cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1mk
title: Data from: Effects of arthropod inquilines on growth and reproductive effort among metacommunities of the purple pitcher plant (Sarracenia purpurea var. montana)

description: Many plant species harbor communities of symbionts that release nutrients
 used by their host plants. However, the importance of these nutrients to
 plant growth and reproductive effort is not well understood. Here, we
 evaluate the relationship between the communities that colonize pitcher
 plant phytotelmata and the pitcher plants’ vegetative growth and flower
 production to better understand the symbiotic role played by phytotelma
 communities. We focus on the mountain variety purple pitcher plant
 (Sarracenia purpurea var. montana), which occurs in small and isolated
 populations in Western North Carolina. We found that greater symbiont
 community diversity is associated with higher flower production the
 following season. We then examined geographic variation in communities and
 found that smaller plant populations supported less diverse symbiont
 communities. We relate our observations to patterns of community diversity
 predicted by community ecology theory.
description: Data set related to arthropod communities living in pitchers of
 <em>Sarracenia purpurea</em> var. <em>montana</em>
 in eight populations in Western North Carolina, USA. Data collected in
 2015-2016.
DOI: 10.5061/dryad.fn2z34tq4
title: Assessing the repeatability, robustness to disturbance, and parent‐offspring colony resemblance of collective behavior

description: Groups of animals possess phenotypes such as collective behaviour, which
 may determine the fitness of group members. However, the stability and
 robustness to perturbations of collective phenotypes in natural conditions
 is not established. Furthermore, whether group phenotypes are transmitted
 from parent to offspring groups with fidelity is required for
 understanding how selection on group phenotypes contributes to evolution,
 but parent-offspring resemblance at the group level is rarely estimated.
 We evaluated the repeatability, robustness to perturbation, and
 parent-offspring resemblance of collective foraging aggressiveness in
 colonies of the social spider Anelosimus eximius. Among-colony differences
 in foraging aggressiveness were consistent over time but changed if the
 colony was perturbed through the removal of individuals, or via
 individuals’ removal and subsequent return. Offspring and parent colony
 behaviour were correlated at the phenotypic level, but only once the
 offspring colony had settled after being translocated, and the correlation
 overlapped with zero at the among-colony level. The parent-offspring
 resemblance was not driven by a shared elevation but could be due to other
 environmental factors. The behaviour of offspring colonies in a common
 garden laboratory setting was not correlated with the behaviour of the
 parent colony nor the same colony’s behaviour once it was returned to the
 field. The phenotypes of groups represent a potentially important tier of
 biological organisation, and assessing the stability and heritability of
 such phenotypes helps us better understand their role in evolution.
description: For full data collection and analysis methods, please see the
 associated paper. But in brief:   We
 located 45 colonies of social spiders (<em>Anelosimus
 eximius</em>) in Ecuador, and repeatedly assayed them for behaviour.
 We then removed some spiders from 2/3 of them (the
 "disturbance"), and tested those subsets in a laboratory. We
 then returned 15 subsets back to their original colony, and the other 15
 were placed into vegetation within 5-10m of the original colony
 ("bud" colonies). We then assayed both the original colonies and
 the newly founded colonies repeatedly.  
 To analyse it we used multivariate mixed effect models in the R
 package "MCMglmm" to determine the among colony covariance in
 foraging aggression between pre- and post-disturbance assays, and if this
 differed between colonies that had individuals removed, individuals
 removed and then returned, and colonies that were not disturbed. We also
 related pre-disturbance assays to tests in the laboratory and to the
 assays on the bud colonies.
description: See ReadMe file ("Herit & robust to disturb
 ReadMe.docx") and R code file ("Herit & robust to
 disturb R code.R") for how to use the dataset
DOI: 10.15468/dl.gdtkdc
title: Occurrence Download

description: A dataset containing 26415 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Podarcis siculus"
 ]
}

