cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3f951q
title: Data from: Effects of Lewy body disease and Alzheimer’s disease on brain atrophy and cognitive dysfunction

description: Objectives: We investigated the independent and interaction effects of
 Alzheimer’s disease (AD) and Lewy body disease (LBD) on cognition and
 brain atrophy. Methods: We consecutively recruited 38 controls and 108
 patients with AD-related cognitive impairment (ADCI) and/or LBD-related
 cognitive impairment (LBCI) from university-based dementia and movement
 clinics. Diagnoses of ADCI and LBCI were supported by 18F-Florbetaben PET
 and 18F-FP-CIT-PET, respectively. There were 38 controls, 26 patients with
 pure ADCI (18 mild cognitive impairment (MCI) and 8 dementia), 28 patients
 with pure LBCI (13 MCI and 15 dementia), and 54 patients with mixed ADCI
 and LBCI (17 MCI and 37 dementia). We performed group-wise comparisons for
 neuropsychological z scores and regional cortical thickness. We also
 evaluated the effects of ADCI and LBCI using general linear models.
 Results: Compared to the controls, pure patients with ADCI group and pure
 LBCI group had focused cortical thinning in the bilateral entorhinal/right
 anterior temporal cortices and bilateral anteromedial temporal/basal
 frontal cortices, respectively, while the mixed disease group had
 additional cortical thinning in the widespread association cortices. The
 independent effects of ADCI and LBCI on regional cortical thinning
 overlapped in the widespread association cortices, especially at the
 bilateral temporo-parietal junction and parietal cortices. ADCI and LBCI
 had independent detrimental effects on the copying item of the
 Rey-Osterrieth Complex Figure Test. Conclusions: Concomitant ADCI and LBCI
 are associated with the accentuation of neurodegeneration to widespread
 association cortices, and both diseases contribute to visuospatial
 dysfunction.
description: supplementary_file
DOI: 10.5281/zenodo.17761191
title: INRIM_Brand1_400F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 400F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.17761192
title: INRIM_Brand1_400F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 400F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.308hs50
title: Data from: Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

description: In order to investigate the contribution of the physical environment to
 variation in multicellular development of Myxococcus xanthus, phenotypes
 developed by different genotypes in a gradient of substrate stiffness
 conditions were quantitatively characterized. Statistical analysis showed
 that plastic phenotypes result from the genotype, the substrate conditions
 and the interaction between them. Also, phenotypes were expressed in two
 distinguishable scales, the individual and the population levels, and the
 interaction with the environment showed scale and trait specificity.
 Overall, our results highlight the constructive role of the physical
 context in the development of microbial multicellularity, with both
 ecological and evolutionary implications.
description: Raw
 dataRaw data of Myxococcus
 xanthus fruiting bodies phenotypic traitsdata_sheet.csv
DOI: 10.5061/dryad.1b5f638
title: Data from: Estimating selection on the act of inbreeding in a population with strong inbreeding depression

description: Inbreeding depression is widely regarded as a driving force in the
 evolution of dispersal, mate choice and sperm selection. However, due to
 likely costs of inbreeding avoidance, which are poorly understood, it is
 unclear to what extent selection to avoid inbreeding is expected in
 nature. Moreover, there are currently very few empirical estimates of the
 strength of selection against the act of inbreeding (mating with a
 relative), as opposed to the fitness costs of being inbred. Here, we use
 data from the individual-based study of red deer on the Scottish island of
 Rum, a strongly polygynous system which harbours a large inbreeding load,
 to estimate selection against the act of inbreeding for each sex. We use
 pedigree and genomic estimates of relatedness between individuals and
 measure fitness using both lifetime breeding success (number of calves
 born) and lifetime reproductive success (number of calves surviving to
 independence), with the latter incorporating inbreeding depression in calf
 survival. We find for both sexes that the repeatability of the act of
 inbreeding was low (&lt;0.1), suggesting little among-individual
 variation for this trait on which selection can act. Using the genomic
 measures there was significant selection against the act of inbreeding in
 males, but not in females, and there was considerable uncertainty in the
 estimate in both sexes. We discuss possible explanations for these
 patterns and their implications for understanding the evolution of
 inbreeding avoidance in natural populations.
description: RawData_MainAnalysisRaw data for the main analyses that appear in the paperRawData_Dryad.txtData for analysis on Harem holdingData for the supplementary analysis on the relationship between relatedness to a mate and harem holding and mating with members of that haremHaremData_ForDryad.txt
DOI: 10.5061/dryad.kk7hq10
title: Data from: Deforestation risks posed by oil palm expansion in the Peruvian Amazon

