cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6g206
title: Data from: Tracking the history and ecological changes of rising double-crested cormorant populations using pond sediments from islands in eastern Lake Ontario

description: In the Laurentian Great Lakes region, the double-crested cormorant
 (Phalacrocorax auritus) has seen a thousand-fold population increase in
 recent decades. These large colonies of birds now often conflict with
 socioeconomic interests, particularly due to perceived competition with
 fisheries and the destruction of terrestrial vegetation in nesting
 habitats. Here we use dated sediment cores from ponds on islands in
 eastern Lake Ontario that receive waste inputs from dense colonies of
 cormorants and ring-billed gulls (Larus delawarensis) to chronicle the
 population rise of these species and assess their long-term ecological
 impacts. Modern water chemistry sampling from these sites reveals
 drastically elevated nutrient and major ion concentrations compared to
 reference ponds not influenced by waterbirds. Geochemical tracers in dated
 sediment cores, particularly δ15N and chlorophyll-a concentrations, track
 waterbird influences over time. Fossil diatom assemblages were dominated
 by species tolerant of hyper-eutrophic and polluted systems, which is in
 marked contrast to assemblages in reference sites. In addition to
 establishing long-term ecological impacts, this multi-proxy
 paleoecological approach can be used to determine whether islands of
 concern have been long-term nesting sites or were only recently colonized
 by cormorant or ring-billed gull populations across the Great Lakes,
 facilitating informed management decisions about controversial culling
 programs.
description: Stewart et al. raw
 dataIncluded in this file
 are raw species counts used in stratigraphic figures, as well as
 radioisotopic activities used to create dates for sediment
 cores.
DOI: 10.5061/dryad.4vp41
title: Data from: Urban environment shortens telomere length in nestling great tits, Parus major

description: Urban environments are expanding rapidly, and with urbanization come both
 challenges and opportunities for wildlife. Challenges include combating
 the anthropogenic disturbances such as light, noise and air pollution and
 lower availability of natural food sources. The benefits are many,
 including the availability of anthropogenic food sources, breeding boxes
 and warmer temperatures. Thus, depending on the context, urbanization can
 have both positive and negative effects on fitness related traits. It is
 well known that early-life conditions can have lifelong implications on
 fitness; little is however known about development in urban environments.
 We reciprocally cross-fostered urban and rural nestling great tits (Parus
 major L.) to study how growing up in an urban versus rural habitat
 affected telomere length (TL)—a suggested biomarker of longevity. We show,
 for the first time, that growing up in an urban environment significantly
 shortens TL, independently of natal origin (i.e. urban or rural). This
 implies that the urban environment imposes a challenge to developing
 birds, with potentially irreversible effects on lifespan.
description: Data.CrossfosteringData for TL and SMI for cross-fostering nestling at day 15
DOI: 10.5061/dryad.8824sd0
title: Data from: Cattle affect regeneration of the palm species Attalea princeps in a Bolivian forest-savanna mosaic

description: Attalea princeps is an important palm species that shapes the
 forest-savanna mosaic in Beni, Bolivia, because it dominates and shapes
 the two principal forest landscape elements (forest islands and gallery
 forest), and it provides a vital microhabitat, food and nesting source for
 numerous plant and animal species. The forest-savanna mosaic is used for
 extensive grazing, and the palm population is declining on the forest
 islands due to a low regeneration rate, which threatens the maintenance of
 this landscape. We therefore examined the (a)biotic factors that influence
 the population structure of Attalea in the centers and edges of forest
 islands and gallery forests. Ninety-one 0.1 ha plots were established and
 500 palm adults and 3700 juveniles were measured for their size, health
 condition and fire damage. For each plot habitat characteristics, such as
 landscape position, grazing pressure, and soil conditions were measured.
 Attalea population density was significantly lower on the forest islands
 than in the gallery forests, especially in the juvenile life stage. A
 structural equation model showed that juvenile density is positively
 related to the health condition of the juveniles and amount of fruits
 present, where the amount of fruits is positively affected by the
 condition of the adults. Juvenile density is negatively influenced by
 grazing, affecting the health condition of the juvenile, as well as
 organic matter and phosphate availability in the soil. Therefore, it is
 recommended to decrease the grazing pressure by decreasing livestock
 densities, fencing off vulnerable forest islands, or by rotating cattle.
description: Palm and soil
 measurements, Beni savannaThis dataset contains
 plot level data collected in the Barba Azul Nature Reserve, Beni Savanna,
 Bolivia between July and October 2016 as part of the MSc thesis project of
 Iris Hordijk, Fabian Meijer and Esther Nissen. Data on palm abundance and
 condition, juvenile abundance and condition, fruit density, soil
 fertility, general plot characteristics and geographic information are
 measured and recorded. The dataset is owned by the data collectors,
 Wageningen University and the Bolivian NGO Armonía.2016-PlotLevelDataPalmsSoilAndGeneralCharacteristics.csv
DOI: 10.15468/dl.pcy3sp
title: Occurrence Download

