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1,052 results for “Structural diversity”
Forest structural diversity at NEON sites in the continuous USA that experienced recent moderate disturbance
Disturbances can change the structural diversity of forests through time, which can be measured from three-dimensional data provided by LiDAR. Discrete-return LiDAR was used to measure a suite of 19 structural diversity metrics that describe the height, cover and openness, vegetation density, and internal and external heterogeneity of forest vegetation at NEON base plots. Discrete-return LiDAR point clouds from the NEON Aerial Observation Platform (DP1.30003.001) were downloaded September of 2020 and used to estimate the metrics within 40 x 40 m base plots. Metrics were estimated from base plots at 15 NEON forested sites from provisional LiDAR data available from 2014 to 2020. The workflow that produced the data was developed in the program R.
NMR screen reveals the diverse structural landscape of a G- quadruplex library
<p>This is the NMR dataset for the manuscript '<span>NMR screen reveals the diverse structural landscape of a G-</span><br><span>quadruplex library</span>'</p> <p>Abstract</p> <p><span>G-quadruplexes are noncanonical nucleic acid structures</span><br><span>formed by stacked guanosine tetrads. Despite their functional and</span><br><span>structural diversity, a single consensus model is typically used to</span><br><span>describe</span><span> </span><span>sequences</span><span> </span><span>with</span><span> </span><span>the</span><span> </span><span>potential</span><span> </span><span>to</span><span> </span><span>form</span><span> </span><span>G-quadruplex</span><br><span>structures. We are interested in developing more specific sequence</span><br><span>models</span><span> </span><span>for</span><span> </span><span>G-quadruplexes.</span><span> </span><span>In</span><span> </span><span>previous</span><span> </span><span>work,</span><span> </span><span>we</span><span> </span><span>functionally</span><br><span>characterized each sequence in a 496-member library of variants of a</span><br><span>monomeric</span><span> </span><span>reference</span><span> </span><span>G-quadruplex</span><span> </span><span>for</span><span> </span><span>the</span><span> </span><span>ability</span><span> </span><span>to</span><span> </span><span>bind</span><span> </span><span>GTP,</span><br><span>promote a model peroxidase reaction, generate intrinsic fluorescence,</span><br><span>and to form multimers. Here we used NMR to obtain a broad overview</span><br><span>of the structural features of this library. After determining the</span><span> </span><span>1</span><span>H NMR</span><br><span>spectrum of each of these 496 sequences, spectra were sorted into</span><br><span>multiple classes, most</span><span> </span><span>of</span><span> </span><span>which could be rationalized based on</span><br><span>mutational patterns in the primary sequence. A more detailed screen</span><br><span>using representative sequences provided additional information about</span><br><span>spectral classes, and confirmed that the classes determined based on</span><br><span>analysis of</span><span> </span><span>1</span><span>H NMR spectra are correlated with functional categories</span><br><span>identified in previous studies. These results provide new insights into</span><br><span>the surprising structural diversity of this library. They also show how</span><br><span>NMR can be used to identify classes of sequences with distinct</span><br><span>mutational signatures and functions.</span></p> <p><span>Link to journal article: <a href="https://doi.org/10.1002/chem.202401437"><span>https://doi.org/10.1002/chem.202401437</span></a></span></p>
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
Structural Diversity from the NEON Discrete-Return LiDAR Point Cloud in 2013-2022
Structural diversity, characterizing the volumetric capacity and physical arrangement of biotic components in an ecosystem, controls critical ecosystem functions like light interception, hydrology, and microclimate. This product generates structural diversity metrics for the NEON sites, sourced from the Discrete-Return LiDAR Point Cloud from the NEON Aerial Observation Platform (DP1.30003.001; collected in March 2023). Using R programming, we computed the metrics detailing height, heterogeneity, and density at 30 m, aligned to the Landsat grids, for 243 site years in 57 NEON sites from 2013 to 2022.
Compiled database, code and raw data for the article "A Comprehensive Database of Leaf Temperature, Water, and CO2 Fluxes in Young Oil Palm Plants Across Diverse Climate Scenarios for the Evaluation of Functional-Structural Models"
<p>This dataset results from an experiment on young oil palm plants (<em>Elaeis guineensis</em>) in the Ecotron facility from CNRS in Montpellier. Four plants were put in a microcosm one by one with varying climatic conditions to investigate the effect of climate on leaf temperature, CO2, and H2O fluxes at the plant scale. The conditions were defined based on typical daily conditions from a location where it is grown (Libo, Indonesia), <em>i.e.</em>, a day with no rainfall and near-average air temperature and humidity. This base condition was then modified by adding more CO2 (400, 600 and 800ppm), less radiation (typical cloudy sky), and more or less temperature and vapour pressure deficit (± 30%).</p> <p>Find more details from the <code>README.md</code> file in the repository or from the associated <a href="https://github.com/PalmStudio/Biophysics_database_palm" target="_blank" rel="noopener">Github repository</a>.</p>
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates
<p>Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates".</p> <p>Preprint available here: <a href="https://doi.org/10.22541/au.167085544.47638352/v1">10.22541/au.167085544.47638352/v1</a></p> <p>Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip</p> <p>Scripts used to generate pipeline outputs as well as other aspects of the final article are available at <a href="https://github.com/thomasdotter/spineless-haplotypes">https://github.com/thomasdotter/spineless-haplotypes</a>.</p> <p> </p>
Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers
<p>The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters. Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r<sup>2</sup> =0.2 and r<sup>2</sup>= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.</p>
Fig. 3 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 3. Haplotype network based on partial sequencing of the D-loop region (mtDNA) of 92 individuals of Brycon nattereri from the Laranjinha River. Circle sizes are pro- portional to haplotype frequency.
