cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v56t9
title: Data from: Predator-free space, functional responses and biological invasions

description: Predator-prey interactions are mediated by the structural complexity of
 habitats, but disentangling the many facets of structure that contribute
 to this mediation remains elusive. In a world replete with altered
 landscapes and biological invasions, determining how structure mediates
 the interactions between predators and novel prey will contribute to our
 understanding of invasions and predator-prey dynamics in general. Here,
 using simplified experimental arenas, we manipulate predator-free space,
 whilst holding surface area and volume constant, to quantify the effects
 on predator-prey interactions between two resident gammarid predators and
 an invasive prey, the Ponto-Caspian corophiid Chelicorophium curvispinum.
 Systematically increasing predator-free space alters the functional
 responses (the relationship between prey density and consumption rate) of
 the amphipod predators by reducing attack rates and lengthening handling
 times. Crucially, functional response shape also changes subtly from
 destabilising Type II towards stabilising Type III, such that small
 increases in predator-free space to result in significant reductions in
 prey consumption at low prey densities. Habitats with superficially
 similar structural complexity can have considerably divergent consequences
 for prey population stability in general and, particularly, for invasive
 prey establishing at low densities in novel habitats.
description: rawFRdataFunctional responses of gammarid predators towards C. curvispinum
DOI: 10.5061/dryad.b7cd6
title: Data from: The evolution of optimal emergence times: bet hedging and the quest for an ideal free temporal distribution of individuals

description: Proper timing of activities is one of the principal challenges faced by
 most organisms. Organisms need to account for various aspects in decision
 making like avoiding inordinate risks, synchronizing with resource
 availability, or finding mates. We provide analytical and simulation
 models to investigate the influence of life expectancy, resource
 competition and unpredictable environmental conditions (environmental
 uncertainty) on the evolutionarily stable distribution of emergence times
 in organisms depending on seasonally available resources. We focus on the
 partitioning of total phenotypic variance in emergence times into 1)
 genetic variance in mean emergence times between lineages and 2)
 environmental trait variance that determines the intra-lineage variance in
 the timing of emergence. Both life expectancy of organisms and intensity
 of competition severely influence the evolutionary response to
 environmental uncertainty. Our main findings can be summarized as follows:
 1) in general diversifying bet hedging (environmental trait variance) is
 the adequate mechanism to reduce the risk arising from environmental
 uncertainty while conservative bet hedging, i.e. delaying emergence into
 ‘safe’ phases of the season is restricted to short lived organisms and to
 situations with vanishing competition. 2) Environmental trait variance
 increases with increasing environmental uncertainty whereas 3) significant
 genetic variance evolves only under severe resource competition; it is
 driven by selection for an ideal free distribution of emergence times. 4)
 The level of genetic variance evolving declines with increasing life
 expectancy of organisms. 5) With sufficiently short life expectancy
 evolutionary branching and coexistence of distinctly different emergence
 strategies occurs; the number of co-occurring strategies is determined by
 the level of environmental uncertainty. Our model provides cues for
 understanding how different ecological factors contribute and interact to
 shape the evolution of emergence strategies.
description: Source code for
 simulations (Pascal/Delphi)ZIP-archive contains 3
 files: "emerge.pas" (source code), "parameters.txt"
 (text file with model parameters to be read by emerge.pas),
 "results.txt" (text file with results written by emerge.pas).
 For compiling and further instructions see the first lines in
 "emerge.pas".emerge.zip
DOI: 10.5061/dryad.dn4f7b3
title: Data from: Simulated hatching failure predicts female plasticity in extra-pair behavior over successive broods

