cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p9c594
title: Data from: Proximity labeling reveals novel interactomes in live Drosophila tissue

description: Gametogenesis is dependent on intercellular communication facilitated by
 stable intercellular bridges connecting developing germ cells. During
 Drosophila oogenesis, intercellular bridges (referred to as ring canals)
 have a dynamic actin cytoskeleton that drives their expansion to a
 diameter of 10μm. While multiple proteins have been identified as
 components of ring canals (RCs), we lack a basic understanding of how RC
 proteins interact together to form and regulate the RC cytoskeleton. We
 optimized a procedure for proximity-dependent biotinylation in live tissue
 using the APEX enzyme to interrogate the RC interactome. APEX was fused to
 four different RC components (RC-APEX baits) and 55 unique high-confidence
 preys were identified. The RC-APEX baits produced almost entirely distinct
 interactomes that included both known RC proteins as well as
 uncharacterized proteins. The proximity ligation assay was used to
 validate close-proximity interactions between the RC-APEX baits and their
 respective preys. Further, an RNAi screen revealed functional roles for
 several high-confidence prey genes in RC biology. These findings highlight
 the utility of enzyme-catalyzed proximity labeling for protein interactome
 analysis in live tissue and expand our understanding of RC biology.
description: Scaffold file of
 Drosophila ovarian ring canal proteomeThe Scaffold
 (http://www.proteomesoftware.com/products/scaffold/) file contains
 proteomics data, including peptide spectral matches (PSM), from localized
 biotinylation experiments using Drosophila ring canal proteins fused to
 ascorbate peroxidase (APEX).RC_APEX_proteome.sf3
DOI: 10.5061/dryad.m88k1c2
title: Data from: Sexually opposite effects of testosterone on mating success in wild rock hyrax

description: Although males and females share traits, their motivations and needs may
 be different, due to life-history disparities that lead to divergent
 selection pressures. Proximate mechanisms underlying differences between
 the sexes include hormones that mediate the development and activation of
 suites of traits. Testosterone is associated with morphological features,
 physiological processes and social behaviours in both sexes. The goal of
 this study is to test whether testosterone affects males and females
 differently in a species where it is present in similar concentrations in
 the circulation. We combined behavioural mating observations of the wild
 polygynandrous rock hyrax (Procavia capensis) with hair testosterone that
 represents long-term integrated levels. We found that whereas copulation
 success increases with the rise in testosterone in males it decreases in
 females. We did not find an association between testosterone and
 choosiness in either sex. However, we found that males with higher
 testosterone mate-guarded females with lower testosterone. Our findings
 show disassortative mating and mate-guarding in respect to testosterone
 and provide clues to the cost of testosterone for females, in terms of
 copulation success. These results open up intriguing questions relating to
 the role of testosterone in mediating a similar trade-off in male and
 female reproductive success.
description: Supp
 dataData for individual
 hyrax involved in mating related and mate guarding
 interactions.
DOI: 10.5061/dryad.bb114b6
title: Data from: Group size and social status affect scent marking in dispersing female meerkats

description: Many animal species use scent marks such as faeces, urine, and glandular
 secretions to find mates, advertise their reproductive status, and defend
 an exclusive territory. Scent marking may be particularly important during
 dispersal, when individuals emigrate from their natal territory searching
 for mates and a new territory to settle and reproduce. In this study, we
 investigated the scent marking behaviour of 30 dispersing female meerkats
 (Suricata suricatta) during the three consecutive stages of dispersal –
 emigration, transience, and settlement. We expected marking patterns to
 differ between dispersal stages and depending on social circumstances such
 as presence of unrelated mates and social status of the individuals within
 each dispersing coalition; but also to be influenced by water and food
 availability. We showed that defecation probability increased with group
 size during the settlement stage, when newly formed groups are expected to
 signal their presence to other resident groups. Urination probability was
 higher in subordinate than in dominant individuals during each of the
 three dispersal stages, and it overall decreased as the dispersal process
 progressed. Urine may thus be linked to advertisement of the social status
 within a coalition. Anal marking probability did not change across
 dispersal stages, but increased with the presence of unrelated males and
 was higher in dominants than in subordinates. We did not detect any effect
 of rain or foraging success on defecation and urination probability. Our
 results suggest that faeces, urine, and anal markings serve different
 communication purposes (e.g. within and between group communication)
 during the dispersal process.
description: Data and code meerkat
 marking behaviourDataset on dispersing
 meerkat marking behaviour (i.e., defecation, urination, anal marking)
 collected in the Kalahari Desert, South Africa; and code for statistical
 analysis in the software R.Data &
 Code.zip
DOI: 10.5061/dryad.229m0tp
title: Data from: North American Douglas-fir (P. menziesii) in Europe: establishment and reproduction within new geographic space without consequences for its genetic diversity

