cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q5s6298
title: Data from: Retention of learned predator recognition in embryonic and juvenile rainbow trout

description: Minimizing predation risk, especially for young or naïve individuals, can
 be achieved by learning to recognize predators. Embryonic learning may
 optimize survival by allowing for the earliest possible response to
 predation threats post-hatch. However, predatory threats often change over
 an individual’s lifetime, and using old information can be detrimental if
 it becomes outdated. Adaptive forgetting allows an individual to discount
 obsolete information in decision-making, and instead emphasize newer, more
 relevant information when responding to predation threats. Little is known
 about the extent to which young individuals can learn and forget
 information about predation threats. Here we demonstrate that rainbow
 trout 1) are capable of learning from both conspecific and heterospecific
 alarm cues as embryos, newly-hatched and free swimming larvae, 2) exhibit
 adaptive forgetting of predator information at all stages, and 3) display
 dynamic adaptive forgetting based on the ontogeny of learning.
 Specifically, fish that learned information as embryos retained that
 information for longer periods than those that learned the same
 information as newly-hatched alevins.
description: Trout Mem Expt
 1aCapacity of embryonic
 rainbow trout to learn to recognize predators - Experiment
 1aExperiment
 1bCapacity of trout that
 learned as embryos to recognize predators to forget those predators -
 Experiment 1bTrout Mem Expt
 1b.csvTrout Mem Experiment
 2Effects of ontogeny on
 retention of learned predator recognition in embryonic, larval and
 juvenile rainbow trout - Expt 2Trout Mem Expt
 2.csv
DOI: 10.5061/dryad.7rn6dd8
title: Data from: Cascading effects of mammalian herbivores on ground-dwelling arthropods: variable responses across arthropod groups, habitats and years

description: 1. Large mammalian herbivores are well known to shape the structure and
 function of ecosystems worldwide and these effects can in turn cascade
 through systems to indirectly influence other animal species. A wealth of
 studies have explored the effects of large mammals on arthropods, but to
 date they have reported such widely varying results that generalizations
 have been elusive. Three factors are likely drivers of this variability:
 the widely varying life-history characteristics of different arthropod
 groups, the highly variable landscapes that mammalian herbivores commonly
 inhabit, and temporal variation in environmental conditions. 2. Here, we
 use an 18-year-old exclosure experiment stratified across three distinct
 coastal prairie habitats in northern California to address the effects of
 a reintroduced mammalian herbivore, tule elk (Cervus canadensis nannodes)
 on the composition, richness, and abundance of ground-dwelling arthropods
 over two years with very different precipitation regimes. 3. We found that
 elk shifted the composition of arthropod communities, increasing the
 abundance of ants, beetles, spiders and mites, decreasing the abundance of
 woodlice and bristletails in some but not all habitats types, and having
 no effect on the abundance of bugs, crickets and springtails. Elk also
 increased richness and changed the composition of ant-genera and beetle
 morpho-species. Interestingly, the effects of elk on arthropod
 composition, richness and abundance varied little between years, despite
 very different precipitation levels, biomass accumulation, and thatch
 height. 4. Elk reduced shrub cover, aboveground herbaceous biomass, and
 thatch height and increased soil compaction, and these changes predicted
 the abundance and richness of arthropods, although taxonomic groups varied
 in their responses, presumably due to differences in environmental
 requirements. 5. Synthesis. Our research highlights the importance of
 using long-term experiments to assess the cascading effects of large
 herbivores on the composition of ground-dwelling arthropod communities and
 to identify the mechanisms that indirectly shape arthropod responses to
 herbivores among variable habitats and years in order to develop a greater
 understanding of the variable responses of arthropods to large mammalian
 herbivores.
description: Cecil et al. 2019 –
 master dataThis file has multiple
 sheets containing data relating to an exclosure experiment that evaluates
 the effect of tule elk on the abundance and composition of ground-dwelling
 arthropods in northern California.
DOI: 10.5061/dryad.3476709
title: Data from: Range-wide population genomics of the Mexican fruit fly: towards development of pathway analysis tools

