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opencc-zeroNov 2023View details →

Data from: Unisexual flowers as a resolution to intralocus sexual conflict in hermaphrodites

In dioecious populations, males and females may evolve different trait values to increase fitness through their respective sexual functions. Because the two sexual functions are expressed by the same individual in hermaphroditic populations, resolving sexual conflict is potentially more difficult. Here, we show that the modularity of plants may allow hermaphrodites to resolve sexual conflict because modules with different genders can promote fitness through their specialized sexual functions by expressing a correspondingly optimal trait value. We analyzed the flowering phenology, sex allocation, and selection gradients on floral traits of flowers of the andromonoecious plant Pulsatilla alpina, which produces both bisexual and male flowers. Our results indicate that strong protogyny prevents early bisexual flowers from profiting from high siring opportunities early in the reproductive season at a time when male flowers are able to achieve high siring success. Andromonoecy therefore resolves sexual conflict experienced by bisexual flowers in strongly protogynous populations. Our study illustrates the resolution of sexual conflict arising from phenological constraints via modular divergence in sex allocation. We discuss the extent to which modular variation in sex allocation in species with other sexual systems involving bisexuality may be explained similarly.

opencc-by-4.0Aug 2024View details →

Improved database of public-private partnerships from World Bank with imputed economic, institutional and conflict data.

The <a href="https://ppi.worldbank.org/en/ppi">World Bank's database</a> on private participation in infrastructure (PPI) projects provides detailed information on these initiatives. However, the original dataset includes imputed macro-level data for the countries that is outdated, lacks assigned ISO country codes, and is not linked to other standard country-level variables necessary for proper analysis and control by territory. In the improved version of the database, 10,958 project observations from 1900 to 2021 have been supplemented with ISO 2 and 3 country codes, enabling accurate integration with other databases. Additionally, 49 new variables related to <a href="https://data.worldbank.org/?cid=ECR_GA_worldbank_EN_EXTP_search&s_kwcid=AL!18468!3!704632427243!b!!g!!world%20bank%20projects&gad_source=1">economic</a>, <a href="https://www.worldbank.org/en/publication/worldwide-governance-indicators">institutional</a>, and <a href="https://www.start.umd.edu/gtd/">conflict data</a> are incorporated by country and year. This enhanced database ensures that researchers can retain critical World Bank information that might otherwise be lost in future updates, as it is not always preserved in repositories

opencc-zeroMay 2022View details →

Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models

Abstract Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

opencc-zeroMay 2022View details →

Data from: Texas field crickets (Gryllus texensis) use visual cues to place learn but perform poorly when intra- and extra-maze cues conflict

Central place foraging field crickets are an ideal system for studying the adaptive value of learning and memory, but more research is needed on ecology-relevant cognition in these invertebrates. Here, we test the visuospatial place learning of Texas field crickets (Gryllus texensis) in a radial arm maze. Our study expands previous work on G. texensis cognition for accuracy measures and extends our previous findings on females to both sexes. Additionally, our study examines whether crickets use intra- or extra-maze cues to locate a food reward using a maze rotation putting the cues in conflict. We found that male and female crickets improved performance over trials when measured by accuracy variables but not latency variables; thigmotaxis negatively impacted performance in both sexes. In a reward-absent trial, both male and female crickets demonstrated place memory. When intra- and extra-maze cues conflicted during a rotation trial, crickets' performance was not better than chance. Our rotation results suggest that crickets may experience reciprocal overshadowing of conflicting cues – a result most often seen in other taxa with conflicting multi-modal cues. We conclude that crickets do not rely solely on: (1) a single-cue association; (2) route-following; or (3) their own scent cues to navigate the maze. Instead, male and female Texas field crickets seem to learn the location of the reward using a combination of proximal and distal cues. The possibility to test large numbers of wild-caught or laboratory-reared individuals opens the door to future investigations on the evolutionary ecology of visuospatial learning in these invertebrates.

opencc-zeroAug 2022View details →

Interrogating genomic data in the phylogenetic placement of treeshrews reveals potential sources of conflict

