Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
26
datasets available to search
ShareScore release 0.9.0
Dataset results
26 results for “hybrid swarm”
Experimental Results for the study "A Modular Hybridization of Particle Swarm Optimization and Differential Evolution"
<p>This repository contains the experiment results and R scripts to analyze the data for the study "A Modular Hybridization of Particle Swarm Optimization andDifferential Evolution", which is accepted in <em>The Genetic and Evolutionary Computation Conference</em> (GECCO) '20 conference: </p> <p>Rick Boks, Hao Wang, and Thomas Bäck. 2020. A Modular Hybridization of Particle Swarm Optimization and Differential Evolution. In <em>Genetic and Evolutionary Computation Conference Companion (GECCO ’20 Companion), July 8–12, 2020, Cancún, Mexico. </em>ACM, New York, NY, USA, 8 pages. <a href="http://https: //doi.org/10.1145/3377929.3398123">https: //doi.org/10.1145/3377929.3398123</a></p> <p>Bibtex:</p> <pre><code class="language-markdown">@inproceedings{BoksWB20, author = {Rick Boks and Hao Wang and Thomas B\"ack}, title = {{A Modular Hybridization of Particle Swarm Optimization and Differential Evolution}}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference, {GECCO} 2020, Canc\'un, Mexico, July 8-12, 2020}, publisher = {{ACM}}, year = {2020}, url = {https://doi.org/10.1145/3321707.3321816}, doi = {doi.org/10.1145/3377929.3398123, }</code></pre> <p><strong>Data description:</strong> we benchmarked <strong>800 </strong>different<strong> </strong>hybridizations of the Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms on a well-known continuous black-box problem set called <a href="https://coco.gforge.inria.fr/">COCO/BBOB</a>, which consists of 24 test functions. 30 independent runs are conducted for each algorithm on each problem.</p> <ul> <li>'ERT.csv': a data frame with columns DIM (5D or 20D), funcId (F1-24), algId (algorithm names), target (<span class="math-tex">\(10^{\{-8,-7, \ldots, 1\}}\)</span>), ERT (expected running time), and sd (standard deviation).</li> <li>'raw-data.csv': the running time recorded in each independent run. </li> <li>'analysis.R': the R script that generates ERT tables in the paper.</li> <li>'ecdf.R': the R script that renders the ECDF (empirical cumulative distribution function) plots in the paper.</li> </ul>
Data from: Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic
Background: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. Results: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. Conclusions: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.
Data from: Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic
Open the record for dataset details and reuse information.
Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)
Open the record for dataset details and reuse information.
Improved hybrid particle swarm optimizer with sine-cosine acceleration coefficients for transient electromagnetic inversion
<p>The Xishan Landslide Research area is located in Sichuan Lixian County, Southwest China. </p> <p>The N.O. 1 profile from Li et al., (2020), containing 15 measuring points, was chosen to test data fitting of IH-PSO-SCAC and to determine the hydrogeological structure of landslides.</p> <p> </p>
Data from: Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds
Abstract: Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (H. himantopus leucocephalus) is less clear. Here we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kakī and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridisation between kakī and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kakī, thus negating a popular belief that kakī represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human-induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male-biased kakī sex ratio. To maximize the evolutionary potential of kakī, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.
Data from: The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Ecological opportunity is frequently proposed as the sole ingredient for adaptive radiation into novel niches. An additional trigger may be genome-wide hybridization resulting from 'hybrid swarm'. However, these hypotheses have been difficult to test due to the rarity of comparable control environments lacking adaptive radiations. Here I exploit such a pattern in microendemic radiations of Caribbean pupfishes. I show that a sympatric three-species radiation on San Salvador Island, Bahamas diversified 1,445 times faster than neighboring islands in jaw length due to evolution of a novel scale-eating adaptive zone from a generalist ancestral niche. I then sampled 22 generalist populations on seven neighboring islands and measured morphological diversity, stomach content diversity, dietary isotopic diversity, genetic diversity, lake/island areas, macroalgae richness, and Caribbean-wide patterns of gene flow. None of these standard metrics of ecological opportunity or gene flow were associated with adaptive radiation, except for slight increases in macroalgae richness. Thus, exceptional trophic diversification is highly localized despite myriad generalist populations in comparable environmental and genetic backgrounds. This study provides a strong counterexample to the ecological/hybrid-swarm theories of adaptive radiation and suggests that diversification of novel specialists on a sparse fitness landscape is constrained by more than ecological opportunity and gene flow.
