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1,598 results for “genetic diversity”
Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice
GEO Series GSE164156. Mycobacterium tuberculosis H37Rv. 123 samples. Type: Other.
Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs
GEO Series GSE62990. Bos taurus. 25 samples. Type: Genome variation profiling by genome tiling array.
Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodes.
GEO Series GSE272535. Caenorhabditis elegans. 24 samples. Type: Expression profiling by high throughput sequencing.
MAIT cells drive chronic inflammation in a genetically diverse model of spontenous colitis
GEO Series GSE253136. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Discovery of a "White-Gray-Opaque" Tristable Phenotypic Switching System in Candida Albicans: Roles of Non-Genetic Diversity in Host Adaption
GEO Series GSE53671. Candida albicans. 3 samples. Type: Expression profiling by high throughput sequencing.
Patient-derived iPSCs faithfully represent the genetic diversity and cellular architecture of human acute myeloid leukemia
GEO Series GSE210889. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Genetic diversity of Collaborative Cross mice reveals FFAR3 as a target for ILC2 anti-inflammatory reprogramming
GEO Series GSE288176. Mus musculus. 26 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional profiles of PBMCs from pigs infected with three genetically diverse PRRSV strains
GEO Series GSE95213. Sus scrofa. 12 samples. Type: Expression profiling by array.
Data from: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines
Background: Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms. Results: Roger's genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely related and showed a low level of heterozygosity. These lines could be divided into 3 major distinct groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles. Conclusions: Allelic frequency differences observed between the germplasms, together with unique alleles identified within each germplasm, shows the potential for a mutual improvement between the sets of germplasm. The results from this study will be useful to breeders in designing inbred-hybrid breeding programs, association mapping population studies and marker assisted breeding.
Data from: Evolutionary processes driving spatial patterns of intra-specific genetic diversity in river ecosystems
Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.
Data from: Genetic diversity of the endemic Canary Island pine tree, Pinus canariensis (Ph.D. thesis)
The Canary Island pine, Pinus canariensis, is an endemic tree that forms one of the main forest ecosystems within the archipelago, and whose distribution has been reduced in the last five centuries by clear cutting for the extraction of timber and tar. It was in the XXth century that exploitation declined and reforestation programs were brought forward for the restoration of an ecosystem that harbours a number of endangered endemic species of plants and animals. In addition to reforestation efforts, an understanding of population genetic processes is also necessary for the successful conservation management of the Canarian pine forest, particularly in light of gathering evidence for local adaptation. In this thesis historical and contemporary gene flow within P. canariensis was studied with nuclear and chloroplast microsatellite markers. High immigration rates (0.68–0.75) were estimated as expected for an outcrossing wind-pollinated tree. Nevertheless, significant population differentiation (FST=0.019, RST=0.044) was detectable for sites separated by only a few kilometres. Within the context of reforestation programs the high levels of gene flow detected would appear to have a positive effect, by facilitating the immigration of local alleles from natural stands into potentially genetically depauperate first generation gene pools of reforested stands. Historical population growth was revealed with chloroplast microsatellites for most populations of P. canariensis. Population expansions for the pine parasite weevil Brachyderes rugatus were also detected, broadly coinciding with the population expansions within the Canary Island pine forests. Given the estimated times of expansion, these population demographic increases would seem likely related to the process of colonisation of newly emerged islands or local patches after volcanic disturbance. Detection and dating of these expansions from chloroplast microsatellites was, to some degree, negatively affected by homoplasy (i.e. parallel and back mutations). Coalescent simulations of the evolution of chloroplast microsatellites were applied to study the effects of homoplasy in the statistical analysis of population structuring. Measures of genetic diversity based on number of haplotypes and measures based on genetic distances were differently affected. Genetic distances were underestimated but were proportional to the actual value. These effects help to explain the lower performance of statistical analyses for the detection and dating of population expansions. Further research on the effects of homoplasy in the analysis of population differentiation using chloroplast microsatellites is essential.
