cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18374939
title: Assessing the Provision of Ecosystem Services Using Forest Site Classification as a Basis for the Forest Bioeconomy in the Czech Republic

description: The ecosystem services (ESs) of forests are the benefits that people derive from forest ecosystems. Their precise recognition is important for differentiating and determining the optimal principles of multifunctional forest management. The aim of this study is to identify some important ESs based on a site classification system at the lowest level—i.e., forest stands, at the forest owner level—as a tool for differentiated management. ESs were assessed within the Czech Republic and are expressed in units in accordance with the very sophisticated Forest Site Classification System. (1) Biomass production: The vertical differentiation of ecological conditions given by vegetation tiers, which reflect the influence of altitude, exposure, and climate, provides a basic overview of biomass production; the highest value is in the fourth vegetation tier, i.e., the Fageta abietis community. Forest stands are able to reach a stock of up to 900–1200 m3·ha−1. The lowest production is found in the eighth vegetation tier, i.e., the Piceeta community, with a wood volume of 150–280 m3 ·ha−1. (2) Soil conservation function: Geological bedrock, soil characteristics, and the geomorphological shape of the terrain determine which habitats serve a soil conservation function according to forest type sets. (3) The hydricity of the site, depending on the soil type, determines the hydric-water protection function of forest stands. Currently, protective forests occupy 53,629 ha in the Czech Republic; however, two subcategories of protective forests—exceptionally unfavorable locations and natural alpine spruce communities below the forest line—potentially account for 87,578 ha and 15,277 ha, respectively. Forests with an increased soil protection function—a subcategory of special-purpose forests—occupy 133,699 ha. The potential area of soil protection forests could be up to 188,997 ha. Water resource protection zones of the first degree—another subcategory of special-purpose forests—occupy 8092 ha, and there is potentially 289,973 ha of forests serving a water protection function (specifically, a water management function) in the Czech Republic. A separate subcategory of water protection with a bank protection function accounts for 80,529 ha. A completely new approach is presented for practical use by forest owners: based on the characteristics of the habitat, they can obtain information about the fulfillment of the habitat’s ecosystem services and, thus, have basic information for the determination of forest categories and the principles of differentiated management.
DOI: 10.5281/zenodo.18374940
title: Assessing the Provision of Ecosystem Services Using Forest Site Classification as a Basis for the Forest Bioeconomy in the Czech Republic

description: The ecosystem services (ESs) of forests are the benefits that people derive from forest ecosystems. Their precise recognition is important for differentiating and determining the optimal principles of multifunctional forest management. The aim of this study is to identify some important ESs based on a site classification system at the lowest level—i.e., forest stands, at the forest owner level—as a tool for differentiated management. ESs were assessed within the Czech Republic and are expressed in units in accordance with the very sophisticated Forest Site Classification System. (1) Biomass production: The vertical differentiation of ecological conditions given by vegetation tiers, which reflect the influence of altitude, exposure, and climate, provides a basic overview of biomass production; the highest value is in the fourth vegetation tier, i.e., the Fageta abietis community. Forest stands are able to reach a stock of up to 900–1200 m3·ha−1. The lowest production is found in the eighth vegetation tier, i.e., the Piceeta community, with a wood volume of 150–280 m3 ·ha−1. (2) Soil conservation function: Geological bedrock, soil characteristics, and the geomorphological shape of the terrain determine which habitats serve a soil conservation function according to forest type sets. (3) The hydricity of the site, depending on the soil type, determines the hydric-water protection function of forest stands. Currently, protective forests occupy 53,629 ha in the Czech Republic; however, two subcategories of protective forests—exceptionally unfavorable locations and natural alpine spruce communities below the forest line—potentially account for 87,578 ha and 15,277 ha, respectively. Forests with an increased soil protection function—a subcategory of special-purpose forests—occupy 133,699 ha. The potential area of soil protection forests could be up to 188,997 ha. Water resource protection zones of the first degree—another subcategory of special-purpose forests—occupy 8092 ha, and there is potentially 289,973 ha of forests serving a water protection function (specifically, a water management function) in the Czech Republic. A separate subcategory of water protection with a bank protection function accounts for 80,529 ha. A completely new approach is presented for practical use by forest owners: based on the characteristics of the habitat, they can obtain information about the fulfillment of the habitat’s ecosystem services and, thus, have basic information for the determination of forest categories and the principles of differentiated management.
DOI: 10.5281/zenodo.18381649
title: 3230-temporal-keys covers A-B
DOI: 10.5281/zenodo.18381650
title: 3230-temporal-keys covers A-B
DOI: 10.5061/dryad.416kv03
title: Data from: The influence of soil communities on the temperature sensitivity of soil respiration