description: While many studies have investigated the occurrence of extra-pair
 paternity (EPP) and its adaptive significance in wild population of birds,
 we still know surprising little about the plasticity in mating behavior of
 females at the individual level and how it affects the patterns of
 paternity. To address this question, we focused on the direct fertility
 benefit hypothesis for the function of EPP and studied if female birds
 react in extra-pair mating behavior after reproductive failures using a
 wild population of the Japanese great tit, Parus minor, a socially
 monogamous passerine with a moderate frequency of EPP and a high multiple
 brooding rate. We simulated hatching failure by replacing with artificial
 eggs during the egg laying period to investigate if females subsequently
 altered their mating behavior and became more promiscuous to improve
 reproductive success in their following clutches. The proportion of
 extra-pair offspring per clutches of both experimental and control pairs
 increased in the second clutches (replacement and repeat), but compared to
 the control pairs, the increase in the experimental pairs was
 significantly greater. The present study suggests that individual females
 appear to be making decisions based on specific cues and flexibly altering
 mating behavior in adaptive ways. Also, our results are compatible with
 one of the long-debated hypotheses for the evolutionary maintenance of EPP
 which predicts females gain direct fitness benefit through increased
 reproductive success from mating multiply.
description: dataBEHECO-2018-0119
DOI: 10.6084/m9.figshare.31140619
title: Replication Package: Adversarial Bug Reports as a Security Risk in Language Model-Based Automated Program Repair

description: Large Language Model (LLM) - based Automated Program Repair (APR) systems are increasingly integrated into modern software development workflows, offering automated patches in response to natural language bug reports. However, this reliance on untrusted user input introduces a novel and underexplored attack surface. In this paper, we investigate the security risks posed by adversarial bug reports---realistic-looking issue submissions crafted to mislead APR systems into producing insecure or harmful code changes.We develop a comprehensive threat model and conduct an empirical study to evaluate the vulnerability of APR systems to such attacks. Our demonstration comprises 51 adversarial bug reports generated across a spectrum of strategies, ranging from manual curation to fully automated pipelines. We test these against a leading LLM-based APR system and assess both pre-repair defenses (e.g., LlamaGuard variants, PromptGuard variants, Granite-Guardian, and custom LLM filters) and post-repair detectors (GitHub Copilot, CodeQL).Our findings show that current defenses are insufficient: 90% of crafted bug reports triggered attacker-aligned patches. The best pre-repair filter blocked only 47%, while post-repair analysis--often requiring human oversight--was effective in just 58% of cases.To support scalable security testing, we introduce a prototype framework for automating the generation of adversarial bug reports. Our analysis exposes a structural asymmetry: generating adversarial inputs is inexpensive, while detecting or mitigating them remains costly and error-prone. We conclude with recommendations for improving the robustness of APR systems against adversarial misuse and highlight directions for future work on secure APR.
DOI: 10.6084/m9.figshare.31140619.v1
title: Replication Package: Adversarial Bug Reports as a Security Risk in Language Model-Based Automated Program Repair

description: Large Language Model (LLM) - based Automated Program Repair (APR) systems are increasingly integrated into modern software development workflows, offering automated patches in response to natural language bug reports. However, this reliance on untrusted user input introduces a novel and underexplored attack surface. In this paper, we investigate the security risks posed by adversarial bug reports---realistic-looking issue submissions crafted to mislead APR systems into producing insecure or harmful code changes.We develop a comprehensive threat model and conduct an empirical study to evaluate the vulnerability of APR systems to such attacks. Our demonstration comprises 51 adversarial bug reports generated across a spectrum of strategies, ranging from manual curation to fully automated pipelines. We test these against a leading LLM-based APR system and assess both pre-repair defenses (e.g., LlamaGuard variants, PromptGuard variants, Granite-Guardian, and custom LLM filters) and post-repair detectors (GitHub Copilot, CodeQL).Our findings show that current defenses are insufficient: 90% of crafted bug reports triggered attacker-aligned patches. The best pre-repair filter blocked only 47%, while post-repair analysis--often requiring human oversight--was effective in just 58% of cases.To support scalable security testing, we introduce a prototype framework for automating the generation of adversarial bug reports. Our analysis exposes a structural asymmetry: generating adversarial inputs is inexpensive, while detecting or mitigating them remains costly and error-prone. We conclude with recommendations for improving the robustness of APR systems against adversarial misuse and highlight directions for future work on secure APR.
DOI: 10.5061/dryad.2dp8877
title: Data from: An alternative water transport system in land plants

