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22 results for “genetic and genotypic diversity”
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
Figure 4 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 4. Prevalence of six different sub-allele types of Pvmsp-3β (A1-A3, B1-B2 and C1) based on PCR-RFLP.
Figure 2 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 2. Prevalence of nine different sub-allele types of Pvmsp- 3α(A1-A4), (B1-B3), C1 and D are the nine different alleles from PCR-RFLP.
Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
<p><span>Spatial patterns in genetic variation compared across species provide information about the predictability of genetic diversity of natural populations and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni – a major river system from the Guiana Shield – to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as goldmining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.</span></p>
Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
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First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping
<p>Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) datasets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted <em>Rhinoptericola megacantha</em> (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of <em>R. megacantha</em> are more host-specific and less broadly distributed than adults of <em>C. gracilis</em>, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For <em>R. megacantha</em>, population structure coincided with geography rather than host species. For <em>C. gracilis</em>, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.</p>
Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
<p><strong>Background: </strong>Sheep breeds native to the United Kingdom are noted for high breed variability and exhibit a striking diversity of different traits in phenotypes and genetic diversity. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.</p> <p><strong>Results: </strong>In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.</p> <p><strong>Conclusion: </strong>Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small populations sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.</p>
Figure 1 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 1. Prevalence of four different alleles of Pvmsp-3α (A, B, C and D) from PCR-RFLP
Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.
Genotype data from: Extent of stream habitat and hybridization influence levels of genetic diversity in Redband Trout (<em>Oncorhynchus mykiss gairdneri</em>) populations
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Data from: Characterizing population structure and documenting rapid loss of genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis) with high throughput microsatellite genotyping
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First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping
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Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
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Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms
<p>Supplementary materials for the porcine astrovirus study in East Africa.</p> <p><strong>Table S1</strong>: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank </p> <p><strong>Table S2</strong>. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S3</strong>. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S4</strong>: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains.</p> <p><strong>Table S5</strong>. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software</p>
Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
<p>Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among <i>R. mangle</i> maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of <i>R. mangle</i>. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.</p>
Data from: Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
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Data from: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination
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Data from: Genetic variation and clonal diversity in introduced populations of Mimulus guttatus assessed by genotyping at 62 single nucleotide polymorphism loci
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Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing
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Taxus genotype data for "Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L."
<p>The data set contains microsatellite genotypes (18 loci) of Taxus baccata trees, together with the information about sampling sites.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.