cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1246
title: Data from: Teasing apart the many effects of lighting environment on opsin expression and foraging preference in bluefin killifish

description: Coloration and color vision covary with lighting in many taxa. Determining
 the mechanisms underlying these patterns is difficult because lighting
 environments can have multiple effects on signaling that occur at multiple
 time scales. Lighting environments can (1) immediately affect signal
 propagation and transmission which determine the radiance spectrum
 reaching the receiver, (2) induce variation in visual systems via
 developmental plasticity, and (3) lead to genetic differences in visual
 systems due to a history of selection in different habitats. We tease
 apart these effects on pecking preference and examine the relationship
 between pecking preference and opsin expression. Using killifish from two
 visually distinct populations (clear vs. tea-stained water), we performed
 crosses (genetics), raised animals under different lighting conditions
 (developmental plasticity), and assayed preference to peck at different
 colored dots under different lighting conditions (immediate effects).
 Pecks are interpreted as foraging preference. Developmental plasticity
 affected both pecking preference and opsin expression. Lighting
 environments also had immediate effects on pecking preference, but these
 depended on the lighting conditions animals experienced during
 development. Genetic effects were detected in opsin expression, but there
 were no corresponding effects on pecking preference. Overall, only 3.36%
 of the variation in pecking preference was accounted for by opsin
 expression.
description: TableA1.xlsThis appendix explains our sample sizes (i.e. number of tanks of fish), family sizes, and replicates for which there is missing data for either the pecking assay or opsin assay.tablea2.xlsThis data set provides the total number of pecks at red, orange, yellow, green, blue, white, and black dots summed across two replicate measures of pecking behavior for each tank in each testing environment. Some tanks only pecked on one occasion. For those, we simply report the number of pecks on that trial. Sire ID, Dam ID, Tank ID, Sire Population, Dam Population, and Rearing Environment are as reported in Table A1. Tanks with fewer than 5 total pecks in a given testing environment were excluded from the analysis.tablea2.xlsThis data set provides behavioral data for a pecking assay designed to assess the preferences of animals among different colors in a non-mating scenario. This data set provides the total number of pecks at red, orange, yellow, green, blue, white, and black dots summed across two replicate measures of pecking behavior for each tank in each testing environment. Some tanks only pecked on one occasion. For those, we simply report the number of pecks on that trial. Sire ID, Dam ID, Tank ID, Sire Population, Dam Population, and Rearing Environment are as reported in Table A1. Tanks with fewer than 5 total pecks in a given testing environment were excluded from the analysis.TableA3.xls
DOI: 10.5061/dryad.97s1k
title: Data from: Low-intensity agricultural landscapes in Transylvania support high butterfly diversity: implications for conservation

description: European farmland biodiversity is declining due to land use changes
 towards agricultural intensification or abandonment. Some Eastern European
 farming systems have sustained traditional forms of use, resulting in high
 levels of biodiversity. However, global markets and international policies
 now imply rapid and major changes to these systems. To effectively protect
 farmland biodiversity, understanding landscape features which underpin
 species diversity is crucial. Focusing on butterflies, we addressed this
 question for a cultural-historic landscape in Southern Transylvania,
 Romania. Following a natural experiment, we randomly selected 120 survey
 sites in farmland, 60 each in grassland and arable land. We surveyed
 butterfly species richness and abundance by walking transects with four
 repeats in summer 2012. We analysed species composition using Detrended
 Correspondence Analysis. We modelled species richness, richness of
 functional groups, and abundance of selected species in response to
 topography, woody vegetation cover and heterogeneity at three spatial
 scales, using generalised linear mixed effects models. Species composition
 widely overlapped in grassland and arable land. Composition changed along
 gradients of heterogeneity at local and context scales, and of woody
 vegetation cover at context and landscape scales. The effect of local
 heterogeneity on species richness was positive in arable land, but
 negative in grassland. Plant species richness, and structural and
 topographic conditions at multiple scales explained species richness,
 richness of functional groups and species abundances. Our study revealed
 high conservation value of both grassland and arable land in low-intensity
 Eastern European farmland. Besides grassland, also heterogeneous arable
 land provides important habitat for butterflies. While butterfly diversity
 in arable land benefits from heterogeneity by small-scale structures,
 grasslands should be protected from fragmentation to provide sufficiently
 large areas for butterflies. These findings have important implications
 for EU agricultural and conservation policy. Most importantly,
 conservation management needs to consider entire landscapes, and implement
 appropriate measures at multiple spatial scales.
description: Data from: Low-intensity
 agricultural landscapes in Transylvania support high butterfly diversity:
 implications for conservationSpecies abundance and
 environmental data from Loos et al. 2014Loos et al 2014
 Butterflies.xls
DOI: 10.15468/dl.syg8wz
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Thamnophis pulchrilatus",
 "Year 1960-2026"
 ]
}