Data from: Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)
Studies of hybrid zones have revealed an array of evolutionary outcomes, yet the underlying structure is typically characterized as one of three types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary objective was to determine which of these three structures best characterizes a zone of hybridization between two divergent lineages of mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These lineages are morphologically, ecologically and genetically distinct, yet hybridize readily along a zone of secondary contact between the east and west slopes of the Cascade Mountains (Washington and Oregon, USA). Using microsatellite and mitochondrial DNA, we found clear evidence for extensive hybridization and introgression between lineages, with varying degrees of admixture across the zone of contact. The pattern of hybridization in this region closely resembles a hybrid swarm; based on data from 10 microsatellite loci, we detected hybrids that extend well beyond the F1 generation, did not detect linkage disequilibrium at the centre of the zone and found that genotypes were associated randomly within the zone of contact. Introgression was characterized as bidirectional and symmetric, which is surprising given that the zone of contact occurs along a sharp ecotone and that lineages are characterized by large differences in body size (a key component of mating success). Regardless of the underlying mechanisms promoting hybrid swarm maintenance, it is clear that the persistence of a hybrid swarm presents unique challenges for management in this region.
Data from: Long-term persisting hybrid swarm and geographic difference in hybridization pattern: genetic consequences of secondary contact between two Vincetoxicum species (Apocynaceae–Asclepiadoideae)
Background: During glacial periods, glacial advances caused temperate plant extirpation or retreat into localized warmer areas, and subsequent postglacial glacial retreats resulted in range expansions, which facilitated secondary contact of previously allopatric isolated lineages. The evolutionary outcomes of secondary contact, including hybrid zones, dynamic hybrid swarm, and resultant hybrid speciation, depends on the strengths of reproductive barriers that have arisen through epistatic and pleiotropic effects during allopatric isolation. The aim of this study was to demonstrate refugia isolation and subsequent secondary contact between two perennial Asclepioid species and to assess the genetic consequences of the secondary contact. We modeled the range shift of two ecologically distinct Vincetoxicum species using the species distribution model (SDM) and assessed the genetic consequences of secondary contact by combining morphological and genetic approaches. We performed morphometric analysis (592 individuals) and examined 10 nuclear microsatellites (671 individuals) in V. atratum, V. japonicum, and putative hybrid populations. Results: Multivariate analysis, model-based Bayesian analysis, and non-model-based discriminant analysis of principal components confirmed the hybridization between V. atratum and V. japonicum. High pollen fertility and a lack of linkage disequilibrium suggested that the hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Moreover, our findings show that the pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. Geographically-isolated hybrid populations exist as genetically distinct hybrid swarms that consist of V. atratum-like genotypes, V. japonicum-like genotypes, or admixed genotypes. In addition, Bayesian-based clustering analysis and coalescent-based estimates of long-term gene flow showed patterns of introgressive hybridization in three morphologically 'pure' V. japonicum populations. Conclusion: In this study, we demonstrated that climatic oscillations during the Quaternary period likely led to species range shift and subsequently secondary contact. Hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. We concluded that these differences in the genetic consequences of secondary contact are caused by historical colonization processes and/or natural selection.
Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species
Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry has received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The range-wide frequency of hybridization among anadromous populations was generally 0-8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.
Data from: Patterns of mating and generation of diversity in a Geum hybrid swarm
To understand the evolutionary consequences of hybridization between the outcrossing plant Geum rivale and the selfer G. urbanum we tested the predictions of two simple models which assume either A). low or B). high pollen fitness in hybrids. Model A predicts only four genotypic classes (G. rivale, G. rivale backcross (BCR), F1 and G. urbanum) and asymmetric introgression from inbreeding to outbreeding species. Model B predicts additional genotypic classes and potential generation of novel inbreeding lines in the hybrid swarm. AFLP analysis of adults revealed only the four genotypes predicted by model A. However, microsatellite analysis of parent-progeny arrays demonstrated production of selfed offspring by F1 and BCR maternal parents and contribution of these genotypes to outcross pollen pools, as predicted by model B. Moreover AFLP and morphological analysis showed that the offspring generation comprised genotypes and phenotypes covering the entire spectrum of variation between the two parental species, in line with model B. A common garden experiment indicated no systematic reduction in fitness of offspring derived from hybrid parents. The genetic structure of the adults in the Geum hybrid swarm cannot be explained by restricted mating patterns but may result from ecological selection acting on a diverse offspring population.
