cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q86rj
title: Data from: Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas)

description: Amphibians support symbiotic bacterial communities on their skin that
 protect against a range of infectious pathogens, including the amphibian
 chytrid fungus. The conditions under which amphibians are maintained in
 captivity (e.g. diet, substrate, enrichment) in ex situ conservation
 programmes may affect the composition of the bacterial community. In
 addition, ex situ amphibian populations may support different bacterial
 communities in comparison to in situ populations of the same species. This
 could have implications for the suitability of populations intended for
 reintroduction, as well as the success of probiotic bacterial inoculations
 intended to provide amphibians with a bacterial community that resists
 invasion by the chytrid fungus. We aimed to investigate the effect of a
 carotenoid-enriched diet on the culturable bacterial community associated
 with captive red-eyed tree frogs (Agalychnis callidryas) and make
 comparisons to bacteria isolated from a wild population from the Chiquibul
 Rainforest in Belize. We successfully showed carotenoid availability
 influences the overall community composition, species richness and
 abundance of the bacterial community associated with the skin of captive
 frogs, with A. callidryas fed a carotenoid-enriched diet supporting a
 greater species richness and abundance of bacteria than those fed a
 carotenoid-free diet. Our results suggest that availability of carotenoids
 in the diet of captive frogs is likely to be beneficial for the bacterial
 community associated with the skin. We also found wild A. callidryas
 hosted more than double the number of different bacterial species than
 captive frogs with very little commonality between species. This suggests
 frogs in captivity may support a reduced and diverged bacterial community
 in comparison to wild populations of the same species, which could have
 particular relevance for ex situ conservation projects.
description: Bacterial communities on
 Agalychnis callidryasBacterial counts from
 swab cultures of captive Agalychnis callidryas grown on R2A media. Frogs
 were fed on carotenoid enriched or normal diets. Data are divided by
 gender.Antwis data for
 Dryad.xls
DOI: 10.5061/dryad.969q5
title: Data from: Bergmann’s Rule rules body size in an ectotherm: heat conservation in a lizard along a 2200-meter elevational gradient

description: Bergmann's Rule predicts larger body sizes in colder habitats,
 increasing organisms’ ability to conserve heat. Originally formulated for
 endotherms, it is controversial whether Bergmann's Rule may be
 applicable to ectotherms, given that larger ectotherms show diminished
 capacity for heating up. We predict that Bergmann's Rule will be
 applicable to ectotherms when the benefits of a higher conservation of
 heat due to a larger body size overcompensate for decreased capacity to
 heating up. We test this hypothesis in the lizard Psammodromus algirus,
 which shows increased body size with elevation in Sierra Nevada (SE
 Spain). We measured heating and cooling rates of lizards from different
 elevations (from 300 to 2500 meters above sea level) under controlled
 conditions. We found no significant differences in the heating rate along
 an elevational gradient. However, the cooling rate diminished with
 elevation and body size: highland lizards, with larger masses, have a
 higher thermal inertia for cooling, which allows them to maintain heat for
 more time and keep a high body temperature despite the lower thermal
 availability. Consequently, the net gaining of heat increased with
 elevation and body size. This study highlights that the heat conservation
 mechanism for explaining Bergmann's Rule works and is applicable to
 ectotherms, depending on the thermal benefits and costs associated with
 larger body sizes.
description: Tasas calentamiento
 Dryad
DOI: 10.5281/zenodo.18383841
title: COVID-19-Todesfälle in Deutschland

description: Im Datensatz "COVID-19-Todesfälle in Deutschland" des Robert Koch-Instituts werden täglich aktualisierte Informationen zu COVID-19-bedingten Todesfällen in Deutschland bereitgestellt. Die Datenerhebung erfolgt im Rahmen des Infektionsschutzgesetzes (IfSG). Der Datensatz umfasst aggregierte Todesfallzahlen nach Berichtsdatum, Altersgruppen und Bundesländern und wird ergänzt durch den Fall-Verstorbenen-Anteil. Der Datensatz ermöglicht fundierte Analysen zur Bewertung der Krankheitsschwere und Verbreitung von COVID-19 in Deutschland.
DOI: 10.5061/dryad.5q034
title: Data from: Brain regions associated with visual cues are important for bird migration

