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66 results for “clonal populations”
Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs
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Data from: Twelve years of repeated wild hog activity promotes population maintenance of an invasive clonal plant in a coastal dune ecosystem
Invasive animals can facilitate the success of invasive plant populations through disturbance. We examined the relationship between the repeated foraging disturbance of an invasive animal and the population maintenance of an invasive plant in a coastal dune ecosystem. We hypothesized that feral wild hog (Sus scrofa) populations repeatedly utilized tubers of the clonal perennial, yellow nutsedge (Cyperus esculentus) as a food source and evaluated whether hog activity promoted the long-term maintenance of yellow nutsedge populations on St. Catherine's Island, Georgia, United States. Using generalized linear mixed models, we tested the effect of wild hog disturbance on permanent sites for yellow nutsedge culm density, tuber density, and percent cover of native plant species over a 12-year period. We found that disturbance plots had a higher number of culms and tubers and a lower percentage of native live plant cover than undisturbed control plots. Wild hogs redisturbed the disturbed plots approximately every 5 years. Our research provides demographic evidence that repeated foraging disturbances by an invasive animal promote the long-term population maintenance of an invasive clonal plant. Opportunistic facultative interactions such as we demonstrate in this study are likely to become more commonplace as greater numbers of introduced species are integrated into ecological communities around the world.
Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when occurring. Tested under various conditions, this model provided accurate inferences of c, especially when the amount of information was modest, i.e. low sample sizes, few loci, low polymorphism and strong linkage disequilibrium. Inferences remained robust when mutation models and rates were misinformed. However, the method was sensitive to moderate frequencies of null alleles and when the time interval between required samplings exceeding two generations. Misinformed rates on mating modes (inbreeding and selfing) also resulted in biased inferences. Our method was tested on eleven datasets covering five partially clonal species, for which the extent of clonality was formerly deciphered. It delivered highly consistent results with previous information on the biology of those species. ClonEstiMate represents a powerful tool for detecting and inferring clonality in finite populations, genotyped with SNPs or microsatellites. It is freely available at http://https://w">https://w w w 6.rennes.inra.fr / igepp_eng/ Productions/ Software.
Data from: Clonality, genetic diversity, and support for the diversifying selection hypothesis, in natural populations of a flower-living yeast
Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights on the ecological and genetic correlates of clonality, and on the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using AFLP markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by AMOVA (Φst = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparths to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality.
Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands
Field elm (Ulmus minor) is a riparian tree that grows in rare, small populations scattered along temporary watercourses in the Balearic Islands, nowadays mostly covered with Mediterranean vegetation. Agriculture and farming on the fertile land along the periodically flooded plains have reduced the elm populations to sparse tree lines along the creek beds. The presence of field elm in this very anthropic landscape has led some authors to consider it as an introduced species in the Balearics. However, pollen data suggest these elms may be the remains of larger populations experiencing continuous population shrinkage during the Holocene, and hence be native to the isles. In this paper, we apply genetic markers to assess whether field elm is or is not indigenous to the Balearic Islands. We compare the genetic variation in nine nuclear microsatellites of six Balearic populations (three in each of the largest islands, Majorca and Minorca) with that of three natural Iberian populations located in two regions, one geologically (Baetic mountains, SE Iberia) and another historically (Catalonia, NE Iberia) related to the islands. Principal coordinates analysis and Bayesian clustering methods reveal a strong genetic differentiation of the Balearic populations from the Iberian ones, and even among islands, which support their native origin. Genotypic variation in the islands is very low and clonal reproduction is very high compared with the mainland, as it is frequently observed in populations of clonal species where sexual reproduction is limited. We discuss the practical implications of these findings for the conservation of elm genetic resources of these findings.
Increased spatial-genetic structure in a population of the clonal aquatic plant Sagittaria latifolia (Alismataceae) following disturbance
<p>The spatial genetic structure (SGS) of plant populations is determined by the outcome of key ecological processes, including pollen and seed dispersal, the intensity of local resource competition among newly recruited plants, and patterns of mortality among established plants. Changes in the magnitude of SGS over time can provide insights into the operation of these processes. We measured SGS in a population of the clonal aquatic plant, <i>Sagittaria latifolia</i> that had been disturbed by flooding, both before and after the flood. . Over the four-year interval between measurements, we found substantial changes in the magnitude of SGS. In the first measurement (pre-flood), SGS was weak, even over short distances. By contrast, there was substantial SGS in the second measurement (post-flood), particularly over short distances. This change in SGS was accompanied by near complete turnover in the genotypic composition of the population. The genotypic richness of the population (the number of unique clones scaled by the sample size) was halved over the four-year interval. The clonal subrange – the distances between shoots within clones – also shrank considerably, with more than 5% of shoots having clone-mates at distances greater than 10 m before the flood, but fewer than 5% of shoots having clone-mates at distances beyond 2 m afterwards. Clonal turnover and the re-establishment of SGS in clonal populations are both expected following local extirpation and recruitment. These data reveal the genetic signatures of disturbance and a subsequent flush of seedling recruitment and subsequent clonal expansion.</p>
Contrasting clonal and population genetic structure in two endangered Costa Rican Vanilla species of commercial interest
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High clonal propagation and low population connectivity in the holothurian Stichopus chloronotus from the Indo-Pacific (Dataset)
<p>Genetic dataset associated to "High clonal propagation and low population connectivity in the holothurian <em>Stichopus chloronotus</em> from the Indo-Pacific" article published in Marine Biology (2019)</p>
Characterization of Clonal B Cell Populations in HCV Infection
ClinicalTrials.gov study NCT00435201. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Data from: Twelve years of repeated wild hog activity promotes population maintenance of an invasive clonal plant in a coastal dune ecosystem
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Data from: Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina
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Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
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Data from: A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae)
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Data from: Genetic variation and clonal diversity in introduced populations of Mimulus guttatus assessed by genotyping at 62 single nucleotide polymorphism loci
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Data from: Clonality, genetic diversity, and support for the diversifying selection hypothesis, in natural populations of a flower-living yeast
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Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands
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Increased spatial-genetic structure in a population of the clonal aquatic plant Sagittaria latifolia (Alismataceae) following disturbance
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Data from: Correlated responses to clonal selection in populations of Daphnia pulicaria: mechanisms of genetic correlation and the creative power of sex
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Data from: Mating system and genetic structure across all known populations of Dyckia brevifolia: a clonal, endemic and endangered rheophyte bromeliad
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Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes
Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (1) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (2) in dioecious populations, male clones are larger and flower more often than female clones because of sex-differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet- and genet-based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in eastern N. America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations there was no difference in clone size between females and males; ramet- and genet-based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.
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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.