cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k6djh9w4j
title: Caenorhabditis elegans dauer recovery in response to range of bacteria

description: Many species use dormant stages for habitat selection by tying recovery
 from the stage to informative external cues. Other species have an
 undiscerning strategy in which they recover randomly despite having
 advanced sensory systems. We investigated whether elements of a
 species' habitat structure and life history can bar it from
 developing a discerning recovery strategy. The
 nematode Caenorhabditis elegans has a dormant stage
 called the dauer larva that disperses between habitat patches. On one
 hand, C. elegans colonization success is profoundly
 influenced by the bacteria found in its habitat patches, so we might
 expect this to select for a discerning strategy. On the other
 hand, C. elegans' habitat structure and life history suggest
 that there is no fitness benefit to varying recovery, which might select
 for an undiscerning strategy. We exposed dauers of three genotypes to a
 range of bacteria acquired from the worms' natural habitat. We found
 that C. elegans dauers recover in all conditions but
 increase recovery on certain bacteria depending on the worm’s genotype,
 suggesting a combination of undiscerning and discerning strategies.
 Additionally, the worms' responses did not match the bacteria's
 objective quality, suggesting that their decision is based on other
 characteristics.
description: 2000 dauer worms of each worm strain were plated
 on 5x10<sup>7</sup> CFU bacteria and allowed to roam around
 the plate for three hours. At the end of this period, worms were washed
 off the plates, treated with 1% SDS for 30 minutes, then washed multiple
 times to remove the SDS. For each worm/bacteria combination, ten small
 aliquots (~20 uL) were spotted onto a fresh plate and examined for dead
 and live worms. 
description: The variable called "LB_uL" is the volume of Luria
 broth in microliters used to maintain the constant number
 of 5x10<sup>7</sup> CFU bacteria, since each bacterial strain
 grows at a different density.  For the variable called
 "Dead_Binary," a value of 1 indicates that the worm was killed
 by 1% SDS and therefore recovered from the dauer stage during the three
 hour exposure. A value of 0 indicates that the worm survived because it
 remained in the dauer stage.' The variable
 "Category" is based on the classification these bacterial
 strains were given in Samuel et al. 2016 "<em>Caenorhabditis
 elegans</em> responses to bacteria from its natural
 habitats"
DOI: 10.5061/dryad.f1vhhmgts
title: Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

description: Phenotypic plasticity allows organisms to alter their phenotype in direct
 response to changes in the environment. Despite growing recognition of
 plasticity’s role in ecology and evolution, few studies have probed
 plasticity’s molecular bases—especially using natural populations. We
 investigated the genetic basis of phenotypic plasticity in natural
 populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally
 develop into an ‘omnivore’ morph that is favored in long-lasting,
 low-density ponds. However, if tadpoles consume freshwater shrimp or other
 tadpoles, they can alternatively develop (via plasticity) into a
 ‘carnivore’ morph that is favored in shallow, high-density ponds. By
 combining natural variation in pond ecology and morph production with
 population genetic approaches, we identified candidate loci associated
 with morph (carnivores versus omnivores) and loci associated with adaptive
 phenotypic plasticity (adaptive versus maladaptive morph choice). Our
 candidate morph loci mapped to two genes, whereas our candidate plasticity
 loci mapped to 14 genes. In both cases, the identified genes tended to
 have functions related to their putative role in spadefoot tadpole
 biology. Our results thereby form the basis for future studies into the
 molecular mechanisms that mediate plasticity in spadefoots. More
 generally, these results illustrate how diverse loci might be deployed to
 mediate adaptive plasticity.Phenotypic plasticity allows organisms to
 alter their phenotype in direct response to changes in the environment.
 Despite growing recognition of plasticity’s role in ecology and evolution,
 few studies have probed plasticity’s molecular bases—especially using
 natural populations. We investigated the genetic basis of phenotypic
 plasticity in natural populations of spadefoot toads (Spea multiplicata).
 Spea tadpoles normally develop into an ‘omnivore’ morph that is favored in
 long-lasting, low-density ponds. However, if tadpoles consume freshwater
 shrimp or other tadpoles, they can alternatively develop (via plasticity)
 into a ‘carnivore’ morph that is favored in shallow, high-density ponds.
 By combining natural variation in pond ecology and morph production with
 population genetic approaches, we identified candidate loci associated
 with morph (carnivores versus omnivores) and loci associated with adaptive
 phenotypic plasticity (adaptive versus maladaptive morph choice). Our
 candidate morph loci mapped to two genes, whereas our candidate plasticity
 loci mapped to 14 genes. In both cases, the identified genes tended to
 have functions related to their putative role in spadefoot tadpole
 biology. Our results thereby form the basis for future studies into the
 molecular mechanisms that mediate plasticity in spadefoots. More
 generally, these results illustrate how diverse loci might be deployed to
 mediate adaptive plasticity.
DOI: 10.5061/dryad.j9kd51c8w
title: Virtual screening for functional foods against the main protease of 2019 novel coronavirus

