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81 results for “heterogeneous environment”
RafanoSet: Dataset of raw, manual and automatically annotated Raphanus Raphanistrum weed images for object detection and segmentation in Heterogenous Agriculture Environment
<p>This dataset is a collection of raw and annotated Multispectral (MS) images acquired in a heterogenous agricultural environment with MicaSense RedEdge-M camera. The spectra particularly Green, Blue, Red, Red Edge and Near Infrared (NIR) were acquired at sub-metre level.. <br><br>The MS images were labelled manually using VIA and automatically using Grounding DINO in combination with Segment Anything Model. The segmentation masks obtained using these two annotation techniqes over as well as the source code to perform necessary image processing operations are provided in the repository. The images are focussed over Horseradish (Raphanus Raphanistrum) infestations in Triticum Aestivum (wheat) crops.</p> <p>The nomenclature of sequecncing and naming images and annotations has been in this format: IMG_<scene number>_<spectral channel number><br><strong>_1</strong>: Blue<br><strong>_2</strong>: Green<br><strong>_3</strong>: Red<br><strong>_4</strong>: Near Infrared<br><strong>_5</strong>: RedEdge<br><br>Example: An image name <strong>IMG_0200_3 </strong>represents the scene number<strong> 200</strong> in <strong>Red channel</strong></p> <p>This dataset 'RafanoSet'is categorized in 6 directories namely 'Raw Images', 'Manual Annotations', 'Automated Annotations', 'Binary Masks - Manual', 'Binary Masks - Automated' and 'Codes'. The sub-directory 'Raw Images' consists of manually acquired 85 images in .PNG format. over 17 different scenes. The sub-directory 'Manual Annotations' consists of annotation file 'region_data' in COCO segmentation format. The sub-directory 'Automated Annotations' consists of 80 automatically annotated images in .JPG format and 80 .XML files in Pascal VOC annotation format.</p> <p>The scientific framework of image acquisition and annotations are explained in the Data in Brief paper which is the course of peer review. This is just a prerequisite to the data article. <br><br>Field experimentation roles:</p> <p>The image acquisition was performed by Mariano Crimaldi, a researcher, on behalf of Department of Agriculture and the hosting institution University of Naples Federico II, Italy.</p> <p>Shubham Rana has been the curator and analyst for the data under the supervision of his PhD supervisor Prof. Salvatore Gerbino. They are affiliated with Department of Engineering, University of Campania 'Luigi Vanvitelli'. </p> <p>Domenico Barretta, Department of Engineering has been associated in consulting and brainstorming role particularly with data validation, annotation management and litmus testing of the datasets.</p>
FIGURE 2 in Population genetics of three threatened catfish species in heterogeneous environments of the Cauca River, Colombia
FIGURE 2 | Population structure suggested by STRUCTURE (A–C) and the Discriminant Analysis of the Principal Components (D–F) for Pimelodus grosskopfii (A, D), Sorubim cuspicaudus (B, E), and Ageneiosus pardalis (C, F).
FIGURE 1 in Population genetics of three threatened catfish species in heterogeneous environments of the Cauca River, Colombia
FIGURE 1 | Location of sampling sites of Pimelodus grosskopfii, Sorubim cuspicaudus, and Ageneiosus pardalis in the middle and lower sections of the Cauca River.
