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648 results for “Local adaptation”
Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)
Functional trait variation within and across populations can strongly influence population, community, and ecosystem processes, but the relative contributions of genetic vs. environmental factors to this variation are often not clear, potentially complicating conservation and restoration efforts. For example, local adaptation, a particular type of genetic by environmental (G*E) interaction in which the fitness of a population in its own habitat is greater than in other habitats, is often invoked in management practices, even in the absence of supporting evidence. Despite increasing attention to the potential for G*E interactions, few studies have tested multiple populations and environments simultaneously, limiting our understanding of the spatial consistency in patterns of adaptive genetic variation. In addition, few studies explicitly differentiate adaptation in response to predation from other biological and environmental factors. We conducted a reciprocal transplant experiment of first-generation eastern oyster (Crassostrea virginica) juveniles from six populations across three field sites spanning 1000 km in the southeastern Atlantic Bight in both the presence and absence of predation to test for G*E variation in this economically valuable and ecologically important species. We documented significant G*E variation in survival and growth, yet there was no evidence for local adaptation. Condition varied across oyster cohorts: Offspring of northern populations had better condition than offspring from the center of our region. Oyster populations in the southeastern Atlantic Bight differ in juvenile survival, growth, and condition, yet offspring from local broodstock do not have higher survival or growth than those from farther away. In the absence of population-specific performance information, oyster restoration and aquaculture may benefit from incorporating multiple populations into their practices.
Data from: Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana
Local adaptation is common, but the traits and genes involved are often unknown. Physiological responses to cold probably contribute to local adaptation in wide-ranging species, but the genetic basis underlying natural variation in these traits has rarely been studied. Using a recombinant inbred (495 lines) mapping population from locally adapted populations of Arabidopsis thaliana from Sweden and Italy, we grew plants at low temperature and mapped quantitative trait loci (QTLs) for traits related to photosynthesis: maximal quantum efficiency (Fv/Fm), rapidly reversible photoprotection (NPQfast), and photoinhibition of PSII (NPQslow) using high-throughput, whole-plant measures of chlorophyll fluorescence. In response to cold, the Swedish line had greater values for all traits, and for every trait, large effect QTLs contributed to parental differences. We found one major QTL affecting all traits, as well as unique major QTLs for each trait. Six trait QTLs overlapped with previously published locally adaptive QTLs based on fitness measured in the native environments over 3 years. Our results demonstrate that photosynthetic responses to cold can vary dramatically within a species, and may predominantly be caused by a few QTLs of large effect. Some photosynthesis traits and QTLs probably contribute to local adaptation in this system.
Data from: Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans
Coral reefs have great biological and socioeconomic value, but are threatened by ocean acidification, climate change, and local human impacts. The capacity for corals to adapt or acclimatise to novel environmental conditions is unknown but fundamental to projected reef futures. The coral reefs of Kāne'ohe Bay, Hawai'i were devastated by anthropogenic insults from the 1930s-1970s. These reefs experience naturally reduced pH and elevated temperature relative to many other Hawaiian reefs which are not expected to face similar conditions for decades. Despite catastrophic loss in coral cover due to human disturbance, these reefs recovered under low pH and high temperature within 20 years after sewage input was diverted. We compare the pH and temperature tolerances of three dominant Hawaiian coral species from within Kāne'ohe Bay to conspecifics from a nearby control site and show that corals from Kāne'ohe are far more resistant to acidification and warming. These results show that corals can have different pH and temperature tolerances among habitats and understanding the mechanisms by which coral cover rebounded within two decades under projected future ocean conditions will be critical to management. Together these results indicate that reducing human stressors offers hope for reef resilience and effective conservation over coming decades.