Data from: Admixture of hybrid swarms of native and introduced lizards in cities is determined by the cityscape structure and invasion history
Introductions of non-native lineages increase opportunities for hybridization. Non-native lineages of the common wall lizard, Podarcis muralis, are frequently introduced in cities where they hybridize with native populations. We aimed at unravelling the invasion history and admixture of native and non-native wall lizards in four German cities using citywide, comprehensive sampling. We barcoded and genotyped 826 lizards and tested if gene flow in populations composed of admixed native and introduced lineages is facilitated by similar environmental factors as in native populations by comparing fine-scale landscape genetic patterns. In cities with non-native lineages, lizards commonly occurred in numerous clusters of hybrid swarms, which showed variable lineage composition, consisting of up to four distinct evolutionary lineages. Hybrid swarms held vast genetic diversity and showed recent admixture with other hybrid swarms. Landscape genetic analyses showed differential effects of cityscape structures across cities, but identified water bodies as strong barriers to gene flow in both native and admixed populations. In contrast, railway tracks facilitated gene flow of admixed populations only. Our study shows that cities represent unique settings for hybridization, caused by multiple introductions of non-native taxa. Cityscape structure and invasion histories of cities will determine future evolutionary pathways at these novel hybrid zones.
Bug Report Analytics for Software Reliability Assessment using Hybrid Swarm-Evolutionary Algorithm
<p><span>There are in total 6 files.</span></p> <p><span><span>1.<span> </span></span></span><span>Out of these files three documents are related to datasets. Two are related to unrefined Eclipse and JDT files and third is refined data of Eclipse and JDT Project Failure Datasets which has been used for experimentation purpose.</span></p> <p><span><span>2.<span> </span></span></span><span>This package also includes code for all the models version wise for all versions of Eclipse and JDT projects.</span></p> <p><span><span>3.<span> </span></span></span><span>Sample Code has also been given for version 4.3 and 4.10. </span></p> <p><span>Steps to run </span></p> <p><span><span>a)<span> </span></span></span><span>In this code, Main ABCDE file needs to be run and different datasets could be executed on this file. This is for one type of datasets that is time domain dataset only. </span></p> <p><span><span>b)<span> </span></span></span><span>If anyone is interested in getting separate results for cumulative sum and failure intensity, separate file has been given. </span></p> <p><span><span>c)<span> </span></span></span><span>Code for ABCDE algorithm that is Swarm Evolutionary algorithm used in the paper has also been given in these files.</span></p>
Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation in hybrid prevalence in populations throughout the main Hawaiian Islands, using genomic data to characterize population structure of koloa, quantify the extent of hybridization, and compare hybrid proportions over time. To accomplish this, we genotyped 3,308 double-digest restriction-site-associated DNA (ddRAD) loci in 425 putative koloa, mallards, and hybrids from populations across the main Hawaiian Islands. We found that despite a population decline in the last century, koloa genetic diversity is high. There were few hybrids on the island of Kauaʻi, home to the largest population of koloa. By contrast, we report that sampled populations outside of Kauaʻi can now be characterized as hybrid swarms, in that all individuals sampled were of mixed koloa × mallard ancestry. Further, there is some evidence that these swarms are stable over time. These findings demonstrate spatial variation in the extent and consequences of interspecific hybridization, and highlight how islands or island-like systems with small population sizes may be especially prone to genetic extinction when met with a congener that is not reproductively isolated.
Data from: Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds
Open the record for dataset details and reuse information.
Data from: Discordant introgression in a rapidly expanding hybrid swarm
Open the record for dataset details and reuse information.
Data from: Patterns of mating and generation of diversity in a Geum hybrid swarm
Open the record for dataset details and reuse information.
Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands
Open the record for dataset details and reuse information.
Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species
Open the record for dataset details and reuse information.
Data from: The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.