cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.573n5tb6g
title: Seasonality in Kgalagadi lizards: inferences from legacy data

description: This data set compiles field and dietary data on Kagalagadi lizards,
 collected in 1969-70. The data are used in: Huey, R. B., D. B. Miles, and
 E. R. Pianka. 2021. Seasonality in Kgalagadi lizards: Inferences from
 llegacy data. American Natualist in press. This paper addresses
 whether legacy data -- or other data that had been
 gathered for unrelated purposes -- can be relevant to contemporary
 ecological issues. The data used here were gathered a
 half-century ago. Natural-history data were compiled for 18 species of
 Kgalagadi lizards and then used to explore aspects of the seasonal ecology
 of these lizards, emphasizing winter. The data include species, body size
 (snout-to-vent length, SVL in mm, mass in g), sex, date, time of day, body
 temperature (°C), air temperature (°C), and food volume (ml). These
 natural history data were not gathered with a study of seasonal ecology in
 mind but nonetheless inform diverse seasonal patterns for a major
 community of lizards. The paper discussed challenges and ambiguities in
 using repurposed data (whether recent or legacy).
description: Most data were collected and recorded directly on the field, but
 dietary data was obtained later from stomach contents.
 Data were originally saved on punch cards, but are saved here as
 Excel files. The original field notes will be deposited at the Los Angeles
 County Museum of Natural History, where all specimens are
 stored.
description: Several data sets are available. Missing values are indicated by
 NA.  All data sets and their variables are described in
 a README.
DOI: 10.5061/dryad.5hqbzkh4w
title: Notes on Fomitiporia Murrill in Amazon region: a list of species and new references

description: Twenty-three specimens of fungi of genus Fomitiporia Murrill, collected in
 the Amazonian region in the states of Amazonas and Roraima in their
 respective rainy periods were analyzed. The present study has both
 resulted in the description of eight species, namely F. apiahyna s. l.
 (Speg.) Robledo, Decock & Rajchenb., F. calkinsii (Murrill) Vlasák
 & Kout, F. conyana Alves-Silva & Drechsler-Santos, F.
 impercepta Morera, Robledo&Urcelay, F. langloisii Murrill, F.
 maxonii Murrill, F. murrillii Alves-Silva, R.M. Silveira &
 Drechsler-Santos and F. neotropica Camp.-Sant., Amalfi, R.M. Silveira,
 Robledo & Decock contributed with new records for the Amazonian
 region, Brazil and the Americas.
description: <i>Fomitiporia </i>specimens were collected from 2016 to 2017, in the states of Amazonas [Adolph Ducke Forest Reserve and Tropical Silviculture Experimental Station (ZF-2)] and Roraima (Maracá Ecological Station and Viruá Nacional Park) (Fig. 1). Specimens were photographed in scale, and, then, removed by hand or with the aid of a pocket knife (Fidalgo and Bononi 1989). They were packed separately in paper bags, and data related to site, date, collector, habitat and basidiomata (shape, consistency, mode of insertion in the substrate, coloring and dimensions), were recorded (Robledo and Urcelay 2009). The material was dried at a temperature close to 40<sup>o </sup>C, for 48–72 hours. Subsequently, all fungal exsiccates were deposited at the INPA Herbarium. Notes were taken regarding the basidiomata length, width and thickness, as well as hymenophore characteristics, pileus surface, pores and tube layers number and basidiomata consistency, in order to carry out the macroscopic analyses. Measurements were made with a ruler and/or caliper and the coloring was determined with the aid of Kueppers (1982). Microscopic structures: hyphal system, basidiospores, sterile elements (setae, cystidia) were characterized and measured, under a micrometer-eyepiece (Teixeira 1995). Melzer’s reagent (IKI) was used to check the dextrinoid or amyloid reaction of basidiospores and/or hyphae, 3% aqueous KOH (Potassium Hidroxide) solution which hydrates structures and determines xanthochroic and Cotton Blue reaction, to ascertain the cyanophilic reaction (Teixeira 1995). Microstructure illustrations were made from photos taken with a microscope-coupled camera (LEICA DM500).
DOI: 10.5061/dryad.2547d7wpr
title: Quantum interference between spin-orbit split partial waves in the F+HD→HF+D reaction

