cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h5v25
title: Data from: Cold-stress responses in the Antarctic basidiomycetous yeast Mrakia blollopis

description: Microbes growing at subzero temperatures encounter numerous growth
 constraints. However, fungi that inhabit cold environments can grow and
 decompose organic compounds under subzero temperatures. Thus,
 understanding the cold-adaptation strategies of fungi under extreme
 environments is critical for elucidating polar-region ecosystems. Here, I
 report that two strains of the Antarctic basidiomycetous yeast Mrakia
 blollopis exhibited distinct growth characteristics under subzero
 conditions: SK-4 grew efficiently, whereas TKG1-2 did not. I analysed the
 metabolite responses elicited by cold stress in these two M. blollopis
 strains by using capillary electrophoresis–time-of-flight mass
 spectrometry. M. blollopis SK-4, which grew well under subzero
 temperatures, accumulated high levels of TCA-cycle metabolites, lactic
 acid, aromatic amino acids and polyamines in response to cold shock.
 Polyamines are recognized to function in cell-growth and developmental
 processes, and aromatic amino acids are also known to improve cell growth
 at low temperatures. By contrast, in TKG1-2, which did not grow
 efficiently, cold stress strongly induced the metabolites of the TCA
 cycle, but other metabolites were not highly accumulated in the cell.
 Thus, these differences in metabolite responses could contribute to the
 distinct abilities of SK-4 and TKG1-2 cells to grow under subzero
 temperature conditions.
description: Concentration of
 targeted metabolites data_M. TsujiIn the CE-TOFMS
 analysis, 219 metabolites (115 cationic, 104 anionic) were detected.
 Moreover, 88 metabolites, which included amino acids, organic acids, sugar
 phosphates, and nucleotides, were quantified using external standards and
 targeted metabolite analysis.MS data set_M.
 Tsuji.xlsx
DOI: 10.5061/dryad.n5b54j0
title: Data from: The influence of environmental gradients on individual behaviour: individual plasticity is consistent across risk and temperature gradients

description: 1. The expression of individual behaviour as a function of environmental
 variation (behavioural plasticity) is recognised as a means for animals to
 modify their phenotypes in response to changing conditions. Plasticity has
 been studied extensively in recent years, leading to an accumulation of
 evidence for behavioural plasticity within natural populations. 2. Despite
 the recent attention given to studying individual variation in behavioural
 plasticity, there is still a lack of consensus regarding its causes and
 constraints. One pressing question related to this is whether individual
 plasticity carries over across temporal and environmental gradients. That
 is, are some individuals more plastic (responsive) than others in general?
 3. Here, we examined the influence of temporal and environmental gradients
 on individual behavioural responses in a marine gastropod, Littoraria
 irrorata. We measured individual boldness repeatedly over time and in
 response to tidal cycle (high vs low an index of risk) and daily
 temperature fluctuations (known to affect metabolism), in a controlled
 field experiment. 4. On average, boldness increased from high to low tide
 and with increasing temperature but decreased marginally over time.
 Individuals also differed in their responses to variation in tide and
 temperature, but not over time. Those that were relatively bold at high
 tide (when predation risk is greater) were similarly bold at low tide,
 whereas shy individuals became much more ‘bold’ at low tide. Most notably,
 individuals that were more responsive to tide (and thus risk) were also
 more responsive to temperature changes, meaning that plasticity was
 correlated across contexts (r = 0.57) and that bolder individuals were
 least plastic overall. 5. This study provides a rare and possibly first
 example of consistency of individual behavioural plasticity across
 contexts, suggesting underlying physiology as a common mechanism, and
 raises the possibility of correlational selection on plasticity.
description: JAE-2018-00480.R2 - raw
 data & SAS codeRaw data collected
 during experiments undertaken at the Virginia Institute of Marine Science,
 Eastern Shore Laboratory, in 2016.
DOI: 10.5061/dryad.33cd137
title: Data from: Predicting the cover and richness of intertidal macroalgae in remote areas: a case study in the Antarctic Peninsula

