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480 results for “spatial structure”

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dryad36/100

Spatial and local environmental factors outperform geo-climatic gradients in structuring taxonomically- and traits-based β‐diversity of benthic algae

Aim: Understanding the variation in biodiversity and its underlying drivers and mechanisms is a core task in biogeography and ecology. In this study, we examined: i) the relative contributions of species replacement (i.e. turnover) and richness difference (i.e. nestedness) to taxonomically- and traits-based β-diversity of stream benthic algae; ii) whether these two facets of β-diversity are correlated with each other; and iii) the relative contributions of local environmental (e.g. water chemistry, flow velocity, habitat quality), geo-climatic (e.g. land use types, elevation, precipitation), and spatial factors (e.g. using principal coordinates of neighborhood matrices) to the two facets of β-diversity and their components (i.e. total β-diversity, turnover, and nestedness). Location: Hun-Tai River Basin, northeastern China Taxon: Stream benthic algae Methods: A total of 157 sites were sampled. Mantel tests were used to examine the complementarities between the two facets of β-diversity and their components. Distance-based redundancy analysis and variation partitioning were utilized to investigate the relative contributions of local environmental, geo-climatic, and spatial factors to each facet of β-diversity and their components. Results: Weak correlations between taxonomically- and traits-based β‐diversity and their components were detected, which indicated complementarity of ecological information. Taxonomically-based total β‐diversity was largely driven by turnover, whereas traits-based total β-diversity was more driven by nestedness. Variation partitioning results indicated that local environmental and spatial factors contributed more than geo-climatic variables to the total explained variation in taxonomically- and traits-based β‐diversity. Main conclusions: Our findings highlighted the importance of the different facets of β‐diversity and their decomposition for understanding diversity patterns of benthic algae relative to abiotic factors. A high level of traits-based convergence among benthic algae communities, despite high taxonomic divergence, demonstrated turnover of species with similar biological traits across our study region. Our study provides a traits-based insight into stream benthic algae communities, which was less documented by previous freshwater studies that focused on regions undergoing recovery following human disturbances.

opencc-zeroFeb 2022View details →

dryad36/100

Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States

The southern pine beetle, Dendroctonus frontalis, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of D. frontalis individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for D. frontalis, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion dynamics in this species using alternate approaches.

opencc-zeroJul 2021View details →

dryad36/100

Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm

Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine-scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large-seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent-mediated seed dispersal has a stronger influence than insect-mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large-seeded plants. Rodent-mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity.

opencc-zeroOct 2022View details →

zenodo36/100

Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America : Dataset

This dataset is linked to the paper “Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America" published in Geoscientific Model Development (https://doi.org/10.5194/gmd-16-1661-2023). It contains the installer of the model, its user guide, as well as all the input files (inventory, thinning, meteorology and soil horizons files for each stand used in the evaluation and calibration steps), the R scripts and associated data used to analyse the model outputs.

opencc-by-4.0Oct 2022View details →

dryad36/100

Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus

Staphylococcus aureus uses quorum sensing and nutrient availability to control the expression of agr-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at high concentration, reduces expression of surface attachment proteins (coa, fnbpA), and increases expression of exotoxins (lukS) and proteases (splA). Nutrient availability can be sensed through the saeS/saeR system. Low nutrients increase expression of saeR, which augments expression of coa and fnbpA distinct from AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. This may impact quorum sensing and/or nutrient acquisition, and thus affect the expression of agr-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of S. aureus using a physical force affects the expression of agr-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of coa, fnbpA, lukS, and splA. Disturbance into a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of coa and fnbpA but increased expression of lukS and splA. Interestingly, at an intermediate amplitude, the overall expression of agr-regulated virulence factors was the lowest; expression of lukS and splA remained unchanged relative to an undisturbed biofilm while expression of coa and fnbpA significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to disturbance.

opencc-zeroJan 2023View details →

dryad36/100

Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing (PSK) systems to coexist

