cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wh70rxwr0
title: Source code and data from: Foraging personalities modify effects of habitat fragmentation on biodiversity

description: Habitat loss undeniably poses a substantial threat to biodiversity, but
 whether fragmentation per se drives the loss of species is still widely
 debated. While negative consequences from fragmentation are often
 anticipated, many empirical studies report positive effects. However, the
 intrinsic mechanisms governing species’ persistence in fragmented
 landscapes are not yet understood. In this study, we investigated
 consistent personality-dependent differences in foraging behavior among
 individuals as a possible mechanism underlying the discrepancy of reported
 fragmentation effects. We devised a mechanistic individual-based model
 simulating the home range behavior of a competitive small mammal community
 based on the availability of a shared resource. Thereby, an individual’s
 risk-taking behavior dictates its foraging decisions at risky habitat
 edges, an inherent property of fragmentation per se. Our simulations show
 that differences in risk-taking while foraging are potentially a further
 mechanism contributing to reconciling the fragmentation debate. The first
 scenario considering risk-seeking communities showed a neutral response
 towards fragmentation, while the second scenario featuring risk-avoiding
 communities confirmed the negative effects of fragmentation. Notably, the
 third scenario, simulating behaviorally diverse communities including
 risk-avoiding and risk-seeking individuals, demonstrated a positive
 influence of fragmentation on biodiversity. Intraspecific differences in
 behavior could also enhance the temporal species coexistence (coviability)
 of communities threatened by an ongoing habitat loss. Our study highlights
 the importance of recognizing the behavioral composition of populations
 and communities for estimating fragmentation effects, because differences
 in risk-taking can influence the coping abilities of animal communities in
 light of fragmentation.
description: This repository provides the source code for the implementation
 of a dynamic and spatially-explicit individual-based community model as
 well as the used input file to derive our results. The dataset was
 simulated using the individual-based community model and is provided as
 csv-files. Their visualization, as in the paper, is included as R-Scripts.
description: The data files do not require a specific software. The model can
 be compiled using a C++ compiler, the setup und usage of the model are
 explained in the respective README. Required are a C++ compiler (e.g.
 clang from XCode) and Qt (https://www.qt.io/download-qt-installer), min.
 version 4.
DOI: 10.5061/dryad.kkwh70s79
title: Artificial waterhole type selection data for elephant and rhino

description: Artificial water provisioning occurs in southern African nature reserves,
 with different game species preferring specific waterhole types. Movement
 patterns and behaviour of elephant and rhino are associated with water
 availability. These mega-herbivores affect the environment and species
 they encounter, especially at waterholes which are focal points for
 congregation and interaction. Understanding artificial waterhole type
 preferences is important, particularly during times of water shortage,
 allowing managers to manipulate numbers and types of waterholes. This
 study investigates elephant and rhino use of waterholes in the Olifants
 West Nature Reserve, South Africa. Waterhole types in the study area are
 earth dams, concrete pans, reservoirs and troughs. Visitation frequency,
 proportion of visits, time visited, and variables affecting frequency of
 visits were investigated using camera traps. Findings indicated that
 elephants preferred reservoirs, black rhino preferred earth dams, and
 white rhino preferred troughs. Different social groupings had distinct
 preferences for different waterhole types. Elephant breeding herds
 preferred reservoirs, while bachelor groups avoided them and preferred
 earth dams. Black and white rhino bachelor groups preferred troughs, and
 cows and bull-and-cow groups preferred earth dams. Data from this study
 will facilitate implementation of efficient conservation plans for
 existing areas containing the study species, and for potential release
 sites.   artificial waterhole use
description: Data was collected in the field using camera traps and visual
 observations. Data was captured into MS Excel and analysed using Binomial
 tests and a series of Poisson GLM's. Graphs and tables were also
 produced from the data.   
description: MS Excel
DOI: 10.5061/dryad.h9w0vt4mq
title: Identifying ‘climate keystone species’ as a tool for conserving ecosystem functioning under climate change

description: Aim: Climate change affects ecological communities via impacts on species.
 The community’s response to climate change can be represented as the
 temporal trend in a climate-related functional property that is quantified
 using a relevant functional trait. Noteworthy, some species influence this
 response in the community more strongly than others. Innovation:
 Leveraging on the concept of keystone species, we propose that species
 with a strong effect on the community’s functional response to climate
 change beyond their relative abundance can be considered as ‘climate
 keystone species’. We develop a stepwise tool to determine species’
 effects on a community’s climate response and identify climate keystone
 species. We quantify the species-specific effect by measuring the
 difference in the community’s climate response with and without the
 species. Next, we identify climate keystone species as those with a strong
 residual effect after weighting with their relative abundances in the
 community. Main Conclusions: To illustrate the use of the stepwise tool
 with empirical data, we identify climate keystone species that have a
 strong effect on the change in the average temperature niche in North
 American bird communities over time and find the identification tool
 ecologically relevant. Identification of climate keystone species can
 serve as an additional conservation method to efficiently protect
 ecosystem functions.
description: R software is needed to open and rerun the code and data
 files.
DOI: 10.15468/dl.a5a7br
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fish occurrence in Tajikistan"
 ]
}

