cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j6q573n7x
title: Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses

description: C4 photosynthesis is a complex trait that sustains fast growth and high
 productivity in tropical and subtropical conditions and evolved repeatedly
 in flowering plants. One of the major C4 lineages is Andropogoneae, a
 group of ~ 1,200 grass species that includes some of the world's most
 important crops and species dominating tropical and some temperate
 grasslands. Previous efforts to understand C4 evolution in the group have
 compared a few model C4 plants to distantly related C3 species, so that
 changes directly responsible for the transition to C4 could not be
 distinguished from those that preceded or followed it. In this study, we
 analyse the genomes of 66 grass species, capturing the earliest
 diversification within Andropogoneae as well as their C3 relatives.
 Phylogenomics combined with molecular dating and analyses of protein
 evolution show that many changes linked to the evolution of C4
 photosynthesis in Andropogoneae happened in the Early Miocene, between 21
 and 18 Ma, after the split from its C3 sister lineage, and before the
 diversification of the group. This initial burst of changes was followed
 by an extended period of modifications to leaf anatomy and biochemistry
 during the diversification of Andropogoneae, so that a single C4 origin
 gave birth to a diversity of C4 phenotypes during 18 million years of
 speciation events and migration across geographic and ecological spaces.
 Our comprehensive approach and broad sampling of the diversity in the
 group reveals that one key transition can lead to a plethora of phenotypes
 following sustained adaptation of the ancestral state.
DOI: 10.5061/dryad.2v6wwpzh0
title: Predicting barrier effects of transportation networks on Asian elephants: Implications for environmental impact assessment

description: The rapid proliferation of transportation networks (TNs) is a threat to
 wide–ranged animals through habitat erosion, road–kill, and indirect
 socio–ecological interaction. In most cases, environmental impact
 assessments of TNs about animals are descriptive and targeted to direct
 impacts of the “linear features”, while indirect and cumulative impacts
 are relatively neglected. Using spatially explicit data of elephant–caused
 damage during 2012–2015 in China, we quantified barrier effects of TN on
 Asian elephants and predicted the effects under a TN expansion scenario
 using maximum entropy algorithms. We found that TN acted as a strong
 barrier even for the elephants that have inhabited highly fragmented
 landscapes for years, with only 18% of the damage occurred on the crossed
 side of roads. Also, the TN expansion will reduce elephant habitats,
 exacerbating herd isolation and human–elephant conflict locally. Thus, we
 suggest that mitigation of the conflicts should be integrated into future
 environmental impact assessments.
description: Please check details in the article.
description: We have prepared a manuscript to explore multi-spatial mechanism
 of elephant-caused damage, any use of this dataset should not be
 competing.
DOI: 10.5061/dryad.sf7m0cg1k
title: Data from: Evolution and disappearance of sympatric Coregonus albula in a changing environment - a case study of the only remaining population pair in Sweden

description: During the past 50 years Fennoscandian populations of spring-spawning
 Baltic cisco (Coregonus albula), sympatric to common autumn-spawners, have
 declined or disappeared; e.g., three out of four known spring-spawning
 populations in Sweden are regarded as extinct. Over the same period,
 climate has changed and populations have been subject to other
 anthropogenic stressors. We compared historic (1960s) and recent
 (1990-2000s) morphological data from the still existent sympatric cisco
 populations in Lake Fegen, Sweden. Phenotypic changes were found for
 spring-spawners making them more similar to the sympatric autumn-spawners
 (that had remained virtually unchanged). Based on results for other
 salmoniform fishes, a phenotypically plastic response to increased
 temperature during early development appears unlikely. The recent material
 was also analysed with microsatellite markers; long-term effective
 population size in spring-spawners was estimated to be about 20 times
 lower than autumn-spawners, with signs of long-term gene flow in both
 directions and a recent genetic bottleneck in spring-spawners. The change
 towards a less distinct phenotype in spring-spawners is suggested to
 reflect a recent increase in gene flow from autumn-spawners. Time since
 divergence was estimated to only c. 1 900 years (95% CI: 400 – 5 900), but
 still the Fegen populations represent the most morphologically and
 genetically distinct sympatric populations studied. Consequently, we
 hypothesise that less distinct population pairs can be even younger, and
 that spring-spawning may have repeatedly evolved and disappeared in
 several lakes since the end of the last glaciation, concurrent with
 changed environmental conditions.
description: Please refer to Material and Methods in Delling & Palm
 (Ecology and Evolution 2019;9:12727-12753).
description: The submitted dataset contains microsatellite genotypes (nine
 loci) from the individuals in Delling & Palm (Ecology and
 Evolution 2019;9:12727-12753). Please see the uploaded "Read me"
 file for details.
DOI: 10.5061/dryad.34tmpg4fm
title: Data from: Assessing species richness trends: declines of bees and bumblebees in the Netherlands since 1945.

