cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dv234
title: Data from: Survival and mortality of pumas (Puma concolor) in a fragmented, urbanizing landscape

description: Wide-ranging large carnivores pose myriad challenges for conservation,
 especially in highly fragmented landscapes. Over a 13-year period, we
 combined monitoring of radio collared pumas (Puma concolor) with
 complementary multi-generational genetic analyses to inform puma
 conservation in southern California, USA. Our goals were to generate
 survivorship estimates, determine causes of mortality, identify barriers
 to movement, and determine the genetic and demographic challenges to puma
 persistence among &gt;20,000,000 people and extensive urban, suburban,
 and exurban development. Despite protection from hunting, annual survival
 for radio collared pumas was surprisingly low (55.8%), and humans caused
 the majority of puma deaths. The most common sources of mortality were
 vehicle collisions (28% of deaths), and mortalities resulting from
 depredation permits issued after pumas killed domestic animals (17% of
 deaths). Other human-caused mortalities included illegal shootings, public
 safety removals, and human-caused wildfire. An interstate highway (I-15)
 bisecting this study area, and associated development, have created a
 nearly impermeable barrier to puma movements, resulting in severe genetic
 restriction and demographic isolation of the small puma population (n ~
 17–27 adults) in the Santa Ana Mountains west of I-15. Highways that
 bisect habitat or divide remaining “conserved” habitat, and associated
 ongoing development, threaten to further subdivide this already fragmented
 puma population and increase threats to survival. This study highlights
 the importance of combining demographic and genetic analyses, and
 illustrates that in the absence of effective measures to reduce mortality
 and enhance safe movement across highways, translocation of pumas, such as
 was done with the endangered Florida panther (P. c. coryi), may ultimately
 be necessary to prevent further genetic decline and ensure persistence of
 the Santa Ana Mountains population.
description: UCDavis Southern
 California Puma Survival and Mortality DataThis dataset represents
 findings from a telemetry study of pumas in southern California from
 2001-2013, and puma mortality data recorded by California Department of
 Fish and Wildlife and others over the period 1981-2013.UCD_Puma_Survival_Manuscript_Final_Dataset_2015_06_10 to Dryad.xlsx
DOI: 10.5061/dryad.3q26p
title: Data from: Differentially expressed mRNA targets of differentially expressed miRNAs predict changes in the TP53 axis and carcinogenesis related pathways in human keratinocytes chronically exposed to arsenic

description: Background: Arsenic is a widely distributed toxic natural element. Chronic
 arsenic ingestion causes several cancers, especially skin cancer.
 Arsenic-induced cancer mechanisms are not well defined, but several
 studies indicate that mutation is not the driving force and that microRNA
 expression changes play a role. Chronic low arsenite exposure malignantly
 transforms immortalized human keratinocytes (HaCaT), serving as a model
 for arsenic-induced skin carcinogenesis. Hypothesis: Early changes in
 miRNA expression in HaCaT cells chronically exposed to arsenite will
 reveal early steps in transformation. Methods: HaCaT cells were maintained
 with 0/100 nM NaAsO2 for 3 and 7 weeks. Total RNA was purified. miRNA and
 mRNA expression was assayed using Affymetrix microarrays. Targets of
 differentially expressed miRNAs were collected from TargetScan 6.2,
 intersected with differentially expressed mRNAs using Partek Genomic
 Suite™ software, and mapped to their pathways using MetaCore™ software.
 MDM2, HMGB1 and TP53 mRNA and protein levels were assayed by western blot.
 Results: Numerous miRNAs and mRNAs involved in carcinogenesis pathways in
 other systems were differentially expressed at 3 and 7 weeks. A TP53
 regulatory network including MDM2 and HMGB1 was predicted by the miRNA and
 mRNA networks. Total TP53 and TP53-S15-phosphorylation were induced.
 However, TP53-K382-hypoacetylation suggested that the induced TP53 is
 inactive in arsenic exposed cells. Conclusions: Our data provide strong
 evidence that early changes in miRNAs and target mRNAs may contribute to
 arsenic-induced carcinogenesis.
description: Supplementary table
 1Differentially expressed
 mRNAs at both 3 and 7 weeks of exposure to arseniteSupplementary table
 2Filtered differentially
 expressed 38 predicted targets of differentially expressed miRNA at 3 and
 7 weeks.Supplementary table
 3Filtered differentially
 expressed mRNA targets of differentially expressed miRNAs (3 weeks time
 point)Supplementary table
 4Filtered differentially
 expressed mRNA targets of differentially expressed miRNAs (3 weeks time
 point)
DOI: 10.5061/dryad.c76q3t7
title: Data from: A century of genetic variation inferred from a persistent soil-stored seed bank

