cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp3/piygpm
title: Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (&lt;em&gt;Ochotona princeps&lt;/em&gt;) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism (SNP)-based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (&lt;em&gt;n&lt;/em&gt;=158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair, some of which have been previously linked to putative high elevation and/or climate adaptation that may serve as important targets in future studies.&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;This research made use of previously archived short-read sequencing data deposited in the NCBI sequence read archive (BioProject ID: PRJNA1075342).&lt;/p&gt;
description: <b>Dryad version number:</b> 2
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.2bvq83bzf
<b>Storage size:</b> 285479572
<b>Visibility:</b> public
DOI: 10.5683/sp3/oyiknb
title: Turkey vulture (Cathartes aura) ingested plastics data

description: This dataset describes the analysis of regurgitated pellets collected from four communal turkey vulture (Cathartes aura) roosts in southern Ontario over three years (2021-2023). The pellets were analyzed for anthropogenic debris (plastics and other garbage), in addition to types of natural non-digestible materials.
DOI: 10.5683/sp3/leerjt
title: ABoVE: Synthesis of Burned and Unburned Forest Site Data, AK and Canada, 1983-2016

description: This record is for the dataset “ABoVE: Synthesis of Burned and Unburned Forest Site Data, AK and Canada, 1983-2016 ” at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1744"&gt;https://doi.org/10.3334/ORNLDAAC/1744&lt;/a&gt;. 
&lt;p&gt;&lt;p&gt;
This dataset is a synthesis of field plot characterization data, derived above-ground and below-ground combusted carbon, and acquired Fire Weather Index (FWI) System components for burned boreal forest sites across Alaska, USA, the Northwest Territories, and Saskatchewan, Canada from 1983-2016. Unburned plot data are also included. Compiled plot-level characterization data include stand age, disturbance history, tree density, and tree biophysical measurements for calculation of the above-ground (ag) and below-ground (bg) biomass/carbon pools, pre-fire and residual post-fire soil organic layer (SOL) depths and estimates of combustion of tree structural classes. The measured slope and aspect for each site and an assigned moisture class based on topography are also provided. Data from 1019 burned and 152 unburned sites are included. From the estimates of combusted ag and bg carbon pools and SOL losses, the total carbon combusted, the proportion of pre-fire carbon combusted, and the proportion of total carbon combusted were calculated for each plot. FWI System components including moisture and drought codes and indices of fire danger were obtained for each plot from existing data sources based on the plot location, year of burn, and a dynamic start-up date (day of burn, DOB) from the global fire weather database. Data for soil characteristics are included in a separate file.&lt;p&gt;
This dataset can be downloaded at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1744"&gt;https://doi.org/10.3334/ORNLDAAC/1744&lt;/a&gt;.
DOI: 10.5683/sp3/xoqmfb
title: Optimization of environmental DNA-based methods: A case study for detecting brook trout (Salvelinus fontinalis)

description: The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and passive sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods reduces the sensitivity of this approach and precludes the reliable comparison of findings across studies, respectively. DNA extraction is a prime target for optimization efforts because the extraction method is highly variable across eDNA studies despite being the most influential factor in detection efficiency across the entire post-collection workflow. Sequence analysis is arguably the least standardized step in the workflow, with new bioinformatics pipelines frequently emerging in the literature and being implemented with innumerable unique combinations of parameter values. The current study aimed to support the optimization and standardization of eDNA methods for fish detection by assessing two commercial DNA extraction kits manufactured by Qiagen and Macherey-Nagel on cost, time, and performance specifications and comparing the success of brook trout detection by metabarcoding across three bioinformatics pipelines, qPCR, and ddPCR. Our protocols were effective in detecting brook trout in all 20 samples analyzed. Brook trout eDNA was detected by ddPCR in nine (90%) Qiagen extracts but only seven (70%) Macherey-Nagel extracts. In comparison, detection success was equal across the two extraction kits using qPCR (70%) and metabarcoding (100%). The metabarcoding pipelines performed equally well in detecting brook trout with no significant differences in read numbers associated with the target species. Under our experimental conditions, the Qiagen kit was selected as the preferred kit due to its overall good performance and considerably lower cost despite a slightly longer extraction time.
DOI: 10.5683/sp3/eaupeo
title: Soil Respiration Maps for the ABoVE Domain, 2016-2017