 The dataset includes 247 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000730-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sm3tg
title: Data from: Plant species richness and shrub cover attenuate drought effects on ecosystem functioning across Patagonian rangelands

description: Drought is an increasingly common phenomenon in drylands as a consequence
 of climate change. We used 311 sites across a broad range of environmental
 conditions in Patagonian rangelands to evaluate how drought severity and
 temperature (abiotic factors) and vegetation structure (biotic factors)
 modulate the impact of a drought event on the annual integral of
 normalized difference vegetation index (NDVI-I), our surrogate of
 ecosystem functioning. We found that NDVI-I decreases were larger with
 both increasing drought severity and temperature. Plant species richness
 (SR) and shrub cover (SC) attenuated the effects of drought on NDVI-I.
 Grass cover did not affect the impacts of drought on NDVI-I. Our results
 suggest that warming and species loss, two important imprints of global
 environmental change, could increase the vulnerability of Patagonian
 ecosystems to drought. Therefore, maintaining SR through appropriate
 grazing management can attenuate the adverse effects of climate change on
 ecosystem functioning.
description: DatasetESM4.xls
DOI: 10.5061/dryad.22pr0
title: Data from: Facilitation consequences for reproduction of the benefactor cushion plant Laretia acaulis along an elevational gradient: costs or benefits?

description: Environmental stress may favour facilitative interactions among plants but
 whether these interactions are positive for the benefactor and how this
 depends on stress factors, remains to be determined. We studied the effect
 of beneficiary cover and biomass on reproduction of the benefactor cushion
 plant Laretia acaulis (Apiaceae) in the central Chilean Andes during three
 years. Study sites were situated along an elevational gradient at 2600,
 2800, 3000 and 3150 m a.s.l. This range comprises a cold- and a
 drought-stress gradient, with moisture increasing and temperature
 decreasing with elevation. We studied the effect of natural gradients in
 beneficiary cover and of experimental cover removal on cushion flower and
 fruit production. Beneficiary cover had a negative effect on flower
 production but not on infructescence and fruit densities or fruit weights.
 A positive effect of beneficiaries on the fraction of flowers converted
 into fruits was detected for hermaphrodite cushions. The effect of
 beneficiary cover on flowering was independent of elevation or cushion
 gender, although these latter factors explained most of the variation.
 Removing the aboveground parts of the beneficiaries positively affected
 flowering at 2800 m a.s.l. but not at the other elevations. Our results
 suggest negative effects of facilitation on L. acaulis flowering, but
 these are neutralized in fruit production. Surprisingly, this conclusion
 holds along the entire elevational or stress gradient. This suggests that
 this system of facilitation is evolutionarily stable and not very
 sensitive to environmental change. It remains to be tested, however,
 whether facilitation affects fitness via growth and long-term survival in
 these slow-growing alpine cushions.
description: Data set of Laretia
 acaulis reproductive outputs in 2012, 2013, and 2014 in the high Andes of
 central ChileDetails of the
 spreadsheet: 1. Data set of Laretia acaulis reproductive output in 2012,
 2013, and 2014 of intact cushions. See also Fig. 1 of the original
 article. 2. Dataset of Laretia acaulis reproductive output in 2012 as
 functions of A) beneficiary cover (n=80, but n=60 at 2800 m a.s.l.) or B)
 biomass (n=40, only 2600, 3000 and 3150 m a.s.l.). For a statistical
 summary see Tables 1 and 2, and Fig. 2 and 3 of the orginal article. 3.
 Data set of Laretia acaulis reproductive output as a function of
 experimental beneficiary removal. A) for three elevations (2600, 3000 and
 3150 m), one or two years after removal, B) for 2800 m a.s.l., one, two or
 three years after removal. For a statistical summary see Table 3 andFig. 4
 of the original article.15.06.09_Dataset.xlsx
DOI: 10.5061/dryad.tc4n6
title: Data from: Arthropod but not bird predation in Ethiopian homegardens is higher in tree-poor than in tree-rich landscapes