description: Estimating and predicting temporal trends in species richness is of
 general importance, but notably difficult because detection probabilities
 of species are imperfect and many datasets were collected in an
 opportunistic manner. We need to improve our capabilities to assess
 richness trends using datasets collected in unstandardized procedures with
 potential collection bias. Two methods are proposed and applied to
 estimate richness change, which both incorporate models for sampling
 effects and detection probability: (1) non-linear species accumulation
 curves with an error variance model and (2) Pradel capture-recapture
 models. The methods are used to assess nationwide temporal trends
 (1945-2018) in the species richness of wild bees in the Netherlands.
 Previously, a decelerating decline in wild bee species richness was
 inferred for part of this dataset. Among the species accumulation curves,
 those with non-constant changes in species richness are preferred.
 However, when analysing data subsets, constant changes became selected for
 non-Bombus bees (for samples in collections) and bumblebees (for spatial
 grid cells sampled in three periods). Smaller richness declines are
 predicted for non-Bombus bees than bumblebees. However, when relative
 losses are calculated from confidence intervals limits, they overlap and
 touch zero loss. Capture-recapture analysis applied to species encounter
 histories infers a constant colonization rate per year and constant local
 species survival for bumblebees and other bees. This approach predicts a
 6% reduction in non-Bombus species richness from 1945 to 2018 and a
 significant 19% reduction for bumblebees. Statistical modelling to detect
 species richness time trends should be systematically complemented with
 model checking and simulations to interpret the results. Data inspection,
 assessing model selection bias and comparisons of trends in data subsets
 were essential model checking strategies in this analysis. Opportunistic
 data will not satisfy the assumptions of most models and this should be
 kept in mind throughout.
DOI: 10.5061/dryad.d2547d7z3
title: Uninterrupted growth in a non-polar hadrosaur explains the gigantism among duck-billed dinosaurs

description: Duck-billed dinosaurs (Hadrosauridae) were the most common ornithopods of
 the Late Cretaceous. Second only to sauropods and in many cases exceeding
 the sizes of the largest land mammals (such as indricotheres or
 proboscideans), they represent the largest terrestrial herbivores that
 walked the Earth. Despite their gigantic sizes, diversity, and abundance,
 their growth strategies remain poorly understood. Herein, we examine the
 bone microstructure of several Mongolian hadrosauroids of varied adult
 sizes. The small and middle-sized species have lines of arrested growth
 (LAGs). On the other hand, one of the largest duck-billed dinosaurs,
 Saurolophus angustirostris, shows an uninterrupted growth, comparable with
 other big hadrosaurs for which the lack of cyclical growth arrests was
 interpreted as a result of living in the polar region. Since both of the
 studied taxa inhabited warmer, continental, monsoon-influenced
 environments of the Late Cretaceous Mongolia, we propose that the absence
 of LAGs is not a climatic-driven condition but rather connected with the
 animal’s size (i.e., ontogeny). Our results show that hadrosaurs, similar
 to sauropods changed their growth dynamics from cyclical to continuous
 during their evolution, which made it possible for them to achieve
 comparable body sizes.
description: The 3D images of the specimens
 were prepared using the Shining 3D EinScan Pro 2X 3D scanner fixed on a
 tripod with EinScan Pro 2X Color Pack (texture scans), EinTurntable
 (alignment based on features), and EXScan Pro 3.2.0.2 software. The number
 of turntable steps was varied, chosen depending on the specimen. The
 models were meshed using the Watertight Model and High Detail
 presets.
description: <strong>File list and descriptions</strong>
 Słowiak et al. Uninterrupted
 growth in a non-polar hadrosaur explains the gigantism among duck-billed
 dinosaurs - Supplementary information.docx Main supplementary file:
 description of additional material of <em>Gobihadros
 mongoliensis</em>, data and results of the phylogenetic analysis,
 supplementary references ZPAL_MgD-III_2.ply
 Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/2, proximal end of the right tibia
 ZPAL_MgD-III_7.ply Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/7, the ungual of the second digit of the left
 pes ZPAL_MgD-III_10.ply Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/10, a small fragment of the right dentary
 representing the lateral (labial) part of the mandible, close to the
 symphysis ZPAL_MgD-III_17.ply Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/17, a proximal caudal vertebra 
 ZPAL_MgD-III_19 proximal.ply Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/19, right fibula, proximal part
 ZPAL_MgD-III_19 distal.ply Bayn Shire Hadrosauroidea
 indet., ZPAL MgD-III/19, right fibula, distal part
DOI: 10.5281/zenodo.18393462
title: Dataset from the PLEAZOL project