description: This record is for the dataset “Soil Respiration Maps for the ABoVE Domain, 2016-2017” at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1935 /"&gt; https://doi.org/10.3334/ORNLDAAC/1935 &lt;/a&gt;
&lt;p&gt;&lt;p&gt; 
This dataset provides gridded estimates of carbon dioxide (CO2) emissions from soil respiration occurring within permafrost-affected tundra and boreal ecosystems of Alaska and Northwest Canada at a 300 m spatial resolution for the period 2016-08-18 to 2018-09-12. The estimates include monthly average CO2 flux (gCO2 C m-2 d-1), daily average CO2 flux and error estimates by season (Autumn, Winter, Spring, Summer), estimates of annual offset of CO2 uptake (i.e., vegetation GPP), annual budgets of vegetation gross primary productivity (GPP; gCO2 C m-2 yr-1), and the fraction of open (non-vegetated) water within each 300 m grid cell. Belowground sources of respiration (i.e., root and microbial) are included. The gridded soil CO2 estimates were obtained using seasonal Random Forest models, information from remote sensing, and a new compilation of in-situ soil CO2 flux from Soil Respiration Stations and eddy covariance towers. The flux tower data are provided along with daily gap-filled flux observations for each Soil Respiration station forced diffusion (FD) chamber record. The data cover the NASA ABoVE Domain.&lt;p&gt;
This dataset can be downloaded at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1935 /"&gt; https://doi.org/10.3334/ORNLDAAC/1935 &lt;/a&gt;
DOI: 10.5683/sp3/vjowt2
title: Infected conspecifics avoidance in Lepomis gibbosus, Laurentides, Quebec [2022]
title: Évitement des congénères infectés chez Lepomis gibbosus, Laurentides, Québec [2022]

description: Data were collected in summer 2022 at the Station de biologie des Laurentides de l’Université de Montréal (Saint-Hippolyte, Quebec, Canada). The experiments were carried out in the laboratory on wild caught pumpkinseed sunfish (Lepomis gibbosus). For each individual, data were recorded on time spent with infected and uninfected conspecifics, lake of origin, total and standard length, body mass, spleen mass, sex, number of cestodes, trematodes and other parasites (yellow grub, white grub, nematodes). The purposes of the data were to assess whether uninfected pumpkinseed sunfish display avoidance behaviour towards infected conspecifics, whether they can detect infection using chemical and/or visual cues and whether the expression of this behaviour is influenced by the level of parasite exposure of focal fish in their natural environment.
description: For each fish (ID), 2 trials were done to measure the time spent on each side:
-Control 1: Uninfected conspecifics VS No fish;
-Control 2: Infected conspecifics VS No fish;
-Treatment: Infected conspecifics VS Uninfected conspecific.

METADATA:
-ID: Identification of the focal fish; 
-Lake: Origin of the focal fish (Triton or Cromwell);
-Treatment: Experiment set up (Control 1, Control 2 or Treatment);
-Tank: Holding tank in lab;
-Trial: First or second focal fish trial (1 or 2);
-Temp_exp: Temperature of the arena during trials (Celcius) ;
-Time_exp: time of the day the test to place (am or pm);
-Side_Fish: Side of the arena where stimuli fish are (for Control 1 and 2);
-Side_Uninf: Side of the arena where uninfected stimuli fish are (for Treatment);
-TL: Total length of focal fish (mm);
-SL: Standard length of focal fish (mm);
-Mass = Mass of focal fish (g);
-a = Constant in the equation Mass = a * SL^b;
-b = Constant in the equation Mass = a * SL^b;
-Spleen_mass: Spleen mass of the focal fish (g);
-Sex: Sex of the focal fish (Male, Female, NA);
-BS_tot: Total number of blackspot parasites; 
-BT_tot: Total number of bass tapeworm parasites;
-Other: Total number of yellow grub and nematode parasites; 
-Total_parasites: Total number of parasites;
-Parasites_density: Total_parasites / Mass; 
-Infected_zone: Time spent with infected conspecifics (s);
-Uninfected_zone: Time spent with uninfected conspecifics (s); 
-None_zone: Time spent with no fish (Control only) (s);
-Neutral_zone: Time spent in the center of the arena (Visual cues only) (s);
-Total_time: Duration of the trial;
-Shoal: Number of the shoal used as stimulus;
-Notes: Any notes taken during the experiment or the dissection.
DOI: 10.5683/sp3/aq4qgi
title: Zooplankton abundance in 45 lakes in La Mauricie National Park [2019]
title: Abondance du zooplancton dans 45 lacs du Parc national de la Mauricie [2019]

