cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kg42p
title: Data from: A nocturnal rail with a simple territorial call eavesdrops on interactions between rivals

description: The behaviour of most animals has evolved in a communication network
 environment, in which signals produced by senders are perceived by many
 intended and unintended receivers. In this study, we tested whether the
 corncrake (Crex crex), a nocturnal rail species with innate (non-learned)
 calls, is able to eavesdrop on the interactions of conspecific males and
 how this eavesdropping affects subsequent responses by the eavesdropper to
 territorial intrusion. In the first step, simulated aggressive or neutral
 interactions between male dyads were presented to a focal male. In the
 second step, the calls of winning, losing or neutral males from the first
 step were played within the territory of the focal male. We measured
 behavioural and vocal responses of focal males. We found that corncrakes
 eavesdropped on signal exchange between rivals. Males often began
 responding to distant aggressive interactions during the eavesdropping
 phase, and they responded strongly during the intrusion phase of the
 experiments. The response was significantly weaker to playback of males
 from neutral interactions than to those involved in aggressive
 interactions, and we found no differences between the responses to Winners
 and Losers entering a focal male territory.
description: Wojas et all_Corncrake
 eavesdroppingData was collected
 during three seasons of field work (2013, 2014, 2015) in Upper Nurzec
 River Valley in Northeast Poland. To create this data we used Avisoft
 SASLab Pro 5.2.x (Avisoft Bioacoustics, Berlin, Germany), STATA v. 14.2
 (StataCorp, College Station, TX, USA) and IBM SPSS Statistics v. 24 (IBM
 Corp, Chicago, IL, USA). The final version is created in Microsoft Excel
 file. Column heading are describe in worksheet called
 ‘legend’.
DOI: 10.5061/dryad.6p823
title: Data from: Effects of temperature and drought on early life stages in three species of butterflies: mortality of early life stages as a key determinant of vulnerability to climate change?

description: Anthropogenic climate change poses substantial challenges to biodiversity
 conservation. Well-documented responses include phenological and range
 shifts, and declines in cold but increases in warm-adapted species. Thus,
 some species will suffer while others will benefit from ongoing change,
 although the biological features determining the prospects of a given
 species under climate change are largely unknown. By comparing three
 related butterfly species of different vulnerability to climate change, we
 show that stress tolerance during early development may be of key
 importance. The arguably most vulnerable species showed the strongest
 decline in egg hatching success under heat and desiccation stress, and
 similar pattern also for hatchling mortality. Research, especially on
 insects, is often focussed on the adult stage only. Thus, collating more
 data on stress tolerance in different life stages will be of crucial
 importance for enhancing our abilities to predict the fate of particular
 species and populations under ongoing climate change.
description: raw
 DataThese is the complete
 raw data file for survival rates of eggs and hatchlings under control,
 heat and desiccation/food stress treatment.
DOI: 10.15468/dl.sf9dpn
title: Occurrence Download

description: A dataset containing 840692 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Moscow University Herbarium (MW))",
 "GadmGid is one of (RUS.43_1, RUS.44_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 840692 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001242-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7t8c
title: Data from: Pleiotropic effect of the Flowering Locus C on plant resistance and defence against insect herbivores

description: 1. Plants vary widely in the extent to which they defend themselves
 against herbivores. Because the resources available to plants are often
 site-specific, variation among sites dictates investment into defence, and
 may reveal a growth-defence trade-off. Moreover, plants that have evolved
 different life-history strategies in different environments may situate
 themselves on this trade-off curve differently. For instance, plants that
 flower later have a longer vegetative lifespan, and may accordingly defend
 themselves differently than those that flower earlier. 2. Here, we tested
 whether late-flowering plants, with a longer vegetative lifespan, invest
 more in defence than early-flowering plants, using recombinant genotypes
 of the annual herb Cardamine hirsuta that differ in flowering time as a
 result of differences in the activity of the major floral repressor
 Flowering Locus C (FLC). 3. We found that variation at FLC was mainly
 responsible for regulating flowering time and allocation to reproduction,
 but this partially depended on where the plants grew. We also found that
 variation at FLC mediated plant allocation to defence, with late-flowering
 plants producing higher levels of total glucosinolates and stress-related
 phytohormones. Nonetheless, plant growth and the qualitative values of
 plant defence and plant resistance against specialist herbivores were
 mainly independent from FLC. 4. Synthesis - Our results highlight
 pleiotropic effects associated with flowering-time genes that might
 influence plant defence and plant-herbivore interactions.
description: all
 dataComplete
 datasetdata.csv
DOI: 10.15468/dl.pvxzqv
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corema album",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 208 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001248-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8b0m1
title: Data from: Resource allocation and seed size selection in perennial plants under pollen limitation