description: Genetic admixture and plasticity along with propagule pressure, large seed
 dispersal distances and fast adaptation support successful establishment
 and spread of introduced species outside their native range. Consequently,
 introductions may display climatic niche shifts in the introduced range.
 Douglas-fir, a controversial forest and ornamental conifer represented by
 two ecologically different and hybridising varieties, was transferred
 multiple times outside the native range in North America. Here, we compare
 climatic and genetic patterns of 38 native populations from North America
 with six old Pseudotsuga menziesii populations with natural regeneration
 in the introduced range in Central Europe. Following variety and
 geographic origin assessment of introduced populations, genotypic and
 climatic data were examined for signatures of inter-varietal gene flow,
 reduced genetic diversity, presence of fine-scale spatial genetic
 structure (SGS), dispersal patterns, and climate similarities between
 native and introduced range. In the introduced range, dominating coastal
 variety originated from a restricted area in the US, whereas the interior
 variety, with limited presence in the European sites, displayed wider
 geographic origin. Variety hybrids with contributing coastal, but not the
 interior parent were identified. Differences in genetic diversity between
 both ranges, but also among the parent and their respective offspring
 populations in Europe were not found. Old populations in general lacked
 any SGS, whereas natural regeneration revealed different patterns of SGS.
 Distances of propagule dispersal ranged between 2.5 and 92 m. The climate
 of the studied European introduced range was most similar to the climate
 of the coastal variety from the western Cascade range from which the
 majority of the analysed coastal European Douglas-fir, but not the
 European interior variety, was assigned to originate. The results we
 present here shed not only light on dynamics of invasive species in the
 introduced range in general, but also allow for refinement of climatic
 niche modeling when using lower than species level.
description: Genotypic data from 6
 populations of Douglas fir in Europe_dataThe file contains
 genotypic data of 435 trees (old trees and natural regeneration) from six
 (6) populations of Douglas-fir in Europe (Austria and Germany). Samples
 were genotyped according to the methods described in the publication. The
 file contains genotypes of 13 nuclear microsatellite
 loci.Douglas_fir_Europe_data.csv
DOI: 10.5061/dryad.7254t7d
title: Data from: Plant defenses interact with insect enteric bacteria by initiating a leaky gut syndrome