description: Soil respiration represents a major carbon flux between terrestrial
 ecosystems and the atmosphere, and is expected to accelerate under climate
 warming. Despite its importance in climate change forecasts, however, our
 understanding of the effects of temperature on soil respiration (RS) is
 incomplete. Using a metabolic ecology approach we link soil biota
 metabolism, community composition and heterotrophic activity, to predict
 RS rates across five biomes. We find that accounting for the ecological
 mechanisms underpinning decomposition processes predicts climatological RS
 variations observed in an independent dataset (n = 312). The importance of
 community composition is evident because without it RS is substantially
 underestimated. With increasing temperature, we predict a latitudinal
 increase in RS temperature sensitivity, with Q10 values ranging between
 2.33 ±0.01 in tropical forests to 2.72 ±0.03 in tundra. This global trend
 has been widely observed, but has not previously been linked to soil
 communities.
description: Soil Biota Metabolic
 DataBody mass and
 temperature dependence of individual metabolic rates for fourteen soil
 biota groups.JohnstonSiblySoilBiotaMetabolicData.csvSoil Respiration DataSoil respiration rates, heterotrophic respiration rates and Q10 values with mean annual temperature across five biomes.JohnstonSiblySoilRespirationData.csvSoil Biota Abundance DataPopulation abundance and biomass dataset for thirteen soil biota groups across five biomes.JohnstonSiblySoilBiotaAbundanceData.csvDataset ReferencesReferences for all studies mentioned in the three datasets for: Johnston, A.S.A & Sibly, R.M. The influence of soil communities on the temperature sensitivity of soil respiration.JohnstonSiblyDatasetReferences.csv
DOI: 10.5061/dryad.cb76d28
title: Data from: Limited consequences of infestation with a blood-feeding ectoparasite for the nestlings of two North Pacific seabirds

description: The seabird tick (Ixodes uriae) parasitizes over 60 host species in the
 circumpolar regions of both hemispheres, and acts as a vector for a number
 of potentially virulent pathogens. On Triangle Island, British Columbia,
 Canada, the nestlings of Cassin’s Auklet (Ptychoramphus aleuticus) and
 Rhinoceros Auklet (Cerorhinca monocerata) are often parasitized by seabird
 ticks, which may affect their growth and survival in the nest. We used a
 logistic growth model to interpolate between successive measures of mass
 (g) and wing chord (mm) for 558 Cassin’s Auklet and 344 Rhinoceros Auklet
 chicks over 11 years from 1996 to 2007. From the model, we estimated the
 asymptotic measure and the age at inflection point for each chick’s growth
 trajectory, and assessed the effect of tick load relative to other sources
 of annual and seasonal variation in growth. Most chicks (72.4% of Cassin’s
 Auklets, and 62.2% of Rhinoceros Auklets) hosted ≥1 ticks at least once
 while in the nest, and the median tick load was two in both species. The
 probability of hosting a tick declined strongly with chick age, such that
 by day 40 after hatching less than 1% hosted ticks. We found evidence that
 tick load had a negative effect on asymptotic weights and wing lengths of
 both species, but the effect was minor relative to that of other sources
 of annual and seasonal variation. Only at very high loads – which were
 rare – did ticks have effects on growth that were likely to be
 biologically relevant. Tick load had little effect on survival to fledging
 in either species.We argue that these mild effects of ticks on their hosts
 are consistent with a co-evolutionary process that results in intermediate
 virulence when parasite transmission is linked to host recovery.
description: Triangle Island tick
 chick growth measures (1996-2007)Morphological measures
 (mass, wing length) of chicks of two seabird species nesting on Triangle
 Island, British Columbia, 1996 to 2007. Data includes day of year, hatch
 day, age, counts of number of ticks found during each burrow check, and
 whether chick fledged (1 = fledged, 0 = fledged).
DOI: 10.5061/dryad.qt3v0t4
title: Data from: Landscape of tumor mutation load, mismatch repair deficiency, and PD-L1 expression in a large patient cohort of gastrointestinal cancers

