cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jm90
title: Data from: Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north-western Pacific Acropora digitifera

description: Coral reefs are suffering a major decline due to the environmental
 constraints imposed by climate change. Over the last 20 years, three major
 coral bleaching events occurred in concomitance with anomalous heat waves,
 provoking a severe loss of coral cover worldwide. The conservation
 strategies for preserving reefs, as they are implemented now, cannot cope
 with global climatic shifts. Consequently, researchers are advocating for
 preservation networks to be set-up to reinforce coral adaptive potential.
 However, the main obstacle to this implementation is that studies on coral
 adaption are usually hard to generalize at the scale of a reef system.
 Here, we study the relationships between genotype frequencies and
 environmental characteristics of the sea (seascape genomics), in
 combination with connectivity analysis, to investigate the adaptive
 potential of a flagship coral species of the Ryukyu Archipelago (Japan).
 By associating genotype frequencies with descriptors of historical
 environmental conditions, we discovered six genomic regions hosting
 polymorphisms that might promote resistance against heat stress.
 Remarkably, annotations of genes in these regions were consistent with
 molecular roles associated with heat responses. Furthermore, we combined
 information on genetic and spatial distances between reefs to predict
 connectivity at a regional scale. The combination of these results
 portrayed the adaptive potential of this population: we were able to
 identify reefs carrying potential heat stress adapted genotypes and to
 understand how they disperse to neighbouring reefs. This information was
 summarized by objective, quantifiable, and mappable indices covering the
 whole region, which can be extremely useful for future prioritization of
 reefs in conservation planning. This framework is transferable to any
 coral species on any reef system, and therefore represents a valuable tool
 for empowering preservation efforts dedicated to the protection of coral
 reefs in warming oceans.
description: The raw genomic data is available under the Bioproject accession:
 PRJDB4188 Refer to the metadatascripts.pdf file for
 information on the methods applied to data.
DOI: 10.5061/dryad.pg4f4qrj3
title: Elevational contrast in predation and parasitism risk to caterpillars in a tropical rainforest

description: Invertebrate predators and parasitoids are among the most important
 natural enemies of insect herbivores. Yet, the strength of natural enemy
 pressure along an altitudinal gradient and interactions between groups of
 natural enemies (such as predation on parasitized prey) are not well
 known. Various methods are used to reveal mortality factors of herbivores.
 Predation pressure is usually assessed through exposure of artificial
 prey. However, this method cannot provide information about the attacks of
 parasitoids, or their eventual interactions with predators. Further,
 artificial or dead prey might not attract predators because they do not
 show expected host behavior, and this method mostly cannot distinguish
 between predation and scavenging. For the first time in a tropical
 rainforest, we quantified mortality factors along an altitudinal gradient
 using exposure of live caterpillars. We exposed a total of 800 live
 caterpillars of Talanga excelsalis moresbyensis Strand (Lepidoptera:
 Crambidae) on saplings of Ficus copiosa Steud. (Moraceae) at two
 elevations in primary tropical rain forest in Papua New Guinea (200 and
 1 200 m a.s.l.). We exposed the caterpillars in two treatments:
 exposed to and protected from invertebrate predators and parasitoids.
 Disappearance of caterpillars was significantly higher in the exposed
 treatment. Further, caterpillar disappearance was significantly higher in
 lowlands than in highlands (43 vs. 12%). We consider the vast majority of
 the disappearance to be due to predation, as migration of the caterpillars
 from the focal trees was not observed (except one caterpillar). This
 estimate of invertebrate predation rate corresponds with studies which
 used artificial caterpillar models. No significant difference in
 parasitism rate between the two elevations was observed (12 vs. 13%). The
 combination of the disappearance and parasitism rate patterns means that
 larval parasitoids face stronger pressure from invertebrate predators
 through higher predation of their hosts in the lowlands than in the
 highlands.
description: The data were collected in the primary rainforest of Papua New
 Guinea. The objects were exposed to predators and parasitoids. After the
 exact periode of time, the caterpillars were collected and reared to
 adults. More info in the methodology.
DOI: 10.5061/dryad.ht76hdr9t
title: Data from: Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