description: 1. Antarctica is an iconic region for scientific explorations as it is
 remote and a critical component of the global climate system. Recent
 climate change causes dramatic retreat of ice in Antarctica with
 associated impacts to its coastal ecosystem. These anthropogenic impacts
 have a potential to increase habitat availability for Antarctic intertidal
 assemblages. Assessing the extent and ecological consequences of these
 changes requires us to develop accurate biotic baselines and quantitative
 predictive tools. 2. In this study, we demonstrated that satellite based
 remote sensing, when used jointly with in-situ ground-truthing and machine
 learning algorithms, provides a powerful tool to predict the cover and
 richness of intertidal macroalgae. 3. The salient finding was that the
 Sentinel-based remote sensing described a significant proportion of
 variability in the cover and richness of Antarctic macroalgae. The highest
 performing models were for macroalgal richness and the cover of brown and
 green algae as opposed to the model of red algal cover. 4. When expanding
 the geographical range of the ground-truthing, even involving only a few
 sample points, it becomes possible to potentially map other Antarctic
 intertidal macroalgal habitats and monitor their dynamics. This is a
 significant milestone as logistical constraints are an integral part of
 the Antarctic expeditions. The method has also a potential in other remote
 coastal areas where extensive in-situ mapping is not feasible.
description: dataSHEET DATA Cover of
 substrate types and cover (%) and richness of macroalgal taxonomic groups
 along with values of the bottom of atmosphere reflectance at different
 spatial resolution (in metres) at an indicative wavelength. SHEET EXTERNAL
 VALIDATION DATASET Percent coverage of different macroalgal taxonomic
 group or macroalgal richness estimated by our BRT modelling together with
 that estimated during a separate field survey.
DOI: 10.5061/dryad.3q5k0
title: Data from: Comparison of historical bottleneck effects and genetic consequences of reintroduction in a critically-endangered island passerine

description: Re-introduction is an important tool for recovering endangered species;
 however, the magnitude of genetic consequences for re-introduced
 populations remains largely unknown, in particular the relative impacts of
 historical population bottlenecks compared to those induced by
 conservation management. We characterize 14 microsatellite loci developed
 for the Seychelles paradise flycatcher and use them to quantify temporal
 and spatial measures of genetic variation across a 134-year time frame
 encompassing a historical bottleneck that reduced the species to ~28
 individuals in the 1960s, through the initial stages of recovery and
 across a second contemporary conservation-introduction-induced bottleneck.
 We then evaluate the relative impacts of the two bottlenecks, and finally
 apply our findings to inform broader re-introduction strategy. We find a
 temporal trend of significant decrease in standard measures of genetic
 diversity across the historical bottleneck, but only a nonsignificant
 downward trend in number of alleles across the contemporary bottleneck.
 However, accounting for the different timescales of the two bottlenecks
 (~40 historical generations versus &lt;1 contemporary generation), the
 loss of genetic diversity per generation is greater across the
 contemporary bottleneck. Historically, the flycatcher population was
 genetically structured; however, extinction on four of five islands has
 resulted in a homogeneous contemporary population. We conclude that severe
 historical bottlenecks can leave a large footprint in terms of sheer
 quantity of genetic diversity lost. However, severely depleted genetic
 diversity does not render a species immune to further genetic erosion upon
 re-introduction. In some cases, the loss of genetic diversity per
 generation can, initially at least, be greater across
 re-introduction-induced bottlenecks.
description: All_Terpsiphone_corvina_genotypes_tableMicrosatellite genotypes table for 338 modern and 53 museum Terpsiphone corvina individuals. Text file contains individual ID, sex, age, collection location, collection date and genotype at 14 icrosatellite loci.All_SPF_genotypes_table.txtLaDigue_tmvp_inputTMVP input file (.prn) for La Digue historical and contemporary Ne.Praslin_tmvp_inputPraslin TMVP input file. Format is .prn file. For calculation of historical (age of the oldest sample) and contemporary Ne from genotype dataInput file for calculating the proportion of alleles capturedInput file for calculating the proportion of alleles present in the La Digue source population that could be captured by translocating differing numbers of individualsinput.txt
DOI: 10.5061/dryad.q8638
title: Data from: Reef accessibility impairs the protection of sharks