description: A dataset containing 610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((65.71493 23.63104,75.49504 6.69214,80.23985 8.80289,74.42988 26.52485,65.71493 23.63104))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Crocodylia"
 ]
}

 The dataset includes 610 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001170-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q7qv2
title: Data from: Experimental demonstration of an Allee effect in microbial populations

description: Microbial populations can be dispersal limited. However, microorganisms
 that successfully disperse into physiologically ideal environments are not
 guaranteed to establish. This observation contradicts the Baas-Becking
 tenet: ‘Everything is everywhere, but the environment selects’. Allee
 effects, which manifest in the relationship between initial population
 density and probability of establishment, could explain this observation.
 Here, we experimentally demonstrate that small populations of Vibrio
 fischeri are subject to an intrinsic demographic Allee effect. Populations
 subjected to predation by the bacterivore Cafeteria roenbergensis display
 both intrinsic and extrinsic demographic Allee effects. The estimated
 critical threshold required to escape positive density-dependence is
 around 5, 20 or 90 cells ml−1 under conditions of high carbon resources,
 low carbon resources or low carbon resources with predation, respectively.
 This work builds on the foundations of modern microbial ecology,
 demonstrating that mechanisms controlling macroorganisms apply to
 microorganisms, and provides a statistical method to detect Allee effects
 in data.
description: R script for data
 analysisThe code associated with
 the manuscript analysis is contained in `DataAnalysis.R’. This file
 contains the maximum likelihood analysis and produces the plots in the
 main text and supplement.DataAnalysis.Rcomplete dataAll data used for analysis is contained in 'completedata.csv'. This file consists of 3 columns. The first 'x' is the natural log transformed value of the inoculum density. The second, 'y', is the binary score of population establishment (1- established; 0- failed to establish). The last column, 'treat', identifies the environmental treatment (1- high carbon, 2- low carbon, 3- low carbon with predation).completedata.csv
DOI: 10.5061/dryad.m9d40
title: Data from: Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy

description: A population genetics approach is used to identify the most likely
 introduction site and introduction pathway for the North American forest
 pathogen Heterobasidion irregulare using 101 isolates from six sites in
 Italy and 34 isolates from five sites in North America. Diversity indices
 based on sequences from ten loci indicate the highest diversity in Italy
 is found in Castelfusano/Castelporziano and that diversity progressively
 decreases with increasing distance from that site. AMOVA, Bayesian
 clustering and principal coordinates analyses based on 12 SSR loci
 indicate high levels of gene flow among sites, high frequency of admixing,
 and fail to identify groups of genotypes exclusive to single locations.
 Cumulatively, these analyses suggest the current infestation is the result
 of multiple genotypes expanding their range from a single site. Based on
 two sequenced loci, a single source site in North America could provide
 enough variability to explain the variability observed in Italy. These
 results support the notion that H. irregulare was introduced originally in
 Castelporziano: because Castelporziano has been sealed off from the rest
 of the world for centuries except for a camp set up by the US military in
 1944, we conclude the fungus may have been transported in infected wood
 used by the military. Finally, spatial autocorrelation analyses using SSR
 data indicate a significant under-dispersion of alleles up to 0.5–10 km,
 while a significant overdispersion of alleles was detected at distances
 over 80 km: these ranges can be used to make predictions on the likely
 dispersal potential of the invasive pathogen.
description: SSR
 repeatsData file including the
 results (number of repeats) of the analysis of 11 SSR loci from haploid
 Heterobasidion irregulare isolates collected from the six pine stands
 reported in the first column. The data file was created with the software
 microsoft excel 2010.Geographical
 coordinatesData file including the
 latitude and longitude coordinates (expressed in UTM) of the collection
 points of the Heterobasidion irregulare isolates submitted to SSR
 analysis.
DOI: 10.5061/dryad.vs213
title: Data from: Phylogenetic distribution of a male pheromone that may exploit a nonsexual preference in lampreys

