cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.dpkxcz
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cestrum auriculatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 133 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000869-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4qt17
title: Data from: Woody flora types to describe phytogeographic units: an insight along a west–east transect in central Italy

description: To improve the phytogeographic characterization of peninsular Italy, we
 analysed and compared the spatial distribution of woody flora at species
 and genus levels along an approximate 160 km west–east transect within the
 central peninsula. Sampling sites were selected using a subjective
 stratified sampling design. A total of 1710 occurrence data, 138 species,
 and 74 genera from 153 floristic relevés was used. The congruence in
 species and genera patterns, supported by Mantel and Procrustes tests,
 confirmed the validity of the higher-taxon approach to analyse woody flora
 patterns. Nonmetric multidimensional scaling and Pearson's chi square
 test pointed out that elevation and related bioclimatic factors were the
 most important drivers of woody species composition. Three well defined
 woody flora types (coastal low-elevation, inland middle-elevation, and
 inland high-elevation) were identified using partition around medoids
 clustering; the species-rich inland middle-elevation type supports the
 recently described Transition unit between the Mediterranean and
 Eurosiberian Regions. Contrary to previous assumptions by other authors,
 floristic and chorological differences between the Tyrrhenian and the
 Adriatic subtypes were detected only in the inland high-elevation type and
 not in the coastal low-elevation one. The adopted methodological approach,
 based on higher-taxon approach, on clustering and on ordination of
 floristic relevés, resulted to be valuable to detect woody flora
 distribution patterns and to delineate the phytogeographic characters of a
 very heterogeneous and biodiverse area.
description: supplementary-material_Appendix ATo improve the phytogeographic characterization of peninsular Italy, we analysed and compared the spatial distribution of woody flora at species and genus levels along an approximate 160 km west–east transect within the central peninsula (Lazio and Abruzzo regions). A total of 1710 occurrence data, 138 species, and 74 genera from 153 floristic relevés was used. Woody flora types and subtypes were identified. Appendix A includes: list of the relevés (environmental variables, surface, data, source, type, and subtype are reported for each relevé); presence/absence data of woody species in each relevé (one table for each subtype is presented); and list of the species data (genus, family, chorotype, and life-form are reported for each species).
DOI: 10.5061/dryad.s07cg
title: Data from: Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

description: Variation in baseline ploidy is seen throughout the tree of life, yet the
 factors that determine why one ploidy level is maintained over another
 remain poorly understood. Experimental evolution studies using asexual
 fungal microbes with manipulated ploidy levels intriguingly reveals a
 propensity to return to the historical baseline ploidy, a phenomenon that
 we term ‘ploidy drive’. We evolved haploid, diploid, and polyploid strains
 of the human fungal pathogen Candida albicans under three different
 nutrient limitation environments to test whether these conditions,
 hypothesized to select for low ploidy levels, could counteract ploidy
 drive. Strains generally maintained or acquired smaller genome sizes size
 (measured as total nuclear DNA through flow cytometry) in minimal medium
 and under phosphorus depletion compared to in a complete medium, while
 mostly maintained or acquired increased genome sizes under nitrogen
 depletion. Improvements in fitness often ran counter to changes in genome
 size; in a number of scenarios lines that maintained their original genome
 size often increased in fitness more than lines that converged towards
 diploidy. Combined, this work demonstrates a role for both the environment
 and genotype in determination of the rate of ploidy drive, and highlights
 questions that remain about the force(s) that cause genome size variation.
description: PloidyDrive: R setup
 fileThis R code file loads
 the required libraries and data for analysis and
 figures.PloidyDrive_setup.RPloidyDrive: R figures fileThis R code file will reproduce the figures in the manuscript.PloidyDrive_figures.RPloidyDrive: R stats fileThis R code file will reproduce the statistics in the manuscript.PloidyDrive_stats.RFlow cytometry dataRaw flow cytometry data used to analyze genome size change. Columns labeled enviro-evol.2 indicate the location of a secondary G1 peak when it was present. Used in the R setup file.Flow_all.csvGR_allSDCAncestral and evolved growth rate and yield data from SDC (complete medium). Used in the R setup file.GR_allSDAncestral and evolved growth rate data from SD (minimal medium). Used in the R setup file.GR_allPlimAncestral and evolved growth rate data from phosphorus depleted (Pdep) medium. Used in the R setup file.GR_allNlimAncestral and evolved growth rate data from nitrogen depleted (Ndep) medium. Used in the R setup file
DOI: 10.5061/dryad.68fr52p
title: Data from: Does metabolism constrain bird and mammal ranges and predict shifts in response to climate change?