description: 1. Reef sharks are declining worldwide under ever increasing fishing
 pressure with potential consequences on ecosystem functioning. Marine
 protected areas (MPAs) are currently one of the management tools to
 counteract the pervasive impacts of fishing. However, MPAs in which reef
 sharks are abundant tend to be located in remote and underexploited areas
 preventing a fair assessment of management effectiveness beyond remoteness
 from human activities. 2. Here we determine the conditions under which
 MPAs can effectively protect sharks along a wide gradient of reef
 accessibility, from the vicinity of a regional capital towards remote
 areas, using 385 records from Baited Remote Underwater Video Systems
 (BRUVS) and 2790 Underwater Visual Censuses (UVC) performed in areas open
 to fishing and inside 15 MPAs across New Caledonia (south-western
 Pacific). 3. We show that even one of the world’s oldest (43 years), large
 (172 km²) and most restrictive (no-entry) MPA (Merlet reserve) on coral
 reefs has between 17.3 % and 45.3% fewer shark species and between 37.2 %
 and 79.8 % fewer shark abundance than remote areas in a context where
 sharks are not historically exploited. 4. On coral reefs situated at less
 than 1 hour of travel time from humans, shark populations are so low in
 abundance (less than 0.05 individuals per 1000 m²) that their functional
 roles is severely limited. 5. Synthesis and applications. Remote areas are
 the last sanctuaries for reef sharks and provide a new baseline to
 evaluate human impacts with no equivalent close to human activities even
 in large, old and strongly restrictive MPAs. As such they deserve strong
 protection efforts. The large and no-entry MPAs close to humans offer
 limited benefits for reef shark populations but provide more realistic
 conservation targets for managers of human-dominated reefs. The exclusion
 of human activities on a sufficiently large area is key to protect reef
 shark populations. However, this strategy remains difficult to apply in
 many countries critically depending on reef resources for food security or
 livelihood.14-Aug-2017
description: Data_Juhel_JAE_2017Shark abundance and richness in New Caledonia using Baited Remote Underwater Systems (BRUVS) and Underwater Visual Censuses (UVC)
DOI: 10.5061/dryad.rc41072
title: Data from: Protoporphyrin-based eggshell pigmentation is associated with female plumage colouration and predicts offspring sex ratio in the barn swallow

description: Inter- and intraspecific variation in eggshell colouration has long
 fascinated evolutionary biologists. Among species, such variation may
 accomplish different functions, the most obvious of which is camouflage
 and background matching. Within species, it has been proposed that
 inter-female variation in eggshell pigmentation patterns can reflect egg,
 maternal or paternal traits and hence may provide cues to conspecifics
 about egg, maternal or paternal phenotypic quality. However, the
 relationship between protoporphyrin-based eggshell pigmentation and egg or
 maternal/paternal traits appears to be highly variable among species. We
 investigated patterns of intraspecific variation in Eurasian barn swallow
 (Hirundo r. rustica) protoporphyrin-based eggshell pigmentation, and
 analysed its association with egg and clutch characteristics,
 maternal/paternal phenotypic traits and parental feeding effort. Eggshell
 pigmentation pattern significantly varied between breeding colonies, was
 significantly repeatable in clutches laid by the same females in different
 years (intraclass correlation coefficient ranging between 0.56 and 0.63),
 but it was not significantly associated with egg traits, such as position
 in the laying sequence, egg mass, yolk testosterone concentration and
 antioxidant capacity. It was weakly or non-significantly associated with
 female and male traits (sexual ornaments), but females laying darker
 (higher pigment intensity) first clutches had higher hatching success,
 suggesting that eggshell pigment intensity may predict fitness.
 Nevertheless, males did not significantly modulate their parental nestling
 feeding effort accordingly. In addition, females with darker breast
 plumage colouration (a melanin-based trait related to fitness) laid highly
 protoporphyrin-covered eggs, suggesting the presence of a previously
 unappreciated link between protoporphyrin biosynthesis and plumage
 melanisation. Moreover, the proportion of male offspring increased in
 clutches originating from highly protoporphyrin-covered eggs, suggesting
 that parents could acquire visual cues about their future brood sex
 composition before egg hatching. Our results support the idea that
 intraspecific signalling via eggshell pigmentation is a species-specific
 rather than a general feature of avian taxa.
description: barn swallow eggshell
 pigmentationdata collected in the
 field and associated laboratory analysesbarnswalloweggs.xlsx
DOI: 10.5061/dryad.5688g40
title: Data from: Increase in CO2 concentration could alter the response of Hedera helix to climate change