 The dataset includes 161 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003225-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2v6wwpzrx
title: Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat

description: The dataset presents data from a laboratory experiment exploring the
 effect of heatwaves of different intensities on benhic bioturbation,
 community excretion and biogeochemical cycling of solutes. We tested the
 effects of short-term, moderate and strong marine heatwaves on macrofauna
 bioturbation and associated solute fluxes as examples of ecosystem
 functioning. We also measured macrofaunal excretion rates to assess
 effects of temperature on macrofauna metabolism. For this experiment, we
 used unmanipulated sediment cores with natural animal communities
 collected from a muddy location at 32 m depth in the northern Baltic Sea.
 Despite the mechanistic effect of bioturbation remaining unchanged between
 the treatments, there were significant differences in oxygen consumption,
 solute fluxes and excretion. Biogeochemical and biological processes were
 boosted by the moderate heatwave, whereas biogeochemical cycling seemed to
 decrease under a strong heatwave.
description: Sediment cores used as experimental units were retrieved with a
 GEMAX twin-corer (diameter 9 cm) from a 32 m deep, muddy site (coordinates
 59° 51 614 N 23° 20 943 E) in the
 northern Baltic Sea. All temperature treatments (in situ, Moderate and
 Strong) had five replicate cores. The following parameters were measured:
 sediment mixing (DbN) using luminophore tracers, maximum penetration depth
 (MPD) using luminophore tracers, porewater exchange rate (Q) using an
 inert bromide tracer, fluxes of nitrate+nitrite, phosphate, silicate and
 ammonium and oxygen (Winkler titration), benthic ocmmunity excretion rates
 of ammonium and phosphate and community composition of macrofauna. The
 solute fluxes were measured as start and end concentrations at the start
 and end of dark incubations and calculated to a flux per square meter per
 day. Excretion rates are given per core per day. Sediment mixing is given
 as square cm per year, porewater exchange rate as ml per day and MPD as cm
 into the sediment. Sediment characteristics are measured at the end of the
 9-day long experiment from one core per treatment which was sliced in 0.5
 cm intervals down to 5 cm, in 1 cm intervals down to 9 cm and in 2 cm
 intervals down to as long as there was sediment in the core. Seidment
 organic content is given as % Loss on Ignition, chl a and phaeophytin as
 ug per gram of sediment and carbon and nitrogen as C/N
 ratio.
DOI: 10.5061/dryad.tht76hf2f
title: Climate change in textbooks

description: Climate change is a potent threat to human society, biodiversity, and
 ecosystem stability. Yet a 2021 Gallup poll found that only 43% of
 Americans see climate change as a serious threat over their lifetimes. In
 this study, we analyze college biology textbook coverage of climate change
 from 1970 to 2019. We focus on four aspects for document analysis: 1) the
 amount of coverage, determined by counting the number of sentences within
 the climate change passage, 2) the start location of the passage in the
 book, 3) the categorization of sentences as addressing a description of
 the greenhouse effect, impacts of global warming, or actions to ameliorate
 climate change, and 4) the presentation of data in figures. We analyzed 57
 textbooks. Our findings show that coverage of climate change has
 continually increased. However, the greatest increase occurred during the
 1990s, despite the growing threats of climate change. The position of the
 climate change passage moved further back in the book, from the last 15%
 to the last 2.5% of pages. Over time, coverage shifted from a description
 of the greenhouse effect to focus mostly on effects of climate change; the
 most addressed impact was shifting ecosystems. Sentences dedicated to
 actionable solutions to climate change peaked in the 1990s at over 15% of
 the passage, then decreased in recent decades to 3%. Data figures present
 only global temperatures and CO2 levels prior to the year 2000, then
 include photographic evidence and changes to species distributions after
 2000. We hope this study will alert curriculum designers and instructors
 to consider implicit messages communicated in climate change lessons.
DOI: 10.15468/dl.3q83cg
title: Occurrence Download

description: A dataset containing 906 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Country is France",
 "GadmGid is FRA.8.4_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Athene noctua",
 "Year 2010-2026"
 ]
}

