cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7m0cfxq0s
title: Nests ocurrence at Community of Madrid (Spain)

description: Organic waste production has greatly increased following human sprawl and
 led to the development of landfills in recent decades. This abundant and
 reliable anthropogenic food source has favoured several species, some of
 which consequently became overabundant. Landfills present hazards to
 wildlife, which may suffocate on plastic materials, tangle on cords, and
 get exposed to pollutants and pathogens. In response to environmental and
 public health concerns over the maintenance of landfills, the European
 Commission proposed to close the landfills. Our objective was to determine
 the impact of the Landfill European Directive on the White
 Stork, Ciconia ciconia, whose population recovery and growth were
 linked to landfill exploitation. We implemented species distribution
 models to project future distribution in the absence of landfills in the
 Community of Madrid (Spain). Habitat suitability was estimated based on
 nest occurrence and we included data from land cover types, human
 population density and two different climate change scenarios (i.e.,
 emissions in low and high shared socioeconomic pathways). Given that
 protection measures, particularly implemented in protected areas, were
 associated with population recovery, we also evaluated the overlapping
 degree between protected areas and projected distribution. Our models
 predicted a sharp decline in breeding population distribution with
 landfill closure, reaching values similar to the 1984 breeding census when
 the species was categorized as threatened. Our results also suggest a
 decrease in maximum habitat suitability. Climate change also contributed
 to a reduction in breeding population distribution given model predictions
 for the extreme emission pathway (ssp5). Measures such as gradual change
 in landfill management, continuous monitoring of breeding populations, and
 evaluation of the Stork use of natural feeding areas before and after
 landfill closure, should be considered. 
description: Direct census searching for nests in the whole Community of
 Madrid.
DOI: 10.5061/dryad.0cfxpnw7c
title: Soil fungal communities contribute to the positive diversity-productivity relationship of tree communities under contrasting water availability

description: Plant diversity has often been linked to increased productivity; however,
 this apparent diversity-productivity relationship may rely on
 inter-trophic interactions such as those between plants and soil microbes.
 Soil fungi can create complementarity between plant species via altered
 plant resource partitioning, facilitation via fungal networks, or biotic
 feedbacks, thereby promoting plant diversity-productivity relationships.
 Furthermore, these relationships are likely to be context-dependent in
 response to resource availability.  We used a
 biodiversity-ecosystem function experiment with trees exposed to high and
 low water availability treatments to determine the contribution of soil
 fungal communities to the diversity-productivity relationship in tree
 communities. We used amplicon sequencing of soil fungi to assess fungal
 richness, community composition, and richness of functional guilds. We
 then applied structural equation modelling to determine relationships
 between tree diversity, fungal communities, and tree productivity and the
 role of water availability in these relationships. Tree species richness
 and functional diversity both increased above-ground tree productivity and
 influenced soil fungal community composition. Fungal community composition
 had a direct impact on tree productivity and enhanced net diversity
 effects on productivity. Therefore, fungal communities mediated a
 positive, indirect effect of tree richness on productivity. While total
 fungal richness was not associated with tree diversity, pathogen richness
 decreased and mycorrhizal richness increased with tree richness. Pathogen
 and mycorrhizal richness had either no impact or a weak negative effect on
 productivity. Tree species traits strongly affected fungal communities and
 these changes promoted productivity. Finally, water availability greatly
 influenced fungal communities but did not interact with tree diversity to
 affect productivity; indicating possible resilience of tree communities to
 altered precipitation regimes and associated changes in fungal
 communities. Synthesis: Our study highlights the crucial role that fungal
 communities play in shaping the relationship between tree diversity,
 traits, and productivity, and resilience to altered water availability.
DOI: 10.5061/dryad.2547d7wwp
title: Challenges of copro-parasitological surveys in wild Iberian ibex (Capra pyrenaica) populations addressed through a combination of molecular and statistical tools

