cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8gd1653
title: Data from: The greatest hits of all time: the histories of dominant genera in the fossil record

description: Certain taxa are noticeably common within collections, widely distributed,
 and frequently long-lived. We have examined these dominant genera as
 compared to rarer genera, with a focus on their temporal histories. Using
 occurrence data from the Paleobiology Database, we determined which genera
 belonging to six target groups ranked among the most common within each of
 49 temporal bins based on occurrences. The turnover among these dominant
 taxa from bin-to-bin was then determined for each of these groups and all
 six groups pooled. Although dominant genera are only a small fraction of
 all genera, the patterns of turnover mimic those seen in much larger
 compilations of total biodiversity. We also found that differences in
 patterns of turnover at the top ranks among the higher taxa reflect
 previously documented comparison of overall turnover among these classes.
 Both dominant and non-dominant genera exhibit on average symmetrical
 patterns of rise and fall between first and last appearances. Dominant
 genera rarely begin at high ranks, but nevertheless tend to be more common
 when they first appear than non-dominant genera. Moreover, dominant genera
 rarely are in the Top 20 when they last appear, but still typically occupy
 more localities than non-dominant genera occupy in their last interval.
 The mechanism(s) that produce dominant genera remain unclear. Nearly half
 of dominant genera are the type genus of a family or subfamily. This is
 consistent with a simple model of morphological and phylogenetic
 diversification and sampling.
description: Plotnick & Wagner
 SupplementaryTwo supplementary tables
 and three supplementary figures.Supplemental
 ReferencesSupplemental
 referencesSupplemental Table
 1Supplemental Table 1 in
 .csv format.Supplemental Table
 2Supplemental Table 2 in
 .csv format
DOI: 10.5061/dryad.94g0tc5
title: Data from: SSR Markers for Filago subgen. Filago (Gnaphalieae: Asteraceae) and cross-amplification in three other subgenera

description: • Premise of the study: Microsatellite primers were developed for the
 first time in the genus Filago (Gnaphalieae: Asteraceae). These markers
 will facilitate low-scale phylogenetic, phylogeographic and population
 genetics studies within the genus Filago. • Methods and Results: Nine
 pairs of microsatellite primers were identified and optimized on two
 species of Filago using a microsatellite-enrichment library method and 454
 GS-FLX technique. The set of primers amplified tri- to hexanucleotide
 repeats, and showed one to six alleles per locus for both species: F.
 gaditana and F. carpetana. Transferability was performed in 29 samples
 corresponding to nine representative species of Filago. • Conclusions: The
 results indicate the utility of the newly developed markers, which will be
 useful to go deeper into the phylogenetic relationships among the taxa
 within Filago. These microsatellites will enable phylogeographic,
 reproductive and genetic variation studies.
description: Genoscreen-project71220_LD-MO-SA_sequences_TOTFASTA File (No FASTAQ available) from: GENO SAT report - High-throughput DNA sequencing by 454-GsFLX Titanium chemistry of a library enriched DNA TG AAC AGG ACAT TC AAG ACG ACTC in microsatellite loci from two samples of Filago carpetana (Lange) Chrtek & Holub and two samples of Filago gaditana (Pau) Andrés-Sánchez & Galbany
DOI: 10.5061/dryad.q53g43n
title: Data from: Species’ ecological functionality alters the outcome of fish stocking success predicted by a food-web model

