cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18346972
title: Android Binary XV Diffing Code and Data

description: This paper presents XvDiff, a high-precision and high-performance cross-version diffing tool for Android binaries that integrates structural code-feature similarity with LLM-based semantic reasoning. XvDiff accurately identifies function-level changes even under heavy obfuscation, substantially outperforming state-of-the-art diffing approaches. Leveraging the diff results produced by XvDiff, we construct XvCKG, a multi-version Android code knowledge graph that unifies both intrinsic version-specific information and cross-version differential information into a single structured representation. Built upon this knowledge graph, we further develop an automated analysis framework that employs agentic retrieval-augmented generation to perform cross-version reasoning, enabling the detection of functional changes and the evolution of security properties throughout app development.
DOI: 10.5061/dryad.wstqjq2jp
title: Meerkat helpers buffer the detrimental effects of adverse environmental conditions on fecundity, growth and survival

description: 1. Recent comparative studies show that cooperative breeding is positively
 correlated with harsh and unpredictable environments and it is suggested
 that this association occurs because helpers buffer the negative effects
 of adverse ecological conditions on fitness. 2. In the Kalahari, rainfall
 varies widely between- and within years, affecting primary production and
 the availability of the principal prey of cooperatively breeding Kalahari
 meerkats, Suricata suricatta. Our study aimed to establish whether the
 presence and number of helpers buffer the negative effects of variation in
 rainfall on the fecundity and body mass of breeding females, and the
 survival and growth of pups. 3. We investigate the relationship between
 group size and variation in rainfall on dominant female fecundity, body
 mass, and offspring survival and growth using an additive modeling
 approach on twenty-one years of individual-based records of the life
 histories of individual meerkats. 4. We show that breeding female
 fecundity is reduced during periods of low rainfall but that the effects
 of low rainfall are mitigated by increases in group size and body mass
 because heavier females and those in larger groups have increased
 fecundity and reduced interbirth intervals. Pup growth and survival are
 also reduced during periods of low rainfall, but more so in smaller
 groups. 5. Our results support the suggestion that cooperative breeding
 mitigates the detrimental effects of adverse environmental conditions and
 may enhance the capacity of species to occupy environments where food
 availability is low and unpredictable.
description: These are long-term data collected from a population of
 habituated Meerkats at the Kalahari Research Center in Northern Cape,
 South Africa. The unique ID's for each individual in this dataset
 have been randomised and do therefore not correspond to similar ID's
 in this dataset or previous work from this population.
description: All columns have been named according to their usage in the
 manuscript and should be intuitive to use. There are no missing values in
 these data.
DOI: 10.5061/dryad.66t1g1k10
title: Breeding system of diploid sexuals within the Ranunculus auricomus complex and its role in a geographical parthenogenesis scenario

description: The larger distribution area of asexuals compared to their sexual
 relatives in geographical parthenogenesis (GP) scenarios has been widely
 attributed to the advantages of uniparental reproduction and polyploidy.
 However, potential disadvantages of sexuals due to their breeding system
 have received little attention so far. Here, we study the breeding system
 of five narrowly distributed sexual lineages of Ranunculus notabilis s.l.
 (R. auricomus complex) and its effects on outcrossing, inbreeding, female
 fitness, and heterozygosity. We performed selfing and intra- and
 interlineage crossings by bagging 481 flowers (59 garden individuals)
 followed by germination experiments. We compared seed set and germination
 rates, and related them to genetic distance and genome-wide heterozygosity
 (41,580 filtered RADseq loci). Selfings (2.5%) unveiled a significantly
 lower seed set compared to intra- (69.0%) and interlineage crossings
 (69.5%). Seed set of intra- (65%) compared to interpopulation crossings
 (78%) was significantly lower. In contrast, all treatments showed
 comparable germination rates (32-43%). Generalized linear regressions
 between seed set and genetic distance revealed positive relationships in
 general and between lineages, and a negative one within lineages. Seed set
 was the main decisive factor for female fitness. Germination rates were
 not related to genetic distance at any level, but were positively
 associated with heterozygosity in interlineage crossings. Experiments
 confirmed full crossability and predominant outcrossing among sexual R.
 notabilis s.l. lineages. However, up to 5% (outliers 15-31%) of seeds were
 formed by selfing, probably due to semi-self-compatibility in a
 multi-locus gametophytic SI system. Less seed set in intrapopulation
 crossings, and higher seed set and germination rates from crossings of
 genetically more distant and heterozygous lineages (interlineage) indicate
 negative inbreeding and positive outbreeding effects. In GP scenarios,
 sexual species with small and/or isolated populations can suffer from
 decreased female fitness due to their breeding system. This factor, among
 others, probably limit range expansion of sexuals.
DOI: 10.5061/dryad.x69p8czgt
title: Data from: Group size elevates inequality in cooperative behaviour

