cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3mf71
title: Data from: Seasonality of soil moisture mediates responses of ecosystem phenology to elevated CO2 and warming in a semi-arid grassland

description: Vegetation greenness, detected using digital photography, is useful for
 monitoring phenology of plant growth, carbon uptake, and water loss at the
 ecosystem level. Assessing ecosystem phenology by greenness is especially
 useful in spatially extensive, water-limited ecosystems such as the
 grasslands of the western United States, where productivity is moisture
 dependent and may become increasingly vulnerable to future climate change.
 We used repeat photography and a novel means of quantifying greenness in
 digital photographs to assess how the individual and combined effects of
 warming and elevated CO2 impact ecosystem phenology (greenness and plant
 cover) in a semi-arid grassland over an 8-year period. Climate variability
 within and among years was the proximate driver of ecosystem phenology.
 Individual and combined effects of warming and elevated CO2 were
 significant at times, but mediated by variation in both intra- and
 inter-annual precipitation. Specifically, warming generally enhanced plant
 cover and greenness early in the growing season but often had a negative
 effect during the middle of the summer, offsetting the early season
 positive effects. The individual effects of elevated CO2 on plant cover
 and greenness were generally neutral. Opposing seasonal variations in the
 effects of warming and less so elevated CO2 cancelled each other out over
 an entire growing season, leading to no net effect of treatments on annual
 accumulation of greenness. The main effect of elevated CO2 dampened
 quickly, but warming continued to affect plant cover and plot greenness
 throughout the experiment. The combination of warming and elevated CO2 had
 a generally positive effect on greenness, especially early in the growing
 season and in later years of the experiment, enhanced annual greenness
 accumulation. However, interannual precipitation variation had larger
 effect on greenness, with 2-3 times greater greenness in wet years than in
 dry years. Synthesis. Seasonal variation in timing and amount of
 precipitation governs grassland phenology, greenness, and the potential
 for carbon uptake. Our results indicate that concurrent changes in
 precipitation regimes mediate vegetation responses to warming and elevated
 atmospheric CO2 in semi-arid grasslands. Even small changes in vegetation
 phenology and greenness in response to warming and rising atmospheric CO2
 concentrations, such as those we report here, can have large consequences
 for the future of grasslands.
description: PHACE_Greenness_DryadPHACE_PlantCover_DryadPHACEGreennessMatlabCode
DOI: 10.5061/dryad.vv121
title: Data from: Cu1-xFexO: hopping transport and ferromagnetism

description: Single phase, sol–gel prepared Cu1–xFexO (0 ≤ x ≤ 0.125) powders are
 characterized in terms of structural, electronic and magnetic properties.
 Using dielectric and magnetic studies we investigate the coupling of
 electron and spin. The electrical conductivities and activation energies
 are studied with increasing Fe content. Modelling of experimental
 conductivity data emphasizes a single hopping mechanism for all samples
 except x = 0.125, which have two activation energies. Hole doping is
 confirmed by confirming a majority Fe3+ substitution of Cu2+ in CuO from
 X-ray photoelectron spectroscopy studies (XPS). Such a substitution
 results in stabilized ferromagnetism. Fe substitution introduces variation
 in coercivity as an intrinsic magnetic property in Fe-doped CuO, and not
 as a secondary impurity phase
description: data
 filescontains XRD, XPS,
 conductivity and magnetic data
DOI: 10.5061/dryad.h43q8
title: Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