description: This record contains three data sets:

Growth_data.csv

Data on the growth performance of synthetic populations of Metschikowia reukaufii (Ascomycota) in different treatments. The dataset contains four columns:



Population: name of the synthetic population (P1, P2, or P3).

Step: propagation step (T01 to T32).

Treatment: IZL_0.5, artificial nectar containing 0.5 μg/mL of imazalil; IZL_0.125, artificial nectar containing 0.125 μg/mL of imazalil; IZL_0.031, artificial nectar containing 0.031 μg/mL of imazalil; and CTRL, artificial nectar containing no fungicide.

CFU_count: colony forming units (CFU) per mL.


MIC_data_strains.csv

Data on the in vitro susceptibility to different fungicides of the ten M. reukaufii strains used to create the aforementioned synthetic populations. The dataset contains eight columns:



Strain: strain name.

AMB: minimum inhibitory concentration (MIC, in μg/mL) to amphotericin B.

CSF: MIC to caspofungin.

EPZ: MIC to epoxiconazole.

FCZ: MIC to fluconazole.

IZL: MIC to imazalil.

KTZ: MIC to ketoconazole.

VCZ: MIC to voriconazole.


MIC_data_evolved.csv

Data on the in vitro susceptibility to different fungicides of M. reukaufii colonies evolved in the same treatments used in the Growth_data.csv data set. The dataset contains eleven columns:



Colony: colony name.

Population: name of the synthetic yeast population (P1 or P2).

Treatment: IZL_0.5, artificial nectar containing 0.5 μg/mL of imazalil; IZL_0.125, artificial nectar containing 0.125 μg/mL of imazalil; IZL_0.031, artificial nectar containing 0.031 μg/mL of imazalil; and CTRL, artificial nectar containing no fungicide.

Step: propagation step (T1 [2 weeks] or T4 [4 months]).

AMB: minimum inhibitory concentration (MIC, in μg/mL) to amphotericin B.

CSF: MIC to caspofungin.

EPZ: MIC to epoxiconazole.

FCZ: MIC to fluconazole.

IZL: MIC to imazalil.

KTZ: MIC to ketoconazole.

VCZ: MIC to voriconazole.
DOI: 10.5281/zenodo.18393463
title: Dataset from the PLEAZOL project

description: This record contains three data sets:

Growth_data.csv

Data on the growth performance of synthetic populations of Metschikowia reukaufii (Ascomycota) in different treatments. The dataset contains four columns:



Population: name of the synthetic population (P1, P2, or P3).

Step: propagation step (T01 to T32).

Treatment: IZL_0.5, artificial nectar containing 0.5 μg/mL of imazalil; IZL_0.125, artificial nectar containing 0.125 μg/mL of imazalil; IZL_0.031, artificial nectar containing 0.031 μg/mL of imazalil; and CTRL, artificial nectar containing no fungicide.

CFU_count: colony forming units (CFU) per mL.


MIC_data_strains.csv

Data on the in vitro susceptibility to different fungicides of the ten M. reukaufii strains used to create the aforementioned synthetic populations. The dataset contains eight columns:



Strain: strain name.

