cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qq340d4
title: Data from: Top–down limits on prey populations may be more severe in larger prey species, despite having fewer predators

description: Variation in the vulnerability of herbivore prey to predation is linked to
 body size, yet whether this relationship is size‐nested or
 size‐partitioned remains debated. If size‐partitioned, predators would be
 focused on prey within their preferred prey size range. If size‐nested,
 smaller prey species should become increasingly more vulnerable because
 increasingly more predators are capable of catching them. Yet, whether
 either of these strategies manifests in top‐down prey population
 limitation would depend both on the number of potential predator species
 as well as the total mortality imposed. Here we use a rare ecosystem scale
 “natural experiment” comparing prey population dynamics between a period
 of intense predator persecution and hence low predator densities and a
 period of active predator protection and population recovery. We use three
 decades of data on herbivore abundance and distribution to test the role
 of predation as a mechanism of population limitation among prey species
 that vary widely in body size. Notably, we test this within one of the few
 remaining systems where a near‐full suite of megaherbivores occur in high
 density and are thus able to include a thirtyfold range in herbivore body
 size gradient. We test whether top‐down limitation on prey species of
 particular body size leads to compositional shifts in the mammalian
 herbivore community. Our results support both size‐nested and
 size‐partitioning predation but suggest that the relative top‐down
 limiting impact on prey populations may be more severe for intermediate
 sized species, despite having fewer predators than small species. In
 addition we show that the gradual recovery of predator populations shifted
 the herbivore community assemblage towards large‐bodied species and has
 led to a community that is strongly dominated by large herbivore biomass.
description: Le_Roux_et_al_2019_ECOGRAPHY_42(1-10)See txt file
DOI: 10.5061/dryad.44v7p60
title: Data from: Small logging roads do not restrict movements of forest rats in Bornean logged forests

description: Selective logging is driving the proliferation of roads throughout
 tropical rainforests, particularly narrow, unpaved logging roads. However,
 little is known about the extent of road edge effects or their influence
 on the movements of tropical understory animal species. Here, we used
 forest rats to address the following questions: (1) Does the occupancy of
 rats differ from road edges to forest interior within logged forests? (2)
 Do roads inhibit the movements of rats within these forests? We
 established trapping grids along a road edge-to-forest interior gradient
 at four roads and in three control sites within a logged forest in Sabah,
 Malaysia. To quantify the probability of road crossing, rats were
 captured, translocated across a road, and then recaptured on subsequent
 nights. We caught 216 individuals of eight species on 3024 trap nights.
 Rat occupancy did not differ across the gradient from road edge to
 interior, and 48 percent of the 105 translocated individuals crossed the
 roads and were recaptured. This proportion was not significantly different
 from that of rats returning in control sites (38% of 60 individuals),
 suggesting that small roads were not barriers to rat movements within
 logged forests. Subadults were significantly more likely to return from
 translocation than adults in both road and control sites. Our results are
 encouraging for the ecology of small mammal communities in heavily logged
 forests, because small logging roads do not restrict the movements of rats
 and therefore are unlikely to create an edge effect or influence habitat
 selection.
description: Mammal_roads_SAFEproject_2016File contains: Information on the small mammals caught, location, distance from the edge, morphometric information.
DOI: 10.34740/kaggle/dsv/14639584
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.n090827
title: Data from: Integrating reproductive phenology in Ecological Niche Models changed the predicted future ranges of a marine invader