description: Molecular data from three chloroplast markers resolve individuals
 attributable to Radula buccinifera in six lineages belonging to two
 subgenera, indicating the species is polyphyletic as currently
 circumscribed. All lineages are morphologically diagnosable, but one pair
 exhibits such morphological overlap that they can be considered cryptic.
 Molecular and morphological data justify the re-instatement of a broadly
 circumscribed ecologically variable R. strangulata, of R. mittenii, and
 the description of five new species. Two species Radula mittenii Steph.
 and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of
 north-east Queensland, suggesting high diversity and high endemism might
 characterise the bryoflora of this relatively isolated wet-tropical
 region. Radula demissa sp. nov. is endemic to southern temperate
 Australasia, and like R. strangulata occurs on both sides of the Tasman
 Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in
 association with waterways in New South Wales and Queensland. Another
 species, R. pugioniformis sp. nov., has been confused with Radula
 buccinifera but was not included in the molecular phylogeny. Morphological
 data suggest it may belong to subg. Odontoradula. Radula buccinifera is
 endemic to Australia including Western Australia and Tasmania, and to date
 is known from south of the Clarence River on the north coast of New South
 Wales. Nested within R. buccinifera is a morphologically distinct plant
 from Norfolk Island described as R. anisotoma sp. nov. Radula australiana
 is resolved as monophyletic, sister to a species occurring in east coast
 Australian rainforests, and nesting among the R. buccinifera lineages with
 strong support. The molecular phylogeny suggests several long-distance
 dispersal events may have occurred. These include two east-west dispersal
 events from New Zealand to Tasmania and south-east Australia in R.
 strangulata, one east-west dispersal event from Tasmania to Western
 Australia in R. buccinifera, and at least one west-east dispersal from
 Australia to New Zealand in R. australiana. Another west-east dispersal
 event from Australia to Norfolk Island may have led to the budding
 speciation of R. anisotoma. In contrast, Radula demissa is
 phylogeographically subdivided into strongly supported clades either side
 of the Tasman Sea, suggesting long distance dispersal is infrequent in
 this species.
description: Buccinifera_concatenated_MUSCLE_final_MrBayesConcatenated dataset for three chloroplast markers aligned separately using MUSCLE on the CIPRES portal. Has nexus block for MrBayes analysis as presented in the manuscript. The datafile should execute as is.
DOI: 10.5061/dryad.9q2v7c4
title: Data from: The effect of range overlap on ecological niche divergence depends on spatial scale in monkeyflowers

description: Patterns of niche divergence and geographical range overlap of closely
 related species provide insights into the evolutionary dynamics of
 ecological niches. When ranges overlap, shared selective pressures may
 preserve niche similarity along coarse‐scale macrohabitat axes (e.g.,
 bioclimates). Alternatively, competitive interactions may drive greater
 divergence along local‐scale microhabitat axes (e.g., micro‐topographical
 features). We tested these hypotheses in 16 species pairs of western North
 American monkeyflowers (Erythranthe and Diplacus, formerly Mimulus) with
 species’ niches, geographic ranges and a robust phylogeny. We found that
 macrohabitat niche divergence decreased with increasing range overlap,
 consistent with convergent selection operating at a coarse scale. No
 significant relationship was detected for microhabitat niches.
 Additionally, niche divergence was greater for young pairs along all
 macrohabitat niche axes, but greater for old pairs along one microhabitat
 axis related to vegetation cover. For a subset of species pairs with
 partially overlapping ranges, greater microhabitat divergence was detected
 in sympatry than in allopatry for at least one niche axis for three pairs,
 consistent with character displacement in sympatry. Thus, coarse‐ and
 local‐scale niche divergence show dissimilar patterns in relation to range
 overlap and evolutionary time, perhaps because the relative importance of
 convergent versus divergent selection depends on spatial scale.
description: Phylogeny, macrohabitat
 and microhabitat data of MimulusThree files: 1) the
 pruned phylogeny of Mimulus (in nexus format); 2) macrohabitat niche data
 for occurrences of 32 species with corresponding latitude/longitude and
 projected coordinates, including five bioclimatic variables, eight edaphic
 variables, and four topographic variables; 3) microhabitat niche data from
 plot-level measurements for each population of 32 species, including five
 variables and corresponding site types.Mimulus_Niche_Phylogeny.zip
DOI: 10.5061/dryad.j0bd4
title: Data from: Plastome mutations and recombination events in barley chloroplast mutator seedlings