description: Hybridization dynamics between co-occurring species in environments where
 human-mediated changes take place is important to quantify for furthering
 our understanding of human impacts on species evolution and for informing
 management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad
 Alosa fallax (Lacépède, 1803), two clupeids sister species, have been
 severely impacted by human activities across Europe. The shrinkage of A.
 alosa distribution range along with the decline of the remaining
 populations’ abundance threaten its persistence. The main objective was to
 evaluate the extent of hybridization and introgression between those
 interacting species. We developed a set of 77 species-specific SNP loci
 that allowed a better resolution than morphological traits as they enabled
 the detection of hybrids up to the third generation. Variable rates of
 contemporary hybridization and introgression patterns were detected in 12
 studied sites across the French Atlantic coast. Mitochondrial markers
 revealed a cyto-nuclear discordance almost invariably involving A. alosa
 individuals with an A. fallax mitochondrial DNA and provided evidence of
 historical asymmetric introgression. Overall, contemporary and historical
 introgression revealed by nuclear and mitochondrial markers strongly
 suggest that a transfer of genes occurs from A. fallax towards A. alosa
 genome since at least four generations. Moreover, the outcomes of
 introgression greatly depend on the catchments where local processes are
 thought to occur. Undoubtedly, interspecific interaction and gene flow
 should not be overlooked when considering the management of those species.
description: Data from: Taillebois et al. "Variable outcomes of
 hybridization between declining Alosa alosa and Alosa fallax"
 Evolutionary Application 2019 Sheets
 description: - MassARRAY_Primers: Primer sequences for
 the MassARRAY Agena Bioscience SNP genotyping plateform ; genotyping
 analysis available at the Genome Transcriptome Facility of Bordeaux
 (pgtb@inra.fr) - GenotypicClasses_3Gen-NewHybrid: The
 genotypic classes expected for three generations hybridization used for
 New Hybrid assignment - SNP-MitoHaplo-Assignement_data:
 The SNP genotype table and mitochondrial sequences and individual metadata
 including sampling localities, gill raker counts, Structure and NewHybrid
 assignment results
DOI: 10.15468/dl.sadb3b
title: Occurrence Download

description: A dataset containing 2344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis lupus baileyi"
 ]
}

 The dataset includes 2344 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001970-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5qfttdz14
title: Vastly underestimated radiation of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification

description: We present data showing that the number of salamander species in Amazonia
 is vastly underestimated. We used DNA sequences of up to five genes (3
 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89
 non-Amazonian nominal species and 177 Amazonian specimens, including types
 or topotypes, of eight of the nine recognized species in the region. By
 including representatives of all known species of Amazonian Bolitoglossa,
 except for one, and 73 % of the currently 132 recognized species of the
 genus, our dataset represents the broadest sample of Bolitoglossa species,
 specimens, and geographic localities studied to date. We performed
 phylogenetic analyses using parsimony with tree-alignment and maximum
 likelihood (ML) with similarity alignment, with indels as binary
 characters. Our optimal topologies were used to delimit lineages that we
 assigned to nominal species and candidate new species following criteria
 that maximize the consilience of the current species taxonomy, monophyly,
 gaps in branch lengths, genetic distances, and geographic distribution. We
 contrasted the results of our species-delimitation protocol with those of
 Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree
 Processes (mPTP). Finally, we inferred the historical biogeography of
 South American salamanders by dating the trees and using
 dispersal-vicariance analysis (DIVA). Our results revealed a clade
 including almost all Amazonian salamanders, with a topology incompatible
 with just the currently recognized nine species. Following our
 species-delimitation criteria, we identified 44 putative species in
 Amazonia. Both ABGD and mPTP inferred more species than currently
 recognized, but their numbers (23–49) and limits vary. Our biogeographic
 analysis suggested a stepping-stone colonization of the Amazonian lowlands
 from Central America through the Chocó and the Andes, with several late
 dispersals from Amazonia back into the Andes. These biogeographic events
 are temporally concordant with an early land bridge between Central and
 South America (~ 10–15 MYA) and major landscape changes in Amazonia during
 the late Miocene and Pliocene, such as the drainage of the Pebas system,
 the establishment of the Amazon River, and the major orogeny of the
 northern Andes.
DOI: 10.5061/dryad.dz08kprsw
title: Data from: Longitudinal structural and metabolic changes in frontotemporal dementia

description: Objective: To compare the sensitivity of structural MRI and
 18F-Fludeoxyglucose PET (18FDG-PET) to detect longitudinal changes in
 frontotemporal dementia (FTD). Methods: Thirty patients with
 behavioral-variant FTD (bvFTD), 7 with non-fluent/agrammatic variant
 primary progressive aphasia (nfvPPA), 16 with semantic variant PPA (svPPA)
 and 43 cognitively normal controls underwent 2-4 MRI and 18FDG-PET scans
 (total scan/visit=270) as part of the Frontotemporal Lobar Degeneration
 Neuroimaging Initiative study. Linear mixed-effects models were carried
 out voxel-wise and in regions of interest to identify areas showing
 decreased volume or metabolism over time in patients as compared to
 controls. Results: At baseline, patients with bvFTD showed bilateral
 temporal, dorsolateral and medial prefrontal atrophy/hypometabolism that
 extended with time into adjacent structures and parietal lobe. In nfvPPA,
 baseline atrophy/hypometabolism in supplementary motor cortex extended
 with time into left greater than right precentral, dorsolateral and
 dorsomedial prefrontal cortex. In svPPA, baseline atrophy/hypometabolism
 encompassed the anterior temporal and medial prefrontal cortex and
 longitudinal changes were found in temporal, orbitofrontal and lateral
 parietal cortex. Across syndromes, there was substantial overlap in the
 brain regions showing volume and metabolism loss. Even though the pattern
 of metabolic decline was more extensive, metabolic changes were also more
 variable and sample size estimates were similar or higher for 18FDG-PET
 compared to MRI. Conclusion: Our findings demonstrated the sensitivity of
 18FDG-PET and structural MRI for tracking disease progression in FTD. Both
 modalities showed highly overlapping patterns of longitudinal change and
 comparable sample size estimates to detect longitudinal changes in future
 clinical trials.
DOI: 10.5061/dryad.4tmpg4f5f
title: A comprehensive survey among statistical members of medical ethics committees in Germany on their personal impression of completeness and correctness of biostatistical aspects of submitted study protocols