description: Copro-parasitological surveys in wildlife face challenges due to the
 secretive nature of many species and the unknown performance of the
 diagnostic tests employed. To overcome these issues, we used a combination
 of hierarchical models (site-occupancy and N-mixture models) applied to
 copro-parasitological data obtained from faecal samples assigned to the
 host species by molecular methods in the Iberian ibex in north-western
 Iberian Peninsula. The aims were to compare the performance of four
 diagnostic tests (Mini-FLOTAC, McMaster, Willis flotation, and natural
 sedimentation) and to use this methodological approach (molecular analysis
 with hierarchical models) to better estimate positivity proportion and
 shedding intensity in a wild ibex population. Pooled faecal samples were
 collected, and those confirmed by molecular analyses to be the host
 species in question were included in the study. Hierarchical models
 confirmed different performances of each diagnostic test, with Mini-FLOTAC
 showing higher sensitivity for eimeriid coccidia, Willis flotation (for
 proportion positive) and McMaster (for shedding intensity) in
 gastrointestinal Strongylida, and equal performance of MiniFlotac/Willis
 flotation (for proportion positive) and MiniFlotac/McMaster (for shedding
 intensity) in Moniezia spp. This study employed a combination of molecular
 and statistical methods that improved the estimates of prevalence and
 shedding intensity and allowed us to compare the performance of four
 diagnostic tests while assessing the effect of covariates. Such
 improvements are critical to enhancing inference in non-invasive wildlife
 copro-parasitological studies.
DOI: 10.5061/dryad.kh18932bx
title: Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi

description: Limiting harm to organisms via genetic sampling is an important
 consideration for rare species. Nondestructive sampling techniques have
 been developed to address this issue in freshwater mussels. Two methods,
 visceral swabbing and tissue biopsies, have proven to be effective for DNA
 sampling, though it is unclear as to which method is preferable for
 genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and
 damage to organisms, while visceral swabbing potentially reduces the
 chance of such harm. Our study compared the efficacy of these two DNA
 sampling methods for generating GBS data for the Unionid freshwater
 mussel, Texas Pigtoe (Fusconaia askewi). Our results find both methods
 generate quality sequence data, though some considerations are in order.
 Tissue biopsies produced significantly higher DNA concentrations and
 larger numbers of reads when compared to swabs, though there was no
 significant association between starting DNA concentration and number of
 reads generated. Swabbing produced greater sequence depth (more reads per
 sequence) while tissue biopsies revealed greater coverage across the
 genome (at lower sequence depth). Patterns of genomic variation as
 characterized in principal component analyses were similar regardless of
 the sampling method, suggesting that the less invasive swabbing is a
 viable option for producing quality GBS data in these organisms.
DOI: 10.5061/dryad.cfxpnvxb7
title: Data from: Testing concordance and conflict in spatial replication of landscape genetics inferences

description: The degree to which landscape genetics findings can be extrapolated to
 different areas of a species range is poorly understood. Here, we used a
 broadly distributed ectothermic lizard (Sceloporus occidentalis, Western
 Fence lizard) as a model species to evaluate the full role of topography,
 climate, vegetation, and roads on dispersal and genetic differentiation.
 We conducted landscape genetics analyses in five areas within the Sierra
 Nevada mountain range. Genetic distances calculated from thousands of
 ddRAD markers were used to optimize landscape resistance surfaces and
 infer the effects of landscape and topographic features. Across study
 areas, we found a great deal of consistency in the primary environmental
 gradients impacting genetic connectivity, along with some site-specific
 differences, and a range in the proportion genetic variance explained by
 environmental factors across study sites. High-elevation colder areas were
 consistently found to be barriers to gene flow, as were areas of high
 ruggedness and slope. High temperature seasonality and high precipitation
 during the winter wet season also presented a substantial barrier to gene
 flow in a majority of study areas. The effect of other landscape variables
 on genetic differentiation was more idiosyncratic and depended on specific
 attributes at each site. Across study areas, canyon valleys were always
 implicated as facilitators to dispersal and key features linking
 populations and maintaining genetic connectivity, though the relative
 importance varied in different areas. We emphasize that spatial data
 layers are complex and multidimensional, and careful consideration of
 spatial data correlation structure and robust analytic frameworks will be
 critical to our continued understanding of spatial genetics processes.
description: This dataset includes script files in R, and bioinformatic
 pipelines provided in markdown format, as well as spatial data layers
 provided in ascii and geo tif format.
description: Open source software: R, QGIS, Markdown and Text editor.
DOI: 10.5061/dryad.ngf1vhj09
title: The shape of kernels and cracks, in a nutshell