description: Design and development of an effective method or technologyto
 combat the 2019 novel coronavirus remains a challenge. In this
 work, the special attention was paid on the interaction between functional
 foods and the main protease of 2019-nCoV. Here, 10870 ligands were
 employed and screened by the molecular docking, which involved 12 kinds of
 functional foods (carbohydrates, fat acids, phospholipids, vitamin,
 β-sitosterol, flavonoids, nordihydroguaiaretic acid, curcumin, nookatone,
 β-pinene, tincturoid, and their isomers/analogs/derivatives). Then, 60
 ligands were obtained with the good docking affinity. Most of them belong
 to quercetin and its isomers/analogs/derivatives, which also showed the
 highest affinity for the main protease of 2019-nCoV. The dynamic
 simulation indicated that quercetin-protease and quercetin-analog-protease
 showed the excellent stability. Thus, quercetin may be the best candidate
 to prevent or inhibit the main protease of 2019-nCoV. Considering the
 green and white tea are rich in quercetin and its
 isomers/analogs/derivatives, tea and relative beverages may become a good
 option to regulate our metabolism and help us to overcome this special
 time.
DOI: 10.5061/dryad.70rxwdbvg
title: Soil microbial legacy drives crop diversity advantage: linking ecological plant-soil feedback with agricultural intercropping

description: Although the importance of the soil microbiome in mediating plant
 community structures and functions has been increasingly emphasized in
 ecological studies, the biological processes driving crop diversity
 overyielding remain unexplained in agriculture. Based on the plant-soil
 feedback (PSF) theory and method, we quantified how much soil microbes
 contributed to intercropping overyielding and detected which microbial
 groups mediated this effect. Soils were collected as inocula and sequenced
 from a unique 10-year field experiment, consisting of monoculture,
 intercropping and rotation planted with wheat (Triticum aestivum), maize
 (Zea mays) or faba bean (Vicia faba). A PSF study was conducted to test
 microbial effects on three crops’ growth in monoculture or intercropping.
 In wheat & faba bean (W&F) and maize & faba bean
 (M&F) systems, soil microbes drove intercropping overyielding
 compared to monoculture, with 28-51% of the overyielding contributed by
 microbial legacies. The overyielding effects resulted from negative PSFs
 in both systems, as crops, in particular faba bean grew better in soils
 conditioned by other crops than itself. Moreover, faba bean grew better in
 soils from intercropping or rotation than from the average of
 monocultures, indicating a strong positive legacy effect of multispecies
 cropping systems. However, with positive PSF and negative legacy benefit
 effect of intercropping/rotation, we did not observe significant
 overyielding in the W&M system. With more bacterial and fungal
 dissimilarities by metabarcoding in heterospecific than its own soil, the
 better it improved faba bean growth. More detailed analysis showed faba
 bean monoculture soil accumulated more putative pathogens with higher
 Fusarium relative abundance and more Fusarium oxysporum gene copies by
 qPCR, while in heterspecific soils, there was less pathogenetic effects
 when cereals were engaged. Further analysis in maize/faba bean
 intercropping also showed an increase of rhizobia relative abundance.
 Synthesis and applications. Our results demonstrate a soil
 microbiome-mediated advantage in intercropping through suppression of the
 negative PSF of pathogens and increasing beneficial microbes. As microbial
 mediation of overyielding is context-dependent, we conclude that the
 dynamics of both beneficial and pathogenic microbes should be considered
 in designing cropping systems for sustainable agriculture, particularly
 including combinations of legumes and cereals.
DOI: 10.5061/dryad.rxwdbrv5w
title: Experimental data from: On Simultaneous Buckling, Contact and Load Carrying Capacity

