cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rn8pk0pcb
title: Brood parasites that care: alternative nesting tactics in a subsocial wasp

description: Hosts and brood parasites are a classic example of conflict. Parasites
 typically provide no offspring care after laying eggs, imposing costs on
 hosts. Female subsocial wasps, Ammophila pubescens, alternated between
 initiating their own nests and an ‘intruder’ tactic of replacing eggs in
 nests of unrelated conspecifics. Hosts could respond by substituting new
 eggs of their own, with up to eight reciprocal replacements. Remarkably,
 intruders usually provisioned offspring in host nests, often alongside
 hosts. We used field data to investigate why intruders provision and to
 understand the basis of interactions. We found that intruders could not
 increase their fitness payoffs by using the typical brood parasite tactic
 of not provisioning offspring. Intruders using the typical tactic would
 benefit when hosts provisioned in their stead, but their offspring would
 starve when hosts failed to provision. Although some hosts obtained
 positive payoffs when intruders mistakenly provisioned their offspring, on
 average utilizing a conspecific nest represents parasitism: hosts pay
 costs while intruders benefit. Both females used the same tactic of egg
 replacement, but intruders more often laid the final egg. Selection should
 favour better discrimination of offspring, which could lead to repeated
 cycles of costly egg replacement.
description: All datasets & R code required to reproduce analyses
 reported in the associated paper have been uploaded to Dryad.
 The 'README_Field_et_al_2023' file contains all
 necessary information on the datasets, methods & R code required
 to reproduce analyses reported in the associated paper.
DOI: 10.5061/dryad.v15dv41xk
title: Pigmentation biosynthesis influences the microbiome associated with sea urchins

description: Organisms living on the seafloor are subject to encrustations by a wide
 variety of animal, plants, and microbes. Sea urchins, however, thwart this
 covering. Despite having a sophisticated immune system, there is no clear
 mechanism that allows sea urchins to remain clean. Here, by using
 CRISPR/Cas9, we test the hypothesis that pigmentation biosynthesis in sea
 urchin spines influences their interactions with microbes in vivo. We have
 three primary findings. First, the microbiome of sea urchin spines are
 species-specific and that much of this community is lost in captivity.
 Second, different color morphs associate with bacterial communities that
 are similar in composition and structure. Lastly, the gene activity of the
 pigmentation biosynthesis genes polyketide synthase and flavin-dependent
 mono-oxygenase induces a shift in which bacterial taxa colonize the
 tissues of sea urchin spines. We, therefore, find it plausible that host
 pigments are involved in host-microbe interactions and potentially in
 symbiotic homeostasis.
DOI: 10.5061/dryad.8pk0p2npx
title: Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses

description: Potyviruses are a large genus of plant-infecting RNA viruses in the family
 Potyviridae. Due to their rapid diversification and frequent
 recombination, reconstructing the phylogenetic history of the potyviruses
 has proven difficult. Phylogenies reconstructed from different
 protein-coding regions of the viral genome often reveal conflicing or
 discordant relationships. But the extent to which discordance is due to
 interspecific recombination versus phylogenetic noise or errors in
 reconstruction is unclear.     To explore the
 recombinant history of the potyviruses, we assembled a dataset containing
 referece genomes for 131 species of potyviruses. High-quality, full-length
 reference genomes for all species were obtained form NCBI GenBank. Viral
 genomes were carefully aligned at the codon-level and screened for
 recombination. The full alignment was then partitioned into several
 sub-alignments between each detected recombination event, such that each
 sub-aligment corresponds to a non-recombinant block (NRB) free of detected
 recombination events. Local phylogenetic trees for each NRB were then
 reconstructed to explore how phylogenetic relationships varied across
 different regions of the potyvirus genome.   We then
 used our program Espalier to disentangle the phylogenetic history of the
 potyviruses. Espalier reconciles and removes discordances between
 phylogenetic trees that are likely attributable to phylogenetic error
 while retaining recombination events that are strongly supported by the
 sequence data. Applying Espalier to the potyviruses revealed that most
 phylogenetic discordace between local trees is likely attributable to
 phylogenetic noise. Removing the discordance attributable to phylogenetic
 error allows us to much more clearly visualize the phylogenetic history of
 the potyviruses.
description: Viral genomes were obtained for 131 Potyvirus species for which
 high-quality, full-length genomes were publically available. Viral genomes
 were retrieved from NCBI GenBank using the accession numbers provided by
 Gadhave et al. (2020). Full genome nucleotide sequences were aligned using
 MAFFT version 7 (Katoh, 2013). K. R. Gadhave, S.
 Gautam, D. A. Rasmussen, and R. Srinivasan. Aphid transmission of
 potyvirus: The largest plant-infecting RNA virus genus.
 <em>Viruses</em>, 12(7):773, 2020.  K. Katoh and D. M. Standley.
 MAFFT multiple sequence alignment software version 7: improvements in
 performance and usability. <em>Molecular Biology and
 Evolution,</em> 30(4):772–780, 2013.
DOI: 10.5061/dryad.8sf7m0cqd
title: Metadata for Jaguarundi Status and Distribution in Texas and Northeastern Mexico