description: Data were collected between 17 June and 11 July 2019. For each sample, data was recorded on the time, date, sample coordinates, time of day, transect location (in macrophytes or in pelagic zones), the presence or absence of macrophytes in the lake and the number of individuals for different zooplankton size-taxa. The samples were collected using a plankton net with a 63-micrometre wick in the first 50 cm of the water column. The aim of the data was to assess the differences in zooplankton abundance between areas with and without macrophytes, and between nearshore and pelagic areas, during the day and at night.
description: The file contains the following variables and units of measurement: date, time, latitude, longitude, period, region, profmoy (m), water temperature (°C), water transparency, external temperature (°C), macrophytes (presence or absence), zooplankton taxa (count).
DOI: 10.5683/sp3/ybnors
title: ABoVE: Landsat-derived Annual Dominant Land Cover Across ABoVE Core Domain, 1984-2014

description: This record is for the dataset “ABoVE: Landsat-derived Annual Dominant Land Cover Across ABoVE Core Domain, 1984-2014” at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1691"&gt;https://doi.org/10.3334/ORNLDAAC/1691&lt;/a&gt;
&lt;p&gt;&lt;p&gt; 
This dataset provides two 30-m resolution time series products of annual land cover classifications over the Arctic Boreal Vulnerability Experiment (ABoVE) core domain for each year of the period 1984-2014. The data are the annual dominant plant functional type in a given 30-m pixel derived from Landsat surface reflectance, landcover training data mapped across the ABoVE domain (using Random Forests modeling, with clustering and interpretation of field photography) and very high resolution imagery to assign land cover classifications. One product has a 15-class land cover classification that breaks out forest and shrub types into several additional classes; the other product provides a simplified, 10-class approach. Classification accuracy assessment results are provided per year. Assessments were based on a probability-based random sample of reference data that supported statistically robust estimation of areas and uncertainties in mapped areas. &lt;p&gt;
This dataset can be downloaded at &lt;a href= "https://doi.org/10.3334/ORNLDAAC/1691"&gt;https://doi.org/10.3334/ORNLDAAC/1691&lt;/a&gt;
DOI: 10.5683/sp3/spbutq
title: Zooplankton data in 3 Lakes in La Mauricie National Park [2020]
title: Données sur le zooplancton dans 3 lacs du Parc national de la Mauricie [2020]

description: Data were collected between 28 August and 15 September 2020. For each sample, data was recorded on the time, date, transect coordinates, time of day, distance from the shore (m), sampling place (surface or bottom) and the number of individuals for different zooplankton size-taxa. The samples were collected using a Schindler-Patalas box. The aim of the data was to assess zooplankton abundance as a function of a horizontal gradient in distance from the bank during the day and at night.
description: The file contains the following variables and units of measurement: date, time, latitude, longitude, period, distance (m), place (surface or bottom), sample depth (m), zooplankton taxa (count).
DOI: 10.5683/sp3/djyu6f
title: ABoVE: Wetland Inundation Coverage at Yukon Flats, AK and PA Delta, Canada, 2017-2019

description: This record is for the dataset “ABoVE: Wetland Inundation Coverage at Yukon Flats, AK and PA Delta, Canada, 2017-2019” at &lt;a href= " https://doi.org/10.3334/ORNLDAAC/1901"&gt;https://doi.org/10.3334/ORNLDAAC/1901&lt;/a&gt;
&lt;p&gt;&lt;p&gt; 

