cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.x8xhmp
title: Occurrence Download

description: A dataset containing 14001 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gamochaeta purpurea (L.) Cabrera"
 ]
}

 The dataset includes 14001 records from 474 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027211-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/f75h7f5m
title: Combined wildfire dataset for the United States and certain territories, 1870-2015

description: The increase in wildfires, particularly in the western U.S., represents one of the greatest threats to multiple native ecosystems. Despite this threat, there is currently no central repository to store both past and current wildfire perimeter data. Currently, wildfire boundaries can only be found in disparate local or national datasets. These datasets are generally restricted to specific locations, fire sizes, or time periods. Our first objective was to create a comprehensive national wildfire perimeter dataset by combining all freely available wildfire datasets that we could download. We combined and dissolved individual wildfire polygons from multiple datasets if they were in the same year and overlapped each other or were within 1km of the fire boundary. This combined dataset includes spatial summary statistics such as number of times burned, earliest fire of record, and most recent fire of record. Our second objective was to create various seasonal weather rasters (for example October-March, April-June, July-September, and October-September precipitation and temperature) using PRISM (http://www.prism.oregonstate.edu/) weather data to identify weather factors from the focal year and 1-3 years previous that may lead to an increase in the number and size of wildfires.
DOI: 10.15468/dl.brbgnk
title: Occurrence Download

description: A dataset containing 2039 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Chile, Argentina)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Fuchsia magellanica Lam."
 ]
}

 The dataset includes 2039 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027214-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/63b8ae3b8b413754f658766f62b12089
title: Hourly Meteorological Data for the Virginia Coast Reserve LTER 1989-present

description: Data from VCR/LTER meteorological stations is listed in comma-separated-value (CSV) files by year. A combined file for all years is also available, sorted by station, date and time, however, unlike the annual files, this combined file is too large for most spreadsheets to handle. A compressed copy of all the .CSV files is included in a single .ZIP file for users who wish to conveniently download a copy of all the data.
DOI: 10.6084/m9.figshare.29039416.v1
title: Standard methods and good practices in <i>Apis</i> honey bee omics research

description: In the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access <i>BEEBOOK</i> volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in <i>Apis mellifera</i>,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other <i>Apis</i> species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipelines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.
DOI: 10.6084/m9.figshare.25576879
title: Effect of protein and lipids in pollen on the developmental success of the native solitary bee <i>Osmia lignaria</i> Say

description: The health of solitary bees is dependent on the pollen they consume, driving their development from larvae to pupae. Nutrients such as proteins and lipids play an important role in bee development and could be an important key in conservation efforts to support declining populations. We examined the concentration of protein, total lipids, and 13 individual lipid classes in pollen provisions collected from the native solitary nesting bee, <i>Osmia lignaria</i> Say, at 22 sites in urban and rural landscapes in western Washington over three years and during two distinct foraging periods. The results indicate that protein concentrations in pollen did not significantly affect larval development. We detected higher lipid concentrations in the second foraging period, which was also associated with increased larval developmental success. Using Next-Generation sequencing on collected pollen, we also ascertained the plant genera in pollen and observed that plant richness did not differ significantly between the two foraging periods even though levels of lipid concentrations did. Individual lipid classes may play a role in the successful development of <i>O. lignaria</i>, as hexosylceramide and cholesterol ester were positively associated with <i>O. lignaria</i> larval developmental success, which emphasizes the need for additional studies on the role of individual lipid classes on bee development.
DOI: 10.6084/m9.figshare.25576879.v1
title: Effect of protein and lipids in pollen on the developmental success of the native solitary bee <i>Osmia lignaria</i> Say

description: The health of solitary bees is dependent on the pollen they consume, driving their development from larvae to pupae. Nutrients such as proteins and lipids play an important role in bee development and could be an important key in conservation efforts to support declining populations. We examined the concentration of protein, total lipids, and 13 individual lipid classes in pollen provisions collected from the native solitary nesting bee, <i>Osmia lignaria</i> Say, at 22 sites in urban and rural landscapes in western Washington over three years and during two distinct foraging periods. The results indicate that protein concentrations in pollen did not significantly affect larval development. We detected higher lipid concentrations in the second foraging period, which was also associated with increased larval developmental success. Using Next-Generation sequencing on collected pollen, we also ascertained the plant genera in pollen and observed that plant richness did not differ significantly between the two foraging periods even though levels of lipid concentrations did. Individual lipid classes may play a role in the successful development of <i>O. lignaria</i>, as hexosylceramide and cholesterol ester were positively associated with <i>O. lignaria</i> larval developmental success, which emphasizes the need for additional studies on the role of individual lipid classes on bee development.
DOI: 10.6084/m9.figshare.29039416
title: Standard methods and good practices in <i>Apis</i> honey bee omics research

