cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3q977
title: Data from: Topsoil removal through scarification improves natural regeneration in high-graded Nothofagus old-growth forests

description: 1.High grading by removing the majority of trees with superior timber
 quality has led to loss of productivity and biodiversity in forests.
 Typically, after high grading, little attention is given to tree
 regeneration. Thus, undesirable understory vegetation often dominates for
 a long time, leading to stagnation in forest recovery and so-called
 arrested succession. In such settings, managing understory vegetation
 using topsoil removal through scarification has been proposed as a
 restoration tool to encourage tree regeneration. 2.We investigated the
 effectiveness of topsoil removal as a restoration technique in high-graded
 Nothofagus old-growth forests in the Chilean Andes. In these forests, high
 grading often leads to understories being dominated by dense thickets of
 native bamboo, Chusquea culeou. These understory conditions typically
 delay succession by preventing tree regeneration. 3.T-tests were used to
 compare vegetation development in areas with topsoil removal against those
 without. Non-parametric multiplicative regression (NPMR) was used to
 investigate which environmental variables were mainly related to
 regeneration of different plant groups (short and long-lived early and
 late-seral tree species) and C. culeou abundance in areas with and without
 topsoil removal. 4.Topsoil removal improved the regeneration of
 early-seral tree species and constrained C. culeou. In areas without
 topsoil scarification, higher abundances of C. culeou were reflected in a
 higher transmitted radiation and litter cover. In these areas, the
 presence of early-seral tree species was related to higher soil water
 content and transmitted radiation. However, topsoil removal altered these
 response patterns for early-seral trees. For instance, the interaction
 between higher soil water content and more exposed mineral soil was
 reflected in a higher likelihood of finding early-seral tree seedlings.
 5.Synthesis and applications. Topsoil removal was a successful restoration
 tool for overcoming arrested succession in Nothofagus old-growth forests
 in the Chilean Andes by encouraging the regeneration of early-seral trees
 in high-graded forests. Contrasting environmental conditions of pre- and
 post-topsoil removal allowed insights into the processes and mechanisms
 responsible for forests with arrested succession and for succession
 progression. This understanding provides guidance regarding the range of
 conditions under which topsoil removal can be used as a successful
 restoration practice.
description: Soto&Puettmann.database.jaethis file has the full data base of the paper published without management and transformation. More details about codes you can send an email to the corresponding author.data.jae.csv
DOI: 10.5281/zenodo.18323365
title: A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

description: Haplotype-resolved nuclear genome assemblies, gene and transposable element annotations, and a complete mitochondrial genome for the barley stripe rust pathogen Puccinia striiformis f. sp. hordei isolate NP85002. 

Genome assemblies



PshNP85002.fasta (both haplotypes combined)

PshNP85002_hap1.fasta

PshNP85002_hap2.fasta


Gene annotations



PshNP85002.gene.gff3

PshNP85002_hap1.gene.gff3

PshNP85002_hap2.gene.gff3


Transposable element annotations



PshNP85002.transposable_element.gff3

PshNP85002_hap1.transposable_element.gff3

PshNP85002_hap2.transposable_element.gff3


Mitochondrial genome assembly & annotations



PshNP85002_mtDNA.fasta

PshNP85002_mtDNA.gene.gff3
DOI: 10.5281/zenodo.18323364
title: A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

description: Haplotype-resolved nuclear genome assemblies, gene and transposable element annotations, and a complete mitochondrial genome for the barley stripe rust pathogen Puccinia striiformis f. sp. hordei isolate NP85002. 

