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1,598 results for “genetic diversity”
Data from: Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate
Species that inhabit naturally fragmented environments are expected to be spatially structured and exhibit reduced genetic diversity at the periphery of their range. Patterns of differentiation may also reflect historical processes such as recolonization from glacial refugia. We examined the relative importance of these factors in shaping the spatial patterns of genetic differentiation across the range of an alpine specialist, the North American mountain goat (Oreamnos americanus). Contrary to fossil evidence which suggests a single southern refugium, we detected evidence for additional refugia in northern British Columbia and the Alaskan coast using both mitochondrial and microsatellite DNA. A core area of elevated genetic diversity characterized both regions, and molecular dating suggested a recent Pleistocene split was followed by demographic expansion. Across their range, mountain goats were highly genetically structured and displayed the expected pattern of declining diversity towards the periphery. Gene flow was high within contiguous mountain ranges, but cross-assignments paradoxically suggest that long-distance contemporary dispersal movements are not uncommon. These results improve our understanding of how historical vicariance and contemporary fragmentation influence population differentiation, and have implications for conserving the adaptive potential of alpine populations and habitat.
Data from: High genetic diversity in the offshore island populations of the tephritid fruit fly Bactrocera dorsalis
Background: Geographic isolation is an important factor that limit species dispersal and thereby affects genetic diversity. Because islands are often small and surrounded by a natural water barrier to dispersal, they generally form discrete isolated habitats. Therefore, islands may play a key role in the distribution of the genetic diversity of insects, including flies. Results: To characterize the genetic structure of island populations of Bactrocera dorsalis, we analyzed a dataset containing both microsatellite and mtDNA loci of B. dorsalis samples collected from six offshore islands in Southern China. The microsatellite data revealed a high level of genetic diversity among these six island populations based on observed heterozygosity (Ho), expected heterozygosity (HE), Nei's standard genetic distance (D), genetic identity (I) and the percentage of polymorphic loci (PIC). These island populations had low F ST values (F ST = 0.04161), and only 4.16 % of the total genetic variation in the species was found on these islands, as determined by an analysis of molecular variance. Based on the mtDNA COI data, high nucleotide diversity (0.9655) and haplotype diversity (0.00680) were observed in all six island populations. F-statistics showed that the six island populations exhibited low or medium levels of genetic differentiation among some island populations. To investigate the population differentiation between the sampled locations, a factorial correspondence analysis and both the unweighted pair-group method with arithmetic mean and Bayesian clustering methods were used to analyze the microsatellite data. The results showed that Hebao Island, Weizhou Island and Dong'ao Island were grouped together in one clade. Another clade consisted of Shangchuan Island and Naozhou Island, and a final, separate clade contained only the Wailingding Island population. Phylogenetic analysis of the mtDNA COI sequences revealed that the populations on each of these six islands were closely related to different populations on mainland China. Conclusions: Our study suggests that these island populations have high genetic diversity, experience frequent gene flow and exhibit low or medium levels of genetic differentiation among some island populations. Therefore, the geographic isolation of the six islands does not appear to be a major dispersal barrier to B. dorsalis. Such knowledge is helpful for a better understanding of evolutionary processes of the species of island populations.
Data from: Effects of postglacial phylogeny and genetic diversity on the growth variability and climate sensitivity of European silver fir
<p>The zip file contains almost 2000 tree ring width data in Tucson format (rwl) from 78 sites across the Carpathian Mountains in Europe. In addition, genetic data used in the study are also attached. The datasets were used in the paper on <strong>Effects of postglacial phylogeny and genetic diversity on the growth variability and climate sensitivity of European silver fir </strong>published in Journal of Ecology.</p>
FIGURE 3 in Morphological diversity and genetic structure within Lerista kalumburu Storr, 1976 (Squamata: Scincomorpha: Sphenomorphidae) — taxonomic implications
FIGURE 3. Lerista kalumburu in life. Specimen from Theda Station. Photo courtesy of H. Cook.