AMB: minimum inhibitory concentration (MIC, in μg/mL) to amphotericin B.

CSF: MIC to caspofungin.

EPZ: MIC to epoxiconazole.

FCZ: MIC to fluconazole.

IZL: MIC to imazalil.

KTZ: MIC to ketoconazole.

VCZ: MIC to voriconazole.


MIC_data_evolved.csv

Data on the in vitro susceptibility to different fungicides of M. reukaufii colonies evolved in the same treatments used in the Growth_data.csv data set. The dataset contains eleven columns:



Colony: colony name.

Population: name of the synthetic yeast population (P1 or P2).

Treatment: IZL_0.5, artificial nectar containing 0.5 μg/mL of imazalil; IZL_0.125, artificial nectar containing 0.125 μg/mL of imazalil; IZL_0.031, artificial nectar containing 0.031 μg/mL of imazalil; and CTRL, artificial nectar containing no fungicide.

Step: propagation step (T1 [2 weeks] or T4 [4 months]).

AMB: minimum inhibitory concentration (MIC, in μg/mL) to amphotericin B.

CSF: MIC to caspofungin.

EPZ: MIC to epoxiconazole.

FCZ: MIC to fluconazole.

IZL: MIC to imazalil.

KTZ: MIC to ketoconazole.

VCZ: MIC to voriconazole.
DOI: 10.5061/dryad.z612jm67f
title: Feeding behaviour is the main driver for microparticle intake in mangrove crabs

description: As marine plastic debris is primarily sourced from terrestrial input,
 coastal environments are particularly affected by deposition. Because of
 their pneumatophores, mangroves have been recognized for their importance
 in confining plastic waste. Crabs are a dominant component of the mangrove
 ecosystem and play a critical role in maintaining healthy and resilient
 mangrove forests. Therefore, the presence of debris fragmented from waste,
 in their habitat is a potential threat. However, the potential ingestion
 of microplastic pieces by mangrove crabs has not yet been investigated.
 Here, we quantified microparticles found in the cardiac stomachs and gill
 chambers of four species of crabs. All specimens collected had
 anthropogenic microparticles present either via their digestive or
 respiratory systems. We observed significant variability in the abundance
 and types of anthropogenic microparticles across sites and species.
 Interspecific differences appear to be explained by their particular
 feeding habits, with less selective species ingesting more particles.
description: Samples were collected near rocks and
 in mud depending on the species. At least two individuals were collected
 for each species depending on their appearance on rocks and muds. The
 number of samples collected for each species are listed in Table 1 on the
 manuscript. All the samples were collected in a bucket with leaves and
 sediments to reduce stress of handling. Samples were gently washed with
 Milli-Q water to remove the mud outside the carapace, legs and chelipeds
 in the laboratory. They were then frozen at -18 °C immediately for later
 sample digestion and examination, in which samples were stored in separate
 clearly named samples bags.
description: See additional descriptions in file - Metadata-Not_etal.docx
DOI: 10.5061/dryad.7h44j0zq9
title: Research Data Management in Health and Biomedical Citizen Science: Practices and Prospects

description: Background: Public engagement in health and biomedical research is being
 influenced by the paradigm of citizen science. However, conventional
 health and biomedical research relies on sophisticated research data
 management tools and methods. Considering these, what contribution can
 citizen science make in this field of research? How can it follow research
 protocols and produce reliable results? Objective: The aim of this paper
 is to analyse research data management practices in existing biomedical
 citizen science studies, so as to provide insights for members of the
 public and of the research community considering this approach to
 research. Methods: A scoping review was conducted on this topic to
 determine data management characteristics of health and bio medical
 citizen science research. From this review and related web searching, we
 chose five online platforms and a specific research project associated
 with each, to understand their research data management approaches and
 enablers. Results: Health and biomedical citizen science platforms and
 projects are diverse in terms of types of work with data and data
 management activities that in themselves may have scientific merit.
 However, consistent approaches in the use of research data management
 models or practices seem lacking, or at least are not evident.
 Conclusions:  There is potential for important data collection
 and analysis activities to be opaque or irreproducible in health and
 biomedical citizen science initiatives without the implementation of a
 research data management model that is transparent and accessible to team
 members and to external audiences. This situation might be improved with
 participatory development of standards that can be applied to diverse
 projects and platforms, across the research data life cycle.
DOI: 10.5061/dryad.ns1rn8pnf
title: How does joint evolution of consumer traits affect resource specialization?