 The dataset includes 26415 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002093-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1vx0b
title: Single-chain heteropolymers transport protons selectively and rapidly

description: Precise protein sequencing and folding are believed to generate the
 natural channel structure and chemical diversity of
 proteins, both of which are essential to synthetically achieve
 proton transport performance comparable to that seen in natural
 systems. Geometrically defined channels have been fabricated using
 peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic
 frameworks; however, none of these channels rivals the performance
 observed in their natural counterparts. Here we show that without forming
 an atomically structured channel, four-monomer-based random heteropolymers
 (RHPs) can mimic membrane proteins and exhibit selective proton
 transport across lipid bilayers at a rate similar to those of natural
 proton channels. Statistical control over the monomer distribution in an
 RHP leads to segmental heterogeneity in hydrophobicity, which facilitates
 the insertion of single RHPs into the lipid bilayers. It also results in
 bilayer-spanning segments containing polar monomers that promote the
 formation of hydrogen-bonded chains for proton transport. Our study
 demonstrates the importance of the adaptability that is enabled by
 statistical similarity and of the modularity provided by the chemical
 diversity of monomers, to achieve uniform behaviour in heterogeneous
 systems. Our results also validate statistical randomness as an unexplored
 approach to realize protein-like behaviour at the single-polymer-chain
 level in a predictable manner.
description: This dataset provides files necessary to reproduce main and
 extended data figures. Final figures are provided as .pdf or .tif files.
 Text and image files necessary to reproduce the final figures are provided
 as .txt or .tif files. Manually highlighted sequences from Extended Data
 Figure 7 are provided as .xlsx files.  Movies in this
 dataset are the same as those included in the supplementary information.
 They are provided as .mp4 files.
DOI: 10.5061/dryad.00000000k
title: Data from: Continent-wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

description: The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic
 across vast regions of North America. We examined the extent of panmixia
 by genotyping 3650 single nucleotide polymorphism (SNP) loci in 1975
 individuals from 128 collections across the continent. We found three
 spatially structured subpopulations: Western (Alaska, Yukon), Central
 (southeastern Yukon to the Manitoba-Ontario border) and Eastern
 (Manitoba-Ontario border and Atlantic). Additionally, the most diagnostic
 genetic differentiation between the Central and Eastern subpopulations was
 chromosomally restricted to a single block of SNPs that may constitute an
 island of differentiation within the species. Geographic differentiation
 in the spruce budworm parallels that of its principal larval host, white
 spruce, Picea glauca, providing evidence that spruce trees survived in the
 Beringian refugium through the Last Glacial Maximum and that at least two
 isolated populations diverged with spruce/fir south of the ice sheets.
 Gene flow in the spruce budworm may also be affected by mountains in
 western North America, habitat isolation in West Virginia, regional
 adaptations, factors related to dispersal, and proximity of other species
 in the spruce budworm species complex. The central and eastern geographic
 regions contain individuals that assign to Eastern and Central
 subpopulations, respectively, indicating that these barriers are not
 complete. Our discovery of previously undetected geographic and genomic
 structure in the spruce budworm suggests that further population modelling
 of this ecologically important insect should consider regional
 differentiation, potentially co-adapted blocks of genes, and gene flow
 between subpopulations.
DOI: 10.5061/dryad.547d7wm49
title: Data from: Testing the importance of harvest refuges for phenotypic rescue of trophy hunted populations