description: The evolution of vascular tissue is a key innovation enabling plants to
 inhabit terrestrial environments. Here, we demonstrate extra-vascular
 water transport in a giant, prop-rooted monocot from Lord Howe Island.
 Pandanus forsteri (Pandanaceae) produces gutter-like leaves that capture
 rainwater, which is then couriered along a network of channels to the tips
 of aerial roots, where it is stored by absorptive tissue. This passive
 mechanism of water acquisition, transport, and storage is critical to the
 growth of aerial prop roots that cannot yet attain water via vascular
 conduction. This species therefore sheds light on the elaborate means by
 which plants have evolved to attain water.
description: Longitudinal
 growthLongitudinal growth of
 roots in three treatments (control, stemflow diverted, and velamen
 removed). Growth is measured in centimeters after 22
 months.longgrowthdata.csvRadial root growthThe radial growth of roots subject to three treatments (control, stemflow diverted, and valamen removed). Units are in the form of post-treatment:pre-treatment ratio. Measurements were taken 22 months after treatment.radialgrowthdata.csvRoot channel water experimentThe volume of water captured by root channels that had water experimentally poured onto them under two treatment conditions (control, channel disabled). Units are in mL of water captured. Root inclination is included as a covariate.rootexp.csvleavesLeaf morphology data (leaf length, width, and channel area).leafexpSimulated rainfall experiment with two treatments (channels present, channels disabled).
DOI: 10.5061/dryad.4387q
title: Data from: Modular color evolution facilitated by a complex nanostructure in birds

description: The way in which a complex trait varies, and thus evolves, is critically
 affected by the independence, or modularity, of its subunits. How modular
 designs facilitate phenotypic diversification is well studied in
 non-ornamental (e.g., cichlid jaws), but not ornamental traits. Diverse
 feather colors in birds are produced by light absorption by pigments
 and/or light scattering by nanostructures. Such structural colors are
 deterministically related to the nanostructures that produce them and are
 therefore excellent systems to study modularity and diversity of
 ornamental traits. Elucidating if and how these nanostructures facilitate
 color diversity relies on understanding how nanostructural traits covary,
 and how these traits map to color. Both of these remain unknown in an
 evolutionary context. Most dabbling ducks (Anatidae) have a conspicuous
 wing patch with iridescent color caused by a two-dimensional photonic
 crystal of small (100–200 nm) melanosomes. Here, we ask how this complex
 nanostructure affects modularity of color attributes. Using a combination
 of electron microscopy, spectrophotometry, and comparative methods, we
 show that nanostructural complexity causes functional decoupling and
 enables independent evolution of different color traits. These results
 demonstrate that color diversity is facilitated by how nanostructures
 function and may explain why some birds are more color-diverse than
 others.
description: Nanostructural and color
 traits measured in dabbling ducksSpecies means calculated
 from natural logarithms of raw nanostructural and color trait data. Data
 were collected from museum specimens and analyzed in R.
 'Diameter_SD' is the standard deviation of natural-log
 transformed diameter values.dryad_duck_species_means.csv
DOI: 10.5061/dryad.78m34
title: Data from: A global synthesis of survival estimates for microbats

description: Accurate survival estimates are needed to construct robust population
 models, which are a powerful tool for understanding and predicting the
 fates of species under scenarios of environmental change. Microbats make
 up 17% of the global mammalian fauna, yet the processes that drive
 differences in demographics between species are poorly understood. We
 collected survival estimates for 44 microbat species from the literature
 and constructed a model to determine the effects of reproductive, feeding
 and demographic traits on survival. Our trait-based model indicated that
 bat species which produce more young per year exhibit lower apparent
 annual survival, as do males and juveniles compared with females and
 adults, respectively. Using 8 years of monitoring data for two Australian
 species, we demonstrate how knowledge about the effect of traits on
 survival can be incorporated into Bayesian survival analyses. This
 approach can be applied to any group and is not restricted to bats or even
 mammals. The incorporation of informative priors based on traits can allow
 for more timely construction of population models to support management
 decisions and actions.
description: C. gouldii
 mark-recapture data setMark-recapture data file
 needed to run Bayesian survival analysis for Chalinolobus gouldii example,
 as detailed in Supplement 4, page 8.CG_Bat_Dat.RData
DOI: 10.5061/dryad.293mk
title: Data from: Distinguishing causes of virulence evolution: reply to Alizon & Michalakis