This dataset provides time series of wetland inundation coverage maps and corresponding inundation frequency maps at ~10-meter resolution estimated every 12 days during the free-water period (May to October) for the years 2017-2019 over the Yukon Flats (YK) portion of the Yukon River, Alaska, USA, and the Peace-Athabasca Delta (PAD), Alberta, Canada. Wetland inundation coverage was determined by a two-step modified decision-tree classification approach that first used Sentinel-1 C-band SAR to identify likely inundated areas across a study site and was followed by a decision-tree classification step with C-band SAR backscatter statistics thresholds to distinguish among different inundation components. The result of this process was five classes for each inundation map, namely Open Water (OW), Floating Plants (FP), Emergent Plants (EP), Flooded Vegetation (FV), and Dry Land (DRY). After all the individual (every 12 days) inundation coverage maps were derived for a study site, they were generalized to two-class maps which maintained only inundation status. These generalized maps were then stacked and summarized to produce the inundation frequency map for the site. In these maps, higher values signify more frequently inundated areas, with the maximum value representing permanently inundated pixels. The Sentinel-1 inundation mapping capability demonstrated here provided frequent, broad-scale mapping of different wetland inundation components. Integration of such products with process-based methane (CH4) models would improve simulation of CH4 emissions from wetlands. &lt;p&gt;
This dataset can be downloaded at &lt;a href= " https://doi.org/10.3334/ORNLDAAC/1901"&gt;https://doi.org/10.3334/ORNLDAAC/1901&lt;/a&gt;
DOI: 10.5683/sp3/rej1ac
title: Black spruce seed availability and viability after fire, Northwest Territories, Canada

description: This record is for the dataset “Black spruce seed availability and viability after fire, Northwest Territories, Canada” at &lt;a href= " https://doi.org/10.5061/dryad.z8w9ghxg4"&gt; https://doi.org/10.5061/dryad.z8w9ghxg4&lt;/a&gt;
&lt;p&gt;&lt;p&gt; 
&lt;b&gt;Context &lt;/b&gt; &lt;p&gt; Black spruce ( Picea mariana ) is an important conifer in boreal North American that develops a semi-serotinous, aerial seedbank and releases a pulse of seeds after fire. Variation in post-fire seed rain has important consequences for black spruce regeneration and stand composition. &lt;p&gt;

&lt;b&gt;Aims &lt;/b&gt;&lt;p&gt; We explore the possible effects of changes in fire regime on the abundance and viability of black spruce seeds following a very large wildfire season in the Northwest Territories, Canada (NWT). &lt;p&gt;

&lt;b&gt;Methods&lt;/b&gt;&lt;p&gt; We measured post-fire seed rain over two years at 25 black spruce dominated sites and evaluated drivers of stand characteristics and environmental conditions on total black spruce seed rain and viability. &lt;p&gt;

&lt;b&gt;Results &lt;/b&gt;&lt;p&gt; We found a positive relationship between black spruce basal area and total seed rain. However, at high basal areas this increasing rate of seed rain was not maintained. Viable seed rain was greater in stands that were older, closer to unburned edges, and where canopy combustion was less severe. Finally, we demonstrated positive relationships between seed rain and seedling establishment, confirming our measures of seed rain were key drivers of post-fire forest regeneration. &lt;p&gt;

&lt;b&gt;Conclusion&lt;/b&gt; &lt;p&gt; These results suggest that black spruce recruitment after fire may be reduced with projected increases in fire activity. &lt;p&gt;
This dataset can be downloaded at &lt;a href= " https://doi.org/10.5061/dryad.z8w9ghxg4"&gt; https://doi.org/10.5061/dryad.z8w9ghxg4&lt;/a&gt;
DOI: 10.5683/sp3/ttwhhf
title: Biennial aerial application of Bacillus thuringiensis Berliner var. kurstaki is the most cost-effective approach of protection against spruce budworm (Choristoneura fumiferana [Clemens])