description: Mechanistic approaches for predicting the ranges of endotherms are needed
 to forecast their responses to environmental change. We test whether
 physiological constraints on maximum metabolic rate and the factor by
 which endotherms can elevate their metabolism (metabolic expansibility)
 influence cold range limits for mammal and bird species. We examine
 metabolic expansibility at the cold range boundary (MECRB) and whether
 species’ traits can predict variability in MECRB and then use MECRB as an
 initial approach to project range shifts for 210 mammal and 61 bird
 species. We find evidence for metabolic constraints: the distributions of
 metabolic expansibility at the cold range boundary peak at similar values
 for birds (2.7) and mammals (3.2). The right skewed distributions suggest
 some species have adapted to elevate or evade metabolic constraints.
 Mammals exhibit greater skew than birds, consistent with their diverse
 thermoregulatory adaptations and behaviors. Mammal and bird species that
 are small and occupy low trophic levels exhibit high levels of MECRB.
 Mammals with high MECRB tend to hibernate or use torpor. Predicted
 metabolic rates at the cold range boundaries represent large energetic
 expenditures (&gt;50% of maximum metabolic rates). We project species
 to shift their cold range boundaries poleward by an average of 3.9°
 latitude by 2070 if metabolic constraints remain constant. Our analysis
 suggests that metabolic constraints provide a viable mechanism for initial
 projections of the cold range boundaries for endotherms. However, errors
 and approximations in estimating metabolic constraints (e.g., acclimation
 responses) and evasion of these constraints (e.g., torpor/hibernation,
 microclimate selection) highlight the need for more detailed,
 taxa‐specific mechanistic models. Even coarse considerations of metabolism
 will likely lead to improved predictions over exclusively considering
 thermal tolerance for endotherms.
description: Metabolic expansibility
 dataSpecies, physiological,
 and environmental data. See README file for explanation of columns. R code
 to run the analysis is available here:
 https://github.com/lbuckley/tnz.MRexpansibility_Buckleyetal_Data.csv
DOI: 10.5061/dryad.f098g
title: Data from: An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea

description: Fitness costs are frequently invoked to explain the presence of genetic
 variation underlying plant defense across many types of damaging agents.
 Despite the expectation that costs of resistance are prevalent, however,
 they have been difficult to detect in nature. To examine the potential
 that resistance confers a fitness cost, we examined the survival and
 fitness of genetic lines of the common morning glory, Ipomoea purpurea,
 that diverged in the level of resistance to the herbicide glyphosate. We
 planted a large field experiment and assessed survival following herbicide
 application as well as fitness of the divergent selection lines in the
 absence of the herbicide. We found that genetic lines selected for
 increased resistance exhibited lower death compared to control and
 susceptible lines in the presence of the herbicide, but no evidence that
 resistant lines produced fewer seeds in the absence of herbicide. However,
 susceptible lines produced more viable seeds than resistant or control
 lines, providing some evidence of a fitness cost in terms of seed
 germination, and thus potential empirical support for the expectation of
 trait trade-offs as a consequence of adaptation to novel environments.
description: Field experiment data,
 G3sAllDataG3FieldDryad.txtGermination data for field collected seedsID's are cross-listed with ID's from Field data fileGermTest.txt
DOI: 10.5061/dryad.v6j70
title: Data from: Plasticity of thermoregulatory behaviour in response to the thermal environment by widespread and alpine reptile species