description: In the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access <i>BEEBOOK</i> volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in <i>Apis mellifera</i>,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other <i>Apis</i> species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipelines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.
DOI: 10.6084/m9.figshare.25435256.v1
title: Inconsistent changes on infuscation and length of the forewing of <i>Heterotrigona itama</i> populations supported by <i>COI</i> Phylogeny

description: No study has been done so far using a large number of data for investigating the morphological changes (infuscation and length of the forewings) of the <i>Heterotrigona itama</i> populations, and constructing its phylogeny using the cytochrome c oxidase (<i>COI</i>) sequences. Through this research, the origin of the plant species of each colony will be estimated and may confirm does the movement of log beehives is supported by the <i>COI</i> phylogeny or not. That information still is not understood and is very crucial as the basis of genetic information and implies evolutionary transition and conservation programmes. In this study, the samples of <i>H. itama</i> from 37 colonies throughout Malaysia were collected from log beehives in varied ecosystems, wild (several forest types) and non-wild (orchards and residential areas). In this study, the non-infuscated front wings found in many <i>H. itama</i> populations are widely distributed in the East and West Malaysia populations, while no significant difference in <i>H. itama</i> populations (F <sub>(36, 369)</sub> = 1.84, <i>p</i> &gt; 0.05) was observed in the length of the forewing. The Neighbour-Joining (NJ), Maximum Parsimony (MP), and Bayesian inference (BI) trees of the <i>COI</i> showed a mixture between colonies and sampling sites on the tree topologies, except the Seberang Perai colony where the beehive log was collected from the mangrove tree. The results of the phylogenetic analyses supported the findings on the morphological changes that are probably due to the movement of log beehives, however, it is not parallel with the changing ecosystem types.
DOI: 10.6084/m9.figshare.25435256
title: Inconsistent changes on infuscation and length of the forewing of <i>Heterotrigona itama</i> populations supported by <i>COI</i> Phylogeny

description: No study has been done so far using a large number of data for investigating the morphological changes (infuscation and length of the forewings) of the <i>Heterotrigona itama</i> populations, and constructing its phylogeny using the cytochrome c oxidase (<i>COI</i>) sequences. Through this research, the origin of the plant species of each colony will be estimated and may confirm does the movement of log beehives is supported by the <i>COI</i> phylogeny or not. That information still is not understood and is very crucial as the basis of genetic information and implies evolutionary transition and conservation programmes. In this study, the samples of <i>H. itama</i> from 37 colonies throughout Malaysia were collected from log beehives in varied ecosystems, wild (several forest types) and non-wild (orchards and residential areas). In this study, the non-infuscated front wings found in many <i>H. itama</i> populations are widely distributed in the East and West Malaysia populations, while no significant difference in <i>H. itama</i> populations (F <sub>(36, 369)</sub> = 1.84, <i>p</i> &gt; 0.05) was observed in the length of the forewing. The Neighbour-Joining (NJ), Maximum Parsimony (MP), and Bayesian inference (BI) trees of the <i>COI</i> showed a mixture between colonies and sampling sites on the tree topologies, except the Seberang Perai colony where the beehive log was collected from the mangrove tree. The results of the phylogenetic analyses supported the findings on the morphological changes that are probably due to the movement of log beehives, however, it is not parallel with the changing ecosystem types.
DOI: 10.5066/f7wd3zrd
title: Western US 30m Heatload Derived Using McCune and Dylan (2002)

description: Heat load, a unitless value from 0 (low incident radiation) to around 1 (high incident radiation), is calculated using aspect, slope, and latitude (McCune and Dylan 2002 ). For the purposes of the planning tool, the data are binned into 6 classes using Geometric Interval. Classes range from very low to very high and are designed to allow the classification of a polygon into its heat load types.
DOI: 10.15468/dl.9a7cbb
title: Occurrence Download

description: A dataset containing 250481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nymphaeales)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1981",
 "Geometry POLYGON((-30 25,50 25,50 75,-30 75,-30 25))"
 ]
}

 The dataset includes 250481 records from 1027 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027206-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nz6mdr
title: Occurrence Download

description: A dataset containing 4016880 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pinales)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1981",
 "Geometry POLYGON((-30 25,50 25,50 75,-30 75,-30 25))"
 ]
}

 The dataset includes 4016880 records from 3355 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027207-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vsp4h3
title: Occurrence Download

description: A dataset containing 4589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((136.28259 14.63557,176.76151 68.92276,125.87912 74.21907,91.83139 36.57743,62.32337 42.06289,69.13292 5.55617,116.61054 -21.3037,133.25608 -2.19915,107.61971 17.83032,108.33467 20.80931,111.37324 21.34553,136.28259 14.63557))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Perilla frutescens"
 ]
}

 The dataset includes 4589 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028735-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xa2hvm
title: Occurrence Download

description: A dataset containing 907 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Afrocarpus falcatus (Thunb.) C.N.Page"
 ]
}

