cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm5s0
title: Data from: Defining the role of Prolamin-box binding factor1 gene during maize domestication

description: The prolamin-box binding factor1 (pbf1) gene encodes a transcription
 factor that controls the expression of seed storage protein (zein) genes
 in maize. Prior studies show that pbf1 underwent selection during maize
 domestication although how it affected trait change during domestication
 is unknown. To assay how pbf1 affects phenotypic differences between maize
 and teosinte, we compared nearly isogenic lines (NILs) that differ for a
 maize versus teosinte allele of pbf1. Kernel weight for the teosinte NIL
 (162mg) is slightly but significantly greater than that for the maize NIL
 (156mg). RNAseq data for developing kernels show that the teosinte allele
 of pbf1 is expressed at about twice the level of the maize allele.
 However, RNA and protein assays showed no difference in zein profile
 between the two NILs. The lower expression for the maize pbf1 allele
 suggests that selection may have favored this change; however, how reduced
 pbf1 expression alters phenotype remains unknown. One possibility is that
 pbf1 regulates genes other than zeins and thereby is a domestication
 trait. The observed drop in seed weight associated with the maize allele
 of pbf1 is counterintuitive but could represent a negative pleiotropic
 effect of selection on some other aspect of kernel composition.
description: pdf all trait
 datadata for kernel
 traits.
DOI: 10.5061/dryad.gt0n2
title: Data from: The importance of terrestrial subsidies in stream food webs varies along a stream size gradient

description: Cross system subsidies of energy and materials can be a substantial
 fraction of food web fluxes in ecosystems, especially when autochthonous
 production is strongly limited by light or nutrients. We explored whether
 assimilation of terrestrial energy varied in specific consumer taxa
 collected from streams of different sizes and resource availabilities.
 Since headwater streams are often unproductive, we expected that inputs
 from surrounding terrestrial systems (i.e. leaf litter, terrestrial
 invertebrates) would be a more important food source for consumers than in
 mid-size rivers that have more open canopies and higher amounts of primary
 production available for consumers. We collected basal resources,
 invertebrates, and fish along a gradient in stream size in the Adirondack
 Mountains (NY, USA) and in Trinidad and Tobago and analyzed all samples
 for hydrogen isotopes as a means of differentiating biomass derived from
 allochthonous versus autochthonous sources. We found significant
 differences in allochthonous energy use within individual consumer taxa,
 showing that some taxa range from being entirely allochthonous to entirely
 autochthonous depending on where they were collected on the stream size
 gradient (grazers and collector–gatherer functional feeding groups), while
 other taxa are relatively fixed in the source of energy they assimilate
 (shredder and predator functional feeding groups). Consistent with
 expectations, allochthonous energy use was positively correlated with
 canopy cover in both regions for most feeding groups, with individuals
 from small, shaded streams having a more pronounced allochthonous signal
 than individuals collected from larger streams with less canopy cover.
 However, consumers in the shredder/detritivore feeding group did not vary
 among sites in their allochthonous energy use, and had a mostly
 allochthonous signal regardless of canopy cover and algal biomass. Our
 results demonstrate that the importance of energy from terrestrial
 subsidies can vary markedly but are similar in both temperate and tropical
 streams, suggesting a widely consistent pattern.
description: Adirondacks solid sample
 deuterium dataDeuterium isotope data
 for food web solid samples from the AdirondacksAdks_solidsample_dD_archive.csvAdirondacks water sample deuterium dataWater sample deuterium data for sites in the AdirondacksAdks_water_dD_archive.csvTrinidad solid sample deuterium dataSolid sample isotope data from Trinidad sitesTdad_solidsample_dD_archive.csvTrinidad water sample deuterium dataWater sample isotope data from Trinidad sitesTdad_water_dD_archive.csv
DOI: 10.5061/dryad.sg546
title: Data from: Bringing habitat information into statistical tests of local adaptation in quantitative traits: a case study of nine-spined sticklebacks

