cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3tn
title: The role of surface adhesion on the macroscopic wrinkling of biofilms

description: Biofilms, bacterial communities of cells encased by a self-produced
 matrix, exhibit a variety of three-dimensional structures. Specifically,
 channel networks formed within the bulk of the biofilm have been
 identified to play an important role in the colonies viability by
 promoting the transport of nutrients and chemicals. Here, we study channel
 formation and focus on the role of the adhesion of the biofilm matrix to
 the substrate in Pseudomonas aeruginosa biofilms grown under constant flow
 in microfluidic channels. We perform phase contrast and confocal laser
 scanning microscopy to examine the development of the biofilm structure as
 a function of the substrates surface energy. The formation of the wrinkles
 and folds is triggered by a mechanical buckling instability, controlled by
 biofilm growth rate and the film's adhesion to the substrate. The
 three-dimensional folding gives rise to hollow channels that rapidly
 increase the overall volume occupied by the biofilm and facilitate
 bacterial movement inside them. The experiments and analysis on mechanical
 instabilities for the relevant case of a bacterial biofilm grown during
 flow enable us to predict and control the biofilm morphology.
description: Raw data (timelapse images) of PAO1 biofilm growing in a
 microfluidic device under constant flow. The images have not been
 processed. The image analysis code can be used to perform DDM and the
 skeletonization to recreate the results from the manuscript "The role
 of surface adhesion on the macroscopic wrinkling of
 biofilms"
description: The image analysis code can be used to perform DDM and the
 skeletonization to recreate the results from the manuscript "The role
 of surface adhesion on the macroscopic wrinkling of
 biofilms"
DOI: 10.5061/dryad.mkkwh7122
title: Morphometric data of two tree frog species and their hybrids from a hybrid zone in Poland

description: Under incomplete reproductive isolation, secondary contact of diverged
 allopatric lineages may form hybrid zones that allow to study recombinants
 over several generations as excellent systems of genomic interactions,
 resulting from the evolutionary forces, acting on certain genes and
 phenotypes. Hybrid phenotypes are expected to either exhibit intermediacy
 or, alternatively, transgressive traits, which exceed the extremes of
 their parents due to epistasis and segregation of complementary alleles.
 While transgressive morphotypes have been examined in fish, reptiles,
 birds, and mammals, studies in amphibians are rare. Here, we associate
 microsatellite-based genotypes and morphometrics-based morphotypes of two
 European tree frog species of the Hyla arborea group,
 sampled across a hybrid zone in Poland, to understand whether the
 genetically differentiated parental species also differ in morphology
 between each other and their hybrids, and whether secondary contact leads
 to the evolution of intermediate or transgressive morphotypes. Using
 univariate approaches, explorative multivariate methods (Principal
 Component Analyses) as well as techniques with prior grouping
 (Discriminant Function Analyses), we find that morphotypes of both
 parental species and hybrids differ from each other. Importantly, hybrid
 morphotypes are neither intermediate nor transgressive but found to be
 more similar to H. orientalis than to H.
 arborea. Our study presents one of the rare datasets, in which genotypes
 along with morphotypes examined the occurrence or absence of transgressive
 morphologies in wild amphibians.
DOI: 10.5061/dryad.15dv41nzs
title: Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness

description: In animals with distinct life stages such as holometabolous insects, adult
 phenotypic variation is often shaped by the environment of immature
 stages, including their interactions with microbes colonizing larval
 habitats. Such carry-over effects were previously observed for several
 adult traits of the mosquito Aedes aegypti after larval exposure to
 different bacteria, but the mechanistic underpinnings are unknown. Here,
 we investigated the molecular changes triggered by gnotobiotic larval
 exposure to different bacteria in Ae. aegypti. We initially screened a
 panel of 16 bacterial isolates from natural mosquito breeding sites to
 determine their ability to influence adult life-history traits. We
 subsequently focused on four bacterial isolates (belonging to
 Flavobacterium, Lysobacter, Paenibacillus, and Enterobacteriaceae) with
 significant carry-over effects on adult survival and found that they were
 associated with distinct transcriptomic profiles throughout mosquito
 development. Moreover, we detected carry-over effects at the level of gene
 expression for the Flavobacterium and Paenibacillus isolates. The most
 prominent transcriptomic changes in gnotobiotic larvae reflected a
 profound remodeling of lipid metabolism, which translated into phenotypic
 differences in lipid storage and starvation resistance at the adult stage.
 Together, our findings indicate that larval exposure to environmental
 bacteria trigger substantial physiological changes that impact adult
 fitness, uncovering a possible mechanism underlying carry-over effects of
 mosquito-bacteria interactions during larval development.
description: This dataset contains all the raw data presented in the figures
 of the article.
DOI: 10.5061/dryad.zs7h44jb9
title: Macronutrient niches and field limitation in a woodland assemblage of harvestmen

description: 1. Description of animals’ trophic niches help us understand interactions
 between species in biological communities that are not easily observed.
 Analyses of macronutrient niches, i.e. the range of macronutrient
 (protein:lipid:carbohydrate) ratios selected by generalist feeders, may be
 a useful alternative approach to inter-species comparisons of diets,
 especially within taxonomic assemblages of predators where species with
 similar nutritional requirements are likely to accept similar types of
 prey. 2. Here we analysed the macronutritional niches of a woodland
 assemblage of seven harvestman species, all supposed to be predators with
 omnivorous tendencies. Five species (Mitopus morio, Leiobunum gracile,
 Oligolophus tridens, O. hanseni, Paroligolophus agrestis) were native and
 two species (Opilio canestrinii, Dicranopalpus ramosus) were recent
 invaders into the community. 3. We compare the fundamental (FMN) and
 realized (RMN) macronutritional niche positions of the species using a
 ‘double-test procedure’, which provides information on whether the species
 were food limited in their natural habitat, and whether they were limited
 by specific macronutrients. 4. All seven species were food limited and six
 species were non-protein limited in the field; of these, four species were
 carbohydrate limited, and in one species females were lipid limited and
 males carbohydrate limited. These findings add to the notion that
 predators are mainly non-protein limited in the field. 5. The FMN
 positions of the assemblage fell within 46-50% protein, 29-38% lipid, and
 16-22% carbohydrate. The amount of carbohydrate in the self-selected diet
 combined with carbohydrate limitation confirms that the species are
 zoophytophagous. Two morphological clusters of species (large long-legged
 vs. small short-legged species) differed not only in microhabitat (upper
 vs. lower forest strata) but also in macronutrient selection, where large
 long-legged species selected higher proportion of carbohydrate than small
 short-legged species. Thus, morphologically similar species occupy the
 same habitat stratum and have similar macronutritional niches. 6. We
 discuss the hypothesis that the invasive O. canestrinii might have an
 impact on native species as it allegedly had in urban environments
 previously. Two basic assumptions about interspecific resource competition
 were fulfilled, i.e. high overlap of nutritional requirements and
 limitation by food and macronutrients.
description: Laboratory experiments.
DOI: 10.5061/dryad.7m0cfxpw3
title: Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice

description: The island syndrome hypothesis (ISH) stipulates that, as a result of local
 selection pressures and restricted gene flow, individuals from island
 populations should differ from individuals within mainland populations.
 Specifically, island populations are predicted to contain individuals that
 are larger, less aggressive, more sociable, and that invest more in their
 offspring. To date, tests of the ISH have mainly compared oceanic islands
 to continental sites, and rarely smaller spatial scales such as inland
 watersheds. Here, using a novel set of genome-wide SNP markers in wild
 deer mice (Peromyscus maniculatus) we conducted a genomic assessment of
 predictions underlying the ISH in an inland riverine island system:
 analysing island-mainland population structure, and quantifying
 heritability of phenotypes thought to underlie the ISH. We found clear
 genomic differentiation between island and mainland populations and
 moderate to high marker-based heritability estimates fo r overall
 variation in traits previously found to differ in line with the ISH
 between mainland and island locations. FST outlier analyses highlighted 12
 loci associated with differentiation between mainland and island
 populations. Together these results suggest that the island populations
 examined are on independent evolutionary trajectories, the traits
 considered have a genetic basis (rather than phenotypic variation being
 solely due to phenotypic plasticity). Coupled with the previous results
 showing significant phenotypic differentiation between island and mainland
 groups in this system, this study suggests that the ISH can hold even on a
 small spatial scale.
DOI: 10.5061/dryad.rfj6q57c2
title: Avoiding obstacles while intercepting a moving target: A miniature fly's solution