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: Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe
Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P-value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.
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: Genetic diversity-area relationships across bird species
The genetic diversity-area relationship (GAR), compared to the extensively explored species-area relationship (SAR), remains poorly recognized despite the importance of understanding it for the development and application of biodiversity theory. It has been hypothesized that maintaining genetic diversity within a population is mechanistically similar to maintaining species diversity within a community, implying that GAR trajectories should mathematically behave as SAR ones. Here we test this prediction by fitting microsatellite heterozygosity and allelic richness in relation to distribution range size across bird species against eight well-known SAR models. The Monod model best described the data of resident and migratory species combined, and especially the data of resident species only, showing that with increasing range size, genetic diversity across species rapidly increased up to a certain level and then tended towards an asymptote. None of the candidate models provided an adequate fit for the data of migratory species, likely because their breeding range size mostly is large in that a GAR curve has become flat. Our work takes the first step towards formulating GARs and applying them to predicting the effect of habitat fragmentation on genetic diversity.
Data from: Species and genetic diversity are not congruent in fragmented dry grasslands
Biological diversity comprises both species diversity (SD) and genetic diversity (GD) and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are, therefore, supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analysed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study it can be concluded that in fragmented dry grasslands the protection of SD does not necessarily ensure the conservation of GD.
Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
Data from: Genetic diversity and drivers of dwarfism in extinct island emu populations
Australia's iconic emu (Dromaius novaehollandiae novaehollandiae) is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the 19th century. While one of these - the King Island emu - has been found to be conspecific with Australian mainland emus, little is known about how the other two forms - Kangaroo Island and Tasmanian emus - relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of Dromaius diversity, including data from one of the few definitively genuine Tasmanian emu specimens known. Our genetic analyses suggest that all the island populations represent sub-populations of mainland D. novaehollandiae. Further, the size of island emus and those on the mainland appears to scale linearly with island size but not time since isolation, suggesting that island size—and presumably concomitant limitations on resource availability—may be a more important driver of dwarfism in island emus, though its precise contribution to emu dwarfism remains to be confirmed.
Data from: Is Hydroides dianthus (Verrill, 1873) really a Mediterranean native? Increased sampling in the eastern United States reveals enhanced genetic diversity
<p>The introduction of non-indigenous species (NIS) is a significant threat to marine biodiversity, facilitated by vectors such as shipping and aquaculture. <em>Hydroides dianthus,</em> a tubicolous polychaete worm, is known for its biofouling capabilities, impacting both shipping and aquaculture. Traditionally, the east coast of the United States has been considered the native range of <em>H. dianthus</em>. However, previous studies have suggested the Mediterranean region as the species' true native range based on higher genetic diversity. This study aims to re-evaluate the genetic diversity patterns of <em>H. dianthus</em> on the east coast of the United States by expanding the cytochrome c oxidase I (COI) dataset currently available for the species. Samples were collected from various locations on the east coast and analyzed using DNA barcoding. The results revealed a three-fold increase in haplotype diversity on the east coast compared to previous findings. A hierarchical AMOVA indicated significant genetic structuring between the Mediterranean and U.S. populations (ϕST = 0.51, P < 0.05). Despite a higher genetic diversity in the Mediterranean, this study highlights the variability of genetic diversity estimates and the challenges in using such metrics to delineate native ranges. Factors such as multiple introductions, genetic drift, and sampling bias can significantly alter genetic variability within populations. The findings suggest that the east coast's genetic diversity is likely underestimated and that more comprehensive data, including high-throughput genomic analyses and ecological studies, are needed to determine the native range of <em>H. dianthus</em> conclusively. This study underscores the complexity of using genetic data to trace the biogeography and invasion pathways of marine species.</p>
Fig. 2 in Preliminary Studies On The Genetic Diversity Of An Endemic And Endangered Species Saussurea Esthonica Baer Ex Rupr. In Latvia
Fig. 2 Band patterns across populations based on AFLP analysis
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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.