description: This paper considers the case of a relatively large number of parallel
 columns that buckle simultaneously. The close proximity between columns
 results in the possibility of contact between adjacent columns as buckling
 proceeds, and this brings with it some interesting observations on load
 carrying capacity. Some experimental results verify the theoretical
 development based on the versatility of high-fidelity 3D-printing. The
 sensitive nature of initial geometric imperfections (slight lack of
 straightness) and load eccentricity strongly influence post-buckled
 contact, load-carrying capacity, and, as the number of columns is
 increased, a statistically-based evaluation of anticipated behavior
 becomes appropriate.
description: Figures 7, 9, 12: The experimental data was collected using a
 digital load cells (Omega 50N with 0.05N precision, and Omega 500N load
 with 0.1 N precision), and two proximity lasers (OPTO NCDT 1302, with a
 precision of 0.025~mm). The data was then placed in the Kaleidograph (Mac)
 and plotted. Figure 3: This is numerical data,
 generated and plotted using Matlab. Also included is a
 typical multi-column design used by the 3D-printer. This was produced
 using the software package Solidworks. This data
 relates to the paper entitled "On Simultaneous Buckling, Contact and
 Load Carrying Capacity"
description: The experimental datasets are simple text files and can be
 imported into any other package. For the data contained
 in "Figures 7 and 9" the data is simply axial load P (measured
 using the above mentioned load cell), and axial displacement e (measured
 using a laser) for various numbers of columns n.
DOI: 10.5061/dryad.4f4qrfj8t
title: Data from: Negative effects of individual heterozygosity on reproductive success in a wild bird population

description: The evolutionary consequences of individual genetic diversity are
 frequently studied by assessing heterozygosity-fitness correlations
 (HFCs). The prevalence of positive and negative HFCs and the predominance
 of general versus local effects in wild populations are far from
 understood, partly because comprehensive studies testing for both
 inbreeding and outbreeding depression are lacking. We studied a
 genetically diverse population of blue tits in southern Germany using a
 genome-wide set of 87 microsatellites to investigate the relationship
 between proxies of reproductive success and measures of multi-locus and
 single-locus individual heterozygosity (MLH and SLH). We used
 complimentary measures of MLH and partitioned markers into functional
 categories according to their position in the blue tit genome. HFCs based
 on MLH were consistently negative for functional loci, whereas
 correlations were rather inconsistent for loci found in non-functional
 areas of the genome. Clutch size was the only reproductive
 variable showing a general effect. We found evidence for local effects for
 three measures of reproductive success: arrival date at the breeding site,
 the probability of breeding at the study site, and male reproductive
 success. For these, we observed consistent, and relatively strong,
 negative effects at one functional locus. Remarkably, this marker had a
 similar effect in another blue tit population from Austria (~400
 km to the east). We suggest that a genetic local effect on timing of
 arrival might be responsible for most negative HFCs detected, with
 carry-over effects on other reproductive traits. This effect could reflect
 individual differences in the distance between overwintering areas and
 breeding sites.
description: Details will be provided in the published paper.
description: Dataset: HFCs_Ccaeruleus Negative effects of
 individual heterozygosity on reproductive success in a wild bird
 population<br> Authors: Botero-Delgadillo, Esteban; Gilsenan, Carol;
 Mueller, Jakob C.; Kempenaers, Bart<br> MS Reference Number:
 MEC-20-0603 The whole dataset contains data for
 evaluating the relationship between individual heterozygosity and
 reproductive success in a population of Blue tit (Cyanistes caeruleus) in
 southern Germany.  The data set is divided into
 three spreadsheets: Breeding-Nonbreeding data; Breeding success data;
 Complete genotypes. These datasets are described in detail in the ReadMe
 file.
DOI: 10.5061/dryad.1jwstqjs3
title: Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes

description: Intraspecific competition has long been considered a key driver of
 evolutionary diversification, but whether it can also promote evolutionary
 innovation is less clear. We examined the interplay between competition
 and phenotypic plasticity in fueling the origins of a novel, complex
 phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles
 (genus Spea) that specializes on fairy shrimp. We specifically sought to
 explore the possible origins of this phenotype by providing shrimp to
 Scaphiopus holbrookii tadpoles (the sister genus to Spea that does not
 produce carnivores) while subjecting them to competition for their
 standard diet of detritus.  Previous research had shown that this
 species will eat shrimp when detritus is limited, and that these
 shrimp-fed individuals produce features that are redolent of a rudimentary
 Spea carnivore. In this study, we found that: 1) behavioral and
 morphological plasticity enabled some individuals to expand their diet to
 include shrimp; 2) there was heritable variation in this plasticity; and
 3) individuals received a growth and development benefit by eating shrimp.
 Thus, novel resource use can arise via plasticity as an adaptive response
 to intraspecific competition. More generally, our results show how
 competition and plasticity may interact to pave the way for the evolution
 of complex, novel phenotypes, such as the distinctive carnivore morph in
 present-day Spea.
DOI: 10.5061/dryad.4b8gtht9f
title: Data from: Too salty for you? Changes of diet in the laughing gull nestlings during the growing period

description: In many seabird and waterbird species, salinity can impose physiological
 stress on recently hatched chicks because they have a limited capacity to
 excrete salt loads. In response, parents can select low-salt food for
 their nestlings in the first stage of their growth. We determined the
 growth-related variation in the diet of laughing gull Leucophaeus
 atricilla nestlings by using stable isotope analysis of feathers. Isotopic
 measurement of hatchling down reflects the mother's diet before
 laying eggs. At the same time, the primary feather tip indicates the food
 intake during the initiation of feather growth (one week of age), and the
 primary feather base indicates the food provided by parents during the
 period immediately before fledging. δ15N and δ13C values among the feather
 types showed a spatiotemporal shift in the nestlings’ diet. Younger chicks
 consumed more terrestrial prey sources (weevil beetles Sphenophorus sp.;
 ~51%) than chicks at fledging (~2%). However, fledging chicks and females
 before egg-laying consumed mostly marine prey sources (Pacific white
 shrimp Litopenaeus vannamei and anchovy Anchoa sp.; &gt; 90%). The
 base and primary tip portions had similar δ15N values, but both sections
 were less enriched than the hatchling down. This change was diet-related,
 as the nestlings showed a lower percentage of anchovy consumption (13.3 –
 14.7%) compared to females before egg-laying (30.4%). Younger chicks had a
 different spatial niche than fledglings and females before egg-laying,
 indicating a diet shift through the chick growth period. Assuming that the
 availability of food in the terrestrial or marine foraging areas did not
 vary through the nestlings’ growth period (five weeks), our findings
 support food resource selectivity by parents for their offspring during
 the first days of life, to reduce the physiological stress caused by high
 salt loads.
DOI: 10.5061/dryad.h70rxwdgb
title: Quantitative analysis of subcellular distributions with an open-source, object-based tool

description: The subcellular localization of objects, such as organelles, proteins, or
 other molecules, instructs cellular form and function. Understanding the
 underlying spatial relationships between objects through colocalization
 analysis of microscopy images is a fundamental approach used to inform
 biological mechanisms. We generated an automated and customizable
 computational tool, the SubcellularDistribution pipeline, to facilitate
 object-based image analysis from 3D fluorescence microcopy images. To test
 the utility of the SubcellularDistribution pipeline, we examined the
 subcellular distribution of mRNA relative to centrosomes within Drosophila
 embryos. Centrosomes are microtubule-organizing centers, and RNA
 enrichments at centrosomes are of emerging importance. Our open-source and
 freely available software detected RNA distributions comparably to
 commercially available image analysis software. The
 SubcellularDistribution pipeline is designed to guide the user through the
 complete process of preparing image analysis data for publication, from
 image segmentation and data processing to visualization.
description: Images were acquired on a Nikon Ti-E system fitted with a
 Yokogawa CSU-X1 spinning disk head, Hamamatsu Orca Flash 4.0 v2 digital
 CMOS camera, Perfect Focus system, and a Nikon LU-N4 solid state laser
 launch (15 mW 405, 488, 561, and 647 nm) using a 100x 1.49 NA Apo TIRF
 oil-immersion objective. This microscope was controlled through Nikon
 Elements AR software on a 64-bit HP Z440 workstation.
description: Images are single molecule fluorescence in situ hybridization
 (smFISH) signals for centrocortin and gapdh (channel 1) and direct
 fluorescence of GFP-Cnn (channel 2) in
 <em>Drosophila</em> embryos at nuclear cycle 12 in interphase
 or metaphase. The raw-data-metadata.csv file documents the type of RNA and
 cell cycle for each image.
DOI: 10.5061/dryad.73n5tb2tw
title: Maladaptive migration behaviour in hybrids links to predator-mediated ecological selection