description: Aim: Phenology of a wide diversity of organisms has a dependency on
 climate, usually with reproductive periods beginning earlier in the year
 and lasting longer at lower latitudes. Temperature and day length are
 known environmental drivers of the reproductive timing of many species.
 Hence, reproductive phenology is sensitive to warming and is important to
 be considered for reliable predictions of species distributions. This is
 particularly relevant for rapidly spreading non-indigenous species (NIS).
 In this study, we forecast the future ranges of a NIS, the seaweed
 Sargassum muticum, including its reproductive phenology. Location: Coastal
 areas of the Northern Hemisphere (Pacific and Atlantic oceans). Methods:
 We used ecological niche modelling to predict the distribution of S.
 muticum under two scenarios forecasting limited (RCP 2.6) and severe (RCP
 8.5) future climate changes. We then refined our predictions with a hybrid
 model using sea surface temperature constraints on reproductive phenology.
 Results: Under the most severe climate change scenario, we predicted
 northward expansions which may have significant ecological consequences
 for subarctic coastal ecosystems. However, in lower latitudes, habitats
 currently occupied by S. muticum will no longer be suitable, creating
 opportunities for substantial community changes. The temperature
 constraints imposed by the reproductive window were shown to restrict the
 modelled future species expansion strongly. Under the RCP 8.5 scenario,
 the total range area was expected to increase by 61.75 % by 2100, but only
 by 1.63 % when the reproductive temperature window was considered. Main
 conclusions: Altogether these results exemplify the need to integrate
 phenology better to improve the prediction of future distributional shifts
 at local and regional scales.
description: Appendix S1 Occurrence
 data Sargassum muticumDatabase of occurrence
 records compiled for Sargassum muticum.
DOI: 10.5061/dryad.d8vs845
title: Data from: Nrf2 ameliorates DDC-induced sclerosing cholangitis and biliary fibrosis and improves the regenerative capacity of the liver.

description: The Nrf2 pathway protects against oxidative stress and induces
 regeneration of various tissues. Here, we investigated whether Nrf2
 protects from sclerosing cholangitis and biliary fibrosis and
 simultaneously induces liver regeneration. Diet containing
 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) was fed to Nrf2-KO mice
 (Nrf2-/-), mice with liver-specific hyper-activated Nrf2 (HKeap1-/-) and
 wild type (WT) littermates to induce cholangitis, liver fibrosis, and oval
 cell expansion. HKeap1-/--mice were protected from almost all DDC-induced
 injury compared to WT and Nrf2-/-. Liver injury in Nrf2-/- and WT mice was
 mostly similar, albeit Nrf2-/- suffered more from DDC diet as seen for
 several parameters. Nrf2 activity was especially important for the
 expression of the hepatic efflux transporters Abcg2 and Abcc2-4, which are
 involved in hepatic toxin elimination. Surprisingly, cell proliferation
 was more enhanced in Nrf2-/-- but also HKeap1-/--mice compared to WT.
 Interestingly, Nrf2-/--mice failed to sufficiently activate oval cell
 expansion after DDC-treatment and showed almost no resident oval cell
 population under control conditions. The resident oval cell population of
 untreated HKeap1-/--mice was increased and DDC-treatment resulted in a
 stronger oval cell expansion compared to WT. We provide evidence that Nrf2
 activation protects from DDC-induced sclerosing cholangitis and biliary
 fibrosis. Moreover, our data establish a possible role of Nrf2 in oval
 cell expansion.
description: Fig. S1 - Cre
 verification Ai9 mouseData of Cre validation
 using Ai9 Cre reporter gene (tdTOMATO) mice. Cre-derived TOMATO
 fluorescence was detected with an IVIS whole animal imager as well as
 microscopically.Fig. S2 - IF higher
 resolutionHigher magnification of
 the immunofluorescence staining shown in Fig. 6 from DDC-treated
 mice.Fig.
 S2 - IF_higher resolution.pdfFig. S3 - A6 IF HKeap1
 Nrf2 double-KOA6 immunoreactivity in
 livers of HKeap1-/-::Nrf2-/- mice under control
 conditions.Fig. S3 - A6 IF HKeap1_Nrf2
 dKO.pdfFragoulis et al. - Nrf2
 protects against DDC (TOXSCI-18-0647.R3)_supplements
DOI: 10.7910/dvn/sgi0vk
title: Linked Multi-Model Data on Russian Domestic and Foreign Policy Speeches