description: Bird and arthropod predation is often associated with natural pest control
 in agricultural landscapes, but the rates of predation may vary with the
 amount of tree cover or other environmental factors. We examined bird and
 arthropod predation in three tree-rich and three tree-poor landscapes
 across southwestern Ethiopia. Within each landscape we selected three
 tree-rich and three tree-poor homegardens in which we recorded the number
 of tree species and tree stems within 100 × 100 m surrounding the central
 house. To estimate predation rates, we attached plasticine caterpillars on
 leaves of two coffee and two avocado shrubs in each homegarden, and
 recorded the number of attacked caterpillars for 7–9 consecutive weeks.
 The overall mean daily predation rate was 1.45% for birds and 1.60% for
 arthropods. The rates of arthropod predation varied among landscapes and
 were higher in tree-poor landscapes. There was no such difference for
 birds. Within landscapes, predation rates from birds and arthropods did
 not vary between tree-rich and tree-poor homegardens in either tree-rich
 or tree-poor landscapes. The most surprising result was the lack of
 response by birds to tree cover at either spatial scale. Our results
 suggest that in tree-poor landscapes there are still enough non-crop
 habitats to support predatory arthropods and birds to deliver strong
 top-down effect on crop pests.
description: bird and arthropod
 predation rateThe bird and arthropod
 predation rates data on plasticine caterpillars was collected from 6 home
 gardens of each six agricultural landscapes of southwest Ethiopia. The
 data also includes the heterogeneity variation among home gardens and
 landscapes.predation_env
 data.xlsx
DOI: 10.5061/dryad.8272
title: Data from: Small-scale variation in fuel loads differentially affects two co-dominant bunchgrasses in a species-rich pine savanna

description: Ecological disturbances frequently control the occurrence and patterning
 of dominant plants in high-diversity communities like C4 grasslands and
 savannas. In such ecosystems disturbance-related processes can have
 important implications for species, and for whole communities when those
 species are dominant, yet mechanistic understanding of such processes
 remains fragmentary. Multiple bunchgrass species commonly co-dominate
 disturbance-dependent and species-rich pine savannas, where small-scale
 fuel heterogeneity may influence bunchgrass survival and growth following
 fires. We quantified how fire in locally varying fuel loads influenced
 dynamics of dominant C4 bunchgrasses in a species-rich pine savanna in
 southeastern Louisiana, USA. We focused on two congeneric, co-dominant
 species (Schizachyrium scoparium and S. tenerum) with similar growth
 forms, functional traits and reproductive strategies to highlight effects
 of fuel heterogeneity during fires. In experimental plots with either
 reduced or increased fuels versus controls with unmanipulated fuels, we
 compared: 1) bunchgrass damage and 2) mortality from fires; 3) subsequent
 growth and 4) flowering. Compared to controls, fire with increased fuels
 caused greater damage, mortality and subsequent flowering, but did not
 affect post-fire growth. Fire with reduced fuels had no effect on any of
 the four measures. The two species responded differently to fire with
 increased fuels – S. scoparium incurred measurably more damage and
 mortality than S. tenerum. Logistic regression indicated that the larger
 average size of S. tenerum tussocks made them resistant to more severe
 burning where fuels were increased. We speculate that locally increased
 fuel loading may be important in pine savannas for creating colonization
 sites because where fuels are light or moderate, dominant bunchgrasses
 persist through fires. Small-scale heterogeneity in fires, and differences
 in how species tolerate fire may together promote shared local dominance
 by different bunchgrasses.
description: Gagnon et al.
 Bunchgrasses & Fuel Treatment DataDataset of bunchgrass
 tussocks (their size and number) collected at Camp Whispering Pines Girl
 Scout Camp in Tangipahoa Parish in SE Louisiana during the growing season
 of 2007 as part of a study of fire and fuel treatment effects on
 bunchgrass dominance.
DOI: 10.5061/dryad.g40f0
title: Data from: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

description: Early pig farmers in Europe imported Asian pigs to cross with their local
 breeds in order to improve traits of commercial interest. Current genomics
 techniques enabled genome-wide identification of these Asian introgressed
 haplotypes in modern European pig breeds. We propose that the Asian
 variants are still present because they affect phenotypes that were
 important for ancient traditional, as well as recent, commercial pig
 breeding. Genome-wide introgression levels were only weakly correlated
 with gene content and recombination frequency. However, regions with an
 excess or absence of Asian haplotypes (AS) contained genes that were
 previously identified as phenotypically important such as FASN, ME1, and
 KIT. Therefore, the Asian alleles are thought to have an effect on
 phenotypes that were historically under selection. We aimed to estimate
 the effect of AS in introgressed regions in Large White pigs on the traits
 of backfat (BF) and litter size. The majority of regions we tested that
 retained Asian deoxyribonucleic acid (DNA) showed significantly increased
 BF from the Asian alleles. Our results suggest that the introgression in
 Large White pigs has been strongly determined by the selective pressure
 acting upon the introgressed AS. We therefore conclude that human-driven
 hybridization and selection contributed to the genomic architecture of
 these commercial pigs.
description: haplotypes_infoInformation on the background of haplotypes (Asian, European or both) for all Large White pigs.phenotypes_infoInformation on the phenotypes backfat and litter size for all Large White pigs in the experiment.
DOI: 10.5061/dryad.k2f0n
title: Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads

description: Several individuals of the Caribbean Zamia clade and other cycad genera
 were used to identify single copy nuclear genes for phylogeographic and
 phylogenetic studies in Cycadales. Two strategies were employed to select
 target loci: 1) a tblastX search of Arabidopsis conserved ortholog
 sequence (COS) set and, 2) a tblastX search of
 Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC)
 against the EST Zamia databases in Genbank. From the first strategy, 30
 loci were selected, and from the second, 16 loci. In both cases the
 matching Genbank accessions of Zamia were used as a query for retrieving
 highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba.
 After retrieving and aligning all the sequences in each locus, intron
 predictions were completed to assist in primer design. PCR was carried out
 in three rounds to detect paralogous loci. A total of 29 loci were
 successfully amplified as a single band of which 20 were likely single
 copy loci. These loci showed different diversity and divergence levels. A
 preliminary screening allowed us to select 8 promising loci (40S, ATG2,
 BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci
 (COS26, GroES, GTP and HTS) for all other cycad genera.
description: MER-13-0343Nexus matrix. see ReadMe file for sample codes
DOI: 10.5061/dryad.22rh6
title: Data from: Experimental evolution reveals that sperm competition intensity selects for longer, more costly sperm

description: It is the differences between sperm and eggs that fundamentally underpin
 the differences between the sexes within reproduction. For males, it is
 theorized that widespread sperm competition leads to selection for
 investment in sperm numbers, achieved by minimizing sperm size within
 limited resources for spermatogenesis in the testis. Here, we empirically
 examine how sperm competition shapes sperm size, after more than 77
 generations of experimental selection of replicate lines under either high
 or low sperm competition intensities in the promiscuous flour beetle
 Tribolium castaneum. After this experimental evolution, populations had
 diverged significantly in their sperm competitiveness, with sperm in
 ejaculates from males evolving under high sperm competition intensities
 gaining 20% greater paternity than sperm in ejaculates from males that had
 evolved under low sperm competition intensity. Males did not change their
 relative investment into sperm production following this experimental
 evolution, showing no difference in testis sizes between high and low
 intensity regimes. However, the more competitive males from high sperm
 competition intensity regimes had evolved significantly longer sperm and,
 across six independently selected lines, there was a significant
 association between the degree of divergence in sperm length and average
 sperm competitiveness. To determine whether such sperm elongation is
 costly, we used dietary restriction experiments, and revealed that
 protein-restricted males produced significantly shorter sperm. Our
 findings therefore demonstrate that sperm competition intensity can exert
 positive directional selection on sperm size, despite this being a costly
 reproductive trait.
description: Godwin et al 2017 Sperm
 competition and sperm length raw dataContains raw data
 collected during all assays described by the paper.
DOI: 10.5061/dryad.c8r43
title: Data from: No effect of seed source on multiple aspects of ecosystem functioning during ecological restoration: cultivars compared to local ecotypes of dominant grasses

description: Genetic principles underlie recommendations to use local seed, but a
 paucity of information exists on the genetic distinction and ecological
 consequences of using different seed sources in restorations. We
 established a field experiment to test whether cultivars and local
 ecotypes of dominant prairie grasses were genetically distinct and
 differentially influenced ecosystem functioning. Whole plots were assigned
 to cultivar and local ecotype grass sources. Three subplots within each
 whole plot were seeded to unique pools of subordinate species. The
 cultivar of the increasingly dominant grass, Sorghastrum nutans, was
 genetically different than the local ecotype, but genetic diversity was
 similar between the two sources. There were no differences in aboveground
 net primary production, soil carbon accrual, and net nitrogen
 mineralization rate in soil between the grass sources. Comparable
 productivity of the grass sources among the species pools for four years
 shows functional equivalence in terms of biomass production. Subordinate
 species comprised over half the aboveground productivity, which may have
 diluted the potential for documented trait differences between the grass
 sources to influence ecosystem processes. Regionally developed cultivars
 may be a suitable alternative to local ecotypes for restoration in
 fragmented landscapes with limited gene flow between natural and restored
 prairie and negligible recruitment by seed.
description: ISSR Data for
 Sorghastrum nutans.xlsxExcel
 spreadsheetISSR data for Sorghastrum
 nutans.xlsxANPP_2006 to 2009_Figs 2
 3 4Soil C and N stock_2006
 2011Net N Mineralization
 Rate 2009