description: Original data of a comprehensive survey among statistical members
 of medical ethics committees in Germany on their personal impression of
 completeness and correctness of biostatistical aspects of submitted study
 protocols. To enable reproduction of the results presented in the
 corresponding paper, the final dataset is freely available here,
 without any information on the medical ethics committee’s federal state to
 avoid any risk of potential re-identification.
DOI: 10.5061/dryad.02v6wwpzq
title: Data from: Phage combination therapies for bacterial wilt disease in tomato

description: Bacteriophage have been proposed as an alternative to pesticides to kill
 bacterial pathogens of crops. However, phage-biocontrol outcomes are still
 highly variable and poorly understood in natural rhizosphere microbiomes
 at timescales considering both ecological and evolutionary processes.
 However, the efficacy of phage-biocontrol is variable and poorly
 understood in natural rhizosphere microbiomes at timescales considering
 both ecological and evolutionary processes. We studied the biocontrol
 efficacy of different phage combinations on Ralstonia solanacearum
 infection in tomato. Increasing the number of phages in combinations
 decreased disease incidence by up to 80% in greenhouse and field
 experiments during single crop season. Disease reduction was explained by
 pathogen density reduction and selection for resistant but slow-growing
 pathogen strains, together with enrichment for bacterial species that were
 antagonistic towards Ralstonia solanacearum. Phage treatment did not
 affect existing rhizosphere microbiota. Specific phage combinations show
 promise as precision tools to reduce pathogen abundance in plants.
description: Spreadsheet tabs contain data underlying figures from the
 associated paper (http://doi.org/10.1038/s41587-019-0328-3)
DOI: 10.5061/dryad.1vhhmgqnw
title: Data from: Right phenotype, wrong place: predator-induced plasticity is costly in a mismatched environment

description: Like many animals, tadpoles often produce different, predator-specific
 phenotypes when exposed to risk of predation. It is generally assumed that
 such plasticity enhances survival in the presence of the predator and is
 costly elsewhere, but evidence remains surprisingly scarce. We measured 1)
 the survival trade-off of opposing phenotypes developed by Dendropsophus
 ebraccatus tadpoles when exposed to different predators and 2) which
 specific aspects of morphology drive any potential survival benefit or
 cost. Tadpoles developed predator specific phenotypes after being reared
 with caged fish or dragonfly predators for two weeks. In 24-hour predation
 trials with either a fish or a dragonfly, survival was highest in the
 groups with their matched predator, and lowest among with those the
 mismatched predator, with predator-naïve controls being relatively
 intermediate. Then, using a large group of phenotypically variable
 predator-naïve tadpoles, we found that increased survival rates are
 directly related to the morphological changes that are induced by each
 predator. This demonstrates that induced phenotypes are indeed adaptive
 and the product of natural selection. Furthermore, our data provide clear
 evidence of an environmental cost for phenotypic plasticity in a
 heterogeneous environment. Such costs are fundamental for understanding
 the evolution and maintenance of inducible phenotypes.
description: The ReadMe.txt file describes the various columns in each data
 set.
DOI: 10.5061/dryad.vt4b8gtn4
title: Data from: Phenological plasticity is a poor predictor of subalpine plant population performance following experimental climate change

