-4.0Dec 2006View details →

Figure 2 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 2: E. alpha forest habitat in Cislano (Lombardy, Italy) (photo by Marco Colombo).

opencc-by-4.0May 2018View details →

Data supplementing Lichtenberg et al. (2018) Costs and benefits of alternative food handling tactics help explain facultative exploitation of pollination mutualisms. Ecology

This dataset contains data and scripts that supplement the publication Lichtenberg et al. (2018) Costs and benefits of alternative food handling tactics help explain facultative exploitation of pollination mutualisms. Ecology 99: 1815-1824. https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.2395   Please cite the above article if you use any of the included data or code.   Files are described in README.md.