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1,598 results for “genetic diversity”
Soil requirements, genetic diversity and population history of the Juniperus sabina L. varieties in Europe and Asia
<p>Dataset comprises genotypes of 335 individuals of J. sabina. </p>
Figure 6 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 6: Haplotype network of 11 haplotypes of Halymenia malaysiana and their distribution. Haplotype names are written beside the circles. Each cross in the lines between two haplotypes is a single mutation. The data were processed by PopART software.
Figure 4 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 4: Maximum likelihood phylogenetic tree inferred from the alignment of ITS1 sequences. Support values are shown as in Figure 3. The ribotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Alaria esculenta was used as an outgroup to root the tree. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site).
Figure 5 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 5: Distribution of haplotypes of Halymenia malaysiana in Sunda Shelf (Malaysia and Viet Nam) and the Philippines. 11 haplotypes (R1–R11) are defined by different colors. Sites 1–9 (S1–S9) were defined by Tan et al. (2018a). S10 is defined in this study. Dotted line represents the border of the Sunda Shelf. The data were processed by PopART software.
Figure 3 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 3: Maximum likelihood phylogenetic tree inferred from the alignment of the combined cox3 and tatC–tLeu sequences. Bootstrap values and Bayesian posterior probabilities>50% are shown, and "-" indicates a value <50%. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site). Refer to Uwai et al. (2006a) for explanation of the haplotype names and classification of the clades I to IV. The haplotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Lessoniopsis littoralis was used as an outgroup to root the tree.
Figure 4 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 4: Halymenia malaysiana from Viet Nam (CDNT-H15) showing cystocarp development. (A) Auxiliary cell and ampullar filaments (white arrowheads). (B) Young cystocarp showing auxiliary cell and medullary filaments (black arrowheads). (C–E) Development of other young cystocarps showing a basal fusion cell, gonimoblast initial (black arrow) and gonimolobe enveloped by elongated ampullar filaments and secondary medullary filaments. (F) Mature cystocarp showing gonimoblast initial (gi, black arrow), basal fusion cell (fc), and gonimolobe (g). Scale bars = 20 µm; aux, auxiliary cell; g, gonimolobe; gi, gonimoblast initial; fc, fusion cell.
Figure 3 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 3: Halymenia malaysiana from Viet Nam showing habit and vegetative morphology. (A) Thallus in Van Phong Bay (VPKH-H2). (B) Herbarium voucher specimen CDNT-H15 collected at Nha Trang Bay. (C) Cross section through middle part of a young blade showing densely arranged cortical cells and sparse. loosely arranged, filamentous medullary cells of CDNT-H15. (D) Magnification of cortex layers from (C). (E) Anomalous refractive ganglionic cell (arrow) with 6 arms from CDNT-H15. Scale bars in (C–E) = 20 µm.
Figure 2 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 2: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of ITS1 sequences. The color areas in the pie charts are proportional to the ribotype frequency in the map. Small circles indicate undetected ribotypes. Each line connecting ribotypes represents one base mutation. The ribotypes detected in the Chinese samples in the present study are indicated in the ribotype network by the same colors as those in the map.
Figure 1 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences
Figure 1: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of the combined cox3 and tatC–tLeu sequences. The color areas in the pie charts are proportional to the haplotype frequency in the map. Refer to Uwai et al. (2006a) and Table 3 for explanation of the haplotype names and classification of the clades I to IV, which are enclosed by boxes with lines of different patterns. Small circles indicate undetected haplotypes. Each line connecting haplotypes represents one base mutation. The haplotypes detected in the Chinese samples in the present study are indicated in the haplotype network with the same colors as those in the map.
Figure 2 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 2: Phylogeny of members of Halymenia inferred from maximum likelihood and Bayesian inference. Data set based on 1207 bp of partial rbcL. Bootstrap values and posterior probability of each method are shown at each node: (left) maximum likelihood/(right) Bayesian inference; *, full support (bootstrap value = 100%, posterior probability = 1.0); -, bootstrap value <50%. Numbers before countries are GenBank accession numbers. In bold face, samples collected in Viet Nam. See Supplementary Table S1 for more information on each taxon.
Figure 1 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific
Figure 1: Map of Viet Nam coast and sampling sites (arrows). See Supplementary Table S1 for more information.
Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions
<p><em><strong>Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions</strong></em></p> <p> </p> <p>Tools and scripts were used to generate results in Zhang et al 2024.</p> <p>Supplementary files that were not included in the initial submission.</p> <p>Full summary statistics of eQTLs including top eQTLs and all SNP-gene pairs of each cell type, consistent.tar.gz for consistent eQTLs per cell and response.tar.gz for response eQTLs, respectively.</p>
Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.
