cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6q573n612
title: Environment regimes play an important role in structuring trait- and taxonomy-based temporal beta diversity of riverine diatoms

description: This dataset is from the manuscript 'Environment regimes play an
 important role in structuring trait-and taxonomy-based temporal beta
 diversity of riverine diatoms' whereby daily riverine diatom data,
 flow, nutrients and metal ions data were used to examine i) the
 relative roles of turnover and nestedness components to trait- and
 taxonomy-based temporal beta diversity of riverine diatoms; ii) whether
 trait-based temporal beta diversity provides complementary information to
 taxonomy-based temporal beta diversity; iii) the relative roles of
 hydrology (e.g., discharge, antecedent precipitation index), metal ions
 (e.g., Mg2+, Si2+), and nutrients (e.g., nitrogen, orthophosphate) to the
 both facets of temporal beta diversity and their components (i.e., total
 beta diversity, turnover, and nestedness); and iv) whether inclusion of
 environment regimes increase their explained variations. Therefore, this
 dataset contains three different data: 1) daily species composition
 (date*species); 2) species trait (species * traits); 3) environmental
 variables (date*environmental variables). 
description: We collected daily mixed water
 samples at the outlet of the catchment (i.e. Kielstau catchment, Germany)
 from April 25, 2013 to April 30, 2014. Using two automatic samplers, daily
 mixed water samples were collected and kept in the refrigerators at 4 °C.
 They were picked once a week (normally on Monday) and taken back to the
 lab of the Department of Hydrology and Water Resources Management of Kiel
 University. In the lab,
 Hydrogen Peroxide Method (30% H2O2 solution) and Naphrax (Northern
 Biological supplies Ltd., UK, R1=1.74) were used to prepare permanent
 diatom slides. We counted
 a minimum of 300 valves for each sample using a Zeiss Axioskop microscope
 at 1000× under oil immersion. Diatoms were identified to the lowest
 taxonomic level possible (mainly species
 level). Water chemical parameters, including metal ions
 (Cl-, K+, Ca+, Na+, Mg2+ and Si2+), ammonium-nitrogen (NH4-N),
 nitrate-nitrogen (NO3-N), orthophosphate (PO4-P), and sulphate (SO42-),
 were measured in the lab (for methods, see Appendix S1). We also collected
 hydrological variables included daily discharge (Q), discharge skewness
 (Sk), precipitation (Prec), and antecedent precipitation index
 (API). We computed both flow (using Q) and nutrient (using NH4-N, NO3-N, and PO4-P) regimes with R package SER (Guo et al., 2019).
DOI: 10.6086/d1dt2t
title: Data for: Community science reveals high diversity of nectaring plants visited by painted lady butterflies (Lepidoptera: Nymphalidae) in California sage scrub

description: California’s sage scrub habitats support a diversity of nectar and host
 plants for migrating and resident populations of painted lady butterflies
 (Vanessa cardui) throughout all seasons. The V. cardui North American
 migration is not an annual occurrence and is instead dependent on winter
 weather patterns at breeding grounds near the US–Mexico border. Thus, the
 irregularity of these migrations makes it difficult to study floral
 resource use along the migration route. Here we used the community science
 platform iNaturalist to quantify patterns in V. cardui nectar resource use
 in sage scrub over time and space during both migratory and non-migratory
 years. We identified over 329 different nectaring plant species of varying
 functional types (72% native to California) visited by adult V. cardui,
 195 of which had not been previously identified as known nectar plants for
 V. cardui. Vanessa cardui butterflies were observed in similar locations
 regardless of whether a migration occurred, indicating the presence of
 resident painted lady populations across California. Moreover, migration
 years were positively correlated with warmer and wetter local conditions
 at observation locations. Our results provide new insights into patterns
 of floral resource use by North American V. cardui by harnessing the power
 of community science data and while highlighting the factors associated
 with its periodic North American migration.
description: Painted lady observations were downloaded from iNaturalist
 (iNaturalist.org) and plants identified from each observation. We also
 extracted date, time, and climate data for the location of each
 observation.
description: data are in the first tab of the xlsx file and the explanation of
 all columns are in the metadata tab.
DOI: 10.5061/dryad.jsxksn0bp
title: SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission

description: Genetic diversity and population structure of Plasmodium falciparum are
 assessed here using three established methods (i) SNP barcoding (panel of
 24-biallelic loci), (ii) microsatellite genotyping (panel of
 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene
 diversity, akin to microhaplotyping) to identify changes in parasite
 population genetics in response to a short-term indoor residual spraying
 (IRS) intervention. Typical of high seasonal transmission in Africa,
 multiclonal infections were found in 82.3% (median 3; range 1–18) and
 57.8% (median 2; range 1–12) of asymptomatic individuals pre- and
 post-IRS, respectively, in Bongo District, Ghana. Since directly phasing
 multilocus haplotypes for population genetic analysis is not possible for
 biallelic SNPs and microsatellites, we chose 200 low-complexity infections
 for analysis. Each genotyping method presented a different pattern of
 change in population diversity and structure as a consequence of
 variability in usable data and the relative polymorphism of the molecular
 markers (SNPs &lt; microsatellites &lt; var). In terms of neutral
 variation, the 24-SNP barcode was the least informative, largely due to
 the bi-allelic nature of SNPs leading to a high proportion of
 double-allele calls (DACs), whereas multiallelic microsatellites showed
 high haplotype diversity with ten markers but no measurable change in
 population structure after IRS. Varcoding provided the most informative
 and nuanced description of changes in population structure, showing high
 diversity with a subtle but measurable change to less related var
 repertoires as a result of the IRS intervention. Relative performance,
 suitability, and cost-effectiveness of the methods relevant to local
 malaria elimination in high-transmission endemic areas are
 discussed. 
description: Data has been provided as a tab-delimited text file in genalex
 format with haploid SNP allele data, sorted by Survey (1 or 3) and
 Population (Bongo). We present the data for "all infections"
 (including MOI=1 and MOI&gt;1) and "single-clone infections"
 (MOI = 1). Sample IDs with the suffix “_M” represent the multi-clonal
 isolates (MOI &gt;1) and those with "_S" represent the
 remaining single-clone isolates that have MOI=1.
DOI: 10.5061/dryad.vmcvdncvc
title: Telomere length links with physiological phenotype and breeding patterns in a long-lived seabird

description: Telomere length (TL) is known to covary with a suite of physiological
 traits involved in energy balances that may influence breeding success.
 Thus, TL may be an indicator of individual-quality, influencing mate
 choice and breeding strategies. In the brown booby (Sula leucogaster), a
 long-lived seabird, we investigated in a total of 72 pairs, whether TL may
 indicate the individual physiological phenotype by examining how it
 relates to mitochondrial DNA copy number (mtDNAcn) and corticosterone
 (CORT) levels. Then, we tested if TL is associated with mating patterns by
 looking for covariation with skin coloration (a condition-dependent sexual
 trait), whether there is assortative mating by TL, and if the degree of TL
 similarity between partners influences an individual’s likelihood of
 changing mates between reproductive seasons. Because environmental
 conditions can have important effects on the condition and reproductive
 strategies of individuals, the study was performed in two colonies with
 contrasting breeding conditions. We found that TL was positively related
 to mtDNAcn (but not CORT levels), suggesting that individuals with shorter
 telomeres may have a reduced mitochondrial density. TL was reflected in
 sexual coloration, but only in the colony with good breeding conditions.
 There was positive assortative mating by TL, however, the degree of
 assortative mating was unrelated to the probability of mate change, which
 greatly varied between the two colonies. Our results suggest that TL is
 associated with the physiological phenotype of individuals and their
 breeding patterns. Importantly, contrasting environmental conditions
 influenced the link between TL and sexual coloration and the propensity of
 individuals to change mate, highlighting the importance of environmental
 variation on mating patterns.
description: Brown boobies (<em>Sula leucogaster</em>) were
 studies in two colonies (Islas Marietas and Isla San Jorge, Mexico) to
 test whether telomere length (TL) may indicate individual pace-of-life by
 examining how it relates to mitochondrial DNA copy number (mtDNAcn),
 baseline corticosterone (cort) levels, and skin coloration—a
 condition-dependent sexual trait. We also tested whether there is
 assortative mating by TL, and whether the degree of TL similarity between
 partners influences an individual’s likelihood of changing mates and
 physiological state (mtDNAcn and cort levels).
description: A description of the variables is included in the file.
DOI: 10.5061/dryad.b5mkkwhfg
title: Data set for: Effects of microstructure evolution on compressive strength of silica sand-enhanced oil well cement at a wide temperature range

description: The influence of microstructure of silica-enhanced cement on the
 mechanical performance of cement is difficult to be described. In this
 study, we used the scanning electron microscope and image processing
 method to investigate the relationship between the complicity of cement
 microstructure and compressive strength under various temperature and
 curing time conditions. Fractal dimension was applied to describe the
 complicity of cement. The relationships among compressive strength,
 fractal dimension, temperature, curing time and pore structure of cement
 were identified. The results show that curing time of cement directly
 control the complicity of cement microstructure and compressive strength
 by altering the pore orientation and macropore ratio in cement. The curing
 temperature affects the complicity of cement microstructure and
 compressive strength indirectly by changing the ratio of micropore and
 small pore. The fractal dimension of silica-enhanced cement shows good
 correlation with compressive strength. Pore size distribution is the most
 important factor that influence the complicity of cement matrix and
 compressive strength of silica-enhanced cement. When building up the
 macroscopic mechanical performance model of cement, we should consider the
 influence of pore size distribution in cement under different curing
 temperatures and times on the complicity of cement microstructure.
DOI: 10.5061/dryad.j3tx95xgh
title: Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)