 The dataset includes 906 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003226-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7m0cfxpxp
title: Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance

description: Despite the obstacles facing marine colonists, most lineages of aquatic
 organisms have colonized and diversified in freshwaters repeatedly. These
 transitions can trigger rapid morphological or physiological change and,
 on longer timescales, lead to increased rates of speciation and
 extinction. Diatoms are a lineage of ancestrally marine microalgae that
 have diversified throughout freshwater habitats worldwide. We generated a
 phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to
 resolve freshwater transitions in one lineage, the Thalassiosirales.
 Although most parts of the species tree were consistently resolved with
 strong support, we had difficulties resolving a Paleocene radiation, which
 affected the placement of one freshwater lineage. This and other parts of
 the tree were characterized by high levels of gene tree discordance caused
 by incomplete lineage sorting and low phylogenetic signal. Despite
 differences in species trees inferred from concatenation versus summary
 methods and codons versus amino acids, traditional methods of ancestral
 state reconstruction supported six transitions into freshwaters, two of
 which led to subsequent species diversification. Evidence from gene trees,
 protein alignments, and diatom life history together suggest that habitat
 transitions were largely the product of homoplasy rather than hemiplasy, a
 condition where transitions occur on branches in gene trees not shared
 with the species tree. Nevertheless, we identified a small set of
 putatively hemiplasious genes, many of which have been associated with
 shifts to low salinity, indicating that hemiplasy played a small but
 potentially important role in freshwater adaptation. Accounting for
 differences in evolutionary outcomes, in which some taxa became locked
 into freshwaters while others were able to return to the ocean or become
 salinity generalists, might help further distinguish different sources of
 adaptive mutation in freshwater diatoms.
DOI: 10.5281/zenodo.18401481
title: The 3DVAR code and data sample

description: Python code and data used in the manuscript
DOI: 10.5281/zenodo.18401480
title: The 3DVAR code and data sample

description: Python code and data used in the manuscript
DOI: 10.5061/dryad.5hqbzkh8n
title: Cyprinodon pupfish gut microbiomes

description: Adaptive radiations offer an excellent opportunity to understand the
 eco-evolutionary dynamics of gut microbiota and host niche specialization.
 In a laboratory common garden, we compared the gut microbiota of two novel
 derived trophic specialist pupfishes, a scale-eater and a molluscivore, to
 closely related and distant outgroup generalist populations, spanning both
 rapid trophic evolution within 10 kya and stable generalist diets
 persisting over 11 Mya. We predicted an adaptive and highly divergent
 microbiome composition in the trophic specialists reflecting their rapid
 rates of craniofacial and behavioral diversification. We sequenced 16S
 rRNA amplicons of gut microbiomes from lab-reared adult pupfishes raised
 under identical conditions and fed the same high-protein diet. In contrast
 to our predictions, gut microbiota largely reflected phylogenetic distance
 among species, rather than generalist or specialist life history, in
 support of phylosymbiosis. However, we did find significant enrichment of
 Burkholderiaceae bacteria in replicated lab-reared scale-eater
 populations. These bacteria sometimes digest collagen, the major component
 of fish scales, supporting an adaptive shift. We also found some
 enrichment of Rhodobacteraceae and Planctomycetia in lab-reared
 molluscivore populations, but these bacteria target cellulose. Overall
 phylogenetic conservation of microbiome composition contrasts with
 predictions of adaptive radiation theory and observations of rapid
 diversification in all other trophic traits in these hosts, including
 craniofacial morphology, foraging behavior, aggression, and gene
 expression, suggesting that the functional role of these minor shifts in
 microbiota will be important for understanding the role of the microbiome
 in trophic diversification.
DOI: 10.5061/dryad.brv15dvck
title: Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

description: Recently, populations of various species with very low genetic diversity
 have been discovered. Some of these persist in the long term, but others
 could face extinction due to accelerated loss of fitness. In this work, we
 characterize 45 individuals of one of these populations, belonging to the
 Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq
 technique, which generated 1,421 SNPs. The heterozygosity values of the
 analyzed individuals were among the lowest recorded for mammals, ranging
 from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the
 localities, highly isolated due to strong barriers, presented extremely
 high inbreeding coefficients, with values above 0.7. Under this scenario
 of low genetic diversity and elevated inbreeding levels, some individuals
 appeared to be almost genetically identical. We used different methods and
 simulations to determine if genetic identification and parentage analysis
 were possible in this population. Only one of the methods, which does not
 assume population homogeneity, was able to identify all individuals
 correctly. Therefore, genetically impoverished populations pose a great
 methodological challenge for their genetic study. However, these
 populations are of primary scientific and conservation interest, so it is
 essential to characterize them genetically and improve genomic
 methodologies for their research.
description: ddRAD_reads.zip Quality-filtered reads for
 each individual in FASTQ format.
DOI: 10.5281/zenodo.18256701
title: The Climate Opportunities of Risks of Contrail Avoidance - Output Climate Data Cases 10-18

description: This repository contains climate data that is outputted to the Aviation Climate and Air Quality Impacts model to generate the climate outputs for the journal publication titled The Climate Opportunities and Risks of Contrail Avoidance. The output files in this repository are files 10 to 18 of 36, denoted by the two-digit number at the start of the file.