description: Consumers regularly experience trade-offs in their ability to find, handle
 and digest different resources. Evolutionary ecologists recognized the
 significance of this observation for the evolution and maintenance of
 biological diversity long ago and continue to elaborate on the conditions
 under which to expect one or several specialists, generalists or
 combinations thereof. Existing theory based on a single evolving trait
 predicts that specialization requires strong trade-offs such that
 generalists perform relatively poorly, while weak trade-offs favor a
 single generalist. Here, we show that this simple dichotomy does not hold
 true under joint evolution of two or more foraging traits. In this case,
 the boundary between trade-offs resulting in resource specialists and
 resource generalists is shifted toward weaker trade-off curvatures. In
 particular, weak trade-offs can result in evolutionary branching leading
 to the evolution of two coexisting resource specialists while the
 evolution of a single resource generalist requires particularly weak
 trade-offs. These findings are explained by performance benefits due to
 epistatic trait interactions enjoyed by phenotypes that are specialized in
 more than one trait for the same resource.
description: Vasconcelos&Rueffler2019AmNat.nb: This notebook is
 written in Wolfram Mathematica 11. It contains all calculations, both
 symbolic and numerical, on which our results are based.
 Vasconcelos&Rueffler2019AmNat_simulations.m: Simulation
 code written in MatLab.  
description: The settings for the notebook are read only. If you want to
 modify the code you can copy and paste code in your own file.
DOI: 10.7272/q65x273x
title: Functionally heterogeneous human satellite cells identified by single cell RNA sequencing

description: Although heterogeneity is recognized within the murine satellite cell
 pool, a comprehensive understanding of distinct subpopulations and their
 functional relevance in human satellite cell population is lacking. We
 used a combination of single cell RNA sequencing and flow cytometry to
 identify, distinguish, and physically separate novel subpopulations of
 human PAX7+ satellite cells (HuSCs) from normal muscles. We found that,
 although relatively homogeneous compared to activated satellite cells and
 committed progenitors, the HuSC pool contains clusters of
 transcriptionally distinct cells with consistency across human
 individuals. New surface marker combinations were enriched in
 transcriptional subclusters, including a subpopulation of HuSCs marked by
 CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ HuSCs are morphologically
 distinct, and are characterized by resistance to activation compared to
 CAV1- HuSCs. In vivo, CAV1+ HuSCs demonstrated increased engraftment
 potential after transplantation in mice. Our findings provide a
 comprehensive transcriptional view of normal HuSCs and describe new
 heterogeneity, enabling separation of functionally distinct human
 satellite cell subpopulations.
description: Freshly harvested human muscle was  stored in DMEM with 30% FBS at 4°C overnight. Muscle was digested, erythrocytes were lysed, and hematopoietic and endothelial cells were depleted with magnetic column depletion. Viable cells were depleted for CD31, CD34, and CD45 expressing cells. Cells that remained after depletion were sorted for CXCR4+/CD29+/CD56+ and collected for single cell rna sequencing (Garcia et al., 2018; Garcia et al., 2017). To capture individual cells, we utilized the Chromium Single Cell 3' Reagent Version 1 or 3 Kit from 10X Genomics (Zheng et al., 2017). For both samples (aged and adult) 18,000 satellite cells isolated as in (Garcia et al., 2018)were loaded onto one well of the 10X chip to produce Gel Bead-in-Emulsions (GEMs). GEMs underwent reverse transcription to barcode RNA before cleanup and cDNA amplification. Libraries were prepared with the Chromium Single Cell 3' Reagent Version 1 or 3 Kit. Each sample was sequenced on 1 lane of the HiSeq2500 (Illumina) run in Rapid Run Mode with paired-end sequencing parameters.  Matrices were obtained via 10x Genomics Cell Ranger pipeline for scRNA seq.
description: Programming languages such as R or Python should be used to load
 the matrices