description: Purpose: The efficacy of immunotherapy varies widely among different
 gastrointestinal cancers. Response to immune checkpoint inhibitors is
 shown to correlate with tumor mutation load (TML), mismatch repair
 deficiency status (dMMR), and programmed cell death-ligand 1 (PD-L1)
 expression. Herein, we attempt to quantify TML, dMMR, and PD-L1 expression
 and determine their interrelationship in gastrointestinal cancers.
 Experimental Design: A total of 4125 tumors from 14 different
 gastrointestinal cancer sites were studied. Next-generation sequencing was
 performed on genomic DNA isolated from formalin-fixed paraffin-embedded
 (FFPE) tumor samples using the NextSeq platform. TML was calculated using
 only somatic nonsynonymous missense mutations sequenced with a 592-gene
 panel. Microsatellite instability (MSI) was assessed by validated direct
 analysis of altered known MSI loci in the target regions of the sequenced
 genes. PD-L1 expression was analyzed by immunohistochemistry. Results:
 Right-sided colon and small bowel adenocarcinomas had the highest
 prevalence of TML-high tumors (14.6% and 10.2%, respectively). Pancreatic
 neuroendocrine tumors and gastrointestinal stromal tumors (GIST) had the
 lowest rates of TML-high (1.3% and 0%, respectively). TML-high status was
 strongly associated with MSI-H (P&lt;0.0001). However, all TML-high
 anal cancers (8.3%) were microsatellite stable (MSS). Higher PD-L1
 expression was more likely to be seen in MSI compared with MSS tumors
 (20.6% vs. 7.8%, P&lt;0.0001). Conclusions: TML-high rate varied
 widely among gastrointestinal cancers. Although microsatellite instability
 is conceivably the main driver for TML-high status, other factors may be
 involved. Future clinical trials are needed to evaluate whether the
 integration of TML, MSI, and PD-L1 could better identify potential
 responders to immunotherapy.
description: TML in GI cancer
 uploaded
DOI: 10.5061/dryad.t8952
title: Data from: Finding politically feasible conservation policies: the case of wildlife trafficking

description: Conservation management is of increasing importance in ecology as most
 ecosystems nowadays are essentially managed ones. Conservation managers
 work within a political-ecological system when they develop and attempt to
 implement a conservation plan that is designed to meet particular
 conservation goals. In this article, we develop a decision support tool
 that can identify a conservation policy for a managed wildlife population
 that is both sustainable and politically feasible. Part of our tool
 consists of a simulation model composed of interacting influence diagrams.
 We build, fit, and use our tool on the case of rhino horn trafficking
 between South Africa and Asia. Using these diagrams, we show how a rhino
 poacher’s belief system can be modified by such a policy and locate it in
 a perceived risks-benefits space before and after policy implementation.
 We statistically fit our model to observations on group actions and rhino
 abundance. We then use this fitted model to compute a politically feasible
 conservation policy.
description: polecolText file of all political actions, rhino abundance, and Kruger National Park vegetation observations used to fit the models described in the paper. Data sets are listed sequentially. Political actions data format: Document Archive Number, Date of news story, Source, Number of actors, Actors, Number of subjects, Subjects, Action, Number of countries, Countries, Number of regions, Regions, Date of action.
DOI: 10.5061/dryad.nt269
title: Data from: Phylogenetic relationships among members of the neotropical clade of Miliuseae (Annonaceae): generic non-monophyly of Desmopsis and Stenanona