description: Plants produce suites of defenses that can collectively deter and reduce
 herbivory. Many defenses target the insect digestive system, with some
 altering the protective peritrophic matrix (PM) and causing increased
 permeability. The PM is responsible for multiple digestive functions,
 including reducing infections from potential pathogenic microbes. In our
 study, we developed axenic and gnotobiotic methods for fall armyworm
 (Spodoptera frugiperda) and tested how particular members present in the
 gut community influence interactions with plant defenses that can alter PM
 permeability. We observed interactions between gut bacteria with plant
 resistance. Axenic insects grew more, but displayed lower immune-based
 responses compared to those possessing Enterococcus, Klebsiella, and
 Enterobacter isolates from field-collected larvae. While gut bacteria
 reduced performance of larvae fed on plants, none of the isolates produced
 mortality when injected directly into the hemocoel. Our results strongly
 suggest that plant physical and chemical defenses not only act directly
 upon the insect, but also have some interplay with the herbivore’s
 microbiome. Combined direct and indirect, microbe-mediated assaults by
 maize defenses on the fall armyworm on the insect digestive and immune
 system reduced growth and elevated mortality in these insects. These
 results imply that plant-insect interactions should be considered in the
 context of potential mediation by the insect gut microbiome.
description: Impacts of bacteria and
 plant defenses on caterpillar performanceGrowth data containing
 mixture of bacteria and different plant genotypescombined-bacteria
 mix.csvFall armyworm immune
 responses to bacteria and plant defensesphenoloxidase,
 pro-phenoloxidase, and hemocyte responses of fall
 armywormimmune response
 data.csvImpacts of bacterial
 isolates and plant defenses of fall armyworm growth and
 mortlaityfaw_bact_geno_fullbioassay.csvInteractions between recombinant chitinases and bacteriachitinase_bactint.csvInteractions between plant physical defenses and chitinaseschitinase_plant_int.csvImpact of bacteiral injection on growth of fall armyworombacterial_injections.xlsxHemolymph colony forming units for fall armywormBacterial colony forming units (per uL) in response to different feeding substrates.bacteiral CFUs .xlsx
DOI: 10.5061/dryad.fg1r11d
title: Data from: Risk of potential pesticide use to honeybee and bumblebee survival and distribution: a country-wide analysis for The Netherlands

description: Aim: Bees play an important role in natural ecosystems and the world’s
 food supply. In the past decades, bee abundance and diversity have
 declined globally. This has resulted in decreased pollination services for
 natural ecosystems and the agricultural sector at the field scale. One of
 the causes of the decline in bee abundance and diversity is the use of
 pesticides. Linking pesticide use, land use and bee presence could provide
 crucial insights into areas and pesticides that pose a significant threat
 to the abundance and diversity of bees. Obtaining actual figures of farmer
 pesticide use is rarely possible. Therefore, we designed a method to study
 the effects of potential pesticide use on the survival and distribution of
 honey- and bumblebees. Location: The Netherlands. Methods: A pesticide
 risk model was implemented incorporating a hazard quotient as the risk
 assessment. The number of allowed pesticide active ingredients per crop
 that could pose a risk to honeybees and bumblebees were linked to the
 Dutch crop parcel locations for 2015 and 2016. The potential pesticide
 risk maps were analyzed using honeybee colony survival and bumblebee
 presence data. Results: Non-significant negative effects of potential
 pesticide risk on honeybee colony survival and bumblebee presence were
 found. A significant negative effect of greenhouses was identified for
 both honeybees and bumblebees. The most important factors in the models
 predicting honeybee colony survival and bumblebee presence were urban land
 areas and natural grasslands respectively, both showing a positive effect.
 Main conclusions: Here, the first attempt to estimate and map pesticide
 risk to bees in the Netherlands in a country-wide manner is presented. The
 results could provide crucial high-resolution insights for bee
 conservation action and facilitate the increase of pollination services in
 natural ecosystems and the agricultural sector on a local and country-wide
 scale.
description: Vegetation structure
 dataThis zip file contains
 the LIDAR vegetation structure data in raster format
 (.img).vegetation_structure_dryad.zip
DOI: 10.5061/dryad.6836p06
title: Data from: Seasonal shifts and complementary use of pollen sources by two bee, a lacewing and a ladybeetle species in European agricultural landscapes