description: Pollen limitation may affect resource allocation patterns in plants, but
 its role in the selection of seed size is not known. Using an
 evolutionarily stable strategy model of resource allocation in perennial
 iteroparous plants, we show that under density-independent population
 growth, pollen limitation (i.e., a reduction in ovule fertilization rate)
 should increase the optimal seed size. At any level of pollen limitation
 (including none), the optimal seed size maximizes the ratio of juvenile
 survival rate to the resource investment needed to produce one seed
 (including both ovule production and seed provisioning); that is, the
 optimum maximizes the fitness effect per unit cost. Seed investment may
 affect allocation to postbreeding adult survival. In our model, pollen
 limitation increases individual seed size but decreases overall
 reproductive allocation, so that pollen limitation should also increase
 the optimal allocation to postbreeding adult survival. Under
 density-dependent population growth, the optimal seed size is inversely
 proportional to ovule fertilization rate. However, pollen limitation does
 not affect the optimal allocation to postbreeding adult survival and ovule
 production. These results highlight the importance of allocation
 trade-offs in the effect pollen limitation has on the ecology and
 evolution of seed size and postbreeding adult survival in perennial
 plants.
description: Data underlying figure
 2Effects of ovule
 fertilization rate on the selected optimal seed size (fig. 2A), allocation
 to post-breeding adult survival (fig. 2B) and number of ovules produced
 (fig. 2C) under density-independent population growth.Data underlying figure
 3Effects of ovule
 fertilization rate on the selected optimal seed size (fig. 3A), allocation
 to post-breeding adult survival (fig. 3B) and number of ovules produced
 (fig. 3C) under density-independent population growth.
DOI: 10.5061/dryad.vb769
title: Data from: The SETDB2 locus: evidence for a genetic link between handedness and atopic disease

description: The gene SETDB2, which mediates aspects of laterality in animal model
 systems, has recently been linked with human handedness as measured
 continuously on a scale from strong left to strong right. By contrast, it
 was marginally associated with a left-right dichotomous measure, and it
 showed no evidence of association with absolute handedness strength
 independent of direction. We genotyped the SETDB2 handedness-associated
 single nucleotide polymorphism, rs4942830, in a large healthy population
 likewise phenotyped for continuous, absolute, and dichotomous handedness
 variables. Our results replicated the previously described pattern of
 association, with significant effects on continuous handedness, and
 weaker, marginal effects on dichotomous handedness, but no effects on
 absolute handedness. These results help to establish the locus marked by
 the SNP rs4942830 as a strong candidate for mediating human handedness.
 Intriguingly, rs4942830 is also in complete linkage disequilibrium with
 rs386770867, a polymorphism recently shown to affect human serum levels of
 IgE production and other atopic phenotypes, which implicates this locus in
 the longstanding links of handedness with asthma and other atopic
 diseases.
description: Data_SETDB2_9aug2017Full description in manuscript - Handedness data: Participants filled out the Waterloo Handedness Questionnaire (WHQ). Scores for each of 32 WHQ items ranging from +2 for strong right, +1 for weak right, 0 for ambidextrous, -1 for weak left and -2 for strong left, giving a total scale range from -64 to +64. Laterality Quotient (LQ) is a continuous measure from -64 to +64 that thus incorporates both direction and strength of handedness; Strength of Handedness (ST) is the absolute value of LQ; and Left-Right (LR) is a dichotomous measure whereby -1 to -64 is designated left and +1 to +64 is right. Genetic data: DNA was extracted from saliva using standard phenol-chloroform protocols. Fluorophore-labeled primers for SETDB2 rs4942830 fluorophore-labeled were used for TaqMan® genotyping on a Roche LightCycler® 96 Real-Time PCR machine. VIC and FAM fluorescence data were analyzed under Endpoint Genotyping using LightCycler® 96 software, version 1.1.0.1320.
DOI: 10.5061/dryad.q8s5k
title: Data from: Has open data arrived at the British Medical Journal (BMJ)? An observational study

