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opencc-zeroSep 2022View details →

Data from: Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

We investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions and contrasting exposure (open/closed tubes). We used four different primer sets targeting bacteria, fungi, protists (cercozoans), and general eukaryotes. We quantified differences in richness, evenness, and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. This repository contains the un-demultiplexed fastq sequences.

opencc-by-4.0Apr 2024View details →

R code and data for: How much is enough? Minimum sample sizes in community ecology

minimum_sample_sizes_code.R includes the complete set of instructions used to carry out the analyses in the related manuscript, plus save the computed data files and generate the text figures. data_files.tar.gz includes all of the files generated by the R code.

opencc-by-4.0Apr 2024View details →

Survey questionnaire data on Perceptions, interactions, and responses to urban natural environments through ecological momentary assessment

Data consist of a R file format and contain the cleaned survey quistionaire data where people were asked about their perceptions, interactions, and responses to urban natural environments. For more information please read the following report Published as part of the Regreen Horizon project.  Panduro, T.E., Zandersen, M., Guell, C., Lovell, R., Garrett, J., Taylor, T., Fullam, J., Amegbor, P. (2024) Perceptions, interactions, and responses to urban natural environments through ecological momentary assessment (EMA). Deliverable D4.6. REGREEN - Fostering nature-based solutions for smart, green and healthy urban transitions in Europe and China. Horizon2020 Grant No. 821016.  https://www.doi.org/10.5281/zenodo.10594764

opencc-by-4.0May 2024View details →

Replication Data and Analyses for: J. Monsimet, S. Sjögersten, N.J. Sanders, M. Jonsson, J. Olofsson & M. Siewert, 2024. UAV data and deep learning: efficient tools to map the ecological footprint of ants mounds, Remote Sensing in Ecology and Conservation.

This dataset corresponds to the article: "Jérémy Monsimet*¹, Sofie Sjögersten², Nathan J. Sanders³, Micael Jonsson¹, Johan Olofsson¹, Matthias Siewert¹, 2024. UAV data and deep learning: efficient tools to map the ecological footprint of ants mounds, Remote Sensing in Ecology and Conservation" DOI: <a href="https://doi.org/10.1002/rse2.400" target="_blank" rel="nofollow noreferrer noopener">10.1002/rse2.400</a> 1 Department of Ecology and Environmental Science, Umeå University, Sweden 2 School of Biosciences, University of Nottingham, Loughborough, UK 3 Department of Ecology and Evolutionary Biology, University of Michigan, US The gitlab repository of this dataset is available at: <a href="https://gitlab.com/Monsimet/uav_ants_treeline/-/tree/main/">https://gitlab.com/Monsimet/uav_ants_treeline/-/tree/main/</a> In this repository, you will find the analyses and results presented in the paper. In each folder, there is a html file that can be read after downloading locally the whole folder. You can either run the .qmd file used to produce the html file or walk through the html files (see the readme.md for more information). Paper abstract: High‐resolution unoccupied aerial vehicle (UAVs) data have alleviated the mismatch between the scale of ecological processes and the scale of remotely sensed data, while machine learning and deep learning methods allow new avenues for quantification in ecology. Ant nests play key roles in ecosystem functioning, yet their distribution and effects on entire landscapes remain poorly understood, in part because they and their mounds are too small for satellite remote sensing. This research maps the distribution and impact of ant mounds in a 20 ha treeline ecotone. We evaluate the detectability from UAV imagery using a deep learning model for object detection and different combinations of RGB, thermal and multispectral sensor data. We were able to detect ant mounds in all imagery using manual detection and deep learning. However, the highest precision rates were achieved by deep learning using RGB data which has the highest spatial resolution (1.9 cm) at comparable UAV flight height. While multispectral data were outperformed for detection, it allows for novel insights into the ecology of ants and their spatial impact on vegetation productivity using the normalized difference vegetation index. Scaling up, this suggests that ant mounds quantifiably impact vegetation productivity for up to 4% of our study area and up to 8% of the Betula nana vegetation communities, the vegetation type with the highest abundance of ant mounds. Therefore, they could have an overlooked role in nutrient‐limited tundra vegetation, and on the shrubification of this habitat. Further, we show the powerful combination UAV multi‐sensor data and deep learning for efficient ecological tracking and monitoring of mound‐building ants and their spatial impact.

opencc-by-4.0May 2024View details →

Data for "The Role of Mood and Stress in Physical Activity Engagement: Insights from Ecological Momentary Assessment

Data collected in the SmartPA study in a joint effort from the Department of Psychology at the University of Salzburg (Jens Blechert) and the Ludwig Boltzmann Institute for Digital Health and Prevention Salzburg.

opencc-by-4.0Dec 2023View details →

Data and code for Reeb, R.A. & Kuebbing, S.E. (2024). Phenology mediates direct and indirect interactions among co-occurring invasive plant species. Ecology, e4446.