description: Pheromones are among the most important sexual signals used by organisms
 throughout the animal kingdom. However, few are identified in vertebrates,
 leaving the evolutionary mechanisms underlying vertebrate pheromones
 poorly understood. Pre-existing biases in receivers’ perceptual systems
 shape visual and auditory signaling systems, but studies on how receiver
 biases influence the evolution of pheromone communication remain sparse.
 The lamprey Petromyzon marinus uses a relatively well-understood suite of
 pheromones and offers a unique opportunity to study the evolution of
 vertebrate pheromone communication. Previous studies indicate that male
 signaling with the mating pheromone 3-keto petromyzonol sulfate (3kPZS)
 may exploit a nonsexual attraction to juvenile-released 3kPZS that guides
 migration into productive rearing habitat. Here, we infer the distribution
 of male signaling with 3kPZS using a phylogenetic comparison comprising
 six of ten genera and two of three families. Our results indicate that
 only P. marinus and Ichthyomyzon castaneus release 3kPZS at high rates.
 Olfactory and behavioral assays with P. marinus, I. castaneus and a subset
 of three other species that do not use 3kPZS as a sexual signal indicate
 that male signaling might drive the evolution of female adaptations to
 detect 3kPZS with specific olfactory mechanisms and respond to 3kPZS with
 targeted attraction relevant during mate search. We postulate that 3kPZS
 communication evolved independently in I. castaneus and P. marinus, but
 cannot eliminate the alternative that other species lost 3kPZS
 communication. Regardless, our results represent a rare macroevolutionary
 investigation of a vertebrate pheromone and insight into the evolutionary
 mechanisms underlying pheromone communication.
description: Data for Phylogenetic
 distribution of a male pheromone that may exploit a nonsexual preference
 in lampreysChemistry,
 electrophysiological, and behavioral data from Phylogenetic distribution
 of a male pheromone that may exploit a nonsexual preference in lampreys.
 3kPZS is 3 keto petromyzonol sulfate. Arg is arginine. M is molar. Bc is
 pre-treatment on the control side, Be is pre-treatment on the experimental
 side, Ac is during the 3kPZS treatment on the control side, and Ae is
 during the 3kPZS treatment on the experimental side. Behavior data are in
 seconds.Data.xlsx
DOI: 10.5061/dryad.kc57603
title: Data from: Elevated oxidative stress in pied flycatcher nestlings of eumelanic foster fathers under low rearing temperatures