Data from: Determining the optimal movement strategies in environments with heterogeneously distributed resources and toxicants
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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>
Leaf size variations in a dominant desert shrub, Reaumuria soongarica, adapted to heterogeneous environments
<p>The climate in arid Central Asia (ACA) has changed rapidly in recent decades, but the ecological consequences of this are far from clear. To predict the impacts of climate change on ecosystem functioning, greater attention should be given to the relationships between leaf functional traits and environmental heterogeneity. As a dominant constructive shrub widely distributed in ACA, <em>Reaumuria soongarica</em> provided us with an ideal model to understand how leaf functional traits of desert ecosystems responded to the heterogeneous environments of ACA. Here, to determine the influences of genetic and ecological factors, we characterized species-wide variations in leaf traits among 30 wild populations of <em>R. soongarica</em> and 16 populations grown in a common garden. We found that the leaf length, width, and leaf length to width ratio (L/W) of the northern lineage were significantly larger than those of other genetic lineages, and principal component analysis based on the <em>in situ</em> environmental factors distinguished the northern lineage from the other lineages studied. With increasing latitude, leaf length, width, and L/W in the wild populations increased significantly. Leaf length and L/W were negatively correlated with altitude, and first increased and then decreased with increasing mean annual temperature (MAT) and mean annual precipitation (MAP). Stepwise regression analyses further indicated that leaf length variation was mainly affected by latitude. However, leaf width was uncorrelated with altitude, MAT or MAP. The common garden trial showed that leaf width variation among the eastern populations was caused by both local adaptation and phenotypic plasticity. Our findings suggest that <em>R. soongarica</em> preferentially changes leaf length to adjust leaf size to cope with environmental change. We also reveal phenotypic evidence for ecological speciation of <em>R. soongarica</em>. These results will help us better understand and predict the consequences of climate change for desert ecosystem functioning.</p>
Directed movement changes coexistence outcomes in heterogeneous environments
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Leaf size variations in a dominant desert shrub, Reaumuria soongarica, adapted to heterogeneous environments
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Effects of species richness and turnover on ecosystem functioning in heterogeneous environments of two tropical mountains
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Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments
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Data from: Mallard resource selection trade‐offs in a heterogeneous environment during autumn and winter
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Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
<p>Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous <i>versus</i> evergreen forests and insular <i>versus</i> mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (<i>F</i><sub>ST</sub> = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (<i>F</i><sub>ST</sub> = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular <i>versus</i> mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.</p>
Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)
<p>Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evoutionary history of a species, providing the premise for studying the response of organisms to rapid cimate change. However, for most species how exacty the spatial heterogeneity promotes popuation divergence and how genomic variations contribute to adaptive evolution remain poorly understood.</p> <p>We examine the contributions of geographica and environmental variables to population divergence of the relictual, alpine herb <i>Circaeaster agrestis</i>, as wel as genetic basis of local adaptation using RAD-seq and plastome data.</p> <p><span>We detected</span> significant genetic structure with <span>an extraordinary disequilibrium of genetic diversity</span><span> among regions</span>, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and <span>redundancy </span>analyses revealed significant association between genetic variation and temperature variables<i>.</i> <span><span>Genome</span></span><span><span>‐</span></span><span><span>environment association analyses identified 16 putatively adaptive loci mainly related </span></span>mainly <span><span>to biotic and abiotic stress resistance.</span></span></p> <p><span>Our genome wide data provide new insights into the important roe of </span>environmenta heterogeneity<span> in shaping genetic structure, and access the footprints of ocal adaptation in an </span>ancient reictual species, informing future conservation efforts<span>.</span></p> <div> <div class="gtx-trans-icon"> </div> </div>
A meta-analysis of effects of physiological integration in clonal plants under homogeneous vs. heterogeneous environments