Data from: Influence of range position on locally adaptive gene-environment associations in Populus flowering time genes
Local adaptation is pervasive in forest trees, which are characterized by large effective population sizes spanning broad climatic gradients. In addition to having relatively contiguous populations, many species also form isolated populations along the rear edge of their range. These rear-edge populations may contain unique adaptive diversity reflecting a history of selection in marginal environments. Thus, discovering genomic regions conferring local adaptation in rear edge populations is a key priority for landscape genomics to ensure conservation of genetic resources under climate change. Here, we report on adaptive gene-environment associations in SNPs from 27 genes in the Populus flowering time gene network, analyzed on a range-wide collection of >1000 balsam poplar trees, including dense sampling of the southern range edge. We use a combined approach of local adaptation scans to identify candidate SNPs, followed by modeling the compositional turnover of adaptive SNPs along multivariate climate gradients using Gradient Forests (GF). Flowering time candidate genes contained extensive evidence of climate adaptation, namely outlier population structure and gene-environment associations, along with allele frequency divergence between the core and edge of the range. GF showed strong allele frequency turnover along gradients of elevation and diurnal temperature variability, as well as threshold responses to summer temperature and precipitation, with turnover especially strong in edge populations that occur at high elevation but southerly latitudes. We discuss these results in light of how climate may disrupt locally adaptivegene-environment relationships, and suggest that rear edge populations hold climate-adaptive variants that should be targeted for conservation.
Data from: Local adaptation for enhanced salt tolerance reduces non-adaptive plasticity caused by osmotic stress
Organisms often respond to environmental change via phenotypic plasticity, where an individual modulates its phenotype according to the environment. Highly variable or changing environments can exceed physiological limits and generate maladapted plastic phenotypes, which is termed non-adaptive plasticity. In some cases, selection may reduce the negative or disruptive impacts of environmental stress and produce locally adapted populations. Salt is an increasingly prevalent contaminant of freshwater systems and can induce non-adaptive plastic phenotypes for freshwater organisms like amphibians. Hyla cinerea is a frog species with populations inhabiting brackish, coastal habitats, so we use this species to test whether coastal populations are locally adapted to tolerate saltwater by determining how salt exposure during the embryonic and larval stages alters mortality and plastic developmental and metamorphic phenotypes of coastal and inland populations. Coastal frogs have higher survival, faster growth rates, and metamorphose sooner than inland frogs across salinities. Coastal frogs also metamorphose smaller (likely a consequence of earlier metamorphosis) yet maintain constant size, while higher salinities reduce metamorphic size for inland frogs. Coastal frogs evolved to minimize non-adaptive and disruptive impacts of saltwater during larval development and accelerate the larval period to reduce time spent in a stressful environment.
Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. Part I: Adaptive local approximate models
<p>The global search stage of Crystal Structure Prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II (Habgood, M., Sugden, I. J., Kazantsev, A. V., Adjiman, C. S. & Pantelides, C. C. (2015).<em> J Chem Theory Comput</em> <strong>11</strong>, 1957-1969) program is presented, where the most efficient use of computational effort is ensured via the use of adaptive Local Approximate Model (LAM) placement. The entire search space of relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimise the computational effort expended in high energy regions whilst maximising the accuracy in low energy regions. As the size, complexity, and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule XXVI from the sixth blind test (Reilly <em>et al.</em>, (2016).<em> Acta Cryst. B, accepted</em>.), which is challenging due its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. </p>
Data supporting "Local Clustering Decoder: a fast and adaptive hardware decoder for the surface code"
<p>The data consists of a CSV file containing the raw performance data collected from running our decoder on a Xilinx Virtex Ultrascale+ VU19P FPGA. The Stim circuits that were used to create the samples are provided in a ZIP file. Our internal fork of Stim with support for leakage is needed to sample noise from the circuits.</p>
Rapid evolution and local adaptation of urban aphids
<p>Publication in preparation: R Scripts and data for analyses and results of an aphid common garden experiment conducted in summer 2019 in Berlin, Germany. This repository is a work in progress.</p>
Data from: Fitness surfaces and local thermal adaptation in Drosophila along a latitudinal gradient