Fig. 6 in Community Structure and Undescribed Species Diversity in Non-Pollinating Fig Wasps Associated with the Strangler Fig Ficus petiolaris
Fig. 6. Phenotypic variation among the four species represented by the first two coordinate axes of a principal component analysis.Twelve morphological characters were analyzed (Table 3). A Mantel test of the multivariate morphological differences among species was highly significant (P <0.0001). In addition, LO1 shows further differentiation based on geography, with distinct clusters recovered for both Baja and Sonora samples.
Fig. 5. Bayesian skyline plots for three Idarnes species. X in Community Structure and Undescribed Species Diversity in Non-Pollinating Fig Wasps Associated with the Strangler Fig Ficus petiolaris
Fig. 5. Bayesian skyline plots for three Idarnes species. X-axes are in units of mutations per site, while y-axes are in units of effective population size scaled by mutation rate. LO1 shows sharp growth in population size, whereas SO1 and SO2 show a similar pattern of consistent population size through time with minimal growth. LO2 was not included as it contains two cryptic species reducing sample sizes too low for analysis.
Fig. 2. A in Community Structure and Undescribed Species Diversity in Non-Pollinating Fig Wasps Associated with the Strangler Fig Ficus petiolaris
Fig. 2. A habitus drawing of an Idarnes wasp. The drawing represents a wasp from the LO1 species associated with host Ficus petiolaris. Illustrated are the 12 morphological characters measured for analysis.The characters are as follows: 1) presence of antennal setulae, 2) number of antennal segments, 3) scape length, 4) scape color (amber vs dark), 5) head width, 6) inter-antennal distance, 7) facial width, 8) collar length, 9) stigmal vein length, 10) femur color (amber vs dark), 11) body length, and 12) ovipositor length.
Fig. 3 in Community Structure and Undescribed Species Diversity in Non-Pollinating Fig Wasps Associated with the Strangler Fig Ficus petiolaris
Fig. 3. Maximum-clade credibility tree for Idarnes mtDNA sequences from wasps associated with Ficus petiolaris. Four distinct clades (LO1, SO1, LO2, SO2) each with a posterior probability of 1.0 were recovered.There is little information in the data as to how these four clades are related. Posterior probabilities ≥0.50 are presented.Taxon names are composed of clade name, locality number, and internal lab numbers. In addition, LO1 sequences show phylogeographic structure, with sequences primarily clustering based on if sampled from Baja California (BC) or Sonora (S). One sequence (denoted with black box) is an exception, where the wasp was sampled from Sonora (locale 12; see Fig. 1) yet clusters with Baja California sequences.
Dataset for "Structural diversity with varying disorder enables the multicolored display in the longhorn beetle Sulawesiella rafaelae"
<p><strong>Dataset for</strong> "Structural diversity with varying disorder enables the multicolored display in the longhorn beetle <em>Sulawesiella rafaelae</em>"</p> <p>The data is arranged into a .zip folder, containing the following files (.txt, .tif, jpg files). This data and the descriptions below should be read in conjunction with the manuscript and “Supporting Info”, both of which may be found on the <em>iScience</em> homepage.</p> <p>Doi: https://doi.org/10.1016/j.isci.2020.101339</p>
Research data supporting "Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils"
<p>Research data supporting the publication:</p> <p>Wang, S.-T. et al., 2017, Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils, ACS Nano, http://dx.doi.org/10.1021/acsnano.7b02325</p>
FIGURE 7 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 7. Boxplot of Tukey HSD test illustrating three major length types (a–c) of single folded sperm packages in Scorpiones. Representatives of the three groups in boldface (see text).
Figure 3 in Diversity and community structure of oribatid mites (Acari: Oribatida) in the dominant habitats of Machakhela National Park (Georgia, Caucasus)
Figure 3. The results of the cluster analysis of the different forest habitats in Machakhela National Park.
Figure 1 in Diversity and community structure of oribatid mites (Acari: Oribatida) in the dominant habitats of Machakhela National Park (Georgia, Caucasus)
Figure 1. Distribution of the sites of the sample collection of the oribatid mite diversity in the Machakhela National Park.
Supplemental data for: Structural polymorphism and diversity of human segmental duplications
<p>Data used for figure generation and analysis in: Structural polymorphism and diversity of human segmental duplications</p> <p> </p> <p>Code used for data analysis is on https://github.com/hrrsjeong/pangenome_SD</p>
FIGURE 3 in Species diversity and community structure of fruit-feeding butterflies (Lepidoptera: Nymphalidae) in an eastern amazonian forest
FIGURE 3: Whittaker plot (rank-abundance distribution) for the total sample of fruit-feeding butterflies in an eastern Amazonian forest. The y axis represents species abundance and the x axis ranks each species in order from most to least abundant.
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