cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6824t
title: Data from: DNA methylation mediates genetic variation for adaptive transgenerational plasticity

description: Environmental stresses experienced by individual parents can influence
 offspring phenotypes in ways that enhance survival under similar
 conditions. Although such adaptive transgenerational plasticity is well
 documented, its transmission mechanisms are generally unknown. One
 possible mechanism is environmentally induced DNA methylation changes. We
 tested this hypothesis in the annual plant Polygonum persicaria, a species
 known to express adaptive transgenerational plasticity in response to
 parental drought stress. Replicate plants of 12 genetic lines (sampled
 from natural populations) were grown in dry versus moist soil. Their
 offspring were exposed to the demethylating agent zebularine or to control
 conditions during germination and then grown in dry soil. Under control
 germination conditions, the offspring of drought-stressed parents grew
 longer root systems and attained greater biomass compared with offspring
 of well-watered parents of the same genetic lines. Demethylation removed
 these adaptive developmental effects of parental drought, but did not
 significantly alter phenotypic expression in offspring of well-watered
 parents. The effect of demethylation on the expression of the parental
 drought effect varied among genetic lines. Differential seed provisioning
 did not contribute to the effect of parental drought on offspring
 phenotypes. These results demonstrate that DNA methylation can mediate
 adaptive, genotype-specific effects of parental stress on offspring
 phenotypes.
description: Herman_Sultan_demethylationThis file contains all raw data for the analyses presented in the article "DNA methylation mediates genetic variation for adaptive transgenerational plasticity" by J.J. Herman and S.E. Sultan.
DOI: 10.5061/dryad.3hk0v
title: Data from: Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction

description: Bacteria engage in a complex network of ecological interactions, which
 includes mobile genetic elements (MGEs) such as phages and plasmids. These
 elements play a key role in microbial communities as vectors of horizontal
 gene transfer but can also be important sources of selection for their
 bacterial hosts. In natural communities, bacteria are likely to encounter
 multiple MGEs simultaneously and conflicting selection among MGEs could
 alter the bacterial evolutionary response to each MGE. Here, we test the
 effect of interactions with multiple MGEs on bacterial molecular evolution
 in the tripartite interaction between the bacterium, Pseudomonas
 fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid,
 pQBR103, using genome sequencing of experimentally evolved bacteria. We
 show that individually, both plasmids and phages impose selection leading
 to bacterial evolutionary responses that are distinct from bacterial
 populations evolving without MGEs, but that together, plasmids and phages
 impose conflicting selection on bacteria, constraining the evolutionary
 responses observed in pairwise interactions. Our findings highlight the
 likely difficulties of predicting evolutionary responses to multiple
 selective pressures from the observed evolutionary responses to each
 selective pressure alone. Understanding evolution in complex microbial
 communities comprising many species and MGEs will require that we go
 beyond studies of pairwise interactions.
description: Selection experiment
 population dynamicsDetails of bacterial and
 phage population dynamics for each of 6 replicate populations from 4
 treatments evolved for 20 transfers (approx 150 bacterial generations).
 Data shown in figure 2 and S2. Date comprises bacterial population
 density, frequency of mucoid colonies, frequency of
 plasmidPopulation
 dynamics.csvSNPeff identifed
 mutationsSummary of mutations
 identified from sequenced clones taken from transfer 20 (bacterial
 generation ~150). Clones were sequenced on the illumina MiSeq platform and
 reads aligned using BWA. Small variants (SNPs and small indels) were
 identified using GATK HaplotypeCaller and SNPeff and structural
 rearrangements identified using BreakDancer. Data are shown in figure 1,
 S1 and table S2.
DOI: 10.5061/dryad.pf28st1
title: Data from: Divergent strategies in pre- and postzygotic reproductive isolation between two closely related Dianthus species