Genome assemblies



PshNP85002.fasta (both haplotypes combined)

PshNP85002_hap1.fasta

PshNP85002_hap2.fasta


Gene annotations



PshNP85002.gene.gff3

PshNP85002_hap1.gene.gff3

PshNP85002_hap2.gene.gff3


Transposable element annotations



PshNP85002.transposable_element.gff3

PshNP85002_hap1.transposable_element.gff3

PshNP85002_hap2.transposable_element.gff3


Mitochondrial genome assembly & annotations



PshNP85002_mtDNA.fasta

PshNP85002_mtDNA.gene.gff3
DOI: 10.5061/dryad.m3r3831
title: Data from: Social immunity in honeybees—Density dependence, diet, and body mass trade‐offs

description: Group living is favourable to pathogen spread due to the increased risk of
 disease transmission between individuals. Similar to individual immune
 defences, social immunity, i.e. anti-parasite defences mounted for the
 benefit of individuals other than the actor, are predicted to be altered
 in social groups. The eusocial honey bee (Apis mellifera) secretes glucose
 oxidase (GOX), an antiseptic enzyme, throughout its colony, thereby
 providing immune protection to other individuals in the hive. We conducted
 a laboratory experiment to investigate the effects of group density on
 social immunity, specifically GOX activity, body mass and feeding
 behaviour in caged honey bees. Individual honey bees caged in a low group
 density displayed increased GOX activity relative to those kept at a high
 group density. In addition, we provide evidence for a trade-off between
 GOX activity and body mass: Individuals caged in the low group density had
 a lower body mass, despite consuming more food overall. Our results
 provide the first experimental evidence that group density affects a
 social immune response in a eusocial insect and that the previously
 reported trade-off between immunity and body mass extends to social
 immunity. GOX production appears to be costly for individuals, and
 potentially the colony, given that low body mass is correlated with small
 foraging ranges in bees. At high group densities individuals can invest
 less in social immunity than at low densities, whilst presumably gaining
 shared protection from infection. Thus, there is evidence that trade-offs
 at the individual level (GOX vs body mass) can affect colony-level
 fitness.
description: All
 DataGOX, Body mass and
 consumption dataALL
 DATA.xlsx
DOI: 10.15468/dl.xsx8pn
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ochotona muliensis"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001250-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kd564
title: Data from: Quantifying the coevolutionary potential of multistep immune defenses

description: Coevolutionary models often assume host infection by parasites depends on
 a single bout of molecular recognition. As detailed immunological studies
 accumulate, however, it becomes increasingly apparent that the outcome of
 host-parasite interactions more generally depends on complex multiple step
 infection processes. For example, in plant and animal innate immunity,
 recognition steps are followed by downstream effector steps that kill
 recognized parasites, with the outcome depending on an escalatory
 molecular arms race. Here, we explore the consequences of such multi-step
 infection processes for coevolution using a genetically explicit model.
 Model analyses reveal that polymorphism is much greater at recognition
 loci than effector loci, that host-genotype by parasite-genotype (Gh x Gp)
 interactions are larger for the recognition step, and that the recognition
 step contributes more to local adaptation than the effector step. These
 results suggest that (1) local adaptation is more likely when fitness
 measures are related to recognition versus downstream effectors, (2)
 effector loci, while mechanistically important, are less likely to harbor
 the Gh x Gp variation that fuels coevolution, and (3) recognition loci are
 better candidates for genomic hotspots of coevolution.
description: Simulation code
 (C++)This C++ code performs
 coevolutionary simulations as described within the
 paper.Two
 step infection for Dryad.cpp
DOI: 10.5061/dryad.j61sp
title: Data from: Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana

description: Early seedling emergence can increase plant fitness under competition.
 Seed oil composition (the types and relative amounts of fatty acids in the
 oils) may play an important role in determining emergence timing and early
 growth rate in oilseeds. Saturated fatty acids provide more energy per
 carbon atom than unsaturated fatty acids but have substantially higher
 melting points (when chain length is held constant). This characteristic
 forms the basis of an adaptive hypothesis that lower melting point seeds
 (lower proportion of saturated fatty acids) should be favored under colder
 germination temperatures due to earlier germination and faster growth
 before photosynthesis, while at warmer germination temperatures, seeds
 with a higher amount of energy (higher proportion of saturated fatty
 acids) should be favored. To assess the effects of seed oil melting point
 on timing of seedling emergence and fitness, high- and low-melting point
 lines from a recombinant inbred cross of Arabidopsis thaliana were
 competed in a fully factorial experiment at warm and cold temperatures
 with two different density treatments. Emergence timing between these
 lines was not significantly different at either temperature, which aligned
 with warm temperature predictions, but not cold temperature predictions.
 Under all conditions, plants competing against high-melting point lines
 had lower fitness relative to those against low-melting point lines, which
 matched expectations for undifferentiated emergence times.
description: coldData was collected in a
 temperature-controlled growth chamber and is described in the readme
 file.warm_treatmentThis data was collected in a temperature-controlled growth chamber and is described in detail in the readme file.warm.csv
DOI: 10.5061/dryad.6vd5d71
title: Data from: Coloration of chicks modulates costly interactions among family members

description: The resolution of family conflicts over parental care involves elaborate
 behavioral interactions where signals and information exchange play a
 central role. Usually the focus is on offspring begging and adult signals
 and their effect on parental provisioning. Yet, despite offspring of many
 animal species display structural ornaments during parental dependency,
 their role in intra-family conflicts remains practically unexplored. In
 the blue tit, Cyanistes caeruleus, we experimentally manipulated nestling
 plumage color and food availability in 60 broods to investigate if family
 members flexibly adjust their decisions according to color under different
 conditions. Feeding rates were not affected by experimental treatments,
 but plumage color did affect parent-offspring interactions in the form of
 prey-testings (when a parent places a prey item into a nestling’s gape but
 removes it again). In non-supplemented nests, fathers but not mothers
 tested more prey on UV reduced offspring, suggesting that fathers evaluate
 less ornamented chicks when food is scarce. As predicted by theoretical
 studies, UV reduced nestlings increased begging in food-supplemented
 nests, although only to mothers. Moreover, UV reduced nestlings increased
 parent-absent begging in all nests, indicating that plumage color affected
 sib-sib competitive interactions. Finally, UV reduced offspring gained
 less body mass and this was probably due to costly intra-family
 interactions. Overall, our results suggest that ornamentation during early
 life plays an important role on social-mediated costs and reveals
 sex-specific parental strategies according to offspring ornaments.
description: Chick individual
 dataDatabase with chick
 individual data (tarsus length, initial body mass, body mass
 change)chickdata.txtBehavioral variables (parents present)Database with behavioral data when parents are present (feeding rates, prey size, begging intensity during feeding bouts, prey-testings). Note that there are 4 data per nest correponding to the behavior of the male and the female parent and UVreduced and non-UV reduced chicks.parents_present.txtBehavioral variables (parents absent)Database with behavioral variables during parent-absent events (number of parent-absent events with begging and begging intensity in parent-absent events) . Note that there are 2 data per nest corresponding to UVreduced and non_UV reduced chicks.parents_absent.txt
DOI: 10.5061/dryad.9g4k6408
title: Data from: Exploring possible human influences on the evolution of Darwin's finches