<p><span>Local adaptation is commonly cited to explain species distribution, but how fitness varies along continuous geographical gradients is not well understood. Here we combine thermal biology and life-history theory to demonstrate that <em>Drosophila </em>populations along a 2,500 km latitudinal cline are adapted to local conditions. We measured how heat tolerance and viability rate across 8 populations vary with temperature in the laboratory, and then simulated their expected cumulative Darwinian fitness employing high-resolution temperature data from their 8 collection sites. Simulations indicate a trade-off between annual survival and cumulative viability, as both mortality and the recruitment of new flies are predicted to increase in warmer regions. Importantly, populations are locally adapted and exhibit the optimal combination of both traits to maximize fitness where they live. In conclusion, our method is able to reconstruct fitness surfaces employing empirical life-history estimates and reconstructs peaks representing locally adapted populations, allowing to study geographic adaptation <em>in silico</em>.</span></p>
Local adaptation in trait-mediated trophic cascades dataset
<p>Predator-induced changes in prey foraging can indirectly influence community dynamics by increasing the abundance of basal resources via a trait-mediated trophic cascade. The strength of these cascades may be altered by eco-evolutionary relationships between predators and prey, but the role of basal resources has received limited attention. We hypothesized that the strength of trait-mediated trophic cascades may be shaped by selection from trophic levels above and below prey. Our field and laboratory experiments utilized snails (<em>Nucella lapillus</em>)<em> </em>from two regions in the Gulf of Maine (GoM) that vary substantially in basal resource (e.g., barnacles, mussels) availability and invasion history with the predatory green crab, <em>Carcinus maenas</em>. <em>Nucella</em> from both regions were provided with mussels as a basal resource and exposed to the presence or absence of green crab risk cues. In both experiments, <em>Nucella</em> from the northern GoM, where basal resources are scarce, displayed weaker responses to risk cues than southern <em>Nucella</em>. In the lab, however, northern <em>Nucella</em> foraged more than southern snails under risk, but foraging rates among the two regions did not differ without risk. Our results suggest that adaptation to basal resource availability may contribute to geographic variation in the strength of trait-mediated trophic cascades.</p>
Data from: Geographic and seasonal variation of the for gene reveal signatures of local adaptation in Drosophila melanogaster
<p>In the early 1980s, the observation that <em>Drosophila melanogaster </em>larvae differed in their foraging behavior laid the foundation for the work that would later lead to the discovery of the foraging gene (<em>for</em>) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of the <em>for</em> gene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying adaptation of populations in response to environmental variation. Here, I present results of a genotype-environment association analysis that quantifies variation at the <em>for</em> gene among samples of <em>D. melanogaster</em> structured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based on Fst values, and an analysis of population structure revealed an east-west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behavior in <em>D. melanogaster</em>.</p>
Weak local adaptation to drought in seedlings of a widespread conifer
<p>Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests.</p> <p>We used a large-scale common-garden drought-to-death experiment to assess range-wide variation in drought tolerance measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (<em>Pseudotsuga menziesii </em>var. <em>menziesii </em>and var. <em>glauca</em>).</p> <p>Local adaptation to drought was weak in var. <em>glauca </em>and nearly absent in <em>menziesii.</em> Var. <em>glauca</em> showed higher tolerance to drought but slower growth than var. <em>menziesii</em>. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. <em>menziesii</em> in response to extreme drought.</p> <p>Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.</p>
Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
<p>Freshwater salinisation is an important threat to biodiversity, ecosystem functioning, and the provision of ecosystem services. Therefore, understanding the capacity of species to adapt to salinity gradients is crucial. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinisation. We studied local genetic adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes - a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. The population-level salinity tolerance range was reduced in more saline bomb crater ponds through an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show genetic adaptation to salinity gradients at different spatial scales and fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.</p>
Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside
<p>Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (<em>Menidia menidia</em>) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.</p>
Data for: Local adaptation of a generalist hemiparasitic plant to one of its potential host plants
