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1,467 results for “Genetic structure”
Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management
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Genetic diversity and structure of wild Vaccinium populations - V. myrtillus, V.vitis-idaea and V. uliginosum in the Baltic States
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The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets
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Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
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Data from: Patterns of fine-scale spatial genetic structure and pollen dispersal in giant sequoia (Sequoiadendron giganteum)
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Standing at the gateway to Europe - the genetic structure of Western Balkan populations based on autosomal and haploid markers
GEO Series GSE59032. Homo sapiens. 70 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genetic networks regulating structure and function of the maize shoot apical meristem
GEO Series GSE137715. Zea mays. 6 samples. Type: Expression profiling by high throughput sequencing.
Nano-structural analysis of engrafted human induced pluripotent stem cell-derived cardiomyocytes in mouse hearts using a genetic-probe APEX2.
GEO Series GSE99470. Homo sapiens. 32 samples. Type: Expression profiling by array.
Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer [SET 14]
GEO Series GSE72906. Homo sapiens. 108 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Somatically Acquired Structural Genetic Differences; a Longitudinal Study of Elderly Danish Twins
GEO Series GSE76390. Homo sapiens. 169 samples. Type: Genome variation profiling by SNP array.
Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer [SET 15]
GEO Series GSE72911. Homo sapiens. 133 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
The genetic basis of structural colour variation in mimetic Heliconius butterflies [erato]
GEO Series GSE190378. Heliconius erato demophoon; Heliconius erato cyrbia. 32 samples. Type: Expression profiling by high throughput sequencing.
Spatial genetic structure to identify populations at risk
<p>Microsatellite genotypes, locality information, and raster data for Miller et al</p>
SNP data: Population genetic structure in bull sharks (Carcharhinus leucas)
<p><span>The bull shark (<em>Carcharhinus leucas</em>) is a large, mobile, circumglobally distributed high trophic level predator that inhabits a variety of remote islands and continental coastal habitats, including freshwater environments. </span>Here, we hypothesise that the barriers to dispersal created by large oceanic expanses and deep-water trenches result in a heterogeneous distribution of the neutral genetic diversity between island bull shark populations compared to populations sampled in continental locations connected through continuous coastlines of continental shelves. <span>We analysed 1,494 high-quality neutral Single Nucleotide Polymorphism (SNP) markers in 215 individual bull sharks from widespread locations across the Indian and Pacific Oceans (South Africa, Indonesia, Western Australia, Papua New Guinea, eastern Australia, New Caledonia and Fiji). Genomic analyses revealed partitioning between remote insular and continental populations, with the Fiji population being genetically different from all other locations sampled (<i>F</i><sub>ST</sub> 0.034-0.044, <i>P </i>< 0.001), and </span>New Caledonia showing marginal isolation (<i>F</i><sub>ST</sub> 0.016-0.024, <i>P </i>< 0.001; albeit based on a small sample size) from most sampled sites<span>.</span> Discriminant Analysis of Principal Components (DAPC) identified samples from Fiji as a distinct cluster with all other sites as one large cluster. Genetic structure analyses (Admixture, STRUCTURE & AssignPOP) further supported the genetic isolation of bull sharks from Fiji, with the analyses in agreement. The observed differentiation in bull sharks from Fiji makes this site of special interest, as it indicates a lack of migration through dispersal across deep-water trenches and large ocean expanses.</p>
Data from: Population genetic structure of Picea engelmannii, P. glauca and their previously unrecognized hybrids in the central Rocky Mountains
Areas of geographic overlap between potentially hybridizing species provide the opportunity to study interspecific gene flow and reproductive barriers. Here we identified hybrids between Picea engelmannii and P. glauca by their genetic composition at 17 microsatellite markers, and determined the broad-scale geographic distribution of hybrids in the central Rocky Mountains of North America, a geographic region where hybrids and isolation between species had not previously been studied. Parameter estimates from admixture models revealed considerable variation in ancestry within and among collection sites, suggesting that within this area of geographic overlap, the interaction of the two species varies extensively. The results document a previously unrecognized patchy distribution of hybrids between P. engelmannii and P. glauca, including locations where hybrids were not known or expected to exist. Further, the ancestry of many hybrids was consistent with multiple generations of hybridization, with probable directional backcrossing to P. engelmannii, suggesting a relatively porous species boundary. The identification and characterization of hybridization between these spruce in this region raises the question of what factors maintain barriers to gene flow in these long-lived forest trees. The current research lays the groundwork for future study of the ecological and evolutionary contexts of their hybridization, as well as of differential introgression and permeability of species boundaries.