description: Recurrently invading pests provide unique challenges for pest management,
 but also present opportunities to utilize genomics to understand invasion
 dynamics and inform regulatory management through pathway analysis. In the
 southern United States, the Mexican fruit fly Anastrepha ludens is such a
 pest, and its incursions into Texas and California represent major threats
 to the agricultural systems of those regions. We developed a draft genome
 assembly for A. ludens, conducted range-wide population genomics using
 restriction-site associated DNA sequencing, and then developed and
 demonstrated a panel of highly-differentiated diagnostic SNPs for source
 determination of intercepted flies in this system. Using 2,081 genome-wide
 SNPs, we identified four populations across the range of A. ludens,
 corresponding to western Mexico, eastern Mexico/Texas,
 Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation
 present between clusters, particularly in Central America. From this
 population genomics framework, we developed a diagnostic panel of 28
 highly-differentiated SNPs that were able to recreate the genome-wide
 population structure in this species. We demonstrated this panel on a set
 of test specimens, including specimens intercepted as part of regular
 trapping surveillance in Texas and California, and we were able to predict
 populations of origin for these specimens. This methodology presents a
 highly applied use of genomic techniques and can be implemented in any
 group of recurrently invading pests.
description: MexFly_ALLPATHS_assemblyALLPATHS assembly used for mapping ddRAD reads.2081_SNPs_vcf2081 SNPs data file, vcf format2081_SNPs.vcf2081_SNPs_str2081 SNPs datafile in structure format2081_SNPs.str2081_SNPs_noRearingIndividuals_str2081 SNPs datafile in structure format, with rearing individuals removed2081_SNPs_noRearingIndividuals.str28_SNPs_str28 SNPs datafile (diagnostic panel) in structure format, including 40 real-world test specimens28_SNPs.str
DOI: 10.5061/dryad.f1bn36c
title: Data from: Dispersal, philopatry and population genetic structure of the mainland dibbler, Parantechinus apicalis

description: Dispersal plays an important role in the population structure and
 resilience of species. To gain a better understanding of dispersal in the
 endangered Australian marsupial, the dibbler (Parantechinus apicalis), we
 screened 199 individuals from seven locations within the Fitzgerald River
 National Park, Western Australia, for genetic variation at 17
 microsatellite loci. There were high levels of genetic variation within
 all sites (gene diversity ranged from 0.68 to 0.71) as well as significant
 genetic differentiation between sites less than 19 km apart that were
 consistent over multiple years (FST = 0.021 – 0.073). A Bayesian
 clustering analysis revealed the presence of two genetic clusters
 separating P. apicalis in the western part from the central and eastern
 parts of the National Park. There was also evidence of fine-scale
 population structure with spatial autocorrelation analysis showing
 positive genetic structure up to distances of 200 m in females. By
 contrast males did not exhibit significant fine-scale population
 structure, thus suggesting P. apicalis exhibits female philopatry and
 male-biased dispersal. We recommend that management should take into
 account the existence of two subpopulations within the National Park and
 manage accordingly. Individuals selected for captive breeding and
 translocation programs, especially females, should be sampled at least 200
 m apart to reduce the likelihood of selecting related individuals.
description: GenotypeMicrosatellite loci of Parantechinus apicalis
DOI: 10.5061/dryad.1rm2290
title: Data from: Artificial light at night causes reproductive failure in clownfish

description: The Earth is getting brighter at night, as artificial light at night
 (ALAN) continues to increase and extend its reach. Despite recent
 recognition of the damaging impacts of ALAN on terrestrial ecosystems,
 research on the impacts of ALAN on marine systems is comparatively
 lacking. To further our understanding of the impacts of ALAN on marine
 organisms, this study examines the impact of ALAN on the reproductive
 fitness of the common clownfish Amphiprion ocellaris. We assessed how
 exposure to low levels of ALAN affects 1) frequency of spawning, 2) egg
 fertilisation success, and 3) hatching success of A. ocellaris under
 control (12:12 day-night) and treatment (12:12 day-ALAN) light regimes.
 While we found exposure to ALAN had no impact on the frequency of spawning
 or fertilisation success, ALAN had dramatic effects on hatching.
 Amphiprion ocellaris eggs incubated in the presence of ALAN simply did not
 hatch, resulting in zero survivorship of offspring. These findings suggest
 ALAN can significantly reduce reproductive fitness in a benthic-spawning
 reef fish. Further research in this field is necessary to fully understand
 the extent of this impact on population and community dynamics in the
 wild.
description: Fobert et al_ALAN causes
 reproductive failure in clownfish_datasetSpawning interval,
 fertilisation success, hatch rate, and fish size data for Amphiprion
 ocellaris
DOI: 10.5061/dryad.574pc6n
title: Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

