cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tqjq2bw2k
title: Assessing the conservation priority of freshwater lake sites based on taxonomic, functional and environmental uniqueness

description: Aim: We propose a novel approach that considers taxonomic uniqueness,
 functional uniqueness and environmental uniqueness, and show how
 it can be used in guiding conservation planning. We illustrate
 the approach using data for lake biota and environment. Location: Lake
 Puruvesi, Finland. Methods: We sampled macrophytes and macroinvertebrates
 from the same 18 littoral sites. By adapting the original
 ‘ecological uniqueness’ approach, we used distance‒based methods to
 calculate measures of taxonomic (LCBD‒t), functional (LCBD‒f) and
 environmental (LCEH) uniqueness for each site. We also considered
 the numbers and locations of the sites needed to protect up to 70% of
 total variation in taxonomic, functional or environmental
 features in the studied part of the lake. Results: Relationships between
 taxonomic (LCBD‒t), functional (LCBD‒f) and environmental
 (LCEH) uniqueness were generally weak, and only the relationship
 between macrophyte LCBD‒t and LCBD‒f was statistically
 significant. Overall, however, if the whole biotic dataset was
 considered, macroinvertebrate LCBD‒f values showed a consistent
 positive relationship with macrophyte LCBD‒f. Depending on the measure of
 site uniqueness, between one third to one half of the sites could
 help protect up to 70% of the ecological uniqueness of the studied part of
 Lake Puruvesi. Main conclusions: Although the dataset examined originated
 from a large lake system, the approach we proposed here can be
 applied in different ecosystems and at various spatial scales. An
 important consideration is that a set of sites has been sampled
 using the same methods, resulting in species and
 environmental matrices that can be analysed using the
 methodological approach proposed here. This framework can be
 easily applied to grid‒based data, sets of islands, or sets of forest
 fragments. We suggest that the approach based on taxonomic,
 functional and environmental uniqueness will be a useful tool
 in guiding nature conservation and ecosystem management,
 especially if associated with meta‒system ideas or network
 thinking.
DOI: 10.57903/uj/7gqap4
title: The Hypoxic Microenvironment of Candida albicans Biofilms Shapes Neutrophil Responses - raw data

description: The dataset contains raw and processed data collected during the NCN PRELUDIUM 21 research project and underlying the publication "The Hypoxic Microenvironment of Candida albicans Biofilms Shapes Neutrophil Responses". The dataset includes confocal and fluorescence microscopy images of neutrophil-biofilm interactions, as well as quantitative analyses of neutrophil activity at different biofilm maturation stages. The data were obtained from biological replicates and are provided in their original formats to ensure reproducibility.
DOI: 10.5061/dryad.gf1vhhmsn
title: Supplemental material for: Multiple routes to color convergence in a radiation of Neotropical poison frogs

description: Convergent evolution is defined as the independent evolution of similar
 phenotypes in different lineages. Its existence underscores the importance
 of external selection pressures in evolutionary history, revealing how
 functionally similar adaptations can evolve in response to persistent
 ecological challenges through a diversity of evolutionary routes. However,
 many examples of convergence, particularly among closely related species,
 involve parallel changes in the same genes or developmental pathways,
 raising the possibility that homology at deeper mechanistic levels is an
 important facilitator of phenotypic convergence. Using the genus
 Ranitomeya, a young, color-diverse radiation of Neotropical poison frogs,
 we set out to (1) provide a phylogenetic framework for this remarkable
 group, (2) leverage this framework to determine if color phenotypes are
 convergent, and (3) to characterize the underlying coloration mechanisms
 to test whether color convergence occurred through the same or different
 physical mechanisms. We generated a phylogeny for Ranitomeya using
 ultraconserved elements and investigated the physical mechanisms
 underlying bright coloration, focusing on skin pigments. Using
 phylogenetic comparative methods, we identified several instances of color
 convergence, involving several gains and losses of carotenoid and pterin
 pigments. We also found a compelling example of nonparallel convergence,
 where, in one lineage, red coloration evolved through the red pterin
 pigment drosopterin, and in another lineage, through red ketocarotenoids.
 Additionally, in another lineage, “reddish” coloration evolved
 predominantly through structural color mechanisms. Our study demonstrates
 that, even within a radiation of closely related species, convergent
 evolution can occur through both parallel and nonparallel mechanisms,
 challenging the assumption that similar phenotypes among close relatives
 evolve through the same mechanisms.
DOI: 10.5061/dryad.sxksn0364
title: Experimental test of selection against hybridization as a driver of avian signal divergence

