cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1s2
title: Data from: Pathogen-mediated selection and management implications for white-tailed deer exposed to chronic wasting disease

description: Pathogens can cause host extinction, affect population dynamics, and
 influence natural selection. Host susceptibility to pathogens can vary by
 species, demographics, and genetics which affect epizootic dynamics;
 ultimately determining population trends and evolution. Chronic
 wasting disease (CWD), a fatal neuro-degenerative prion disease of
 cervids, has varying host susceptibility conferred by polymorphisms of the
 prion protein gene (PRNP) at the 96 codon for white-tailed deer
 (Odocoileus virginianus). Deer with the homozygous Glycine allele (96GG)
 are most susceptible and a single Serine allele (96GS/96SS) reduces the
 risk of infection and mortality. We developed epizootiological
 models that demonstrate CWD infection and disease-associated mortality
 were higher for the more susceptible (96GG) genotype; and, infection was
 higher for males than females. We used population models to evaluate
 future shifts in genotype frequencies under alternative harvest and
 infection rate scenarios. Genetic shifts towards less susceptible
 genotypes were predicted as CWD prevalence increased during the course of
 an outbreak. This further increased CWD prevalence, and likely
 environmental contamination from prion shedding, due to longer incubation
 periods. Alternative harvest management strategies directly influenced CWD
 prevalence and spread, the rate of genetic selection, and deer population
 growth.  Synthesis and applications: We show that CWD
 transmission varied by sex, age classes, and genotypes, and that CWD
 disease-associated mortality varied by genotype. Together, these forces
 lead to CWD-mediated genetic selection for a white-tailed deer population.
 We predict that genetic selection pressure increases when hunter harvest
 pressure is lowered, and conversely, increasing hunter harvest can reduce
 genetic selection rates of antlered deer. Our results support the control
 of CWD prevalence by aggressive harvest of adult males because they have
 the highest infection rates. Our results have strong implications for
 evolution, disease ecology, geographic spread, disease mitigation, and
 cervid population management.
description: # Data from: Pathogen-mediated selection and management implications for
 white-tailed deer exposed to chronic wasting disease
 [https://doi.org/10.5061/dryad.866t1g1s2](https://doi.org/10.5061/dryad.866t1g1s2) ## Description of the data and file structure There are 3 data files available here. 1\. DeerTested.csv is hunter-harvested surveillance data from the core area in south-central Wisconsin. 2\. PRNPtable.csv is a subset of the hunter-harvested surveillance data (i.e. DeerTested.csv), for which there are genotyped deer. 3\. Corrected_Prevalence.csv are the estimates from the first part of the analysis, which were then used in the subsequent epizootiological models and simulations.
DOI: 10.5061/dryad.08kprr53v
title: Dietary abundance distributions: Dominance and diversity in vertebrate diets

description: Diet composition is among the most important yet least understood
 dimensions of animal ecology. Inspired by the study of species-abundance
 distributions (SADs), we tested for generalities in the structure of
 vertebrate diets by characterizing them as dietary-abundance distributions
 (DADs). We compiled data on 1167 population-level diets, representing
 &gt;500 species from 6 vertebrate classes, spanning all continents and
 oceans. DADs near-universally (92.5%) followed a hollow-curve shape, with
 scant support for other plausible rank-abundance-distribution shapes. This
 strong generality is inherently related to, yet incompletely explained by,
 the SADs of available food taxa. By quantifying dietary generalization as
 the half-saturation point of the cumulative distribution of dietary
 abundance (sp50, minimum number of foods required to account for 50% of
 diet), we found that vertebrate populations are surprisingly specialized:
 in most populations, fewer than three foods accounted for at least half
 the diet. Variation in sp50 was strongly associated with consumer type,
 with carnivores being more specialized than herbivores or omnivores. Other
 methodological (sampling method and effort, taxonomic resolution),
 biological (body mass, frugivory), and biogeographic (latitude) factors
 influenced sp50 to varying degrees. Future challenges include identifying
 the mechanisms underpinning the hollow-curve DAD, its generality beyond
 vertebrates, and the biological determinants of dietary generalization.
description: See Hutchinson et al. 2022 <em>Ecology
 Letters</em>
description: DADs_data.RData: Each element in the list is one population-level
 diet. Element names correspond to the DietID column in DADs_metadata.csv
 and include the consumer's Latin binomial name as well as the BibTeX
 key (i.e., the unique identifier of each primary source; reported in the
 Bibkey column of DADs_metadata.csv and in the DADs_bibliography.bib file).
 Each population-level diet is a vector describing the percent dietary
 abundance of each consumed food taxon. 
 DADs_bibliography.bib: BibTeX bibliography file
 containing references for all of the primary sources used to compile
 the diet data used in our study DADs_metadata.RData:
 Metadata for each diet. See Metadata_ReadME.txt for complete descriptions
 of each variable. DADSAD_data.RData: Abundances of food
 taxa in the environments and the diets for six case studies shown in
 Figure 5 of the article. See DADSAD_ReadMe.txt for further
 details.
DOI: 10.15468/dl.ddc4ts
title: Occurrence Download