description: The main goal of this study is to evaluate the efficacy of different protection scenarios in reducing tree mortality and growth losses over a 11-year period (2010-2020) in mixed fir-spruce stands that are dominated by mature balsam fir trees. We hypothesize that a less-intensive protection approach (Btk applications every 2 years) may provide a level of protection similar to the standard program currently used in the Province of Quebec. In 2007, we established nineteen 100-ha experimental units in Quebec’s Côte-Nord region to determine the efficacy of different Btk spraying scenarios for reducing tree mortality and volume losses in mixed stands of balsam fir (Abies balsamea [L.] Mill.), white spruce (Picea glauca [Moench] Voss) and black spruce (P. mariana [Mill.] BSP). Tree mortality was monitored annually in three circular plots of 400 m2 within each experimental unit. Growth losses were evaluated using stem analyses. This dataset contains the rawdata used in the related paper publish in Annals of Forest Science. The variables included in the dataset are tree mortality, annual volume increment (AVI), specific volume increment (SVI), and defoliation by host species and year since the first aerial application of Btk in the experimental unit.
description: The data is in the sheet named "raw data" and the description of the variables is in the sheet named "variables".
DOI: 10.5683/sp3/pep31x
title: Replication Data for: Misallocation in the Chinese Land Market

description: The data and programs replicate tables and figures from "Misallocation in the Chinese Land Market", by Fei, Hu, and Xu. Please see the ReadMe file for additional details.
DOI: 10.5683/sp3/svcvxv
title: Comparing PolSAR, SAR and Optical Imagery Integration for Forest Canopy Height Estimation in Interior British Columbia, Canada

description: Forest canopy height is an important indicator for estimating forest carbon stock and biomass, which have implications for multiple environmental issues. In remote sensing, canopy height is most commonly measured using light detection and ranging (LiDAR), which comes with satisfactory accuracy but also high costs. This study looked at the potential of using synthetic aperture radar (SAR) and polarimetric synthetic aperture radar (PolSAR), together with optical imagery, to estimate canopy height in an interior coniferous forest in British Columbia, Canada. A machine learning approach was used to derive the canopy height values. SAR backscatter coefficients from Sentinel-1 and ALOS-2, as well as PolSAR parameters from Sentinel-1, were used as independent variables. Sentinel-2 optical indices and bands were fused as independent variables in some trials in an attempt to further enhance model performance. LiDAR-extracted canopy height values served as ground truth for both model training and validation. We compared between using SAR backscatter and PolSAR parameters, as well as between using SAR backscatter from Sentinel-1 and ALOS-2. Results show that PolSAR parameters outperforms SAR backscatter in predicting canopy height, while ALOS-2 achieved better accuracy in canopy height estimation than Sentinel-1. Optical indices and bands were capable of enhancing model accuracy in all scenarios. To conclude, Sentinel-1 PolSAR parameters were the best predictor variables due to PolSAR’s ability to capture different scattering mechanisms under different canopy heights. Future studies should examine the potential of polarimetric synthetic aperture radar interferometry (PolInSAR) and ALOS-2 PolSAR to yield more accurate canopy height estimation over interior coniferous forests.
description: R
DOI: 10.5683/sp3/zyiq2u
title: Mapping the Unseen: Identifying Data Gaps and Proposing New Sampling Points in Northern Boreal Mountain Eco-province, BC Using K-Means Clustering and cLHS

description: This study investigates the soil variability within the Northern Boreal Mountains Ecoprovince in British Columbia, with a particular focus on wetland soils and soil organic carbon mapping. Utilizing the BCSOIL2020 dataset and an array of environmental covariates, we employed Principal Component Analysis (PCA), k-means clustering, and conditioned Latin Hypercube Sampling (cLHS) to develop a comprehensive environmental covariate space. This approach allowed for the evaluation of the BCSOIL2020 dataset's representativeness of the current distribution of wetland soils and the generation of new, strategically placed sampling plots aimed at enhancing future research efforts. Through this methodology, the study identifies critical data gaps in existing datasets and proposes a methodological framework for improving soil mapping practices, thereby contributing to more informed resource management and conservation strategies.