description: Further expansion of agriculture in the tropics is likely to accelerate
 the loss of biodiversity. One crop of concern to conservation is African
 oil palm (Elaeis guineensis). We examined recent deforestation associated
 with oil palm in the Peruvian Amazon within the context of the region’s
 other crops. We found more area under oil palm cultivation (845 km2 ) than
 did previous studies. While this comprises less than 4% of the cropland in
 the region, it accounted for 11% of the deforestation from agricultural
 expansion from 2007 to 2013. Patches of oil palm agriculture were larger
 and more spatially clustered than for other crops, potentially increasing
 their impact on local habitat fragmentation. Modeling deforestation risk
 for oil palm expansion using climatic and edaphic factors showed that
 sites at lower elevations, with higher precipitation, and lower slopes
 than those typically used for intensive agriculture are at long-term risk
 of deforestation from oil palm agriculture. Within areas at long-term
 risks, based on CART models, areas near urban centers, roads, and
 previously deforested areas are at greatest short-term risk of
 deforestation. Existing protected areas and officially recognized
 indigenous territories cover large areas at long-term risk of
 deforestation for oil palm (&gt;40%). Less than 7% of these areas are
 under strict (IUCN I-IV) protection. Based on these findings, we suggest
 targeted monitoring for oil palm deforestation as well as strengthening
 and expanding protected areas to conserve specific habitats.
description: Vijay_et_al_2018_oilpalmrisk
DOI: 10.5061/dryad.43n9j1p
title: Data from: Why is Amazonia a ‘source’ of biodiversity? climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae)

description: Amazonia is a ‘source’ of biodiversity for other Neotropical ecosystems,
 but which conditions trigger in situ speciation and emigration is
 contentious. Three hypotheses for how communities have assembled include
 (1) a stochastic model wherein chance dispersal events lead to gradual
 emigration and species accumulation, (2) diversity-dependence wherein
 successful dispersal events decline through time due to ecological limits,
 and (3) barrier displacement wherein environmental change facilitates
 dispersal to other biomes via transient habitat corridors. We sequenced
 thousands of molecular markers for the Neotropical Tityrinae (Aves) and
 applied a novel filtering protocol to identify loci with high utility for
 dated phylogenomics. We used these loci to estimate divergence times and
 model Tityrinae’s evolutionary history. We detected a prominent role for
 speciation driven by barriers including synchronous speciation across the
 Andes, and found that dispersal increased toward the present. Because
 diversification was continuous but dispersal was non-random over time, we
 show that barrier displacement better explains Tityrinae’s history than
 stochasticity or diversity-dependence. We propose that Amazonia is a
 source of biodiversity because (1) it is a relic of a biome that was once
 more extensive, (2) environmentally-mediated corridors facilitated
 emigration, and (3) constant diversification is attributed to a spatially
 heterogeneous landscape that is perpetually dynamic through time.
description: Tityrinae-mafft-nexus-clean-54taxa-95perThe zip file includes all loci and gene trees (produced in RAxML) for the 95% complete dataset (all UCE loci for which 95% of individuals had sequence). It additionally contains a spreadsheet with the characteristics of each of these loci.
DOI: 10.5061/dryad.ht3823d
title: Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

