cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.jc977s
title: Occurrence Download

description: A dataset listing the 1462 species recorded in GBIF matching the query:
{
 "and" : [
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 "IucnRedListCategory is one of (NE, DD, LC, NT)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1462 records were derived from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001932-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dbrv15dwp
title: Human influences on antipredator behaviour in Darwin’s finches

description: 1) Humans exert dramatic influences upon the environment, creating novel
 selective pressures to which organisms must adapt. On the Galapagos,
 humans have established a permanent presence and have altered selective
 pressures through influences such as invasive predators and urbanization,
 affecting iconic species such as Darwin’s finches. 2) Here, I ask two key
 questions: (i) does antipredator behaviour (e.g. flight initiation
 distance – FID) change depending on whether invasive predators are
 historically absent, present, or eradicated? and (ii) to what degree does
 urbanization affect antipredator behaviour? This study is one of the first
 to quantify antipredator behaviour in endemic species after the
 eradication of invasive predators. This will help to understand the
 consequences of invasive predator eradication and inform conservation
 measures. 3) I quantified FID, an antipredator behaviour, in Darwin’s
 finches, across multiple islands in the Galapagos that varied in the
 presence, absence, or successful eradication of invasive predators. On
 islands with human populations, I quantified FID in urban and non-urban
 populations of finches. 4) FID was higher on islands with invasive
 predators compared to islands with no predators. On islands from which
 invasive predators were eradicated ~11 years previously, FID was also
 higher than on islands with no invasive predators. Within islands that had
 both urban and non-urban populations of finches, FID was lower in urban
 finch populations, but only above a threshold human population size. FID
 in larger urban areas on islands with invasive predators was similar to or
 lower than FID on islands with no history of invasive predators. 5)
 Overall, these results suggest that invasive predators can have a lasting
 effect on antipredator behaviour, even after eradication. Furthermore, the
 effect of urbanization can strongly oppose the effect of invasive
 predators, reducing antipredator behaviour to levels lower than found on
 pristine islands with no human influences. These results improve our
 understanding of human influences on antipredator behaviour which can help
 inform future conservation and management efforts on islands.
DOI: 10.5061/dryad.jwstqjq4m
title: Prenatal androgen exposure and transgenerational susceptibility to polycystic ovary syndrome

description: The effects of how obesity and elevated androgen levels in women with
 polycystic ovary syndrome (PCOS) affect their offspring are unclear. We
 found that daughters of PCOS mothers are more likely to be diagnosed with
 PCOS in a Swedish nationwide register-based cohort and a clinical
 case-control study from Chile. Further, female mice (F0) with PCOS-like
 traits induced by late gestation injection of dihydrotestosterone, with
 and without obesity, produced female F1–F3 offspring with a PCOS-like
 reproductive and metabolic phenotypes. Sequencing of single MII oocytes
 from F1–F3 offspring revealed common and unique altered gene expression
 across all generations. Notably, four genes were also differentially
 expressed in serum samples from daughters in the case-control study and
 unrelated women with PCOS. Our findings provide evidence of
 transgenerational effects in female offspring of PCOS mothers and identify
 possible candidate genes for the prediction of a PCOS phenotype in future
 generations.
description: <b>Data availability. </b>Raw data of
 F1-F3 females and of clinical characteristics of daughters are available
 through https://datadryad.org/stash. All raw and analysed single cell RNA-sequencing data of mouse MII oocytes from F1-F3 females is available at GEO database via accession number GSE133100. Both will be released on publication. For the Swedish register-based cohort, original data is held by Swedish National Board of Health and Welfare and Statistics Sweden and because of Swedish data privacy laws we cannot make the data publicly available. Any researcher can access the data by obtaining an ethical approval from a regional ethical review board and thereafter asking the Swedish National Board of Health and Welfare and Statistics Sweden for the original data. However, aggregated data used in the analysis of this study are available from the authors upon a reasonable request and with approved data sharing and data processing agreements in line with the General Data Protection Regulation (GDPR). Further use of this data must be authorized by the local ethics committee regarding the merit of the project involved. A detailed description of the unrelated case-control study including global gene expression analyzes is subcutaneous adipose tissue has previously been published<sup>28</sup>.
DOI: 10.5061/dryad.ksn02v707
title: Data from: Long-term demographic surveys reveal a consistent relationship between average occupancy and abundance within local populations of a butterfly metapopulation

