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1,659 results for “Population: structure”
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
<p><strong>PREMISE</strong>: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function.</p> <p><strong>METHODS</strong>: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass <em>Leymus chinensis</em>. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.</p> <p><strong>RESULTS</strong>: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.</p> <p><strong>CONCLUSIONS</strong>: We found strong genetic structure among patches of <em>L. chinensis</em>. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.</p>
Data from: Drastic shift in flowering phenology of F1 hybrids explains the population structure of Imperata cylindrica in Japan
<p>Hybridization is a major source of phenotypic variation and a driving force for evolution. On the other hand, these novel traits can often disrupt adaptive relationships between the parental phenotypes and their environments. However, it remains unclear how new hybrid traits disrupt local adaptation. Here, we report how a new phenotype of hybrids between two ecotypes of Imperata cylindrica contributes to rapid reproductive isolation from their parents and affects hybrid fitness.</p> <p>We analyzed 350 accessions of I. cylindrica collected from the 1980s to the 2010s throughout Japan to explore the genetic population structure of the hybrids. We surveyed flowering periods, seed sets, and germination of two ecotypes and their hybrids in both natural habitats and common gardens.</p> <p>Genetic analyses of population structure revealed that the hybrid populations consisted of only F1 individuals, without post-F1 hybrids. The flowering phenology of the F1 plants was delayed to autumn, 5–6 months later than the parental ecotypes.</p> <p>The drastic shift in flowering phenology prevents F1s from backcrossing. In addition, it changes their seed dispersal time to winter. Germination is inhibited by low temperatures, and the seeds likely decay before the next spring, resulting in the absence of an F2 generation. For the first time in the field, we found environmental mismatch of F1 as a specific mechanism for the maintenance of only F1 populations.</p> <p>Synthesis. We have demonstrated that this flowering phenology mismatch promotes reproductive isolation between the parents and F1s and affects various temporal components of the hybrids, resulting in a unique hybrid population consisting only of F1s. This system sheds light on the importance of hybrid traits in terms of rapid reproductive isolation.</p>
Fig. 2 in Population Densities And Community Structure Of Birds Breeding In A Suburban Wooded Grassland In The Highveld Of Lesotho
Fig. 2. Numbers (right axis; dot or square signs) of species (A), all breeding pairs (B), and breeding pairs of selected bird species (C: Ss — Streptopelia senegalensis, Sc — Streptopelia capicola; D: RwS — Onychognathus morio, ES — Sturnus vulgaris; E — Passer griseus; F — Ploceus velatus; G — Columba guinea, H — Lanius collaris) in relation to the rainfall (columns; in mm per annum; left axis).
Fig. 2 in Population Structure Of Ungulates In Waterberg National Park, Namibia
Fig. 2. Location of Waterberg N. P., the different vegetation types and the distribution of the seven (7) water holes in the park (Jankowitz, 1983).
Fig. 4 in Population Structure Of Ungulates In Waterberg National Park, Namibia
Fig. 4. Herd size and number of herds of White and Black Rhino based on water point census only in Waterberg Plateau Park.
Fig. 1 in Population Structure Of Ungulates In Waterberg National Park, Namibia
Fig. 1. Rainfall in the Waterberg N. P. for the years 1980 to 2017 (Sasscalweathernet.org/station_datasheet_ we.php).
Fig. 6 in Population Structure Of Ungulates In Waterberg National Park, Namibia
Fig. 6. Year to year changes in age structure (adults: black bar, Juveniles: grey bars) in ungulates in the Waterberg Plateau Park in 2008–2013, based on water point census.
Fig. 5 in Population Structure Of Ungulates In Waterberg National Park, Namibia
Fig. 5. Year to year changes in the proportion of sex (males: black bar, females: grey bars) in ungulates in the Waterberg Plateau Park in 2008–2013, based on water point census.
Fig. 2 in Species Structure Of Oribatid Mite Population (Acari, Oribatea) In The Forest Floor Litter In The Reclaimed Territories (Ukraine)
Fig. 2. Stratigraphic types of artificial edaphotopes within the experimental-production reclamation site.
Fig. 1 in Species Structure Of Oribatid Mite Population (Acari, Oribatea) In The Forest Floor Litter In The Reclaimed Territories (Ukraine)
Fig. 1. Location of the Western Donbas coal basin in the Dnipropetrovsk Region, Ukraine: WD — Western Donbas.
Fig. 6 in Species Structure Of Oribatid Mite Population (Acari, Oribatea) In The Forest Floor Litter In The Reclaimed Territories (Ukraine)
Fig. 6. Average population density and species richness of oribatid mites on different recultivation types within red cedar plantation.
T a b l e 2 in Species Structure Of Oribatid Mite Population (Acari, Oribatea) In The Forest Floor Litter In The Reclaimed Territories (Ukraine)
T a b l e 2. Species structure of oribatid mite population, collected from coniferous floor litter within red cedar plantation on the humified calcic chernozem layer with loess-like loam interlayer (3rd stratigraphic type)
Fig. 3 in Ornithological Fauna Of The Waste Water Treatment Plants In The Northern Left Bank Ukraine (Chernihiv And Kyiv Regions): Winter Populations And Ecological Structure
Fig. 3. Similarity clusters of bird populations' species composition in winter according to the water treatment facilities' biotopic zones: 1 — zone of water bodies; 2 — dam zone; 3 — technological zone 4 — meadows agricultural zone.