description: Multiple nuclear markers provide genetic polymorphism data for molecular
 systematics and population genetic studies. They are especially required
 for the coalescent-based analyses that can be used to accurately estimate
 species trees and infer population demographic histories. However, in
 avian evolutionary studies, these powerful coalescent-based methods are
 hindered by the lack of a sufficient number of markers. In this study, we
 designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by
 scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch
 (Taeniopygia guttata) genomes. To test their utility, we amplified these
 loci in 41 bird species representing 23 Aves orders. The sixty-three
 best-performing NPCLs, based on high PCR success rates, were selected
 which had various mutation rates and were evenly distributed across 17
 avian autosomal chromosomes and the Z chromosome. To test phylogenetic
 resolving power of these markers, we conducted a Neoavian phylogenies
 analysis using 63 concatenated NPCL markers derived from 48 whole genomes
 of birds. The resulting phylogenetic topology, to a large extent, is
 congruence with results resolved by previous whole genome data. To test
 the level of intraspecific polymorphism in these makers, we examined the
 genetic diversity in four populations of the Kentish Plover (Charadrius
 alexandrinus) at 17 of NPCL markers chosen at random. Our results showed
 that these NPCL markers exhibited a level of polymorphism comparable with
 mitochondrial loci. Therefore, this set of pan-avian nuclear
 protein-coding loci has great potential to facilitate studies in avian
 phylogenetics and population genetics.
description: alignments of universal
 nuclear protein-coding loci and Perl script for BLAST1. Alignment of
 48species at 65genes; 2. Alignment of the four populations of Kentish
 Plover at 19 genes; 3. Partition of 48species at 65 genes; 4. Partition of
 the four populations of Kentish Plover at 19 genes; 5.Perl Script for
 BLASTDRYAD_NPCL_Data.zip
DOI: 10.5061/dryad.h010451
title: Data from: Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq

description: Background Anthocyanins are water-soluble colored flavonoids present in
 multiple organs of various plant species including flowers, fruits,
 leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic
 helix–loop–helix (bHLH) transcription factors, and WD40 repeat proteins
 are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the
 transcription of structural genes in the anthocyanin pathway. Although
 black cultivars of carrots (Daucus carota L.) can accumulate large
 quantities of anthocyanin in their storage roots, the regulatory genes
 responsible for their biosynthesis are not well characterized. The current
 study aimed to analyze global transcription profiles based on RNA
 sequencing (RNA-Seq), and mine MYB, bHLH and WD40 genes that may function
 as positive or negative regulators in the carrot anthocyanin biosynthesis
 pathways. Results RNA was isolated from differently colored calli, as well
 as tissue samples from taproots of various black carrot cultivars across
 the course of development, and gene expression levels of colored and
 non-colored tissue and callus samples were compared. The expression of 32
 MYB, bHLH and WD40 genes were significantly correlated with anthocyanin
 content in black carrot taproot. Of those, 11 genes were consistently up-
 or downregulated in a purple color-specific manner across various calli
 and cultivar comparisons. The expression of 10 out of these 11 genes was
 validated using real-time quantitative reverse transcriptase polymerase
 chain reaction (qRT-PCR). Conclusions The results of this study provide
 insights into regulatory genes that may be responsible for carrot
 anthocyanin biosynthesis, and suggest that future focus on them may help
 improve our overall understanding of the anthocyanin synthesis pathway.
description: Kodama_et_al_2018_Gene_Count_12Sep18This file contains the raw gene counts for all samples used in Kodama et al. (2018). On the "count" tab, the data are organized as: Gene number, LOC ID, chromosome, start position of the gene, end position of the gene and the gene product.
DOI: 10.5061/dryad.q6c9891
title: Data from: Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program