description: The barley chloroplast mutator (cpm) is an allele of a nuclear gene that
 when homozygous induces several types of cytoplasmically inherited
 chlorophyll deficiencies. In this work, a plastome TILLING (Targeting
 Induced Local Lesions in Genomes) strategy based on mismatch digestion was
 used on families that carried the cpm genotype through many generations.
 Extensive scanning of 33 plastome genes and a few intergenic regions was
 conducted. Numerous polymorphisms were detected on both genic and
 intergenic regions. The detected polymorphisms can be accounted for by at
 least 61 independent mutational events. The vast majority of the
 polymorphisms originated in substitutions and small indels
 (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes
 were the most polymorphic. Interestingly, the variation observed in the
 rpl23 gene consisted of several combinations of five different one
 nucleotide polymorphisms. Besides, four large indels that have direct
 repeats at both ends were also observed, which appear to be originated
 from recombinational events. The cpm mutation spectrum suggests that the
 CPM gene product is probably involved in plastome mismatch repair. The
 numerous subtle molecular changes that were localized in a wide range of
 plastome sites show the cpm as a valuable source of plastome variability
 for plant research and/or plant breeding. Moreover, the cpm mutant appears
 to be as an interesting experimental material for investigating the
 mechanisms responsible for maintaining the stability of plant organelles
 DNA.
description: Landau SupMat 1
 genealogy of the plant materialGraphic describing the
 genealogy of the plant material used in this work.Landau SupMat 2 table of
 primers and ampliconsTable of primers and
 amplicons used for chloroplast TILLING
DOI: 10.5061/dryad.rr78s
title: Data from: A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

description: Northern and central European Arabidopsis lyrata ssp. petraea populations
 are locally adapted to prevailing climatic conditions through differences
 in timing of life history events. The timing of flowering, and in
 perennials, the timing of growth cessation influence fitness. Phytochrome
 A may have an important role in regulating these life-history traits as it
 perceives changes in daylength. We asked, whether PHYA has contributed to
 local adaptation to the northern conditions in A. l. petraea. To search
 for signals of directional selection at the PHYA locus, we resequenced
 PHYA and 9 short fragments around PHYA from a 57 kb region from a German
 (Plech) and a Norwegian (Spiterstulen) population and compared patterns of
 differentiation and diversity to a set of 19 reference loci around the
 genome. First, we found that the populations were highly differentiated:
 there were three nonsynonymous fixed differences at the PHYA locus, which
 was in stark contrast with the total four fixed differences in the 19
 reference loci. Compatible with a sweep hypothesis, variation was almost
 completely removed from the 9.4 kb region around PHYA in the northern
 Spiterstulen population. The overall level of linkage disequilibrium (LD)
 was higher in Spiterstulen, but there was no LD across the PHYA locus in
 the population, which is also a known consequence of a selective sweep.
 The sweep has likely occurred after the last glacial maximum, which
 suggests that it has contributed to adaptation to the northern conditions.
description: Input files (and output
 file) for sweep testingssw_clsw.zipAlignment files for fragments 1-11Alignment_files.zipLinkage disequilibrium patterns across 57 kb region (figures 2A and 2B)LD_across 57 kb region.fasLinkage disequilibrium patterns between flanking loci (2 and 9, figure 2D)LD_2 and 9_loci.fasFragment and sample specific Accession nosFile includes table of Accession nos for each sample in each sequenced fragment
DOI: 10.5061/dryad.sf34t61
title: Data from: Inbreeding intensifies sex- and age-dependent disease in a wild mammal