To persist a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if it has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do. Accordingly, plasmids with PSK systems can displace other plasmids. In nature, plasmids with and without PSK systems coexist and prior theory has suggested this is expected to be very rare or unstable, such that one or the other type of plasmid eventually takes over. Here, we show that if there is spatial structure and plasmids confer benefits to hosts, coexistence of plasmids occurs broadly. Often plasmids confer benefits (even ones with a PSK system) and bacteria are often spatially structured. So, our results may be generally applicable.

opencc-zeroJan 2023View details →

dryad36/100

Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass

This raw data set contains multilocus genotypes for 1,312 individual samples from 44 locations. Aim: Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterise intraspecific genetic diversity and its spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Location: Temperate Australian coastal waters Methods: Predictive modelling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Results: Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognised biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional bioregions. Clonal diversity was highly variable, but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Main conclusions: Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonisation of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.

opencc-zeroMar 2023View details →

zenodo36/100

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas"

Table 1. CCF Specimen, Biological Structure, and Spatial Ontology. For each ontology, we provide all class names, property names, entity Internationalized Resource Identifier (IRI), definition when available, and entity type. Table 2. 3D Reference Objects. The 3rd HRA release features 53 Spatial Entities of type Spatial Object Reference that are linked to anatomical structures in the ASCT+B tables plus 43 Spatial Entities of type Extraction Site. For each entity, we provide the spatial entity name, 3D object file name, ID and version number, organ label, sex, and type. Note that a landmark is a Spatial Entity that has been tagged as an Extraction Set for a specific Extraction Site, see Table 3. Table 3. Registered Tissue Data. This table shows 364 Extraction Site entities that either represent the registration location for Tissue Blocks or Registration Sites. For each, we provide consortium name and entity ID, HuBMAP ID if available, and experimental data donor sex as well as HRA data such as organ name, sex, Uberon ID, and GLB file. The data comes from four consortia. HuBMAP data includes 306 tissue blocks, and many of these have derived tissue sections with one or more associated datasets. The 29 well-defined GTEx extraction set sites link to 5,397 datasets. The 26 SPARC blocks link to one paper while the three KPMP tissue blocks link to two data publications.

opencc-by-4.0Sep 2022View details →

zenodo36/100

Figure 5 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan

Figure 5. Spatial distribution of snow leopards in the Sarychat–Ertash Reserve.

opencc-by-4.0Jul 2020View details →

zenodo36/100

Datasets for "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents"

Datasets used in the manuscript titled, "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents" are uploaded here.  Brightfield and fluorescent stained images of brain tissue used for Fig. 5(a): Malt3-20190624_Region 009_DAPI.png Malt3-20190624_Region 009_qCy5.png Malt3-20190624_Region 009_qFITC.png Malt3-20190624_Region 009_qTexasRed.png Malt3_BF20190628_Region 001.png Fluorescent image of brain with embedded CFETs: MALT2_Rat_100um_MOR1_x500_TSA_AF488.jpg Rat_100um_MOR1_x500_TSA.czi In vivo dopamine recording data for Fig. 3: ratarrays822_163.mat ratarrays822_57.mat

opencc-by-4.0Apr 2023View details →

dryad36/100

Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.

opencc-zeroJul 2023View details →

zenodo36/100

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"   compressed FASTA files for 16s amplicon sequences relating to two separate projects,  "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities" and "Habitat filtering leads to phylogenetic clustering in synthetic microbial communities". DADA22 pipeline is included, which pools all samples for better accuracy. A Julia script bioinfo.jl is then used to select only the samples relevant to spatial structure project.   All csv filenames are appended with "_q" indicating an increase in the stringency of quality filtering parameters (also increasing minimum hamming distance used in DADA2 algorithm to 5) to produce a taxa table with a sensible number of ASVs (given a known number of input strains) with each ASV uniquely aligning to an individual sequence from colony PCR of said input strains.

opencc-by-4.0May 2023View details →

dryad36/100

Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms – a process which involves both the domestication and the transfer of lumpfish between geographic regions. Here, we have 70K SNP array data and whole genome re-sequencing data (WGS) for a variety of sample sites across the Northwest Atlantic.

opencc-zeroSep 2023View details →

dryad36/100