description: Sustainable exploitation must minimize its impact on the ecology and
 evolution of exploited wildlife. Intense phenotype-based selective
 harvests can induce evolutionary change. Refuges could mitigate those
 evolutionary effects if individuals not subject to selective hunting in
 harvest refuges migrated and reproduced in hunted areas. The role of
 harvest refuges on phenotypic rescue of trophy-hunted species, however,
 has rarely been tested. We investigated spatial and temporal variation in
 the effect of refuges on horn size and age at harvest in bighorn sheep
 (Ovis canadensis). We analyzed data on 5 826 males harvested over 39 years
 in Alberta, Canada. Horn length, a trait targeted by hunters, and age at
 harvest increased with the amount of protected areas 5-40 km around each
 kill. Horn base circumference, however, was independent of proximity to
 refuges. The number of males harvested increased during the last 10 days
 of the hunting season in late October, corresponding with the timing of
 bighorn male breeding migrations. Males shot during those 10 days were on
 average 17% closer to a refuge than males shot earlier in the season.
 Apparently, some large males exit refuges late in the hunting season, are
 shot, and cannot contribute to rescue. Uncertainty remains about the
 proportion of males exiting refuges after the hunting season and how many
 survive to reproduce. Synthesis and applications. Harvest refuges are
 unlikely to rescue hunted populations of bighorn sheep in Alberta, because
 some males exiting refuges are at risk of harvest before they mate. For
 phenotypic rescue to be effective, unselected males must reproduce before
 they are shot. Closing the hunting season 10 days earlier would increase
 survival of unselected rams exiting refuges.
DOI: 10.5061/dryad.hx3ffbg9s
title: Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis

description: Premise of the study: Nutrients, light, water, and temperature
 are key factors limiting the growth of individual plants in
 nature. Mutualistic interactions between plants and microbes
 often mediate resource limitation for both partners. In the mutualism
 between legumes and rhizobia, plants provide rhizobia with carbon in
 exchange for fixed nitrogen. Because partner quality in mutualisms is
 genotype-dependent, within-species genetic variation is expected to alter
 the responses of mutualists to changes in the resource environment. Here
 we ask whether partner quality variation in rhizobia mediates the response
 of host plants to changing light availability, and conversely, whether
 light alters the expression of partner quality variation. 
 Methods: We inoculated clover hosts with 11 rhizobium strains
 that differed in partner quality, grew plants under either ambient or low
 light conditions in the greenhouse, and measured plant growth, nodule
 traits, and foliar nutrient composition.  Key
 results: Light availability and rhizobium inocula interactively
 determined plant growth, and rhizobium partner quality variation was more
 apparent in ambient light.  Conclusions: Our results
 suggest that variation in the costs and benefits of rhizobium symbionts
 mediate host responses to light availability, and that rhizobium variation
 might more important in higher-light environments. Our work adds
 to a growing appreciation for the role of microbial intraspecific
 and interspecific diversity in mediating extended phenotypes in their
 hosts and suggests an important role for light availability in the ecology
 and evolution of legume-rhizobium symbiosis.
DOI: 10.5061/dryad.83bk3j9mz
title: SSR genotypes and geographical locations of collections of three Asian butternuts and two species of Quercus

description: In the file, we display the genotypes of 502 adult individuals of
 17 natural Q. mongolica populations (QM), 139
 individuals of 5 populations of northeast Q.
 liaotungensis (QL_ CBS), 240 individuals from 8
 populations of northwest Q. liaotungensis (QL_
 NWC), 596 individuals in 25 J. cathayensis (JC)
 populations, 399 individuals in 14 J.
 mandshurica populations (JM) and 107 individuals in 5 J.
 ailantifolia populations (JA). In addition, the sample
 information:  geographical locations of collections and sample
 size of the populations.
DOI: 10.5061/dryad.73n5tb2t0
title: The evolution of broadly polylectic behaviour in Lasioglossum (Chilalictus) (Halictidae, Apoidea)