description: Phenotypic plasticity plays a central role in determining how organisms
 respond to environmental change over short timescales. Despite this, we
 know little about how phenotypic plasticity varies between populations or
 species. We tested the extent of plasticity in basking behaviour in low-
 and high-altitude populations of two widespread lowland and two highland
 species of a cool-climate lizard genus: Niveoscincus. We found evidence of
 divergence in basking behaviour between populations and species, with
 highland species and high-altitude populations of all species basking more
 than the widespread lowland species and low-altitude populations.
 Furthermore, we found differences in the extent of behavioural plasticity
 between species. Widespread lowland species altered their basking
 behaviour depending on basking opportunity whereas the highland species
 maintained high levels of basking independent of basking opportunity.
 These differences in basking behaviour were concordant with the
 differences in body temperature across all populations, species and
 treatments. Combined, this suggests that divergence in thermoregulatory
 behaviour and thermophysiology between populations and species may have
 been facilitated by adaptive behavioural plasticity within populations. We
 discuss this and the implications of our findings for the ability of these
 animals to cope with ongoing climate change.
description: Data from Caldwell et al
 Animal BehaviourAll morphological,
 behavioural and thermophysiological data for all
 species/populations/treatments collected as part of this
 study.Caldwelletal_AniBeh_DATA.csv
DOI: 10.5061/dryad.8p165g9
title: Data from: Variation in age, body size, and reproductive traits among urban and rural amphibian populations

description: Although amphibians use human-created habitats in urban landscapes, few
 studies have investigated the quality of these habitats. To assess habitat
 quality of stormwater management ponds and adjacent urban uplands forwood
 frogs (Lithobates sylvaticus) and American toads (Anaxyrus americanus), we
 compared life history characteristics between populations breeding across
 an urbanization gradient. Specifically, we compared body size, ages of
 breeding adults, and female reproductive investment among urban, suburban,
 and rural populations in Baltimore County, Maryland, USA. Although there
 was variation in age at maturity among populations, ages of breeding
 adults did not differ among urban, suburban, and rural areas. Maternal
 body size strongly influenced reproductive investment in both species, but
 relationships did not vary among urban, suburban, and rural populations.
 Adult wood frogs and American toads from more urbanized landscapes were
 significantly smaller at age than conspecifics from rural landscapes; the
 magnitude of differences was similar across adult age classes. Our results
 suggest that in the urban and rural landscapes that we studied, adult
 habitats are similar in quality, but either larval or juvenile habitats
 may be of lower quality in urban areas.
description: ToadAgeReduceEggsWood.csvEggsToadMalestoadagefemalestoadageMaleswoodagefemaleswoodagesummarymalewoodsummarymaletoadsummaryfemalewoodsummaryfemaletoadsToadAgeReduceFrogAgeReduce
DOI: 10.5061/dryad.tt47r
title: Data from: The legend of the Canadian horse: genetic diversity and breed origin

description: The Canadian breed of horse invokes a fascinating chapter of North
 American history and as such it is now a heritage breed and the national
 horse of Canada. The aims of this study were to determine the level of
 genetic diversity in the Canadian, investigate the possible foundation
 breeds and the role it had in the development of the US horse breeds, such
 as Morgan Horse. We tested a total of 981 horses by using 15
 microsatellite markers. We found that Canadian horses have high values of
 genetic diversity indices and show no evidence of a serious loss of
 genetic diversity and the inbreeding coefficient was not significantly
 different from zero. Belgian, Percheron, Breton and Dales Pony, unlike the
 light French horses, may have common ancestries with the Canadian and
 could be important founders. However, the Shire and Clydesdale influenced
 the Canadian to a lesser extent than French and Belgian draft breeds.
 Furthermore, our finding indicated that there was no evidence of a clear
 relationship between Canadian and Oriental or Iberian breeds. Also, the
 Canadian likely contributed to the early development of the Morgan.
 Finally, these findings support the ancient legends of the Canadian Horse
 as North America’s first equine breed and the foundation bloodstock to
 many American breeds and may help in the management and breeding program
 of this outstanding breed in North America.
description: Genotypes data
 fileGenotypes_Genepop
DOI: 10.5061/dryad.sc833
title: Data from: The large X-effect on secondary sexual characters and the genetics of variation in sex comb tooth number in Drosophila subobscura