description: Objective: To quantify data sharing policy compliance at the BMJ by
 analysing the rate of data sharing practices, and investigate attitudes
 and examine barriers towards data sharing. Design: Observational study.
 Setting: The BMJ research archive. Participants: 160 randomly sampled BMJ
 research articles, excluding meta-analysis and systematic reviews. Main
 outcome measures: Percentages of research articles that indicated the
 availability of their raw datasets in their data sharing statements and
 those that provided their datasets upon request. Results: Fifty out of 160
 (31%) research articles indicated the availability of their datasets.
 Twelve used publicly available data and the remaining 38 were sent email
 requests to access their datasets. Only 1 publicly available dataset could
 be accessed and only 6 out of 38 shared their data via e-mail. So only
 7/160 research articles shared their datasets, 4.4% (95% confidence
 interval: 1.8% to 8.8%). Conclusions: Despite the BMJ’s strong data
 sharing policy, sharing rates are low. Possible explanations for low data
 sharing rates could be: the wording of the BMJ data sharing policy, which
 leaves room for individual interpretation and possible loopholes; that our
 email requests ended up in researchers spam folders; and, that researchers
 are not rewarded in the scientific community for sharing their data. It
 might be time for a more effective data sharing policy and better
 incentives for health and medical researchers to share their data.
description: Data sharing at the BMJ
 from 2009-2015Data sharing at the BMJ
 from 2009-2015. This data was collected using publicly available data (BMJ
 research archive) and then by emailing authors to request access to their
 raw datasets.BMJ_DataSharing.xlsx
DOI: 10.5061/dryad.m69t2
title: Data from: Male receiver bias for red agonistic signaling in a yellow-signaling widowbird: a field experiment

description: Receiver bias models of signal evolution are typically regarded as
 alternatives or complements to ornament evolution due to coevolving mate
 choice, whereas sexually or socially selected agonistic signals are rarely
 studied with respect to receiver psychology. Against the background of
 convergent evolution of red agonistic signals from yellow ancestors in the
 genus Euplectes (widowbirds and bishops), we experimentally test the
 function of a yellow signal in the montane marsh widowbird (E.
 psammocromius), as well as a hypothesized receiver bias for redder (longer
 wavelength) hues. In a field experiment in southern Tanzania, males that
 had their yellow wing patches blackened lost their territories or lost
 territorial contests more often than controls or reddened males, which
 together with a longer wavelength hue in territory holders, indicates an
 agonistic signal function. Males painted a novel red hue, matching that of
 red-signalling congeners, retained their territories and won contests more
 often than controls. To our knowledge, this is the first demonstration of
 a receiver bias driving agonistic signal evolution. Although the sensory
 or cognitive origin of this bias is yet unknown, it strengthens our view
 that genetically constrained signal production (i.e. carotenoid
 metabolism), rather than differential selection, explains the carotenoid
 colour diversification in Euplectes.
description: Bias for red article
 dataThe excel file consists
 of three spreadsheets. The labeling of the spreadsheets and the column
 headers, together with details in the article, are
 self-explanatory.
DOI: 10.5061/dryad.2jp32
title: Data from: Genomic analysis of demographic history and ecological niche modeling in the endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