description: The phylogenetic relationships among members of the Neotropical clade of
 Miliuseae were inferred using Bayesian inference, maximum likelihood, and
 parsimony on a dataset of six plastid regions (ndhF, matK, psbA-trnH,
 rbcL, rps16-trnQ, and trnL-F). The phylogenetic hypothesis obtained
 indicate that the Neotropical clade of Miliuseae is a monophyletic group,
 composed of two distinct lineages: the first comprises the genera
 Sapranthus and Tridimeris, and the second is composed of Desmopsis,
 Stenanona, and two potentially new taxa, which together form the
 Desmopsis-Stenanona clade. However, the relationships within the
 Desmopsis-Stenanona clade are not fully resolved; the phylogenetic results
 indicate that Desmopsis and Stenanona, as currently circumscribed, are not
 monophyletic. The morphological characteristics that distinguish each
 genus and potential synapomorphies are discussed. We conclude that the
 observed variation in floral and fruit characteristics among the members
 of the Desmopsis-Stenanona clade could be driven by interactions with
 their main pollinators and fruit dispersers. Based on these results we
 propose that the Neotropical clade of Miliuseae needs to be recognized at
 the subtribe level, under the name of Sapranthinae.
description: Neotropical
 Miliuseae_concatenated aligmentThis Nexus file is a
 concatenated alignment containing chloroplast (ndhF, matK, psbA-trnH,
 rbcL, rps16-trnQ and trnL-F) sequences of the Neotropical Miliuseae
 (Annonaceae) used in this study.Neotropical_Miliuseae_concatenated aligment.nex
DOI: 10.5061/dryad.94pv0
title: Data from: Genomic basis of life history evolution in Drosophila melanogaster

description: Natural diversity in aging and other life history patterns is a hallmark
 of organismal variation. Related species, populations, and individuals
 within populations show genetically based variation in life span and other
 aspects of age-related performance. Population differences are especially
 informative because these differences can be large relative to
 within-population variation and because they occur in organisms with
 otherwise similar genomes. We used experimental evolution to produce
 populations divergent for life span and late-age fertility and then used
 deep genome sequencing to detect sequence variants with nucleotide-level
 resolution. Several genes and genome regions showed strong signatures of
 selection, and the same regions were implicated in independent
 comparisons, suggesting that the same alleles were selected in replicate
 lines. Genes related to oogenesis, immunity, and protein degradation were
 implicated as important modifiers of late-life performance. Expression
 profiling and functional annotation narrowed the list of strong candidate
 genes to 38, most of which are novel candidates for regulating aging. Life
 span and early-age fecundity were negatively correlated among populations;
 therefore the alleles we identified also are candidate regulators of a
 major life-history trade-off. More generally, we argue that hitchhiking
 mapping can be a powerful tool for uncovering the molecular bases of
 quantitative genetic variation.
description: life50LongLifespan data for virgin males and females. Selection and Control populations are indicated in column 'Line' (S, C). Population replicate is indicated by column 'replicate' (1,2,3). The x,y columns were used only for plotting.FecundityFecundity data. Line column gives Treatment (Selection, S, or Control, C) populations. Set is the population replicate (1,2,3). Column 'offspring' gives total number of offspring produced at a given age in a given vial. Column 'alivefem' is the number of females that contributed offspring to the vial. Column 'fec' is the total number of offspring divided by the number of alive females.lifeMatedLongLifespan data for mated females and males. Population Treatment is indicated by variable 'Line' (S or C), 'dead' is number dead at that census, censor is censoring variable, day is the age of flies at that census. Population replicate is indicated by variable 'set' (1,2,3).
DOI: 10.5061/dryad.pv18p
title: Data from: Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus)