description: The jaguarundi (Puma yagouaroundi) is a small felid with a historical
 range from central Argentina through southern Texas. Information on the
 current distribution of this reclusive species is needed to inform
 recovery strategies in the United States (U.S.) where its last record was
 in 1986 in Texas. From 2003 to 2021, we conducted camera-trap surveys
 across southern Texas and northern Tamaulipas, México to survey for
 medium-sized wild cats (i.e., ocelots [Leopardus pardalis], bobcats [Lynx
 rufus], and jaguarundi). After 350,366 trap nights at 685 camera sites, we
 did not detect jaguarundis at 16 properties or along two highways (1,050
 km2) in Texas. However, we recorded 126 jaguarundi photographic detections
 in 15,784 trap nights on two properties (125.3 km2) in the northern Sierra
 of Tamaulipas, Tamaulipas, México. On these properties, latency to
 detection was 72 trap nights, with a 0.05 probability of detection per day
 and 0.73 photographic event rate every 100 trap nights. Due to a lack of
 confirmed class I sightings (e.g., specimen, photograph) in the 18 years
 of this study, and no other class I observations since 1986 in the U.S.,
 we conclude that the jaguarundi is likely extirpated from the United
 States. Based on survey effort and results from México, we would have
 expected to detect jaguarundis over the course of the study if still
 extant in Texas. We recommend that state and federal agencies consider
 jaguarundis as extirpated from the U.S. and initiate recovery actions as
 mandated in the federal jaguarundi recovery plan. These recovery actions
 include identification of suitable habitat in Texas, identification of
 robust populations in México, and re-introduction of the jaguarundi to
 Texas. 
description: This is the metadata of the camera trap surveys we conducted over
 18 years used to summarize our results for this analysis. 
description: This is summarized metadata and does not include occurrence
 locations (GPS coordinates)
DOI: 10.5061/dryad.3r2280gj3
title: Data for: Evaluating conditions for MFAD fisheries development in the Caribbean and Bermuda

description: Moored fish aggregating devices (MFADs) are promoted in small-scale
 fisheries around the world as tools to increase fisher incomes, enhance
 food security, and ease pressure on degraded inshore fisheries. Despite
 their growing popularity, the biophysical and socioeconomic contexts in
 which MFAD fisheries are implemented - and the implications of these
 contexts for MFAD fishery success - remain poorly understood. Here we
 develop a framework identifying and evaluating factors likely to influence
 MFAD fishery outcomes and apply it across states in the insular Caribbean
 region. We highlight the heterogeneity in MFAD regulatory strength, catch
 marketability, social need, and costs among states and discuss best
 approaches for optimizing MFAD benefits across different socioeconomic
 scenarios.
description: Refer to the README.txt file.
DOI: 10.5061/dryad.vx0k6djtd
title: Data from: Climate affects the outbreaks of a forest defoliator indirectly through its tree hosts

