cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k4pf189
title: Data from: Higher incubation temperatures produce long-lasting upward shifts in cold tolerance, but not heat tolerance, of hatchling geckos

description: Heatwaves are a regular occurrence in Australia, and are predicted to
 increase in intensity and duration in the future. These changes may
 elevate temperatures inside lizard nests, shortening the incubation
 period, so that hatchlings are more likely to emerge during heatwaves.
 Potentially, developmental plasticity or heat hardening could buffer
 hatchings from future warming. For example, higher incubation temperatures
 could shift critical thermal maxima upwards, enabling lizards to withstand
 higher temperatures. To investigate whether developmental plasticity
 affects hatchling thermal tolerance, we incubated eggs of the velvet gecko
 Amalosia lesueurii under two fluctuating incubation treatments to mimic
 current warm (mean = 24.3°C, range 18.4 - 31.1°C) and future hot (mean =
 28.9°C, range 19.1 - 38.1°C) nest temperatures. We maintained the
 hatchlings under identical conditions, and measured their thermal
 tolerance (CTmax) at age 14 d and 42 d. We then released hatchlings at
 field sites, and recaptured individually marked lizards at age six months,
 to determine whether incubation induced shifts in thermal tolerance were
 transitory or long-lasting. We found that at age 14 d, hatchlings from the
 future hot temperature incubation treatment had higher CTmax (mean = 39.96
 ± 0.25°C) than hatchlings from the current warm incubation treatment (mean
 = 39.70 ± 0.36°C). Hatchlings from the warm-incubation treatment also had
 significantly higher heat hardening capacity (mean = 0.79 ± 0.37°C) than
 hatchlings from hot-temperature incubation treatment (mean = 0.47 ±
 0.17°C). However, both of these incubation-induced effects did not persist
 into later life. By contrast, incubation treatment had significant and
 long-lasting effects on the cold tolerance of hatchlings. At age 14 d,
 warm-incubated hatchlings tolerated colder temperatures (CTmin = 11.24 ±
 0.41°C) than hot-incubated hatchlings (CTmin = 14.11 ± 0.25°C). This
 significant difference in cold tolerance persisted into the juvenile life
 stage, and was present in 6 month old lizards that we recaptured from
 field sites. This finding indicates that upward shifts in cold tolerance
 caused by higher nest temperatures might impact negatively on overwinter
 survival of lizards, but field studies linking fitness to thermal
 tolerance are necessary to test this idea. Overall, our results suggest
 that developmental plasticity for heat tolerance is unlikely to buffer
 lizard populations from increasing temperatures.
description: Data from Abayarathna et
 al.Excel file with five
 spreadsheets that contain the raw data that was used in the statistical
 analyses. The spreadsheet column headings are self-explanatory so a readme
 file has not been attached.
DOI: 10.5061/dryad.nr1hs48
title: Data from: A superb solo, or a deviant duet? Overlapping songs in superb fairy-wrens

description: Avian duets are formed when two birds coordinate their songs. Most
 research on the evolution and function of duetting has focused on species
 with highly coordinated duets, and less is known about the context and
 function of overlapping songs that are more loosely coordinated, in part
 due to the challenge of determining whether such vocalisations coincide by
 chance or through coordination between the partners. Here, we use field
 recordings and playback experiments to test whether breeding pairs of
 superb fairy-wrens Malurus cyaneus, coordinate their territorial songs to
 form duets. We test three key characteristics of duetting; whether
 partners’ songs 1) overlap more than expected by chance; 2) have a
 stereotyped structure that occurs repeatedly and predictably in time, and
 3) show evidence of a constant time lag between the contributions of the
 two participants, indicating that individuals are coordinating their
 songs. This is the first study to quantify the temporal precision of song
 between partners to investigate coordination in the Malurus genus, an
 important model taxon for song, sexual selection, and speciation. We found
 variation in the extent to which partners’ songs overlapped, with some
 individuals overlapping their partners’ songs more than expected by
 chance, no difference in structure of solo and overlapping songs, and no
 evidence of a consistent response interval. Thus song overlap in superb
 fairy-wrens meets only some criteria for duetting. We suggest that
 overlapping songs in this species may be due to individuals responding
 independently to the same stimulus and/or ‘call and answer’ between pair
 members.
description: Data for all
 analysesThis data was collected
 in the field. Each file contains the data for a different analysis and the
 column headings are the same as the variables stated in the paper. The
 title specifies the analysis the data is used.Data
 files.ZIP
DOI: 10.5061/dryad.7dd64gs
title: Data from: Palaeoproteomics resolves sloth phylogeny