description: A dataset containing 3775194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantae, Undaria pinnatifida, Lindavia intermedia)",
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 0",
 "DecimalLongitude is greater than or equal to -180",
 "DecimalLatitude is greater than or equal to -90",
 {
 "not" : {
 "or" : [
 "Issue is Zero coordinate",
 "Issue is Coordinate out of range",
 "Issue is Country coordinate mismatch"
 ]
 }
 }
 ]
}

 The dataset includes 3775194 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003001-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h18931znb
title: Same place, different stories: Disparate evolutionary trends of Mygalomorphae from the peripampasic orogenic arc

description: Aim: Comparative phylogeography seeks to unravel similarities in the
 population structure and evolutionary processes undergone by
 co-distributed taxa under the assumption that they will have experienced
 the same geoclimatic events. However, small differences in functional
 traits, particularly those related to dispersal abilities, may translate
 into incongruent evolutionary histories. Here, we used a sequence target
 multi-locus approach to infer and compare the phylogeographical patterns
 of three sympatric mygalomorph spiders in the Argentinean peripampasic
 orogenic arc. Location: The mountainous systems of central and northern
 Argentina. Taxon: Mygalomorphae spiders (Araneae) Methods: We inferred the
 phylogeny of three species of mygalomorph spiders based on 16S+L1+nad1 and
 ITS sequences from one hundred and thirty-four individuals by using a
 Bayesian and Maximum likelihood approaches and we also estimated
 divergence dates. Also, nuclear networks were inferred. Based on our
 molecular phylogeny, we reconstructed ancestral areas using the the
 Bayesian Binary MCMC method. Results: A deep genetic divergence and highly
 structured populations was obtained in the pycnothelid Acanthogonatus
 centralis, whereas the theraphosids Plesiopelma longisternale and
 Grammostola vachoni showed shallow divergences and poorly structured
 populations. Additionally, we uncovered potentially overlooked species
 diversity within G. vachoni, which warrants conducting a full taxonomic
 revision of Grammostola. Main conclusions: We propose that differences in
 dispersion rates and time of colonization between the theraphosids and the
 pycnothelid led to divergent lineage history despite common environmental
 conditions. Our results further corroborate the key role played of the
 Plio-Pleistocene geoclimatic events in shaping the present-day diversity
 of mygalomorph spiders along the peripampasic orogenic arc.
DOI: 10.5061/dryad.bzkh189b5
title: Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods

description: Aim: Specialisation to the soil environment is expected to constrain the
 spatial scale of diversification within animal lineages. In this context,
 the existence of flightless arthropod lineages, adapted to soil
 environments, but with broad geographic ranges, represent something of an
 anomaly. Here we investigate the diversification process within one such
 ‘anomalous’ soil specialist: Geomitopsis franzi Coiffait, 1978, an eyeless
 and flightless beetle species strongly adapted to the endogean environment
 but distributed across several oceanic islands. Location: Canary Islands
 Taxon: Geomitopsis (Coleoptera, Staphylinidae) Methods: We performed an
 integrative study, including molecular phylogenetics, population genomics,
 and morphometry. Four DNA regions (two mitochondrial and two nuclear) were
 amplified and sequenced for 159 specimens from 58 localities sampled
 across five islands for phylogenetic analyses, and a dated phylogenetic
 tree was obtained using a mitogenome dataset. ddRAD-seq data was generated
 to evaluate mtDNA lineages in sympatry against the biological species
 concept. Results: We found high levels of genetic differentiation
 (&gt;8% COI gene divergence) among populations from different islands
 and among geographically coherent lineages within single islands. Lineages
 within Tenerife presented significant patterns of isolation by distance,
 with ddRAD-seq providing evidence that lineages represent biological
 species. Morphometric analyses revealed limited variation, with most
 lineages lacking diagnostic characters. Main conclusions: Geomitopsis
 franzi is comprised of at least seven lineages that merit consideration as
 biological species, and is best considered as a complex of cryptic
 species. The limited morphological variation across these lineages is
 consistent with adaptation to the endogean environment placing strong
 constraints on morphological change. The evolution of cryptic species
 should be favoured when such constraints are coupled with limited
 dispersal ability, which characterises G. franzi, and is a trait that
 broadly characterises the soil mesofauna. We suggest that cryptic species
 diversity is likely to be a recurrent feature across soil adapted
 arthropod species with range sizes that appear inconsistent whith a low
 potential for dispersal.
description: See publication
DOI: 10.5061/dryad.w6m905qqz
title: Computationally modelled structure of type IV pilus PilA of Aggregatibacter actinomycetemcomitans

description: Some bacterial type IV pili structures have been determined with Cryo-EM,
 X-ray diffraction or similar method. The type IVa pilus PilA
 of Aggregatibacter actinomycetemcomitans, an oral pathogen,
 shares sequence identity with other bacterial type IVa pili. To understand
 the structure of AaPilA at the molecular level, we performed computational
 modeling studies. To model the filament, we utilized the GalaxyGemini web
 server using different monomer conformations from molecular dynamics
 simulations as a seed; then, we extended the structure to 14-mer by
 employing the cryo-EM map file of type IV pilus from enterohemorrhagic E.
 coli. The structures were predicted for a full-length monomer PilA_D7S,
 N-terminally truncated monomer PilA_D7S_Δ1-27 and 14-homo-oligomer
 PilA_D7S_14mer. PilAD7S_Δ1-27 and PilAD7S share the same secondary
 structural elements: an N-terminal α-helix, four antiparallel β-strands, a
 hypervariable segment and a flexible C-terminus. The homo-oligomeric
 PilAD7S from our computational model resembles the interface seen in the
 cryo-EM structure of N. meningitidis type IV pili.
description: Methods are described in detail in Vahvelainen et al. 2022 (https://doi.org/10.1016/j.micpath.2022.105843).
description: README file describes the dataset.
DOI: 10.5061/dryad.rjdfn2zcc
title: Momordica janarthanamii (Cucurbitaceae): a remarkable new species from Maharashtra state, India

description: Momordica janarthanamii, a new species is described and illustrated from
 Nashik district of Maharashtra state, India. The new species is closely
 related to Momordica dioica Roxb. ex Willd. Colored photographs,
 distribution, ecological note and economical value of the new species are
 provided. A key for the dioecious species of Momordica from India has also
 been provided to facilitate identification.
description: The specimens of new species of <i>Momordica</i> were collected from Karanjali ghat (Kumbharbari), Nashik in July 2020. The morphological characters were studied under Leica EZ4 Stereo Zoom microscope. Diagnostic characters of the unknown species were compared with protologue and type specimens of its closely related species <i>i.e</i>. <i>M. dioica.</i> Photographs in the field and different parts of the plants were taken by using M50 Canon camera. The type specimens have been deposited at BSI, CAL and SUK herbaria.
DOI: 10.57760/sciencedb.ecodb.00246
title: A dataset of carbon and water fluxes at the Changling grassland flux observation site from 2019 to 2020
title: 2019-2020年长岭草地生态系统碳水通量观测数据集