description: Stratigraphic accretion of dormant propagules in soil can result in
 natural archives useful for studying ecological and evolutionary responses
 to environmental change. Few attempts have been made, however, to use
 soil-stored seed banks as natural archives, in part because of concerns
 over non-random attrition and mixed stratification. Here we examine the
 persistent seed bank of Schoenoplectus americanus, a foundational brackish
 marsh sedge, to determine whether it can serve as a resource for
 reconstructing historical records of demographic and population genetic
 variation. After assembling profiles of the seed bank from radionuclide
 dated soil cores, we germinated seeds to ‘resurrect’ cohorts spanning the
 20th century. Using microsatellite markers, we assessed genetic diversity
 and differentiation among depth cohorts, drawing comparisons to extant
 plants at the study site and in nearby and more distant marshes. We found
 that seed density peaked at intermediate soil depths. We also detected
 genotypic differences among cohorts as well as between cohorts and extant
 plants. Genetic diversity did not decline with depth, indicating that the
 observed pattern of differentiation is not due to attrition. Patterns of
 differentiation within and among extant marshes also suggest that local
 populations persist as aggregates of small clones, likely reflecting
 repeated seedling recruitment and low immigration from admixed regional
 gene pools. These findings indicate that persistent and stratified
 soil-stored seed banks merit further consideration as resources for
 reconstructing decadal-to-century long records that can lend insight into
 the tempo and nature of ecological and evolutionary processes that shape
 populations over time.
description: sample_id_namesThis file includes the names of samples provided in shorthand in MSA input filesdryad_idsmsa.xlsxSERC_KirkpatrickMarsh_MSA_summaryoutputThis is a summary output file generated in MSA for samples taken in Kirkpatrick Marsh / SERC in Edgewater, MDSummary_serc_trimmed.xlsChesapeake_MSA_summaryoutputSummary output generated by MSA for Chesapeake Bay samples of extant S. americanusSummary - Copy.xlsAtlantic_MSA_summaryoutputSummary output generated for Atlantic coast samples of extant S. americanus (microsatellites)Summary - Copy.xlsGulf_MSA_summaryoutputOutput generated by MSA for Gulf coast samples of extant S. americanus (microsatellites)Gulf_summary_MSA.xls
DOI: 10.5061/dryad.d2kv0
title: Data from: Greenhouse gas emissions from reservoir water surfaces: a new global synthesis

description: Collectively, reservoirs created by dams are thought to be an important
 source of greenhouse gases (GHGs) to the atmosphere. So far, efforts to
 quantify, model, and manage these emissions have been limited by data
 availability and inconsistencies in methodological approach. Here, we
 synthesize reservoir CH4, CO2, and N2O emission data with three main
 objectives: (1) to generate a global estimate of GHG emissions from
 reservoirs, (2) to identify the best predictors of these emissions, and
 (3) to consider the effect of methodology on emission estimates. We
 estimate that GHG emissions from reservoir water surfaces account for 0.8
 (0.5–1.2) Pg CO2 equivalents per year, with the majority of this forcing
 due to CH4. We then discuss the potential for several alternative pathways
 such as dam degassing and downstream emissions to contribute significantly
 to overall emissions. Although prior studies have linked reservoir GHG
 emissions to reservoir age and latitude, we find that factors related to
 reservoir productivity are better predictors of emission.
description: Reservoir Greenhouse Gas
 Fluxes and Potential Predictor Variables This data file contains
 reservoir greenhouse gas emission estimates as well as categorical and
 continuous data for tested predictors of these fluxes. There is one row
 reserved for each reservoir included in the study. The associated
 references for this data are included in a second spreadsheet
 tab.
DOI: 10.5061/dryad.vk3ns
title: Data from: Prozac in the water: chronic fluoxetine exposure and predation risk interact to shape behaviors in an estuarine crab

