Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

Data from: The extreme rainfall gradient of the Cape Horn Biosphere Reserve and its impact on forest bird richness. Biodiversity and Conservation

Description of dataset This dataset contains information about forest bird species richness and climatic variables in 61 sample sites of the Cape Horn Biosphere Reserve. This dataset was analysed in : Quilodrán CS, Sandvig EM, Aguirre F, Rivero de Aguilar J, Barroso O, Vásquez RA, and R Rozzi. 2022. Effects of the extreme rainfall gradient in the Cape Horn Biosphere Reserve on forest bird richness. Biodiversity and Conservation.    Acknowledgments  This study was funded by grants for Technological Centers of Excellence with Basal Financing of the National Agency for Research and Development (ANID-Chile), granted to the Cape Horn International Center (CHIC- FB210018) and the Institute of Ecology and Biodiversity (IEB-AFB170008). CSQ acknowledges support from the Swiss National Science Foundation (N°P5R5PB_203169).

opencc-zeroMay 2022View details →

Data from: Evaluating staging habitat quality to advance the conservation of a declining migratory shorebird, Red Knot Calidris canutus

Identifying where and when population "bottlenecks" occur is critical to the conservation of migratory species, many of which are declining precipitously worldwide. Especially challenging is the evaluation of changes to staging sites. These sites are indispensable links in the migratory cycle but are typically used only briefly. We devised a field-based approach to assess the quality and carrying capacity of a critical staging site in Nanpu, China, for the declining, migratory Red Knot (Calidris canutus rogersi & C. c. piersmai) during northward migration. The Nanpu tidal flat supports 50,000-100,000 Red Knots annually, and while there, the knots feed almost exclusively on the bivalve Potamocorbula laevis. We simultaneously monitored changes in the abundance of Red Knots and bivalves across the entire staging site in spring 2018. After taking into account potential competition with other shorebird species, we estimated that the Nanpu tidal flat was capable of supporting approximately 1.46-1.70 times the current observed level of usage of the site by Red Knots, and therefore is operating below, but close, to carrying capacity with respect to food resources for Red Knots. This result suggests that any further development of this site could harm the EAAF Red Knot population. Synthesis and applications: Quantitative monitoring and evaluation of habitat quality of staging sites are essential to successfully conserve declining migratory species. In particular, researchers and conservation practitioners should incorporate both population size and staging duration in order to more accurately assess the importance of different sites and to quantify how changes in staging habitat quality may translate into changes in migrant population sizes at both local and global scales.

opencc-zeroJul 2022View details →

Data from: Diversity among rare and common congeneric plant species from the Garry oak and Okanagan shrub-steppe ecosystems in British Columbia: implications for conservation

Using universal non-coding chloroplast DNA markers (cpDNA), we investigated genetic diversity and genetic structure in four rare and common plant species pairs inhabiting threatened ecosystems (Garry Oak and Okanagan shrub-steppe) in British Columbia. The species found in the Garry oak ecosystem are: Sanicula bipinnatifida (purple sanicle; Apiaceae; rare), Sanicula crassicaulis (Pacific sanicle; Apiaceae; common), and Balsamorhiza deltoidea (deltoid balsamroot; Asteraceae; rare). The species found in the Okanagan shrub-steppe ecosystem are: Balsamorhiza sagittata (arrowleaf balsamroot; Asteraceae; common), Orthocarpus barbatus (Grand Coulee owl-clover; Orobanchaceae; rare), Orthocarpus luteus (yellow owl-clover; Orobanchaceae; common), Phacelia ramosissima (branching phacelia; Hydrophyllaceae; rare), and Phacelia linearis (thread-leaved phacelia; Hydrophyllaceae; common). Eight cpDNA regions were sequenced for each study species. Sequences were aligned and concatenated within each species, and single nucleotide polymorphisms (SNPs) were used to analyze patterns of regional genetic diversity and phylogeographic structure within genera and species. Results include: total gene diversity (Ht), nucleotide diversity (π), number of private alleles, haplotype networks, isolation by distance, and analysis of molecular variance.