description: Striking variation in melanin coloration within natural populations is
 likely due to the different fitness outcomes of alternative phenotypes in
 varying environmental conditions. There are two types of melanins.
 Eumelanins yield blackish hues, while pheomelanins yield reddish hues. The
 production of eumelanins requires low levels of glutathione (GSH), which
 is the most important intracellular antioxidant, while the production of
 pheomelanins requires high levels of GSH. We investigated the oxidative
 status of male pied flycatchers (Ficedula hypoleuca) with different
 degrees of melanin coloration under different temperatures during the
 nestling period. Moreover, we assessed the oxidative status of offspring
 in relation to their biological or foster father's melanin coloration
 and ambient temperature. To separate offspring genotype effects and
 paternal effects in different temperatures, we used a partial cross-foster
 design. The temperature differently affected the oxidative status of
 differently colored male pied flycatchers and their foster offspring. When
 the weather was relatively cold, black males had higher glutathione
 S-transferase levels compared to brown males, indicating enhanced stress
 in black males. Foster offspring of black males had lower ratio between
 reduced and oxidized GSH followed by higher total amount of GSH than
 foster offspring of brown males. Thus, foster offspring of black males
 seem to suffer from oxidative stress under relatively cold weather
 compared to those of brown males, and vice versa under relatively warm
 weather. While differently colored males experienced changes in their
 oxidative status under different temperatures, the link between father
 melanin coloration and offspring oxidative stress appears to be
 environmentally induced.
description: Pied flycatcher melanin
 oxidative stress dataThe file contains two
 data sheets "chicks" and "males". Measurements of SOD,
 CAT, GP, GSHratio, GSHtotal, CARB and GST as indicators of oxidative
 stress are assigned to each individual. Temperature measure is an average
 temperature value for nestling period (day 4 to day 11) and individually
 assigned for each box.Melanin_ox_Teerikorpi­_etal.xlsx
DOI: 10.5061/dryad.716kr
title: Data from: On the inconsistency of pollinator species traits for predicting either response to land-use change or functional contribution

description: The response and effect trait framework, if supported empirically, would
 provide for powerful and general predictions about how biodiversity loss
 leads to loss in ecosystem function. This framework proposes that species
 traits will explain how different species respond to disturbance (i.e.
 response traits) as well as their contribution to ecosystem function (i.e.
 effect traits). However, predictive response and effect traits remain
 elusive for most systems. Here, we use data on crop pollination services
 provided by native, wild bees to explore the role of six commonly used
 species traits in determining both species' response to land-use
 change and the subsequent effect on crop pollination. Analyses were
 conducted in parallel for three crop systems (watermelon, cranberry, and
 blueberry) located within the same geographical region (mid-Atlantic USA).
 Bee species traits did not strongly predict species' response to
 land-use change, and the few traits that were weakly predictive were not
 consistent across crops. Similarly, no trait predicted species'
 overall functional contribution in any of the three crop systems, although
 body size was a good predictor of per capita efficiency in two systems.
 Overall we were unable to make generalizable predictions regarding species
 responses to land-use change and its effect on the delivery of crop
 pollination services. Pollinator traits may be useful for understanding
 ecological processes in some systems, but thus far the promise of
 traits-based ecology has yet to be fulfilled for pollination ecology.
description: repository to reproduce
 analysis (includes data)Code (Analysis.R) and
 data (in folder data_) to reproduce a paper about response and effect
 traits. Main data is in three files: specimens.csv: Data on specimens
 collected per site gis.csv: Data on landscape characteristics per sites.
 Can be combined with specimens.csv by site. traits.csv: Data on ecological
 traits at species level. Can be combined with specimens by genus and
 species.RE_traits-master.zip
DOI: 10.5061/dryad.qt71v
title: Data from: Benzene exposure is associated with cardiovascular disease risk