description: In cooperatively breeding species where rearing effort is shared among
 multiple group members, increases in group size typically reduce average
 per capita contributions to offspring care in all group members
 (load-lightening) but it is not known how changes in group size affect the
 distribution of workload among group members. The socioeconomic collective
 action theory suggests that, in larger groups, the incentives for free
 riding are stronger, leading to greater inequalities in work-division
 among group members. Here, we use the Gini index to measure inequality at
 the group level in the contributions of helpers to three different
 cooperative behaviours (babysitting, pup-provisioning and raised guarding)
 in groups of varying size in wild Kalahari meerkats (Suricata suricatta).
 In larger groups, inequality in helpers’ contributions to cooperative
 activities and the frequency of free riding both increased. Elevated
 levels of inequality were generated partly as a result of increased
 differences in contributions to cooperative activities between helpers in
 different sex and age categories in larger groups. Increasing levels of
 inequality in contributions to cooperative behaviour were associated with
 reductions in total pup-provisioning conducted by the group and reductions
 in total pup provisioning were, in turn, associated with reductions in the
 growth and survival of pups. Our results support the prediction of
 collective action theory described above and show how the Gini index can
 be used to investigate the distribution of cooperative behaviour within
 the group.
DOI: 10.5061/dryad.zw3r22870
title: Insights into short and long-term crop-foraging strategies in a chacma baboon (Papio ursinus) from GPS and accelerometer data

description: Crop-foraging by animals is a leading cause of human-wildlife ‘conflict’
 globally, affecting farmers and resulting in the death of many animals in
 retaliation, including primates. Despite significant research into
 crop-foraging by primates, relatively little is understood about the
 behaviour and movements of primates in and around crop fields, largely due
 to the limitations of traditional observational methods. Crop-foraging by
 primates in large scale agriculture has also received little attention. We
 used GPS and accelerometer bio-loggers, along with environmental data, to
 gain an understanding of the spatial and temporal patterns of activity for
 a female in a crop-foraging baboon group in and around commercial farms in
 South Africa over one year. Crop fields were avoided for most of the year,
 suggesting that fields are perceived as a high-risk habitat. When field
 visits did occur, this was generally when plant primary productivity was
 low, suggesting that crops were a ‘fallback food’. All recorded field
 visits were at or before 15:00. Activity was significantly higher in crop
 fields than in the landscape in general, evidence that crop-foraging is an
 energetically costly strategy and that fields are perceived as a risky
 habitat. In contrast, activity was significantly lower within 100m of the
 field edge than in the rest of the landscape, suggesting that baboons wait
 near the field edge to assess risks before crop-foraging. Together this
 understanding of the spatiotemporal dynamics of crop-foraging can help to
 inform crop protection strategies and reduce conflict between humans and
 baboons in South Africa.
description: NDVI data: Data from the Moderate Resolution
 Imaging Spectrometer (MODIS) on board of NASA's TERRA satellite were
 retrieved using the Google Earth Engine website
 (https://earthengine.google.com, Gorelick et al., 2017) and monthly NDVI
 values were downloaded from the MOD13Q1 data set (250m spatial resolution)
 over the home range of the study group (based on a minimum convex polygon
 of 62.7km<sup>2</sup>). Pixels were discarded based on
 associated quality assessment data sets, where only pixels with associated
 quality values of 0 (good) were retained. Average NDVI values were then
 taken from the remaining pixels for each month. GPS
 and accelerometer data: One adult female chacma baboon
 was fitted with a GPS and accelerometer collar with an automatic timer
 activated drop-off (Vectronic GPS‐PLUS collars 18; VECTRONIC Aerospace,
 Berlin, Germany). The collar recorded data for full days between
 26/10/2013 and 18/10/2014. The collar took hourly GPS fixes from 05:00 to
 19:00 South African Standard Time, with a further nocturnal fix at 24:00
 to identify sleeping sites (<i>N</i> = 5728 fixes).  The
 collar also contained a bi-axial accelerometer, positioned at the back of
 the baboon’s neck, which recorded acceleration in the x-axis and y-axis at
 4 Hz. The collar averaged acceleration in the two axes over 120s for
 storage.
DOI: 10.5061/dryad.d51c5b01v
title: Gregariousness, foraging effort, and social interactions in lactating bonobos and chimpanzees