description: Quantifying the relative contribution of multiple isolation barriers to
 gene flow between recently diverged species is essential for understanding
 speciation processes. In parapatric populations, local adaptation is
 thought to be a major contributor to the evolution of reproductive
 isolation. However, extrinsic postzygotic barriers assessed in reciprocal
 transplant experiments are often neglected in empirical assessments of
 multiple isolation barriers. We analyzed multiple isolation barriers
 between two closely related species of the plant genus Dianthus, a genus
 characterized by the most rapid species diversification in plants reported
 so far. Although D. carthusianorum L. and D. sylvestris Wulf. can easily
 be hybridized in crossing experiments, natural hybrids are rare. We found
 that in parapatry, pollinator mediated prezygotic reproductive isolation
 barriers are important for both D. carthusianorum (0.761) and D.
 sylvestris (0.468). In contrast to D. carthusianorum, high hybrid
 viability in D. sylvestris (-0.491) was counteracted by strong extrinsic
 postzygotic isolation (0.900). Our study highlights the importance of
 including reciprocal transplant experiments for documenting extrinsic
 postzygotic isolation and demonstrates clearly divergent strategies and
 hence asymmetric pre- and postzygotic reproductive isolation between
 closely related species. It also suggests that pollinator-mediated and
 ecological isolation could have interacted in synergistic ways, further
 stimulating rapid speciation in Dianthus.
description: Raw_dataData.txt
DOI: 10.5281/zenodo.17936465
title: SHM_415748_HST_3D

description: Photogrammetric 3D model of a spoon scraper from the Late Neolithic collected from Skåne and currently held in the collection of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=654

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/BD65C0B3-76A0-4C80-93A7-8AF541F401A1
DOI: 10.5281/zenodo.17936466
title: SHM_415748_HST_3D

description: Photogrammetric 3D model of a spoon scraper from the Late Neolithic collected from Skåne and currently held in the collection of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=654

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/BD65C0B3-76A0-4C80-93A7-8AF541F401A1
DOI: 10.5061/dryad.8kb4m
title: Data from: Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments

description: Wastewater discharges introduce antibiotic residues and
 antibiotic-resistant bacteria (ARB) into surface waters. Both inputs
 directly affect the streambed resistome, either by exerting a selective
 pressure that favor the proliferation of resistant phenotypes or by
 enriching the resident communities with wastewater-associated ARB. Here,
 we investigated the impact of raw and treated urban wastewater discharges
 on epilithic (growing on rocks) and epipsammic (growing on sandy
 substrata) streambed biofilms. The effects were assessed by comparing
 control and impact sites i) on the composition of bacterial communities;
 ii) on the abundance of twelve antibiotic resistance genes (ARGs) encoding
 resistance to β-lactams, fluoroquinolones, sulfonamides, tetracyclines,
 macrolides and vancomycin, as well as the class 1 integron-integrase gene
 (intI1); and iii) on the occurrence of wastewater-associated bacteria,
 including putative pathogens, and their potential linkage to target ARGs.
 We measured more pronounced effects of raw sewage than treated wastewater
 at the three studied levels. This effect was especially noticeable in
 epilithic biofilms, which showed a higher contribution of
 wastewater-associated bacteria and ARB than in epipsammic biofilms.
 Comparison of correlation coefficients obtained between the relative
 abundance of both target ARGs and operational taxonomic units (OTUs)
 classified as either potential pathogens or non-pathogens yielded
 significant higher correlations between the former category and genes
 intI1, sul1, sul2 and ermB. Altogether, these results indicate that
 wastewater-associated microorganisms, including potential pathogens,
 contribute to maintain the streambed resistome and that epilithic biofilms
 appear as sensitive biosensors of the effect of wastewater pollution in
 surface waters.
description: qPCR data Subirats et al
 _ Mol EcolThe data file provides
 the relative abundance of twelve antibiotic resistance genes (ARGs)
 detected in streambed biofilms (epilithic and epipsammic biofims) impacted
 by both treated and raw effluents.
DOI: 10.5061/dryad.2kj8p
title: Data from: Tracking plant preference for higher-quality mycorrhizal symbionts under varying CO conditions over multiple generations