description: Long-distance migratory birds have relatively smaller brains than
 short-distance migrants or residents. Here, we test whether reduction in
 brain size with migration distance can be generalized across the different
 brain regions suggested to play key roles in orientation during migration.
 Based on 152 bird species, belonging to 61 avian families from six
 continents, we show that the sizes of both the telencephalon and the whole
 brain decrease, and the relative size of the optic lobe increases, while
 cerebellum size does not change with increasing migration distance. Body
 mass, whole brain size, optic lobe size and wing aspect ratio together
 account for a remarkable 46% of interspecific variation in average
 migration distance across bird species. These results indicate that visual
 acuity might be a primary neural adaptation to the ecological challenge of
 migration.
description: Brain region sizes, body
 mass, wing morphology and migration distance in 152 species of
 birdsThis table contain data
 on 152 species of birds, from 61 avian orders and from six continents.
 Data covers: migration distance (km), body mass (g), brain mass (g), size
 of cerebellum (g), size of telencephalon (g), size of optic lobe (g), wing
 aspect ratio (dimensionless) and wing area (m2).Supplementary
 Dataset.xls
DOI: 10.5061/dryad.6824n
title: Data from: Ecological relevance of energy metabolism: transcriptional responses in energy sensing and expenditure to thermal and osmotic stresses in an intertidal limpet

description: For rocky intertidal species that experience changes in a number of
 potential stressors seasonally and during the tidal cycle, sensing
 cellular energy status and modulating it adaptively may be crucial for
 responding to stressor effects. However, the responses of energy
 metabolism of intertidal species to multiple sublethal stressors are still
 unclear. Here, we examined gene expression profiles of biomarkers related
 to sensing of cellular energy status and regulation of catabolism and
 energy expenditure in a mid-intertidal limpet Cellana toreuma for
 elucidating the species’ cellular energy responses stresses from high
 temperature, desiccation and rainfall. Expression levels of genes encoding
 metabolic regulators [two subunits of AMP-activated protein kinase, ampkα,
 ampkβ; Fu gene inhibition axis formation, axin; two sirtuins,
 NAD-dependent deacetylase sirtuin-1 (sirt1); NAD-dependent deacetylase
 sirtuin-5 (sirt5)], metabolic enzymes (hexokinase, hk; pyruvate kinase,
 pk; isocitrate dehydrogenase, idh) and heat shock protein 70 (hsp70) were
 quantified in specimens exposed to different temperatures and
 aerial/freshwater spray conditions. Based on the gene expression patterns,
 all individuals could be divided into three groups with divergent cellular
 energy status, indicating that the selected target genes are appropriate
 indicators of cellular metabolism. The divergent gene expression patterns
 indicated a sequence in which individuals from group 1, group 2 and group
 3 were faced with increasing energy stress. The frequency distributions of
 individuals in the three groups were different among different time points
 and treatments, indicating that high temperature, desiccation, and
 rainfall, singly or in combination, could cause energy stress. Compared to
 the high percentage (100%) of individuals placed in the highest-stress
 group (group 3), after 2 h of freshwater spray at 18 °C, the lower
 percentage (77·8%) of individuals in group 3 after 2 h of freshwater spray
 at 30 °C indicated the existence of interactive effects of high
 temperature and rain; high temperature resulted in a lower response of
 cellular energy metabolism to rainfall. Sublethal environmental stresses
 from single stressors such as temperature or osmotic challenges can lead
 to cellular energy stress. Interactions among stressors may lead to a
 complex overall effect on cellular energy status in intertidal species.
description: Gene expression of
 limept Cellana toreuma in different thermal and osmotic
 conditionsGene expression data
 20151128.xlsx
DOI: 10.5061/dryad.8557
title: Data from: Evolution of specialization: a phylogenetic study of host range in the red milkweed beetle (Tetraopes tetraophthalmus)