description: The miniature robber fly Holcocephala fusca intercepts its targets using a
 system whose behaviour is approximated by the proportional navigation
 guidance law. During predatory trials, we challenged Holcocephala's
 interception performance by placing a large object in its potential flight
 path. In response, Holcocephala deviated from the path predicted by
 pure-proportional navigation, but in many cases still eventually contacted
 the target. We show that such flight deviations can be explained as the
 output of two competing navigational systems; pure-proportional navigation
 and a simple obstacle avoidance algorithm. Obstacle avoidance by
 Holcocephala is here described by a simple feedback loop that uses the
 visual expansion of the approaching obstacle to mediate the magnitude of
 the turning-away response. We name the integration of this this steering
 law with pro-nav "Combined Guidance". The results demonstrate
 that predatory intent does not operate a monopoly on the fly's
 steering when attacking a target, and that simple guidance combinations
 can explain obstacle avoidance during interceptive tasks.
description: The enclosed data features the trajectories
 of <em>Holcocephala fusca</em> intercepting a moving dummy
 target whilst avoiding a static obstacle. This data was collected under
 field conditions using time-synchronised Photron Fastcam 2 cameras
 recording at 1000 frames per second. The data has been converted into 3D
 trajectories using checker-board calibration of the cameras immediately
 after capturing interception flights.
description: The obstacle (termed "bar") took the form of a flat
 sheet of painted black acetate. 'Thick' and 'Thin' in
 the bar descriptor refers to either a 5 cm width or 2.5 cm width, as
 detailed within the manuscript. A ReadMe file is included that details
 each of the files within each data folder, and what they tell you.
 Separately, there is an example plotting script which should demonstrate
 the use of all the included data to reproduce figures similar to those in
 the manuscript.
DOI: 10.5061/dryad.z8w9ghxdq
title: Data from: Determining ground-state phase diagrams on quantum computers via a generalized application of adiabatic state preparation

description: Quantum phase transitions materialize as level crossings in the
 ground-state energy when the parameters of the Hamiltonian are varied. The
 resulting ground-state phase diagrams are straightforward to determine by
 exact diagonalization on classical computers, but are challenging on
 quantum computers because of the accuracy needed and the near degeneracy
 of competing states close to the level crossings. In this work, we use a
 local adiabatic ramp for state preparation to allow us to directly compute
 ground-state phase diagrams on a quantum computer via time evolution. This
 methodology is illustrated by examining the ground states of the XY model
 with a magnetic field in the z-direction in one dimension. We are able to
 calculate an accurate phase diagram on both two and three site systems
 using IBM quantum machines.
description: For the two sites, the quantum computer data is obtained from IBM
 Santiago after readout error correction. For the three sites, the quantum
 computer data is obtained from IBM Yorktown, IBM Montreal, IBM Casablanca
 after readout error correction. Other data is from computer
 simulations.
DOI: 10.6071/m3196r
title: Shape multistability in flexible tubular crystals through interactions of mobile dislocations: Simulation data