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-zeroMay 2024View details →

Data from: Growth and longevity of the endangered freshwater pearl mussel (Margaritifera margaritifera): Implications for conservation and management

Key life-history data, such as growth and age, are necessary to effectively manage and conserve threatened freshwater mussel species. Traditionally growth and age studies require large yet destructive sample sizes covering all age classes. Such methods pose a risk to populations of conservation concern, and therefore alternative methods that need only limited sample sizes are necessitated to prevent further threats to such populations. We applied retrospective shell growth at age reconstructions to 98 critically endangered freshwater pearl mussel (FPM) individuals from 34 populations across Finland and Sweden, enabling the use of extremely small sample sizes (n = 1–6 per population). We compared the performance of six different growth models with the reconstructed size-at-age data across FPM juvenile (<20 years old) and adult life stages. The growth reconstruction model showed reasonable skill in reconstructing FPM growth patterns. The von Bertalanffy model was shown to be a good general descriptor of growth for FPM, but it systematically underestimated the asymptotic size. The power law model was the most accurate in estimating juvenile growth (lowest deviances from the size-at-age data). FPM showed great variability in longevity (Amax = 54–254 years) and growth constant k (0.018– 0.057 year-1). Our results show that reasonable estimates of growth can be attained even when sample sizes are extremely limited. The results can be further applied to gain knowledge on the population's age structure, size at maturation, and recovery potential. The methodology is applicable to other freshwater mussel species of conservation concern.

opencc-by-4.0May 2024View details →

Supporting data for: Angiosperms in a conservation area in the semiarid region of Paraíba State, Northeastern Brazil

<h3>Title: Angiosperms in a conservation area in the semiarid region of Paraíba State, Northeastern Brazil.</h3> Contact information: Bernardo de Farias Rocha, bernardorocha284@gmail.com, and José Iranildo Miranda de Melo, tournefort@gmail.com, Universidade Estadual da Paraíba. Figures and table produced to illustrate an article, disponibilized as supporting data. Geographical Coordinates of the Study Area: 6º27'S, 36º18'W

opencc-by-4.0Jul 2024View details →

Raw data for: Spatial and temporal variation in farmland bird nesting ecology: Implications for effective Corn Bunting Emberiza calandra conservation

These are raw data accompanying the study "Spatial and temporal variation in farmland bird nesting ecology: Implications for effective Corn Bunting Emberiza calandra conservation". All information on data origin, data analysis, and derived implications will be available with the original publiation.

opencc-by-4.0Sep 2019View details →

Processed data for "Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses"

tar.gz of processed data in the form of compressed R files (rds) of SingleCellExperiment (<a href="https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html">https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html</a>) objects and a metadata csv for the data in the publication Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses (O'Flanagan et al. 2019).

opencc-by-4.0Jul 2020View details →

Fig. 1 in Problems with imperfect locality data: distribution and conservation status of an enigmatic pitviper

Fig. 1. Geographic distribution of the Guatemalan Palm-pitviper, Bothriechis bicolor, based on a review of the literature and museum collections. Circles indicate previously published records, diamonds indicate new records, and question marks approximate the locations of selected problematic records discussed in the text. The easternmost question mark represents the type locality for B. bicolor. The inset illustrates specimen MZFC-HE 33491 (juvenile, snout-vent length 322 mm) in life.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status.

Natural history specimen data linked to collectors and determiners held within, "Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a>. Formatted as a Frictionless Data package.

opencc-zeroDec 2017View details →

Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums

Interspecific hybridization can lead to adaptation and speciation, especially in the context of recent radiations. The emblematic Crocodylus (true crocodiles) is the most broadly distributed, ecologically diverse, and species-rich crocodylian genus. Nonetheless, their within-species evolutionary processes are poorly resolved mainly due to their potential for hybridization. Notably, the evolutionary outcomes when hybridization is ancient and involves long-lived species, like crocodiles, remain largely unexplored. Here, we evaluate the genomic admixture between the American (Crocodylus acutus) and the Morelet's (Crocodylus moreletii) species, and demonstrate that this hybridization system challenges the definition of species boundaries and poses a triple conservation conundrum: what has been recognized as C. acutus is actually two distinct species, therefore its taxonomic reassessment is needed; we identified two evolutionary distinct hybrids lineages, which are genetically discernible from the parental species; the remaining C. moreletii populations evidence its likely extinction as a species and/or evolution via hybridization. Hence, the crocodiles' distinct species and hybrids lineages warrant recognition and need urgent conservation efforts.

opencc-zeroJul 2021View details →

Data from: Native shade trees aid bird conservation in tea plantations in southern India

In the Western Ghats, India, we study how different intensities of tea cultivation influence birds. We compared bird communities in conventional monoculture tea and mixed-shade tea plantations, both of which use agrochemicals, with organic tea plantations, a rainforest fragment, and continuous rainforest within the Anamalai Tiger Reserve. In 225 point count surveys, overall bird species richness and abundance were lowest in conventional tea and up to 33% higher in organic tea. Mixed-shade tea had 40% higher species richness (including 15 canopy and 4 shrub and mid-storey species – primarily frugivores, nectarivores and insectivores), and 83% higher bird abundance than conventional tea, with a greater proportion of forest-affiliated birds and similarity in species composition with forest sites. The rainforest fragment and continuous rainforest had a higher proportion, richness and abundance of forest-affiliated birds and fewer open-country birds, unlike tea plantations where the pattern was reversed. Habitat associations of 62 bird species in indicator species analysis revealed similar patterns. Thus organic tea is better than conventional tea for birds, but mixed-shade tea is even better, although still poorer than forests. Retaining or promoting native shade trees in tea plantations will increase bird diversity and abundance, including of forest-affiliated species and support landscape-level bird conservation.