description: Specialization is common in most lineages of insect herbivores, one of the
 most diverse groups of organisms on earth. To address how and why
 specialization is maintained over evolutionary time, we hypothesized that
 plant defense and other ecological attributes of potential host plants
 would predict the performance of a specialist root feeding herbivore (the
 red milkweed beetle, Tetraopes tetraophthalmus). Using a comparative
 phylogenetic and functional trait approach, we assessed the determinants
 of insect host range across 18 species of Asclepias. Larval survivorship
 decreased with increasing phylogenetic distance from the true host, A.
 syriaca, suggesting that adaptation to plant traits drives specialization.
 Among several root traits measured, only cardenolides (toxic defense
 chemicals) correlated with larval survival, and cardenolides also
 explained the phylogenetic distance effect in phylogenetically controlled
 multiple regression analyses. Additionally, milkweed species having a
 known association with other Tetraopes beetles were better hosts than
 species lacking Tetraopes herbivores, and milkweeds with similar specific
 leaf area values (a trait related to leaf function and habitat
 affiliation) to A. syriaca were better hosts than species having divergent
 values. We thus conclude that phylogenetic distance is an integrated
 measure of phenotypic and ecological attributes of Asclepias species,
 especially defensive cardenolides, which can be used to explain
 specialization and constraints on host shifts over evolutionary time.
description: Rasmann_AgrawalDatafile contains raw and mean value of phenotipic data of 18 species of milkweeds (Asclepias spp.) collected from common garden experiments.
DOI: 10.5061/dryad.bb7q8
title: Data from: An experimental comparison of three Towed Underwater Video Systems using species metrics, benthic impact and performance

description: 1. Managing ecological systems, which operate over large spatial scales is
 inherently difficult and often requires sourcing data from different
 countries and organizations. The assumption might be made that data
 collected using similar methodologies are comparable but this is rarely
 tested. Here, benthic video data recorded using different towed underwater
 video systems (TUVSs) were experimentally compared. 2. Three technically
 different TUVSs were compared on different seabed types (rocky, mixed
 ground and sandy) in Kingmere Marine Conservation Zone, off the south
 coast of England. For each TUVS, species metrics (forward facing camera),
 seabed impact (backward facing camera).and operational performance
 (strengths and limitations of equipment and video footage) were compared
 with the aim of providing recommendations on their future use and
 comparability of data between different systems. 3. Statistically
 significant differences between species richness, density, cover and
 assemblage composition were detected amongst devices and were believed to
 be mostly due to their optical specifications. As a result of their high
 image definition and large field of vision both the Benthic Contacting
 Heavy and benthic tending TUVS provided good quality footage and
 ecological measurements. However the heaviest TUVS proved difficult to
 operate on irregular ground and was found to cause the most impact to the
 seabed. The lightest TUVS (Benthic Contacting Light) struggled to maintain
 contact with the seabed. The benthic tending TUVS was able to fly over
 variable seabed relief and was comparably the least destructive. 4.
 Results from this study highlight that particular care should be given to
 sled and optic specifications when developing a medium or long term MPA
 monitoring programme. Furthermore, when using data gathered from multiple
 sources to test ecological questions, different equipment specifications
 may confound observed ecological differences. 5. A benthic tending TUVS is
 recommended for benthic surveys over variable habitat types, particularly
 in sensitive areas such as marine protected areas.
description: Impact, Taxa, Cover,
 Count and Assemblage dataImpact, Taxa, Cover and
 count data show metrics as described in the paper. The assemblage data is
 averaged over frame grabs per site as described in the paper. Details of
 Towed Underwater Video System, Habitat, Area and Site are included.
 Metrics are labelled on separate tabs in the same file.Panache data for dryad
 storage.xlsx
DOI: 10.5061/dryad.p2gq8
title: Data from: "Disentangling nestedness" disentangled

description: Analytical research indicates that the ‘nestedness’ of mutualistic
 networks facilitates the coexistence of species by minimizing the costs of
 competition relative to the benefits of facilitation. In contrast, James
 et al. recently argued that a more parsimonious explanation exists: the
 persistence of a community and its constituent species depends more on
 their having many interactions (high connectance and high degree,
 respectively) than for these interactions to be organized in any
 particular manner. Here we demonstrate that these conclusions are an
 unintended consequence of the fact that the methodology of ref. 2 directly
 changed the number of interactions of each species—and hence their
 expected persistence. When these changes are taken into account, we find a
 significant, positive relationship between nestedness and network
 persistence that reconfirms the importance of nestedness in mutualistic
 communities. There is a Reply to this Brief Communication Arising by
 James, A., Pitchford, J. W. & Plank, M. J. Nature 500,
 http://dx.doi.org/10.1038/nature12381 (2013).
description: Network data, Dynamic
 simulation code, and Statistical analysis codeanalysis-code.zip
DOI: 10.5061/dryad.8nm35
title: Data from: Late Oligocene caviomorph rodents from Contamana, Peruvian Amazonia