description: The raw observation data acquired by the eddy covariance system at the Changling grassland flux observation site from 2019 to 2020 were processed based on the ChinaFLUX data processing standards to produce this standardized dataset of ecosystem carbon and water fluxes and key meteorological elements. The site was established by Shanxi University and is located in Changling county, Jilin province. In this dataset, the annual data includes 8 Excel data files, divided into two categories: LITE, which includes major fluxes and meteorological variables, and ALL, which adds data quality and interpolation indicators on the basis of LITE. Each category has four data files, including data files at four scales: half-hour (HH), day (DD), month (MM), and year (YY). 
description: The raw observation data acquired by the eddy covariance system at the Changling grassland flux observation site from 2019 to 2020 were processed based on the ChinaFLUX data processing standards to produce this standardized dataset of ecosystem carbon and water fluxes and key meteorological elements. The site was established by Shanxi University and is located in Changling county, Jilin province. In this dataset, the annual data includes 8 Excel data files, divided into two categories: LITE, which includes major fluxes and meteorological variables, and ALL, which adds data quality and interpolation indicators on the basis of LITE. Each category has four data files, including data files at four scales: half-hour (HH), day (DD), month (MM), and year (YY).
DOI: 10.5061/dryad.fqz612jtt
title: Data from: The evolutionary pathways for local adaptation in mountain hares

description: Understanding the evolution of local adaptations is a central aim of
 evolutionary biology and key for the identification of unique populations
 and lineages of conservation relevance. By combining RAD sequencing and
 whole-genome sequencing, we identify genetic signatures of local
 adaptation in mountain hares (Lepus timidus) from isolated and distinctive
 habitats of its wide distribution: Ireland, the Alps and Fennoscandia. We
 recovered full mitochondrial DNA sequences from whole-genome sequencing
 data and used it to recontruct the evolutionary relationships among
 mountain hare haplotypes.
description: Complete mitochondrial DNA (mtDNA) genomes were
 recovered for each mountain hare individual for which the whole genome was
 sequenced at lower coverage, using the ABySS assembler (Jackman et al.,
 2017; Simpson et al., 2009). The standard ABySS run was done with k-mer
 size of 64 bp (k=64), but modified to k=96 and/or randomly subsampling
 input reads, when it allowed increasing the contig length. For each
 individual, the nearly full mtDNA sequence was retrieved by inspecting the
 longest contigs and then aligning with a mountain hare mtDNA reference
 (GenBank Acc. Nr KJ397605; Melo-Ferreira, Seixas, Cheng, Mills, &
 Alves, 2014). Final alignments were produced using ClustalW (Thompson,
 Higgins, & Gibson, 1994), followed by manual corrections in
 BioEdit (Hall, 1999).
description: Mitochondrial DNA alignment of 59 mountain hare individuals from
 Ireland, Alps and Fennoscandia.
DOI: 10.5061/dryad.k6djh9w7q
title: A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster

description: Exposing sires to various environmental manipulations has demonstrated
 that paternal effects can be non-trivial also in species where male
 investment in offspring is almost exclusively limited to sperm. Whether
 paternal effects also have a genetic component (i.e. paternal indirect
 genetic effects - PIGEs) in such species is however largely unknown,
 primarily because of methodological difficulties separating indirect from
 direct effects of genes. PIGEs may nevertheless be important, since they
 have the capacity to contribute to evolutionary change. Here we use
 Drosophila genetics to construct a breeding design that allows testing
 nearly complete haploid genomes (&gt;99%) for PIGEs. Using this
 technique, we estimate the variance in male lifespan due to PIGEs among
 four populations and compare this to the total paternal genetic variance
 (the sum of paternal indirect and direct genetic effects). Our results
 indicate that a substantial part of the total paternal genetic variance
 results from PIGEs. A screen of 38 haploid genomes, randomly sampled from
 a single population, suggests that PIGEs also influence variation in
 lifespan within populations. Collectively, our results demonstrate that
 PIGEs may constitute an underappreciated source of phenotypic variation.
DOI: 10.5061/dryad.bg79cnpc2
title: Habitat use and foraging parameters of breeding Skylarks indicate no seasonal decrease in food availability in heterogeneous farmland