description: Signal divergence may be pivotal in the generation and maintenance of new
 biodiversity by allowing closely related species to avoid some costs of
 co-occurrence. In birds, closely related, sympatric species are more
 divergent in their colour patterns than those that live apart, but the
 selective pressures driving this pattern remain unclear. Traditionally,
 signal divergence among sympatric species is thought to result from
 selection against hybridization, but broad evidence is lacking. Here, we
 conducted field experiments on naïve birds using spectrometer-matched,
 painted 3D-printed models to test whether selection against hybridization
 drives colour pattern divergence in the genus Poecile. To address
 selection for male colour pattern divergence without the influence of
 learning or the evolution of female discrimination in sympatry, we
 simulated secondary contact between Poecile species, and conducted mate
 choice experiments on naïve, allopatric females. We found that female
 black-capped chickadees (P. atricapillus) are equally likely to perform
 copulation solicitation displays to sympatric and allopatric
 heterospecific congeners when they are paired with conspecifics, but
 exhibit a strong preference for less divergent males when presented with
 paired heterospecific congeners. These results suggest that increased
 colour pattern divergence among sympatric species can reduce the
 likelihood of mixed mating in some contexts, and therefore should be
 favoured by selection against hybridization.
DOI: 10.5061/dryad.4b8gthtfr
title: Forage evaluation in acidic soil and dry areas of Rwanda

description: A study aimed at characterising nutritive value of introduced Brachiaria
 grasses in Rwanda was conducted. Four Brachiaria grasses including,
 Brachiaria decumbens cv. Basilisk, Brachiaria brizantha cv. MG4,
 Brachiaria brizantha cv. Piatã and Brachiaria cv. Cayman with Panicum
 coloratum as control were planted in two contrasting areas (low
 rainfall-Kirehe district and acidic soils - Nyamagabe district) and
 harvested after 60 days and 90 days. The experiment was set in a
 randomized complete block design (RCBD) with four replications. The data
 collected were dry matter (DM), crude proteins (CP) and  In vitro
 gas production was used to estimate metabolisable energy (ME). Also, soill
 composition, especially carbon and Nitrogen were recorded. The data,
 further contains yield for ME and DM.
description: forage biomass samples and soil under forage samples
description: Excel spread sheets
DOI: 10.5061/dryad.9ghx3ffkt
title: ITS and LSU sequences, phylogenetic trees

description: Russula kashmiriana sp. nov (subg. Tenellula, sect. Laricinae) has been
 collected and described from Himalayan coniferous forest of Azad Jammu and
 Kashmir (AJ&K), Pakistan. The taxon is characterized by bright
 reddish orange pileus with cracked margins and obvious reddish orange
 circle on the pileus, yellow context and light olive to yellowish amyloid
 basidiospores. Micro and macroscopic features along with molecular
 phylogenetic analysis based on large subunit (LSU) and internal
 transcribed spacer (ITS) sequences data confirmed the status of Russula
 kashmiriana as a distinct species. AJ&K, LSU, Phylogeny,
 Russulaceae.
description: DNA was extracted from gills of dried fruiting bodies by modified
 CTAB method and the rDNA ITS region was amplified using universal primer
 pair ITS1F and ITS 4 (Gardes and Bruns, 1993; Bruns, 1995). The LSU
 regions were amplified by using LR0R and LR5 primers (Ge et al., 2014).
 The PCR products was sequenced using the same primers (Macrogen,
 Korea). To generate consensus sequences of both LSU and
 ITS regions BioEdit version 7.2.5 (Hall, 1999) was used. Nucleotide
 sequence comparisons were performed with Basic Local Alignment Search Tool
 (BLAST) network services using National Center for Biotechnology
 Information (NCBI), USA database (http://www.ncbi.nlm.nih.gov/). For phylogenetic tree construction and alignment of sequences, closely related sequences were retrieved from GenBank. Published sequences and data from the literature were also added in final data set. An online software MUSCLE was used for alignment purpose (http://www.ebi.ac.uk/Tools/msa/muscle/). Phylogenetic analyses were performed in MEGA6.
description: BioEdit, MUSCLE and MEGA6.
DOI: 10.5061/dryad.p2ngf1vt4
title: Data from: Metabolites from the fungal pathogen Batrachochytrium dendrobatidis (Bd) reduce Bd load in Cuban treefrog tadpoles