description: This Dataverse entry incldues a dataset of interlinked multimodal political communications from the Russian government, addressing persistent deficiencies in the availability of social text- and image-based data for authoritarian politics contexts. The dataset comprises two large corpora of official speeches delivered by senior actors within the Kremlin and the Russian Ministry of Foreign Affairs over multiple decades. For each speech, we provide Russian- and English-language texts, associated images and captions where available, and harmonized metadata including (e.g.) dates, speakers, (geo)locations, and official government content tags. Unique identifiers link images to speeches and align Russian and English versions of the same communication texts. We further augment these linked datasets with validated topical annotations for both speech texts and speech images, which are generated via transformer-based multimodal topic modeling and refined by a Russian politics expert. The resulting data resources support multimodal, multilingual, temporal, and/or spatial analyses of (authoritarian) political communication and offer a valuable testbed for social science research and large language model (LLM) applications in political domains.
DOI: 10.5061/dryad.21b52d0
title: Data from: Diurnal variation in the production of vocal information about food supports a model of social adjustment in wild songbirds

description: Wintering songbirds have been widely shown to make economic foraging
 decisions to manage the changing balance of risks from predation and
 starvation over the course of the day. In this study, we ask whether the
 communication and use of information about food availability differ
 throughout the day. First, we assessed temporal variation in food-related
 vocal information produced in foraging flocks of tits (Paridae) using
 audio recordings at RFID-equipped feeding stations. Vocal activity was
 highest in the morning and decreased into the afternoon. This pattern was
 not explained by there being fewer birds present, as we found that group
 sizes increased over the course of the day. Next, we experimentally tested
 the underlying causes for this diurnal calling pattern. We set up bird
 feeders with or without playback of calls from tits, either in the morning
 or in the afternoon, and compared latency to feeder discovery,
 accumulation of flock members, and total number of birds visiting the
 feeder. Irrespective of time of day, playbacks had a strong effect on all
 three response measures when compared to silent control trials,
 demonstrating that tits will readily use vocal information to improve food
 detection throughout the day. Thus, the diurnal pattern of foraging
 behaviour did not appear to affect use and production of food-related
 vocalizations. Instead, we suggest that, as the day progresses and
 foraging group sizes increase, the costs of producing calls at the food
 source (e.g. competition and attraction of predators) outweigh the
 benefits of recruiting group members (i.e. adding individuals to large
 groups only marginally increases safety in numbers), causing the observed
 decrease in vocal activity into the afternoon. Our findings imply that
 individuals make economic social adjustments based on conditions of their
 social environment when deciding to vocally recruit group members.
description: example
 callsParid calls recorded at
 feeding stations. 1: frequency-modulated churr call, 2: churr call with
 introductory tonal elements), 3: three-note churr call, 4: three-note
 chirp call, 5 and 6: ptew call and complete dä/D call with introductory
 tonal element and dä/D-elementsHillemann et al 2019
 Parid diurnal patterns at feederData and R code
 underlying the analysis of Parid diurnal patterns at feeders (number of
 individuals and number of calls recorded throughout the
 day)Hillemann et al 2019
 Parid playbackData and R code
 underlying the analysis of the playback experiment
DOI: 10.5061/dryad.p2gs002
title: Data from: Metapopulation vicariance, age of island taxa and dispersal: a case study using the pacific plant genus Planchonella (Sapotaceae)