description: Genetic studies of secondary sexual traits provide insights into whether
 and how selection drove their divergence among populations, and these
 studies often focus on the fraction of variation attributable to genes on
 the X-chromosome. However, such studies may sometimes misinterpret the
 amount of variation attributable to the X-chromosome if using only simple
 reciprocal F1 crosses, or they may presume sexual selection has affected
 the observed phenotypic variation. We examined the genetics of a secondary
 sexual trait, male sex comb size, in Drosophila subobscura. This species
 bears unusually large sex combs for its species group, and therefore, this
 trait may be a good candidate for having been affected by natural or
 sexual selection. We observed significant heritable variation in number of
 teeth of the distal sex comb across strains. While reciprocal F1 crosses
 seemed to implicate a disproportionate X-chromosome effect, further
 examination in the F2 progeny showed that transgressive autosomal effects
 inflated the estimate of variation associated with the X-chromosome in the
 F1. Instead, the X-chromosome appears to confer the smallest contribution
 of all major chromosomes to the observed phenotypic variation. Further, we
 failed to detect effects on copulation latency or duration associated with
 the observed phenotypic variation. Overall, this study presents an
 examination of the genetics underlying segregating phenotypic variation
 within species and illustrates two common pitfalls associated with some
 past studies of the genetic basis of secondary sexual traits.
description: R codeR code used for QTL
 mapping sex comb variation and QTL effect size
 estimatesR_code.txtStrain Variation DataAverage of distal & proximal sex comb size for individual males from 5 lines of D. subobscuraPopulationVariationData.csvX-chromosome mapping filerQTL-formatted data file with male genotypes from 13 loci along X-chromosome. Relative map locations also listed in row 3. Individual proximal or distal sex combs measured as prox1, distal1, prox2, distal2, and then average sex comb size (when one sex comb was lost, the remaining assumed to be average). Plate, row, and column depict location in 96-well plates, and cytoplasm indicates grandmother strain (used to test for maternal effects).subf2rqtlonlyx.csvMapping data filerQTL-formatted data file as above but with single marker genotypes from each chromosome.subMapMain.csvCourtship/ mating experiments dataData include time prior to copulation (TimePreCop) and duration of copulation (TimeCop). Distal sex comb sizes given as "Bigger" and "Smaller", and the average is given as well as the difference. The file also indicates if the flies mated as well as notes. Notes like "D2=7+2" mean one distal sex comb was "broken" into two segments with 7 and 2 teeth respectively.SubMate.csv
DOI: 10.5061/dryad.b8d0g
title: Data from: Anthrax toxin receptor 1 is essential for arteriogenesis in a mouse model of hindlimb ischemia

description: Anthrax toxin receptor 1/tumor endothelial marker 8 (Antxr1 or TEM8) is
 up-regulated in tumor vasculature and serves as a receptor for anthrax
 toxin, but its physiologic function is unclear. The objective of this
 study was to evaluate the role of Antxr1 in arteriogenesis. The role of
 Antxr1 in arteriogenesis was tested by measuring gene expression and
 immunohistochemistry in a mouse model of hindlimb ischemia using wild-type
 and ANTXR1-/- mice. Additional tests were performed by measuring gene
 expression in in vitro models of fluid shear stress and hypoxia, as well
 as in human muscle tissues obtained from patients having peripheral artery
 disease. We observed that Antxr1 expression transiently increased in
 ischemic tissues following femoral artery ligation and that its expression
 was necessary for arteriogenesis. In the absence of Antxr1, the mean
 arterial lumen area in ischemic tissues decreased. Antxr1 mRNA and protein
 expression was positively regulated by fluid shear stress, but not by
 hypoxia. Furthermore, Antxr1 expression was elevated in human peripheral
 artery disease requiring lower extremity bypass surgery. These findings
 demonstrate an essential physiologic role for Antxr1 in arteriogenesis and
 peripheral artery disease, with important implications for managing
 ischemia and other arteriogenesis-dependent vascular diseases.
description: Andersen PLoS One
 2015This file contains data
 used to generate the figures in this manuscript.
DOI: 10.5061/dryad.47nm0
title: Data from: Population genetic structure within and among seasonal site types in the little brown bat (Myotis lucifugus) and the northern long-eared bat (M. septentrionalis)