description: Batrachochytrium dendrobatidis (Bd) has been associated with massive
 amphibian population declines worldwide. Wildlife vaccination campaigns
 have proven effective for mitigating damage from other pathogens, and
 there is evidence that adult frogs can acquire resistance to Bd when
 exposed to killed Bd zoospores and the metabolites they produced. Here, we
 investigated whether Cuban treefrogs tadpoles (Osteopilus septentrionalis)
 can gain protection from Bd through exposure to a prophylaxis treatment
 composed of killed zoospores or soluble Bd metabolites. We used a 2x2
 factorial design, crossing the presence or absence of killed zoospores
 with the presence or absence of Bd metabolites. All hosts were
 subsequently exposed to live Bd to evaluate susceptibility. Exposure to
 killed zoospores did not induce a protective response. However, tadpoles
 exposed to Bd metabolites had significantly lower Bd intensity and
 prevalence than tadpoles that were not exposed to metabolites. The
 metabolites Bd produce pose no risk of Bd infection and therefore make an
 epidemiologically safe prophylaxis treatment, protecting tadpoles against
 Bd. This work provides a promising potential for protecting amphibians in
 the wild as a disease management strategy for controlling Bd associated
 declines.
description: These data were collected through a manipulative lab experiment
 using a 2x2 factorial design.
DOI: 10.15468/dl.e4zajz
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus hillianus"
 ]
}

 The dataset includes 157 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003156-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/1496
title: Quantifying language experience in bilingual and trilingual children

description: The data in this repository were collected in France, the Netherlands and the UK between 2020 and 2022 to inform the validation of the Q-BEx questionnaire (www.q-bex.org). Children between the ages of 5 and 9 were tested individually to assess their proficiency in the societal language (i.e., French, Dutch or English), as well as their non-verbal intelligence and working memory. One of their parents or caregivers also filled in the full version of the Q-BEx questionnaire. The repository includes data from 299 children (FR: n=78, NL: n=117, UK: n=104), although some measures are not available for all children.
DOI: 10.5061/dryad.dncjsxm2n
title: Data supporting: Molecular, behavioural and morphological comparisons of sperm adaptations in a fish with alternative mating tactics

description: In species with alternative reproductive tactics, there is much empirical
 support that sneaker males have larger testes size and greater sperm
 numbers. However, support for higher sperm performance by sneakers is
 inconsistent. We used the sand goby (Pomatoschistus minutus) to test
 whether sperm performance differed between breeding-coloured males (small
 testes, but large mucus-filled sperm-duct glands; builds a nest lined with
 a sperm-containing mucus, provides care) and sneaker-morph males (no
 breeding colouration, large testes, rudimentary sperm-duct glands; no
 nest, no care). We compared motility (proportion motile sperm), velocity
 and longevity of sperm, between the two morphs. Furthermore, we compared
 gene expression of testes, and tested if the sperm-duct gland contents
 affected sperm performance, and if sperm morphometrics differed between
 male morphs. We found a clear difference in gene expression of testes
 between the male morphs with 109 transcripts differentially expressed
 between the morphs. Notably, several mucin genes were upregulated in
 breeding-coloured males and two ATP-related genes were upregulated in
 sneaker-morph males. There was some evidence of higher sperm velocity in
 sneaker-morph males, but no difference in sperm motility. Presence of the
 sperm-duct gland contents significantly increased sperm velocity, but
 equally so for the two morphs. The same was true for sperm motility
 although the difference was not significant. The sand goby has remarkably
 long-lived sperm, with only small or no decline in motility and velocity
 over time (5 min vs. 22 hours), but again, this was equally true for both
 morphs. Sperm length (head, tail, total) did not differ between morphs,
 and did not correlate with sperm velocity for either morph. Thus, other
 than a clear difference in testes gene expression, we found only modest
 differences between the two male morphs, confirming previous findings that
 high sperm performance as an adaptation to sperm competition is not a
 primary target of evolution.
description: Please see publication for details.
description: Please see publication for details.
DOI: 10.5061/dryad.7d7wm37z1
title: Acute stress and restricted diet reduce bill-mediated heat dissipation in the song sparrow (Melospiza melodia): Implications for optimal thermoregulation

