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1,052 results for “structure diversity”
A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types
<p class="MsoNormal"><span>Teleost fish form the largest group of vertebrates, making them critically important for the study on the</span> <span>mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar</span> <span>to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We</span> <span>performed a systematic comparative survey of the goldfish telencephalon: the seat of plastic behavior,</span> <span>learning, and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using</span> <span>single-cell RNA-seq and spatial transcriptomics, resulting in de novo molecular neuroanatomy</span> <span>parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse</span> <span>and goldfish, while neurons showed diversity and modularity in gene expression. Specifically,</span> <span>somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory</span> <span>input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved.</span> <span>Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly conserved goldfish homologs. We further suggest different elements of a hippocampal formation across</span> <span>the goldfish pallium. Finally, aiding study of the teleostan everted telencephalon, we describe substantial</span> <span>molecular similarities between the goldfish and zebrafish neuronal taxonomies. Together, our atlas</span> <span>provides new insights into organization and evolution of vertebrate forebrains and may serve as a resource</span> <span>for the functional study underlying cognition in teleost fish.</span></p>
A Toroidal Zr70 Oxysulfate Cluster and Its Diverse Packing Structures
<p>Supplementary material: Syntheses, XRD, TGA, SEM, PXRD</p>
Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: Implications for conservation and management
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Genetic diversity, structure, and demography of Pandanus boninensis(Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands
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Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei)
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Changes in vertical and horizontal diversities mediated by the size structure of introduced fish collectively shape food-web stability
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Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
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Going with the flow? Relative importance of riverine hydrologic connectivity versus tidal influence for spatial structure of genetic diversity and relatedness in a foundational submersed aquatic plant
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A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types
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Data from: Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak
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Genetic Diversity and Spatial Structure of Spartina alterniflora in on the Eastern Shore of Virginia
Nine polymorphic microsatellite loci were used to quantify the genetic characteristics (e.g., allelic richness,diversity, polyploidy, fixation index) of the S. alterniflora populations at five salt marshes on the Eastern Shore of Virginia (Northampton Co.), as well as to measure the spatial structure (size and shape of clones) of a single population in Upper Phillips Creek marsh (UPC), a marsh that experienced dieback. Over 250 individual plant samples were collected at three spatial scales for these experiments
Data from: Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance
<p>Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae<i> </i>spp.) are both vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati (Christmas) atoll) in the central equatorial Pacific, and quantified the sequence assemblages and community structure of their associated Symbiodiniaceae<i> </i>and bacterial communities. Although Symbiodiniaceae alpha diversity did not vary with chronic human disturbance, disturbance was consistently associated with higher bacterial Shannon diversity and richness, with bacterial richness by sample almost doubling from sites with low to very high disturbance. Chronic disturbance was also associated with altered microbial beta diversity for Symbiodiniaceae and bacteria, including changes in community structure for both and increased variation (dispersion) of the Symbiodiniaceae communities. We also found concordance between Symbiodiniaceae and bacterial<i> </i>community structure, when all corals were considered together, and individually for two massive species, <i>Hydnophora microconos</i> and <i>Porites lobata, </i>implying that symbionts<i> </i>and bacteria respond similarly to human disturbance in these species. Finally, we found that the dominant Symbiodiniaceae ancestral lineage in a coral colony was associated with differential abundances of several distinct bacterial taxa. These results suggest that increased beta diversity of Symbiodiniaceae<i> </i>and bacterial communities may be a reliable indicator of stress in the coral microbiome, and that there may be concordant responses to chronic disturbance between these communities at the whole-ecosystem scale.</p>
Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America
<p>Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.</p>
Data from: Structural colours in diverse Mesozoic insects
Structural colours, nature's most pure and intense colours, originate when light is scattered via nanoscale modulations of the refractive index. Original colours in fossils illuminate the ecological interactions among extinct organisms and functional evolution of colours. Here we report multiple examples of vivid metallic colours in diverse insects from mid-Cretaceous amber. Scanning and transmission electron microscopy revealed a smooth outer surface and five alternating electron-dense and electron-lucent layers in the epicuticle of a fossil wasp, suggesting that multilayer reflectors, the most common biophotonic nanostructure in animals and even plants, are responsible for the exceptional preservation of colour in amber fossils. Based on theoretical modeling of the reflectance spectra, a reflective peak of wavelength of 514 nm was calculated, corresponding to the bluish green colour observed under white light. The green to blue structural colours in fossil wasps, beetles, and a fly most likely functioned as camouflage, although other functions such as thermoregulation cannot be ruled out. This discovery not only provides critical evidence of evolution of structural colours in arthropods, but also sheds light on the preservation potential of nanostructures of ancient animals through geological time.