description: 1. Continuous availability of food resources, such as pollen, is vital for
 many insects that provide pollination and pest control services to
 agriculture. However, there is a lack of knowledge about the shared or
 complementary use of floral resources by such species, which hampers more
 effective landscape management to simultaneously promote them in
 agroecosystems. 2. Here, we simultaneously quantified pollen use by a
 bumblebee (Bombus terrestris) and a mason bee (Osmia bicornis), two bee
 species recognized as important crop pollinators, as well as a lacewing
 (Chrysoperla carnea) and a ladybeetle species (Harmonia axyridis), both
 common predators of crop aphids, throughout the season in 23 agricultural
 landscapes in Germany and Switzerland. 3. Pollen diets were more diverse
 and similar among C. carnea and H. axyridis compared to the two bee
 species, but all four species shared key pollen types early in the season
 such as Acer, Quercus, Salix and Prunus. All species exhibited a
 pronounced shift in pollen sources from primarily woody plants (mainly
 trees) in spring to primarily herbaceous plants in summer. The majority of
 pollen (overall ≥64%) came from non-agricultural plants even in
 crop-dominated landscapes. 4. Synthesis and applications. Our results
 highlight the importance of trees as pollen sources for many insect
 species, particularly early in the season. Our findings support incentives
 that promote heterogeneous agricultural landscapes including both woody
 and herbaceous semi-natural habitats, ensuring phenological
 complementarity of floral resources for insect species that can provide
 pollination and pest control services to agriculture. The identified key
 plant species can help to design and optimize agri-environment schemes to
 promote these functionally important insects.
description: Data of pollen collected
 by four insect speciesThe file includes data
 regarding pollen samples collected by four insect species: Bombus
 terrestris (BT), Osmia bicornis (OB), Chrysoperla carnea (CC) and Harmonia
 axyridis (HA). Samples were collected from April to early July in 23
 agricultural landscapes in Germany and Switzerland.PollenData_Bertrand-et-al-2019.xlsx
DOI: 10.5061/dryad.493rk16
title: Data from: Genetic dissection of complex behaviour traits in German Shepherd dogs

description: A favourable genetic structure and diversity of behavioural features
 highlights the potential of dogs for studying the genetic architecture of
 behaviour traits. However, behaviours are complex traits, which have been
 shown to be influenced by numerous genetic and non-genetic factors,
 complicating their analysis. In this study, the genetic contribution to
 behaviour variation in German Shepherd dogs (GSDs) was analysed using
 genomic approaches. GSDs were phenotyped for behaviour traits using the
 established Canine Behavioral Assessment and Research Questionnaire
 (C-BARQ). Genome-wide association study (GWAS) and regional heritability
 mapping (RHM) approaches were employed to identify associations between
 behaviour traits and genetic variants, while accounting for relevant
 non-genetic factors. By combining these complementary methods we
 endeavoured to increase the power to detect loci with small effects.
 Several behavioural traits exhibited moderate heritabilities, with the
 highest identified for Human-directed playfulness, a trait characterised
 by positive interactions with humans. We identified several genomic
 regions associated with one or more of the analysed behaviour traits. Some
 candidate genes located in these regions were previously linked to
 behavioural disorders in humans, suggesting a new context for their
 influence on behaviour characteristics. Overall, the results support dogs
 as a valuable resource to dissect the genetic architecture of behaviour
 traits and also highlight the value of focusing on a single breed in order
 to control for background genetic effects and thus avoid limitations of
 between-breed analyses.
description: Friedrich_BehavGenetDogs_25062019Contains all files for the Publication "Genetic dissection of complex behaviour traits in German Shepherd dogs"
DOI: 10.5061/dryad.h7nj6qn
title: Data from: Implications of existing local (mal)adaptations for ecological forecasting under environmental change