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In this study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. The results suggest that the data has statistical support for two hypotheses for the placements of treeshrews, sister to Primatomorpha and to Primatomorpha + Glires. While we observe differences in properties of loci of different types (e.g., CDS, intron, etc.) with respect to the strength of the signal, the support for any particular topology is not dependent on the properties of the data. Rather, we show that the method of phylogenetic signal assessment, as well as whether the signal is measured using the full dataset or only loci with the strongest signal, impacts the results much more.

opencc-zeroApr 2024View details →

Data from: Flying without fear: shooting disturbance has little effect on site preferences in a conflict goose species

Human-modified landscapes have created opportunities for numerous taxa. Agricultural expansion has proven advantageous for several Arctic-breeding goose species, leading to increased abundance and intensified conflict with farmers. Shooting is frequently implemented as a mitigation strategy to control population and via scaring to alter the spatial distribution of conflict species. However, the efficacy of such regimes in manipulating the fear landscape is not always investigated. We developed resource selection functions using GPS-tracking data for Greenland barnacle geese (Branta leucopsis) wintering on Islay, Scotland to assess foraging site choice. We assessed overall foraging site preference and evaluated the influence of shooting management on foraging site selection of key habitats. Barnacle geese selected for improved grassland areas and the likelihood of utilisation varied between these fields according to field-specific management. Protected areas were strongly selected for along with newly reseeded grassland. Field-level exposure to shooting disturbance did not cause a notable change in site selection. Synthesis and Applications: Our results demonstrate the importance of providing refuges within managed agricultural landscapes to encourage site use and minimise conflict. We highlight how low intensity shooting disturbance may be ineffective in altering winter habitat selection of high-value foraging sites (especially near roosts). If future management aimed to stimulate redistribution higher intensity shooting disturbance along with the spatial and temporal coordination of shooting effort would likely be required to create a stronger perceived gradient of disturbance risk.

opencc-zeroJun 2024View details →

Data from: Coordination of care reduces conflict and predation risk in a cooperatively breeding bird

When two or more individuals cooperate to provision a shared brood, each carer may be able to maximize their payoffs by coordinating provisioning in relation to what others are doing. This investment 'game' is not simply a matter of how much to invest, but also of the relative timing of investment. Recent studies propose that temporal coordination of care in the forms of alternation (i.e. turn-taking) and synchrony (i.e. provisioning together) function to mitigate conflict between carers and reduce brood predation risk, respectively. Such coordination is widespread in biparental and cooperatively breeding birds, yet the fitness consequences have rarely been empirically tested. Here, we use a long-term study of long-tailed tits Aegithalos caudatus, a facultative cooperatively breeding bird with active coordination of care, to assess the support for these hypothesized functions for coordination of provisioning visits. First, we found evidence that turn-taking mitigates conflict between carers because, in cooperative groups, provisioning rates and offspring recruitment increased with the level of active alternation exhibited by carers, and with the associated increase in provisioning rate parity between carers. In contrast, offspring recruitment did not increase with alternation in biparental nests, although it was positively correlated with parity of provisioning between carers, which is predicted to result from conflict mitigation. Secondly, synchronous nest visits were associated with a reduced probability of nest predation and thus increased brood survival, especially when provisioning rates were high. We attribute this effect to synchrony reducing carer activity near the nest. We conclude that temporal coordination of provisioning visits in the forms of alternation and synchrony both confer fitness benefits on carers, and despite being intrinsically linked, these different kinds of coordination appear to serve different functions.

Figure 5. Final Ranking-Data Conflict Resolution among Same Entities in Web of Data

Finally, the last score with regard to the equation 4 has been calculated and is shown in figure 5. As it shows Geonames gains the highest score. Considering the proposed idea, Geonames' data is the most accurate. So when we are faced with data conflicts, Geonames' data must be chosen. The WordFactbook is also illustrated in the above table. We can see if WordFactbook is not removed from the synonyms list it would have more accurate data compared with DBpedia data.

Figure 3. Result of first fraction-Data Conflict Resolution among Same Entities in Web of Data

Finally we count the entities that contain any words in the synonyms list. The result of first the fraction in equation 4 is shown in figure 3.

Figure 2. Ranking datasets by Page Rank-Data Conflict Resolution among Same Entities in Web of Data

As depicted in Figure 2 DBpedia is the top ranked data set while GeoLinked Data and Eurostat are the low ranked data sets. In this stage the data sets whose rank scores are less than half of the rank scores belonging to the top ranked data set are removed from the assessment.