description: Loss of biodiversity is accelerating, including the loss of genetic
 diversity. Conservation of small, isolated populations may be important,
 as they can provide valuable contributions to overall genetic variation
 and long-term viability of species. Furthermore, such populations may play
 an essential role in adaptation to new environments following changes in
 e.g. land-use and climate. Dracocephalum ruyschiana is a threatened plant
 species throughout its European distribution, but 25% of the European
 populations are situated within Norway. Therefore, the species has its own
 action plan in Norway, which includes demographic monitoring. However,
 this monitoring does not cover genetic variation nor is the selection of
 monitored populations based on genetic differentiation, therefore this
 fundamental level of biodiversity is overlooked. We analyzed 43 sites
 using 96 SNPs developed for D. ruyschiana, to investigate whether the
 monitored populations cover the genetic variation and differentiation
 found within the Norwegian distribution. The results show structuring and
 differentiation between populations and indicate that there are at least
 four distinct genetic groups, of which only two are covered extensively by
 current demographic monitoring. We suggest that two sites representing the
 two other genetic groups should be included in the national monitoring
 program to better conserve the genetic variation found in the Norwegian
 population of D. ruyschiana. Overall, our results highlight the importance
 of an integrated, interdisciplinary framework to better monitor and
 conserve biodiversity at several levels.
description: Genomic DNA was extracted from the silica dried leaves of
 <em>D. ruyschiana</em> sampled from 43 sites across the
 Norwegian distribution range. All samples were genotyped at 96 presumably
 non-coding SNPs applying a SNP-typing assay recently developed specifcally
 for the purpose of facilitating monitoring of the northern dragonhead (see
 Kleven et al. 2019 for details). Briefy, SNPs were genotyped on a 96.96
 Dynamic Array using the Fluidigm EP1 instrument according to the
 manufacturer’s protocol and scored using the Fluidigm SNP genotyping
 analysis software (https:// www.fuidigm.com/software). Please see metadata in the README file for additional details on the dataset.
description: Dracocephalum ruyschiana is an endangered
 species in Norway and Europe. The datafile contains geo references, but
 with lower accuracy then available from other sources, e.g. Norwegian
 Biodiversity Information Centre. Thus, geo refrences in the dataset should
 not impact conservation efforts or introduce unintended
 risk to the species.
DOI: 10.5061/dryad.547d7wmb0
title: Data from: The Matthew effect: common species become more common and rare ones become more rare in response to artificial light at night

description: Artificial light at night (ALAN) has been and still is rapidly spreading,
 and has become an important component of global change. Although numerous
 studies have tested its potential biological and ecological impacts on
 animals, very few studies have tested whether it affects alien and native
 plants differently. Furthermore, common plant species, and particularly
 common alien species, are often found to benefit more from additional
 resources than rare native and rare alien species. Whether this is also
 the case with regard to increasing light due to ALAN is still unknown.
 Here, we tested how ALAN affected the performance of common and rare alien
 and native plant species in Germany directly, and indirectly via flying
 insects. We grew five common alien, six rare alien, five common native and
 four rare native plant species under four combinations of two ALAN (no
 ALAN vs ALAN) and two insect-exclusion (no exclusion vs exclusion)
 treatments, and compared their biomass production. We found that common
 plant species, irrespective of their origin, produced significantly more
 biomass than rare species, and that this was particularly true under ALAN.
 Furthermore, alien species tended to show a slightly stronger positive
 response to ALAN than native species did (p = 0.079). Our study shows that
 common plant species benefited more from ALAN than rare ones. This might
 lead to competitive exclusion of rare species, which could have cascading
 impacts on other trophic levels and thus have important community-wide
 consequences, when ALAN becomes more widespread. In addition, the slightly
 more positive response of alien species indicates that ALAN might increase
 the risk of alien plant invasions.
description: We did a common garden experiment and collected data from the
 experiment. For more details, please see the following paper.
 Liu Y*, Speißer B, Knop E, van Kleunen M (2022) Matthew effect:
 common species become more common and rare ones become more rare in
 response to artificial light at night, Global Change Biology, https://doi.org/10.1111/gcb.16126.
description: Details please see README file.
DOI: 10.15468/dl.2e6wwk
title: Occurrence Download

description: A dataset containing 1875 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hypoponera punctatissima",
 "Year 1000-2025"
 ]
}