description: We explore the shape of walnut shells and kernels. We analyze 1264
 individual 3D X-ray CT scan reconstructions of walnuts, corresponding to
 150 walnut accessions. We exploit the nondestructiveness of X-rays to
 digitally segment and measure the 4 main tissues of interest for each
 walnut, namely shell, kernel, packing tissue, and sealed air. From these,
 we extract a total of 38 size- and shape-specific descriptors, many of
 them unexplored in the current literature. We focus on several allometric
 relationships of interest, from which we draw theoretical upper and lower
 bounds of possible walnut and kernel sizes. We then study correlations and
 variations of these morphological descriptors with qualitative data
 corresponding to traits of commercial interest like ease of kernel removal
 and shell strength.
description: All plant materials represent walnut breeding lines, germplasm,
 and cultivars maintained by the Walnut Improvement Program at the
 University of California, Davis. A total of 150 walnuts accessions were
 harvested into mesh bags at hull split, oven-dried overnight at 95F, and
 then air-dried for several weeks before moving into cold storage at 35F. 5
 to 16 individuals were selected for each accession, for a total of 1301
 individual walnuts to be scanned at Michigan State University. The walnuts
 were scanned in 171 batches. The scans were produced using the North Star
 X3000 system and the included efX-DR software. The X-ray source was set at
 75 kV and 100~\micro{A}, with 720 projections per scan, at 3 frames per
 second and with 3 frames averaged per projection. The data was obtained in
 continuous mode. The 3D X-ray CT reconstruction was computed with the
 efX-CT software, obtaining voxel-based images with voxel size of 75.9
 microns.
description: All the files are either 3D TIFF images, CSVs with associated
 metadata, or JPGs for visualization and inspection purposes.
 All the TIFF files were manipulated as 3D numpy arrays with
 Python. A GitHub repository is referenced with plenty of Jupyter notebooks
 that provide more detail on how the images were handled and how the CSVs
 and images were produced.
DOI: 10.5061/dryad.2280gb5xs
title: Mean species responses predict effects of environmental change on coexistence

description: Environmental change research is plagued by the curse of dimensionality:
 the number of communities at risk and the number of environmental drivers
 are both large. This raises the pressing question if a general
 understanding of ecological effects is achievable. These data show that
 this is indeed possible. It contains code that calculates the feasibility
 domain size (a proxy for coexistence) for bi- and tritrophic communities
 challenged by environmental change. Some of this code simply returns the
 output of a closed-form expressions (i.e. simple equations), while some
 rely on simulations that require specific packages. The data also contain
 presence/absence data of macroinvertebrate taxa and water chemistry
 variables measured across sites (that are either severely or weakly
 modified by human activity, quantified via land use) at US streams. With
 these data, we were able to test if sites that share the same community
 have similar water chemistry, in other words: how tightly is a community
 linked to a certain water chemistry? This analysis demonstrates how to
 apply our theory to the analysis of field data, and lends support to
 effects of land use change on coexistence in natural invertebrate
 communities.
description: Full description of invertebrate data collection: https://www.science.org/doi/10.1126/sciadv.adf4896
description: RStudio, Version 2023.03.1+446 (2023.03.1+446).
DOI: 10.5061/dryad.ksn02v799
title: Supporting data for: Whole genome sequencing reveals fine-scale environment associated divergence near the range limits of a temperate reef fish