Fig. 4 in Conservation importance of Nakai-Nam Theun National Protected Area, Laos, for small carnivores based on camera trap data

Fig. 4. Distribution of camera-trap records for Mustelidea and Herpestidea in Nakai-Nam Theun NPA from 2006–2011.

Fig. 3 in Conservation importance of Nakai-Nam Theun National Protected Area, Laos, for small carnivores based on camera trap data

Fig. 3. Distribution of camera-trap records for Viverridae and linsang in Nakai-Nam Theun NPA from 2006–2011.

Fig. 2 in Conservation importance of Nakai-Nam Theun National Protected Area, Laos, for small carnivores based on camera trap data

Fig. 2. Total survey effort (in camera trap days) per month over the 2006–2011 survey period (bars) and relative species encounter rate (i.e., total independent photos of small carnivore spp./total camera trap day for the month). Relative encounter rates were highest during the warmest and well-surveyed months—peaks are observed in March (start of the warm season) and October (still within the warm season). Despite high survey effort in January and December (cold season), encounter rates were low.

Fig. 1 in Conservation importance of Nakai-Nam Theun National Protected Area, Laos, for small carnivores based on camera trap data

Fig. 1. Camera-trap sampling effort within Nakai–Nam Theun NPA in 2006–2011 (c.f. Table 1; Johnson et al., 2007) at 10 survey blocks; in chronological order of survey: (1) Khamkeut – Nam San; (2) Nam On – Boualapha; (3) Nam On – Gnomalath; (4) Khamkeut – Thong Pae; (5) Nam Chae – Makfuang; (6) Nam Chae – Navang; (7) Phou Vang – Houay Nam Heuy; (8) Thong Xet; (9) Nam Mon – Thongkacheng; (10) Nam Theun – reservoir.

opencc-by-4.0Jun 2021View details →

Fig. 3. Land use and land cover data for 2014 in Population trends and conservation status of proboscis monkeys (Nasalis larvatus) in the face of habitat change in the Klias Peninsula, Sabah, Borneo, Malaysia

Fig. 3. Land use and land cover data for 2014/2015 within the 1-km buffer distance from surveyed rivers, overlaid with proboscis monkey sightings from the 2004/2005 and 2014 surveys, Protected Areas, and Production Forest Reserve boundaries.

opencc-zeroNov 2022View details →

Data for: Brood parasitism of Hooded Warblers by Brown-headed Cowbirds: Severe impact on individual nests but modest consequences for seasonal fecundity and conservation

<div> <div> <div> <div> Brood parasitism by Brown-headed Cowbirds (Molothrus ater) often has pronounced negative effects on host nests. However, the extent to which parasitism reduces annual reproduction and presents conservation challenges for host species is unclear. We address this issue with data from a color-banded population of Hooded Warblers (Setophaga citrina) in Pennsylvania, where Hooded Warblers have increased dramatically despite frequent nest parasitism. Our analysis is based on both an extensive dataset (8 years, 847 nests) on the per-nest impacts of cowbird parasitism, and female-based stochastic simulations that accurately reflect the reproductive biology and parasitism rate (30%) of our study population. Cowbird parasitism has multiple negative consequences for Hooded Warbler nests, including: (1) reduced host clutch size, (2) increased nest abandonment, (3) increased risk of complete failure due to predation, and (4) in surviving nests increased egg loss, hatching failure, and nestling mortality. We estimate that parasitism reduces success of Hooded Warbler nests 68%, from 1.29 to 0.41 fledglings per nest. For females and populations, however, the consequences of nest parasitism are considerably less extreme; female annual fecundity decreases 25% for each nesting attempt parasitized, and population-level fecundity drops 5.6% for each 10% increase in the frequency of parasitism. These more modest impacts are attributable to: (1) steep declines in rates of cowbird parasitism as the nesting season progresses, (2) rapid re-nesting following abandonment or failure of parasitized nests, and (3) regular double brooding, with second broods initiated in late June and July when the incidence of cowbird parasitism is low. Our results help resolve the paradox of how cowbird parasitism can have both severe consequences for individual host nests but more modest and sustainable conservation impacts on the seasonal fecundity of females and populations. They further underscore the importance of determining population-level effects of brood parasites before investing in costly management efforts. </div> </div> </div> </div>

opencc-zeroJan 2023View details →

Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth's total biodiversity and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.