Research data for "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining"
<p>This dataset supports the paper: "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining", available at the following DOI: 10.1039/d0sc03287e.</p> <p>The cleaned-up, coarse-grained, and re-scaled structures are provided here in both XYZ and CIF format. The data presented in the journal publication is also included; namely, MDS coordinates, T densities, and A-site heterogeneities for each structure in the dataset. T densities -- defined as: metals per unit volume (nm-3) -- are calculated using the re-scaled structures.</p>
Patch size and vegetation structure drive changes to mixed-species flock diversity and composition across a gradient of fragment sizes in the Western Andes of Colombia
<p>This data set represents a series of 502 mixed-species bird flock compositions, and derived taxonomic, functional, and phylogenetic diversity indices, that were gathered along a gradient of forest fragment sizes (range = 10-173 ha) in the Colombian Western Andes. We sampled mixed-species flocks using transect surveys along 14 transects in 8 fragments and a continuous forest reference site in the same landscape and at the same elevation (~1900-2200 m.a.s.l.). We also used buffer analysis to quantify the proportion of forest cover and forest edge within 1 km of each transect, and calculated local vegetation density and complexity, as well as distance from edge, for each 100-meter transect segment (<em>n</em> = 70 segments). Flock composition data observed on a transect were used to calculate overall species richness and flock size as well as two indices of functional and phylogenetic diversity; we calculated the stadardized effect size (SES) of each measure to account for the correlation between these measures and species richness. We also provide the raw counts of each species for each flock composition. These data were used for the analyses in Jones and Robinson (2020). </p>
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
<p>Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread <i>Elymus</i> species. <i>Elymus excelsus</i> Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of <i>E. excelsus</i> germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of <i>E. excelsus</i> from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of <i>E. excelsus</i> germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (<i>F</i><sub><i>st</i></sub> = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (<i>H</i><sub><i>e</i></sub> = 0.197) was greater than that of the GSC (<i>H</i><sub><i>e</i></sub> = 0.176) and XJC (<i>H</i><sub><i>e</i></sub> = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that <i>E. excelsus</i> accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable <i>E. excelsus</i> germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.</p>
Data from: Genetic structure and diversity of the blueface darter Etheostoma cyanoprosopum, a microendemic freshwater fish in the southeastern United States
Darters represent one of the most diverse groups of freshwater fishes in North America, but approximately 33% of the 215 recognized species are considered imperiled on the IUCN Red List. Discovery and description of new darter species continues at a relatively rapid pace, with many exhibiting microendemic geographic distributions and little baseline data for conservation decisions. The Blueface Darter Etheostoma cyanoprosopum is a newly described species that occupies < 20 km of stream reaches in the Bear Creek system of the Tennessee River drainage and the Hubbard Creek system of the Black Warrior River drainage in the Mobile Basin (Alabama, USA). In addition to restricted distribution, the species is threatened by habitat degradation and several natural and man-made barriers that putatively fragment connectivity among populations. This study used microsatellite and mitochondrial (mt) DNA data with comparisons to the relatively broadly distributed sister species (Bandfin Darter E. zonistium) to evaluate multiple objectives about genetic connectivity and diversity among Blueface Darter populations. Analysis of mtDNA data indicated a lack of historical structuring across the Tennessee-Black Warrior river drainage divide and within the Bear Creek system. However, microsatellite-based Bayesian cluster analyses and F-statistics suggested contemporary isolation across the drainage divide and evidence for reservoir-induced fragmentation within the Bear Creek system. Compared to the sister Bandfin Darter, Blueface Darter populations exhibited reduced levels of genetic diversity, rendering them more susceptible to local extirpation and reduced fitness. Continued monitoring and quantitative ecological studies are recommended to understand population-specific measures of occurrence and abundance.
Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence significantly predicted community diversity; (iii) the presence of aphids on genetically susceptible trees increased the stability of arthropod communities across years; and (iv) the experimental removal of aphids affected community network structure (network degree, modularity and tree genotype contribution to modularity). These findings demonstrate that the interactions of foundation species are genetically based, which in turn significantly contributes to community diversity, stability and species interaction networks. These experiments provide an important step in understanding the evolution of Darwin's 'entangled bank', a metaphor that characterizes the complexity and interconnectedness of communities in the wild.
Liana communities exhibit different species composition, diversity and community structure across forest types in the Congo Basin
<p>Lianas are poorly characterized for central African forests. We quantify variation in liana composition, diversity and community structure in different forest types in the Yangambi Man and Biosphere Reserve, Democratic Republic of Congo. These attributes of liana assemblages were examined in 12 1-ha plots, randomly demarcated within regrowth forest, old-growth monodominant forest, old-growth mixed forest and old-growth edge forest. Using a combination of multivariate and univariate community analyses, we visualize the patterns of these liana assemblage attributes and/or test for their significant differences across forest types. The combined 12 1-ha area contains 2,638 lianas (≥ 2 cm diameter) representing 105 species, 49 genera and 22 families. Liana species composition differed significantly across forest types. Taxonomic diversity was higher in old-growth mixed forests compared to old-growth monodominant and regrowth forests. Trait diversity was higher than expected in the regrowth forest as opposed to the rest of forest types. Similarly, the regrowth forest differed from the rest of forest types in the pattern of liana species ecological traits and diameter frequency distribution. The regrowth forest was also less densely populated in lianas, and had lower liana total basal area than the rest of forest types. We speculate that the mechanism of liana competitive exclusion by dominant tree species is mainly responsible for the lower liana species diversity in monodominant compared to mixed forests. We attribute variation in liana community structure between regrowth and old-growth forests mostly to short development time of size hierarchies.</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)
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.