Figure 1. General Workflow of Algorithm-.Data Conflict Resolution among Same Entities in Web of Data

The Page Rank algorithm which is widely used in most search engines such as Google could be easily used to rank linked data. By starting from a point and random surfing, this algorithm evaluates the probability of finding any given page. The algorithm assumes a link between a page i to a page j demonstrates the importance of page j. In addition, the importance of page j is associated to the importance of page i itself and inversely proportional to the number of pages i point to. To adapt this algorithm to web of data, any page considered as a dataset and links between pages considered as links between datasets.

Figure 4. Result of Second Fraction-Data Conflict Resolution among Same Entities in Web of Data

In the last stage the size of the data set is examined. The number of instances of specialized entities and total entities are calculated. For example "London" is an instance of a specialized entity. In table 2 one of the properties of "London" is displayed in form of a triple. As is shown, the object of the triple is dbpedia-owl:Place that contains "place" as a member of the specialized entity. And 'A Trip to the Moon' is an instance of non-specialized entity because neither the subject nor the object is in the specialized entities list. After calculating the number of specialized instances and total instances the result of the second fraction of equation 4 is shown in figure 4.

opencc-zeroJul 2021View details →

Data supporting Fear of sex: Sexual conflict exposed as avoidance in a parthenogenetic invertebrate

Males and females often have divergent evolutionary interests, generating sexual conflicts. This is particularly true in organisms that exhibit facultative sexuality, whereby females are capable of reproducing without fitness costs of mating. Here we provide the first documented evidence with quantitative tracking showing that sex interacts with social context to determine space-use of females, in a pattern resembling predator avoidance. To achieve this, we labeled Daphnia magna with fluorescent nanoparticles and utilized a 3-D tracking platform to record pairs of individuals swimming. The recordings comprised either same-sex or opposite-sex pairings. We found that females swam faster, deeper, more horizontally and more linearly when exposed to males than when exposed to females. Simultaneously, we found that male behavior did not differ depending on swimming partner and, importantly, we observed no sexual dimorphism in swimming behaviors when swimming with the same sex. Our results suggest that the presence of males in a population has the potential to influence the distribution of individuals, similarly to known threats, such as predation. This highlights that sexual conflict has clear spatial consequences and should be considered in such ecological frameworks, like the Landscape of Fear (LOF) concept. In a broader context, the connection of the evolutionary and social concept of sexual conflict and the ecological concept of LOF may improve our understanding of population dynamics and the spatial and temporal distribution of individuals in natural ecosystems.

opencc-zeroJan 2023View details →

Data from: Reproductive senescence and mating tactic interact and conflict to drive reproductive success in a passerine

An understanding of the drivers of individual fitness is a fundamental component of evolutionary ecology and life-history theory. Reproductive senescence, mate and mating tactic choice, and latent heterogeneity in individual quality interact to affect individual fitness. We sought to disentangle the effects of these fitness drivers, where longitudinal data are required to understand their respective impacts. We used reproductive allocation and success data from a long-term (1989-2018) study of white-throated dippers (Cinclus cinclus) in Switzerland to simultaneously examine the effects of female and male age, mating tactic, nest initiation date, and individual heterogeneity on reproductive performance. We modeled quadratic and categorical effects of age on reproductive parameters. The probability of polygyny increased with age in both sexes before declining in older age classes. Similarly, hatching probability in monogamous pairs and the number of nestlings hatched in both monogamous and polygynous pairs increased with female age before declining later in life. As predicted, offspring survival in monogamous pairs increased with male age before declining in older age classes, but male age had no effect on offspring survival in polygynous nesting attempts. Our results demonstrate that parental age, mating tactic, and individual heterogeneity all affect reproductive success, and that the impacts of senescent decline are expressed across different demographic components as a function of sex-specific senescent decline and mating tactic.

opencc-zeroJan 2023View details →

Data from: Modelling harvest of Greenland barnacle geese and its implications in mitigating human-wildlife conflict