<p>This database contains the coordinates of individuals of <em>Aechmea mariae-reginae</em> and <em>Werauhia ampla</em> in phorophytic trees and the genotypes for 8 microsatellite loci.</p>
Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations
<p>With the two-fold cost of sex, derived asexual organisms have an immediate reproductive advantage over their sexual sisters. Yet the "twiggy'' phylogenetic distribution of asexual lineages implies that they go extinct relatively quickly over evolutionary time. Meanwhile, bacteria and archaea have persisted for billions of years without requiring sexual reproduction. A simple explanation for this difference is that prokaryotes have very large population sizes that are not subject to the accumulation of deleterious mutations, but this implies that drift and mutational meltdown dominate derived asexual populations. </p> <p>We explored a different hazard, quantifying the degree to which genetic variation is lost in asexual populations experiencing selective sweeps. Even though large populations generate diversity by mutation during sweeps, we find that populations that are safe from mutational meltdown may still be reduced to dangerous effective population sizes by sweeps. Thus, ironically, adaptation itself reduces further adaptive potential and may predispose asexual populations to extinction. Our data give results for the probability of mutational meltdown across various population sizes, the critical population size required to avoid meltdown, and the effect of selective sweeps on heterozygosity. Analytical predictions are confirmed by simulation.</p> <p>We also derive a simple approximation for the effective population size after a hard sweep, and quantify the impact of recent sweeps on evolutionary rescue. These factors may help to explain the phylogenetic twigginess of asexuals, the maintenance of sex and recombination, and the evolutionary persistence of prokaryotes.</p>
Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA
<p>The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching, and fragmentation. Here we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186bp and cytochrome b 487bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared to the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126,cytochrome b 0.0528) and high FST statistics (D-loop 0.725,cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.</p>
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant
<p><span>Anthropogenic environmental change threatens many species and can be especially challenging for rare species given their potentially limited capacity for migration and adaptation relative to more common species.</span> The ability to acclimate via phenotypic plasticity could provide an important path to persistence, especially for rare species. We investigated the responses of an endangered plant species endemic to a highly dynamic riparian habitat in southeastern Tennessee, USA, and its most widespread congener to environmental change to elucidate their current statuses and future vulnerability. Specifically, we compared the population- and species-level plasticity of rare <i>Pityopsis ruthii</i> and common <i>P. graminifolia </i>to contrasting light, temperature, and water conditions in a growth chamber experiment to evaluate their potential to acclimate to environmental change. Contrary to our expectations, <i>P. ruthii</i> had greater phenotypic plasticity than its common congener in response to both altered light and water availability. But this plasticity was not associated with increased fitness, suggesting that it was not adaptive. Concurrently, we genotyped these individuals at nine putatively neutral microsatellite loci to contrast genetic diversity across the range of each species. As expected, <i>P. ruthii </i>exhibited reduced genetic diversity relative to its more common congener. Overall, our findings accord with the narrow range and current habitat specificity of <i>P. ruthii</i>, especially its tolerance of highly variable water, and highlight its potential vulnerability to future environmental change.</p>
Genetic diversity, differentiation and historical origin of the isolated population of rooksCorvus frugilegusin Iberia
<p>Current bird populations in southern temperate latitudes often represent relicts of glacial refugia from which northern populations expanded as the climate became suitable following the last glacial maximum, 18 000 years before present. Alternatively, these southern populations could be the result of the fragmentation of large distributions and other processes not related to glaciations, like recent recolonization from northern populations and human impact in historical times. Here, we investigate the origin of a small, isolated population of rooks Corvus frugilegus in north-western Iberia. We use genetic data from mitochondrial sequence markers and seven microsatellite loci to assess levels of genetic diversity, structure and gene flow among extant populations in Iberia and its broad distribution across western Europe. Microsatellite markers revealed the existence of two genetic clusters corresponding to Iberia and the remaining European populations, respectively. Haplotype networks based on mtDNA markers revealed a marked star-like phylogenetic pattern and evidence of a recent population expansion in northern Europe, but not in the Iberian population. Our results suggest that contemporary gene flow between Iberia and western Europe is restricted, and that breeding recruitment over recent generations in the Iberian population is local. The results are consistent with a relatively recent post-glacial colonization of Europe and western Siberia by rooks surviving the last glacial maximum in an Iberian refugium, and likely from refugia in other southern peninsulas. The unique ecological features and genetic differentiation of the Iberian rooks underscore the importance of ensuring the long-term conservation of this declining population.</p>
Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China
Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica as one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (NST > GST, p > 0.05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plots (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period, and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.
Linking genetic diversity and species diversity through plant-soil feedback
<p>Genetic diversity and species diversity are typically studied in isolation despite theory showing they likely influence one another. Here, we used simplified communities of one or two populations of one or two species to test whether linkages between genetic and species diversity can be mediated by interactions between plants and their soil microbiota, or microbe-mediated plant-soil feedback (PSF). Interspecific PSF promotes the maintenance of species diversity when plants grow better with heterospecific soil microbes than with conspecific microbes. Similarly, intraspecific PSF promotes the maintenance of genetic diversity when plants grow better with heterogenotypic than with congenotypic microbes. In a two-generation greenhouse experiment, we conditioned the soil microbial community with pairs of plants that were either two individuals of the same species (lower species diversity) or one individual of each of two species (higher species diversity), and with pairs of plants that were either two individuals from the same population (lower genetic diversity) or one individual from each of two populations (higher genetic diversity). We then tested the effects of these microbial communities on plant growth in a second generation. We found that higher genetic diversity reduced the ability of interspecific PSF to promote plant species diversity, and for one of our two study species, higher species diversity reduced the ability of intraspecific PSF to promote plant genetic diversity. If these patterns occur in more diverse communities, then our results suggest that PSF may dampen the negative effects of diversity loss by promoting diversity at other levels of biological organization.</p>
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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)
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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.