description: • Increasing CO2 concentrations ([CO2]) is likely to affect future species
 distributions, in interaction with other climate change drivers. However,
 current modelling approaches still seldom consider interactions between
 climatic factors and the importance of these interactions therefore
 remains mostly unexplored. • Here, we combined dendrochronological and
 modelling approaches to study the interactive effects of increasing [CO2]
 and temperature on the distribution of one of the main European liana
 species, Hedera helix. We combined a classical continent-wide species
 distribution modelling approach with a case study using H. helix and
 Quercus cerris tree rings, where we explored the long term influence of a
 variety of climate drivers, including increasing [CO2], and their
 interactions, on secondary growth. Finally, we explored how our findings
 could influence the model predictions. • Climate-only model predictions
 showed a small decrease in habitat suitability for H. helix in Europe,
 however this was accompanied by a strong shift in the distribution toward
 the north and east. Our growth ring data suggested that H. helix can
 benefit from high [CO2] under warm conditions, more than its tree hosts,
 which showed a weaker response to [CO2] coupled with higher cavitation
 risk under high temperature. Increasing [CO2] might therefore offset the
 negative effects of high temperatures on H. helix and we illustrate how
 this might translate into maintenance of H. helix in warmer areas. Our
 results highlight the need to consider carbon fertilization and
 interactions between climate variables in ecological modelling. Combining
 dendrochronological analyses with spatial distribution modelling may
 provide opportunities to refine predictions of how climate change will
 affect species distributions.
description: RESULTS_VesselsRessult of the vessel analysis of Hedera helix and Quercus cerris cores with yearly information on the wood characteristics: analyzed area of the core, number of vessels, vessel diameter, VF, REC, vulnerability to cavitation, and tree, core an species identification.
DOI: 10.5061/dryad.8577
title: Data from: Do convergent ecomorphs evolve through convergent morphological pathways? Cranial shape evolution in fossil hyaenids and borophagine canids (Carnivora, Mammalia)

description: Cases of convergent evolution, particularly within ecomorphological
 contexts, are instructive in identifying universally adaptive
 morphological features across clades. Tracing of evolutionary pathways by
 which ecomorphological convergence takes place can further reveal
 mechanisms of adaptation, which may be strongly influenced by phylogeny.
 Ecomorphologies of carnivorous mammals represent some of the most
 outstanding cases of convergent evolution in the Cenozoic radiation of
 mammals. This study examined patterns of cranial shape change in the dog
 (Canidae) and hyena (Hyaenidae) families, in order to compare the
 evolutionary pathways that led to the independent specialization of
 bone-cracking hypercarnivores within each clade. Geometric morphometrics
 analyses of cranial shape in fossil hyaenids and borophagine canids
 provided evidence for deep-time convergence in morphological pathways
 toward the independent evolution of derived bone-crackers. Both clades
 contained stem members with plesiomorphic generalist/omnivore cranial
 shapes, which evolved into doglike species along parallel pathways of
 shape change. The evolution of specialized bone-crackers from these
 doglike forms, however, continued under the constraint of a full cheek
 dentition and restriction on rostrum length reduction in canids, but not
 hyaenids. Functionally, phylogenetic constraint may have limited
 borophagine canids to crack bones principally with their carnassial
 instead of the third premolar as in hyaenids, but other cranial shape
 changes associated with durophagy nevertheless evolved in parallel in the
 two lineages. Size allometry was not a major factor in cranial shape
 evolution in either lineage, supporting the interpretation of functional
 demands as drivers for the observed convergence. The comparison between
 borophagines and hyaenids showed that differential effects of alternative
 functional “solutions” that arise during morphological evolution may be
 multiplied with processes of the “macroevolutionary ratchet” already in
 place to further limit the evolutionary pathways available to specialized
 lineages.
description: Tseng&Wang_Paleobiology10007_SISupplementary Information for Tseng and Wang. Contains list of specimens used in the study.
DOI: 10.5061/dryad.jf2c0
title: Data from: The temporal dimension in individual-based plant pollination networks