description: Environmental variation is increasingly recognized as an important driver
 of diversity in marine species despite the lack of physical barriers to
 dispersal and the presence of pelagic stages in many taxa. A robust
 understanding of the genomic and ecological processes involved in
 structuring populations is lacking for most marine species, often
 hindering management and conservation action. Cunner (Tautogolabrus
 adspersus), is a temperate reef fish with both pelagic early life history
 stages and strong site-associated homing as adults; the species is also of
 interest for use as a cleaner fish in salmonid aquaculture in Atlantic
 Canada. We aimed to characterize genomic and geographic differentiation of
 cunner in the Northwest Atlantic. To achieve this, a chromosome-level
 genome assembly for cunner was produced and used to characterize spatial
 population structure throughout Atlantic Canada using whole genome
 resequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes;
 whole genome resequencing of 803 individuals from 20 locations from
 Newfoundland to New Jersey identified approximately 11 million genetic
 variants. Principal component analysis revealed four regional Atlantic
 Canadian groups. Pairwise FST and selection scans revealed signals of
 differentiation and selection at discrete genomic regions, including
 adjacent peaks on chromosome 10 across multiple pairwise comparisons
 (i.e., FST 0.5–0.75). Redundancy analysis suggested association of
 environmental variables related to benthic temperature and oxygen range
 with genomic structure. Results suggest regional scale diversity in this
 temperate reef fish and can directly inform the collection and
 translocation of cunner for aquaculture applications and the conservation
 of wild populations throughout the Northwest Atlantic.
DOI: 10.5281/zenodo.18390146
title: A high-throughput microphysiological system to quantify key events leading to liver fibrosis

description: New approach methodologies (NAMs), including microphysiological systems (MPS), are emerging as alternatives to animal testing. In the liver, chronic hepatocellular damage can progress to fibrosis, which has been described by an Adverse Outcome Pathway (AOP). However, standardized in vitro models that capture and quantify key AOP events and cell-cell interactions are lacking. 

We developed a scalable liver fibrosis model using the 384-well Akura™ Twin microplate featuring 168 interconnected well pairs. We studied fibrosis progression by seeding HepaRG microtissues (MTs), with or without THP-1 cells in alpha wells and hepatic stellate cell (hTERT-HSC) MTs in beta wells. Cell health and metabolic activity were monitored via specific sensors that detect glucose and lactate levels. Transforming growth factor beta 1 (TGF‑β1), methotrexate (MTX) and acetaminophen (APAP) reduced albumin production, indicating hepatocellular injury. TGF‑β1 activated THP-1, increasing ALOX5AP, TREM2, and TGF-β1 mRNA expression. PAI-1 protein levels increased following treatment with TGF-β1, particularly in HepaRG-THP-1 co-cultures. In hTERT-HSCs, TGF-β1 also induced expression of fibrosis markers (ACTA2, COL1A1, COL3A1 and FN1) and increased stress fibers and fibronectin expression. Extracellular matrix remodeling was confirmed by elevated Pro-Collagen 1A1 and CTGF protein levels upon TGF-β1 treatment. 

The Akura™ Twin platform enables high-throughput modeling of liver fibrosis, mimicking the key events of the liver fibrosis AOP. This model, combining a high-throughput MPS with established cell lines, offers a promising tool to investigate fibrosis mechanisms and advancing quantitative AOP development.
DOI: 10.5281/zenodo.18390147
title: A high-throughput microphysiological system to quantify key events leading to liver fibrosis

description: New approach methodologies (NAMs), including microphysiological systems (MPS), are emerging as alternatives to animal testing. In the liver, chronic hepatocellular damage can progress to fibrosis, which has been described by an Adverse Outcome Pathway (AOP). However, standardized in vitro models that capture and quantify key AOP events and cell-cell interactions are lacking. 

We developed a scalable liver fibrosis model using the 384-well Akura™ Twin microplate featuring 168 interconnected well pairs. We studied fibrosis progression by seeding HepaRG microtissues (MTs), with or without THP-1 cells in alpha wells and hepatic stellate cell (hTERT-HSC) MTs in beta wells. Cell health and metabolic activity were monitored via specific sensors that detect glucose and lactate levels. Transforming growth factor beta 1 (TGF‑β1), methotrexate (MTX) and acetaminophen (APAP) reduced albumin production, indicating hepatocellular injury. TGF‑β1 activated THP-1, increasing ALOX5AP, TREM2, and TGF-β1 mRNA expression. PAI-1 protein levels increased following treatment with TGF-β1, particularly in HepaRG-THP-1 co-cultures. In hTERT-HSCs, TGF-β1 also induced expression of fibrosis markers (ACTA2, COL1A1, COL3A1 and FN1) and increased stress fibers and fibronectin expression. Extracellular matrix remodeling was confirmed by elevated Pro-Collagen 1A1 and CTGF protein levels upon TGF-β1 treatment. 

