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109 results for “Data race”
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
<p>Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of <i>Rhagoletis pomonella </i>to their sibling species <i>R. mendax</i> that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and <i>R. mendax</i> show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on <i>R. mendax</i> revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in <i>Rhagoletis</i>. The generality of this result is placed in the context of other similar systems.</p>
A Study of Real-world Data Races in Golang (Artifact)
<p>The concurrent programming literature is rich with tools and techniques for data race detection. Less, however, has been known about real-world, industry-scale deployment, experience, and insights about data races. Golang (Go for short) is a modern programming language that makes concurrency a first-class citizen. Go offers both message passing and shared memory for communicating among concurrent threads. Go is gaining popularity in modern microservice-based systems. Data races in Go stand in the face of its emerging popularity.</p> <p>In this paper, using our industrial codebase as an example, we demonstrate that Go developers embrace concurrency and show how the abundance of concurrency alongside language idioms and nuances make Go programs highly susceptible to data races. <br> Google's Go distribution ships with a built-in dynamic data race detector based on ThreadSanitizer. Dynamic race detectors pose scalability and flakiness challenges; we discuss various software engineering trade-offs to scale this detector to work effectively at scale.</p> <p>We have deployed this detector in our 50-million lines of Go codebase hosting 2100 distinct microservices, found over 2000 data races, fixed over 1000 data races, spanning 790 distinct code patches submitted by 210 unique developers over a six-month period. Based on a detailed investigation of these data race patterns in Go, we make seven high-level observations relating to the complex interplay between the Go language paradigm and data races. </p>
Data from: Asynchronous life histories generate uneven arms races and impact the maintenance of mutualisms
<p>Mutualisms constitute a diverse class of ecologically important interactions, yet their ecological and evolutionary stability remain topics of debate in coevolutionary theory. Recent theoretical and empirical work has suggested that coevolutionary arms races may be involved in the maintenance of mutualistic interactions, sustaining mutually beneficial outcomes for interacting species while producing exaggerated traits. Here we present an individual-based model that evaluates how asynchronous life histories – i.e., partners with different average lifespans – change the dynamics of trait coevolution, the expected fitness outcomes for species involved, and the dynamics of selection differentials across time for each species. Results indicate that a longer-lived mutualist will consistently 'lose' an otherwise balanced coevolutionary arms race, being outpaced in both the mean trait value and fitness outcome compared to a shorter-lived partner. Furthermore, linear selection differentials on mutualistic traits become increasingly divergent as life histories become increasingly asynchronous, with the longer-lived species experiencing persistent directional selection and the shorter-lived species experiencing weaker, more inconsistent selection. These results suggest that asynchronous life histories can complicate the maintenance of mutualistic interactions via coevolutionary arms-races and that detecting coevolution via selection differentials may be difficult when life histories are sufficiently divergent.</p>
LAGOS-US Race and Ethnicity: Dataset classifying conterminous US lake communities based on racial and ethnic demographic data (v 2.0)
<p>Knowing the consistency of water quality sampling in lakes surrounded by a variety of racial and ethnic communities is important for potential policy uses and to assess community impacts. By using the 2010 US Census race and ethnicity demographic block group data, we analyzed the frequency (i.e., number of years and consistency) of lake water quality sampling according to racial and ethnic demographics in surrounding neighborhoods. Our approach classified human communities near lakes as predominantly White or people of color (POC), and Hispanic or non-Hispanic (NH). Associated R analysis scripts can also be found in this folder. Our data and approach can be used for future studies seeking to analyze environmental monitoring practices in relation to human demographic variables, particularly from US Census data.</p>
Ocean Data Hours - Ocean Race - Ocean Village - Genova Pavilllion - Cape Town 23.02.2023
<p>The ocean plays a significant role in the Earth's system, and understanding its importance is crucial for ensuring sustainable management and exploitation. Ocean observation should not be a task for experts and scientists alone.</p> <p>Citizen science is a form of scientific collaboration where members of the public participate in scientific research projects, providing data and observations that can be analyzed by researchers.</p> <p>This workshop presents a series of CS initiatives exploiting low cost technologies for ocean data collection by showing and discussing their maturity level and how scientists can already use these data.</p> <p>By supporting citizen science initiatives, policymakers can democratize marine observation science, creating a new type of self-driven, sustainable, and cost-efficient observatory concept, and at the same time, providing for the making of informed decisions based on the best available information.</p> <p>Ocean Data Hours is a series of workshops and talks organized in the Genova Pavillion at the Ocean Village - Ocean Race 2023. </p>
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