description: Predators exert considerable top-down pressure on ecosystems by directly
 consuming prey or indirectly influencing their foraging behaviors and
 habitat use. Prey is, therefore, forced to balance predation risk with
 resource reward. A growing list of anthropogenic stressors such as rising
 temperatures and ocean acidification has been shown to influence prey risk
 behaviors and subsequently alter important ecosystem processes. Yet,
 limited attention has been paid to the effects of chronic pharmaceutical
 exposure on risk behavior or as an ecological stressor, despite widespread
 detection and persistence of these contaminants in aquatic environments.
 In the laboratory, we simulated estuarine conditions of the shore crab,
 Hemigrapsus oregonensis, and investigated whether chronic exposure (60
 days) to field-detected concentrations (0, 3, and 30 ng/L) of the
 antidepressant fluoxetine affected diurnal and nocturnal risk behaviors in
 the presence of a predator, Cancer productus. We found that exposure to
 fluoxetine influenced both diurnal and nocturnal prey risk behaviors by
 increasing foraging and locomotor activity in the presence of predators,
 particularly during the day when these crabs normally stay hidden. Crabs
 exposed to fluoxetine were also more aggressive, with a higher frequency
 of agonistic interactions and increased mortality due to conflicts with
 conspecifics. These results suggest that exposure to field-detected
 concentrations of fluoxetine may alter the trade-off between resource
 acquisition and predation risk among crabs in estuaries. This fills an
 important data gap, highlighting how intra- and interspecific behaviors
 are altered by exposure to field concentrations of pharmaceuticals; such
 data more explicitly identify potential ecological impacts of emerging
 contaminants on aquatic ecosystems and can aid water quality management.
description: EE_crab_behav_dataBehavioral data recorded for Hemigrapsus oregonensis exposed to fluoxetine (Control=0ng/L, 3ng/L, and 30ng/L) over a 60 day study. Data recorded as counts of behavioral acts during no predator and predator trials at day and night
DOI: 10.5061/dryad.sm7p8
title: Data from: Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

description: Phytoplankton are the basis of marine food webs, and affect biogeochemical
 cycles. As CO2 levels increase, shifts in the frequencies and physiology
 of ecotypes within phytoplankton groups will affect their nutritional
 value and biogeochemical function. However, studies so far are based on a
 few representative genotypes from key species. Here, we measure changes in
 cellular function and growth rate at atmospheric CO2 concentrations
 predicted for the year 2100 in 16 ecotypes of the marine picoplankton
 Ostreococcus. We find that variation in plastic responses among ecotypes
 is on par with published between-genera variation, so the responses of one
 or a few ecotypes cannot estimate changes to the physiology or composition
 of a species under CO2 enrichment. We show that ecotypes best at taking
 advantage of CO2 enrichment by changing their photosynthesis rates most
 should increase in relative fitness, and so in frequency in a high-CO2
 environment. Finally, information on sampling location, and not
 phylogenetic relatedness, is a good predictor of ecotypes likely to
 increase in frequency in this system.
description: (Figure1) Photosynthesis
 (measured as oxygen evolution rates) for 16 Ostreococcus ecotypes at
 ambient and elevated pCO2This file contains
 oxygen evolution data per cell per hour for all ecotypes in both CO2
 treatments as measured with a Clark-type electrode. Note that these are
 means for biological (n=3-6) and technical (n=3) replicates. Also, the ppm
 CO2 given are the pCO2 we aimed to reach. For the actual values and
 detailed carbonate chemistry, please see our SI files, which are available
 from nature climate change.DatadryadPS.xlsx(Figure1)Growth rates of 16 Ostreococcus ecotypes at ambient and elevated CO2 levelsThis file contains growth rate data for 16 Ostreococcus ecotypes, measured as OD and verified on an Accuri (AWI) and a FACS Calibur (Edinburgh) flow cytometre.DatadryadGrowth.xlsx(Figure1) CN ratio of five representative ecotypes of Ostreococcus at ambient and elevated pCO2 levelsThis file contains CN ratios, as measured through combustion, for five representative ecotypes of Ostreococcus. There were at least three biological and three technical replicates of each ecotype.DatadryadCN.xlsx(Figure1) Cell size of 16 Ostreococcus ecotypes at ambient and elevated pCO2 levelsCell size of Ostreococcus was measured in relation to calibration beads using an Accuri (AWI) and a FACS Calibur flow cytometre. This file already contains the standard error (calculated as standard deviation divided by square root of number of replicates)CellsizeDatadryad.xlsx
DOI: 10.5061/dryad.qn1cj
title: Data from: Temporally dynamic habitat suitability predicts genetic relatedness among caribou