description: Species distribution models are the tool of choice for large-scale
 population monitoring, environmental association studies, and predictions
 of range shifts under future environmental conditions. Available data and
 familiarity of the tools rather than the underlying population dynamics
 often dictate the choice of specific method — especially for the case of
 presence–absence data. Yet, for predictive purposes, the relationship
 between occupancy and abundance embodied in the models should reflect the
 actual population dynamics of the modelled species. To understand the
 relationship of occupancy and abundance in a heterogeneous landscape at
 the scale of local populations, we built a spatio-temporal regression
 model of populations of the Glanville fritillary butterfly (Melitaea
 cinxia) in a Baltic Sea archipelago. Our data comprised nineteen years of
 habitat surveys and snapshot data of land use in the region. We used
 variance partitioning to quantify relative contributions of land use,
 habitat quality, and metapopulation covariates. The model revealed a
 consistent and positive, but noisy relationship between average occupancy
 and mean abundance in local populations. Patterns of abundance were highly
 variable across years, with large uncorrelated random variation and strong
 local population stochasticity. In contrast, the spatio-temporal random
 effect, habitat quality, population connectivity, and patch size explained
 variation in occupancy, vindicating metapopulation theory as the basis for
 modelling occupancy patterns in fragmented landscapes. Previous abundance
 was an important predictor in the occupancy model, which points to a
 spillover of abundance into occupancy dynamics. While occupancy models can
 successfully model large-scale population structure and average occupancy,
 extinction probability estimates for local populations derived from
 occupancy-only models are overconfident, as extinction risk is dependent
 on actual, not average, abundance.
description: The data collection and processing are described in the published
 study. The code for analysis is included with the files.
description: <strong>ECOG-04799</strong> This file contains the data, workflow and scripts of the study. The associated README file in text and html format describe the data and how to re-run the analyses.
DOI: 10.5061/dryad.83bk3j9mj
title: Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae)

description: Genetic variation in natural populations often occurs at levels
 suggesting the action of processes such as frequency-dependent selection,
 heterozygote advantage, and variable selection. However, the maintenance
 of genetic variation in fitness-related traits remains incompletely
 explained.  Obligately self-fertilizing populations
 of Lobelia inflata(Campanulaceae L.) are characterized by high
 levels of genetic variation, strongly implying balancing
 selection.  L. inflataoffers an exceptional opportunity
 for an empirical test of genotype-environment interaction (GxE) as a
 variance-maintaining mechanism under fluctuating selection: L.
 inflatais monocarpic and reproduces only by seed, facilitating assessment
 of lifetime fitness; genome-wide homozygosity precludes some mechanisms of
 balancing selection, and microsatellites are, in effect, genotypic lineage
 markers. Here, we find support for the temporal GxE hypothesis
 using a manipulated space-for-time approach across four environments: a
 field environment, an outdoor experimental plot and two differing growth
 chamber environments.  High genetic variance was
 confirmed: 83 field-collected individuals consisted of 45 distinct
 microsatellite lineages with on average 4.5 alleles per
 locus. Rank-order fitness, measured as lifetime fruit production
 in sixteen replicated multilocus genotypes, changed significantly across
 environments.  Phenotypic differences among
 microsatellite lineages were detected.  Although results
 support the GxE hypothesis in principle, evaluation of the effect size of
 this mechanism and fitness effects of life-history traits will require
 long-term study of fluctuating selection on labelled genotypes in the
 field.
DOI: 10.5061/dryad.qv9s4mw9c
title: Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

description: Aim: Wetland habitats, and the ecological restrictions imposed by them,
 structure patterns of genetic variation in constituent taxa. As
 such, genetic variation may reflect properties of the specific
 biomes species inhabit, or shared life history traits among
 species may result in similar genetic structure. We evaluated these
 hypotheses jointly by quantifying the similarity of genetic
 structure in three South American marsh rat species (Holochilus),
 and test how genetic variation in each species relates to
 biome‐specific environmental space and historical stability. Location:
 South America. Taxon: Rodentia. Methods: Using complementary analyses
 (Mantel tests, dbRDA, Procrustes, covariance structure of allele
 frequencies and environmental niche models [ENMs])
 with 8,000–32,000 SNPs per species, we quantified the association
 between genomic variation and geographic and/or environmental
 differences. Results: Significant association between genetic variation
 and geography was identified for all species. Similarity in the
 strength of the association suggests connectivity patterns
 dictated by shared species‐traits predominate at the biome scale.
 However, substantial amounts of genetic variation are not
 explained by geography. Focusing on this portion of the variance,
 we demonstrate a significant quantitative association between
 genetic variation and the environmental space of a biome, and a
 qualitative association with varying regional stability.
 Specifically, historically stable areas estimated from ecological
 niche models are correlated with local levels of
 geographic structuring, suggesting that local biome‐specific
 histories affect population isolation/ connectivity.
DOI: 10.5061/dryad.k98sf7m2m
title: An effective mutualism? The role of theoretical studies in ecology and evolution