description: During late summer and early autumn, temperate bats migrate from their
 summering sites to swarming sites, where mating likely occurs. However,
 the extent to which individuals of a single summering site migrate to the
 same swarming site, and vice versa, is not known. We examined the
 migratory connectivity between summering and swarming sites in two
 temperate, North American, bat species, the little brown bat (Myotis
 lucifugus) and the northern long-eared bat (Myotis septentrionalis). Using
 mitochondrial and microsatellite DNA markers, we examined population
 structuring within and among summering and swarming sites. Both species
 exhibited moderate degrees of mitochondrial DNA differentiation (little
 brown bat: FST(SWARMING) = 0.093, FST(SWARMING) = 0.052; northern
 long-eared bat: FST(SWARMING) = 0.117, FST(SWARMING) = 0.043) and little
 microsatellite DNA differentiation among summering and among swarming
 sites. Haplotype diversity was significantly higher at swarming sites than
 summering sites, supporting the idea that swarming sites are comprised of
 individuals from various summering sites. Further, pairwise analyses
 suggest that swarming sites are not necessarily comprised of only
 individuals from the most proximal summering colonies.
description: MYLU_microsatellites_Genepop_infile.txtThis file contains the genotypes (at 9 loci) of M. lucifugus bats at 29 sites in New Brunswick and Nova Scotia, Canada.MYSE_microsatellites_Genepop_infileThis file contains the genotypes (at 9 loci) of M. septentrionalis bats at 15 sites in New Brunswick and Nova Scotia, Canada.
DOI: 10.5061/dryad.6n89r74
title: Data from: Planning protected areas network that are relevant today and under future climate change is possible: the case of Atlantic Forest endemic birds

description: Background. A key strategy in biodiversity conservation is the
 establishment of protected areas. In the future, however, the
 redistribution of species in response to ongoing climate change is likely
 to affect species’ representativeness in those areas. Here we quantify the
 effectiveness of planning protected areas network to represent 151 birds
 endemic to the Brazilian Atlantic Forest hotspot, under current and future
 climate change conditions for 2050. Methods. We combined environmental
 niche modeling and systematic conservation planning using both a county
 and a regional level planning strategy. We recognized the conflict between
 biodiversity conservation and economic development, including
 socio-economic targets (as opposed to biological only) and using planning
 units that are meaningful for policy-makers. Results. We estimated an
 average contraction of 29,500 km² in environmentally suitable areas for
 birds, representing 52% of currently suitable areas. Still, the most
 cost-effective solution represented almost all target species, requiring
 only ca. 10% of the Atlantic Forest counties to achieve that
 representativeness, independent of strategy. More than 50% of these
 counties were selected both in the current and future planned networks,
 representing &gt; 83% of the species. Discussion. Our results indicate
 that: i) planning protected areas network currently can be useful to
 represent species under climate change; ii) the overlapped planning units
 in the best solution for both current and future conditions can be
 considered as “no regret” areas; iii) priority counties are spread
 throughout the biome, providing specific guidance wherever the opportunity
 of creating protected area arises, and iv) decision can occurs at
 different administrative spheres (Federal, State or County) as we found
 quite similar numerical solutions using either county or regional level
 strategies.
description: Vale et al PeerJ
 Supplemental Table S1Vale et al PeerJ
 Supplemental Table S2