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2,445 results for “Genetics: population”
Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations
<p>Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (<em>N</em> = 690) of the terrestrial orchid, <em>Epidendrum radicans</em>, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (<em>N</em> = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (<em>H<sub>e</sub></em> = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from <em>in</em> <em>situ</em> reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).</p>
Oenothera Section Calylophus population genetic study
<p><strong>Premise</strong>: Animal pollinators play an important role in pollen dispersal. Differences in foraging patterns, flight distances and grooming behaviors are assumed to have consequences for genetic diversity of plants but are rarely tested explicitly. Here, we assess the role of pollinator functional groups with different foraging behaviors (hawkmoth and bee) in generating patterns of genetic diversity over similar geographic ranges for two closely related taxa.</p> <p><strong>Methods</strong>: This study focuses on two members of <em>Oenothera</em> section <em>Calylophus</em> that co-occur on gypsum outcrops throughout the Chihuahua Desert but differ in floral phenotype and primary pollinator: <em>Oenothera</em> <em>gayleana</em> (bee) and <em>O</em>. <em>hartwegii</em> subsp. <em>filifolia</em> (hawkmoth). We measured breeding system and floral traits in the greenhouse and conducted a population genetic study at the local (<13km; four populations) and landscape (60–440km; five populations) scales using 10–11 nuclear (pollen dispersal) and three plastid (seed dispersal) microsatellite markers. </p> <p><strong>Key Results</strong>: Both taxa were self-incompatible and floral traits were consistent with expectations for different pollinators. We found no evidence of genetic structure at the local scale, but at the landscape scale, <em>O</em>. <em>gayleana</em> showed greater differentiation and significant isolation by distance than <em>O</em>. <em>hartwegii</em> subsp. <em>filifolia</em>. The plastid data were consistent with gravity dispersal of seeds and suggest that pollen dispersal is the principal driver of genetic structure in both species.</p> <p><strong>Conclusions</strong>: We demonstrate that pollinator functional groups can impact genetic differentiation in different and predictable ways. Hawkmoths, with larger foraging distances, can maintain gene flow across greater spatial scales than bees.</p>
Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars
<p>The VCF file contains the information of 1662 SNP sites of 820 cauliflower inbred lines that were filtered according to a series of stringent conditions.</p>
Figure 6. One chromosome from the population and the five chromosomes existing in the evaluation partition.-Genetic Algorithms Principles Towards Hidden Markov Model
<p>For example comparing the<br> chromosome given in Figure 6 with the first chromosome in the evaluation partition, the<br> difference between the relation Med-Med and Med-High as a pair is 0.0 and the difference<br> between the relation High-High and High-Med as a pair is 0.1. Similarly the difference between<br> the relation Med-Cold and Med-Hot as a pair is 0.1 and the difference between the relation<br> High-Cold and High-Hot as a pair is 0.2. We sum all these differences to get the value of<br> compare(i,j), the sum value is 0+0.1+0.1+0.2 = 0.4. Using the same approach we compute the<br> compare function with the other four chromosomes and we get values 0.4, 0.5,0.4 and 0.6. Now<br> we sum the five values 0.4 + 0.4 + 0.5+ 0.4 +0.6 = 2.3. The fitness value is then 1/ 2.3 = 0.434.<br> The highest is the fitness value, the better is the performance of the chromosome.</p>
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
<p>A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French <em>Arabidopsis thaliana</em> population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.</p>
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
<p>Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (<em>Pinus pinaster</em> Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.</p>
Fig. 2 in Genetic diversity of Egyptian populations of the African Common Toad (Sclerophrys regularis, Reuss 1833)
Fig. 2. Phylogenetic tree of African Common Toad, using COI haplotypes based on the Maximum Likelihood method. Numbers refer to localities mentioned in the text: 1. Sharm El-Shaikh; 2. Arish; 3. Ismailia; 4. Damietta; 5. Alexandria; 6. Matrouh; 7. Gharbiya; 8. Cairo; 9. SiwaOasis; 10. Bani Sweif; 11. Menia; 12. Sohag; 13. Qena; 14. Aswan.
Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)
<p>Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.</p> <p>We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow <em>Salix herbacea</em> L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.</p> <p>We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. </p> <p>Synthesis: Our results suggest that sex ratio bias in <em>S. herbacea</em> is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of <em>Salix</em> may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.</p>
Fig. 2 in Population Genetics Of Philaenus Spumarius On The Istranca Mountains: Ii. Polymorphism And Phenotype Frequency
Fig. 2. The chart for the combined four major phenotype categories of Philaenus spumarius showing the frequency distributions on the Istranca Mountains, Turkey. From left to right, three groups of bars blank, dotted hatched, and dark coloured bars of the diagrams indicate POP, TYP, TRI+VIT, and melanic (MAR+LAT+FLA+LCE). The height of the bar indicates the percentage (numbers are given at
Fig. 1 in Population Genetics Of Philaenus Spumarius On The Istranca Mountains: Ii. Polymorphism And Phenotype Frequency
Fig. 1. Dorsal colour/pattern phenotypes of Philaenus spumarius found on the Istranca Mountains, Turkey (abbreviations are described in the text)
Fig. 3 in Population Genetics Of Philaenus Spumarius On The Istranca Mountains: Ii. Polymorphism And Phenotype Frequency
Fig. 3. Combined phenotype frequency distributions of Philaenus spumarius for three types of habitat on the Istranca Mountains, Turkey. Separate diagrams for females and males denote the habitats from top to the bottom: Mixed, Oak, and Beech forests respectively. From left to right, the bars of the diagrams indicate; 1: POP, 2: TYP, 3: TRI+VIT, 4: MAR+LAT, 5: FLA+LCE. The height of the bar
Fig. 2 in Genetic Differentiation And Linkage Disequilibrium In A Spatially Fragmented Population Of Cheilosia Vernalis (Diptera: Syrphidae) From The Balkan Peninsula
Fig. 2. Standardized variance of allelic frequencies FST (open symbols) and genetic distance D (NEI 1978) (filled symbols) plotted against corresponding geographic distance between subpopulation pairs of Cheilosia vernalis: Durmitor-Morinj (75 km), Fruška Gora- Durmitor (240 km), and Fruška Gora-Morinj (306 km). Pearson correlation coefficients between geographic distance and FST and D
Fig. 1 in Genetic Differentiation And Linkage Disequilibrium In A Spatially Fragmented Population Of Cheilosia Vernalis (Diptera: Syrphidae) From The Balkan Peninsula
Fig. 1. Map of Serbia and Montenegro showing sampling sites for the studied subpopulations of Chelosia vernalis, and genotype distribution at the Pgm locus. The Pgm locus was the most variable locus in the surveyed subpopulations, and along with differences of allele frequency variances at the
Fig. 1 in Genetic Diversity In Peripheral And Central Populations Of Rusty-Necklaced Partridge (Alectoris Magna) Based On Mitochondrial And Microsatellite Dna
Fig. 1. Rusty-necklaced partridge sampling sites: 1 = Lanzhou, 2 = Jingyuan, 3 = Haiyuan, 4 = Dingxi, 5 = Huining, 6 = Wushan, 7 = Beidao, 8 = Lixian
Fig. 1 in On The Limit Of Altitudinal Range Shifts - Population Genetics Of Relict Butterfly Populations
Fig. 1. Neighbour-joining tree based on genetic distances (CAVALLI-SFORZA & EDWARDS 1967) performed on five microsatellite loci, representing the analysed populations of Scandinavia, Finland, eastern Europe (Poland, Lithuania, Romania) and the Vosges. Genetic distances are projected on a map. Solid lines display the genetic distance, arrows show the locations of the sampling sites. Data
Fig. 2 in On The Limit Of Altitudinal Range Shifts - Population Genetics Of Relict Butterfly Populations
Fig. 2. Allele frequency distributions of L. helle populations of the Pyrenees and the western low-altitude mountains (Massif Central, Vosges, Ardennes). The colours in the pie charts indicate the distribution of alleles (white: occurring in several mountain areas, black: exclusive to a single mountain area, grey: exclusively occurring in the respective population). Data taken from FINGER et al. (2009)
Fig.5 in Genetic And Morphological Variability Of Small Vendace (Coregonus Albula (Linnaeus, 1758)) Population In Three Latvian Lakes
Fig.5. Principal component analysis (PCA) plot of the genetic structuring among the three vendace populations. A). PC1 and PC2 explain 25.50% and 21.88% of the total variation, respectively (by allozyme markers); B). PC1 and PC2 explain 19.52% and 13.73% of the total variation, respectively (by RAPD markers).
Fig. 4 in Genetic And Morphological Variability Of Small Vendace (Coregonus Albula (Linnaeus, 1758)) Population In Three Latvian Lakes
Fig. 4. Number of RAPD loci and gene diversity of Coregonus albula in three Latvian lakes, based on RAPD markers.
Fig.3 in Genetic And Morphological Variability Of Small Vendace (Coregonus Albula (Linnaeus, 1758)) Population In Three Latvian Lakes
Fig.3. Allelic richness and polymorphism in Coregonus albula populations in studied lakes based on allozyme markers.
Fig. 4 in MORPHOLOGICALAND GENETIC DIFFERENTIATION OF SAXIFRAGA HIRCULUS L. (SAXIFRAGACEAE) POPULATIONS IN LITHUANIA Edita Meškauskaitė, Donatas Naugžemys, Donatas Žvingila, Jonas Remigijus
Fig. 4. UPGMA dendrogram of genetic relationships among 20 S. hirculus individuals from Merkinė population
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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.