description: 1. The mutation accumulation theory of senescence predicts that
 age-related deterioration of fitness can be exaggerated when inbreeding
 causes homozygosity for deleterious alleles. A vital component of fitness,
 in natural populations, is the incidence and progression of disease. 2.
 Evidence is growing for natural links between inbreeding and ageing;
 between inbreeding and disease; between sex and ageing; and between sex
 and disease. However, there is scant evidence, to date, for links among
 age, disease, inbreeding and sex in a single natural population. 3. Using
 ecological and epidemiological data from a long-term longitudinal field
 study, we show that in wild European badgers (Meles meles) exposed
 naturally to bovine tuberculosis (bTB), inbreeding (measured as
 multi-locus homozygosity) intensifies a positive correlation between age
 and evidence of progressed infection (measured as an antibody response to
 bTB), but only among females. Male badgers suffer a steeper relationship
 between age and progressed infection than females, with no influence of
 inbred status. We found no link between inbreeding and the incidence of
 progressed infection during early-life in either sex. 4. Our findings
 highlight an age-related increase in the impact of inbreeding on a
 fitness-relevant trait (disease state) among females. This relationship is
 consistent with the predictions of the mutation accumulation theory of
 senescence, but other mechanisms could also play a role. For example,
 late-life declines in condition, arising through mechanisms other than
 mutation accumulation might have increased the magnitude of inbreeding
 depression in late-life. 5. Whichever mechanism causes the observed
 patterns, we have shown that inbreeding can influence age-dependent
 patterns of disease and, by extension, is likely to affect the magnitude
 and timing of the late-life declines in components of fitness that
 characterise senescence. Better understanding of sex-specific links
 between inbreeding, disease and ageing provides insights into
 population-level pathogen dynamics and could influence management
 strategies for wildlife reservoirs of zoonotic disease.
description: Benton2018_InbreedingDataset_DryadMicrosatellite data, individual inbreeding coefficients and demographic data from a subset of badgers from the Woodchester Park Study Population. Results of TB diagnostic tests are also included. For those interested on collaborating on the use of these data or data from the wider Woodchester Park study, please contact Professor Dez Delahay (dez.delahay@apha.gsi.gov.uk).
DOI: 10.5061/dryad.14hj1
title: Data from: Stage-dependence of phenotypical and phenological maternal effects: insight into squamate reptile reproductive strategies

description: Enhanced thermal conditions have been credited as a driving force for the
 evolution of viviparity, particularly in squamate reptiles, among which it
 has independently evolved more than 100 times. However, maternal
 thermoregulation is also a critical component of reproduction in oviparous
 squamates, for which considerable embryonic development occurs prior to
 oviposition. When carrying eggs, oviparous mothers modify thermoregulation
 in a manner similar to that of pregnant females. To further understand the
 role of temperature in influencing reproductive strategies, it is critical
 that we elucidate the degree to which thermal sensitivity varies across
 developmental stages. We studied stage-dependent embryonic sensitivity in
 a viviparous snake, the aspic viper (Vipera aspis). We manipulated female
 body temperature at different stages of pregnancy—early development, early
 embryonic growth, and late embryonic growth—by imposing two contrasting
 daily thermal cycles that mimicked reproductive (warm) and nonreproductive
 (cool) female temperature profiles. Thermal sensitivity of offspring
 phenotype was stage dependent, with offspring quality more negatively
 affected when exposure to cool temperatures occurred early in development.
 In contrast, developmental rate was slowed by the cooler cycle,
 independent of the timing of the exposure. Given the more persistent
 effect on phenology, phenological effects likely provide a greater driving
 force for complete embryonic retention (i.e., viviparity).
description: DRYAD_MorphologyDataMorphological data on neonates. data collected in the laboratory.DRYAD_MetabolismMetabolic rate collected one vipers neonates at one month of ageDRYAD_ExploExploratory behaviour measured in neonates snakes from the different thermal treatments. Data collected at birth in the laboratory.DRYAD_First preyScore of first prey acceptance in aspic viper neonates. Data collected 5 month after birth in the laboratory.DRYAD_TractionTraction force measured in aspic vipers one month after birth.
DOI: 10.5061/dryad.mb2sf
title: Data from: Genetic evidence for polygamy as a mating strategy in Caiman crocodilus