description: Mule deer (Odocoileus hemionus) are an excellent nonmodel species for
 empirically testing hypotheses in landscape and population genomics due to
 their large population sizes (low genetic drift), relatively continuous
 distribution, diversity of occupied habitats and phenotypic variation.
 Because few genomic resources are currently available for this species, we
 used exon data from a cattle (Bos taurus) reference genome to direct
 targeted resequencing of 5935 genes in mule deer. We sequenced
 approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule
 deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or
 adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69
 genes) with putatively fixed allele frequency differences between the two
 major lineages of mule deer (mule deer and black-tailed deer), and our
 estimate of mean genetic divergence (genome-wide FST = 0.123) between
 these lineages was consistent with previous findings using microsatellite
 loci. We detected an over-representation of gamete generation and amino
 acid transport genes among the genes with SNPs exhibiting potentially
 fixed allele frequency differences between lineages. This targeted
 resequencing approach using exon capture techniques has identified a suite
 of loci that can be used in future research to investigate the genomic
 basis of adaptation and differentiation between black-tailed deer and mule
 deer. This study also highlights techniques (and an exon capture array)
 that will facilitate population genomic research in other cervids and
 nonmodel organisms.
description: Mule deer targeted
 re-sequencing dataPowell_et_al_mule_deer_exon_capture.geneious
DOI: 10.5061/dryad.nf57p95
title: Data from: Environmental drivers of forest structure and stem turnover across Venezuelan tropical forests

description: Using data from 50 long-term permanent plots from across Venezuelan
 forests in northern South America, we explored large-scale patterns of
 stem turnover, aboveground biomass (AGB) and woody productivity (AGWP),
 and the relationships between them and with potential climatic drivers. We
 used principal component analysis coupled with generalized least squares
 models to analyze the relationship between climate, forest structure and
 stem dynamics. Two major axes associated with orthogonal temperature and
 moisture gradients effectively described more than 90% of the
 environmental variability in the dataset. Average turnover was 1.91 ±
 0.10% year-1 with mortality and recruitment being almost identical, and
 close to average rates for other mature tropical forests. Turnover rates
 were significantly different among regions (p &lt; 0.001), with the
 lowland forests in Western alluvial plains being the most dynamic, and
 Guiana Shield forests showing the lowest turnover rates. We found a weak
 positive relationship between AGB and AGWP, with Guiana Shield forests
 having the highest values for both variables (204.8 ± 14.3 Mg C ha-1 and
 3.27 ± 0.27 Mg C ha-1 year-1 respectively), but AGB was much more strongly
 and negatively related to stem turnover. Our data suggest that moisture is
 a key driver of turnover, with longer dry seasons favoring greater rates
 of tree turnover and thus lower biomass, having important implications in
 the context of climate change, given the increases in drought frequency in
 many tropical forests. Regional variation in AGWP among Venezuelan forests
 strongly reflects the effects of climate, with greatest woody productivity
 where both precipitation and temperatures are high. Overall, forests in
 wet, low elevation sites and with slow turnover stored the greatest
 amounts of biomass. Although faster stand dynamics are closely associated
 with lower carbon storage, stem-level turnover rates and woody
 productivity did not show any correlation, indicating that stem dynamics
 and carbon dynamics are largely decoupled from one another.
description: DataFileThis file contains the main results from the analysis of stem turnover, aboveground biomass and woody productivity from 50 permanent forest plots in Venezuela. The file includes coordinates of site location, main environmental characteristics, the scores of the first two PCA axes from a Principal Component Analysis, values of stem turnover (recruitment and mortality) and forest structure.Vilanova_RScript_PONE_FinalR script used for the analysis and preparation of figures related to the publication.
DOI: 10.15468/dl.rdkmk3
title: Occurrence Download

description: A dataset containing 3359 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Lasiurus cinereus"
 ]
}

 The dataset includes 3359 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000577-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.