description: Fish stocking is used worldwide in conservation and management but its
 effects on food-web dynamics and ecosystem stability are poorly known. To
 better understand these effects and predict the outcomes of stocking, we
 used an empirically validated network model of a well-studied lake
 ecosystem. We simulate two stocking scenarios with two native fish species
 valuable for fishing. In the first scenario, we stock planktivorous fish
 (whitefish) larvae in the ecosystem. This leads to 1% increase in adult
 whitefish biomasses and decreases the biomasses of the top predator
 (perch). In the second scenario, we also stock perch larvae in the
 ecosystem. This decreases the planktivorous whitefish and the oldest top
 predator age class biomasses, and destabilizes the ecosystem. Our results
 demonstrate that the effects of stocking depend on the species’ position
 in the food web and thus cannot be assessed without considering
 interacting species. We further show that stocking can lead to undesired
 outcomes from both management and conservation perspectives. The gains of
 stocking can remain minor and have adverse effects on the entire
 ecosystem.
description: Data of whitefish
 baseline stocking (Wht200)Daily biomasses of each
 trophic level in response to whitefish baseline stocking (Wht200) in the
 absence and presence of fishing.data200.txtData of increased whitefish stocking (Wht300)Daily biomasses of each trophic level in response to increased whitefish stocking (Wht300) in the absence and presence of fishing.data300.txtData of perch stocking (Wht300+Per50)Daily biomasses of each trophic level in response to perch stocking (Wht300+Per50) in the absence and presence of fishing.data300_50.txtCatch data of whitefish baseline stocking (Wht200)Catch biomasses of adult fish in response to whitefish baseline stocking (Wht200) in the absence and presence of fishing (1 = 2 year old whitefish, 2 = 3 year old whitefish, 3 = 4 year old whitefish, 4 = 2 year old perch, 5 = 3 year old perch, 6 = 4 year old perch).data200_C.txtCatch data of increased whitefish stocking (Wht300)Catch biomasses of adult fish in response to increased whitefish baseline (Wht300) in the absence and presence of fishing (1 = 2 year old whitefish, 2 = 3 year old whitefish, 3 = 4 year old whitefish, 4 = 2 year old perch, 5 = 3 year old perch, 6 = 4 year old perch).data300_C.txtCatch data of perch stocking (Wht300+Per50)Catch biomasses of adult fish in response to perch stocking (Wht300+Per50) in the absence and presence of fishing (1 = 2 year old whitefish, 2 = 3 year old whitefish, 3 = 4 year old whitefish, 4 = 2 year old perch, 5 = 3 year old perch, 6 = 4 year old perch).data300+50_C.txt
DOI: 10.5061/dryad.6kv1198
title: Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

description: 1. Contemporary techniques predicting habitat suitability under climate
 change projections often underestimate availability of thermal refuges.
 Habitat structure contributes to thermal heterogeneity at a variety of
 spatial scales, but quantifying microclimates at organism‐relevant
 resolutions remains a challenge. Landscapes that appear homogeneous at
 large scales may offer patchily distributed thermal refuges at finer
 scales. 2. We quantified the relationship between vegetation structure and
 the thermal environment at a scale relevant to small, terrestrial animals
 using a new approach for mapping fine‐scale thermal heterogeneity. We
 expected that vegetation would create attenuated microclimates and that
 the influence of vegetation structure would vary seasonally. We measured
 shrub volume, horizontal cover, and operative temperature (Te) in a
 sagebrush‐steppe habitat in Idaho, USA, at 534 microsites across two study
 sites of approximately 1 km2 each. We modeled relationships between
 habitat structure and both mean daily maximum temperature
 (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0001max) and mean
 diurnal temperature range
 (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0002) for each study
 site during summer and winter. Aerial imagery from unmanned aerial systems
 was used to estimate shrub volume and canopy cover at 1‐m resolution, and
 we applied the best fit model to map thermal heterogeneity across broader
 extents. 3. Increasing shrub volume and cover was associated with lower
 urn:x-wiley:2041210X:media:mee313008:mee313008-math-0003max and
 (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0004, but strengths
 of the relationships differed between study sites. There was considerable
 heterogeneity in availability of thermal refuges across sagebrush‐steppe
 rangelands that have traditionally been considered relatively homogeneous.
 4. This technique can help ecologists and land managers identify critical
 thermal refuges that large‐scale climate modelling can overlook and thus
 contribute to an understanding of animal‐habitat relationships under
 changing climates and land uses.
description: Operative
 temperatureAbbreviations and
 descriptions of data contained in
 Milling_etal_SageTe.csv.Milling_etal_SageTe.csvUAS and Thermal GeotiffsAbbreviations and descriptions of Geotiffs contained in Dryad-Thermal_UAS.zip.Dryad-Thermal-UAS.zip
DOI: 10.5061/dryad.qd7t1s8
title: Data from: Hepatocyte-specific deletion of TIPARP, a negative regulator of the aryl hydrocarbon receptor, is sufficient to increase sensitivity to dioxin-induced wasting syndrome