description: Detection of footprints of historical natural selection on quantitative
 traits in cross-sectional data sets is challenging, especially when the
 number of populations to be compared is small and the populations are
 subject to strong random genetic drift. We extend a recent Bayesian
 multivariate approach to differentiate between selective and neutral
 causes of population differentiation by the inclusion of habitat
 information. The extended framework allows one to test for signals of
 selection in two ways: by comparing the patterns of population
 differentiation in quantitative traits and in neutral loci, and by
 comparing the similarity of habitats and phenotypes. We illustrate the
 framework using data on variation of eight morphological and behavioral
 traits among four populations of nine-spined sticklebacks (Pungitius
 pungitius). In spite of the strong signal of genetic drift in the study
 system (average FST = 0.35 in neutral markers), strong footprints of
 adaptive population differentiation were uncovered both in morphological
 and behavioral traits. The results give quantitative support for earlier
 qualitative assessments, which have attributed the observed
 differentiation to adaptive divergence in response to differing ecological
 conditions in pond and marine habitats.
description: Microsatellite data for
 Fennoscandian Pungitius pungitiusThis data set covers 183
 individuals from 4 local populations genotyped for 12 microsatellite loci.
 The genotypes refer to sequence lengths.KarhunenEtAl_Evolution_genotypes.txtMorphological and behavioral measurements from Pungitius pungitiusThis data set involves 92 individuals from four local populations. The entry for each individual covers data needed for animal-model type analyses (parents, sex, origin of parents), behavioral and morphometric measurements. The behavioral variables involve number of attacks against stimulus conspecific, time to orient and time to 'full out' in seconds and feeding behavior recorded as a binary variable. All morphometric measurements are given in millimetres. SL refers to standard length.KarhunenEtAl_Evolution_phenotypes.txt
DOI: 10.15468/dl.vng94v
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Histioteuthis macrohista",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001207-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.25v031b
title: Data from: Testing rangeland health theory in the Northern Great Plains

description: • Correctly assessing whether rangeland ecosystem services are stable,
 improving, or degrading is of global importance. Soil aggregate stability
 (SAS) is widely used to infer rangeland health, partly because high SAS is
 thought to reduce runoff by increasing infiltration. We studied the
 sensitivity of SAS to grazing and other disturbances, the effects of SAS
 on infiltration, and the utility of alternative indicators of infiltration
 in the Northern Great Plains.• To test grazing effects on SAS, we compared
 SAS between paired areas that were lightly to moderately grazed or
 excluded from grazing for 6 years. Additionally, we compared SAS between
 grazed and not-grazed plots of a two-year controlled grazing experiment
 with moderate and severe grazing. Also, we applied herbicide, mowing, and
 fungicide treatments to test SAS responses to disturbances more generally,
 as well as effects of SAS and other factors on infiltration. To more
 generally test for a SAS-infiltration relationship, we performed a
 meta-analysis of our data combined with other data from the region. •
 Grazing often reduced stability of small macroaggregates (0.25-1 mm) in
 the controlled grazing experiment but not the paired grazing area
 experiment. Grazing had no detectible effect on SAS of larger
 macroaggregates (1-2 mm). Herbicide tended to reduce SAS, and mowing
 sometimes increased SAS. Infiltration exhibited high plot-to-plot
 variation and was not significantly affected by treatments. Variation in
 infiltration was best explained by plant community composition variables
 and was not explained by either SAS or other soil properties. Our
 meta-analysis revealed no general SAS-infiltration relationship. •
 Synthesis and applications. Our findings counter prevailing expectations
 that SAS is consistently sensitive to rangeland disturbance(s) and a
 leading indicator of soil water transport. Plant community composition
 properties were better predictors of infiltration. Our findings support
 theory that excessive grazing increases the prevalence of a grazing
 tolerant species, which was associated with low levels of infiltration
 irrespective of SAS.
description: controlled grazing
 experiment dataSoil aggregate stability
 data for the controlled grazing experiment.controlled_graz_exp.csvDisturbance experimentPlant and soil data for multi-disturbance (biocide, grazing, mowing) experiment.disturb_exp_env.csvplant community composition data for disturbance experimentPlant community composition data for disturbance experiment.disturb_exp_plant_comp.csvparameters for meta-analysisRegional data (Montana and North Dakota) describing effect sizes for aggregate stability and infiltration associations.meta-analysis_parameters.csvpaired plot grazing experimentSoil aggregate stability data for the paired plot grazing experiment.paired_plot_graz_exp.csv
DOI: 10.5061/dryad.v1ss7
title: Data from: Interspecific interactions influence contrasting spatial genetic structures in two closely related damselfly species