 The dataset includes 907 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010764-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3s235
title: Occurrence Download

description: A dataset containing 36817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36817 records from 429 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005974-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9ehe2
title: Occurrence Download

description: A dataset containing 9372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "Depth 200.0-1000.0m",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 9372 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005976-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sabeu7
title: Occurrence Download

description: A dataset containing 74656 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Handroanthus Mattos"
 ]
}

 The dataset includes 74656 records from 570 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002011-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.br8pqj
title: Occurrence Download

description: A dataset containing 8238 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-14.86945 23.37456,87.61631 23.37456,87.61631 64.90477,54.38071 74.86774,-14.86945 64.90477,-14.86945 23.37456))",
 "HasGeospatialIssue is false",
 "TaxonKey is Asclepias syriaca L."
 ]
}

 The dataset includes 8238 records from 209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000132-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15275987
title: Parasites alter interaction patterns in fish social networks

description: The data and code for the paper "Parasites alter interaction patterns in fish social networks" published in Proceedings of the Royal Society B. For a description of data and code see "README.txt".
DOI: 10.5281/zenodo.15275988
title: Parasites alter interaction patterns in fish social networks

description: The data and code for the paper "Parasites alter interaction patterns in fish social networks" published in Proceedings of the Royal Society B. For a description of data and code see "README.txt".
DOI: 10.15468/dl.hdefbd
title: Occurrence Download

description: A dataset containing 9370 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus maritimus Phipps, 1774"
 ]
}

 The dataset includes 9370 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012748-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hqkkwt
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Matsumurides okinawanus (Matsumura, 1931), Matsumurides lateritia (Hering, 1931), Matsumurides bicolor (Shiraki, 1913), Matsumurides lola (Swinhoe, 1904), Matsumurides bisuroides (Hering, 1931), Matsumurides lateritia (Hering, 1931), Matsumurides thaumasta (Hering, 1933), Matsumurides lola (Swinhoe, 1904), Matsumurides lola (Swinhoe, 1904), Allothosea lola, Matsumurides bicolor (Shiraki, 1913), Matsumurides montana (Holloway, 1986), Matsumurides lateritia (Hering, 1931), Matsumurides lola (Swinhoe, 1904), Matsumurides thaumasta (Hering, 1933), Matsumurides bisuroides (Hering, 1931), Matsumurides okinawanus (Matsumura, 1931), Matsumurides okinawanus (Matsumura, 1931), Matsumurides montana (Holloway, 1986), Matsumurides thaumasta (Hering, 1933))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001790-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcfwj6
title: Occurrence Download

description: A dataset containing 62602 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cercopidae"
 ]
}

 The dataset includes 62602 records from 630 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0223733-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11577540
title: Supplement - Structure from Motion Metadata and Outcomes

description: Ground control points used to ensure Structure from Motion (SfM) terrain models were georectified (Westoby et al. 2012; Wolf 2021) using Emlid R2 RTK (real-time kinematic) GNSS (global navigation satellite system) system consisting of a base station set up over an established known point (established with Canadian Geodetic Survey of Natural Resources Canada (NRCAN) service Canadian Spatial Reference System Precise Point Positioning (CSRS- PPP)) and a rover. 

Once the ground control points were surveyed, aerial drone images were acquired. We created flight polygons in Drone Deploy. Pictures were captured with a DJI Mavic II drone with minimum 80 % overlap of photos. Drone Deploy was chosen because it has an option to account for the doming error commonly found in models created from drone imagery and structure from motion (SfM). The doming effect is a systematic error that impacts the DEMs vertical component and can provide errors larger than the usual centimeter level (Sanz-Ablanedo et al. 2020). Generally, each site was flown once in fall of 2020 and once in spring of 2021. 

We created orthorectified images and digital terrain models using Agisoft Metashape, a photogrammetric processing software application that uses SfM. We followed the workflow outlined in Bywater-Reyes and Pratt-Sitaula (2022). Once processed, orthorectified imagery and Digital Elevation Models (DEMs) were exported to ArcGIS Pro for additional analysis. Data collection metadata and postprocessing outcomes can be found in this Zenodo repository.
DOI: 10.5281/zenodo.11580803
title: Supplement - Structure from Motion Raster Data

description: We created orthorectified images and digital elevation models using Agisoft Metashape, a photogrammetric processing software application that uses SfM. We followed the workflow outlined in Bywater-Reyes and Pratt-Sitaula (2022). Once processed, orthorectified imagery and Digital Elevation Models (DEMs) were exported to ArcGIS Pro for additional analysis. Data collection metadata and postprocessing outcomes can be found in this repository. 
description: Projected Coordinate System
NAD 1983 UTM Zone 13N


Projection
Transverse Mercator


WKID
26913


Authority
EPSG


Linear Unit
Meters (1.0)




 




Geographic Coordinate System
NAD 1983


WKID
4269


Authority
EPSG


Datum
D North American 1983




Orthometric HeightCGVD2013(CGG2013a)