The Akura™ Twin platform enables high-throughput modeling of liver fibrosis, mimicking the key events of the liver fibrosis AOP. This model, combining a high-throughput MPS with established cell lines, offers a promising tool to investigate fibrosis mechanisms and advancing quantitative AOP development.
DOI: 10.5061/dryad.5dv41nsbk
title: Evolution of butterfly seasonal plasticity driven by climate change varies across life stages

description: Photoperiod is a common cue for seasonal plasticity and phenology, but
 climate change can create cue-environment mismatches for organisms that
 rely on it. Evolution could potentially correct these mismatches, but
 phenology often depends on multiple plastic decisions made during
 different life stages and seasons that may evolve separately. For example,
 Pararge aegeria (Speckled wood butterfly) has photoperiod-cued seasonal
 life history plasticity in two different life stages: larval development
 time and pupal diapause. We tested for climate-change-associated evolution
 of this plasticity by replicating common garden experiments conducted on
 two Swedish populations 30 years ago. We found evidence for evolutionary
 change in the contemporary larval reaction norm—although these changes
 differed between populations—but no evidence for evolution of the pupal
 reaction norm. This variation in evolution across life stages demonstrates
 the need to consider how climate change affects the whole life cycle to
 understand its impacts on phenology.
description: Please see the main paper and readme files for full details on
 the methods associated with this dataset. Data on the
 historic experiment was digitized for this study from the original data
 sheets associated with Nylin et al 1989, 1995 (see main text for full
 citations). Data for the contemporary experiment was
 generated by the authors for this study, following the methods of the
 historic experiment. Temperature data came from the
 Swedish Hydrological and Meteorological Institute weather stations and was
 restructured, but otherwise used as provided by SHMI.
description: Readme file is also plain text compatible (.txt).
 Data files are comma-separated values (.csv) format. 
 Software files (.R) are written in in R.
DOI: 10.5061/dryad.dfn2z3576
title: Data for: Repeatable negotiation rules? only females show repeatable response to partner removal in a brood-provisioning songbird

description: Theoretical models indicate that the evolution of biparental care depends
 on how parents behaviorally negotiate their level of care in response to
 those of their partner and whether sexes and individuals consistently vary
 in their response (compensatory response). While compensatory response has
 been widely investigated empirically, its repeatability has rarely been
 assessed. In this study, we used a reaction norm approach to investigate
 the repeatability of the compensatory offspring provisioning of a parent
 after temporary removal of its partner in the pied flycatcher (Ficedula
 hypoleuca) across different breeding seasons and partners. We found that
 only females partially compensated for the short-term removal of the
 partner and their response was significantly repeatable across years while
 breeding with different partners. This study highlights the importance of
 considering among individual differences in negotiation rules to better
 understand the role of negotiation mechanisms in the evolution of parental
 care strategies.
DOI: 10.5061/dryad.dncjsxm4t
title: Valley–dimensionality-locking of superconductivity in cubic phosphides

description: Two-dimensional superconductivity is primarily realized in atomically-thin
 layers through extreme exfoliation, epitaxial growth, or interfacial
 gating. Apart from their technical challenges, these approaches lack
 sufficient control over the Fermiology of superconducting systems. Here,
 we offer a Fermiology-engineering approach, allowing to desirably tune the
 coherence length of Cooper pairs and the dimensionality of superconducting
 states in arsenic phosphides AsxP1−x under hydrostatic pressure. We
 demonstrate how this turns these compounds into tunable two-dimensional
 superconductors with a dome-shaped phase diagram even in the bulk limit.
 This peculiar behavior is shown to result from an unconventional
 valley-dimensionality locking mechanism, driven by a delicate competition
 between three-dimensional hole-type and two-dimensional electron-type
 energy pockets spatially separated in momentum space. The resulting
 dimensionality crossover is further discussed to be systematically
 controllable by pressure and stoichiometry tuning. Our findings pave a
 unique way to realize and control superconducting phases with special
 pairing and dimensional orders.