description: Standing genetic variation represents a genetic load on population fitness
 but can also support a rapid response to short-term environmental change,
 and the greatest potential source of such standing genetic variation
 typically exists among locally adapted populations living along an
 environmental gradient. Here we develop a spatially-explicitly simulation
 model to quantify the contribution of existing genetic variation arising
 from migration-mutation-selection-drift balance to time to extinction
 under environmental change. Simulations reveal that local adaptation
 across a species range associated with an underlying environmental
 gradient could extend time to extinction by nearly three–fold irrespective
 of the rate of environmental change. The potential for pre-adapted alleles
 to increase the rate of adaptation changes the relative importance of
 established extinction risk factors, in particular it reduced the
 importance of the breadth of environmental tolerance and it increased the
 relative importance of fecundity. Although migration of preadapted alleles
 generally increased persistence time, it decreased it at rates of
 environmental change close to the critical rate of change by creating a
 population bottleneck, which ultimately limited the rate at which de novo
 mutations could arise. An analysis of the extinction dynamics further
 revealed that one consequence of gene flow is the potential to maximise
 population growth rate in at least part of the species range, which is
 likely to have consequences for forecasting the consequences of ecological
 interactions. Our study shows that predictions of persistence time change
 fundamentally when existing local adaptations are explicitly taken into
 account, underscoring the need to preserve and manage genetic diversity.
description: EvolApp sim
 dataSummary simulation data
 for figures
DOI: 10.57745/f8hfrf
title: 1. Sugar.tab

description: :unav
DOI: 10.57745/p4yr19
title: Data for the paper Song et al. (2025) SBB

description: Hemicellulosic sugar composition of casts produced by 9 earthworm species
DOI: 10.5061/dryad.7q22r2m
title: Data from: Soil hydraulic properties determined by inverse modeling of drip infiltrometer experiments extended with pedotransfer functions

description: A transient flow experiment using automated drip infiltrometers (ADIs) was
 performed on soil columns (about 6 dm3) large enough to incorporate
 macropore flow effects. We investigated to what extent the estimated soil
 hydraulic parameters obtained from inverse modeling of these experiments
 are reliable. A machine learning based pedotransfer function (PTF) for
 prediction of water content at −1, −10, and −158 m pressure head was
 developed. Sensitivity analysis of the van Genuchten parameters (residual
 and saturated water content r and s, fitting parameters , n, and , and
 saturated hydraulic conductivity Ks) in soils of sandy, silty, and clayey
 textures showed that the temporal variation of pressure heads in ADI
 scenarios was not sensitive to r and s. The other parameters were
 accurately estimated from numerically synthesized data. The uniqueness of
 the estimated parameters did not change when a bias, representing
 experimental error, was added to the data set. In actual columns, using
 the temporal and spatial pressure head data from the ADIs and the water
 contents in the drier range predicted by the developed PTF resulted in a
 precise estimation of the van Genuchten parameters. Not including the PTF
 water contents resulted in non-uniquely estimated van Genuchten
 parameters.
description: dataupSoil Hydraulic
 parameters of 15 columns modelled in the paper. These data include
 summrized version output of drip infiltrometer data used for inverse
 modelling.
DOI: 10.5061/dryad.ms12t45
title: Data from: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

description: The synthetic 17α-ethinylestradiol (EE2) is a common estrogenic pollutant
 that has been suspected to affect the demography of river-dwelling
 salmonids. One possibility is that exposure to EE2 tips the balance during
 initial steps of sex differentiation, so that male genotypes show
 female-specific gene expression and gonad formation. Here we study EE2
 effects on gene expression around the onset of sex differentiation in a
 population of European grayling (Thymallus thymallus) that suffers from
 sex ratio distortions. We exposed singly-raised embryos to one dose of 1
 ng/L EE2, studied gene expression 10 days before hatching, at the day of
 hatching, and around the end of the yolk-sac stage, and related it to
 genetic sex (sdY genotype). We found that exposure to EE2 affects
 expression of a large number of genes, especially around hatching. These
 effects were strongly sex-dependent. We then raised fish for several
 months after hatching and found no evidence of sex reversal in the
 EE2-exposed fish. We conclude that ecologically relevant (i.e. low) levels
 of EE2 pollution do not cause sex reversal by simply tipping the balance
 at early stages of sex differentiation, but that they interfere with
 sex-specific gene expression.
description: Selmoni et
 al_HistologyHistological analyses of
 gonad development over 5 time points in grayling (Thymallus thymallus)
 exposed or not to 17α-ethinylestradiol (EE2) and/or to Pseudomonas
 fluorescens (PF). The table also provides the total lengths of the fish
 and the genetic sex of individuals sampled at the last two time
 points.