description: Oceanic islands originate from volcanism or tectonic activity without
 connections to continental landmasses, are colonized by organisms, and
 eventually vanish due to erosion and subsidence. Colonization of oceanic
 islands occurs through long-distance dispersals or metapopulation
 vicariance, the latter resulting in lineages being older than the islands
 they inhabit. If metapopulation vicariance is valid, island ages cannot be
 reliably used to provide maximum age constraints for molecular dating. We
 explore the relationships between the ages of members of a widespread
 plant genus (Planchonella, Sapotaceae) and their host islands across the
 Pacific to test various assumptions of dispersal and metapopulation
 vicariance. We sampled three nuclear DNA markers from 156 accessions
 representing some 100 Sapotaceae taxa, and analyzed these in BEAST with a
 relaxed clock to estimate divergence times and with a phylogeographic
 diffusion model to estimate range expansions over time. The phylogeny was
 calibrated with a secondary point (the root) and fossils from New Zealand.
 The dated phylogeny reveals that the ages of Planchonella species are, in
 most cases, consistent with the ages of the islands they inhabit.
 Planchonella is inferred to have originated in the Sahul Shelf region, to
 which it back-dispersed multiple times. Fiji has been an important source
 for range expansion in the Pacific for the past 23 myr. Our analyses
 reject metapopulation vicariance in all cases tested, including between
 oceanic islands, evolution of an endemic Fiji–Vanuatu flora, and westward
 rollback vicariance between Vanuatu and the Loyalty Islands. Repeated
 dispersal is the only mechanism able to explain the empirical data. The
 longest (8900 km) identified dispersal is between Palau in the Pacific and
 the Seychelles in the Indian Ocean, estimated at 2.2 Ma (0.4–4.8 Ma). The
 first split in a Hawaiian lineage (P. sandwicensis) matches the age of
 Necker Island (11.0 Ma), when its ancestor diverged into two species that
 are distinguished by purple and yellow fruits. Subsequent establishment
 across the Hawaiian archipelago supports, in part, progression rule
 colonization. In summary, we found no explanatory power in metapopulation
 vicariance and conclude that Planchonella has expanded its range across
 the Pacific by long-distance dispersal. We contend that this will be seen
 in many other groups when analyzed in detail.
description: Supplementary Appendix
 S1Vouchers and GenBank
 accession numbers.Supplementary Appendix
 S2Aligned data
 matrix.Supplementary Appendix
 S3Visualization KML-file
 to be used in Google Earth.Supplementary Appendix
 S5Avi-film showing
 Imperial-pigeon in New Caledonia swallowing Planchonella endlicheri
 fruit.Supplementary Appendix
 S4
DOI: 10.5061/dryad.4h98fq7
title: Data from: Time of emergence of novel climates for North American migratory bird populations

description: To better understand the ecological implications of global climate change
 for species that display geographically and seasonally dynamic
 life-history strategies, we need to determine where and when novel
 climates are projected to first emerge. Here, we use a multivariate
 approach to estimate time of emergence (ToE) of novel climates based on
 three climate variables (precipitation, minimum and maximum temperature)
 at a weekly temporal resolution within the Western Hemisphere over a
 280-year period (2021-2300) under a high emissions scenario (RCP8.5). We
 intersect ToE estimates with weekly estimates of relative abundance for 77
 passerine bird species that migrate between temperate breeding grounds in
 North America and southern tropical and subtropical wintering grounds
 using observations from the eBird citizen-science database. During the
 non-breeding season, migrants that winter within the tropics are projected
 to encounter novel climates during the second half of this century.
 Migrants that winter in the subtropics are projected to encounter novel
 climates during the first half of the next century. During the beginning
 of the breeding season, migrants on their temperate breeding grounds are
 projected to encounter novel climates during the first half of the next
 century. During the end of the breeding season, migrants are projected to
 encounter novel climates during the second half of this century. Thus,
 novel climates will first emerge ca. 40-50 years earlier during the second
 half of the breeding season. These results emphasize the large seasonal
 and spatial variation in the formation of novel climates, and the
 pronounced challenges migratory birds are likely to encounter during this
 century, especially on their tropical wintering grounds and during the
 transition from breeding to migration. When assessing the ecological
 implications of climate change, our findings emphasize the value of
 applying a full annual cycle perspective using standardized metrics that
 promote comparisons across space and time.
description: ToE_analysis_resultsResults from the time of emergence (ToE) analysis for 77 migratory bird species by week (see Fig. 6). The field Class identifies the three classes of species considered in the analysis. The fields with U and L identify the upper and lower limits of the 95% confidence bands for each metric.
DOI: 10.5061/dryad.75t5382
title: Data from: The temporal dynamics and infectiousness of subpatent Plasmodium falciparum infections in relation to parasite density