description: Based on the number of pollen hosts utilised, bees have been categorised
 as generalists (polylectic) or specialists (oligolectic). Faced with a
 changing habitat, polylectic bees can diversify their pollen ‘portfolio’,
 while oligolectic bees cannot and therefore may go locally extinct.
 Research into the evolution and maintenance of broad polylecty is scant.
 Instead, research has mainly focussed on the factors that constrain
 oligolectic species to a narrow diet. Here, we developed a molecular
 phylogeny of a native Australian subgenus Lasioglossum (Chilalictus),
 (Halictidae), to study the evolution of pollen host breadth within the
 group. We find that broad polylecty has evolved independently at least
 four times in L. (Chilalictus) and did not result in subsequent
 speciation. Oligolecty has evolved once and is found in at least three
 related species. In addition, broadly polylectic species have
 significantly larger areas of occurrence than oligolectic and polylectic
 species. Taken together, these results suggest that there is less
 opportunity for speciation in broadly polylectic than in polylectic and
 oligolectic species. As broad polylecty is uncommon in bees, we
 hypothesise the existence of genetic constraints to its evolution. Future
 studies on the evolution of broad polylecty should examine both the
 existence of constraints and selective advantages for host broadening in
 polylectic species.
description: Data S1. A morphological datamatrix comprising 80 characters was
 compiled by Ken Walker (Museums Victoria), an expert in Australian
 <i>Lasioglossum</i>, who kindly provided it to us for
 constructing a morphological phylogeny of <em>L</em>.
 (<em>Chilalictus</em>). Data S2 and S3.
 Posterior probabilities of the ancestral states were produced by adding
 diet width characters into a data matrix of molecular sequence characters
 of <em>L</em>. (<em>Chilalictus</em>) and then
 conducting phylogenetic analysis while simulteneously reconstructing the
 ancestral diet width states of 12 well supported nodes of interest (with
 posterior probabilities ≥ 87). We used the full hierarchical Bayesian
 approach in MrBayes (v3.2) with a symmetric evolutionary model for the
 diet width character and without ordering the diet width character states
 (Data S2). The topology prior was constrained to fix the 12 well-supported
 nodes in every sampled tree during the analysis, so that their
 reconstructed ancestral states could be reported. The analysis was
 conducted 4 times and parameter and log files were analysed for
 convergence following guidelines from the Mr.Bayes manual. We repeated the
 analysis with ordered character states of the diet width, where we
 restricted the rate parameters for the transition between the two extreme
 diet width states (oligolecty and broad polylecty) to zero (Data
 S3).
DOI: 10.15139/s3/k3pnnf
title: Data Management and Sharing Plan for: Role of DNA damage and cellular senescence in osteoarthritis pathophysiology

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.fttdz08p0
title: Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize

description: In most plants, centromeric DNA contains highly repetitive sequences,
 including tandem repeats and retrotransposons; however, the roles of these
 sequences in the structure and function of the centromere are unclear.
 Here, we found that multiple RNA sequences from centromeric
 retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and
 back spliced RNAs were generated from CRM1. We identified three types of
 CRM1-derived circular RNAs with the same back-splicing site based on the
 back-spliced sequences. These circular RNAs bound to the centromere
 through R-loops. Two R-loop sites inside a single circular RNA promoted
 the formation of chromatin loops in CRM1 regions. When RNAi was used to
 target the back-splicing site of the circular CRM1 RNAs, the levels of
 R-loops and chromatin loops formed by these circular RNAs decreased, while
 the levels of R-loops produced by linear RNAs with similar binding sites
 increased. Linear RNAs with only one R-loop site could not promote
 chromatin loop formation. Higher levels of R-loops and lower levels of
 chromatin loops in the CRM1 regions of RNAi plants led to a reduced
 localization of the centromeric H3 variant (CENH3). Our work reveals
 centromeric chromatin organization by circular CRM1 RNAs via R-loops and
 chromatin loops, which suggested that CRM1 elements might help build a
 suitable chromatin environment during centromere evolution. These results
 highlight that R-loops are integral components of centromeric chromatin
 and proper centromere structure is essential for CENH3 localization.
description: Raw images in PDF format: Fig. 2A The 354-nt
 RNA was stable after an RNase R treatment. <i>Cenh3</i> mRNA
 was used as a linear RNA control. The black arrows in the right panel show
 the positions of primers used. Fig. 2E Divergent PCR showed that the
 607-nt and 277- to 296- nt RNAs were stable after RNase R treatment. The
 right panel shows the compositions of the amplified sequences mentioned in
 Fig S2E, 2C, and 2D. Fig. 3F 3C-PCR confirms the
 potential ligations of chromatin loops after <i>DpnII</i>
 digestion. The left panel shows the PCR results in the undigested,
 unligated samples and 3C samples under potential ligation forms. The right
 panel shows the sequences from the bands on the left, including the
 expected sequences, the first and the second part of the expected
 sequences, and the amplified sequences. S1D Fig. RT-PCR
 analysis of the 354-nt RNA without and with reverse
 transcription. S3C Fig. Detection of the R-loop
 structure by T7 endonuclease I digestion and subsequent ligation. The red
 arrows show the shortened sequences. S3F Fig. RNA-85,
 RNA-269 and RNA-85+269 were sensitive to RNase R treatment. The right
 panel shows the positions of the primers. S5 Fig. The
 sense strand transcribed CRM1 RNA can be spliced into the 354-nt-like
 back-spliced RNA after being transformed into oat (A), rice (B), wheat and
 sorghum (E), and soybean (H) protoplasts.
DOI: 10.5061/dryad.brv15dv5r
title: Mapping species richness using opportunistic samples: a case study on ground-floor bryophyte species richness in the Belgian province of Limburg