description: Humans are an increasingly common influence on the evolution of natural
 populations. Potential arenas of influence include altered evolutionary
 trajectories within populations and modifications of the process of
 divergence among populations. We consider this second arena in the medium
 ground finch (Geospiza fortis) on Santa Cruz Island, Galápagos, Ecuador.
 Our study compared the G. fortis population at a relatively undisturbed
 site, El Garrapatero, to the population at a severely disturbed site,
 Academy Bay, which is immediately adjacent to the town of Puerto Ayora.
 The El Garrapatero population currently shows beak size bimodality that is
 tied to assortative mating and disruptive selection, whereas the Academy
 Bay population was historically bimodal but has lost this property in
 conjunction with a dramatic increase in local human population density. We
 here evaluate potential ecological-adaptive drivers of the differences in
 modality by quantifying relationships between morphology (beak and head
 dimensions), functional performance (bite force), and environmental
 characteristics (diet). Our main finding is that associations among these
 variables are generally weaker at Academy Bay than at El Garrapatero,
 possibly because novel foods are used at the former site irrespective of
 individual morphology and performance. These results are consistent with
 the hypothesis that the rugged adaptive landscapes promoting and
 maintaining diversification in nature can be smoothed by human activities,
 thus hindering ongoing adaptive radiation.
description: EvolDataDescription# field data on the morphology (beak and head dimensions) of Geospiza fortis from Santa Cruz Island, Galapagos, Ecuador. # file type = text file # meaning of the column headings: Indi=individual ID, Year=year of colection, Location=site of colection, Species=species (G.fortis), Mean_b.length=mean beak length, Mean_b.depth=mean beak depth, Mean_b.width=mean beak width, Head.Length=mean head length, Head.Width=mean beak width, Head.Depth=mean beak depth, mean.tip=mean bite force for the tip of the beak, mean.side=mean bite force for the side of the beak, H.index.item=index of hardness for different food items, H.index.seed=index of hardness for different seed types, seeds.only=seed type items onlyEvolData
DOI: 10.5061/dryad.rs3q8
title: Data from: Experience and motivation shape leader-follower interactions in fish shoals

description: Leadership is an important process shaping collective movement in some
 species. Recent work has demonstrated that experienced or motivated
 individuals can emerge as leaders, and provides insight into the
 mechanisms by which this occurs. Ultimately, leadership depends on the
 effectiveness with which would-be leaders can entrain followers, and
 although the properties of leaders have received much attention, less is
 known about the factors that affect the propensity of their groupmates to
 follow them. Here, the roles of experience and state (hunger) in shaping
 leader and follower behavior were investigated using shoals of
 sticklebacks (Gasterosteus aculeatus). A first experiment revealed that
 individuals trained to approach a target could entrain and lead their
 naive groupmates out of a refuge toward it, and that they did so more
 effectively when they (the trained fish) were food deprived. In the second
 experiment, the hunger level of the trained fish was held constant,
 whereas that of the naive fish was varied. Here, leadership by trained
 fish was only apparent when the hunger levels of the naive group members
 were intermediate. When naive fish were recently fed, they took a long
 time to visit the target and their arrival times were not affected by the
 presence of a trained individual. Very hungry groups recruited to the
 target most rapidly, but again with no evidence of influence by their
 trained groupmates. These experiments demonstrate that leadership in
 animal groups depends not only on the state and experience of the leader
 but also on that of the potential followers.
description: Webster (2016)
 Leader-follower data for DRYADArrival times
 data
DOI: 10.5061/dryad.f0n35
title: Data from: Evolution of an application profile: advancing metadata best practices through the Dryad data repository

description: Dryad is a general-purpose curated repository for data underlying
 scholarly publications. Dryad’s metadata framework is supported by a
 Dublin Core Application Profile (DCAP, hereafter referred to as
 application profile). This paper examines the evolution of Dryad’s
 application profile, which has been revised over time, in an operational
 system, serving day-to-day needs of stakeholders. We model the
 relationships between data packages and data files over time, from its
 initial implementation in 2007 to its current practice, version 3.2, and
 present a crosswalk analysis. Results covering versions 1.0 to 3.0 show an
 increase in the number of metadata elements used to describe Dryad’s data
 objects in Dryad. Results also confirm that Version 3.0, which envisioned
 separate metadata element sets for data package, data files, and
 publication metadata, was never fully realized due to constraints in Dryad
 system architecture. Version 3.1 subsequently reduced the number of
 metadata elements captured by recombining the publication and data package
 element sets. This paper documents a real world application profile
 implemented in an operational system, noting practical system and
 infrastructure constraints. Finally, the analysis presented informs an
 ongoing effort to update the application profile to support Dryad's
 diverse and expanding community of stakeholders.
description: Appendix_A_Dryad.DCAP_DatasetDryad Metadata Application Profile, Version 3.2
DOI: 10.15468/dl.62w8b4
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cosmelia rubra",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 155 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001251-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.22c0m
title: Data from: Palaeoecological implications of the preservation potential of soft-bodied organisms in sediment-density flows: testing turbulent waters