description: In a recent study of the symbiosis between bacteria and plasmids, the
 available evidence suggests that experimental evolution of plasmid
 virulence was primarily driven by within-host competition caused by
 superinfection. The data do not exclude the possibility, however, that a
 trade-off between virulence and infectious transmission to uninfected
 bacteria also played a minor role.
description: dataTab-delimited text file
 with column headings. Full methods are described in smith (2010) Evolution
 65: 831-841. Briefly: "plasmid.treatment" is the source from
 which the plasmid was sampled (immigration line, no.immigration line, or
 the ancestral plasmid genotype). "selection.coefficient" is a
 measure of the fitness of plasmid-infected strains in competition against
 a common plasmid-resistant competitor. "infection.constant" is a
 measure of the plasmid's ability to infect uninfected bacteria of the
 ancestral genotype. "superinfection.constant" is a measure of
 the palsmid's ability to infect bacteria infected with an
 incompatible competitor plasmid. "ratio.super.to.infect" is the
 ratio of the two constants (the values in the figure this data was used
 for). "NA" values indicate missing data.
DOI: 10.5061/dryad.fp7s8
title: Data from: Host social behavior decreases exposure to vector-borne disease: a field experiment in a “hotspot” of West Nile virus transmission

description: Animals can decrease their individual risk of predation by forming groups.
 The encounter-dilution hypothesis extends the potential benefits of
 gregariousness to biting insects and vector-borne disease by predicting
 that the per capita number of insect bites should decrease within larger
 host groups. Although vector-borne diseases are common and can exert
 strong selective pressures on hosts, there have been few tests of the
 encounter-dilution effect in natural systems. We conducted an experimental
 test of the encounter-dilution hypothesis using the American robin (Turdus
 migratorius), a common host species for the West Nile virus (WNV), a
 mosquito-borne pathogen. By using sentinel hosts (house sparrows, Passer
 domesticus) caged in naturally occurring communal roosts in the suburbs of
 Chicago, we assessed sentinel host risk of WNV exposure inside and outside
 of roosts. We also estimated per capita host exposure to infected vectors
 inside roosts and outside of roosts. Sentinel birds caged inside roosts
 seroconverted to WNV more slowly than those outside of roosts, suggesting
 that social groups decrease per capita exposure to infected mosquitoes.
 These results therefore support the encounter-dilution hypothesis in a
 vector-borne disease system. Our results suggest that disease-related
 selective pressures on sociality may depend on the mode of disease
 transmission.
description: Sentinel Bird Exposure
 DataData describing exposure
 status of each sentinel bird and amount of time spent housed in field
 cagesVector Index Data Roost
 and Non-RoostData used for
 calculating average vector index at roost and non-roost
 sitesBird Baited Trap and
 Paired Light Trap DataCulex abundance and
 infection data from bird baited traps and paired light traps used to
 estimate per capita vector index from 2012
DOI: 10.5061/dryad.md880
title: Data from: Wolbachia increases the susceptibility of a parasitoid wasp to hyperparasitism