description: Background: Genomic variation is widespread, and both neutral and
 selective processes can generate similar patterns in the genome. These
 processes are not mutually exclusive, so it is difficult to infer the
 evolutionary mechanisms that govern population and species divergence.
 Boechera stricta,is a perennial relative of Arabidopsis thaliana native to
 largely undisturbed habitats with two geographic and ecologically
 divergence subspecies. Here we delineate the evolutionary processes
 driving genetic diversity and population differentiation in this species.
 Results: Using whole genome re-sequencing data from 517 Boechera stricta
 accessions, we identify four genetic groups that diverged around 30 - 180
 thousand years ago, with long-term small effective population sizes and
 recent population expansion after the Last Glacial Maximum. We find three
 genomic regions with elevated nucleotide diversity, totaling about 10% of
 the genome. These three regions of elevated nucleotide diversity show
 excess of intermediate-frequency alleles, higher absolute divergence (dXY)
 and lower relative divergence (FST) than genomic background, and
 significant enrichment in immune-related genes, reflecting long-term
 balancing selection. Scattered across the genome we also find regions with
 both high FST and DXY among groups, termed FST-islands. Population genetic
 signatures indicate that FST-islands with elevated divergence, which have
 experienced directional selection, are derived from divergent sorting of
 ancient polymorphisms. Conclusions: Our results suggest that long-term
 balancing selection on disease resistance genes may have maintained
 ancestral haplotypes across different geographical lineages, and unequal
 sorting of balanced polymorphisms may have generated genomic regions with
 elevated divergence. This study highlights the importance of ancestral
 balanced polymorphisms as crucial components of genome-wide variation.
description: SNPs genotyped in this
 studyThis file contains
 4,125,395 high-quality SNPs genotyped in this study. For each SNP, the
 location (Scaffold name and position on scaffold), and reference and
 alternative alleles were provided.Boechera_stricta.snp.gzGeographical location of 517 sequenced Boechera stricta accessions.This file contains geographical information of 517 sequenced B. stricta accessions. 484 genotypes were each assigned into a genetic group based on populaton structure analyses. 33 genotypes were excluded from data analyses due to low data quality, duplicates or incomplete sampling information.Geographical_location_of 517_samples.xlsxpython scriptpython scripts used to estimate Fst and Dxyscript.py.txt
DOI: 10.5281/zenodo.18299875
title: Dataset Respuesta del sector publicitario valenciano a la DANA

description: Esta base de datos recopila el material empírico utilizado en el estudio que analiza la respuesta del sector publicitario valenciano ante la DANA del 29 de octubre de 2024, que provocó lluvias torrenciales en varios municipios de la Comunidad Valenciana. El estudio examina cómo las agencias incorporaron la crisis en sus estrategias comunicativas desde el enfoque del activismo de marca, entendido como la integración del compromiso social en la gestión empresarial y publicitaria.

La base de datos incluye 121 publicaciones relacionadas con la DANA, seleccionadas de un total de 3.771 en Instagram, YouTube y LinkedIn, difundidas durante los ocho meses posteriores al desastre por 110 agencias de publicidad y tres entidades sectoriales (el Colegio Oficial, ComunitAD y Asociación 361º). La muestra se seleccionó mediante una estrategia intencional y sistemática, orientada al sector publicitario organizado y visible, priorizando la identificación de patrones comunicativos significativos sobre la representatividad estadística. Este conjunto de datos es útil para estudiar las dinámicas comunicativas del sector ante una crisis climática reciente y resulta de interés tanto para investigaciones sobre comunicación corporativa en contextos de emergencia como para el análisis de activismo de marca, gestión del compromiso social y estrategias de comunicación digital.
DOI: 10.5281/zenodo.18299874
title: Dataset Respuesta del sector publicitario valenciano a la DANA

description: Esta base de datos recopila el material empírico utilizado en el estudio que analiza la respuesta del sector publicitario valenciano ante la DANA del 29 de octubre de 2024, que provocó lluvias torrenciales en varios municipios de la Comunidad Valenciana. El estudio examina cómo las agencias incorporaron la crisis en sus estrategias comunicativas desde el enfoque del activismo de marca, entendido como la integración del compromiso social en la gestión empresarial y publicitaria.