description: 1. Different migratory species have evolved distinct migratory
 characteristics that improve fitness in their particular ecological
 niches. However, when such species hybridize, migratory traits from
 parental species can combine maladaptively and cause hybrids to fall
 between parental fitness peaks, with potential consequences for hybrid
 viability and species integrity. 2. Here, we take advantage of a natural
 cross-breeding incident to study migratory behaviour in naturally
 occurring hybrids as well as in their parental species and explore links
 between migratory traits and predation risk. 3. To achieve this, we used
 electronic tags and passive telemetry to record detailed individual
 migration patterns (timing and number of migratory trips) in two common
 freshwater fish species, roach (Rutilus rutilus), common bream (Abramis
 brama) as well as their hybrids. Next, we scanned for tags regurgitated by
 a key avian predator (great cormorant, Phalacrocorax carbo) at nearby
 roosting sites, allowing us to directly link migratory behaviour to
 predation risk in the wild. 4. We found that hybrid individuals showed a
 higher number of short, multi-trip movements between lake and stream
 habitats as compared to both parental species. The mean date of first lake
 departure differed between bream and roach by more than 10 days, while
 hybrids departed in two distinct peaks that overlapped with the parental
 species’ averages. Moreover, the probability of cormorant predation
 increased with multi-trip movement frequency across species and was higher
 for hybrids. 5. Our data provide novel insights into hybrid viability,
 with links to predator-mediated ecological selection. Increased exposure
 to predators via maladaptive migratory behaviour reduces hybrid survival
 and can thereby reinforce species integrity.
DOI: 10.5061/dryad.stqjq2c1k
title: The effect of parasite dose on disease severity in the rodent malaria Plasmodium chabaudi

description: Experiments were designed to look at the relationship between infective
 dose and disease severity using two clones of Plasmodium chabaudi
 that differ in virulence. We asked whether there were dose–severity
 relationships, whether clone differences in virulence were maintained over
 a range of doses, and whether disease severity could be accounted for by
 parasite dynamics. Groups of mice were infected with parasite doses
 differing by an order of magnitude, ranging from 100 to 1×108 parasites.
 Infective dose affected the probability of death, but only with the more
 virulent clone. Dose also affected morbidity. For both clones, higher
 doses induced greater anaemia. Larger doses caused greater weight loss,
 but only for infections with the more virulent clone. Here, for a given
 dose, mice lost a fixed amount of weight, irrespective of their initial
 weight. Larger doses induced earlier mortality and morbidity than did
 lower dose treatments. Finally, dose affected parasite dynamics, with
 earlier and higher peak parasite densities in larger dose infections. All
 these effects were small relative to clone differences in disease
 severity, which were apparent across the range of doses. Dose effects were
 manifested through the timing and/or magnitude of peak parasite densities,
 broadly supporting the idea that dose affects disease severity by altering
 the time the host has to control parasite densities and ameliorate the
 effects of parasites. We discuss the possible efficacy of intervention
 strategies aimed at reducing human disease severity by reducing infective
 parasite dose.
description: Rodent malaria data on asexual parasite densities, weight and red
 blood cell densities throughout course of infection, for mice infected
 with different doses of parasites, for two parasite clones. The experiment
 was repeated in a second experimental block. Full methods are given
 in Timms, B., Colegrave, N., Chan, B.H.K., & Read, A.F. 2001. The
 effect of parasite dose on severity of disease in the rodent
 malaria <em>Plasmodium chabaudi. Parasitology.</em> 123:
 1-11
description: See Timms, B., Colegrave, N., Chan, B.H.K., & Read, A.F.
 2001. The effect of parasite dose on severity of disease in the rodent
 malaria <em>Plasmodium chabaudi. Parasitology.</em> 123:
 1-11. File names: b1, b2 = blocks 1 and 2. Anaemia =
 coulter count data; slides = parasitemias and parasite densities;
 weights=body weight