description: The effect of electron spin-orbit interactions on chemical reaction
 dynamics has been a topic of much research interest. Here we report a
 combined experimental and theoretical study on the effect of electron spin
 and orbital angular momentum in the F + HD → HF + D reaction. Using a
 high-resolution imaging technique, we observed a peculiar horseshoe-shaped
 pattern in the product rotational-state–resolved differential cross
 sections around the forward-scattering direction. The unusual dynamics
 pattern could only be explained properly by highly accurate quantum
 dynamics theory when full spinorbit characteristics were considered.
 Theoretical analysis revealed that the horseshoe pattern was largely the
 result of quantum interference between spin-orbit split–partial-wave
 resonances with positive and negative parities, providing a distinctive
 example of how spin-orbit interaction can effectively influence reaction
 dynamics.
DOI: 10.5061/dryad.4mw6m908k
title: Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured

description: Antarctic krill (Euphausia superba) are amongst the most abundant animals
 on Earth, with a circumpolar distribution in the Southern Ocean. Genetic
 and genomic studies have failed to detect any population structure for the
 species, suggesting a single panmictic population. However, the
 hyper-abundance of krill slows the rate of genetic differentiation,
 masking potential underlying structure. Here we use high-throughput
 sequencing of bacterial 16S rRNA genes to show that krill bacterial
 epibiont communities exhibit spatial structuring, driven mainly by
 distance rather than environmental factors, especially for strongly
 krill-associated bacteria. Estimating the ecological processes driving
 bacterial community turnover indicated this was driven by bacterial
 dispersal limitation increasing with geographic distance. Furthermore,
 divergent epibiont communities generated from a single krill swarm split
 between aquarium tanks under near identical conditions suggests physical
 isolation in itself can cause krill-associated bacterial communities to
 diverge. Our findings show that Antarctic krill-associated bacterial
 communities are geographically structured, in direct contrast with the
 lack of structure observed for krill genetic and genomic data.
description: High-throughput DNA sequencing of bacterial 16S rRNA genes. See
 paper for more details.
DOI: 10.5061/dryad.tht76hdz0
title: Raw data for predicting sample success for large-scale ancient DNA studies on marine mammals

description: In recent years, non-human ancient DNA studies have begun to focus on
 larger sample sizes and whole genomes, offering the potential to reveal
 exciting and hitherto unknown answers to ongoing biological and
 archaeological questions. However, one major limitation to the feasibility
 of such studies is the substantial financial and time investments still
 required during sample screening, due to uncertainty regarding successful
 sample selection. This study investigates the effect of a wide range of
 sample properties including latitude, sample age, skeletal element,
 collagen preservation, and context on endogenous content and DNA damage
 profiles for 317 ancient and historic pinniped samples collected from
 across the North Atlantic. Using generalised linear and mixed-effect
 models, we found that a range of factors affected DNA preservation within
 each of the species under consideration. The most important findings were
 that endogenous content varied significantly according to context, the
 type of skeletal element, the collagen content and collection year. There
 also appears to be an effect of the sample’s geographic origin, with
 samples from the Arctic generally showing higher endogenous content and
 lower damage rates. Both latitude and sample age were found to have
 significant relationships with damage levels, but only for walrus samples.
 Sex, ontogenetic age and extraction material preparation were not found to
 have any significant relationship with DNA preservation. Overall, the
 skeletal element and sample context were found to be the most influential
 factors and should therefore be considered when selecting samples for
 large-scale ancient genome studies.
description: Full details regarding data collection and processing can be
 found in the Molecular Ecology Resources article.
description: Samples listed are all those included in the study, not only
 those that were successfully sequenced.  Values for
 certain samples are not available if the sample was collected but did not
 provide a usable extraction. In such cases fields are filled with
 'NOT SCREENED'. As this represents a large
 number of samples of different species, collected by different individuals
 and prepared in two different labs not all information is available for
 some samples as this was never available/collected. In such cases either
 'NA' or 'Unknown' is used.  The
 first row provides a header for the table, with the second row providing a
 more detailed description of the data found in each column.
DOI: 10.5061/dryad.dv41ns1x1
title: Cryptic diversity on cliffs: Aster sanqingensis, a new species of Asteraceae from Eastern China