description: Benzene is a ubiquitous, volatile pollutant present at high concentrations
 in toxins (e.g. tobacco smoke) known to increase cardiovascular disease
 (CVD) risk. Despite its prevalence, the cardiovascular effects of benzene
 have rarely been studied. Hence, we examined whether exposure to benzene
 is associated with increased CVD risk. The effects of benzene exposure in
 mice were assessed by direct inhalation, while the effects of benzene
 exposure in humans was assessed in 210 individuals with mild to high CVD
 risk by measuring urinary levels of the benzene metabolite
 trans,trans-muconic acid (t,t-MA). Generalized linear models were used to
 assess the association between benzene exposure and CVD risk. Mice
 inhaling volatile benzene had significantly reduced levels of circulating
 angiogenic cells (Flk-1+/Sca-1+) as well as an increased levels of plasma
 low-density lipoprotein (LDL) compared with control mice breathing
 filtered air. In the human cohort, urinary levels of t,t-MA were inversely
 associated several populations of circulating angiogenic cells
 (CD31+/34+/45+, CD31+/34+/45+/AC133–, CD34+/45+/AC133+). Although t,t-MA
 was not associated with plasma markers of inflammation or thrombosis,
 t,t-MA levels were higher in smokers and in individuals with dyslipidemia.
 In smokers, t,t-MA levels were positively associated with urinary
 metabolites of nicotine (cotinine) and acrolein (3-hydroxymercapturic
 acid). Levels of t,t-MA were also associated with CVD risk as assessed
 using the Framingham Risk Score and this association was independent of
 smoking. Thus, benzene exposure is associated with increased CVD risk and
 deficits in circulating angiogenic cells in both smokers and non-smokers.
description: Figure 2
 datamouse
 data.xlsxFigure 3
 dataFigure3data.XLSX
DOI: 10.5061/dryad.320bv7b
title: Data from: Social network analysis of psychological morbidity in an urban slum of Bangladesh: a cross-sectional study based on a community census

description: Background Social ties are believed to play important roles in mitigating
 depression and anxiety, as well as fostering mental health in the
 population. We test this association for young urban men in Bangladesh.
 Methods Using a locally adapted GHQ-12 instrument, we enumerate
 self-reported mental health outcomes for 824 post-adolescent young men
 between the ages of 18 and 29 in a low-income urban community in Dhaka,
 Bangladesh. We further measure the social network for all our subjects and
 estimate the association of social network of the respondents with
 self-reported mental health outcomes controlling for possible confounders.
 Results We find there are considerable variations in both the mental
 health outcomes and social network across respondents. The GHQ scores
 (mean = 9.2, SD = 4.9) suggest significant psychological morbidity among
 the respondents. However, our findings imply better social ties and
 connections can potentially mitigate negative mental health outcomes
 (0.05-0.65 lower standardized GHQ score). Among other factors, being
 married and a recent migrant are also associated with better mental health
 status (0.17-0.20 and 0.16-0.17 lower standardized GHQ scores
 respectively). Conclusion Our results underscore the importance of social
 connection in providing buffer against stress and anxiety through
 psychosocial support from one’s peer in a resource constraint urban
 setting. Our findings also suggest incorporating social network and ties
 in designing mental health policies and interventions.
description: Mental Health and Social
 Network DataThis dataset contains
 data used for the analyses included in "A social network analysis of
 psychological morbidity in an urban slum of Bangladesh" paper. The
 zip file contains both the data and also the codes that can replicate all
 the results reported in the main paper and the
 appendix.bmjopen-2017-020180.zip
DOI: 10.5061/dryad.588g0cf
title: Data from: Mutational load, inbreeding depression and heterosis in subdivided populations

description: This paper examines the extent to which empirical estimates of inbreeding
 depression and inter-population heterosis in subdivided populations, as
 well as the effects of local population size on mean fitness, can be
 explained in terms of current estimates of mutation rates, and the
 distribution of selection coefficients against deleterious mutations
 provided by population genomics data. Using population genetics models,
 numerical predictions of the genetic load, inbreeding depression and
 heterosis were obtained for a broad range of selection coefficients and
 mutation rates. The models allowed for the possibility of very high
 mutation rates per nucleotide site, as is sometimes observed for
 epiallelic mutations in plants. There was fairly good quantitative
 agreement between the theoretical predictions and empirical estimates of
 heterosis and the effects of population size on genetic load, on the
 assumption that the deleterious mutation rate per individual per
 generation is approximately one, but there was less good agreement for
 inbreeding depression. Weak selection, of the order of magnitude suggested
 by population genomic data, is required to explain the observed patterns.
 Possible caveats concerning the applicability of the models are discussed.
description: Computer code and
 outputTextfile containing
 computer code and outputCode for load
 calculations.rtf