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1,467 results for “Genetic structure”
Figure 3 from: Boyd OF, Philips TK, Johnson JR, Nixon JJ (2020) Geographically structured genetic diversity in the cave beetle Darlingtonea kentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechini). Subterranean Biology 34: 1-23. https://doi.org/10.3897/subtbiol.34.46348
Figure 3 Cave localities of currently known sites for Darlingtonea kentuckensis. White dots were the caves sampled for this study while black dots represent caves unsampled.
Figure 2 from: Boyd OF, Philips TK, Johnson JR, Nixon JJ (2020) Geographically structured genetic diversity in the cave beetle Darlingtonea kentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechini). Subterranean Biology 34: 1-23. https://doi.org/10.3897/subtbiol.34.46348
Figure 2 Gravid female Darlingtonea kentuckensis photographed in Fletcher Spring Cave, Rockcastle County, Kentucky. Photo courtesy of Dr. Matthew Niemiller, University of Alabama, Huntsville.
The genetic architecture of human brainstem structures and their involvement in common brain disorders
<p>GWAS data described in Elvsåshagen, Bahrami, ..., Kaufmann. The genetic architecture of human brainstem structures and their involvement in common brain disorders (https://www.biorxiv.org/content/10.1101/811711v1).</p>
Figure 7 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 7 Classification of Pontoscolex corethrurus individuals according to a Bayesian assignment algorithm implemented in NEWHYBRIDS (Anderson and Thompson 2002) to detect gene flow. Each unit represents an individual corresponding to parental lineages (Lineage A and Lineage B), F1 generation, F2 (F1 x F1) and later generation or introgressive hybrids B1 (Lineage A x F1) and B2 (e.g., Lineage B x F1).
Figure 6 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 6 Genetic structure using ISSR data for 35 Pontoscolex corethrurus individuals based on discriminant analysis of principal components (DAPC). Proportion of eigenvalues in discriminant analysis (bottom left plot) and PCA eigenvalues (bottom right), with the first 12 significant principal components highlighted in black.
Figure 4 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 4 UPGMA dendrogram of genetic distance between MGLs (A) and between populations (B) observed in the distinct populations of Pontoscolex corethrurus collected in central Veracruz State, Mexico. Only bootstrap values higher than or equal to 70% are shown.
Figure 2 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 2 Rarefaction curve of expected number of MLGs captured per earthworm of Pontoscolex corethrurus sampled (A), and a MLG accumulation curve according to the number of loci sampled (B).
Figure 3 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 3 A Principal Components Analysis, where colors indicate specimens of the population (A) and a Minimum Spanning Network where each node denotes a different MLG, with size matching the number of individuals. Edge thickness and color are proportional to absolute genetic distance. Edge lengths are arbitrary (B). Both analyses show the relationship between multilocus genotypes (MLGs) for four different earthworm populations of Pontoscolex corethrurus living in central Veracruz State, Mexico.
Figure 1 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 1 Pastures sampled in the central region of Veracruz State, Mexico. LV, Laguna verde; AC, Actopan; LC, La Concepción; NA, Naolinco. The digital elevation model was created using data provided by Instituto Nacional de Estadística y Geografía, México.
Figure 5 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure 5 Estimated population genetic structure with a summary plot of Q estimates based on the ISSR data observed for four populations of Pontoscolex corethrurus in central Veracruz State, Mexico. Each individual is shown by a vertical line, which is partitioned into colored segments representing the fraction of the number of members in cluster K (%).
Supplementary material 1 from: Ortíz-Gamino D, Gregorio J, Cunha L, Martínez-Romero E, Fragoso C, Ortíz-Ceballos ÁI (2020) Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico. ZooKeys 941: 49-69. https://doi.org/10.3897/zookeys.941.49319
Figure S1
Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique
Little is known about the extent of genetic connectivity along continuous coastlines in manta rays or whether site visitation is influenced by relatedness. Such information is pertinent to defining population boundaries and understanding localised dispersal patterns and behaviour. Here, we use 3057 genome-wide single nucleotide polymorphisms (SNPs) to evaluate population genetic structure and assess levels of relatedness at aggregation sites of reef manta rays (Mobula alfredi) in southern Mozambique (n = 114). Contrary to indications of limited dispersal along the southern Mozambican coastline inferred from photo identification and telemetry studies, our results show no evidence of population structure (non-significant FST <0.001) for M. alfredi along this coast. We also found no evidence that individuals sampled at the same site were more related than expected by chance for males, females or across both sexes, suggesting kinship may not influence visitation pattern s at these sites. We estimated the effective population size (Ne) of this population to be 375 (95% CI = 369-380). Comparison to a distant eastern Indian Ocean site (Western Australia; n = 15) revealed strong genetic differentiation between Mozambique and Western Australia (FST = 0.377), identifying the Indian Ocean basin as a barrier to dispersal. Our findings show that genetic connectivity in M. alfredi extends for several hundred kilometres along continuous coastlines. We therefore recommend the population in Mozambique be considered a discrete management unit and future conservation plans should prioritize integrated strategies along the entire southern coastline.