description: We used thermal imaging to show that two environmental factors—acute
 stress and diet—influence thermoregulatory performance of a known thermal
 window, the avian bill. The bill plays important roles in thermoregulation
 and water balance. Given that heat loss through the bill is adjustable
 through vasoconstriction and vasodilation, and acute stress can cause
 vasoconstriction in peripheral body surfaces, we hypothesized that stress
 may influence the bill’s role as a thermal window. We further hypothesized
 that diet influences heat dissipation from the bill given that body
 condition influences the surface temperature of another body region (the
 eye region). We measured the surface temperature of the bills of song
 sparrows (Melospiza melodia) before, during, and after handling by an
 observer at 37°C ambient temperature. We fed five birds a restricted diet
 intended to maintain bodyweights typical of wild birds, and we fed six
 birds an unrestricted diet for five months prior to experiments. Acute
 stress caused a decrease in the surface temperature of the bill, resulting
 in a 32.4% decrease in heat dissipation immediately following acute
 stress, before recovering over approximately 2.3 minutes. The initial
 reduction and subsequent recovery provide partial support for the
 haemoprotective and thermoprotective hypotheses, which predict a reduction
 or increase in peripheral blood flow, respectively. Birds with
 unrestricted diets had larger bills and dissipated more heat, indicating
 that diet and body condition influence bill-mediated heat dissipation and
 thermoregulation. These results indicate that stress-induced vascular
 changes and diet can influence mechanisms of heat loss and potentially
 inhibit optimal thermoregulation.
description: These data were extracted from thermal images collected during
 experiments on Song Sparrows (<em>Melospiza melodia</em>)
 during the summer of 2013. In summary, the experiments were conducted at
 37°C (above the thermoneutral zone) and involved the use of a thermal
 imaging camera to measure the surface temperatures of birds during a
 stress response (elicited by handling the bird in photographer's
 grip). The data are measurements of the surface temperature of the bill,
 eyeball, and eye region, which are regions of interest for
 thermoregulation and/or stress monitoring via thermography.
description: R is
 necessary for the analysis, and we recommend using R Studio for
 convenience and ease of installation for the necessary R packages
 associated with the analysis.
DOI: 10.5061/dryad.h70rxwdmt
title: Drivers of zooplankton dispersal in a pond metacommunity

description: Dispersal success is integral to survival of species in metacommunities.
 For species that disperse passively like zooplankton, reliance on
 dispersal vectors is paramount for colonization of water bodies.
 Zooplankton species engage in dispersal in time (resting eggs) and space
 (overland). For dispersal in time, resting eggs are deposited in the
 sediment during adverse conditions and recolonize aquatic systems when
 beneficial conditions resume
DOI: 10.5061/dryad.f1vhhmh0g
title: Data for: Latent functional diversity may accelerate microbial community responses to temperature fluctuations