description: Spatial variation in climate is known to affect the survival and
 reproduction of herbivorous forest insects and tree-species compositions,
 but the importance of indirect effects of climate on outbreaks of forest
 insects through its effects on forest composition is unclear. This data
 was compiled to examine the direct and indirect effects of climate, water
 capacity of the soil, host tree density, and non-host density on the
 spatial extent of Lymantria dispar outbreaks in the Eastern USA over a
 period of 44 years (1975-2018). Host species were subdivided into four
 taxonomic and ecologically distinct groups: red oaks (Lobatae), white oaks
 (Lepidobalanus), other preferred hosts, and intermediate (less preferred)
 hosts. The data offer quantitative evidence that geographic variation in
 climate can indirectly affect outbreaks of a forest insect through its
 effects on tree species composition.
description: A detailed description of the methods descibing how this dataset
 was collected are provided in the associated publication in
 <em>Oecologia</em>.
description: A README file is provided.
DOI: 10.5281/zenodo.17104023
title: Untrustworthiness in LLM-based Vulnerability Repair: Benchmark and Detection

description: This is the replication package accompanying our paper "Untrustworthiness in LLM-based Vulnerability Repair: Benchmark and Detection."

 



Codebase structure




The project is structured as follows.

.├── scripts/                        # bash scripts to run Gumtree├── src/                              # source code of the project├── raw_predictions         # the original predictions (patches + interpretations) made by 5 LLMs

├── processed_data         # the processed data├── requirements.txt        # required Python libraries

 





Run SusVF


Step 1. Run Gumtree 

bash scripts/gumtree.sh processed_data/src processed_data/<pred_pack>

where pred_pack is the directory containing processed data of predictions made by an LLM under a prompting technique (zero-shot CoT or few-shot CoT)

 

Step 2. Filter Gumtree's output

python gumtree_filter.py \

--diff_dir processed_data/<pred_pack>/gumtree_diff \--ast_dir  processed_data/<pred_pack>/gumtree_ast \--src_dir  processed_data/src \--dst_dir  processed_data/<pred_pack>/src \--out_dir  processed_data/<pred_pack>/gumtree_filter

 

Step 3. Generate NL patch descriptions

python gpt_gumtree2nl.py \

--diff_dir processed_data/<pred_pack>/gumtree_filter \--patch_desc_dir processed_data/<pred_pack>/patch_desc \

 

Step 4. Run SusVF's main program

python susvf_main.py \

--data_file processed_data/<pred_pack>/merge_data.csv \--working_dir=processed_data/<pred_pack> \--src_dir=processed_data/src
DOI: 10.5061/dryad.3bk3j9kmj
title: Dataset, statistical analysis code, and supplementary material of juvenile ravens' responses towards acoustic cues of different social categories

description: Social competence i.e., defined as the ability to adjust the expression of
 social behaviour to the available social information, is known to be
 influenced by early-life conditions. Brood size might be one of the
 factors determining such early conditions, particularly in species with
 extended parental care. We here tested in ravens, whether growing up in
 families of different sizes affects the chicks’ responsiveness to social
 information. We experimentally manipulated the brood size of 20 captive
 raven families, creating either small or large families. Simulating
 dispersal, juveniles were separated from their parents and temporarily
 housed in one of two captive non-breeder groups. After five weeks of
 socialization, each raven was individually tested in a playback setting
 with food-associated calls from three social categories: sibling, familiar
 unrelated raven they were housed with, and unfamiliar unrelated raven from
 the other non-breeder aviary. We found that individuals reared in small
 families were more attentive than birds from large families, in particular
 towards the familiar unrelated peer. These results indicate that variation
 in family size during upbringing can affect how juvenile ravens value
 social information. Whether the observed attention patterns translate into
 behavioural preferences under daily life conditions remains to be tested
 in future studies.
description: The Supplementary material contains Tables and Figures of
 additional analyses referred to in the manuscript. The
 .csv file contains the behavioral responses of tested individuals and
 their life history, including data referring to their family ID and brood
 size. The R code describes step by step the statistical
 analyses reported in the current manuscript.
DOI: 10.5061/dryad.pnvx0k6pk
title: Pulsed supplies of small fish facilitate short-term intraguild predation in salmon-stocked streams