description: It is generally believed that cliffs bear low biodiversity because of its
 harsh habitats. However, another reason, i.e. insufficient investigation
 caused by the inaccessibility of the cliffs, could not be excluded. In the
 genus Aster, two cliff species, Aster fanjingshanicus and Aster
 tianmenshanensis, respectively growing on the slate and limestone cliffs,
 were established. During our extensive field investigations, the third
 cliff species of Aster growing on granite cliffs from Eastern China was
 found. Based on the evidence from molecular phylogeny, morphology, and
 micro-morphology, we proposed that it should be treated as a new species
 and named Aster sanqingensis. It is described and illustrated
 here. Considering its limited number of individuals, highly localized
 distribution, and disturbed habitat, we proposed to treat it as a
 critically endangered species. Our new finding indicates there is cryptic
 biodiversity on the cliffs remaining to be discovered.
DOI: 10.15468/dl.uuftgb
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cytisopsis pseudocytisus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 32 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002729-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uphm7z
title: Occurrence Download

description: A dataset containing 2031 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Engelhardia roxburghiana"
 ]
}

 The dataset includes 2031 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002730-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ht76hdrdq
title: Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America

description: Three distinct Canada jay (Perisoreus canadensis) morphotypes with easily
 recognizable plumage traits come into contact in western North America.
 Recent work demonstrated high genetic structure across the species’ range;
 however, patterns of genetic variation in these contact zones remain
 unknown. We categorized 605 individuals into one of three morphotypes
 (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped
 individuals at the mtDNA control region and 12 microsatellite loci to
 assess the extent of hybridization between morphotypes. Our data showed
 cryptic genetic diversity and high cytonuclear discordance among
 morphotypes within contact zones, which is likely the result of recent and
 historical admixture. The distributions of the Boreal and Pacific
 morphotypes each showed a strong association with a single, distinct
 genetic group, whereas the Rocky Mountain morphotype exhibited higher
 genetic diversity and was associated with multiple genotypes. Our analyses
 show the importance of considering both plumage and genetic traits when
 examining contact zones between closely related taxa. Finally, the data
 presented in this study reaffirm that the Pacific morphotype is distinct
 from the Boreal and Rocky Mountain morphotypes based on genetic,
 phenotypic, and ecological data, indicating that the Pacific morphotype
 should be re-elevated to a full species.
description: This file contains microsatellite genotyping data, as well as
 morphotype and mtDNA clade information.
DOI: 10.5061/dryad.pk0p2ngmh
title: Data from: Natural resistance to worms exacerbates bovine tuberculosis severity independently of worm coinfection

description: Pathogen interactions arising during coinfection can exacerbate disease
 severity, for example, when the immune response mounted against one
 pathogen negatively affects defense of another. It is also possible that
 host immune responses to a pathogen, shaped by historical evolutionary
 interactions between host and pathogen, may modify host immune defenses in
 ways that have repercussions for other pathogens. In this case, negative
 interactions between two pathogens could emerge even in the absence of
 concurrent infection. Parasitic worms and tuberculosis (TB) are involved
 in one of the most geographically extensive of pathogen interactions, and
 during coinfection, worms can exacerbate TB disease outcomes. Here, we
 show that in a wild mammal, natural resistance to worms affects bovine
 tuberculosis (BTB) severity independently of active worm infection. We
 found that worm-resistant individuals were more likely to die of BTB than
 were non-resistant individuals, and their disease progressed more quickly.
 Anthelmintic treatment moderated, but did not eliminate, the resistance
 effect, and the effects of resistance and treatment were opposite and
 additive with untreated, resistant individuals experiencing the highest
 mortality. Furthermore, resistance and anthelmintic treatment had
 non-overlapping effects on BTB pathology. The effects of resistance
 manifested in the lungs (the primary site of BTB infection), while the
 effects of treatment manifested almost entirely in the lymph nodes (the
 site of disseminated disease), suggesting that resistance and active worm
 infection affect BTB progression via distinct mechanisms. Our findings
 reveal that interactions between pathogens can occur as a consequence of
 processes arising on very different timescales.
description: The zip directory (Data.zip) contains data reported in the
 associated publication.
DOI: 10.5061/dryad.z612jm6b8
title: Volcanism and paleoclimate change drive diversification of world’s largest whip spider (Amblypygi)