description: In species richness studies, citizen-science surveys where participants
 make individual decisions regarding sampling strategies provide a
 cost-effective approach to collect a large amount of data. However, it is
 unclear to what extent the bias inherent to opportunistically collected
 samples may invalidate our inferences. Here, we compare spatial
 predictions of forest ground-floor bryophyte species richness in Limburg
 (Belgium), based on crowd- and expert-sourced data, where the latter are
 collected by adhering to a rigorous geographical randomisation and data
 collection protocol. We develop a log-Gaussian Cox process model to
 analyse the opportunistic sampling process of the crowd-sourced data and
 assess its sampling bias. We then fit two geostatistical Poisson models to
 both data-sets and compare the parameter estimates and species richness
 predictions. We find that the citizens had a higher propensity for
 locations that were close to their homes and environmentally more
 valuable. The estimated effects of ecological predictors and spatial
 species richness predictions differ strongly between the two
 geostatistical models. Unknown inconsistencies in the sampling process,
 such as unreported observer’s effort, and the lack of a hypothesis-driven
 study protocol can lead to the occurrence of multiple sources of sampling
 bias, making it difficult, if not impossible, to provide reliable
 inferences.
DOI: 10.15468/dl.bxzkup
title: Occurrence Download

description: A dataset containing 8531 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Meuschenia scaber",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 8531 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002094-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tmpg4f4v3
title: Water potential gradient, root conduit size and root xylem hydraulic conductivity determine the extent of hydraulic redistribution in temperate trees

description: 1. Hydraulic redistribution (HR) of soil water through plant roots is
 widely described, however its extent, especially in temperate trees,
 remains unclear. Here, we quantified redistributed water of five temperate
 tree species. We hypothesized that both, HR within a plant and into the
 soil increases with higher water-potential gradients, larger root conduit
 diameters and root-xylem hydraulic conductivities. 2. Saplings of conifer
 (Picea abies, Pseudotsuga menziesii), diffuse-porous (Acer pseudoplatanus)
 and ring-porous species (Castanea sativa, Quercus robur) were planted in
 split-root systems, where one plant had its roots split between two pots
 with different water-potential gradients (0.23 to 4.20 MPa). Hydraulic
 redistribution was quantified via deuterium labeling. 3. On average,
 species redistributed 0.39 ± 0.14 ml water overnight (0.08 ± 0.01 ml g-1
 root mass). Higher pre-dawn water-potential gradients, xylem hydraulic
 conductivities and larger conduit diameters significantly increased HR.
 Hydraulic conductivity had the greatest influence on HR, within the plants
 (0.03 ± 0.01 ml g-1) and into the soil (0.06 ± 0.01 ml g-1). 4. Additional
 factors as soil-root contact should be considered, especially when
 calculating water transfer into the soil. Nevertheless, trees maintaining
 high xylem hydraulic conductivity showed higher HR amounts, potentially
 making them valuable ‘silvicultural tools’ to improve plant water-status.