description: The symbiosis between plants and root-colonizing arbuscular mycorrhizal
 (AM) fungi is one of the most ecologically important examples of
 interspecific cooperation in the world. AM fungi provide benefits to
 plants; in return plants allocate carbon resources to fungi,
 preferentially allocating more resources to higher-quality fungi. However,
 preferential allocations from plants to symbionts may vary with
 environmental context, particularly when resource availability affects the
 relative value of symbiotic services. We ask how differences in
 atmospheric CO2-levels influence root colonization dynamics between AMF
 species that differ in their quality as symbiotic partners. We find that
 with increasing CO2-conditions and over multiple plant generations, the
 more beneficial fungal species is able to achieve a relatively higher
 abundance. This suggests that increasing atmospheric carbon supply enables
 plants to more effectively allocate carbon to higher-quality mutualists,
 and over time helps reduce lower-quality AM abundance. Our results
 illustrate how environmental context may affect the extent to which
 organisms structure interactions with their mutualistic partners and have
 potential implications for mutualism stability and persistence under
 global change.
description: Full Experimental
 DataThis file contains the
 full experimental data analysed, specifically: Plant Number (plantnr),
 Generation (gen), CO2-level (co2), AMF inoculation (amf), full plant
 weight (fpw), G. aggregatum copy number (agg_cp), R. irregularis copy
 number (irr_cp), G. aggregatum copy number at detection limit
 (agg_cp_det_lim) and R. irregularis copy numbers at detection limit
 (irr_cp_det_lim). We analysed copy numbers below the detection limit at
 the detection limit, i.e. we used the agg/irr_cp_det_lim columns (see
 Methods for full justification), but additionally we provide full copy
 number data here including the uncorrected copy numbers
 (agg/irr_cp).Werner_CO2_Data.csvPilot Study DataThis data file contains the data for the pilot study performed, i.e. Plant Number (plantnr), AMF treatment (treatment), generation (generation) and AMF copy number (amf_cp).Werner_CO2_PilotData.csvAnalyses R-ScriptThis R-script performs the analyses presented in Werner et al. (2017), and generates the associated Figures presented in the manuscript. Use with the two data files provided in DataDryad.Werner_EE_CO2_Analyses.R
DOI: 10.5061/dryad.cd7jv41
title: Data from: Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model

description: Species interactions can shift along the parasitism-mutualism continuum.
 However, the consequences of these transitions for coevolutionary
 interactions remain unclear. We experimentally coevolved a novel species
 interaction between Caenorhabditis elegans hosts and a mildly parasitic
 bacterium, Enterococcus faecalis, with host-protective properties against
 virulent Staphylococcus aureus. Coinfections drove the evolutionary
 transition of the C.elegans-E. faecalis relationship towards a
 reciprocally beneficial interaction. As E. faecalis evolved to protect
 nematodes against S. aureus infection, hosts adapted by accommodating
 greater numbers of protective bacteria. The mutualism was strongest in
 pairings of contemporary coevolved populations. To generally assess the
 conditions under which these defensive mutualisms can arise and coevolve,
 we analysed a model which showed that they are favoured when mild
 parasites confer an intermediate level of protection. Our results reveal
 that coevolution can shape the transition of animal-parasite interactions
 towards defensive symbioses in response to co-infections.
description: All data from "
 Mutual fitness benefits arise during coevolution in a nematode-microbe
 model"Excel file of data, one
 spreadsheet per figure.Data_Dryad.xlsx
DOI: 10.5061/dryad.jm2m1
title: Data from: Lateral plate number in low-plated threespine stickleback: a study of plasticity and heritability

description: In the threespine stickleback Gasterosteus aculeatus model system,
 phenotypes are often classified into three morphs according to lateral
 plate number. Morph identity has been shown to be largely genetically
 determined, but substantial within-morph variation in plate number exists.
 In this study, we test whether plate number has a plastic component in
 response to salinity in the low-plated morph using a split-clutch
 experiment where families were split in two, one half raised in water at 0
 and the other at 30 ppt salt. We find a small salinity-induced plastic
 effect on plate number in an unexpected direction, opposite to what we
 predicted: Fish raised in freshwater on average have slightly more plates
 than fish raised in saltwater. Our results confirm that heritability of
 plate number is high. Additionally, we find that variance in plate number
 at the family level can be predicted from other family level traits, which
 might indicate that epistatic interactions play a role in creating the
 observed pattern of lateral plate number variation.
description: Hansson et al. Plates
 count dataThis file includes the
 raw data from the study 'Lateral plate number in low-plated
 threespine stickleback: a study of plasticity and heritability' by
 Truls H. Hansson, Barbara Fischer, Anna B. Mazzarella, Kjetil L. Voje and
 Leif Asbjørn Vøllestad published 2016 in Ecology and Evolution. For 739
 threespine stickleback offspring individuals, which were either raised in
 saltwater or freshwater, lateral plates were counted. For each of these
 individuals (in rows), the file has the following information (in
 columns): FishID (individual fish ID), FamilyID (ID for the 16 Crosses),
 Treatment (F for freshwater, S for saltwater), Plates left (no of lateral
 plates on the left side of the fish), Plates right (no of lateral plates
 on right side of the fish), Density (no of individuals per tank, in which
 they were raised) and Size (body length, in mm).Hansson_Platescountdata.csv
DOI: 10.5061/dryad.8db34
title: Data from: Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography

description: Background: Lethal amanitas (Amanita section Phalloideae) are a group of
 wild, fatal mushrooms causing many poisoning cases worldwide. However, the
 diversity and evolutionary history of these lethal mushrooms remain poorly
 known due to the limited sampling and insufficient gene fragments employed
 for phylogenetic analyses. In this study, five gene loci (nrLSU, ITS,
 rpb2, ef1-α and β-tubulin) with a widely geographic sampling from East and
 South Asia, Europe, North and Central America, South Africa and Australia
 were analysed with maximum-likelihood, maximum-parsimony and Bayesian
 inference methods. Biochemical analyses were also conducted with intention
 to detect amatoxins and phalloidin in 14 representative samples. Result:
 Lethal amanitas were robustly supported to be a monophyletic group after
 excluding five species that were provisionally defined as lethal amanitas
 based on morphological studies. In lethal amanitas, 28 phylogenetic
 species were recognised by integrating molecular phylogenetic analyses
 with morphological studies, and 14 of them represented putatively new
 species. The biochemical analyses indicated a single origin of cyclic
 peptide toxins (amatoxins and phalloidin) within Amanita and suggested
 that this kind of toxins seemed to be a synapomorphy of lethal amanitas.
 Molecular dating through BEAST and biogeographic analyses with LAGRANGE
 and RASP indicated that lethal amanitas most likely originated in the
 Palaeotropics with the present crown group dated around 64.92 Mya in the
 early Paleocene, and the East Asia–eastern North America or Eurasia–North
 America–Central America disjunct distribution patterns were primarily
 established during the middle Oligocene to Miocene. Conclusion: The
 cryptic diversity found in this study indicates that the species diversity
 of lethal amanitas is strongly underestimated under the current taxonomy.
 The intercontinental sister species or sister groups relationships among
 East Asia and eastern North America or Eurasia–North America–Central
 America within lethal amanitas are best explained by the diversification
 model of Palaeotropical origin, dispersal via the Bering Land Bridge,
 followed by regional vicariance speciation resulting from climate change
 during the middle Oligocene to the present. These findings indicate the
 importance of both dispersal and vicariance in shaping the
 intercontinental distributions of these ectomycorrhizal fungi.
description: sequences of nrLSU, ITS,
 RPB2, EF1-alpha and beta-tubulinsequences.rar
DOI: 10.5061/dryad.bj001
title: Data from: Sugar provisioning maximizes the biocontrol service of parasitoids

description: There is increasing interest in the use of food supplements in agriculture
 to enhance the performance of parasitoids as part of conservation
 biological control. Nevertheless, there is limited evidence demonstrating
 the effectiveness of this approach, and this shortage of successful
 examples raises doubt regarding the validity of this approach. The use of
 sugar sources relies on tiered premises that: (i) parasitoids are sugar
 limited and (ii) this limitation is alleviated through the provision of
 sugar sources, thereby increasing both (iii) parasitoid fitness and (iv)
 the population density, which together lead to (v) an increase in
 parasitism. In the present study, we address these five premises through
 experiments examining the release of the parasitoid Aphytis melinus DeBach
 (Hymenoptera: Aphelinidae) into the citrus agroecosystem with and without
 sugars. The results demonstrated that A. melinus is sugar limited when
 honeydew producers are scarce in the field. The provision of sugars did
 not increase the sugar contents in A. melinus females but rather increased
 the realized fecundity in these parasitoids, suggesting that females use
 energy for foraging and oviposition. Sugar sources increased the
 parasitoid population density twofold, and this increase most likely
 reflects the enhanced parasitoid longevity. Higher population densities
 and the increased realized fecundity of A. melinus obtained from trees
 with sugars were reflected in a twofold increase of parasitized hosts.
 Synthesis and applications: this study provides the first evidence
 supporting the five premises underlying sugar provisioning for parasitoids
 and demonstrates the potential value of sugar provisioning to enhance
 natural pest control in agricultural systems.
description: 0_Hemipterans_per_tree1_Parasitoid_density_Fig_22_Sugar_content_Figs_3-43_Fecundity_Fig_54_Parastism_Fig_65_Migration_S16_Survival_S27_sex_ratio_S2Data analysis
DOI: 10.5061/dryad.251q438
title: Data from: Trait correlation network analysis identifies biomass allocation traits and stem specific length as hub traits in herbaceous perennial plants