description: Pulsed supplies of prey generally increase predator food intake. However,
 it is unclear whether this holds true when predators and pulsed prey are
 in same guild (i.e., intraguild [IG] predators and prey). IG prey may
 increase IG-predator food intake through predation, but they may decrease
 food intake through competition. To test these hypotheses, we compared the
 food intake of white-spotted charr (Salvelinus leucomaenis) (IG predator)
 in streams that were stocked or unstocked with masu salmon (Oncorhynchus
 masou) fry (IG prey) in streams in Hokkaido, Japan. One day after
 stocking, mean stomach content weight of charr was six-times higher than
 in unstocked streams due to fry consumption. In particular, large charr
 showed intense piscivory. However, predation on fry was rare on other
 days. Decreasing small fry may be partially responsible for the short-term
 occurrence of predation. In addition, acquisition of predator-avoidance
 behavior by fry and/or a lack of accommodation by charr to the sudden
 emergence of a new prey source may explain this time-limited intraguild
 predation. In days other than the first day post-stocking, food intake by
 charr did not differ between stocked and unstocked streams. No effects of
 interspecific competition on charr food intake were observed.
DOI: 10.5061/dryad.931zcrjmw
title: Chimeric inheritance and crown-group acquisitions of Carbon fixation genes within Chlorobiales

description: The geological record of microbial metabolisms and ecologies primarily
 consists of stable isotope fractionations and the diagenetic products of
 biogenic lipids. Carotenoid lipid biomarkers are particularly useful
 proxies for reconstructing this record, providing information on microbial
 phototroph primary productivity, redox couples, and oxygenation. The
 biomarkers okenane, chlorobactane, and isorenieratene are generally
 considered to be evidence of anoxygenic phototrophs, and provide a record
 that extends to ~1.64 Ga. The utility of the carotenoid biomarker
 record may be enhanced by examining the carbon isotopic ratios in these
 products, which are diagnostic for specific pathways of biological carbon
 fixation found today within different microbial groups. However, this
 joint inference assumes that microbes have conserved these pathways across
 the duration of the preserved biomarker record. Testing this hypothesis,
 we performed phylogenetic analyses of the enzymes constituting the
 reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of
 anoxygenic phototrophic bacteria usually implicated in the deposition of
 chlorobactane and isorenieretane. We find phylogenetically
 incongruent patterns of inheritance across all enzymes, indicative of
 horizontal gene transfers to both stem and crown Chlorobiales from
 multiple potential donor lineages. This indicates that a complete rTCA
 cycle was independently acquired at least twice within Chlorobiales and
 was not present in the last common ancestor. When combined with recent
 molecular clock analyses, these results predict that the Mesoproterzoic
 lipid biomarker record diagnostic for Chlorobiales should not preserve
 isotopic fractionations indicative of a full rTCA cycle. Furthermore, we
 conclude that coupling isotopic and biomarker records is insufficient for
 reliably reconstructing microbial paleoecologies in the absence of a
 complementary and consistent phylogenomic narrative.
description: README
 This is the
 README file for all supplementary data associated with: Paoletti MP,
 Fournier GP. Chimeric Inheritance and Crown-Group Acquisition of Carbon
 Fixation Genes within Chlorobiales   <strong>LUT.csv</strong> Lookup table providing the full names for abbreviations used in all subsequent files Alignment files Multiple sequence alignments, containing files 1-17 (described fully in README file). alignments.zip Phylogenetic trees Phylogenetic tree topologies, containing files 18-23 (described fully in README file). phylogenetic trees.zip Supplemental results Supplemental results, containing files 54-56 (described fully in README file). supplemental_results.zip
DOI: 10.5061/dryad.2280gb5ts
title: Plasticity and evolution shape the scaling of metabolism and excretion along a geothermal temperature gradient