description: The tropics contain many of the most biodiverse regions on Earth but the
 processes responsible for generating this diversity remain poorly
 understood. This study investigated the drivers of diversification in
 arthropods with stenotopic ecological requirements and limited dispersal
 capability using as model the monotypic whip spider (Amblypygi) genus
 Acanthophrynus, widespread in the tropical deciduous forests of Mexico. We
 hypothesized that for these organisms, the tropical deciduous forests
 serve as a conduit for dispersal, with their disappearance imposing
 barriers. Given that these forests are located in a region of complex
 geological history and fluctuated in extent during the
 Pliocene–Pleistocene glacial/interglacial cycles we couple molecular clock
 dating, paleoclimatic niche modeling and ancestral area reconstruction to
 test if and how habitat fragmentation promoted diversification in
 Acanthophrynus. Concomitant with the expected role of landscape change, we
 demonstrate that orogeny of the Trans-Mexican Volcanic Belt, in the Late
 Miocene/Early Pliocene (6.95–5.21 mya), drove the earliest divergence of
 Acanthophrynus through vicariance. Similarly, as expected, the later onset
 of glaciations strongly impacted diversification. Whereas a more stable
 climate in the southern part of the distribution enabled further
 diversification, a marked loss of suitable habitat during the glaciations
 only allowed dispersal and diversification in the north to occur later,
 resulting in a lower overall diversity in this region. Importantly,
 barriers and diversification patterns identified in Acanthophrynus are
 reflected in the phylogeography of codistributed vertebrates and
 arthropods, emphasizing the profound impact of Trans-Mexican Volcanic Belt
 orogeny and glacial/interglacial cycles as drivers of diversification in
 the Mexican Neotropics.
description: Complete dataset and scripts required to reproduce the analyses
 of the study “Volcanism and paleoclimate change drive diversification of
 world’s largest whip spider (Amblypygi)”. A usage guide is provided as a
 README file.
DOI: 10.5281/zenodo.11058509
title: Harmonized livestock number dataset for Europe

description: This dataset comprises spatial and temporal data on ruminant livestock distributions on detailed spatial level. We collected statistics on cattle, sheep and goats distribution for 43 countries and territories in Europe: for 31 countries  and territories we collected data on the level of local administrative units, for 8 countries on regional level (NUTS 3), and on national level (NUTS 0) for 4 countries. We provide data for over 73 thousand administrative units, making them more detailed than publicly provided by the European Statistical Office (which reports data for 325 adminstrative units). The data are available for the periods corresponding to 2000, 2010 and 2020.

Harmonizing to livestock units:

We harmonized the data to livestock units (LSU), making them easy to use and compare between different countries and regions. We used livestock coefficients provided by EUROSTAT (https://ec.europa.eu/eurostat/statistics-explained/index.php?title=Glossary:Livestock_unit_(LSU) ) to harmonize numbers of different livestock types, with more detail on the processing provided in the accompanying data_sources.xlsx file.File description:

