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154 results for “local structure”
Local structure and dynamics in methylammonium, formamidinium and cesium tin(II) mixed−halide perovskites from 119Sn solid−state NMR
<p>Raw and processed NMR data in Bruker Topspin format</p>
Vasp calculation and local structures of NdFeB substituted structures
<p>This dataset summary Density Functional Theory calculations using VASP[1] with Nd-Fe-B substituted structures. The source calculated VASP results are found in [2]. In addition, the dataset includes local structures extracted from the Nd-Fe-B substituted structures and Nd-Fe-B structures collected from OQMD that used to create tSNE maps of local structures. Details information e.g. OFM descriptor, Xray diffraction descriptor, 5967 Lanthanide-Transition metal-Light element from OQMD are also included in this dataset.<br> <br> [1] VASP: Vienna Ab initio Simulation Package: <a href="https://www.vasp.at/">https://www.vasp.at/</a></p> <p>[2] VASP calculation of Nd-Fe-B at NOMAD repository: https://dx.doi.org/10.17172/NOMAD/2020.07.30-1</p> <p>[3] OQMD: Open Quantum Materials Database: <a href="http://www.oqmd.org/">http://www.oqmd.org/</a></p>
Changes in stream food web structure across a gradient of acid mine drainage increases local community stability
<p>Understanding what makes food webs stable has long been a goal of ecologists. Topological structure and the distribution and magnitude of interaction strengths in food webs have been shown to confer important stabilizing properties. However, our understanding of how variable species interactions affect food web structure and stability is still in its infancy. Anthropogenic stress, such as acid mine drainage, is likely to place severe limitations on the food web structures possible due to changes in community composition and body mass distributions. Here, we used mechanistic models to infer food web structure and quantify stability in streams across a gradient of acid mine drainage. Multiple food webs were iterated for each community based on species pairwise interaction probabilities, in order to incorporate the variability of realistic food web structure. We found that food web structure was altered systematically with a 32-fold decrease in the number of links and a 2-fold increase in connectance across the gradient. Stability generally increased 6-fold with increasing acid mine drainage stress, regardless of how interaction strengths were estimated. However, the distribution of the stability measure, s, for some impacted communities separated into clusters of higher and lower magnitude depending on how interaction strengths were estimated. Management and restoration of impacted sites needs to consider their increased stability, as this may have important implications for the re-colonization of desirable species. Furthermore, active species introductions may be required to overcome the internal ecological inertia of affected communities.</p>
Genetic population structure constrains local adaptation in sticklebacks
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene<i> Pitx1</i>, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the <i>Pitx1</i> regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2x stronger population structuring among freshwater populations and >10x stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Local genetic structure in the critically endangered, cave-associated perennial herb Primulina tabacum (Gesneriaceae)
The local spatial genetic structures of cave-associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave-associated plant, and provides valuable information for the sustainable conservation of such species.
Data from: Network structure and local adaptation in coevolving bacteria-phage interactions
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so called 'bipartite networks', reflected observed coevolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts. We found a consistent nested network structure for two phage types, one previously demonstrated to exhibit arms race coevolutionary dynamics and the other fluctuating coevolutionary dynamics. Both phages increased their host ranges through evolutionary time, but we found no evidence for a trade off with impact on bacteria. Finally, only bacteria from the arms race phage showed local adaptation, and we provide preliminary evidence that these bacteria underwent (sometimes different) molecular changes in the wzy gene associated with the LPS receptor, while bacteria coevolving with the fluctuating selection phage did not show local adaptation and had partial deletions of the pilF gene associated with Type IV pili. We conclude that the structure of phage-bacteria interaction networks is not necessarily specific to coevolutionary dynamics, and discuss hypotheses for why only one of the two phages was, nevertheless, locally adapted.
Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management
<p>Incorporating species' eco-evolutionary responses to human-caused disturbances remains a challenge in marine management efforts. A prerequisite is knowledge of geographic structure and scale of genetic diversity and connectivity - the so-called seascape genetic patterns. The Baltic Sea is an excellent model system for studies linking seascape genetics with effects of anthropogenic stress. However, seascape genetic patterns in this area are only described for a few species and are completely unknown for invertebrate herbivores, which constitute a critical part of the ecosystem. This information is crucial for sustainable management, particularly under future scenarios of rapid environmental change. Here, we investigate the population genetic structure among 31 locations throughout the Baltic Sea, of which 45 % were located in marine protected areas, in one of the most important herbivores of this region, the isopod crustacean <i>Idotea balthica</i>, using an array of 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. In addition, we generate a biophysical connectivity matrix for <i>I. balthica</i> from a combination of oceanographic current models and estimated life history traits. We find population structure on scales of hundreds of kilometers across the Baltic Sea, where genomic patterns in most cases closely match biophysical connectivity, indicating passive transport with oceanographic currents as an important mean of dispersal in this species. We also find a reduced genetic diversity in terms of heterozygosity along the main salinity gradient of the Baltic Sea, suggesting periods of low population size. Our results provide crucial information for management of a key ecosystem species under expected changes in temperature and salinity following global climate change in a marine coastal area.</p>
Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Fig. 6. Screening the study area for habitat structures, 6.VI.2020 in The northernmost discovery of Aradus brenskei (Reuter, 1884) (Heteroptera: Aradidae). Considerations on the local distribution and the habitat preferences of this new Belgian species following a nine-months field survey
Fig. 6. Screening the study area for habitat structures, 6.VI.2020. © Brecht Verkempinck.
Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks
A central problem in ecology is to understand how human impacts affect plant-animal interactions that lead to effective seed dispersal services for plant communities. Seed dispersal services are the outcome of plant-frugivore interactions that often form local networks of interacting species. Recent work has shown that some frugivorous bird species are more critical to network organization than others. Here, we explore how patch size and the potential local extinctions of obligate frugivorous birds affect the reorganization of seed dispersal networks. We examined the structure of 20 empirical seed dispersal networks documented across tropical avian assemblages occupying widely variable habitat patch sizes, a surrogate of the amount of remaining habitat. Networks within small forest patches consistently supported both lower plant and bird species richness. Forest patch size was positively associated with nestedness, indicating that reductions in patch size disrupted the nested organization of seed dispersal networks. Obligate frugivores, especially large-bodied species, were almost entirely absent from small forest patches. Analysis at the species level showed that obligate frugivores formed the core of interacting species, connecting species within a given seed dispersal network. Our combined results revealed that patch size reduction erodes frugivorous bird diversity, thereby affecting the integrity of seed dispersal networks. We highlight the importance of conserving large forest patches to maintain tropical forest functionality.
Text-fig. 8. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seedbearing capsule. a, b: general morphology; c–e: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a, b; same scale for both figures), 100 µm (c–e). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 8. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seedbearing capsule. a, b: general morphology; c–e: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a, b; same scale for both figures), 100 µm (c–e).
Data from: Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes
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Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
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Data from: Network structure and local adaptation in coevolving bacteria-phage interactions
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Genetic population structure constrains local adaptation in sticklebacks
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Changes in stream food web structure across a gradient of acid mine drainage increases local community stability
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Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks
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Data from: Local genetic structure in the critically endangered, cave-associated perennial herb Primulina tabacum (Gesneriaceae)
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Data from: Habitat heterogeneity, host population structure and parasite local adaptation
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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