description: Physiological rates are heavily dependent on temperature and body size.
 Most current predictions of organisms’ response to environmental warming
 are based on the assumption that key physiological rates like metabolism
 and excretion scale independently with body size and temperature and will
 not evolve. However, temperature is a significant driver for phenotypic
 variability in the allometric scaling and thermal sensitivity of
 physiological rates within ectotherm species, suggesting that evolution
 may play a role in shaping these parameters. We common-reared six
 populations of western mosquitofish that have recently established (~100
 years ago) in geothermal springs along a broad thermal gradient (19-33°C)
 to determine whether these scaling parameters are affected by evolutionary
 and/or plastic responses to warming over ecological timescales. Each
 population was reared at four different temperatures (23, 26, 30 and
 32°C). We measured routine metabolic and nitrogen excretion rates on
 mosquitofish across a wide body size range. We found evidence for
 plasticity, but not evolution, increasing the allometric scaling of
 metabolic rate with temperature. Plasticity in metabolism allometry
 reflected a decrease in thermal sensitivity at smaller body sizes. We
 found evidence for evolution of phenotypic plasticity on the allometry of
 excretion rate, reflecting evolutionary differences in how thermal
 sensitivity varies with body size across different populations.
 Evolutionary differences in excretion rate scaling did not influence the
 relationship between excretion and metabolism across rearing temperatures,
 suggesting that warming does not affect the balance between mosquitofish
 energy demands and nutrient recycling rates.
description: Data metabolism, excretion and body size data were obtained from
 introduced mosquitofish populations established in six geothermal springs
 spanning a broad thermal gradient (19-33°C) t and reared at four different
 temperatures (23, 26, 30 and 32°C). Routine metabolic
 rate was measured as oxygen consumption
 (<em>MO<sub>2</sub></em>) of individual fish for
 ten to fifteen minutes inside closed-system respirometers. Nitrogen
 excretion rate was estimated as change in ammonia
 (NH<sub>4+</sub>-N) concentrations in the closed respirometers
 over the metabolism assays. Body size was measured as blotted wet
 weight.
description: There are missing values (<em>NA</em>) for routine
 metabolic rate in the case of fish with highly fluctuating oxygen
 consumption traces and <em>NA</em> for excretion rate in the
 case of issues analysing water samples. Please see
 README file for key of column names.
DOI: 10.5061/dryad.m905qfv31
title: Identifying potential cues of species identity in complex animal signals

description: Communication signals are often key for encoding information on species
 identity, but determining the features important in conveying those cues
 is challenging. This is especially the case when attempting to compare
 across closely related sympatric taxa, where the need for accurate species
 recognition is critical. We developed an analytical framework to
 comprehensively quantify the complex movement displays used by male
 lizards to advertise territory ownership in 11 taxa of Puerto
 Rican Anolis, many of which were sympatric. Our analyses were
 able to assign the majority of individuals to the correct population of a
 given species based on only a handful of displays, showing ample
 information exists in these displays for species recognition. Instances
 where lizards were misassigned appeared to have occurred because of
 similarities in display design resulting from local adaptation to similar
 environments or recent shared evolutionary history. Our analyses also
 revealed there was no common (‘magic’) display characteristic for
 recognition across the 11 taxa. Instead, lizards likely assess the entire
 display or a combination of different display cues. Taken together, we
 illustrate a powerful approach that offers a rigorous statistical and
 holistic evaluation of complex animal signals for elucidating features
 likely to be important in species recognition. We provide a guide for
 implementing this analytical framework in R, with associated code and
 worked examples. Information obtained from these analyses can then be used
 to design experiments testing the utility of identifying cues or
 comparative studies investigating how those cues contribute to
 reproductive isolation among populations and ultimately speciation.
description: Details on methods, data collection and processing are given in
 full in the published paper associated with this data set.
description: Information on data format is provided in the README text
 file.
DOI: 10.5061/dryad.sn02v6x5w
title: Supplementary materials sequences of soluble chemical communication proteins in Anagrus nilaparvatae

description: Anagrus nilaparvatae is an important egg parasitoid wasp of pests such as
 the rice planthopper. Based on the powerful olfactory system of sensing
 chemical information in nature, A. nilaparvatae shows complicated life
 activities and behaviors, such as feeding, mating and hosting. We
 constructed a full-length transcriptome library and used this to identify
 the characteristics of soluble chemical communication proteins. We
 analyzed the sequence characteristics of soluble chemical communication
 protein genes and identified eight genes: AnilOBP2, AnilOBP9, AnilOBP23,
 AnilOBP56, AnilOBP83, AnilCSP5, AnilCSP6 and AnilNPC2. After sequence
 alignment and conserved domain prediction, the eight proteins encoded by
 the eight genes above were found to be consistent with the typical
 characteristics of odorant-binding proteins (OBPs), chemosensory proteins
 (CSPs) and Niemann-pick type C2 proteins (NPC2s) in other insects.
 Phylogenetic tree analysis showed that the eight genes share low homology
 with other species of Hymenoptera. This study provides the first data for
 A. nilaparvatae’s molecular characteristics of soluble chemical
 communication proteins, as well as an opportunity for understanding how A.
 nilaparvatae behaviors are mediated via soluble chemical communication
 proteins.