Genetic diversity and structure of wild Vaccinium populations - V. myrtillus, V.vitis-idaea and V. uliginosum in the Baltic States
<p>V. myrtillus L., V. vitis-idaea L. and V. uliginosum L. belong to the genus Vaccinium. These wild species are widely distributed and ecologically important within the Baltic countries but they have not been extensively studied using molecular markers. EST-SSR and cpSSR markers were used to investigate the population structure and genetic diversity of these species to obtain information useful for the development of in situ conservation strategies for these species.</p> <p>Wild Vaccinium species populations are moderately genetically differentiated, with some populations more highly differentiated, but without higher order clustering of groups of populations, indicating that there are no dispersal barriers for these species within the Baltic countries. Genetic diversity of populations growing in protected areas, managed forests and intensively utilised public recreational areas is similar.</p>
Genetic population structure constrains local adaptation in sticklebacks
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene<i> Pitx1</i>, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the <i>Pitx1</i> regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2x stronger population structuring among freshwater populations and >10x stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Environmental and genetic control of brain and song structure in the zebra finch
Birdsong is a classic example of a learned trait with cultural inheritance, with selection acting on trait expression. To understand how song responds to selection, it is vital to determine the extent to which variation in song learning and neuroanatomy is attributable to genetic variation, environmental conditions, or their interactions. Using a partial cross fostering design with an experimental stressor, we quantified the heritability of song structure and key brain nuclei in the song control system of the zebra finch and the genotype-by-environment (G × E) interactions. Neuroanatomy and song structure both showed low levels of heritability and are unlikely to be under selection as indicators of genetic quality. HVC, in particular, was almost entirely under environmental control. G × E interaction was important for brain development and may provide a mechanism by which additive genetic variation is maintained, which in turn may promote sexual selection through female choice. Our study suggests that selection may act on the genes determining vocal learning, rather than directly on the underlying neuroanatomy, and emphasizes the fundamental importance of environmental conditions for vocal learning and neural development in songbirds.
Data from: Dispersal capacity predicts both population genetic structure and species richness in reef fishes
Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.
Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Data from: Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread
Historical invasion scenarios based on observational records are usually incomplete and biased, but these can be supplemented by population genetic data. The western flower thrips (WFT), Frankliniella occidentalis, invaded China in the last 13 years and has rapidly become one of the most serious pests in the country. To assess whether this invasion involved a single event or multiple events, we examined patterns of genetic diversity and population structure of WFT across 12 Chinese populations and a native US population based on mitochondrial DNA and/or 18 microsatellite loci. The average allelic richness and haplotype diversity in Chinese populations were significantly lower than in a population from its native range. The distribution of mitochondrial haplotypes suggested multiple independent invasions of WFT into China, including two invasions into the Beijing region. Based on microsatellite data, two distinct clusters were identified, with both of them splitting further into two clusters; in the Beijing region, the microsatellite data also provided evidence for two introductions. Both the absence of isolation by distance and the fact that distant populations were similar genetically suggest patterns of WFT movement linked to human activities. Our study therefore suggests multiple introductions of WFT into China and human-assisted spread.
Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association
In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia facilitates its spread through vertical transmission via the eggs by inducing feminization of genetic males. The spread of feminizing Wolbachia within and across populations is therefore expected to influence mtDNA genetic structure by hitchhiking. To test this hypothesis, we analysed nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to 100% of sampled females) was highly variable among populations. All three Wolbachia strains previously observed in A. vulgare were present (wVulC, wVulM and wVulP) with wVulC being the most prevalent (9 out of 13 populations). The host showed a genetic structure on five microsatellite loci that is compatible with isolation by distance. The strong genetic structure observed on host mtDNA was correlated to Wolbachia prevalence: three mitotypes were in strong linkage disequilibrium with the three strains of Wolbachia. Neutrality tests showed that the mtDNA polymorphism is not neutral and we thus suggest that this unusual pattern of mtDNA polymorphism found in A. vulgare was due to Wolbachia.
Data from: Genetic structure and differentiation of the Italian Catria horse
Catria is one of the 22 native Italian horse breeds that now survive from a larger number. 30 individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared to data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average FST values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the three approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.
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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.