 The dataset includes 1875 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003057-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pk0p2ngq6
title: Dataset for: Body size and sexual selection shaped the evolution of parrot calls

description: Morphology, habitat and various selective pressures (e.g., social and
 sexual selection) can influence the evolution of acoustic signals, but the
 relative importance of their effects is not well understood. The order
 Psittaciformes (parrots, sensu lato) is a large clade of very vocal and
 often gregarious species for which large-scale comparative studies of
 vocalizations are lacking. We measured acoustic traits (duration, sound
 frequency, frequency bandwidth and sound entropy) of the predominant call
 type for &gt;200 parrot species to test: (1) for associations with
 body size; (2) the acoustic adaptation hypothesis (predicting differences
 between forest and open-habitat species); (3) the social complexity
 hypothesis (predicting more complex calls in gregarious species); and (4)
 influences of sexual selection (predicting correlated evolution with
 colour ornamentation). Larger species had on average longer calls, lower
 sound frequency and wider frequency bandwidth. These associations with
 body size are all predicted by physical principles of sound production. We
 found no evidence for the acoustic adaptation and social complexity
 hypotheses, but perhaps social complexity is associated with vocal traits
 not studied here, such as call repertoire sizes. More sexually dichromatic
 species had on average simpler calls (shorter, with lower entropy and
 narrower frequency bandwidth) indicating an influence of sexual selection,
 namely an evolutionary negative correlation between colour ornamentation
 and elaborate acoustic signals, as predicted by the transference
 hypothesis. Our study is the first large-scale attempt at understanding
 acoustic diversity across the Psittaciformes, and indicates that body size
 and sexual selection influenced the evolution of species differences in
 vocal signals.
DOI: 10.5061/dryad.rxwdbrvb1
title: Code and data from: Familiarity, dominance, sex and season shape common waxbill social networks.

description: In gregarious animals, social network positions of individuals may
 influence their life-history and fitness. Although association patterns
 and the position of individuals in social networks can be shaped by
 phenotypic differences and by past interactions, few studies have
 quantified their relative importance. We evaluated how phenotypic
 differences and familiarity influence social preferences and the position
 of individuals within the social network. We monitored wild-caught common
 waxbills (Estrilda astrild) with radio-frequency identifiers in a large
 mesocosm during the non-breeding and breeding seasons of two consecutive
 years. We found that social networks were similar, and that the centrality
 of individuals was repeatable, across seasons and years, indicating a
 stable social phenotype. Nonetheless, there were seasonal changes in
 social structure: waxbills associated more strongly with opposite-sex
 individuals in breeding seasons, while in non-breeding seasons they
 instead assorted according to similarities in social dominance. We also
 observed stronger assortment between birds that were introduced to the
 mesocosm at the same time, indicating long-lasting bonds among familiar
 individuals. Waxbills that had been introduced to the mesocosm more
 recently occupied more central network positions, especially during
 breeding seasons, perhaps indicating that these birds had less
 socially-differentiated associations with flock members. Finally,
 individual differences in color ornamentation and behavioral assays of
 personality, inhibitory control and stress were not related to network
 centrality or association patterns. Together, these results suggest that,
 in gregarious species like the common waxbill, social networks may be more
 strongly shaped by long-lasting associations with familiar individuals
 than by phenotypic differences among group members.
DOI: 10.5061/dryad.4mw6m90c8
title: Survival of antimicrobial peptide resistant Staphylococcus aureus in mealworm beetles (Tenebrio molitor) with manipulated AMPexpression

description: Antimicrobial peptides (AMP) are essential immune effectors of
 multicellular organisms. Bacteria can evolve resistance to AMPs.
 Surprisingly, when used to challenge the insect Tenebrio molitor,
 Staphylococcus aureus resistant to an abundant beetle AMP (tenecin 1) and
 also pleiotropically to phagocytosis did not increase host mortality or
 bacterial load compared to infections with wild-type S. aureus. A possible
 explanation is that antimicrobial resistance is costly due to collaterally
 increased sensitivity of AMP-resistant strains to other immune effectors.
 Here, we studied the sensitivity of a group of AMP-resistant S. aureus
 strains (which are either resistant to tenecin 1 or a combination of both
 tenecin 1 and tenecin 2) to other immune effectors such as phenoloxidase
 (PO) and other AMPs (specifically tenecin 1, tenecin 2 and tenecin 4) in
 vivo. Using RNAi-based knockdown (KD), we investigated S. aureus in vivo
 survival in insect hosts lacking particular immune effectors. We found
 that all except one AMP-resistant strain displayed collateral sensitivity
 toward phenoloxidase. Moreover, some AMP-resistant mutant strains showed
 sensitivity to one or more components of the beetle AMP defence cocktail.
 Our findings are consistent with the idea that resistance to AMPs and
 phagocytosis does not translate into changes in virulence because it is
 balanced by collaterally increased sensitivity to other host immune
 effectors. AMP resistance fails to provide a net survival advantage to S.
 aureus in a host environment that is dominated by AMPs because of the
 greater sensitivity to other immune effectors.