description: The Deseadan South American Land Mammal Age (late Early Oligocene – Late
 Oligocene) attests to a time of great diversification in the caviomorph
 rodent fossil record. Nevertheless, Deseadan rodent-bearing localities in
 Neotropical lowlands are few and poorly known. Here we describe the rodent
 assemblages from two Late Oligocene localities, near Contamana, Loreto,
 Peru. Seven taxa are new to science: Palaeosteiromys amazonensis gen. et
 sp. nov., Plesiosteiromys newelli gen. et sp. nov., Loretomys minutus gen.
 et sp. nov., Scleromys praecursor sp. nov, Ucayalimys crassidens gen. et
 sp. nov., Chambiramys sylvaticus gen. et sp. nov. and Chambiramys
 shipiborum gen. et sp. nov. These rodent faunas show that caviomorphs were
 relatively diverse in Peruvian Amazonia during the Late Oligocene, with
 the co-occurrence of at least three extant superfamilies: Erethizontoidea,
 Octodontoidea and Chinchilloidea. Additionally, they mark the earliest
 known occurrences of Scleromys, of a small erethizontid closely related to
 Microsteiromys and of an adelphomyine closely reminiscent of Ricardomys
 (all taxa previously restricted to Miocene localities thus far). They also
 document a form potentially related to Eosallamys (previously known from
 around the Eocene–Oligocene transition at Santa Rosa in Peruvian
 Amazonia). Finally, the geographical range of Adelphomyinae and of
 Deseadomys is widely expanded to the lower latitudes of South America for
 the Deseadan interval. The latter elements, in addition to the record of a
 very primitive species of Scleromys, suggest the absence of
 palaeogeographical and palaeoenvironmental barriers within the southern
 cone of South America before the Oligocene–Miocene transition.
description: taxaAppendix S1. Palaeogene
 and Miocene caviomorph taxa used for comparisons in this
 study.
DOI: 10.5061/dryad.s34n8
title: Data from: Immunosenescence and the ability to survive bacterial infection in the red flour beetle Tribolium castaneum

description: 1. In most animals, ageing is associated with a decline in immune function
 (immune senescence). However, different components of the immune system
 seem to age differentially, and many studies do not measure the ultimate
 fitness consequences of immune function after infection. Previous work
 shows that immune function may be traded off with other fitness components
 such as reproduction. It is possible that age alters the nature of these
 trade-offs, particularly in conjunction with factors such as gender and
 mating that can also affect investment in immune function. 2. We tested
 the impact of age, sex and mating on post-infection survivorship in
 Tribolium castaneum flour beetles, as well as the components of baseline
 constitutive innate immunity and external (secreted) immune function in
 uninfected individuals. We also tested whether the reproductive ability of
 uninfected females is traded off with immune function (baseline innate and
 external immunity) and post-infection survivorship across age groups. 3.
 We found that age, sex and mating significantly affected immune components
 and infection outcome, although the magnitude and nature of the impact
 varied in each case. We found that older beetles were more susceptible to
 infection by the pathogen Bacillus thuringiensis even though major
 components of the constitutive innate immune defence (antibacterial and
 phenoloxidase activity) remained unchanged or improved with age. Thus,
 these aspects of innate immunity cannot explain the observed decline in
 post-infection survival of older beetles. We did not find trade-offs
 between the reproductive ability of uninfected females and their immune
 function. In contrast to innate immunity, external immunity showed an
 overall decline with age but was also affected by sex and mating. Finally,
 we show that bacterial infection alters external immunity via complex
 interactions between age, sex and mating status. 4. Our work uncovers
 novel interactions between age, sex and mating that can determine the
 evolution and outcome of immunosenescence by affecting the time course of
 relative investment in different immune and fitness components.
description: data
 submissionthe file contains raw
 data used for the analysisData submission
 Dryad.xlsx
DOI: 10.5061/dryad.58mg2
title: Data from: Mating system and genetic diversity of progenies before and after logging: a case study of Bagassa guianensis (Moraceae), a low-density dioecious tree of the Amazonian forest