La base de datos incluye 121 publicaciones relacionadas con la DANA, seleccionadas de un total de 3.771 en Instagram, YouTube y LinkedIn, difundidas durante los ocho meses posteriores al desastre por 110 agencias de publicidad y tres entidades sectoriales (el Colegio Oficial, ComunitAD y Asociación 361º). La muestra se seleccionó mediante una estrategia intencional y sistemática, orientada al sector publicitario organizado y visible, priorizando la identificación de patrones comunicativos significativos sobre la representatividad estadística. Este conjunto de datos es útil para estudiar las dinámicas comunicativas del sector ante una crisis climática reciente y resulta de interés tanto para investigaciones sobre comunicación corporativa en contextos de emergencia como para el análisis de activismo de marca, gestión del compromiso social y estrategias de comunicación digital.
DOI: 10.5061/dryad.js6j0pr
title: Data from: All routes are not created equal: an ungulate’s choice of migration route can influence its survival

description: 1. Our knowledge of migration ecology has progressed quickly in concert
 with technological advances that collect fine-scale movement data through
 time. We now know that migration plays a critical role in the annual
 nutritional cycle of large herbivores and that sustaining functional
 migratory routes is key to long-term conservation. Yet, we lack basic
 information on whether one migratory route may function better than
 another, or more specifically, if choosing one route over another has
 fitness consequences – knowledge that could help inform conservation and
 restoration efforts. 2. Here, we examined how a suite of migratory
 parameters influenced the survival of mule deer (Odocoileus hemionus) that
 shared a common winter range in New Mexico, USA, but migrated to various
 summer ranges in Colorado, USA. We used a Cox proportional hazard model
 and GPS data collected over a 7-year period to investigate whether the
 mortality risk of 66 deer was affected by choice of migratory route,
 summer range, migration distance, speed, or the number of administrative
 boundaries each route crossed. 3. We found mule deer survival was not
 influenced by migratory distance, speed, or number of administrative
 boundaries, but was strongly affected the choice of migratory route and
 summer range. The magnitude of these effects was surprisingly large,
 doubling or tripling mortality risk. Cumulative survival rates showed that
 regardless of summer range, individuals migrating along high-use exterior
 routes had cumulative survival rates approximately 30% lower than
 individuals migrating along high-use interior routes. To our knowledge,
 this is the first direct evidence that a mammal’s choice of migration
 route can influence its probability of survival. 4. Synthesis and
 applications. Our finding that large herbivores may experience up to 3
 times higher mortality risk by using a different migratory route reveals a
 novel link between migration and demography. Importantly, our results also
 suggest that spatially explicit model parameters and predictions could
 help in the conservation and restoration of migratory populations by
 identifying specific migratory routes or seasonal ranges that reduce
 survival.
description: Migratory routes and
 survival parametersData files include: 1) A
 spreadsheet (Final Survival Table) that includes: Year identifier (1-7),
 animal ID (AID), start day interval, stop day interval, death (1 or 0),
 migration distance (MigDis), summer range (SumRange: 1, 2, or 3), high-use
 migration route (A, B, C, D, or E), mean ownership index, and route
 category (threeroute: Exterior, Interior, Low-use) 2) A shapefile
 (HighAndLowUseRoutes.shp) that contains high (GridCode 2) and low-use
 (GridCode 1) population-level migration routes depicted in Fig.1. 3) A
 shapefile (MigrationLinesRisk.shp) that contains predicted survival
 probabilities on individual routes as depicted in
 Fig.3.DryadData.zip
DOI: 10.5061/dryad.7b980d8
title: Data from: Thyroid hormone protects primary cortical neurons exposed to hypoxia by reducing DNA methylation and apoptosis

