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927 results for “genetic study”
Data from: Sex change and effective population size: implications for population genetic studies in marine fish
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.
Data from: When can refuges mediate the genetic effects of fire regimes? A simulation study of the effects of topography and weather on neutral and adaptive genetic diversity in fire-prone landscapes
Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection-driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which microrefuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically complex landscapes, with fire refuges and fire-prone "hotspots" apparent. Interannual weather variability reduced the effect of topography on fire patterns, with refuges less apparent under high weather variability. Neutral genetic diversity was correlated with long-term fire frequency under spatially heterogeneous fire regimes, being higher in fire refuges than fire-prone areas, except under high dispersal or low fire severity (low mortality). This generated different spatial genetic structures in fire-prone and fire-refuge components of the landscape, despite similar dispersal. In contrast, genetic diversity was only associated with time since the most recent fire in flat landscapes without predictable refuges and hotspots. Genetic effects of selection driven by fire-related conditions depended on selection pressure, migration distance and spatial heterogeneity in fire regimes. Allele frequencies at a locus conferring higher fitness under successional environmental conditions followed a pattern of "temporal adaptation" to contemporary conditions under strong selection pressure and high migration. However, selected allele frequencies were correlated with spatial variation in long-term mean fire frequency (relating to environmental predictability) under weak dispersal, low selection pressure and strong spatial heterogeneity in fire regimes.
Data from: Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments
Red deer and wild boar are two major game species whose populations are managed and live in areas impacted by human activities. Measuring and understanding the impact of landscape features on individual movements and spatial patterns of genetic variability in these species is thus of importance for managers. A large number of individuals sampled across Wallonia (Belgium) for both species have been genotyped using microsatellite markers (respectively >1700 and >1200 genotyped individuals) and some individuals have also been followed using a capture-mark-recapture (CMR) protocol. The combined data set represents an unprecedented opportunity to study and compare the environmental factors impacting the interconnectivity of these large mammals. The present study describes and uses a landscape genetic workflow to compare spatial patterns of genetic variability and the impact of environmental factors on genetic differentiation. For the latter analyses, we investigate the correlation between genetic and environmental distances (pairwise approach) and also between local genetic dissimilarity and environmental conditions (point approach). Preliminary analyses of CMR data confirm that motorways act as significant barriers to dispersal. However, analyses performed with the pairwise approach do not highlight any evidence of an impact of motorways on genetic differentiation, which is presumably due to their recent establishment. Complementary analyses performed with the point approach reveal that low altitude tends to be associated with higher genetic dissimilarity. From a methodological point of view, the present workflow illustrates the complementary application of both pairwise and point approaches as well as univariate and multivariate analyses.
Data from: New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies.
The mutualistic symbioses between reef-building corals and micro-algae form the basis of coral reef ecosystems, yet recent environmental changes threaten their survival. Diversity in host-symbiont pairings on the sub-species level could be an unrecognized source of functional variation in response to stress. The Caribbean elkhorn coral, Acropora palmata, associates predominantly with one symbiont species (Symbiodinium 'fitti'), facilitating investigations of individual-level (genotype) interactions. Individual genotypes of both host and symbiont were resolved across the entire range of the species. Most colonies of a particular animal genotype were dominated by one symbiont genotype (or strain) that may persist in the host for decades or more. While Symbiodinium are primarily clonal, the occurrence of recombinant genotypes indicates sexual recombination is the source of this genetic variation, and some evidence suggests this happens within the host. When these data are examined at spatial scales spanning the entire distribution of A. palmata, gene flow among animal populations was an order of magnitude greater than among populations of the symbiont. This suggests that independent micro-evolutionary processes created dissimilar population genetic structures between host and symbiont. The lower effective dispersal exhibited by the dinoflagellate raises questions regarding the extent to which populations of host and symbiont can co-evolve during times of rapid and substantial climate change. However, these findings also support a growing body of evidence suggesting that genotype by genotype interactions may provide significant physiological variation; influencing the adaptive potential of symbiotic reef corals to severe selection.