IGM Population of HFF structures using Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE data
<p>This repository accompanies the manuscript "<strong>Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations</strong>", to appear in Nat. Methods (2022), see also https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1.</p> <p>It contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE) for the HFF fibroblast cell line to be used in the Integrative Genome Modeling platform (IGM) developed in the Alber lab at UCLA (https://github.com/alberlab/igm).</p> <p>Also, we provide the configuration file to run IGM with those datasets, as we did in generating the HDSF population discussed in the accompanying manuscript. Such population is also provided as an "hss" file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @ https://github.com/alberlab/igm.</p> <p>All files can be read in using the <em>h5py</em> and <em>alabtools</em> (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file. </p> <p>For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna (bonimba@g.ucla.edu) or Dr. Frank Alber (falber@g.ucla.edu).</p> <p> </p>
Population structure of the scleractinian coral, Montastraea cavernosa, in southeast Florida
The persistence of scleractinian coral populations on the Florida Reef Tract (FRT) is controlled in part by metapopulation dynamics and larval dispersal. Nine polymorphic microsatellite loci were analyzed to identify contemporary population structure and gene flow as well as historical migration rates of Montastraea cavernosa at five sites off Martin, Palm Beach, and Broward counties in southeast Florida. The sampled populations demonstrated evidence of genetic isolation by distance over a geographic range of 85 km. Population genetic structure was divided into two genetic clusters, northern and southern, with admixture along a latitudinal gradient. Historical migration models indicated likely panmixia throughout all sites sampled, identifying a potential reduction in connectivity among the sampled populations through time. Though M. cavernosa populations demonstrated evidence of historical connectivity, contemporary patterns of isolation by distance suggest that effective management will require localized actions to maximize the likelihood of sustaining individual populations in the northern FRT. Given the results of this study, coupled with recent coral mortality events in the region, we recommend regional conservation efforts and management initiatives throughout southeast Florida within a more comprehensive FRT-wide management network.
Generation time in stage-structured populations under fluctuating environments (Simulations)
<p>The study is about the computation of the generation time when individuals are classified based on their stage and the environment stochastically fluctuates with time. This folder contains simulation code in R to plot Figure 2 of the manuscript.</p>
Discordant population structure among rhizobium divided genomes and their legume hosts
<p>Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole-genome resequencing of a hierarchically-structured sample of 191 strains of <em>Sinorhizobium meliloti</em> collected from 21 locations in southern Europe to characterize the population structures of this bacterial symbiont and its host plant <em>Medicago truncatula</em>. <em>Sinorhizobium meliloti</em> genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.</p>
Рис. 2. Размерная структура G. lacustris в ΛитораΛьной зоне озера АрахΛей: 1 — июнь; 2 — август; 3 — октябрь Fig. 2. G. lacustris population size structure in the Lake Arakhley littoral zone: 1 — June, 2 — August, 3 — October in The life cycle of Gmelinoides fasciatus (Stebbing, 1899) and Gammarus lacustris (Sars, 1863) amphipods in the lake Arakhley littoral during the extreme low-water phase of the hydrological cycle
Рис. 2. Размерная структура G. lacustris в ΛитораΛьной зоне озера АрахΛей: 1 — июнь; 2 — август; 3 — октябрь Fig. 2. G. lacustris population size structure in the Lake Arakhley littoral zone: 1 — June, 2 — August, 3 — October
Рис. 1. Размерная структура Gm. fasciatus в ΛитораΛьной зоне озера АрахΛей: 1 — в июне; 2 — в августе; 3 — в октябре; 4 — в Αекабре 2017 г. и июне 2018 г. Fig. 1. Gm. fasciatus population size structure in the Lake Arakhley littoral zone: 1 — June; 2 — August; 3 — October; 4 — December, 2017 and June, 2018 in The life cycle of Gmelinoides fasciatus (Stebbing, 1899) and Gammarus lacustris (Sars, 1863) amphipods in the lake Arakhley littoral during the extreme low-water phase of the hydrological cycle
Рис. 1. Размерная структура Gm. fasciatus в ΛитораΛьной зоне озера АрахΛей: 1 — в июне; 2 — в августе; 3 — в октябре; 4 — в Αекабре 2017 г. и июне 2018 г. Fig. 1. Gm. fasciatus population size structure in the Lake Arakhley littoral zone: 1 — June; 2 — August; 3 — October; 4 — December, 2017 and June, 2018
Рис. 4. Фотографии жиΛых гнезΑ в заказнике «Амурский» на искусственных гнезΑовых треногах (сΛева — «активное», справа — «засеΛенное») Fig. 4. Photos of inhabited nests in the Amursky wildlife reserve that are located on artificial nesting structures ("active" on the left and "inhabited" on the right) in Oriental stork (Ciconia boyciana Swinhoe) breeding population survey in the Amur region in 2018-2019
Рис. 4. Фотографии жиΛых гнезΑ в заказнике «Амурский» на искусственных гнезΑовых треногах (сΛева — «активное», справа — «засеΛенное») Fig. 4. Photos of inhabited nests in the Amursky wildlife reserve that are located on artificial nesting structures ("active" on the left and "inhabited" on the right)
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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.