description: Correlations among plant traits often reflect important trade‐offs or
 allometric relationships in biological functions like carbon gain,
 support, water uptake, and reproduction that are associated with different
 plant organs. Whether trait correlations can be aggregated to “spectra” or
 “leading dimensions,” whether these dimensions are consistent across plant
 organs, spatial scale, and growth forms are still open questions. To
 illustrate the current state of knowledge, we constructed a network of
 published trait correlations associated with the “leaf economics
 spectrum,” “biomass allocation dimension,” “seed dimension,” and carbon
 and nitrogen concentrations. This literature‐based network was compared to
 a network based on a dataset of 23 traits from 2,530 individuals of 126
 plant species from 381 plots in Northwest Europe. The observed network
 comprised more significant correlations than the literature‐based network.
 Network centrality measures showed that size traits such as the mass of
 leaf, stem, below‐ground, and reproductive tissues and plant height were
 the most central traits in the network, confirming the importance of
 allometric relationships in herbaceous plants. Stem mass and stem‐specific
 length were “hub” traits correlated with most traits. Environmental
 selection of hub traits may affect the whole phenotype. In contrast to the
 literature‐based network, SLA and leaf N were of minor importance. Based
 on cluster analysis and subsequent PCAs of the resulting trait clusters,
 we found a “size” module, a “seed” module, two modules representing C and
 N concentrations in plant organs, and a “partitioning” module representing
 organ mass fractions. A module representing the plant economics spectrum
 did not emerge. Synthesis. Although we found support for several trait
 dimensions, the observed trait network deviated significantly from current
 knowledge, suggesting that previous studies have overlooked trait
 coordination at the whole‐plant level. Furthermore, network analysis
 suggests that stem traits have a stronger regulatory role in herbaceous
 plants than leaf traits.
description: PlantTraitDataKleyerEtAl2018JECOLThe data file comprises 23 different traits from 2530 plant individuals of 126 sppecies sampled on 381 plots, established on dry semi-natural grasslands, heaths, mesic and wet pastures and meadows, reeds, and saltmarshes, geographically ranging from Switzerland to Germany, The Netherlands and Denmark. All traits were measured using a common protocol. Find more details including the protocol in the paper "Trait correlation network analysis identifies biomass allocation traits and stem specific length as hub traits in herbaceous perennial plants"Kleyer2018.csv
DOI: 10.5061/dryad.908ds
title: Data from: Crosstalk between growth and somatic maintenance in young animals

description: Growing animals face allocation problems whenever receiving suboptimal
 amounts of resources in very stochastic natural environments, possibly
 through a trade-off between growth and somatic maintenance. However, the
 extent to which such a trade-off exists has remained an open question. We
 used an insulin-like growth factor 1 (IGF-1) injection treatment in
 free-living pied flycatcher (Ficedula hypoleuca) nestlings to see how
 IGF-1 levels mediate the development of an antioxidant phenotype via
 glutathione peroxidase (GPx). Our study showed that IGF-1 levels underlie
 variation in GPx activity and provides important information for
 understanding the mechanisms behind the growth variation of passerines.
description: DATA_Lodjak_Magi_2017Glutathione peroxidase (GPx) activity data of free-living pied flycatcher (Ficedula hypoleuca) nestlings. Data is in an Excel file.