Data from: Multiplexed microsatellite markers for genetic studies of beech
European beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects. Multiplex PCR of microsatellites is a fast and cost-effective technique allowing high throughput genotyping. Here we present the procedure used to develop two multiplex kits (8-plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the multiplex kits amplify 16 loci largely devoid of null alleles and allow rapid and cost-effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.
Informative data about the biological sample studied in the article "Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background"
<p>Informative data about the biological sample studied in the article "Nineteenth century French rose (<em>Rosa </em>sp.) germplasm shows a shift over time from a European to an Asian genetic background" published in Journal of Experimental Botany (https://doi.org/10.1093/jxb/erw269)</p>
FIGURE 7. Spiophanes uschakowi Zachs, 1933 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 7. Spiophanes uschakowi Zachs, 1933: A. Anterior end, dorsal view. B. Chaetiger 5–12, lateral view; arrow indicates simple vertical opening of glandular organ in chaetiger 11. C. Neuropodial hooks with reduced hood from chaetiger 19. — All Syntype, RAS 1/25826. Scale: A, B 0.5 mm; C 10 µm.
FIGURE 8 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 8. First presence of neuropodial hooks in relation to body width on chaetiger 4 in both Spiophanes bombyx and S. norrisi sp. nov.
FIGURE 5 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 5. Spiophanes norrisi sp. nov.: A. Anterior end, dorsal view; methyl green stained nuchal and dorsal ciliated organs. B. Anterior end, lateral view; methyl green stained openings of glandular organs on chaetigers 5, 7, and 8; arrow indicates simple vertical opening of glandular organ in chaetiger 14. C–F. Parapodium from chaetiger 2, 5, 11, and 19, all anterior view. G. Neuropodial hooks with reduced hood from chaetiger 19. H. Neuropodial chaeta from chaetiger 5. I. Sabre chaeta from chaetiger 11. K. Neuropodial chaeta from chaetiger 2. — B = LACM–AHF V. 1962–50 (Paratype); all others LACM–AHF V5102. Scale: A, B 0.5 mm, C–F 0.1 mm. G–K 5 µm.
FIGURE 2 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 2. Spiophanes bombyx (Claparède, 1870): A. Anterior end, dorsal view. B. Chaetigers 9–15 with dorsal ciliated organs and dorsal ciliated crests, dorsal view. — Specimens from the North Sea, German Bight, depth 24 m, leg. K. Meißner, Jul 2008. Scale: in µm.
FIGURE 10 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 10. Phylogenetic relationships among five Spiophanes species based on partial mitochondrial and nuclear sequences. A. Maximum–likelihood bootstrap consensus tree (1000 replicates) based on COI haplotypes. Numbers above branches are likelihood bootstrap values; numbers below branches are Bayesian posterior probabilities and parsimony consensus percentages. Trees are rooted using sequences of Prionospio as outgroup (P. steenstrupi EU835668; Prionospio sp.1 EU835667). B. Maximum–parsimony bootstrap consensus tree (1000 replicates) based on 18S haplotypes. Numbers above branches are parsimony bootstrap values; numbers below branches are Bayesian posterior probabilities and likelihood bootstrap percentages. Trees are rooted using sequences of Prionospio as outgroup (P. ehlersi EU340095; P. dubia EU418859).
FIGURE 3 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 3. Spiophanes bombyx (Claparède, 1870): Chaetiger 10–18, dorsal view, methyl green stained nuchal organs. — Specimen from Turkey, Iskenderum Bay, sublittoral, leg. E. Dagli, Sep 2005. Scale: 0.5 mm.