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Data from: Asynchronous life histories generate uneven arms races and impact the maintenance of mutualisms
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Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
Data from: Common protein-coding variants and the racing phenotype in galloping racehorse breeds
<p>Centuries-long selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, <em>G6PC2</em>, <em>HDAC9</em>, <em>KTN1</em>, <em>MYLK2</em>, <em>NTM</em>, <em>SLC16A1</em> and <em>SYNDIG1</em>, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.</p>
SNP data set of Peruvian highland maize races
<p>Peruvian maize exhibits significant morphological diversity, with landraces cultivated from sea level up to 3,500 meters above sea level. Previous research based on morphological descriptors identified at least 52 Peruvian maize races, but their genetic diversity and population structure remain largely unknown. In this study, we used genotyping-by-sequencing (GBS) to infer the genetic structure and diversity of 423 maize accessions from the Genebank of La Molina National Agrarian University (UNALM). These accessions represent nine races and one sub-race, along with 15 open-pollinated lines (purple corn) and two yellow maize hybrids. We obtained 14,235 high-quality SNPs distributed along the 10 maize chromosomes. Gene diversity ranged from 0.33 (Pachia) to 0.362 (Ancashino), with Cusco showing the lowest inbreeding coefficient (0.205) and Ancashino the highest (0.274) among the landraces. Population divergence (FST) was very low (mean = 0.017), indicating extensive interbreeding among Peruvian maize varieties. Population structure analysis revealed that these 423 distinct genotypes could be grouped into 10 clusters, with some maize races clustering together. Peruvian maize races did not form monophyletic groups; instead, our phylogenetic tree identified two clades corresponding to the chronological classification of Peruvian maize races: <em>Anciently Derived or Primary Races</em> (ADPR) and <em>Lately Derived or Secondary Races</em> (LDSR). These clades also align with the geographic origins of the maize races, reflecting their mixed evolutionary backgrounds. Further investigation of Peruvian maize germplasm using modern technologies is essential to enhance their use in breeding programs, particularly in the Andean region of Peru.</p>
Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant" [Dataset]
<p>Data from de Vega et al_Flora "Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant"</p>
Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early versus late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430 km transect, where the host races co-occur in sympatry in the Midwest USA. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.
Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race
<p>Decades of research have shown that the coevolutionary arms race between avian brood parasites and their hosts can promote phenotypic diversification in hosts and brood parasites. However, relatively little is known about the role of brood parasitism in promoting phenotypic diversification of nestlings. We review field data collected over four decades in Australia, New Caledonia and New Zealand to assess potential for coevolutionary interactions between the shining bronze-cuckoo (<em>Chalcites lucidus</em>) and its hosts, and how diversification at the nestling stage may be generating different subspecies. The shining bronze-cuckoo is a specialist parasite of a few hosts in the family Acanthizidae. It has diversified into subspecies, of which the nestlings closely mimic the respective host nestlings in each region. Additionally, some cuckoo subspecies have polymorphic nestlings. The Acanthizidae hosts have similar breeding and nesting habits and only moderately effective frontline defences against parasitism at cuckoo egg laying or at the egg stages. However, some hosts have developed highly effective defences at the nestling stage by recognising and ejecting cuckoo nestlings from the nest. As with the cuckoo nestlings, some hosts have polymorphic nestlings. The coevolutionary interactions in each region suggest different evolutionary stages of the arms race in which either the parasite or the host is currently in the lead. The presence of moderately effective defences at the egg laying and egg stages might explain why some hosts do not have defences at the nestling stage. The south-Pacific cuckoo – host systems are excellent models to explore the evolutionary mechanisms driving the diversification at the nestling stage in the coevolutionary arms race between avian brood parasites and their hosts.</p>
High-frequency location data show that race affects citations and fines for speeding
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Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race
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Data from: Common protein-coding variants and the racing phenotype in galloping racehorse breeds
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Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies
Open the record for dataset details and reuse information.
Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Open the record for dataset details and reuse information.
SNP data set of Peruvian highland maize races
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Data from: The geographic mosaic of arms race coevolution is closely matched to prey population structure
<p>Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (<i>Thamnophis sirtalis</i>) and toxic newts (<i>Taricha granulosa</i>). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.</p>
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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)
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DANDI Archive for NWB datasets
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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.