description: Malaria infections occurring below the limit of detection of standard
 diagnostics are common in all endemic settings. However, key questions
 remain surrounding their contribution to sustaining transmission and
 whether they need to be detected and targeted to achieve malaria
 elimination. In this study we analyse a range of malaria datasets to
 quantify the density, detectability, course of infection and
 infectiousness of subpatent infections. Asymptomatically infected
 individuals have lower parasite densities on average in low transmission
 settings compared to individuals in higher transmission settings. In
 cohort studies, subpatent infections are found to be predictive of future
 periods of patent infection and in membrane feeding studies, individuals
 infected with subpatent asexual parasite densities are found to be
 approximately a third as infectious to mosquitoes as individuals with
 patent (asexual parasite) infection. These results indicate that subpatent
 infections contribute to the infectious reservoir, may be long lasting,
 and require more sensitive diagnostics to detect them in lower
 transmission settings.
description: shareable_data_master_fig1_2_3Parasite density data for each study and positivity by microscopy or RDT. Used for figures 1,2,3shareable_data_master_fig4Longitudinal data with positivity by PCR and microscopy. Used for figure 4.shareable_data_master_fig5Data on probability of being slide-positive in the future. Used for figure 5.shareable_data_master_fig6Gametocyte and asexual parasite density data. Used for figure 6.shareable_data_master_fig7_8Infectivity data and asexual parasite density. Used for figures 7,8.shareable_data_master_S1_seasonalData on seasonal variation in slide positivity. Used for supplementary figure 1.
DOI: 10.5061/dryad.27js55v
title: Data from: Genomic, ecological, and morphological approaches to investigating species limits: a case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes

description: A wide variety of species are distinguished by slight color variations.
 However, molecular analyses have repeatedly demonstrated that coloration
 does not always correspond to distinct evolutionary histories between
 closely related groups, suggesting that this trait is labile and can be
 misleading for species identification. In the present study, we analyze
 the evolutionary history of sister species of Prionurus surgeonfishes in
 the Tropical Eastern Pacific (TEP), which are distinguished by the
 presence or absence of dark spots on their body. We examined the species
 limits in this system using comparative specimen-based approaches, a
 mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved
 Elements), and abiotic niche comparisons. The results indicate there is a
 complete overlap of meristic counts and morphometric measurements between
 the two species. Further, we detected multiple individuals with
 intermediate spotting patterns suggesting that coloration is not
 diagnostic. Mitochondrial data recovered a single main haplotype shared
 between the species and all locations resulting in a complete lack of
 structure (ST = 0). Genomic analyses also suggest low levels of genetic
 differentiation (FST = 0.013), and no alternatively fixed SNPs were
 detected between the two phenotypes. Furthermore, niche comparisons could
 not reject niche equivalency or similarity between the species. These
 results suggest that these two phenotypes are conspecific and widely
 distributed in the TEP. Here we recognize Prionurus punctatus Gill 1862 as
 a junior subjective synonym of P. laticlavius (Valenciennes 1846). The
 underlying causes of phenotypic variation in this species is unknown.
 However, this system gives insight into general evolutionary dynamics
 within the TEP.
description: COI
 alignmentAlignment file for mtDNA
 COI sequences.COI_alignment.nexEnvironmental_PC_axis1Principal component axis 1 for all environmental layers used in niche comparisons.pc1_all.ascEnvironmental_PC_axis2Principal component axis 2 of all environmental layers used in niche comparisons.pc2_all.ascLocality_pointsLocality points for Prionurus laticlavius and P. punctatus prior to niche modeling. Duplicates were filtered out in the modeling script.locality_points.xlsxConcatenated UCE alignment for phylogenetic approach in studyUCE alignment file for phylogenetic analysis in RAxML. This is a 70% complete alignment file.70_percent_for_RAxML.phylipComplete SNP file after all filteringThis VCF file contains all of the SNPs for P. laticlavius and P. punctatus after all quality and maf filtering (P. biafraensis outgrip not included in this file). Datasets for the manuscript used a single randomly chosen SNP for each UCE locus taken from this file.Nobia-maf02_SNPS.vcf