description: While the goal of supplementation programs is to provide positive,
 population-level effects for species of conservation concern, these
 programs can also present an inherent fitness risk when captive-born
 individuals are fully integrated into the natural population. In order to
 evaluate the long-term effects of a supplementation program and estimate
 the demographic and phenotypic factors influencing the fitness of a
 threatened population of Chinook salmon (Oncorhynchus tshawytscha), we
 genotyped tissue samples spanning a 19-year period (1998-2016) to generate
 pedigrees from adult fish returning to Johnson Creek, Idaho USA. We
 expanded upon previous estimates of relative reproductive success (RRS) to
 include two full generations and used generalized linear models to
 determine if origin (hatchery or natural) or phenotypic traits (timing of
 arrival to spawning grounds, body length, and age) significantly predicted
 reproductive success (RS) across multiple years. Our results provide
 evidence that this supplementation program with 100% natural-origin
 broodstock provided a long-term demographic boost to the population (mean
 of 4.56 times in the 1st generation and mean of 2.52 times in the 2nd
 generation). Overall when spawning in nature, hatchery-origin fish
 demonstrated a trend towards lower RS compared to natural-origin fish
 (p&lt;0.05). However, when hatchery-origin fish successfully spawned
 with natural-origin fish, they had similar RS compared to natural by
 natural crosses (1st generation mean hatchery by natural cross RRS = 1.11
 females, 1.13 males; 2nd generation mean hatchery by natural cross RRS =
 1.03 females, 1.08 males). While origin, return year, and body length were
 significant predictors of fitness for both males and females
 (p&lt;0.05), return day was significant for males but not females
 (p&gt;0.05). These results indicate that supplementation programs that
 reduce the potential for genetic adaptation to captivity can be effective
 at increasing population abundance while limiting long-term fitness
 effects on wild populations.
description: Master_Genotype_DataThis is the raw genetic data for all samples used in the analyses of this manuscript.Gt-Seq_Primers_ProbesThis is the list of the primers and probes used for GT-seq SNP genotyping.Koch_et_al_2018_Rscripts_DataAnalysesThis is the R script used for all analyses associated with this manuscript.final_genetics_dataThis is the R object to load into the Rscript for easy start-up of script.
DOI: 10.4121/485bd11f-f97e-4be9-96b2-46b1f740b8cd
title: WadSED Winter 2023-24 frame measurements

description: Measurement data of hydrodynamics, sediment transport, and morphology, collected with measurement frames during the WadSED field campaign in the Dutch Wadden Sea in November 2023 - January 2024.
DOI: 10.5061/dryad.t351v0b
title: Data from: Unequal contributions of species’ persistence and migration on plant communities’ response to climate warming throughout forests

description: Community reshuffling is lagging behind climate warming for many taxa,
 thereby generating a climatic debt. However, only few studies have
 attempted to assess the underlying factors that explain this debt. Here I
 examine how effects of species’ migration and persistence on the current
 climatic debt vary spatially in forest herbaceous communities throughout
 the French territory. I show that Mediterranean communities are responding
 to climate warming through both high species’ migration and persistence
 effects, while alpine forest is the only ecosystem where species’
 migration overtakes species’ persistence mechanisms. Such an approach
 seems promising in assessing the underlying mechanisms of the biodiversity
 response to climate change locally, and it can be applied for conservation
 issues to assess biodiversity sensitivity and optimize its management.
description: Data used for the
 spatio-temporal analysis of the climatic debt observed in understory plant
 communitiesDetails about the
 variables' computation and definition are provided in Bertrand 2018
 and Bertrand et al. 2016. References: Bertrand, R.et al. (2016) Ecological
 constraints increase the climatic debt in forests. Nature communications
 7: 12643. Bertrand, R. (2018) Unequal contributions of species’
 persistence and migration on plant communities’ response to climate
 warming throughout forests. Ecography. Accepted Author
 Manuscript.1993-2008_FrenchForestClimaticDebtSpatioTemporalExplanation_data.xlsx
DOI: 10.4121/485bd11f-f97e-4be9-96b2-46b1f740b8cd.v1
title: WadSED Winter 2023-24 frame measurements

description: Measurement data of hydrodynamics, sediment transport, and morphology, collected with measurement frames during the WadSED field campaign in the Dutch Wadden Sea in November 2023 - January 2024.
DOI: 10.5061/dryad.5670c6n
title: Data from: The relationship between spatial structure and the maintenance of diversity in microbial populations