description: The pollination success of animal-pollinated plants depends on the
 temporal coupling between flowering schedules and pollinator availability.
 Within a population, individual plants exhibiting disparate flowering
 schedules will be exposed to different pollinators when the latter exhibit
 temporal turnover. The temporal overlap between individual plants and
 pollinators will result in a turnover of interactions, which can be
 analyzed through a network approach. We have explored the temporal
 dynamics of individual-based plant networks resulting from pairwise
 similarities in pollinator composition. During two flowering seasons, we
 surveyed the phenology and pollinator fauna of the individual plants from
 a population of Erysimum mediohispanicum (Brassicaceae). We analyzed the
 topology of these networks by means of their modularity, clustering, and
 core–periphery structure. These metrics are related to network functional
 properties such as cohesion, transitivity and centralization respectively.
 Afterwards, we analyzed the influence of each pollinator functional group
 on network topology. We found that network topology varied widely over
 time as a consequence of the differences in plant phenology and the
 idiosyncratic and contextual effect of pollinators. When integrating all
 temporary networks, the network became cohesive (non modular), transitive
 (locally clusterized), and centralized (core–periphery topology). These
 topologies could entail important consequences for plant reproduction. Our
 results highlight the importance of considering the entire flowering
 season and the necessity of making comprehensive temporal sampling when
 trying to build reliable interaction networks.
description: Flowering
 dataIn this file the
 flowering status and number of flowers for each plant at each surveyed day
 is shownFlowering_data.txtFunctional group abundancesThis file contains data of the total number of contacts per pollinator functional group and dayFG_abundances.txtPlant-pollinator surveysThis file contains the individual plant-pollinator interactions for each time-lap considered i our study.Plant_pollinator_surveys.txt
DOI: 10.5281/zenodo.18253022
title: Annotations of human skin-associated fungi

description: Description

This repository contains genome annotations for skin-associated fungi sequenced and analysed in the manuscript:Comparative Genomic Analysis of Clinically Relevant Human Skin-Associated Fungi, S. Agerbaek et al., https://doi.org/10.21203/rs.3.rs-6700810/v1 (under review)

The data provided here represent the original genome assemblies and annotations generated prior to any downstream processing, and are deposited to ensure full reproducibility of the results reported in the study.

Clean assemblies and raw reads are available under the Bioproject: PRJNA126044, which also contains metadata about the strains sequenced. Note that some genomes were excluded from the analysis following the initial upload, which is why there are fewer annotations here than assemblies in the Bioproject. 

Annotations available in this repo under Annotations/species_ID were annotated with Funannotate v1.8.13. Functional annotations were generated with Eggnog-mapper v2.1.7, InterProScan v5.56-89.0, antiSMASH v6.0.0 and SignalP v6.0. 

Content

For each genome, the following files are provided: 



.scaffolds.fa



Initial assembly 



.gff3



Structural gene annotation including gene, transcript, and CDS features



.proteins.fa



Predicted protein sequences 



.rn.proteins.fasta 



Predicted protein sequences with re-named fasta headers containing functional annotation in the format: >Species | Strain_ID | Gene accession | Gene name | Gene description | COG | Antismash | GO term | EC number(s) | Pfam term(s) | Interpro term(s) 



.cds-transcripts.fa 



Nucleotide coding sequences 



.annotations.txt



Functional annotation summary table



.stats.json



Assembly and annotation statistics generated during the annotation process




 

For questions regarding these data, please contact: 

Sofie Agerbaek, sofie.agerbaek@sund.ku.dk