description: Spatial genetic structure (SGS) is largely determined by colonization
 history, landscape and ecological characteristics of the species.
 Therefore, sympatric and ecologically similar species are expected to
 exhibit similar SGSs, potentially enabling prediction of the SGS of one
 species from that of another. On the other hand, due to interspecific
 interactions, ecologically similar species could have different SGSs. We
 explored the SGSs of the closely related Calopteryx splendens and C. virgo
 within Finland and related the genetic patterns to characteristics of the
 sampling localities. We observed different SGSs for the two species.
 Genetic differentiation even within short distances in C. splendens
 suggests genetic drift as an important driver. However, we also observed
 indication of previous gene flow (revealed by a negative relationship
 between genetic differentiation and increasing potential connectivity of
 the landscape). Interestingly, genetic diversity of C. splendens was
 negatively related to density of C. virgo, suggesting that interspecific
 interactions influence the SGS of C. splendens. In contrast, genetic
 differentiation between C. virgo sub-populations was low and only
 exhibited relationships with latitude, pointing to high gene flow,
 colonization history and range margin effects as the drivers of SGS. The
 different SGSs of the two ecologically similar species cautions indirect
 inferences of SGS based on ecologically similar surrogate species.
description: Kahilainen_et_al_Calopteryx_dataThe data package includes two different folders containing a total of three datafiles, each of which is accompanied by detailed information on the provided data in a ReadMe file. Folder: Genotypes contains two tab delimited txt-files containing the diploid microsatellite genotypes for 567 Calopteryx splendens and 1401 C. virgo individuals (collected from 18 and 40 sub-populations, for C. splendens and c. virgo, respectively). Folder: Locality_data contains a single tab delimited txt-file including information on the sampling localities (i.e. sub-populations). Data provided by: Kahilainen A., Keränen I., Knott K.E.K., Kuitunen K. & Kotiaho J. S. Institution: University of Jyvaskyla, Department of Biological and Environmental Science, P.O. Box 35, FI-40014, University of Jyvaskyla, Finland.
DOI: 10.5061/dryad.9s380
title: Data from: Do male fish prefer them big and colourful? Non-random male courtship effort in a viviparous fish with negligible paternal investment

description: In the majority of sexual species, there are asymmetries in reproductive
 effort, with males typically investing more in securing matings and
 females investing more in producing offspring. This causes males to mate
 less discriminately than females. Yet males may also become choosy if the
 following conditions are met: (a) that females vary in their reproductive
 value, (b) that males can perceive this variation, and (c) that mating
 with one female reduces the possibility of mating with another. These
 conditions may be met in the livebearing Goodeidae, a clade of Mexican
 fish whose females are often brightly coloured and whose males display
 costly ornaments and courtship as the only means to obtain matings. Males
 of the black-finned goodeid (Girardinichthys viviparus) have relatively
 simple, yet costly courtship behaviour, with mating probability depending
 on the duration of one-to-one courtship episodes, thus by courting one
 female they must ignore others. We evaluated whether the decision to court
 a female depends on her phenotype. Three variables of female phenotype
 were positively linked to the duration of male visits and to the frequency
 of displays performed by males: belly area, hue (“orangeness”) and size.
 Since fecundity and offspring survival were also a positive function of
 female size, we conclude that male G. viviparus evaluate the potential
 female reproductive value and allocate their courtship effort accordingly.
 Since male courtship effort is also influenced by female colouration, we
 suggest that our findings may help explaining the recurrent evolution of
 sexually dimorphic female colouration in this clade.
description: Mendez Janovitz and
 Macias Garcia dataThis is an Excel file
 containing data in three spreadsheet (Male choice trial, Brood size,
 Offspring survival). The top row from all the spreadsheets contains the
 label of each column with the variable name and the units. The first
 spreadsheet named “Male choice trial” contains the phenotypic data from 40
 females (standard body length, belly area, dorsal fin area, hue,
 saturation and brightness) and the response of 10 males (Visit duration
 and Display frequency). The second spreadsheet named “Brood size” have the
 phenotypic data from 27 females (standard body length, belly area, dorsal
 fin area, hue, saturation and brightness) and the number of offspring they
 gave birth. The third spreadsheet named “Offspring survival” contains the
 phenotypic data from 11 females (standard body length, belly area, dorsal
 fin area, hue, saturation and brightness) as well as the number of
 offspring born, the number of offspring alive at sex weeks of age and the
 survival measured as the proportion of offspring with six weeks of age
 from those who were born.
DOI: 10.5061/dryad.16qk7vf
title: Data from: Female assortative mate choice functionally validates synthesized male odors of evolving river-lake stickleback ecotypes