description: Fission-fusion dynamics have evolved in a broad range of animal taxa and
 are thought to allow individuals to mitigate feeding competition. While
 this is the principal benefit of fission-fusion, few studies have
 evaluated its costs. We compared gregariousness, foraging budgets, and
 social budgets between lactating bonobos and chimpanzees from wild
 populations to evaluate such costs. Both species exhibit fission-fusion
 dynamics, but chimpanzees, particularly in East African populations,
 appear to experience higher feeding competition than bonobos. We expected
 lactating chimpanzees to be less gregarious than lactating bonobos;
 reduced gregariousness should allow lactating chimpanzees to mitigate
 costs of higher feeding competition without requiring more foraging
 effort. However, we expected the reduced gregariousness of lactating
 chimpanzees to limit their time available for affiliative social
 interactions. Using long-term data from LuiKotale bonobos and Gombe
 chimpanzees, we found that lactating chimpanzees were indeed less
 gregarious than lactating bonobos while feeding and travel time did not
 differ between species. Contrary to our predictions, lactating females did
 not differ in social interaction time, and lactating chimpanzees spent
 proportionately more time interacting with individuals other than their
 immature offspring. Our results indicate that lactating chimpanzees can
 maintain social budgets comparable to lactating bonobos despite reduced
 gregariousness and without incurring additional foraging costs. We discuss
 potential explanations for why lactating bonobos are more gregarious.
DOI: 10.5061/dryad.k0p2ngf6t
title: Data from: An assay to investigate factors influencing initial orientation in nocturnally fledging seabirds.

description: The first solitary migration of juvenile birds is difficult to study
 because of a low juvenile survival rates and sometimes long delays in
 return to the breeding grounds. Consequently, little is known about this
 crucial life event for many bird species, in particular the sensory
 guidance mechanisms facilitating the first migratory journey. Initial
 orientation during the first migration is a key measure to investigate
 these mechanisms. Here, we developed an assay to measure initial
 orientation as flight direction upon first take-off in nocturnally
 fledging juvenile seabirds. We dorsally deployed a coloured LED on
 juvenile birds to allow researchers to observe the vanishing bearings of
 individuals as they flew out to sea. Additionally, we co-deployed either a
 small Neodymium magnet or glass bead (control) on top of the bird’s head
 to investigate the use of magnetoreception, previously unexplored in this
 early life stage.   We used this assay to observe the first
 flight of Manx shearwaters (Puffinus puffinus) and found that they did not
 orient towards their wintering ground straight after taking off. Further,
 we did not find an effect of the magnetic treatment on juveniles’ flight
 direction, though whether this is due to the birds not using
 magnetoreception, other salient cues being available or
 a lack of motivation to orient to the migratory beeline is
 unclear. We were, however, able to identify wind direction and topography
 as drivers of first flight direction in Manx shearwaters, which fledged
 with wind component between a crosswind and a tailwind and directed their
 maiden flight towards the sea and away from the land.   
 This novel assay will facilitate the study of the maiden flight of
 nocturnally fledging birds and will help advance the study of sensory
 guidance mechanisms underpinning migratory orientation in a wide range of
 taxa, including species which are traditionally challenging to
 study.
DOI: 10.5061/dryad.cnp5hqc3c
title: No water, no eggs: insights from a warming outdoor mesocosm experiment