description: The aryl hydrocarbon receptor (AHR) mediates the toxic effects of dioxin
 (2,3,7,8-tetrachlorodibenzo-p-dioxin; TCDD), which include thymic atrophy,
 steatohepatitis, and a lethal wasting syndrome in laboratory rodents.
 Although the mechanisms of dioxin toxicity remain unknown, AHR signaling
 in hepatocytes is necessary for dioxin-induced liver toxicity. We
 previously reported that loss of TCDD-inducible poly(ADP-ribose)
 polymerase (TIPARP/PARP7/ARTD14), an AHR target gene and
 mono-ADP-ribosyltransferase, increases the sensitivity of mice to
 dioxin-induced toxicities. To test the hypothesis that TIPARP is a
 negative regulator of AHR signaling in hepatocytes, we generated
 Tiparpfl/fl mice in which exon 3 of Tiparp is flanked by loxP sites,
 followed by Cre-lox technology to create hepatocyte-specific
 (Tiparpfl/flCreAlb) and whole-body (Tiparpfl/flCreCMV; TiparpEx3-/-)
 Tiparp null mice. Tiparpfl/flCreAlb and TiparpEx3-/- mice given a single
 injection of 10 g/kg dioxin did not survive beyond day 7 and 9,
 respectively, while all Tiparp+/+ mice survived the 30-day treatment.
 Dioxin-exposed Tiparpfl/flCreAlb and TiparpEx3-/- mice had increased
 steatohepatitis and hepatotoxicity as indicated by greater staining of
 neutral lipids and serum alanine aminotransferase activity than similarly
 treated wild-type mice. Tiparpfl/flCreAlb and TiparpEx3-/- mice exhibited
 augmented AHR signalling, denoted by increased dioxin-induced gene
 expression. Metabolomic studies revealed alterations in lipid and amino
 acid metabolism in liver extracts from Tiparpfl/flCreAlb mice compared
 with wild-type mice. Taken together, these data illustrate that TIPARP is
 an important negative regulator of AHR activity, and that its specific
 loss in hepatocytes is sufficient to increase sensitivity to
 dioxin-induced steatohepatitis and lethality.
description: Supplementary Table
 S1Supplementary Table S1
 containing genotyping and qPCR primers.Supplemental Table
 1.pdfSupplementary Figures S1
 to S3This is a single file
 that contains supplementary figure S1 which describes the truncated Tiparp
 protein resulting from exon 3 excision. It contains supplementary figure
 S2 and S3 that show the hepatic inflammation and hepatosteatosis in
 TiparpEx3-/- mice.Suppl figures
 1-3.pdfSupplementary Tables S2
 to S7This excel file contains
 metabolomic data that is presented in supplementary tables S2 to
 S7.Supplementary
 Tables_S2_S7.xlsx
DOI: 10.5061/dryad.q78sb73
title: Data from: Nature, extent and ecological implications of night-time light from road vehicles

description: 1.The erosion of night‐time by the introduction of artificial lighting
 constitutes a profound pressure on the natural environment. It has altered
 what had for millennia been reliable signals from natural light cycles
 used for regulating a host of biological processes, with impacts ranging
 from changes in gene expression to ecosystem processes. 2.Studies of these
 impacts have focused almost exclusively on those resulting from stationary
 sources of light emissions, and particularly streetlights. However, mobile
 sources, especially road vehicle headlights, contribute substantial
 additional emissions. 3.The ecological impacts of light emissions from
 vehicle headlights are likely to be especially high because these are (i)
 focused so as to light roadsides at higher intensities than commonly
 experienced from other sources, and well above activation thresholds for
 many biological processes; (ii) projected largely in a horizontal plane
 and thus can carry over long distances; (iii) introduced into much larger
 areas of the landscape than experience street lighting; (iv) typically
 broad ‘white’ spectrum, which substantially overlaps the action spectra of
 many biological processes; and (v) often experienced at roadsides as
 series of pulses of light (produced by passage of vehicles), a dynamic
 known to have major biological impacts. 4.The ecological impacts of road
 vehicle headlights will markedly increase with projected global growth in
 numbers of vehicles and the road network, increasing the local severity of
 emissions (because vehicle numbers are increasing faster than growth in
 the road network) and introducing emissions into areas from which they
 were previously absent. The effects will be further exacerbated by
 technological developments that are increasing the intensity of headlight
 emissions and the amounts of blue light in emission spectra. 5.Synthesis
 and applications. Emissions from vehicle headlights need to be considered
 as a major, and growing, source of ecological impacts of artificial
 night‐time lighting. It will be a significant challenge to minimize these
 impacts whilst balancing drivers’ needs at night and avoiding risk and
 discomfort for other road users. Nonetheless, there is potential to
 identify solutions to these conflicts, both through the design of
 headlights and that of roads.
description: Headlight
 emissionsVariation in intensity
 (lux) and correlated colour temperature (CCT) of emissions measured from
 headlights on full beam for cars of a variety of ages (year) and with
 different kinds of lamps (I - Halogen, L - LED, X -
 Xenon)Roadside light
 measurementsLight intensity (lux)
 over time at three road sides.
DOI: 10.5061/dryad.p564p61
title: Data from: Admixture of hybrid swarms of native and introduced lizards in cities is determined by the cityscape structure and invasion history