Data from: Global mtDNA genetic structure and hypothesized invasion history of a major pest of citrus, Diaphorina citri (Hemiptera: Liviidae)
The Asian citrus psyllid Diaphorina citri Kuwayama, is a key pest of citrus as the vector of the bacterium causing the 'huanglongbing' disease (HLB). To assess the global mtDNA population genetic structure, and possible dispersal history of the pest, we investigated genetic variation at the COI gene collating newly collected samples with all previously published data. Our dataset consists of 356 colonies from 106 geographic sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017), low nucleotide diversity (π-mean = 0.003), and significant positive selection (Ka/Ks = 32.92) were observed. Forty-four haplotypes (Hap) were identified, clustered into two matrilines: Both occur in southeastern and southern Asia, North and South America, and Africa; Lineages A and B also occur in eastern and western Asia, respectively. The most abundant haplotypes were Hap4 in lineage A (35.67%), and Hap9 in lineage B (41.29%). The haplotype network identified them as the ancestral haplotypes within their respective lineages. Analysis of molecular variance showed significant genetic structure (FST = 0.62, p < 0.0001) between the lineages, and population genetic analysis suggests geographic structuring. We hypothesize a southern and/or southeastern Asia origin, three dispersal routes, and parallel expansions of two lineages. The hypothesized first route involved the expansion of lineage B from southern Asia into North America via West Asia. The second, the expansion of some lineage A individuals from Southeast Asia into East Asia, and the third involved both lineages from Southeast Asia spreading westward into Africa and subsequently into South America. To test these hypotheses and gain a deeper understanding of the global history of D. citri more data-rich approaches will be necessary from the ample toolkit of next generation sequencing (NGS). However, the current paper may serve to guide such sampling and in the development of biological control programs against the global pest D. citri.
Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.
Data from: A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds
Background: The native cattle breeds are an important genetic resource for meat and milk production throughout Asia. In Asia cattle were domesticated around 10,000 years ago and in Korea cattle are being raised since 2000 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo, Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is a part of a Food and Agricultural Organization and national genetic evaluation plans, others get little attention. This study is an effort to understand and provide a detailed insight into the population structure and genetic variability of the Korean cattle breeds along with other Asian breeds using various methods. In this study we report the genetic variation and structure of the Korean cattle breeds and their comparison with five other Asian cattle breeds along with a panel of animals from European taurine, African taurine and indicine cattle breeds. Results: Asian cattle were found to be least differentiated which reflects their recent history. Amongst the Asian breeds Hainan, which is an indicine breed, had the lowest gene diversity while Yanbian had the highest followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju Black. The genetic diversity in Asian cattle breeds was found comparable to the European taurines and more than the African taurines and Zebu cattle. Korean cattle breed, Brown Hanwoo was consistently found to be closer to Yanbian, a Chinese cattle breed. We found low divergence and moderate levels of genetic diversity among the native Korean breeds. Indicine introgression from Hainan was seen in other Asian breeds. From Europe, Limousin, Holstein and Hereford introgression was found in Asian breeds. Conclusions: In this study we provide a genome-wide insight into the genetic history of the native cattle breeds of Korea. The outcomes of this study will help in prioritization and designing of the conservation plans.
Data from: Population genetic structure of the Pocillopora damicornis morphospecies along Ningaloo Reef, Western Australia
The effective management of a coral reef system relies on a detailed understanding of the population structure of dominant habitat-forming species. For some corals, however, high levels of phenotypic plasticity have made species delineation based on morphological characteristics alone unreliable, suggesting that previous studies of population genetic structure may have been influenced by the inclusion of multiple genetic lineages in the analyses. We examined the population structure of the Pocillopora damicornis morphospecies along the World Heritage Ningaloo Coast, Western Australia, and recovered 2 mitochondrial haplotypes from sympatrically occurring colonies possessing morphological characteristics consistent with taxonomic classification of P. damicornis. Despite a high degree of genetic differentiation between these lineages, we detected low levels of unidirectional admixture between them, suggesting that reproductive barriers are not fully developed. We found dual modes of reproduction for both lineages with considerable variation in the contribution of sexual reproduction among sample sites. Lastly, we identified a high dispersal potential of sexually produced propagules in the most common lineage with positive spatial autocorrelation detected over distances up to 60 km. Based on these results, it appears that populations of P. damicornis have a high capacity to recover from environmental perturbations as long as the effects of disturbances are patchy across Ningaloo Reef.
Data from: Riverine barriers have little influence on genetic structure of Rattus tanezumi
Rivers may hinder population migration and promote genetic differentiation of terrestrial animals. Most studies testing the riverine barrier hypothesis have yielded positive results, while very few studies do not support this hypothesis. In this study, 384 Asian house rats (Rattus tanezumi) were collected fromYunnan,China. By combined use of the sequence markers of mitochondrial (mtDNA) and nuclear (IRBP), we tested the influence of five local rivers on the population genetics of R. tanezumi. A total of 81 mtDNA haplotypes and 135 IRBP haplotypes were determined, and many of which were shared by two or more of the six geographic regions. AMOVA analyses showed that most variations happened either within populations or among populations, while very few variations (<15%) happened among the six geographic regions formed by the five rivers. SAMOVA analysis classified the mtDNA sequences into three groups, while no genetic differentiation was detected on IRBP. Our results concluded that riverine barriers in the study area have little influence on the genetic structure of R. tanezumi.
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Allen Brain Atlas
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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.
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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.
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