The data-set consists of the following files:



a spreadsheet describing in detail the sources of data and how the data was processed (file data_sources.xlsx)

three geopackage files (archived as a zip file) for each year (2000, 2010, 2020) for harmonized ruminant livestock numbers for all 43 countries and territories (livestock2000.zip, livestock2010.zip, livestock2020.zip )

three geopackage files (archived as a zip file) for each year (2000, 2010, 2020) for sheep and goats for Poland (as the numbers are provided on a different level for these two livestock type for Poland) (poland_sheep_goats2000.zip , poland_sheep_goats2010.zip , poland_sheep_goats2020.zip )

a geopackage file (archived as a zip file) with (estimated) shares of cattle grazing for each country, in many cases for subnational units (grazing_share.zip )


Source information:

The raw data on livestock numbers are available from each country individually, and we provide the sources in the data_sources.xlsx file , to enable future updates.

 



This dataset has been created as part of LAMASUS Project under the scope of Deliverable 2.1 titled "The LUM Geodatabase and Area Estimates of Land Use Change to 2018 ". The full text of the deliverable can be accessed via: https://www.lamasus.eu/wp-content/uploads/LAMASUS_D2.1_LUMGeodatabase.pdf.
DOI: 10.5281/zenodo.12696960
title: LAMASUS Annual Corine Land Cover Time Series (2000 to 2018)

description:  

This dataset consists of an annual times series of Corine land cover from 2000 to 2018. The layers for 2000, 2006, 2012 and 2018 are the accounting layers of Corine land cover, produced by the European Environment Agency as part of the European Union's Copernicus Land Monitoring Service. These layers are being redistributed as part of this data package according to the data policy of the Copernicus Land Monitoring service. 

The annual layers for years in between 2000 and 2018 have been generated using the Corine change layers and a method to identify the year of change. This was based on using the high resolution land cover time series of Witjes et al. (2022) to extract the year when a change had occurred. This allowed 82.9%, 80.5% and 80.4% of cases for 2000 to 2006, 2006 to 2012 and 2012 to 2018 to be identified. MODIS and the BFAST algorithm were then applied to the remaining changes, which allowed an additional 7%, 11.2% and 7.5% of cases for 2000 to 2006, 2006 to 2012 and 2012 to 2018, respectively. Finally, for the remaining cases, a year was randomly allocated between the six year time period. A transition matrix was applied to account for a logical sequence of changes, which is inluded here in the file TransitionsinEurope4CLCTS.xlsx. 

This dataset has been created as part of LAMASUS Project under the scope of Deliverable 2.1 titled "The LUM Geodatabase and Area Estimates of Land Use Change to 2018 ". The data is directly linked to the work described on pages 10-11, belonging to section 2. Corine Land Cover Time Series. The full text of the deliverable can be accessed via: https://www.lamasus.eu/wp-content/uploads/LAMASUS_D2.1_LUMGeodatabase.pdf.
DOI: 10.5281/zenodo.13254324
title: LAMASUS Land Use Management Data Set

description: The land use management classes developed as part of the LAMASUS project have been aggregated to a 1 km grid (INSPIRE) provided as three geopackages files (LIST THEM) and NUTS2 regions (LUMClassesNUTS2.xlxs), provided as shares in each grid cell and region, respectively. The NUTS2 data can be joined to the NUTS2 shapefile (contained in NUTS0_2016_01M_3035_corrected.zip, including all NUTS levels), which is provided here as some corrections to the NUTS layer have been made. A list of the land use management classes is provided on the LUM Classes sheet of the LUMClassesNUTS2.xlxs file. Note that these aggregated files are consistent with official statistics from the Forest Resources Assessment of the Food and Agriculture Organization (FRA-FAO) for forest areas and Eurostat for cropland and grassland areas. 



This dataset has been created as part of LAMASUS Project under the scope of Deliverable 2.1 titled "The LUM Geodatabase and Area Estimates of Land Use Change to 2018 ". The data is directly linked to the work described on pages 12-34, belonging to section 3. The Land Use Management (LUM) Geodatabase. The full text of the deliverable can be accessed via: https://www.lamasus.eu/wp-content/uploads/LAMASUS_D2.1_LUMGeodatabase.pdf.