description: How complex microbial communities respond to climatic fluctuations remains
 an open question. Due to their relatively short generation times and high
 functional diversity, microbial populations harbor great potential to
 respond as a community through a combination of strain-level phenotypic
 plasticity, adaptation, and species sorting. However, the relative
 importance of these mechanisms remains unclear. We conducted a laboratory
 experiment to investigate the degree to which bacterial communities can
 respond to changes in environmental temperature through a combination of
 phenotypic plasticity and species sorting alone. We grew replicate soil
 communities from a single location at six temperatures between 4°C and
 50°C. We found that phylogenetically- and functionally-distinct
 communities emerge at each of these temperatures, with K-strategist taxa
 favoured under cooler conditions, and r-strategist taxa under warmer
 conditions. We show that this dynamic emergence of distinct communities
 across a wide range of temperatures (in essence, community-level
 adaptation), is driven by the resuscitation of latent functional
 diversity: the parent community harbors multiple strains pre-adapted to
 different temperatures that are able to "switch on" at their
 preferred temperature without immigration or adaptation. Our findings
 suggest that microbial community function in nature is likely to respond
 rapidly to climatic temperature fluctuations through shifts in species
 composition by resuscitation of latent functional diversity.
description: Bacterial isolates were collected from a species sorting
 experiment. Isolates were grown at different temperatures, their growth,
 respiration and ATP content measured in order to produce thermal
 performance curves for these traits. Please see the accompanying published
 article: Smith, T.P., Mobrikotb, S., Ransome, E., Kontopoulos, D-G.,
 Pawar, S., Bell, T. 2022. Latent functional diversity may accelerate
 microbial community responses to temperature fluctuations. eLife.
 Accepted.
description: Data files provided in csv format. Please see the README document
 for full details of files and contents (README.md).
DOI: 10.4121/0899eca1-f918-41f0-b2da-1da4cd56a873
title: North Sea Quality-Controlled Sea Level Dataset

description: <strong>North Sea Quality-Controlled Sea Level Dataset</strong> comprises rigorously quality-controlled sea level observations from 29 tide gauge stations distributed across the North Sea region. The dataset includes original quality-controlled sea level time series, residual time series (with the tidal signal removed), and both high-frequency (T &lt; 2 hours) and low-frequency (T &gt; 2 hours) components. Data are provided at temporal resolutions ranging from 1 to 15 minutes, covering the period specified for each individual station.<br>This dataset supports the forthcoming publication <em>"</em> <em>Investigation of North Sea high-frequency sea-level extremes using long-term sea level measurements" </em>(Mia Pupić Vurilj, Gozde Guney Dogan, Marijana Balić, José A. A. Antolínez, Jadranka Šepić; to be submitted to <em>Natural Hazards</em>) and is made publicly available to encourage its reuse in related scientific studies.<br>Comprehensive documentation of the data sources, quality control procedures, preprocessing methodology, and technical specifications is provided in the accompanying README.txt file.<br>The dataset can be used for multiple coastal and climate applications, as it provides long, quality-controlled, sub-hourly sea-level records. Some of key applications are:a) Analysis of storm surge events (timing, magnitude, duration) along the North Sea coastb) Detection and characterization of high-frequency oscillations (i.e. seiches, meteotsunamis)c) Assessment of coastal flooding, compound events and their impact on coastal risk
DOI: 10.4121/0899eca1-f918-41f0-b2da-1da4cd56a873.v1
title: North Sea Quality-Controlled Sea Level Dataset

description: <strong>North Sea Quality-Controlled Sea Level Dataset</strong> comprises rigorously quality-controlled sea level observations from 29 tide gauge stations distributed across the North Sea region. The dataset includes original quality-controlled sea level time series, residual time series (with the tidal signal removed), and both high-frequency (T &lt; 2 hours) and low-frequency (T &gt; 2 hours) components. Data are provided at temporal resolutions ranging from 1 to 15 minutes, covering the period specified for each individual station.<br>This dataset supports the forthcoming publication <em>"</em> <em>Investigation of North Sea high-frequency sea-level extremes using long-term sea level measurements" </em>(Mia Pupić Vurilj, Gozde Guney Dogan, Marijana Balić, José A. A. Antolínez, Jadranka Šepić; to be submitted to <em>Natural Hazards</em>) and is made publicly available to encourage its reuse in related scientific studies.<br>Comprehensive documentation of the data sources, quality control procedures, preprocessing methodology, and technical specifications is provided in the accompanying README.txt file.<br>The dataset can be used for multiple coastal and climate applications, as it provides long, quality-controlled, sub-hourly sea-level records. Some of key applications are:a) Analysis of storm surge events (timing, magnitude, duration) along the North Sea coastb) Detection and characterization of high-frequency oscillations (i.e. seiches, meteotsunamis)c) Assessment of coastal flooding, compound events and their impact on coastal risk