description: The vertebrate extinction rate over the past century is approximately
 22–100 times greater than background extinction rates, and large mammals
 are particularly at risk. Quaternary megafaunal extinctions have been
 attributed to climate change, overexploitation, or a combination of the
 two. Rhinoceroses (Family: Rhinocerotidae) have a rich fossil history
 replete with iconic examples of climate-induced extinctions, but current
 pressures threaten to eliminate this group entirely. The Sumatran
 rhinoceros (Dicerorhinus sumatrensis) is among the most imperiled mammals
 on earth. The 2011 population was estimated at ≤216 wild individuals, and
 currently the species is extirpated, or nearly so, throughout the majority
 of its former range. Understanding demographic history is important in
 placing current population status into a broader ecological and
 evolutionary context. Analysis of the Sumatran rhinoceros genome reveals
 extreme changes in effective population size throughout the Pleistocene.
 Population expansion during the early to middle Pleistocene was followed
 by decline. Ecological niche modeling indicated that changing climate most
 likely played a role in the decline of the Sumatran rhinoceros, as less
 suitable habitat on an emergent Sundaland corridor isolated Sumatran
 rhinoceros populations. By the end of the Pleistocene, the Sundaland
 corridor was submerged, and populations were fragmented and consequently
 reduced to low Holocene levels from which they would never recover. Past
 events denuded the Sumatran rhinoceros of genetic diversity through
 population decline, fragmentation, or some combination of the two and most
 likely made the species even more susceptible to later exploitation and
 habitat loss.
description: Sumatran Rhinoceros
 occurence dataGeoreferenced occurrence
 data for Sumatran Rhinoceros (Dicerorhinus sumatrensis) compiled from
 literature and including recent, historical and putative fossil
 occurrences.rhino_occurrences_20171021-2.xlsx
DOI: 10.5061/dryad.k87m52h
title: Data from: Jasmonic acid regulation of the anti-herbivory mechanism conferred by fungal endophytes in grasses

description: 1. The most studied mechanism of protection against herbivores in grasses
 associated with Epichloë fungal endophytes has been the fungal production
 of alkaloids. However, the contribution of the plant immune responses on
 the level of resistance to herbivores in symbiotic grasses has been poorly
 explored. We studied the relationship between the plant hormone, jasmonic
 acid (JA), and Epichloë fungal endophytes on herbivore defenses in
 symbiotic grasses. We hypothesized that an exogenous application of methyl
 jasmonate (MeJA), an activator of the plant JA defense response, would
 increase the level of resistance of endophyte-symbiotic and non-symbiotic
 plants to a chewing insect. As Epichloë endophytes produce alkaloids, an
 enhancement of the JA defense would complement to the resistance given by
 these alkaloids. 2. Lolium multiflorum plants symbiotic and non-symbiotic
 with the endophyte Epichloë occultans were subjected to an exogenous
 application of MeJA followed by a challenge with the generalist chewing
 insect Spodoptera frugiperda. We measured the level of plant resistance to
 chewing insects, and the defenses conferred by host plants and fungal
 endophytes. 3. Symbiotic plants were more resistant to S. frugiperda than
 their non-symbiotic counterparts. However, despite the fact that the JA
 concentration significantly increased in all plants with the MeJA
 exposure, neither endophyte-symbiotic nor non-symbiotic plants showed an
 enhanced resistance to insects. Unexpectedly, the exposure of
 endophyte-symbiotic plants to MeJA led to a reduction in the concentration
 of loline alkaloids (i.e. N-formyllolines and N-acetylnorlolines),
 consequently decreasing the level of plant resistance to the herbivore. 4.
 Synthesis. Our results suggest that, rather than complementing the
 alkaloid-based defense, the JA hormone weakens the anti-herbivore
 mechanism conferred by endophytes. The present study highlights that the
 interaction between the JA hormone and the presence of leaf fungal
 endophytes can be of importance for the effectiveness of the
 anti-herbivore defenses of symbiotic plants.
description: Concentration of defense
 hormones and lolines of L. multiflorum plants and S. frugiperda
 performance measurementsMeJA: methyl jasmonate;
 SA: salicylic acid; JA: jasmonic acid; nanl: N-acetylnorlolines; nfl:
 N-formyllolines; DW: dry weight.Data Bastias, Daniel A. et
 al_2018.xlsx
DOI: 10.5061/dryad.g7g45
title: Data from: What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow

description: Hybridization is a potent evolutionary process that can affect the origin,
 maintenance, and loss of biodiversity. Because of its ecological and
 evolutionary consequences, an understanding of hybridization is important
 for basic and applied sciences, including conservation biology and
 agriculture. Herein, we review and discuss ideas that are relevant to the
 recognition of hybrids and hybridization. We supplement this discussion
 with simulations. The ideas we present have a long history, particularly
 in botany, and clarifying them should have practical consequences for
 managing hybridization and gene flow in plants. One of our primary goals
 is to illustrate what we can and cannot infer about hybrids and
 hybridization from molecular data; in other words, we ask when genetic
 analyses commonly used to study hybridization might mislead us about the
 history or nature of gene flow and selection. We focus on patterns of
 variation when hybridization is recent and populations are polymorphic,
 which are particularly informative for applied issues, such as
 contemporary hybridization following recent ecological change. We show
 that hybridization is not a singular process, but instead a collection of
 related processes with variable outcomes and consequences. Thus, it will
 often be inappropriate to generalize about the threats or benefits of
 hybridization from individual studies, and at minimum, it will be
 important to avoid categorical thinking about what hybridization and
 hybrids are. We recommend potential sampling and analytical approaches
 that should help us confront these complexities of hybridization.
description: R script to simulate
 hybridsWe used this R script to
 simulate hybrids for the second section of the paper ("what if
 anything are hybrids"). It includes code to extract ancestry data,
 perform PCA, and generate plots.sims.Rnemo initialization filesInitialization files for nemo simulations. *ini files are provided for the different sets of simulations run for the paper. The *freq.txt files provide starting allele frequencies for the simulations, and the shell script runNemo.sh runs the sets of simulations.nemo_init.tar.gz
DOI: 10.5061/dryad.n6sn0
title: Data from: Heterozygosity-fitness correlations in a declining seabird population

description: Loss of genetic diversity is thought to lead to increased risk of
 extinction in endangered populations due to decreasing fitness of
 homozygous individuals. Here, we evaluated the presence of inbreeding
 depression in a long-lived seabird, the European shag (Phalacrocorax
 aristotelis), after a severe decline in population size by nearly 70%.
 During three reproductive seasons, 85 breeders were captured and genotyped
 at seven microsatellite loci. Nest sites were monitored during the
 breeding season to estimate reproductive success as the number of chicks
 surviving to full size-grown per nest. Captured birds were tagged with a
 ring with an individual code, and resighting data was collected during
 seven-year period. We found a strong effect of multilocus heterozygosity
 on female reproductive performance, and a significant, although weaker,
 effect on breeder survival. However, our matrix population model suggests
 that this relatively small effect of genetic diversity on breeder survival
 may have a profound effect on fitness. This highlights the importance of
 integrating life-history consequences in HFC studies. Importantly,
 heterozygosity was correlated across loci, suggesting that genome-wide
 effects, rather than single loci, are responsible for the observed HFCs.
 Overall, the HFCs are a worrying symptom of genetic erosion in this
 declining population. Many long-lived species are prone to extinction, and
 future studies should evaluate the magnitude of fitness impact of genetic
 deterioration on key population parameters, such as survival of breeders.
description: Heterozygosity-Fitness
 correlation in European ShagData file includes 3
 spreadsheets: 1) Micros spreadsheet; Number: numeric code for each bird;
 year: year of capture; colony: island of capture, Sex: sex of each bird;
 Phaari02 to Phaari16: alleles at seven microsatellite loci; HL:
 homozygosity weighted by locus by using CERNICALIN 2) Survival
 spreadsheet; Number: numeric code for each bird; year: year of capture;
 colony: island of capture; HL: homozygosity weighted by locus by using
 CERNICALIN; Sex: sex of each bird; V2007toV2013: capture recapture data 3)
 Reproduction spreadsheet; Number: numeric code for each bird; RS:
 Reproductive success; year: year of capture; colony: island of capture;
 Sex: sex of each bird; HL: homozygosity weighted by locus by using
 CERNICALINbase_mol_ecol.xlsx