description: The living tree sloths Choloepus and Bradypus are the only remaining
 members of Folivora, a major xenarthran radiation that occupied a wide
 range of habitats in many parts of the western hemisphere during the
 Cenozoic, including both continents and the West Indies. Ancient DNA
 evidence has played only a minor role in folivoran systematics, as most
 sloths lived in places not conducive to genomic preservation. Here we
 utilize collagen sequence information, both separately and in combination
 with published mitochondrial DNA evidence, to assess the relationships of
 tree sloths and their extinct relatives. Results from phylogenetic
 analysis of these datasets differ substantially from morphology-based
 concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus
 and Megalonyx pair together as megatherioids, while monophyletic Antillean
 sloths may be sister to all other folivorans. Divergence estimates are
 consistent with fossil evidence for mid-Cenozoic presence of sloths in the
 West Indies and an early Miocene radiation in South America.
description: protein_data_MrBayesNexus file containing collagen alignments for extinct and extant xenarthrans. Also includes MrBayes block with specifications for running Bayesian topology searchcombined_data_MrBayesalignment in nexus format containing collagen protein sequences and mitochondrial genomes as available for living and extinct xenarthrans. Also includes MrBayes block.protein_mtDNA_morphology_sloths_MRBnexus file containing protein and mtDNA data plus the morphological character dataset from Varela et al., 2019.BEAST_protein_Xenarthraxml file to run BEAST under fossilized birth death process with xenarthran proteomic dataBEAST_combined_data_bradypus_constraintxml file to run beast with combined proteomic and mitochondrial genome data. Note that this file enforces a monophyly constraint on Bradypus, which can be removed by commenting out the associated lines of the xmlprotein_only_xenarthra_beastmaximum clade crediibility chronogram from analysis of xenarthran proteomic datacombined_protein_mtDNA_xenarthra_bradypus_constraint_beastmaximum clade credibility chronogram from beast analysis of xenarthran proteomic and mitochondrial genome data.
DOI: 10.25625/g1rf9v
title: Dataset_Mashera et al._Terrestrial laser scanning-based allometric models for East-African tropical rainforest trees

description: Dataset supporting the analyses of Mashera et al.,Terrestrial laser scanning-based allometric models for East-African tropical rainforest trees
DOI: 10.25625/g1rf9v/rttyi2
title: Dataset_TFP_D_25_00989_Mashera.tab

description: :unav
DOI: 10.5061/dryad.kp7r8b4
title: Data from: The cost of chemical defence: the impact of toxin depletion on growth and behaviour of cane toads (Rhinella marina).

description: Many animals capable of deploying chemical defences are reluctant to use
 them, suggesting that synthesis of toxins imposes a substantial cost.
 Typically, such costs have been quantified by measuring the elevation in
 metabolic rate induced by toxin depletion (i.e., during replenishment of
 toxin stores). More generally, we might expect that toxin depletion will
 induce shifts in a broad suite of fitness-relevant traits. In cane toads
 (Rhinella marina), toxic compounds that protect against predators and
 pathogens are stored in large parotoid (shoulder) glands. We used
 correlational and experimental approaches in field and laboratory settings
 to investigate impacts of toxin depletion on growth rate and behaviour in
 cane toads. In free-ranging toads, larger toxin stores were associated
 with smaller gonads and livers, suggesting energetic trade-offs between
 toxin production and both reproduction and energy metabolism. Experimental
 removal of toxin (by manually squeezing parotoid glands) reduced rates of
 growth in body mass in both captive and free-ranging toads. Radio-tracking
 demonstrated that de-toxined toads dispersed more slowly than did control
 toads. Given that toxin stores in cane toads take several months to fully
 replenish, deploying toxin to repel a predator may impose a substantial
 cost, explaining why toads use toxin only as a final line of defence.
description: Cane toad toxin
 manuscript dataExcel file containing
 worksheets with data on dissected, radio tracked and captive cane toads
 used in this study
DOI: 10.5061/dryad.sk67tn8
title: Data from: Effects of forest wildfire on inner-Alpine bird community dynamics