description: Spatial structure is pervasive in the microbial world, yet we know little
 about how it influences the evolution of microbial populations. It is
 thought that spatial structure limits the scale of competitive
 interactions and protracts selective sweeps. This may allow microbial
 populations to simultaneously explore multiple evolutionary paths. But how
 structured must a microbial population be before this effect is realized?
 We used experimental and simulation studies to explore the relationship
 between spatial structure and the maintenance of diversity. The degree of
 spatial structure experienced by Escherichia coli metapopulations was
 manipulated by varying the migration rate between its component
 subpopulations. Each subpopulation was inoculated with an equal number of
 two equally fit genotypes and their frequencies in 12 subpopulations were
 determined during 150 generations of evolution. We observed that the
 frequency of the ‘loser’ genotypes decreased exponentially as the
 migration rate between the subpopulations was increased and that higher
 frequencies of the “loser” genotypes were maintained in structured
 metapopulations. These results demonstrate that structured microbial
 populations can evolve along multiple evolutionary trajectories even when
 migration rates between the subpopulations are relatively high.
description: Variant_abundance_gen150Frequency of the cycloserine resistant and sensitive variants in each subpopulation after 150 generations of evolution in environments with varying degrees of spatial structure.gen150_variant_abundance.xlsxsubpopulation_growth_kinetics_dataFile contains growth kinetic parameters for each subpopulation at 0, 50, 100, and 150 generations of evolution. Parameters were estimated using the R package "grofit" from OD600 measures over a 24 hour period at 15 minute intervals. Plates were incubated at 37 and shaking.growth_kinetics_data.xlsxsimulation_ouput_dataFile contains the data output from 1000s of replicate metapopulation evolution simulations under varying degrees of spatial structure and mutation rates. Every 250 generations of the evolution the simulation recorded: Average fitness, variance in fitness across the metapopulation, frequency of the minor allele, and variance in frequeny of the minor allele. Variance was estimated from the 12 subpopulations values of fitness or minor allele frequency.simulation_data_all.xlsxsas_analysis_codeContains the SAS code used to analyze the data.evol_metapopulation_sim.pySimulation for evolution of metapopulations experiencing differing degrees of spatial structure (migration rate). Simulation was written in python 2.7. Input parameters that can be varied appear in line 577 and include: migration rate, mutation rate, population size, generations of evolution, and number of replicates.structured_evol_v2.py
DOI: 10.5061/dryad.95n3j32
title: Data from: High soil test phosphorus effect on corn yield

description: Phosphorus removal in crop harvest has increased as yields have increased.
 Fertilizer P use guidelines are based on calibrations often developed for
 much lower yield levels and may need recalibration. Corn yields may be
 greater with higher than recommended soil test P when springs are
 relatively wet and cool. Research was conducted across 12 irrigated and
 five rainfed siteyr in Nebraska with initial Bray-1 P ≤ 11 mg kg–1 to
 evaluate P application strategies for yield and P uptake of continuous
 corn (Zea mays L.) with and without tillage. The fertilizer P treatments
 were maintained on the same plots and included: (i) no P applied (0P);
 (ii) P applied according to the University of Nebraska-Lincoln deficiency
 correction recommendation (UNL_P); (iii) P applied to replace P removed in
 the previous harvest (Replace_P); (iv) Bray-1 P increased and maintained
 at 25 mg kg–1 (Bray_25); and (v) Bray-1 P increased and maintained at 35
 mg kg–1 (Bray_35). Interactions of P practice with other factors were not
 significant indicating consistency of P practice effects across varied
 climate conditions near planting and plant emergence. Grain yield was 9.3%
 and 0.89 Mg ha–1 more with the P-applied treatments compared with 0P.
 Grain yield was 3.3% more due to the additional 5.9 kg ha–1 yr–1 P applied
 with Replace_P compared with UNL_P. Grain yield did not differ for
 Replace-P, Bray_25, and Bray_35. Plant P uptake was on average linearly
 increased by 0.27 kg kg–1 P applied. Fertilizer P application for
 continuous corn should be by Replace_P.
description: UNL STP data Oct 14
 2018The potential to
 evaluated the benefit of maintaining high soil test P was evaluated in
 terms of corn yield. The results of the data set were published in
 Wortmann, C.S., C. Shapiro, T. Shaver, and M. Mainz. 2018. High soil test
 phosphorus effect on corn yield. Soil Sci. Soc Amer. J.
 doi:10.2136/sssaj2018.02.0068