<p class="CxSpFirst"><span><b>Summary</b></span></p> <p class="CxSpMiddle"><span>1. Clonal plants play key roles in maintaining community productivity and stability in many ecosystems. Connected individuals (ramets) of clonal plants can translocate and share e.g. photosynthates, water and nutrients, and such physiological integration may affect performance of clonal plants both<a name="_Hlk51046980"> in heterogeneous and homogeneous environments. </a>However, we still lack a general understanding of whether or how physiological integration in clonal plants differs across homogeneous vs. heterogeneous environments. </span></p> <p class="CxSpMiddle"><span>2. We compiled data from 198 peer reviewed scientific studies conducted in 19 countries with 108 clonal plant species from 35 families, and carried out a meta-analysis of effects of physiological integration on 16 traits related to plant growth, morphology, physiology or allocation. Our analyses evaluated these relationships in A) heterogeneous environments where at least one resource essential for plant growth (e.g. light, soil water and mineral nutrients) or non-resource factor (e.g. grazing, trampling and burial) is spatially non-uniformly distributed, and B) homogeneous environments where all these factors are spatially uniformly distributed.</span></p> <p class="CxSpMiddle"><span>3. Physiological integration increased growth of whole clones in both homogeneous and heterogeneous environments due to its highly significant contribution to growth of recipient ramets. Integration did not affect growth of donor ramets in heterogeneous environments, but decreased it in homogeneous environments. </span></p> <p class="CxSpMiddle"><span>4. Integration affected physiological traits of donor ramets in neither homogeneous nor heterogeneous environments. It did not affect any physiological traits of recipient ramets in homogeneous environments, but increased most of them in heterogeneous environments. For donor ramets, integration increased height by 53% and internode length by 37% in heterogeneous environments, but had no effect in homogeneous environments. For recipient ramets, integration increased height by 73% in homogeneous environments and by 115% in heterogeneous environments, and increased internode length by 35% only under heterogeneous environments. In heterogeneous environments, integration increased biomass allocation to roots of donor ramets under high water/nutrient conditions and decreased it under high light. </span></p> <p>5. Physiological integration plays a strong role in clonal plant physiology, morphology, and growth, especially for recipient ramets in heterogeneous environments. Therefore, physiological integration may have contributed to the widespread of clonal plants in nature and their dominance in many ecosystems. It may also play important roles in invasion success of alien clonal plants and in maintaining functions and stability of ecosystems where clonal plants are abundant.</p>
Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment
Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.
Data from: Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics
Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km2 in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.
Data from: Genet dynamics of a regenerating dwarf bamboo population across heterogeneous light environments in a temperate forest understorey
Despite the advantage of plant clonality in patchy environments, studies focusing on genet demography in relation to spatially heterogeneous environments remain scarce. Regeneration of bamboos in forest understoreys after synchronous die-off provides an opportunity for assessing how they come to proliferate across heterogeneous light environments. In a Japanese forest, we examined genet demography of a population of Sasa kurilensis over a 7-year period starting 10 years after die-off, shortly after which some genets began spreading horizontally by rhizomes. The aboveground biomass was estimated and genets were discriminated in 9-m2 plots placed under both canopy gaps and closed canopies. Overall, the results suggest that the survival and spread of more productive genets and the spatial expansion of genets into closed canopies underlie the proliferation of S. kurilensis. Compared to canopy gaps, the recovery rate of biomass was much slower under closed canopies for the first 10 years after the die-off, but became accelerated during the next seven years. Genet survival was greater for more productive genets (with greater initial number of culms), and the spaces occupied by genets that died were often colonized afterward by clonal growth of surviving genets. The number of genets decreased under canopy gaps due to greater mortality, but increased under closed canopies where greater number of genets colonized clonally from outside the plots than genets died. The colonizing genets were more productive (having larger culms) than those originally germinated within the plots, and the contribution of colonizing genets to the biomass was greater under closed canopies. Our study emphasizes the importance of investigating genet dynamics over relevant spatio-temporal scales to reveal processes underlying the success of clonal plants in heterogeneous habitats.
Data from: Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment
Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized their mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, "start early and grow slowly" or "start late and grow fast", driven by precipitation seasonality. Populations following the "start early and grow slowly" strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.
Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments
Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armor plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analyzing 28,888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genome-wide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results.
Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments
The Australian koala is an iconic marsupial with specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene-flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for taxonomic classification of three koala sub-species, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (ie. Blue Mountains region; AvHecorr=0.20, PL%=68.6). Broad-scale population differentiation is primarily driven by an Isolation by Distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene-flow and adapt across divergent environments as long as the required food source is available.
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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)
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.