description: Traumatic Brain Injury (TBI) is associated with disruption of cerebral
 blood flow leading to localized brain hypoxia. Thyroid hormone (TH)
 treatment, administered shortly after injury, has been shown to promote
 neural protection in rodent TBI models. The mechanism of TH protection,
 however, is not established. We used mouse primary cortical neurons to
 investigate the effectiveness and possible pathways of T3-promoted cell
 survival after exposure to hypoxic injury. Cultured primary cortical
 neurons were exposed to hypoxia (0.2% oxygen) for 7 hours with or without
 T3 (5 nM). T3 treatment enhanced DNA 5-hydroxymethylcytosine (5-hmc)
 levels and attenuated the hypoxia-induced increase in DNA 5-methylcytosine
 (5-mc). In the presence of T3, mRNA expression of Tet family genes was
 increased and DNA methyltransferases, (Dnmt) 3a and Dnmt3b, were
 downregulated, compared to conditions in the absence of T3. These
 T3-induced changes decreased hypoxia-induced DNA de novo methylation,
 which reduced hypoxia-induced neuronal damage and apoptosis. We utilized
 RNA-seq to characterize T3-regulated genes in cortical neurons under
 hypoxic conditions and identified 22 genes that were upregulated and 15
 genes that were downregulated. Krupple-like factor 9 (KLF9), a
 multifunctional transcription factor that plays a key role in CNS
 development, was highly upregulated by T3 treatment in hypoxic conditions.
 Knockdown of the KLF9 gene resulted in early apoptosis and abolished the
 beneficial role of T3 in neuronal survival. KLF9 mediates, in part, the
 neuronal protective role of T3. T3 treatment reduces hypoxic damage,
 although pathways that reduce DNA methylation and apoptosis, remains to be
 elucidated.
description: Validation of selected
 genes obtained from RNA-seq by q-PCR.Figure S1. Viladation of
 selected genes obtained from RNA-seq by q-PCR. Primary cortical neurons
 were exposed to hyoixa (0.2% oxygen) for 7 hours either in the presence or
 absence of 5nm T3. Total RNA was isolated from cells, reverse transcribed,
 and evaluated by q-PCR. The q-PCR was performed in triplicates and three
 housekeeping genes were included as controls (GAPDH, B-actin and
 cyclophilin A).supplemental figure
 1.tif
DOI: 10.5061/dryad.m2mf542
title: Data from: Quantity and quality of seed dispersal by a large arboreal frugivore in small and large Atlantic forest fragments

description: Seed dispersal is a key process driving the structure, composition, and
 regeneration of tropical forests. Larger frugivores play a crucial role in
 community structuring by dispersing large seeds not dispersed by smaller
 frugivores. We assessed the hypothesis that brown howler monkeys (Alouatta
 guariba clamitans) provide seed dispersal services for a wide assemblage
 of plant species in both small and large Atlantic forest fragments.
 Although fruit availability often decreases in small fragments compared
 with large ones, we predicted that brown howlers are efficient seed
 dispersers in quantitative and qualitative terms in both forest types
 given their high dietary flexibility. After a 36-month study period and
 2,962 sampling hours, we found that howlers swallowed and defecated intact
 the vast majority of seeds (96%-100%) they handled in all study sites.
 Overall, they defecated ca. 315,600 seeds belonging to 98 species
 distributed in eight growth forms. We estimated that each individual
 howler dispersed an average of 143 (SD = 49) seeds &gt;2 mm per day or
 52,052 (SD = 17,782) seeds per year. They dispersed seeds of 58% to 93% of
 the local assemblages of fleshy-fruit trees. In most cases, the richness
 and abundance of seed species dispersed was similar between small and
 large fragments. However, groups inhabiting small fragments tended to
 disperse a higher diversity of seeds from rarely consumed fruits than
 those living in large fragments. We conclude that brown howlers are
 legitimate seed dispersers for most fleshy-fruit species of the angiosperm
 assemblages of their habitats, and that they might favor the regeneration
 of Atlantic forest fragments with the plentiful amount of intact seeds
 that they disperse each year.
description: Dataset_seeds_dispersedHere we provided data on seed dispersal by six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (&lt;10 ha: S1, S2, and S3) and three large (&gt;90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.Dataset_seed_handlingHere we provided data on seed/fruit handling by six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (&lt;10 ha: S1, S2, and S3) and three large (&gt;90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.