<p>Coevolution is often found in parasite-host interactions but has not yet been described for hemiparasitic plants and their hosts. Root hemiparasites like <em>Rhinanthus alectorolophus</em> perform photosynthesis but also parasitize other plant species, some of which (e.g. <em>Plantago lanceolata</em>) may defend themselves against parasite attack by blocking the haustoria of the parasites. We grew seedlings of the hemiparasite <em>Rhinanthus alectorolophus</em> and the potential host <em>Plantago lanceolata</em> from seven grassland sites in a factorial design. To detect differences in host defence, we also included hosts from two 'naïve' populations from regions where the parasite does not occur.<em> R. alectorolophus</em> grew consistently larger and had higher fitness with sympatric than with allopatric hosts, suggesting parasite adaptation to local host populations. Moreover, <em>R. alectorolophus</em> remained smallest with allopatric hosts from the same region and reached intermediate sizes with allopatric hosts from other regions or naïve hosts, suggesting host adaptation to parasites at the regional scale. Parasite presence reduced the size of the host plants already after four weeks, but only that of hosts with 'experience' of the parasite, suggesting an early host response. Follow-up experiments confirmed that parasites attach to hosts already after four weeks and hosts respond by changing belowground allocation patterns. However, parasite roots did not preferentially grow towards sympatric hosts. Our results suggest that local adaptation to hosts can occur even in generalist parasites and does not require specialization on individual hosts. We discuss the role of potential mechanisms, including variation in chemical signalling (early) and in host defence (late effects).</p>
Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments
<p><span>Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in <i>Liriodendron</i> to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between <i>L. chinense</i> and <i>L. tulipifera</i>, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in <i>L. chinense</i>, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in <i>Liriodendron</i>. Our findings reveal ecological adaptive divergence pattern between <i>Liriodendron</i> species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future <i>L. chinense</i> conservation efforts. </span></p>
Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover
<p>Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (<i>Trifolium repens</i>). This widespread species displays a well-studied chemical defense polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F<sub>2</sub> mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL X E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL co-localization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favored early investment in flowering at the cost of multi-year survival in the southernmost site vs. delayed flowering and multi-year persistence in the northern environments. Our findings demonstrate that multi-locus genetic tradeoffs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.</p>
Gene flow influences the genomic architecture of local adaptation in six riverine fish species
<p>Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation-based outlier tests and three genotype-environment association analyses to define neutral SNPs and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall <em>F</em><sub>ST</sub> (0.0303 - 0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest <em>F</em><sub>ST</sub> (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (<em>F</em><sub>ST</sub> ~ 0.0025 - 0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. </p>
Demonstration of local adaptation in maize landraces by reciprocal transplantation
<p><span><span>Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparison between phenotypic patterns and population genetic structure.</span></span></p> <p><span><span>We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (Q<sub>ST</sub>) was greater than neutral allele frequency differentiation (F<sub>ST</sub>) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits are stronger in the highland site than the lowland site, supporting their status as highland-adaptive. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.</span></span></p>
Divergence in Heliconius flight behaviour is associated with local adaptation to different forest structures
<p>Micro-habitat choice plays a major role in shaping local patterns of biodiversity. In butterflies, stratification in flight height has an important role in maintaining community diversity. The speciation in <em>Heliconius</em> butterflies is often associated with strong assortative mating, but ecological isolation and local adaptation is also considered essential. Despite its presumed importance, the role of behavioural shifts in early stages of speciation in response to differences in habitat structure is yet to be established. Here, we investigated variation in flight height behaviour in two closely related species, <em>H. erato cyrbia</em> and <em>H. himera</em>, which produce viable hybrids but are isolated across an environmental gradient, spanning lowland wet forest to high altitude scrub forest. We show that the two species fly at different heights in the wild, and demonstrate that this can be explained by differences in the vertical distribution of plant resources. We subsequently explored whether this divergence in flight height has a genetic component using common garden experiments. In both the wild and captivity, <em>H. himera</em> choose to fly lower and feed at lower positions, mirroring differences in resource availability in the wild. We suggest that this shift in foraging behaviour may reflect local adaptation to divergent forest structures highlighting the role of behaviour during early stages of speciation.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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