description: As major disturbance agents, natural catastrophes impact habitats, thereby
 maintaining the dynamics of ecological communities. Such discrete events
 are expected to positively affect biodiversity because they generate high
 habitat heterogeneity and thus numerous ecological niche opportunities.
 Species typical of open and semi-open habitats, which are often of high
 conservation concern in modern anthropized landscapes, may benefit most
 from recurrent natural catastrophes that regularly reset ecosystems. We
 investigated bird community changes and species-specific responses to
 wildfire at two recently burnt temperate, montane-subalpine forest stands
 in an inner-Alpine Swiss valley, with a special focus on red-listed and
 conservation priority species. We compared bird community changes in burnt
 forests (spanning 13 years) with bird assemblages occurring in adjacent
 non-burned forest stands that served as quasi-experimental controls.
 Strong species-specific responses to wildfire were evidenced, resulting in
 a dramatic post-fire decrease in overall bird abundance and species
 richness. Yet, red-listed bird species and conservation priority species
 in Switzerland were substantially more common in burnt than in control
 forest stands. Many red-listed species showed a bell-shaped numeric
 response to wildfire over time, suggesting low habitat suitability just
 after fire, high habitat suitability at pioneer and early stages of
 vegetation succession, followed by a long-term decrease in suitability
 while vegetation becomes denser, especially at ground level. As
 established for Mediterranean regions where wildfires are especially
 frequent, this study shows that forest fires can also boost the
 populations of red-listed and priority bird species typical of open and
 semi-open habitats in temperate biomes. Prescribed forest fire might
 represent a management option for preserving threatened elements of
 biodiversity despite the intense public debate it will trigger.
description: Reyetal_dataTable 1: Number of territories and disturbance index for all bird species, collected in the field during our study. Table 2: Species Richness and Abundance within the study area.
DOI: 10.5061/dryad.jj946rq
title: Data from: Plant functional indicators of vegetation response to climate change, past present and future: I. Trends, emerging hypotheses and plant functional modality

description: Plant functional traits are widely applied in models that simulate the
 effects of climate change on biodiversity and resource management. Here
 the aim is to examine the potential role of specific plant functional
 traits and their whole-plant syndromes (Plant Functional Types or PFTs as
 specific ‘modal’ trait assemblages) as indicators of vegetation response
 to climate change, past, present and future. Because plant functional
 characteristics have evolved through time, it is widely argued that models
 of vegetation performance under future climates should benefit from a
 study of plant response under previous climates. This paper presents an
 overview first, of developmental concepts underlying the current use of
 PFTs as indicators of plant response to environmental change, second,
 implications arising from species acclimation and third, process-based
 models used in reconstruction of vegetation under mainly Holocene
 environments but also with respect to present and future climates. In this
 regard the role of individual functional traits in ‘biomization’
 procedures in vegetation response models is briefly discussed. It is
 concluded that, while PFTs possess limited indicator value at biome scale,
 uncertainties in the delimitation of local paleohabitats greatly restrict
 their use as indicators for paleovegetation reconstruction at community
 level. Emerging hypotheses are: 1) A whole-plant system of modal PFTs
 based on a novel set of functional traits can provide an improved
 alternative to PFTs and traits used in models of vegetation response to
 climate change, 2) Modal PFTs are potentially more efficient indicators of
 vegetation response to climate change than individual traits, 3) Improved
 plant functional selection criteria can lead to more efficient
 parameterization of Earth System and Dynamic Global Vegetation Models.
description: Readme file accompanying
 data filesSee Readme file and file
 listDryad_Gillison.zip
DOI: 10.5061/dryad.nd637r5
title: Data from: Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak

description: 1. Parasitic diseases represent one of the greatest challenges for
 aquaculture worldwide and there is an increasing emphasis on ecological
 solutions to prevent infections. One proposed solution is enriched
 rearing, where traditional stimulus-poor rearing tanks are equipped with
 different types of structures to increase habitat complexity. Such spatial
 enrichment is known to increase survival of fish during parasite
 epidemics, but the underlying mechanisms are still unclear. 2. We studied
 whether enriched rearing affected infection of an important fish pathogen
 Flavobacterium columnare in young Atlantic salmon (Salmo salar) and
 sea-migrating brown trout (Salmo trutta). First, we used natural bacterial
 exposures and multiple fish populations in a common garden experiment to
 address the role of host genetic background in effects of enriched
 rearing. Second, fish from standard and enriched rearing were
 experimentally exposed to controlled bacterial doses in standard and
 enriched environments in a full factorial design to explore the relative
 roles of rearing background and environment of exposure on survival of
 fish. 3. Enriched rearing significantly increased survival of fish during
 the natural bacterial outbreak. This effect was also fairly consistent and
 observed in eight of the ten fish populations. In the controlled exposure,
 fish exposed in enriched environment had higher survival regardless of
 their rearing background, suggesting a stronger impact of the environment
 on the disease progression. Additionally, the survival in the enriched
 environment was highest among the fish of enriched rearing background,
 supporting the idea of their higher resistance. 4. Synthesis and
 applications. Our result suggests that the enhanced survival of fish in
 enriched rearing results from a combined effect of the environment and
 improved fish condition, and to a lesser degree from host genetic
 background. This has important implications for when and how environmental
 enrichment should be applied. Overall, these results indicate that
 environmental enrichment has the potential to improve survival of fish
 during parasitic epidemics and thus reduce use of antibiotics in
 aquaculture.
description: Mortality
 dataThe file contains
 mortality data of fish species, populations and different rearing
 treatments in experiment 1, and of fish populations and different
 rearing/exposure environments in experiment 2.data_Räihä et
 al.xlsx
DOI: 10.5061/dryad.2rd9406
title: Data from: Refuges from fire maintain pollinator-plant interaction networks

description: Fire is a major disturbance factor in many terrestrial ecosystems, leading
 to landscape transformation in fire‐prone areas. Species in mutualistic
 interactions are often highly sensitive to disturbances like fire events,
 but the degree and complexity of their responses are unclear. We use
 bipartite insect–flower interaction networks across a recently burned
 landscape to explore how plant–pollinator interaction networks respond to
 a recent major fire event at the landscape level, and where fire refuges
 were present. We also investigate the effectiveness of these refuges at
 different elevations (valley to hilltop) for the conservation of displaced
 flower‐visiting insects during fire events. Then, we explore how the
 degree of specialization of flower‐visiting insects changes across
 habitats with different levels of fire impact. We did this in natural
 areas in the Greater Cape Floristic Region (GCFR) biodiversity hotspot,
 which is species rich in plants and pollinators. Bees and beetles were the
 most frequent pollinators in interactions, followed by wasps and flies.
 Highest interaction activity was in the fire refuges and least in burned
 areas. Interactions also tracked flower abundance, which was highest in
 fire refuges in the valley and lowest in burned areas. Interactions
 consisted mostly of specialized flower visitors, especially in refuge
 areas. The interaction network and species specialization were lowest in
 burned areas. However, species common to at least two fire classes showed
 no significant difference in species specialization. We conclude that
 flower‐rich fire refuges sustain plant–pollinator interactions, especially
 those involving specialized species, in fire‐disturbed landscape. This may
 be an important shelter for specialized pollinator species at the time
 that the burned landscape goes through regrowth and succession as part of
 ecosystem recovery process after a major fire event.
description: Species and Network
 MetricsThis is the overall data
 set with pollinator and flower abundance and species richness, Network
 metrics, Z scores of network metrics, species level specialization and
 normalized degree. The network metrics have been grouped into fire classes
 (Refuge, Unburned and Burned) and also sub-grouped into sites located at
 different elevations.Data.zip
DOI: 10.5061/dryad.8t87571
title: Data from: Is high-sensitivity troponin, alone or in combination with copeptin, sensitive enough for ruling out NSTEMI in very early presenters at admission? A post-hoc analysis performed in emergency departments