description: Theoretical models often have fundamentally different goals than do
 empirical studies of the same topic. Models can test the logic of existing
 hypotheses, explore the plausibility of new hypotheses, provide
 expectations that can be tested with data, and address aspects of topics
 that are currently inaccessible empirically. Theoretical models are common
 in ecology and evolution, and are generally well-cited, but I show that
 many citations appearing in non-theoretical studies are general to topic
 and a substantial proportion are incorrect. One potential cause of this
 pattern is that some functions of models are rather abstract, leading to
 miscommunication between theoreticians and empiricists. Such
 misunderstandings are often triggered by simplifying, logistical
 assumptions that modelers make. The 2018 Vice Presidential Symposium of
 the American Society of Naturalists included a variety of mathematical
 models in ecology and evolution from across several topics. Common threads
 that appear in the use of the models are identified, highlighting the
 power of a theoretical approach and the role of the assumptions that such
 models make.
description: Data from a survey of how theoretical authors perceive citations
 of their papers by non-theoretical papers.  Each entry shows the survey
 respondent, their theoretical paper that they assessed, the year, whether
 they consider the paper to be "ecological" (Ec) or
 "evoltionary" (Ev),  followed by the numbers adnd percentages of
 citations that the theoretical authors perceived to be Incorrect, General
 to topic (and correct), and Specific and appropriate. The three sheets
 contain the same data, just with different summary figures.
 The exact wording of the survey used to obtain this data is also
 included.
DOI: 10.5061/dryad.d2547d7z8
title: Fragmentation and the context-dependence of dispersal syndromes: matrix harshness modifies resident-disperser phenotypic differences in microcosms

description: Habitat fragmentation, the conversion of landscapes into patchy habitats
 separated by unsuitable environments, is expected to reduce dispersal
 among patches. However, its effects on dispersal should depend on
 dispersal syndromes, i.e. how dispersal covaries with phenotypic traits,
 because these syndromes can drastically alter dispersal and subsequent
 ecological and evolutionary dynamics. Our comprehension of whether
 environmental factors such as habitat fragmentation generate and/or modify
 dispersal syndromes (i.e. conditional dispersal syndromes) is therefore
 key for biodiversity forecasting. Here we tested whether habitat
 fragmentation modulates dispersal syndromes by experimentally manipulating
 matrix harshness, a critical feature of habitat fragmentation, in ciliate
 microcosms. We found evidence for dispersal syndromes involving multiple
 traits linked to morphology (elongation and size), movement (velocity and
 linearity) and demography (growth rate and maximal population density).
 More importantly, these syndromes were modified by matrix harshness, with
 increased differences between residents and dispersers in morphology and
 movement traits, and decreased differences in growth rate as the matrix
 became increasingly harsh. Our findings thus reveal that habitat
 fragmentation can mediate the intensity and form of dispersal syndromes, a
 context-dependence that could have important consequences for ecological
 and evolutionary dynamics under environmental changes.
DOI: 10.5061/dryad.m905qftwt
title: Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