The climate data that has been deposited relates to the effective radiative forcing and global surface temperature rise due to carbon dioxide emissions from aviation and contrails, produced using Monte Carlo simulations of uncertain parameters, under various contrail avoidance and modified fuel composition scenarios. The data is separated and labelled with respect to these scenarios. Levels of contrail avoidance effectiveness of 0%, 25%, 50% and 75% are labelled as “no_action”, “eff=25%”, “eff=50%”, “eff=75%” respectively. The scenario with a of contrail avoidance effectiveness of 100% is unlabelled. The aviation growth projections (AGPs) of AGP 0.36, AGP 0.29, AGP 0.21 and AGP 0.14 are labelled as “exp_no_sat”, “exp_sat”, “lin” and “no_growth”, respectively. Scenarios that assume a modified fuel composition have the label “SAF”. Fuel burn penalties of 0.35%, 5% and 10% have the labels “0035”, “0500” and “1000”, respectively. Please see The Climate Opportunities and Risks of Contrail Avoidance for more information.
DOI: 10.5281/zenodo.18256700
title: The Climate Opportunities of Risks of Contrail Avoidance - Output Climate Data Cases 10-18

description: This repository contains climate data that is outputted to the Aviation Climate and Air Quality Impacts model to generate the climate outputs for the journal publication titled The Climate Opportunities and Risks of Contrail Avoidance. The output files in this repository are files 10 to 18 of 36, denoted by the two-digit number at the start of the file.

The climate data that has been deposited relates to the effective radiative forcing and global surface temperature rise due to carbon dioxide emissions from aviation and contrails, produced using Monte Carlo simulations of uncertain parameters, under various contrail avoidance and modified fuel composition scenarios. The data is separated and labelled with respect to these scenarios. Levels of contrail avoidance effectiveness of 0%, 25%, 50% and 75% are labelled as “no_action”, “eff=25%”, “eff=50%”, “eff=75%” respectively. The scenario with a of contrail avoidance effectiveness of 100% is unlabelled. The aviation growth projections (AGPs) of AGP 0.36, AGP 0.29, AGP 0.21 and AGP 0.14 are labelled as “exp_no_sat”, “exp_sat”, “lin” and “no_growth”, respectively. Scenarios that assume a modified fuel composition have the label “SAF”. Fuel burn penalties of 0.35%, 5% and 10% have the labels “0035”, “0500” and “1000”, respectively. Please see The Climate Opportunities and Risks of Contrail Avoidance for more information.
DOI: 10.5061/dryad.fn2z34txq
title: Geographical modelling of language decline for Cornish and Welsh

description: Competition between languages affects the lives of people all over the
 globe, and a huge number of languages are at risk of extinction. In this
 work, statistical physics is applied to modelling the decline of one
 language in competition with another. A model from the literature is used
 and adapted to model the interactions among speakers in a population
 distribution over time, and is applied to historical data for Cornish and
 Welsh. Visual, geographical models show the simulated decline of the real
 languages studied, and a number of qualitative and quantitative features
 from the historical data are captured by the model. The applicability of
 the model to further real situations is discussed, as well as adaptations
 that would be needed to better take account of migration and population
 dynamics.
DOI: 10.5061/dryad.59zw3r2bd
title: Supplemental data for: Classification of the Celastrales based on integration of genomic, morphological, and Sanger-sequence characters

description: We present the best sampled phylogenetic analysis of Celastrales, with
 respect to both character and taxon sampling, and use it to present a
 natural classification of the order.  Parnassiaceae are highly
 supported as sister to Celastraceae; we recognize both families as
 distinct. Pottingeria is highly supported as a member of an early derived
 lineage within Celastraceae.  We recognize and circumscribe 13
 subfamilies in Celastraceae, including the new subfamilies
 Crossopetaloideae, Maytenoideae, Microtropioideae, Monimopetaloideae, and
 Salaciopsioideae. We identified five genera that likely require generic
 recircumscriptions: Cassine, Elachyptera, Gymnosporia, Salacia, and
 Semialarium.  Genera that had not been previously sampled in
 Sanger-sequence-based studies are resolved as follows: Arnicratea is
 sister to Reissantia, Bequaertia is in a clade with Campylostemon and
 Tristemonanthus, Goniodiscus is sister to Wilczekra, Ptelidium is nested
 within Elaeodendron, and Tetrasiphon is most closely related to Gyminda.
description: Morphological, genomic, and Sanger-sequence characters for
 Celastrales, Oxalidales, and Malpighiales were analyzed using
 non-parametric phylogenetic methods.
description: Text editor
DOI: 10.15468/dl.2qfy9k
title: Occurrence Download

description: A dataset containing 518 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Arion vulgaris",
 "Year 1990-2026"
 ]
}

 The dataset includes 518 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003227-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.