description: Landscape heterogeneity plays a central role in shaping ecological and
 evolutionary processes. While species utilization of the landscape is
 usually viewed as constant within a year, the spatial distribution of
 individuals is likely to vary in time in relation to particular seasonal
 needs. Understanding temporal variation in landscape use and genetic
 connectivity has direct conservation implications. Here, we modelled the
 daily use of the landscape by caribou in Quebec and Labrador, Canada and
 tested its ability to explain the genetic relatedness among individuals.
 We assessed habitat selection using locations of collared individuals in
 migratory herds and static occurrences from sedentary groups. Connectivity
 models based on habitat use outperformed a baseline isolation-by-distance
 model in explaining genetic relatedness, suggesting that variations in
 landscape features such as snow, vegetation productivity and land use
 modulate connectivity among populations. Connectivity surfaces derived
 from habitat use were the best predictors of genetic relatedness. The
 relationship between connectivity surface and genetic relatedness varied
 in time and peaked during the rutting period. Landscape permeability in
 the period of mate searching is especially important to allow gene flow
 among populations. Our study highlights the importance of considering
 temporal variations in habitat selection for optimizing connectivity
 across heterogeneous landscape and counter habitat fragmentation.
description: Yannic_data_DRYAD_RSPB-2014-0502Introductory information: Caribou (Rangifer tarandus) capture and genotype data. Please contact either Glenn Yannic (glenn-dot-yannic-at-gmail-dot-com) or Steeve D. Côté (Steeve-dot-Cote-at-bio-dot-ulaval-dot-ca) with any questions of location and genotype data. Identification – lab ID (ID number used in lab), capture ID (ID number used in field), sex (male or female). Capture Location - latitude (Y) and longitude (X) coordinates (datum = WGS84) of capture. Loci - names of microsatellite loci analyzed - 16 in total, two alleles provided per loci in adjacent columns, missing data given 000.
DOI: 10.15468/dl.4hchs8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "InstitutionCode is iNaturalist",
 "TaxonKey is ",
 "Elevation is greater than 5000m"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000718-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.9r2h3
title: Data from: Bayesian inference of a complex invasion history revealed by nuclear and chloroplast genetic diversity in the colonizing plant, Silene latifolia

description: Species invading new ranges are subject to a series of demographic events
 that can strongly shape genetic diversity. Describing this demographic
 history is important for understanding where invasive species come from
 and how they spread, and is critical to testing hypotheses of
 post-invasion adaptation. Here, we analyze nuclear and chloroplast genetic
 diversity to study the invasion history of the widespread colonizing weed,
 Silene latifolia (Caryophyllaceae). Bayesian clustering and PCA revealed
 strong population structure in the native range of Europe and although
 genotypes from multiple native sources were present in the introduced
 range of North America, the spatial distribution of genetic variance was
 dramatically reorganized. Using approximate Bayesian computation (ABC), we
 compared support for different invasion scenarios, including the number
 and size of independent introduction events and the amount of admixture
 occurring between sources of introduced genotypes. Our results supported
 independent introductions into eastern and western North America, with the
 latter forming a bridgehead for a secondary invasion into the Great Lakes
 region of central North America. Despite small estimated founder
 population sizes, the duration of the demographic bottleneck after the
 initial introduction appeared extremely short-lived. This pattern of
 repeated colonization and rapid expansion has effectively eroded the
 strong population structure and cyto-nuclear associations present in
 Europe, but has retained overall high genetic diversity since invasion.
 Our results highlight the flexibility of the ABC approach for constructing
 a narrative of the demographic history of species invasions, and provide
 baseline for future studies of evolutionary changes in introduced S.
 latifolia populations.
description: Kelleretal2012MEC_genotypesGenotypic data from 16 nuclear microsatellites and 1 chloroplast indel marker.Kelleretal2012_MEC_genotypes.xlsxDIYABC_5POPData input file for DIYABC demographic modeling.Keller_etal_MolEcol_2012_DIYABCReference table for DIYABC demographic modeling.Keller_etal_2012_MEC_samplinglocationsGeographic regions and continent of origin associated with each genetic sample. These geographic regions form the basis of the hierarchical tests of genetic structure and the ABC model comparisons.
DOI: 10.5061/dryad.4js7n
title: Data from: The sentinel behaviour of Arabian babbler floaters