FIGURE 4 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 4. Spiophanes bombyx (Claparède, 1870): A. Chaetigers 4–9 with openings of glandular organs on chaetigers 5, 7, 8, 9, lateral view. B. Neuropodial hooks from chaetiger 16, dorsal apical view. C. Chaetigers 9–11, lateral view. D. Posterior end with stout curved notochaeta, dorsal view. — A, B, D specimens from the North Sea, German Bight, depth 24 m, leg. K. Meißner, Jul 2008; C specimen from the Gulf of Naples, depth 20 m, leg. P. Lanera, March 2005. Scale: in µm.
FIGURE 9 in Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) — a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies
FIGURE 9. Number of neuropodial hooks in relation to body width on chaetiger 4 in both Spiophanes bombyx and S. norrisi sp. nov.
FIGURE 4 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 4. Inter- (gray) and intraspecific (open) genetic differences in Tettigonia species for CO1 calculated using the pdistance method and treatment of pairwise deletion for gaps with the range of genetic difference within clusters. The box plot displays the median (internal transverse thick line) and interquartile range (box). Short lines indicate maximum and minimum genetic differences. Asterisk denotes a sequence from NCBI; T. viridissima, JN609414–JN609420; T. hispania, EF515121; T. chinensis, HQ609468–HQ609470. (JJ-TU = Jeju Island population of T. ussuriana; JS-TU = Jeongseon population of T. ussuriana; PC-TU = Pyeongchang population of T. ussuriana; MJ-TU = Muju population of T. ussuriana; MG-TU = Mungyeong population of T. ussuriana)
FIGURE 3 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 3. Neighbor-joining tree inferred from the concatenated dataset of all five genetic loci: CO1, CO2, ND1, TA1, and ITS2. Neighbor-joining (left) and parsimony (right) bootstrap values are indicated above internodes; Bayesian posterior probabilities are shown below internodes.
FIGURE 2 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 2. Neighbor-joining (A), parsimony (B), and Bayesian inference (C) trees inferred from the combined dataset of three mtDNA loci (CO1 + CO2 + ND1). Numbers next to nodes are bootstrap or posterior probability values.
FIGURE 1 in A molecular phylogenetic study on South Korean Tettigonia species (Orthoptera: Tettigoniidae) using five genetic loci: The possibility of multiple allopatric speciation
FIGURE 1. Neighbor-joining phylogenetic tree of each mtDNA gene analysis: (A) CO1, (B) CO2, (C) ND1. Numbers next to nodes are bootstrap values. Numbers on arrows are genetic differences between two clusters.
FIGURE 12 in On the identity of Spio filicornis (O. F. Müller, 1776) — with the designation of a neotype, and the description of two new species from the North East Atlantic Ocean based on morphological and genetic studies
FIGURE 12. Spio symphyta sp. nov.: A. Anterior end, dorsal view. B. Anterior dorsum, dorsal view. C. Anterior end, dorsal view; nuchal organ and dorsal ciliated organs well observable in specimen stained with methyl green. D. Neuropodial hooks from chaetiger 20, lateral view. E. Neuropodial hook from 18th last chaetiger, anterior oblique view; arrow points at uppermost 3rd tooth. F. Anteriormost region, dorsal view; arrow points at fusion between prostomium and peristomium; specimen stained with methyl green. G. Ventrum of chaetigers 13–15, with pattern of white dots (arrows) discernible in specimen stained with methyl green. — A, B (without number, 53°43.941N, 6°31.310E, 23.9 m, 23.07.2008), C, F (ZMH P-25911), D (ZSRO- P2065), E (ZSRO-P2063), G (ZSRO-P1862).
FIGURE 10 in On the identity of Spio filicornis (O. F. Müller, 1776) — with the designation of a neotype, and the description of two new species from the North East Atlantic Ocean based on morphological and genetic studies
FIGURE 10. Spio arndti sp. nov.: A. Anterior dorsum, prostomium and peristomium turned ventrally and not seen in the image. B. Chaetigers 15–18, dorsal view. — All from Kiel Bight (ZSRO-P2052).
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.