Data and analysis code for: Reeb, R.A. & Kuebbing, S.E. (2024). Phenology mediates direct and indirect interactions among co-occurring invasive plant species. Ecology, e4446. <a href="https://doi.org/10.1002/ecy.4446">https://doi.org/10.1002/ecy.4446</a> Repository contains R markdown analysis code, datasets, and the associated metadata file.

opencc-zeroDec 2023View details →

Data from: A multifaceted ecological assessment reveals the invasion of the freshwater red macroalga Montagnia macrospora (Batrachospermales, Rhodophyta) in Taiwan

Invasive freshwater macroalgae are rarely described. Montagnia macrospora is a freshwater red alga introduced from South America to East Asia via the global aquarium trade. The earliest occurrence record of this alga in Taiwan is dated 2005. To determine whether M. macrospora has become invasive in Taiwan and to understand the traits that facilitated its invasion, we took a multifaceted approach that combines examination of ecological background and population genetic analysis. Our island-wide survey showed that M. macrospora is widespread in the field across Taiwan, where the climate greatly differs from that of South America, and can self-sustain for nearly a decade. Our population genetic analysis revealed a lack of genetic diversity of M. macrospora in Taiwan, consistent with the hypothesis that the alga expanded through asexual reproduction. Moreover, during our long-term ecological assessments and field surveys, we observed thatM. macrospora is an ecological generalist that can survive in a wide range of temperature, pH, illumination, and nutrient enrichment. Taken together, our data suggest that M. macrospora has successfully invaded the freshwater ecosystems ofTaiwan, likely due to its ability to disperse asexually and to grow under broad environmental conditions. We hope that our study brings attention to invasive freshwater algae, which have been overlooked in conservation planning and management.

opencc-zeroMay 2024View details →

Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)

Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated. We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias. We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. Synthesis: Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of Salix may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.

opencc-zeroJul 2024View details →

Data from: The importance of biotic interactions in distribution models of wild bees depends on the type of ecological relations, spatial scale and range

Studies have found that biotic information can play an important role in shaping the distribution of species even at large scales. However, results from species distribution models are not always consistent among studies, and the underlying factors that influence the importance of biotic information to distribution models, are unclear. 2. We studied wild bees and plants, and cleptoparasite bees and their hosts in the Netherlands to evaluate how the inclusion of their biotic interactions affects the performance of species distribution models. We assessed model performance through spatial block cross-validation and by comparing models with interactions to models where the interacting species were randomized. Finally, we evaluated how, (i) spatial resolution, (ii) taxonomic rank (genus or species), (iii) degree of specialization, (iv) distribution of the biotic factor, (v) bee body size and (vi) type of biotic interaction, affect the importance of biotic interactions in shaping the distribution of wild bee species using generalized linear models. 3. We found that the models of wild bees improved when the biotic factor was included. The model performance improved the most for parasitic bees. Spatial resolution, taxonomic rank, distribution range of the biotic factor, and degree of specialization of the modelled species all influenced the importance of the biotic interaction to the models. 4. We encourage researchers to include biotic interactions in species distribution models, especially for specialized species and when the biotic factor has a limited distribution range. However, before adding the biotic factor we suggest considering different spatial resolutions and taxonomic ranks of the biotic factor. We recommend using single species or genus data as a biotic factor in the models of specialist species and for the generalist species, we recommend using an approximate measure of interactions, such as flower richness.

opencc-zeroJul 2024View details →

Data from: Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

opencc-by-4.0Jun 2018View details →

Figure 1 in New data on pond snails (Mollusca: Gastropoda: Lymnaeidae) inhabiting the Ukrainian Transcarpathian: diversity, distribution and ecology

Figure 1. Map showing the localities of samples studied. Details for each sampling point are given in Table 1.

Figure 28 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 28: E. flavicaudis collecting sites. Liguria, Tuscany (Italy) and Var (France): 1. Fayence; 2. Mont Faron; 3. Andora Castello; 4. Toirano; 5. Finale Ligure; 6. Levigliani; 7. Castelfalfi.

Figure 24 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 24: E. naupliensis collecting sites. Zakynthos Island (Greece): 1. Skoulikado; 2. Louha; 3. Anafonitria; 4. Volimes; 5. near Volimes.

Figure 22 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 22: Euscorpius (Polytrichobothrius) naupliensis, subadult male (color variation), Louha (Zakynthos Island, Greece) (photo by Marco Colombo).

Figure 21 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 21: Euscorpius (Polytrichobothrius) naupliensis, adult male, Skoulikado (Zakynthos Island, Greece) (photo by Marco Colombo).

Figure 18 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 18: A subadult female of E. italicus surprised catching a caterpillar (Malacosoma neustria) in Peschiera Maraglio (Lombardy, Italy) (photo by Giorgio Colombo).

Figure 15 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 15: Humid forests appear to host weaker species in interspecific ecological competition such as E. concinnus in Castel San Gimignano (Tuscany, Italy) (photo by Marco Colombo).

Figure 11 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 11: E. tergestinus collecting sites. Emilia Romagna, Lombardy, and Veneto (Italy): 1. Cislano; 2. Lubiara; 3. Ceraino; 4. Venezia; 5. Torrechiara.

Figure 13 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 13: An adult female of E. concinnus with remains of a queen wasp (Vespula vulgaris) photographed in Monterosso (Genova, Liguria) (photo by Giorgio Colombo).

Figure 25 in New data on distribution and ecology of seven species of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae)

Figure 25: Euscorpius (Tetratrichobothrius) flavicaudis, subadult female, Castelfalfi (Tuscany, Italy) (photo by Giorgio Colombo).