description: The sentinel behaviour of 38 Arabian babbler adult floaters, who lived
 alone within a territory belonging to a foreign group, was studied and
 compared with their own sentinel behaviour in the past, when they were
 group members. All floaters acted as sentinels and uttered ‘alarm calls’.
 This suggests that sentinel activity is due at least, in part, to selfish
 motives. Floaters sentinelled less than they did as group members, with
 the decrease in sentinel activity sharper for ex-dominants than for
 ex-subordinates. One possible explanation for these differences is that
 sentinel activity is aimed not only at detecting predators, but also at
 detecting foreign conspecifics. Within a group, the latter incentive is
 stronger for breeding dominants than for subordinates, whereas all
 floaters alike may be trying to detect the owners of the territory in
 which they were roaming but also to avoid being detected by them. Other
 possible explanations are that floaters have less time and energy for
 sentinel activity because they are weaker or because foraging is more
 difficult in a foreign territory. This may be especially so for dominants
 who used to enjoy privileged access to food in their group. No significant
 difference was found in the rate of sentinels' ‘alarm calls’ between
 floaters and group members, suggesting that their main purpose is
 predator–prey communication, of which warning groupmates may be a side
 benefit.
description: Sentinel, Refugees,
 Arabian babblerExcel data set for the
 manuscriptSentinel,
 Refugees.xlsx
DOI: 10.5061/dryad.th6g8
title: Data from: Accounting for groundwater in stream fish thermal habitat responses to climate change

description: Forecasting climate change effects on aquatic fauna and their habitat
 requires an understanding of how water temperature responds to changing
 air temperature (i.e., thermal sensitivity). Previous efforts to forecast
 climate effects on brook trout (Salvelinus fontinalis) habitat have
 generally assumed uniform air–water temperature relationships over large
 areas that cannot account for groundwater inputs and other processes that
 operate at finer spatial scales. We developed regression models that
 accounted for groundwater influences on thermal sensitivity from measured
 air–water temperature relationships within forested watersheds in eastern
 North America (Shenandoah National Park, Virginia, USA, 78 sites in nine
 watersheds). We used these reach-scale models to forecast climate change
 effects on stream temperature and brook trout thermal habitat, and
 compared our results to previous forecasts based upon large-scale models.
 Observed stream temperatures were generally less sensitive to air
 temperature than previously assumed, and we attribute this to the
 moderating effect of shallow groundwater inputs. Predicted groundwater
 temperatures from air–water regression models corresponded well to
 observed groundwater temperatures elsewhere in the study area. Predictions
 of brook trout future habitat loss derived from our fine-grained models
 were far less pessimistic than those from prior models developed at
 coarser spatial resolutions. However, our models also revealed spatial
 variation in thermal sensitivity within and among catchments resulting in
 a patchy distribution of thermally suitable habitat. Habitat fragmentation
 due to thermal barriers therefore may have an increasingly important role
 for trout population viability in headwater streams. Our results
 demonstrate that simple adjustments to air–water temperature regression
 models can provide a powerful and cost-effective approach for predicting
 future stream temperatures while accounting for effects of groundwater.
description: Stream temperature
 dataAir and water
 temperature for streams in Shenandoah National Park,
 VirginiaSnyderEtal_Data.xlsx