description: During mate choice decisions, females of many vertebrates use male
 olfactory cues to achieve immunogenetic optimality of their offspring.
 Three-spined sticklebacks (Gasterosteus aculeatus) populating habitats
 that differ in their parasite communities evolve locally adapted
 combinations of genetic variants encoded at the Major Histocompatibility
 Complex (MHC). Such adaptation confers optimal resistance to the local
 parasite fauna. Immunogenetic signatures co-evolved with local parasites
 favor population-specific assortative mate choice behaviour. Previous
 studies have shown that female sticklebacks evaluate male MHC-associated
 olfactory cues during the process of mate choice, but how habitat-specific
 information is exchanged between males and females has remained elusive.
 Here, we directly demonstrate the molecular nature of the olfactory cue
 providing habitat-specific information. Under controlled laboratory
 conditions females that are ready to mate prefer mixtures of synthetic MHC
 peptide ligands mimicking the optimal allele number of their original
 population. These results imply that female sticklebacks can determine the
 number of MHC alleles of their prospective mates, compare it to their own
 immunogenetic status, and, if optimal with respect to the immunogenetic
 complementarity, accept the male as mate. Our results suggest a
 potentially common mechanism of ecological speciation in vertebrates that
 is based on the olfactory assessment of habitat-specific immunogenetic
 diversity.
description: Gahr et al. Data Fig.
 2aMHC
 measurements used for Fig. 2aGahr et al. Data Figure
 2bMate choice results used
 to create Fig. 2b
DOI: 10.5061/dryad.7154q
title: Data from: Speed kills: ineffective avian escape responses to oncoming vehicles

description: Animal–vehicle collisions cause high levels of vertebrate mortality
 worldwide, and what goes wrong when animals fail to escape and ultimately
 collide with vehicles is not well understood. We investigated alert and
 escape behaviours of captive brown-headed cowbirds (Molothrus ater) in
 response to virtual vehicle approaches of different sizes and at speeds
 ranging from 60 to 360 km h−1. Alert and flight initiation distances
 remained similar across vehicle speeds, and accordingly, alert and flight
 initiation times decreased at higher vehicle speeds. Thus, avoidance
 behaviours in cowbirds appeared to be based on distance rather than time
 available for escape, particularly at 60–150 km h−1; however, at higher
 speeds (more than or equal to 180 km h−1) no trend in response behaviour
 was discernible. As vehicle speed increased, cowbirds did not have enough
 time to assess the approaching vehicle, and cowbirds generally did not
 initiate flight with enough time to avoid collision when vehicle speed
 exceeded 120 km h−1. Although potentially effective for evading predators,
 the decision-making process used by cowbirds in our study appears
 maladaptive in the context of avoiding fast-moving vehicles. Our
 methodological approach and findings provide a framework to assess how
 novel management strategies could affect escape rules, and the sensory and
 cognitive abilities animals use to avoid vehicle collisions.
description: cowbird responses to
 virtual vehicle approachThese data were
 collected in a video laboratory in 2012. Brown-headed cowbirds were
 exposed to video playback of an approaching vehicle with two sizes and
 eight vehicle speeds. Alert responses (alert distance and alert time to
 collision) and flight responses (flight initiation distance and flight
 time to collision) were recorded based on the median of a group of three
 cowbirds.DeVault et al BHCO - video lab
 data.xlsx
DOI: 10.5061/dryad.c52kp
title: Data from: Cumulative and partially recoverable impacts of nitrogen addition on a temperate steppe