description: Introductions of non-native lineages increase opportunities for
 hybridization. Non-native lineages of the common wall lizard, Podarcis
 muralis, are frequently introduced in cities where they hybridize with
 native populations. We aimed at unravelling the invasion history and
 admixture of native and non-native wall lizards in four German cities
 using citywide, comprehensive sampling. We barcoded and genotyped 826
 lizards and tested if gene flow in populations composed of admixed native
 and introduced lineages is facilitated by similar environmental factors as
 in native populations by comparing fine-scale landscape genetic patterns.
 In cities with non-native lineages, lizards commonly occurred in numerous
 clusters of hybrid swarms, which showed variable lineage composition,
 consisting of up to four distinct evolutionary lineages. Hybrid swarms
 held vast genetic diversity and showed recent admixture with other hybrid
 swarms. Landscape genetic analyses showed differential effects of
 cityscape structures across cities, but identified water bodies as strong
 barriers to gene flow in both native and admixed populations. In contrast,
 railway tracks facilitated gene flow of admixed populations only. Our
 study shows that cities represent unique settings for hybridization,
 caused by multiple introductions of non-native taxa. Cityscape structure
 and invasion histories of cities will determine future evolutionary
 pathways at these novel hybrid zones.
description: All input
 ascisResistance models of all
 environmental factors of all cities used for landscape genetic
 optimization (ASCI-format).All INPUT
 ASCIS.zipMicrosatellites_all_cititesMicrosatellites of all individuals genotyped in this study.
DOI: 10.5061/dryad.k6r1mk8
title: Data from: Heritability estimates from genome wide relatedness matrices in wild populations: application to a passerine, using a small sample size

description: Genomic developments have empowered the investigation of heritability in
 wild populations directly from genome wide relatedness matrices (GRM).
 Such GRM based approaches can in particular be used to improve or
 substitute approaches based on social pedigree (PED-social). However,
 measuring heritability from GRM in the wild has not been widely applied
 yet, especially using small samples and in non-model species. Here, we
 estimated heritability for four quantitative traits (tarsus length, wing
 length, bill length and body mass), using PED-social and a pedigree
 corrected by genetic data (PED-corrected) and GRM from a small sample (n =
 494) of blue tits from natural populations in Corsica genotyped at nearly
 50,000 filtered SNPs derived from RAD-seq. We also measured genetic
 correlations among traits and we performed chromosome partitioning.
 Heritability estimates were slightly higher when using GRM compared to
 PED-social, and PED-corrected yielded intermediate values, suggesting a
 minor underestimation of heritability in PED-social due to incorrect
 pedigree links, including extra-pair paternity, and to lower information
 content than the GRM. Genetic correlations among traits were similar
 between PED-social and GRM but credible intervals were very large in both
 cases, suggesting a lack of power for this small dataset. Although a
 positive linear relationship was found between the number of genes per
 chromosomes and the chromosome heritability for tarsus length, chromosome
 partitioning similarly showed a lack of power for the three other traits.
 We discuss the usefulness and limitations of the quantitative genetic
 inferences based on genomic data in small samples from wild populations.
description: BLUPSBLUPS for the four
 phenotypic traits studied. Each row corresponds to one
 individual.blups.txtplink bfilesPlink files (bed, bim, fam) containing genomic data for the 494 individuals.plink.zipPED-socialPairwise relatedness obtained from social pedigree.PED.txtPhenotypic traitsPhenotypic traits for the genotyped individuals.traits.txt
DOI: 10.15468/dl.j3tq5t
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphorbia serpyllifolia"
 ]
}