description: Insects are susceptible to dehydration and change in atmospheric humidity
 could affect their fitness. To understand the impacts of humidity changes
 on insect’s reproductive fitness we released an outcrossed Drosophila
 melanogaster population to outdoor mesocosm units and tracked their
 fecundity over ninety days under progressively developing summer season.
 The study was carried out in a tropical urban garden. Often temperature
 has been found to be the key player in changes in reproductive output in a
 considerable number of laboratory based studies. Our work suggested that
 temperature and humidity interactions determine the physiological state of
 an organism which could untimely impact organismal fitness in a given
 environmental set-up. This work suggested that fecundity in Drosophila
 populations was significantly influenced by relative humidity and its
 interaction with temperature. This together suggested that while
 temperature was an important parameter for fecundity, relative humidity
 individually and in combination with temperature also played an important
 role for fecundity in Drosophila. Thus, the combination of temperature and
 relative humidity was a better metric to predict the fecundity in
 Drosophila populations than considering these parameters individually
 under natural conditions. It clearly indicated that future warming events
 could drastically impact insects’ reproductive output.
description: <strong>File: Cages Fecundity and Climatic Data
 File</strong>: For this, we used three indoor
 (Laboratory) and three outdoor cages (Ahmedabad University Experimental
 Evolution Station, East Campus). Each mesocosm was a 5x5x5 feet in
 dimension (custom designed at Ahmedabad University Workshop) outdoor
 insect rearing enclosure surrounding a mature (dwarf) sapota tree. Each
 cage was founded with 500 males and 500 females. Every morning 08.00 hr
 fresh food (75 ml of standard cornmeal–molasses medium) in a half-pint
 bottle was placed in each enclosure (3 indoor and 3 outdoor cages) for the
 entire duration of the experiment (4<sup>th</sup> April 2018
 to 2<sup>nd</sup> July 2018). Flies were allowed to oviposit
 on the fresh food for 24 hours. Each morning, bottles were examined for
 eggs laid in the previous 24 hours. Data shows number of eggs laid each
 day. Temperature and relative humidity in all six cages
 (3 indoor and 3 outdoor) were recorded using HOBO U23 Pro v2 data loggers
 (Onset Computer Corp., Bourne, MA, USA). This file contains data in
 <b>°</b>C and in percent for temperaature and relative
 humidity respectively.
description: All the data has been organized in MS Excel file. These files
 can easily be downloaded on a local PC or Laptop. No conversion or
 permision is required and data does not contain any missing
 values.
DOI: 10.5061/dryad.tmpg4f4x5
title: Colorful traits in avian females, individual condition, reproductive performance, and male mate preferences: A meta-analytic approach

description: Colorful ornaments in females are suggested to have evolved and be
 maintained by sexual selection. Although several studies have evaluated
 this idea evidence is still equivocal. Results from empirical studies have
 been compilated in reviews, but quantitative analyses have seldom been
 performed. Here, using a meta-analytic approach, we show that evidence
 from empirical studies conducted in birds, supports the ideas that
 colorful female ornaments are positively associated with individual
 condition, reproductive performance, and male-mate preferences. Hence,
 females’ colorful traits, in birds, likely evolved and are maintained by
 sexual selection.
description: A systematic search of literature was performed using PRISMA
 method (Preferred Reporting Items for Systematic Reviews and
 Meta-Analyses). We looked for literature trough the search engines Scholar
 Google and Web of Science, using the keywords: “<i>female bird
 ornament”, “female bird ornamentation”, “female bird traits”, “female bird
 quality”, “female bird condition”, “female bird attractiveness”, “female
 bird color”, “female bird colour”, “female bird coloration”, “male bird
 choice”, “male bird preference”</i>. References within papers were
 also checked. Last search was conducted on October 2020.
 Studies with missing reports on statistical values, independent
 estimates for each sex, and type of coloration were excluded. Seventy-six
 studies were found but only 52 satisfied the inclusion criteria. Studies
 included were performed in 37 species with monogamous mating system, four
 with facultative polygamous, and only one with polygamous (eight species
 were used in more than one study). Carotenoid-dependent ornaments were
 present in 25 species, melanin based in 16, and structural colorations in
 10. Intensity of coloration was estimated as number and/or size of colored
 structures/patches, spectrophotometry, digital image analysis (RGB or
 LBA), and visual rank scales (color charts and visual rank
 score). Through independent meta-analyses we evaluated
 evidence for the association of colorful female ornaments with condition,
 reproductive performance, and male preferences. Studies assessing more
 than one of these associations were included in more than one
 meta-analysis. Effect sizes reported as Pearson’s correlation coefficients
 (<i>r</i>) were directly extracted from papers, otherwise were
 calculated using the square root of determination coefficients in
 regression models (<i>R<sup>2</sup></i>).
 Pearson’s coefficients were subsequently transformed to Fisher’s
 <i>z</i>-values for statistical analyses. When studies
 reported <i>t</i> or <i>F</i> values, Hedges’ g
 was calculated to obtain effect size. All effect sizes were weighted using
 the variance value.
DOI: 10.5061/dryad.nzs7h44qc
title: Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments

description: Emerging bacterial pathogens threaten global health and food security, and
 so it is important to ask whether these transitions to pathogenicity have
 any common features. We present a systematic study of the claim that
 pathogenicity is associated with genome reduction and gene loss. We
 compare broad-scale patterns across all bacteria, with detailed analyses
 of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has
 undergone multiple transitions between disease and carriage forms. We find
 that pathogenicity is consistently associated with reduced genome size
 across three scales of divergence (between species within genera, and
 between and within genetic clusters of S. suis). While genome reduction is
 also found in mutualist and commensal bacterial endosymbionts, genome
 reduction in pathogens cannot be solely attributed to the features of
 their ecology that they share with these species, i.e. host restriction or
 intracellularity. Moreover, other typical correlates of genome reduction
 in endosymbionts (reduced metabolic capacity, reduced GC content, and the
 transient expansion of non-functional elements) are not consistently
 observed in pathogens. Together, our results indicate that genome
 reduction is a predictive marker of pathogenicity in bacteria.
description: For each genus containing at least one pathogen and one
 non-pathogen, we downloaded all available complete genomes (see Table S2).
 (Draft genomes were excluded because we observed that they varied
 substantially in length for a few species.) We then used
 <i>Phylosift</i> (Darling et al. 2014) to align 37 single copy
 orthologs identified as universal to all bacteria. Concatenated alignments
 of these loci were checked and corrected by eye.
DOI: 10.5061/dryad.8cz8w9gnx
title: Data from: Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (S. canadensis) in two large reservoirs: insights from genotyping-by-sequencing

description: Anthropogenic activities may facilitate undesirable hybridization and
 genomic introgression between fish species. Walleye (Sander vitreus) and
 sauger (Sander canadensis) are economically valuable freshwater species
 that can spontaneously hybridize in areas of sympatry. Levels of genomic
 introgression between walleye and sauger may be increased by modifications
 to waterbodies (e.g., reservoir development) and inadvertent propagation
 of hybrids in stocking programs. We used genotyping by sequencing (GBS) to
 examine 217 fish from two large reservoirs with mixed populations of
 walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake).
 Analyses with 20,038 (r90) and 478 (r100) SNPs clearly resolved walleye
 and sauger, and classified hybrids with high confidence. F1, F2, and
 multi-generation hybrids were detected in Lake Diefenbaker, indicating
 potentially high levels of genomic introgression. In contrast, only F1
 hybrids were detected in Tobin Lake. Field classification of fish was
 unreliable; 7% of fish were misidentified based on broad species
 categories. Important for activities such as brood stock selection, 12/173
 (7%) fish field-identified as pure walleye, and 1/24 (4%) identified as
 pure sauger were actually hybrids. In addition, 2/15 (13%)
 field-identified hybrids were actually pure walleye or sauger. We conclude
 that hybridization and introgression are occurring in Saskatchewan
 reservoirs, and that caution is warranted when using these populations in
 stocking programs. GBS offers a powerful and flexible tool for examining
 hybridization without pre-identification of informative loci, eliminating
 some of the key challenges associated with other marker types.