description: Atmospheric nitrogen (N) deposition has been shown to decrease
 biodiversity and change nutrient cycles in terrestrial ecosystems.
 However, our understanding of ecological responses to chronic N addition
 and ecological recovery from N enrichment to grassland is limited. Here we
 present evidence from an 11-year grassland experiment with a range of N
 addition rates (0, 30, 60, 120, 240, and 480 kg N ha−1 yr−1) in Inner
 Mongolia, China. Chronic N addition led to a reduction in species
 richness, Shannon Diversity Index and soil pH, and an increase in
 aboveground biomass, foliar N and soil mineral N. High N addition rates
 (240 and 480 kg N ha−1 yr−1) showed significant effects in the first and
 second years, which stabilized over time. Nitrogen addition at low rates
 (30 and 60 kg N ha−1 yr−1) took longer (e.g., ≥ 3 years) to achieve
 significant effects. The negative impacts of high N addition (480 kg N
 ha−1 yr−1) were reduced and species richness, etc., showed a limited but
 rapid recovery with the cessation of N addition. Our findings suggest
 serious and cumulative impacts of N addition on plant and soil communities
 but the potential for partial system recovery over time if N inputs
 decline or cease.
description: Figs'
 dataThe data was collected
 in field, including species richness and aboveground biomass at community
 and functional groups levels (2005-2015,except 2007 and 2012),Shannon
 diversity index at community level (2005-2014,except 2007 and 2012),
 species loss during 2005-2008 and 2013-2015.Figs
 data.xlsx
DOI: 10.5061/dryad.rr7q5
title: Data from: Quantitative analysis of the ecological dominance of benthic disaster taxa in the aftermath of the end-Permian mass extinction

description: The end-Permian mass extinction, the largest extinction of the
 Phanerozoic, led to a severe reduction in both taxonomic richness and
 ecological complexity of marine communities in its aftermath, eventually
 culminating in a dramatic ecological restructuring of communities. During
 the Early Triassic recovery interval, disaster taxa proliferated and
 numerically dominated many marine benthic invertebrate assemblages. These
 disaster taxa include the bivalve genera Claraia, Unionites, Eumorphotis
 and Promyalina, and the inarticulate brachiopod Lingularia. The exact
 nature and extent of their dominance remains uncertain. Here, a
 quantitative analysis of the dominance of these taxa within the fossil
 communities of Panthalassa and Tethys benthic realms is undertaken for the
 stages of the Early Triassic to examine temporal and regional changes in
 disaster taxon dominance as recovery progresses. Community dominance and
 disaster taxon abundance is markedly different between Panthalassic and
 Tethyan communities. In Panthalassa, community evenness is low in the
 Induan stage, but increases significantly in the Smithian and Spathian.
 This is coincident with a significant decrease in the relative abundance
 and occurrence frequency of the disaster taxa, most notably of low-oxygen
 affinity taxa Claraia and Lingularia. While the disaster taxa are present
 in post-Induan assemblages, other taxa, including two articulate
 brachiopod genera, outrank the disaster taxa in relative abundance. In the
 Tethys, assemblages are generally more even than contemporaneous
 Panthalassic assemblages. We observe an averaged trend towards more even
 communities with fewer disaster taxa in both Panthalassic and Tethyan
 assemblages over time.
description: Supplemental
 DataSupplemental data
 includes a table summarizing number of Paleobiology Database collection
 entries and fossil individuals used in the analysis per time bin,
 collection references, and localities.Supplemental.docx