description: Interpreting how far organisms within fossil assemblages may have been
 transported and if they all originated from the same location is
 fundamental to understanding whether they represent true
 palaeocommunities. In a three-factorial experimental design, we used an
 annular flume to generate actualistic sandy sediment-density flows that
 were fast (2 ms−1) and fully turbulent in order to test the effects of
 flow duration, sediment concentration, and grain angularity on the states
 of bodily damage experienced by the freshly euthanized polychaete Alitta
 virens. Results identified statistically significant effects of flow
 duration and grain angularity. Increasing sediment concentration had a
 statistically significant effect with angular sediment but not with
 rounded sediment. Our experiments demonstrate that if soft-bodied
 organisms such as polychaetes were alive and then killed by a flow then
 they would have been capable of enduring prolonged transport in fast and
 turbulent flows with little damage. Dependent upon sediment concentration
 and grain angularity, specimens were capable of remaining intact over flow
 durations of between 5 and 180 min, equating to transport distances up to
 21.6 km. This result has significant palaeoecological implications for
 fossil lagerstätten preserved in deposits of sediment-density flows
 because the organisms present may have been transported over substantial
 distances and therefore may not represent true palaeocommunities.
description: Table of experimental
 trials with recorded states of bodily damageExperimental
 combinations of flow duration, sediment concentration and grain angularity
 with corresponding recorded states of bodily damage.Table of raw
 data.docx
DOI: 10.57745/cap5uw
title: PGD_ STRUCTURE_lSC AgroResonance.pdf

description: PGD Structure
DOI: 10.57745/ndzdyr
title: PGD Structure_AgroResonace_V2.pdf

description: :unav
DOI: 10.5061/dryad.r36d6k6t
title: Data from: An evaluation of the possible adaptive function of fungal brood covering by attine ants

description: Fungus-growing ants (Myrmicinae: Attini) live in an obligate symbiotic
 relationship with a fungus that they rear for food, but they can also use
 the fungal mycelium to cover their brood. We surveyed colonies from 20
 species of fungus-growing ants and show that brood-covering behavior
 occurs in most species, but to varying degrees, and appears to have
 evolved shortly after the origin of fungus-farming, but was partly or
 entirely abandoned in some genera. To understand the evolution of the
 trait we used quantitative phylogenetic analyses to test whether brood
 covering behavior covaries among attine ant clades and with two hygienic
 traits that reduce risk of disease: mycelial brood cover did not correlate
 with mutualistic bacteria that the ants culture on their cuticles for
 their antibiotics, but there was a negative relationship between
 metapleural gland grooming and mycelial cover. A broader comparative
 survey showed that the pupae of many ant species have protective cocoons
 but that those in the subfamily Myrmicinae do not. We therefore evaluated
 the previously proposed hypothesis that mycelial covering of attine ant
 brood evolved to provide cocoon-like protection for the brood.
description: Armitage_et_al_field_survey_mycelial_coverPercent mycelial cover on eggs, larvae and pupae across different attine ant species, data at the colony level. Colonies collected in the field and mycelial cover observed in the lab. Microsoft Excel was used to create the data file.Armitage_et_al_MG_useMetapleural gland use by different attine species for the 60 minutes following infection of the fungus garden with a fungal pathogen (Metarhizium anisopliae), data at the colony level. Microsoft Excel was used to create the data file.
DOI: 10.57745/0jb6pf
title: PGD_StructureAgroResonanceV3.pdf

description: PGD structure de l'ISC AgroResonance
DOI: 10.57745/rpoxlm
title: Plan de Gestion de données Structure AgroResonance

description: Ce PGD Structure décrit la politique générale de gestion données de l'ISC AgroResonance. Il sert de modèle aux PGD projet de la plateforme