description: We study avenues to shape multistability and shape-morphing in flexible
 crystalline membranes of cylindrical topology, enabled by glide mobility
 of dislocations. Using computational modeling, we obtain states of
 mechanical equilibrium presenting a wide variety of tubular crystal
 deformation geometries, due to an interplay of effective defect
 interactions with out-of-tangent-plane deformations that reorient the tube
 axis. Importantly, this interplay often stabilizes defect configurations
 quite distinct from those predicted for a two-dimensional crystal confined
 to the surface of a rigid cylinder. We find that relative and absolute
 stability of competing states depend strongly on control parameters such
 as bending rigidity, applied stress, and spontaneous curvature. Using
 stable dislocation pair arrangements as building blocks, we demonstrate
 that targeted macroscopic three-dimensional conformations of thin
 crystalline tubes can be programmed by imposing certain sparse patterns of
 defects. Our findings reveal a broad design space for controllable and
 reconfigurable colloidal tube geometries, with potential relevance also to
 architected carbon nanotubes and microtubules.
DOI: 10.15468/dl.gq2p5w
title: Occurrence Download

description: A dataset containing 647 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "TaxonKey is Antigone antigone"
 ]
}

 The dataset includes 647 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003014-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t76hdr82h
title: Trans-specific polymorphism and the convergent evolution of supertypes in MHC class II genes in Darters (Etheostoma)

description: Major Histocompatibility Complex (MHC) genes are one of the most
 polymorphic gene groups known in vertebrates. MHC genes also exhibit
 allelic variants that are shared among taxa, referred to as trans-specific
 polymorphism (TSP). The role that selection plays in maintaining such high
 diversity within species, as well as TSP, is an ongoing discussion in
 biology. In this study we used deep-sequencing techniques to characterize
 MHC class IIb gene diversity in three sympatric species of darters. We
 found at least 5 copies of the MHC gene in darters, with 126 genetic
 variants encoding 122 unique amino acid sequences. We identified four
 supertypes based on the binding properties of proteins encoded by the
 sequences. Although each species had a unique pool of variants, many
 variants were shared between species pairs and across all three species.
 Phylogenetic analysis showed that the variants did not group together
 monophyletically based on species identity or on supertype. An expanded
 phylogenetic analysis showed that some darter alleles grouped together
 with alleles from other percid fishes. Our findings show that TSP occurs
 in darters, which suggests that balancing selection is acting at the
 genotype level. Supertypes, however, are most likely evolving
 convergently, as evidenced by the fact that alleles do not form
 monophyletic groups based on supertype. Our research demonstrates that
 selection may be acting differently on MHC genes at the genotype and
 supertype levels, selecting for the maintenance of high genotypic
 diversity while driving the convergent evolution of similar MHC phenotypes
 across different species.
description: See Million and Lively 2021 for detailed methods.
 DNA was extracted from fin clips of three species of darter
 (genus <em>Etheostoma</em>). Two rounds of PCR amplified a
 fragment of MHC class IIb exon 2 using custom primers. Sequencing was
 performed using Illumina MiSeq. After demultiplexing and quality control,
 genetic variants were identified using an Excel macro for genotyping MHC
 in fish. Verified genetic variants were assigned titles and stored in the
 attached .fasta file (DarterMHC.fasta). DNA sequences
 were translated into amino acid sequences. Positively selected sites (PSS)
 were identified using the software MEGA. PSS codons are highlighted in the
 attached .csv file (PSSTN2.csv). Amino acid
 physicochemical properties (Z1-Z5) were obtained using a published
 database. The properties were read into a matrix of positively selected
 codon sites in the sequences (AAproperties.csv). MHCs
 were assigned to one of four functional supertypes via a discriminant
 analysis of principal components (DAPC) using the software adegenet in R
 (supertypeassignments.csv).
DOI: 10.5061/dryad.gmsbcc2pn
title: Data from: Proximity to parasites reduces host fitness independent of infection in a Drosophila-Macrocheles system