Arctic-breeding goose populations have increased in recent decades and their expansion into agricultural areas has caused increasing conflict with farmers due to the damage they cause. Lethal control and scaring are common management strategies of conflict mitigation. Management typically focuses on local/national scales, making addressing the impact of localised control on the wider population challenging, particularly when populations move over large areas and cross international borders. We construct an integrated population model (IPM) to assess the cumulative impact of all shooting harvest (hunting and derogation shooting) on the Greenland barnacle goose, Branta leucopsis. We use data from monitoring schemes throughout the migratory flyway and use population projections to evaluate the impact of potential future shooting strategies on abundance. Our model suggests flyway abundance has declined since its 2012 peak, consistent with an increase in harvest rate and low productivity. Harvest rate increase was most pronounced on Islay (rising from 2% to 7% from 2011 to 2017), suggesting this was a probable cause of flyway abundance decline. Islay abundance has declined since derogation shooting began in 2000, whilst abundance at other wintering sites has increased. This may indicate that declines in Islay abundance may be due to both shooting mortality and emigration from Islay. Should future flyway-level harvest rates increase, further declines in abundance could be expected, and are likely to be more pronounced if harvests are extended to the entire winter range. Conversely, should harvest rates decline, an increase in abundance is predicted. Projections can therefore be used to allocate flyway-level harvest rates to alleviate local pressure without hindering flyway-level management objectives. Synthesis and applications. Our findings demonstrate the impact of local harvests on global abundance, emphasising the importance of internationally coordinated monitoring and management strategies of migratory species. IPMs provide a framework for adaptation to incorporate additional data when they become available and enable comparisons of future harvest scenarios to inform management strategies throughout the flyway.

opencc-zeroMar 2023View details →

Data and codes from: Individuality matters in human-wildlife conflicts: patterns and fraction of damage-making brown bears in the North-eastern Carpathians

Effective, evidence-based management is required to ensure long-term coexistence between people and wildlife in an increasingly humanised world. Although behavioural individuality is recognised as a key factor affecting evolutionary and ecological processes, it has rarely been explicitly assessed in relation to human-wildlife conflicts. The 'problem individuals' paradigm states that some conspecifics within a given population have a disproportionately large contribution to conflicts. To the best of our knowledge, no studies have so far systematically tested this assumption in large carnivores. Here, we investigated the variation in conflict behaviour among brown bears Ursus arctos within the population inhabiting the Polish Eastern Carpathians. We inspected all sites notified as damaged by bears in 2014-2017 to determine the number and sex of the individuals involved. We conducted systematic non-invasive genetic sampling to estimate the size of the local population by spatially explicit capture-recapture models. We assessed the fraction and sex ratio of damage-making bears in relation to the population, as well as the behavioural patterns by classifying and differentiating between occasional and repetitive damage-makers. Approximately one-third of the estimated 72 (95% CI 45.2–115.5) brown bears inhabiting the Polish Eastern Carpathians were responsible for damage occurrence in the region. The majority of damage-makers were female (65% vs. 35% of male), which reflected the sex ratio of the local population (0.57). Thirty-three percent of the damage-making bears (i.e. 9 individuals) were classified as 'problem individuals', exhibiting repetitive conflict behaviour. Synthesis and applications. This study provides evidence of intraspecific differences in conflict behaviour in a large carnivore species, the brown bear, and indicates that damage-making behaviour is not exhibited with the same frequency by all individuals within a population. Managers and policy-makers should be aware that targeting individuals involved in conflicts without reference to the whole population may lead to misleading conclusions or an incomplete picture of the mechanisms underlying the conflicts, and thus, to mismanagement. Unravelling the behavioural patterns of individual engagement in damage through large-scale and population-wide studies is needed to accurately assess the magnitude of damage and enhance human-wildlife coexistence in areas experiencing conflicts.

opencc-zeroMar 2023View details →

Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic datasets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic datasets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated datasets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic datasets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

opencc-by-4.0Mar 2023View details →

Data from: Work-Life Conflict Among Higher Education Institution Workers' During COVID-19: A Demands-Resources Approach

Dataset from: Work-Life Conflict Among Higher Education Institution Workers' During COVID-19: A Demands-Resources Approach

opencc-by-4.0Apr 2023View details →

Proactive Conflict Detection for Collaborative Model-driven Software Engineering (Evaluation Data)

Results of the evaluation for the paper "Proactive Conflict Detection for Collaborative Model-driven Software Engineering"