description: The logging of large trees in tropical forests causes a decrease in the
 density of reproductive individuals, which likely affects the pattern of
 pollen dispersal and the mating system of the remaining trees in the
 population. Here, we investigate the impact of logging on mating system
 and genetic diversity of the low-density, thrip-pollinated, dioecious tree
 Bagassa guianensis within a 500-ha plot at Tapajós National Forest, Pará
 State, Brazil. Mating system parameters of the logged population were
 estimated using mixed-mating model. Six microsatellite loci were used to
 genotype 232 seeds from ten remnant female trees over three seasons (2006,
 2007, and 2008). The data were compared with the mating system of the
 unlogged population of B. guianensis (18 female trees, 488 seeds) in the
 same plot. The overall number of alleles found in the open-pollinated
 progenies decreased after logging (K = 71 before logging and K = 57 after
 logging, considering the three after logging seasons pooled), as well as
 the average number of alleles per locus (A = 11.8 and 9.5, respectively).
 Similarly, the number of private alleles, which is defined in the context
 of this study as the number of alleles observed in the population
 exclusively before or after logging, also decreased after logging (15 and
 1, respectively). However, the average number of alleles per locus and the
 observed and expected heterozygosities were not significantly higher
 before logging than after logging. Logging also did not affect the
 inbreeding of progenies in the population. Somewhat unexpectedly, the
 effective number of pollen donors was consistently higher after (N ep =
 14.5 in 2006, 8.1 in 2007, and 6.3 in 2008) than before logging (N ep =
 3.4), suggesting that the loss of alleles in the population was
 compensated by the higher heterogeneity in the pollen pool after the
 removal of the largest trees by logging. Potential causes explaining the
 patterns found here include the maintenance of large patches of forest
 around the logged plot and the species’ ability to perform long-distance
 pollination by airborne thrips. Maintenance of landscape integrity as
 logged and unlogged forests around the exploited areas is recommended to
 enhance pollen migration and to avoid long-term losses in genetic
 diversity.
description: MLTR_input_Bg
 alinhado_2002_min_6lociGenotypes of Bagassa
 guianensis based on six microsatellite loci; population sampled in
 2012MLTR_input_Bg
 alinhado_2006_MIN_6LOCISix microsatellite loci
 of Bagassa guianensis; population sampled in 2006MLTR_input_Bg
 alinhado_2007_MIN_6LOCISix microsatellite loci
 of Bagassa guianensis; population sampled in 2007MLTR_input_Bg
 alinhado_2008_MIN_6LOCISix microsatellite loci
 of Bagassa guianensis; population sampled in 2006
DOI: 10.5061/dryad.qm7gg
title: Data from: Ants medicate to fight disease

description: Parasites are ubiquitous, and the ability to defend against these is of
 paramount importance. One way to fight diseases is self-medication, which
 occurs when an organism consumes biologically active compounds to clear,
 inhibit or alleviate disease symptoms. Here, we show for the first time
 that ants selectively consume harmful substances (Reactive Oxygen Species,
 ROS) upon exposure to a fungal pathogen, yet avoid these in the absence of
 infection. This increased intake of ROS, while harmful to healthy ants,
 leads to higher survival of exposed ants. The fact that ingestion of this
 substance carries a fitness cost in the absence of pathogens rules out
 compensatory diet choice as the mechanism, and provides evidence that
 social insects medicate themselves against fungal infection, using a
 substance that carries a fitness cost to uninfected individuals.
description: Survival
 dataSurvival of ants fed on
 either control or ROS diet, and afterwards being exposed to either Fungus
 or Control.survivalrosfeeding.txtSpore ViabilityViability of spores after being in contact with varying concentrations of ROS. Spores were counted as either alive or dead in one 'field of view'.sporeviability.txtFood choiceResults of the diet choice of either control or infected ants. The column 'time' depicts hours after treatment.selfmedication4percent.txtROS concentration in bodyROS concentration measurements. Note that these are the raw values straight from the spectrophotometer.Amplex_Red_FF_ROS_06June2015.txtR scriptsR scripts used for final analysis of the data.analysisDRYAD.R