description: We assayed the longevity and reproductive output of Drosophila
 nigrospiracula exposed or not exposed to
 ectoparasitic Macrocheles subbadius accross a mesh barrier. As
 such we measured the non-consumptive effects (extending the ecology of
 fear to host-parasite systems) of an ectoparasite on host
 fecundity and survival. We found that exposure to mites, without
 infection, caused flies to live shorter lives and produce fewer offspring.
description: Experimental female flies were held in vials with either 1) a
 male fly (mated groups) or 2) a companion female (unmated groups - the
 companion fly had a wing clipped to distinguish them from the experimental
 fly. Flies were moved to new vials every 3 or 4 days,
 replacing the companion as needed. Flies were checked for survival every
 24 hours. Exp 1: Flies were held on agar vials and only
 survival was measured. Exp 2: Flies were held on a
 drosophila media-potato-cactus blend and the vials were retained after
 experimental flies died/were moved. Vials were retained for 2 weeks and
 the number of offspring (adult offspring + pupae) was calculated for each
 fly.
description: A meta sheet describes all variables.
 Experiments are more fully described in "Proximity to
 parasites reduces host fitness independent of infection in
 a Drosophila–Macrocheles system". In Exp 2, 1 fly outlived the
 experimental period. This fly was excluded from longevity but not
 fecundity analysis. (doi.org/10.1017/S0031182018000379)
DOI: 10.5061/dryad.stqjq2c4j
title: The individual-based network structure of palm-seed dispersers is explained by a rainforest gradient

description: How species interactions change in space and time is a major question in
 ecology. In tropical forests, plant individuals share mutualistic partners
 (pollinators or seed dispersers), yet we have little understanding of the
 factors affecting these individual interaction patterns. We used a seed
 dispersal individual-based network describing interactions between
 individuals of a palm species with bird species to investigate how
 intrinsic and extrinsic characteristics of individual plants influence the
 network structure. In our work we evaluated if average canopy height,
 number of fruits, distance to forest gap, and habitat type influence the
 role of palm individuals in the network. From 102 palms, 62 individuals
 had their seeds dispersed at least once: 17 individual palms in the
 restinga, 15 in the lowland and 30 in the pre-montane habitat. Twelve bird
 species were recorded dispersing Euterpe edulis seeds in our study area.
description: Focal palm observations of birds consuming
 <i>Euterpe edulis</i> fruits were conducted for a total of 102
 palm individuals across three different habitats in Cardoso Island, São
 Paulo (Brazil). Interactions between birds and palm individuals were
 considered a seed dispersal event only when the birds swallowed or carried
 the fruit away, thus ensuring seed deposition at a distance from the
 maternal plant. 
description: Binary and quantitative matrices of interaction between palm
 individuals and seed dispersing birds.<br> The first letter of palm
 individuals name refers to the habitat in which their were observed (R =
 restinga habitat, L = lowland habitat and P = pre-montane
 habitat).
DOI: 10.5061/dryad.fxpnvx0tb
title: Mammals adjust diel activity across gradients of urbanization

description: Time is a fundamental component of ecological processes. How animal
 behavior changes over time has been explored through well-known ecological
 theories like niche partitioning and predator-prey dynamics. Yet, changes
 in animal behavior within the shorter 24-hour light-dark cycle have
 largely gone unstudied. Understanding if an animal can adjust their
 temporal activity to mitigate or adapt to environmental change has become
 a recent topic of discussion and is important for effective wildlife
 management and conservation. While spatial habitat is a fundamental
 consideration in wildlife management and conservation, temporal habitat is
 often ignored. We formulated a temporal resource selection model to
 quantify the diel behavior of eight mammal species across ten U.S. cities.
 We found high variability in diel activity patterns within and among
 species and species-specific correlations between diel activity and human
 population density, impervious land cover, available greenspace,
 vegetation cover, and mean daily temperature. We also found that some
 species may modulate temporal behaviors to manage both natural and
 anthropogenic risks. Our results highlight the complexity with which
 temporal activity patterns interact with local environmental
 characteristics, and suggest that urban mammals may use time along the
 24-hour cycle to reduce risk, adapt, and therefore persist in
 human-dominated ecosystems.
description: Data collected using remotely-triggered wildlife cameras.
description: Refer to README file for file descriptions.