description: The success of maternally transmitted endosymbiotic bacteria, such as
 Wolbachia, is directly linked to their host reproduction but in direct
 conflict with other parasites that kill the host before it reaches
 reproductive maturity. Therefore, symbionts that have evolved strategies
 to increase their host’s ability to evade lethal parasites may have high
 penetrance, while detrimental symbionts would be selected against, leading
 to lower penetrance or extinction from the host population. In a natural
 population of the parasitoid wasp Hyposoter horticola in the Åland Islands
 (Finland), the Wolbachia strain wHho persists at an intermediate
 prevalence (∼50%). Additionally, there is a negative correlation between
 the prevalence of Wolbachia and a hyperparasitoid wasp, Mesochorus cf.
 stigmaticus, in the landscape. Using a manipulative field experiment, we
 addressed the persistence of Wolbachia at this intermediate level, and
 tested whether the observed negative correlation could be due to Wolbachia
 inducing either susceptibility or resistance to parasitism. We show that
 infection with Wolbachia does not influence the ability of the wasp to
 parasitize its butterfly host, Melitaea cinxia, but that hyperparasitism
 of the wasp increases in the presence of wHho. Consequently, the symbiont
 is detrimental, and in order to persist in the host population, must also
 have a positive effect on fitness that outweighs the costly burden of
 susceptibility to widespread parasitism.
description: WolbVSMeso-March16-DryadFile
DOI: 10.5061/dryad.vk29h
title: Data from: Realised niche changes in a native herbivore assemblage associated with the presence of livestock

description: Habitat partitioning is a common ecological mechanism to avoid competition
 among coexisting species, and the introduction of new species into
 existing assemblages can increase competitive pressures. However,
 situations of species in allopatry and sympatry only differing in species
 presence but not in environmental conditions are scarce. Thus, discerning
 whether niche segregation arises from competition or from different
 habitat preferences is usually unfeasible. Here, we analyse species'
 habitat niches in an assemblage of native and introduced herbivores in
 southern Patagonia. We test if niche overlap is higher between native and
 domestic herbivores than among natives as expected from the relatively
 short time of coexistence, and we evaluate the effect of intra- and
 interspecific competition on niche breadth. We use a probabilistic
 multidimensional approach and null models to evaluate overlap and changes
 in niche dimensions. Overlap among native species is low as expected for
 species coexisting in evolutionary time. In native-domestic species pairs,
 niche overlap was higher than among natives, although showing some niche
 segregation indicating niche differentiation in ecological time. Moreover,
 the presence of domestic species was associated with niche narrowing of
 both native and introduced species, revealing interspecific
 density-dependent effects on their habitat niche during resource shortage
 periods.
description: Niche breadth
 dataNiche breadth data on
 guanaco and sheep and explanatory variables, on 15 sectors on Torres del
 Paine National ParkNB.txt
DOI: 10.5061/dryad.1bm5t
title: Data from: No assortative mating based on size in black guillemots breeding in the Canadian Arctic

description: The Black Guillemot (Cepphus grylle) is a monomorphic, socially monogamous
 member of the Alcidae. Although aspects of their breeding and foraging
 ecology have been extensively studied, less is known about possible
 sex-based differences in morphology, nor whether Black Guillemots mate
 assortatively based on body size. Using molecular techniques, we
 identified the sex of 26 male and 21 female Black Guillemots captured in
 the Canadian Arctic, and measured six external body measurements: outer
 tarsus length, wing length, culmen length, bill depth, head plus bill
 length and body mass to test for sexual size dimorphism (SSD) and
 assortative mating. Overall, males were 1.7% and 8% larger than females in
 outer tarsus length and bill depth, respectively. Within breeding pairs,
 bill depth was the most dimorphic trait. Despite these morphological
 differences no evidence of assortative mating based upon body size was
 found. Thus, mate choice for body size does not appear to be an underlying
 mechanism of SSD in bill depth in Black Guillemots.
description: Black guillemot
 discriminant function analysisThis is the data file
 used for the discriminant function analysis.
DOI: 10.5061/dryad.8f14k
title: Data from: Phenomenological vs. biophysical models of thermal stress in aquatic eggs

description: [No abstract entered]
description: Oxygen consumption
 before hatching of fish embryos as a function of egg
 sizeThis dataset contains
 information on the size (radius and volume), experimental temperature, and
 oxygen consumption rate (micrograms O2/hr) of embryos of 14 species of
 fish measure before hatching.NfuncRdatabaseFinalTableDRYAD.csv