 The dataset includes 111 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001532-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.968nq8n
title: Data from: A worldwide model for boundaries of urban settlements

description: The shape of urban settlements plays a fundamental role in their
 sustainable planning. Properly defining the boundaries of cities is
 challenging and remains an open problem in the science of cities. Here, we
 propose a worldwide model to define urban settlements beyond their
 administrative boundaries through a bottom-up approach that takes into
 account geographical biases intrinsically associated with most societies
 around the world, and reflected in their different regional growing
 dynamics. The generality of the model allows one to study the scaling laws
 of cities at all geographical levels: countries, continents and the entire
 world. Our definition of cities is robust and holds to one of the most
 famous results in social sciences: Zipf’s law. According to our results,
 the largest cities in the world are not in line with what was recently
 reported by the United Nations. For example, we find that the largest city
 in the world is an agglomeration of several small settlements close to
 each other, connecting three large settlements: Alexandria, Cairo and
 Luxor. Our definition of cities opens the doors to the study of the
 economy of cities in a systematic way independently of arbitrary
 definitions that employ administrative boundaries.
description: CLCA
 codeThe City Local
 Clustering Algorithm (CLCA) code is in FORTRAN 90 and it was implemented
 with OpenMP for parallel programming. We also provide the compilation and
 run script.clca_codes.zip
DOI: 10.5061/dryad.5h2vr7c
title: Data from: Time-integrated habitat availability is a resource attribute that informs patterns of use in intertidal areas

description: In dynamic environments, resource availability may change by several
 orders of magnitude, over hours to months, but the duration of resource
 availability is not often included as a characteristic attribute of
 resources even though temporal resource dynamics might limit patterns of
 use. In our study of wading birds foraging in intertidal areas, tides
 cause large changes in the areal extent of shallow-water foraging habitat
 (i.e., the resource), but tides also constrain the duration of
 availability, which is often overlooked. We hypothesized that temporal
 constraints on habitat availability from tides would be reflected in
 patterns of habitat use by foraging birds. We estimated the
 time-integrated habitat availability and compared it to traditional
 habitat attributes (seagrass cover, substrate type, instantaneous water
 depth, and proximity to mangrove islands or deep water) that have strong
 evidential support for influencing patterns of use. To evaluate our
 hypotheses, we quantified habitat attributes at intertidal areas in the
 Florida Keys, U.S.A, where wading birds were observed foraging (Little
 Blue Heron, Egretta caerulea: N=183; Great White Heron, Ardea herodias
 occidentalis: N=162). We tested for non-random use by sampling habitat
 attributes at two spatial scales around the observed feeding locations and
 we analyzed the data using a conditional logistic regression model. There
 was no evidence that seagrass cover or substrate explained patterns of
 use. The proximity of foraging locations relative to mangroves and to deep
 water were important at both spatial scales but had lower effect sizes
 (odds-ratios) than time-integrated habitat availability and water depth,
 and the latter may only serve as a physical constraint on access. We found
 support that time-integrated habitat availability was a distinct resource
 attribute, had the greatest effect size (4-8-fold change in relative
 probability of use), and best explained patterns of habitat use at the
 largest spatial scale. In studies of resource use where changes in
 resource availability are non-linear or when strong constraints on access
 are imposed by behavior, incorporating time-integrated estimates of
 resource availability into analyses can improve insights into
 spatiotemporal patterns of resource use.
description: data_and_scriptsThe zip file contains two folders ./data and ./scripts, with README files within each folder describing the contents in detail, including description of variables in the datasets, sample code for accessing and viewing data, and procedures for running the scripts. The data are in the RDS format, a data format for R Statistical Software. The analysis and plotting scripts are also written for R.