description: Soil microbial communities play a key role in ecosystem functioning but
 still little is known about the processes that determine their turnover
 (β-diversity) along ecological gradients. Here, we characterize soil
 microbial β-diversity at two spatial scales and at multiple phylogenetic
 grains to ask how archaeal, bacterial and fungal communities are shaped by
 abiotic processes and biotic interactions with plants. We characterized
 microbial and plant communities using DNA metabarcoding of soil samples
 distributed across and within eighteen plots along an elevation gradient
 in the French Alps. The recovered taxa were placed onto phylogenies to
 estimate microbial and plant β-diversity at different phylogenetic grains
 (i.e. resolution). We then modeled microbial β-diversities with respect to
 plant β-diversities and environmental dissimilarities across plots
 (landscape scale) and with respect to plant β-diversities and spatial
 distances within plots (plot scale). At the landscape scale, fungal and
 archaeal β-diversities were mostly related to plant β-diversity, while
 bacterial β-diversities were mostly related to environmental
 dissimilarities. At the plot scale, we detected a modest covariation of
 bacterial and fungal β-diversities with plant β-diversity; as well as a
 distance–decay relationship that suggested the influence of ecological
 drift on microbial communities. In addition, the covariation between
 fungal and plant β-diversity at the plot scale was highest at fine or
 intermediate phylogenetic grains hinting that biotic interactions between
 those clades depends on early-evolved traits. Altogether, we show
 how multiple ecological processes determine soil microbial community
 assembly at different spatial scales and how the strength of these
 processes change among microbial clades. In addition, we emphasized the
 imprint of microbial and plant evolutionary history on today’s microbial
 community structure.
description: Details about the methods are available in the article
 Chalmandrier et al. Environmental and biotic drivers of soil microbial
 β-diversity across spatial and phylogenetic scales. Ecography
 This dataset contains: - environmental DNA
 data for 378 soil samples of subalpine/alpine grasslands (Valloire,
 France, 2012) for four clades: Archaea, Tracheophyta, Fungi and
 Bacteria - associated environmental
 conditions - Fasta files for the four clades.
 Furthermore the analysis procedure used to do the analysis is
 included.
DOI: 10.5061/dryad.zkh18935j
title: Combined effects of global climate change and nutrient enrichment on the physiology of three temperate maerl species

description: Made up of calcareous coralline algae, maerl beds play a major role as
 ecosystem engineers in coastal areas throughout the world. They undergo
 strong anthropogenic pressures, which may threaten their survival. The aim
 of this study was to gain insight into the future of maerl beds in the
 context of global and local changes. We examined the effects of rising
 temperatures (+3ºC) and ocean acidification (-0.3 pH units) according to
 temperature and pH projections (i.e. the RCP8.5 scenario), and nutrient (N
 and P) availability on three temperate maerl species (Lithothamnion
 corallioides, Phymatolithon calcareum, Lithophyllum
 incrustans) in the laboratory in winter and summer conditions.
 Physiological rates of primary production, respiration and calcification
 were measured on all three species in each treatment and season. The
 physiological response of maerl to global climate change was
 species-specific and influenced by seawater nutrient concentrations.
 Future temperature-pH scenario enhanced maximal gross primary production
 rates in P. calcareum in winter and in L.
 corallioides in both seasons. Nevertheless, both species suffered
 an impairment of light harvesting and photo-protective mechanisms in
 winter. Calcification rates at ambient light intensity were negatively
 affected by the future temperature-pH scenario in winter, with net
 dissolution observed in the dark in L.
 corallioidesand P. calcareumunder low nutrient concentrations.
 Nutrient enrichment avoided dissolution under future scenarios in winter
 and had a positive effect on L. incrustanscalcification rate in
 the dark in summer. In winter conditions maximal calcification rates were
 enhanced by the future temperature-pH scenario on the three species,
 but P. calcareum suffered inhibition at high
 irradiances. In summer conditions, the maximal calcification rate dropped
 in L. corallioides under the future global climate
 change scenario, with a potential negative impact
 on CaCO3budget for maerl beds in the Bay of Brest where this
 species is dominant. Our results highlight how local changes in nutrient
 availability or irradiance levels impact the response of maerl species to
 global climate change and thus point out how it is important to consider
 other abiotic parameters in order to develop management policies capable
 to increase the resilience of maerl beds under the future global climate
 change scenario.
DOI: 10.5061/dryad.j9kd51c7d
title: A primal role for the vestibular sense in the development of coordinated locomotion

description: Mature locomotion requires that animal nervous systems coordinate distinct
 groups of muscles. The pressures that guide the development of
 coordination are not well understood. To understand how and why
 coordination might emerge, we measured the kinematics of spontaneous
 vertical locomotion across early development in zebrafish (Danio rerio) .
 We found that zebrafish used their pectoral fins and bodies
 synergistically during upwards swims. As larvae developed, they changed
 the way they coordinated fin and body movements, allowing them to climb
 with increasingly stable postures. This fin-body synergy was absent in
 vestibular mutants, suggesting sensed imbalance promotes coordinated
 movements. Similarly, synergies were systematically altered following
 cerebellar lesions, identifying a neural substrate regulating fin-body
 coordination. Together these findings link the vestibular sense to the
 maturation of coordinated locomotion. Developing zebrafish improve
 postural stability by changing fin-body coordination. We therefore propose
 that the development of coordinated locomotion is regulated by vestibular
 sensation.
DOI: 10.6071/m3hw93
title: Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollock

description: Detailed supplemental datasets: inputs and output information and emission
 factors for ingredients, non-ingredient materials, and embodied
 energy of pollock products.