description: Objectives: Copeptin and high-sensitivity cardiac troponin (HS-cTn) assays
 improve the early detection of NSTEMI. Their sensitivities may however be
 reduced in very early presenters. Setting: We performed a post-hoc
 analysis of three prospective studies that included patients who presented
 to the Emergency Department for chest pain onset (CPO) of less than 6
 hours. Participants: 449 patients were included, in whom 12% had NSTEMI.
 CPO occurred &lt;2h from ED presentation in 160, between 2-4h in 143,
 and &gt;4h in 146 patients. The prevalence of NSTEMI was similar in
 all groups (9%, 13% and 12%, respectively, p=0.281). Measures: Diagnostic
 performances of HS-cTn and copeptin at presentation were examined
 according to CPO. The discharge diagnosis was adjudicated by 2 experts,
 including cTnI. HS-cTn and copeptin were blindly measured. Results:
 Diagnostic accuracies of cTnI, cTnI+copeptin and HS-cTnT (but not
 HS-cTnT+copeptin) lower through CPO categories. For patients with
 CPO&lt;2h, the choice of a threshold value of 14 ng/L for HS-cTnT
 resulted in 3 false negative (Sensitivity 80% [95%CI: 51-95]; specificity
 85% [78-90]; 79% of correctly ruled-out patients) and that of 5 ng/L in 2
 false negative ( Sensitivity 87% [59-98]; specificity 58% [50-66]; 52% of
 correctly ruled-out patients). The addition of copeptin to HS-cTnT induced
 a decrease of misclassified patients to 1 in patients with CPO&lt;2h
 (Sensitivity 93% [66-100]; specificity 41% [33-50]). Conclusion: A single
 measurement of HS-cTn, alone or in combination with copeptin at admission,
 seems not safe enough for ruling out NSTEMI in very early presenters (with
 CPO&lt;2h). Trial registrations: French Health Ministry (no.
 DC-2009-1052), French Local Ethic comity « Comité de Protection des
 Personnes Ile-de-France » III (Hôpital Cochin) et VI (CHU
 Pitié-Salpétrière).
description: README 2019_GOBEAUX et
 al copeptin in early presenters2019_GOBEAUX et al
 copeptin in early presenters data
DOI: 10.5061/dryad.707d540
title: Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state

description: The concept of lakes “evolving” phosphorus (P) limitation has persisted in
 limnology despite limited direct evidence. Here, we developed a simple
 model to broadly characterize nitrogen (N) surpluses and deficits relative
 to P in lakes, and compared the magnitude of this imbalance to estimates
 of N gains and losses through biological N transformations. The model
 suggested that approximately half of oligotrophic lakes in the US had a
 stoichiometric N deficit, but almost 90% of the most productive lakes had
 a similar N deficit. Although reactive N appeared to accumulate in the
 most oligotrophic lakes, net denitrification perpetuated the N deficit in
 more productive lakes. Productive lakes tended to export reactive N via
 biological N transformations regardless of their N deficit. The lack of N
 accumulation through N fixation has important implications for our
 understanding of lake biogeochemistry, ecology, and eutrophication
 management.
description: LO Letters format
 metadataMetadata-LO-Letters-data.docTable_S1Table_S2