description: Reduced food availability during chick raising is a major driver of
 farmland bird declines. For the Eurasian Skylark (Alauda arvensis), food
 availability is determined by various factors (i.e., arthropod
 abundance/diversity, accessibility of the vegetation, distance to foraging
 sites). In modern farmland, it is supposed to decrease over the breeding
 season due to less penetrable vegetation. We explored foraging habitat
 selection by chick-raising Skylarks with a focus on the seasonal dynamics
 of habitat use and food availability. We investigated i) habitat selection
 concerning prey biomass/diversity, vegetation cover, and distance to
 foraging sites, ii) the overall and seasonal habitat use, and iii)
 seasonal developments of foraging parameters (e.g., the feeding frequency)
 as indicators of food availability. We collected data on foraging habitats
 and foraging parameters of chick-raising Skylark pairs at 51 nests from a
 Central European population in 2018 and 2019. Prey biomass/diversity and
 vegetation cover were measured for all habitats around 42 of these nests.
 As revealed by multivariate and compositional analyses, Skylarks mainly
 selected foraging habitats based on the proximity to nests. The most
 frequent habitats within home ranges could not be ranked according to an
 overall importance for foraging and their use partially changed over time.
 The feeding frequency increased throughout the breeding season, while
 other foraging parameters did not show significant changes. In contrast to
 our expectations, our data indicated therefore an increase, not a decrease
 in food availability in the late breeding season. This also implies that
 the habitat use was constantly suitable to raise offspring. We interpret
 this to be a consequence of the heterogeneous farmland composition of the
 study area that enabled Skylarks to establish a diverse home range and to
 benefit from synergetic effects of neighboring habitat types. Thus, our
 findings provide support for the high importance of crop diversity in
 Skylark conservation.
DOI: 10.57760/sciencedb.27285
title: A dataset of the statistics on beef wholesale prices in the market in China from 2011 to 2022
title: 2011-2022年中国牛肉市场批发价格统计数据集

description: This dataset includes China's beef market wholesale price data from 2011-2022, consisting of 2 parts: (1) text data includes the average monthly wholesale price of beef markets across the country and 16 provinces (autonomous regions, municipalities) from 2011 to 2022 Price and change rate information data; (2) the image data includes the monthly average beef wholesale price and change rate line chart of the country and 16 provinces (autonomous regions and municipalities) from 2011 to 2022.
description: This dataset includes China's beef market wholesale price data from 2011-2022, consisting of 2 parts: (1) text data includes the average monthly wholesale price of beef markets across the country and 16 provinces (autonomous regions, municipalities) from 2011 to 2022 Price and change rate information data; (2) the image data includes the monthly average beef wholesale price and change rate line chart of the country and 16 provinces (autonomous regions and municipalities) from 2011 to 2022.
DOI: 10.15468/dl.gms4hh
title: Occurrence Download

description: A dataset containing 41032 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen)",
 "Continent is Europe",
 "Country is one of (Sweden, Norway)",
 "TaxonKey is Rangifer tarandus"
 ]
}

 The dataset includes 41032 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003010-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xpnvx0kh2
title: Digital research data from: Biochar stability in a highly weathered sandy soil under four years of continuous corn production

description: Biochar is being considered a climate change mitigation tool by increasing
 soil organic carbon contents (SOC), however, questions remain concerning
 its longevity in soil. We applied 30,000 kg ha−1 of biochars to plots
 containing a Goldsboro sandy loam (Fine-loamy, siliceous, sub-active,
 thermic Aquic Paleudults) and then physically disked all plots.
 Thereafter, the plots were agronomically managed under 4 years (Y) of
 continuous corn (Zea Mays, L.) planting. Annually, incremental soil along
 with corresponding bulk density samples were collected and SOC
 concentrations were measured in topsoil (down to 23-cm). The biochars were
 produced from Lodgepole pine (Pinus contorta) chip (PC) and Poultry litter
 (PL) feedstocks. An untreated Goldsboro soil (0 biochar) served as a
 control.
description: Methods are described in
 the manuscript https://doi.org/10.3390/en14196157
description: Descriptions corresponding to each data table in the manuscript
 are placed on separate tabs in the Excel file to clarify abbreviations and
 summarize the data headings and units.