description: The mating system of the spectacled caiman (Caiman crocodilus) was
 investigated in the Piagaçu-Purus Sustainable Development Reserve,
 Amazonas, Brazil. We used six polymorphic microsatellite loci to genotype
 15 females and 174 hatchlings representing 20 nests sampled over four
 consecutive reproductive seasons (2007 to 2010). Paternity was determined
 by two methods: simple counts, and statistical analysis using Gerud 2.0.
 Results were congruent between the two approaches, and the null hypothesis
 of single paternity was rejected in 19 of the 20 nests analyzed, thereby
 demonstrating that C. crocodilus females are polyandrous and that the
 breeding system of the species can be characterized as polygamous. The
 data suggest that one to four fathers were responsible for the paternity
 of the offspring, and that the males contributed differently (9%-100%) to
 each of the 20 nests. A total of 53 males copulated with the 20 females
 mothering the nests. This is the first study on the mating system of C.
 crocodilus and the frequency of multiple paternity is among the highest
 values (95%) reported thus far for crocodilians.
description: Paternity_Deyla_080214_SI_1Genotypes of all individuals analyzed; inferred genotypes of malesPaternity_Deyla_100214_SI_1.docPaternity_Deyla_100214_SI_2Minimum number of males and their relative contribution to each clutch
DOI: 10.5061/dryad.vt87n
title: Data from: Submerged macrophytes mitigate direct and indirect insecticide effects in freshwater communities

description: Understanding how ecological interactions mitigate the impacts of
 perturbations such as pesticides in biological communities is an important
 basic and applied question for ecologists. In aquatic ecosystems, new
 evidence from microcosm experiments suggests that submerged macrophytes
 can buffer cladocerans from pulse exposures to the widely used insecticide
 malathion, and that mitigation increases with macrophyte density. However,
 whether these results scale up to more complex aquatic communities where
 ecological interactions such as competition can alter toxicity is unknown.
 Further, macrophyte abilities to mitigate different insecticide exposure
 scenarios (i.e. single versus repeated pulses) have never been tested. To
 address these gaps, we performed a factorial mesocosm experiment examining
 the influence of four macrophyte treatments (0, 10, 50, or 100 Elodea
 Canadensis shoots planted per mesocosm) crossed with three malathion
 exposure scenarios (no insecticide, single pulse, repeated pulses) on
 aquatic communities containing zooplankton, phytoplankton, periphyton, two
 snail species, and larval amphibians. In the absence of macrophytes,
 single malathion pulses caused short-term declines in cladoceran abundance
 followed by their rapid recovery, which precluded any indirect effects
 (i.e. trophic cascades). However, repeated malathion pulses caused
 cladoceran extinctions, resulting in persistent phytoplankton blooms and
 reduced abundance of one snail species. In contrast, with macrophytes
 present, even at low density, malathion had no effect on any taxa. We also
 discovered novel effects of macrophytes on the benthic food web. In the
 two highest macrophyte treatments, we observed trends of reduced
 periphyton biomass, decreased abundance of one snail species, and
 decreased amphibian time to and mass at metamorphosis. To our knowledge,
 this is the first evidence of negative submerged macrophyte effects on
 amphibians, a taxa of global conservation concern. Our findings suggest
 that facilitating macrophytes could be an important strategy for buffering
 freshwater communities from insecticides, though consideration of their
 impacts on animal species is necessary.
description: SnailAbundance&AvgMass_PLOSOneMetadata for pond snail and rams horn snail abundance and average mass.Synthesized data for analysisAll data used to analyze response variables. Some data were log-transformed before analysis.WetlandSecurity_AllData_PLOSOne.xlsxGrayTreefrogTimetoMeta&SurvivalMetadata for Gray treefrog time to metamorphosis and survival.ZooplanktonDataAllSamples_PLOSOneMetadata for Cladoceran density, Copepod density, and rotifer density.GTFMetamorphMASSPLOSOneMetadata for Gray treefrog mass.GTFMetamorphMASSandSVL_PLOSOne.xls