description: Phenological shifts, changes in the seasonal timing of life cycle events,
 are among the best documented responses of species to climate change.
 However, the consequences of these phenological shifts for population
 dynamics remain unclear. Population growth could be enhanced if species
 that advance their phenology benefit from longer growing seasons and gain
 a pre-emptive advantage in resource competition. However, it might also be
 reduced if phenological advances increase exposure to stresses, such as
 herbivores and, in colder climates, harsh abiotic conditions early in the
 growing season. We exposed subalpine grasslands to ~ 3 K of warming by
 transplanting intact turfs from 2000 m to 1400 m elevation in the eastern
 Swiss Alps, with turfs transplanted within the 2000 m site acting as a
 control. In the first growing season after transplantation, we recorded
 species’ flowering phenology at both elevations. We also measured species’
 cover change for three consecutive years as a measure of plant
 performance. We used models to estimate species’ phenological plasticity
 (the response of flowering time to the change in climate) and analysed its
 relationship with cover changes following climate change. The phenological
 plasticity of the 18 species in our study varied widely but was unrelated
 to their changes in cover. Moreover, early- and late-flowering species did
 not differ in their cover response to warming, nor in the relationship
 between cover changes and phenological plasticity. These results were
 replicated in a similar transplant experiment within the same subalpine
 community, established one year earlier and using larger turfs. We discuss
 the various ecological processes that can be affected by phenological
 shifts, and argue why the population-level consequences of these shifts
 are likely to be species- and context-specific. Our results highlight the
 importance of testing assumptions about how warming-induced changes in
 phenotypic traits, like phenology, impact population dynamics.
description: This dataset contains all the data and code required to reproduce
 the results reported in the associated paper.
DOI: 10.5061/dryad.pvmcvdngc
title: Competition induces silver spoon effects in developing anuran larvae

description: Early life conditions can have persistent, lifelong impacts on survival
 and fitness.  Silver spoon effects occur when favorable early
 life conditions provide advantages through adulthood, even if conditions
 worsen.  Alternatively, compensatory growth can allow organisms
 initially reared in unfavorable conditions to grow more quickly than
 expected should conditions improve.  We examined these
 possibilities in the American Toad, Anaxyrus americanus, by rearing larvae
 in low competition and high competition environments and then transferring
 them to either high- or low-resource levels.  We measured growth
 one-week post-transfer and toadlet size after metamorphosis.  We
 also dissected larvae and toadlets from each treatment to examine effects
 on organ size.  Before transfer, larvae in low competition
 environments grew significantly faster than those in high competition
 environments.  Consistent with the silver spoon hypothesis, these
 larvae ate significantly more food, continued to grow faster
 post-transfer, and metamorphosed into larger toadlets than those initially
 reared with competition, despite having the same food availability within
 a resource level.  There were also significant effects on
 internal organ sizes.  Overall, our study demonstrates that
 larvae initially reared in favorable conditions maintain a growth
 advantage through metamorphosis even if resource levels decline. 
 Future studies should explore the effects of this advantage
 post-metamorphosis and into adulthood.
DOI: 10.5061/dryad.xgxd254bv
title: Data from: Mechanisms of trophic niche compression: evidence from landscape disturbance

description: 1. Natural and anthropogenic disturbances commonly alter patterns
 of biodiversity and ecosystem functioning. However, how networks of
 interacting species respond to these changes remains poorly understood. We
 described aquatic food webs using invertebrate and fish community
 composition, functional traits, and stable isotopes from twelve
 agricultural streams along a landscape disturbance gradient. 2. We
 predicted that excessive deposition of fine inorganic sediment
 (sedimentation) associated with agricultural activities would negatively
 influence aquatic trophic diversity (e.g., reduced vertical and horizontal
 trophic niche breadths). We hypothesized that multiple mechanisms might
 cause trophic niche ‘compression’, as indicated by changes in realized
 trophic roles. 3. Food-web properties based on consumer stable isotope
 data (δ13C and δ15N) showed that increasing sediment disturbance was
 associated with reduced trophic diversity. In particular, the aquatic
 invertebrate community occupied a smaller area in isotopic niche space
 along the sedimentation gradient that was best explained by a narrowing of
 the invertebrate community δ13C range. 4. Decreased niche partitioning,
 driven by increasing habitat homogeneity, environmental filtering, and
 resource scarcity all seemingly lead to greater trophic equivalency caused
 by the collapse of the autochthonous food-web channel. Bayesian
 mixing-model analyses supported this contention with invertebrate
 consumers increasingly reliant on detritus along the sedimentation
 gradient, and predatory invertebrates relying more on the prey using these
 basal resources.   5. The narrowing of the fish
 community δ13C range along the sedimentation gradient contributed to an
 apparent ‘trophic shift’ towards terrestrial carbon, further indicating
 the loss of the autochthonous food-web channel. On the vertical trophic
 niche axis, fish became increasingly separated from aquatic invertebrates
 with an increase in their estimated trophic position. In combination,
 these responses were most likely mediated through reduced fish densities
 and a diminished reliance on aquatic prey. 6. Although species losses
 remain a major threat to ecosystem integrity, the functional roles of
 biota that persist dictate how food webs and ecosystem functioning respond
 to environmental change. Sedimentation was associated with non-linear
 reductions in trophic diversity which could affect the functioning and
 stability of aquatic ecosystems. Our study helps explain how multiple
 mechanisms may radically reshape food-web properties in response to this
 type of disturbance.