Supplementary material 1 from: Kitabatake K, Izumi K, Kondo NI, Okoshi K (2023) Phylogeography and genetic diversity of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda, Upogebiidae): Natural or anthropogenic dispersal? ZooKeys 1182: 259-287. https://doi.org/10.3897/zookeys.1182.105030
Molecular and morphometric analyses of Upogebia major
Supplementary material 1 from: Berteloot OH, Kuhn A, Peusens G, Beliën T, Hautier L, Van Leeuwen T, De Clercq P (2024) Distribution and genetic diversity of the invasive pest Halyomorpha halys (Hemiptera, Pentatomidae) in Belgium. NeoBiota 90: 123-138. https://doi.org/10.3897/neobiota.90.113421
Metadata of all samples
Genetic divergence and diversity reflect a predominant freshwater resident life history in Rainbow Trout from southwestern Alaska
<p>Rainbow Trout <i>Oncorhynchus mykiss</i> in southwestern Alaska occupy coastal watersheds near the northern boundary of the species native range and support a world class wild trout sport fishery. Although low freshwater temperatures and a short growing season in this region may favor anadromy, these populations appear to exhibit a freshwater resident life history strategy. In this study we used genetic data to evaluate two hypotheses regarding the influence of the presumed migratory behavior of these Rainbow Trout on reproductive isolation among and within watersheds. The results were largely consistent with the predictions but there were exceptions. The data supported the hypothesis that the freshwater resident behavior precludes marine-mediated gene flow resulting in large genetic divergence and low admixture among watersheds. The estimate of <i>F<sub>CT</sub></i> (among-watershed differentiation, 0.350) was large and reflected over 96% of the variation among all sampled aggregations (<i>F<sub>ST</sub></i> = 0.363). However, evidence of admixed individuals in two adjacent watersheds and five first generation migrants among five watersheds suggests that the potential for coastal migration with gene flow exists in these populations. The data also supported the hypothesis that aggregations formed within watersheds during the spawning period (May-June) represent reproductively isolated populations. The pairwise estimates of <i>F<sub>ST</sub></i> and the <i>G</i>-test results revealed population structure in four of the six watersheds tested. However, not all aggregation pairs were found genetically distinct and there was notable variation in the pairwise <i>F<sub>ST</sub></i> estimates (0.000 – 0.067). In summary, the data reflected the predicted results for each hypothesis, but also revealed exceptions that, consistent with tagging studies, demonstrate the complexity of migratory behavior in southwestern Alaska Rainbow Trout. We discuss the implications of these results for fishery management and conservation.</p>
Supplementary material 3 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure S1
Supplementary material 2 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Table S2
Figure 2 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 2 Neighbor-Net of S. lapponum individuals based on Nei (1973) coefficient. Population abbreviations are the same as in Table 1.
Supplementary material 1 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Table S1
Figure 1 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 1 Location of the studied populations of S. lapponum. Population abbreviations are the same as in Table 1.
Figure 3 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 3 Results of the Bayesian admixture analysis data for populations of S. lapponum using STRUCTURE software. Population abbreviations are the same as in Table 1.
Retrotransposon-based genetic diversity of Deschampsia antarctica Desv. from King George Island (Maritime Antarctic)
<p><span><i>Deschampsia antarctica</i> Desv. can be found in diverse Antarctic habitats which may vary considerably in terms of environmental conditions and soil properties. As a result, the species is characterized by wide ecotypic variation in terms of both morphological and anatomical traits. The species is a unique example of an organism that can successfully colonize inhospitable regions due to its phenomenal ability to adapt to both the local mosaic of microhabitats and to general climatic fluctuations. For this reason, <i>D. antarctica </i>has been widely investigated in studies analyzing morphophysiological and biochemical responses to various abiotic stresses (frost, drought, salinity, increased UV radiation). However, there is little evidence to indicate whether the observed polymorphism is accompanied by the corresponding genetic variation.</span></p> <p>In the present study, retrotransposon-based iPBS markers were used to trace the genetic variation of <i>D. antarctica</i> collected in nine sites of the Arctowski oasis on King George Island (Western Antarctic). The genotyping of 165 individuals from nine populations with seven iPBS primers revealed 125 amplification products, 15 of which (12%) were polymorphic, with an average of 5.6% polymorphic fragments per population. Only one of the polymorphic fragments, observed in population 6, was represented as a private band. The analyzed specimens were characterized by low genetic diversity (uH<sub>e</sub> = 0.021, I = 0.030) and high population differentiation (<i>F<sub>ST</sub></i> = 0.4874). An analysis of Fu's <i>F<sub>S</sub></i> statistics and mismatch distribution in most populations (excluding population 2, 6 and 9) revealed demographic/spatial expansion, whereas significant traces of reduction in effective population size were found in three populations (1, 3 and 5). The iPBS markers revealed genetic polymorphism of <i>D. antarctica</i>, which could be attributed to the mobilization of random transposable elements, unique features of reproductive biology, and/or geographic location of the examined populations.</p>
Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation
<p>Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. <i>Horsfieldia tetratepala</i> is an economically important rainforest tree which has declined steadily, mainly though habitat destruction, and an endangered, narrow endemic in China where it is also classified as a Plant Species with Extremely Small Populations (PSESP). Effective conservation strategies for <i>H. tetratepala</i> are required urgently, but limited information about its<i> </i>genome is available. Accordingly, restriction site-associated DNA sequencing (RAD_seq) was used to sequence sixty-three <i>H. tetratepala</i> trees covering ten isolated populations to assess genome-level diversity and population structure, generating 8,103 high-quality SNPs. Low genetic diversity and moderate genetic differentiation was observed among populations, but Bayesian clustering divided the sampled <i>H. tetratepala</i> populations into two genetic clusters, though with some populations from Guangxi and Yunnan intermixed. Because of increasing of habitat fragmentation and human disturbance, conservation priority should be placed on populations with higher genetic variation (e.g., BB, TKH, DWS, and GLQ). Overall, our study provides valuable genomic resources for <i>H. tetratepala</i> that will significantly advance the formulation of effective conservation strategies.</p>
Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
<p>Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003.</p> <p>Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The <em>StCDF1</em> locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.</p>
Patterns of volatile diversity yield insights into the genetics and biochemistry of the date palm fruit volatilome
<p>Volatile organic compounds are key components of the fruit metabolome that contribute to traits such as aroma and taste. Here we report on the diversity of 90 flavor-related fruit traits in date palms (<em>Phoenix dactylifera</em> L.) including 80 volatile organic compounds, which collectively represent the fruit volatilome, as well as 6 organic acids, and 4 sugars in tree-ripened fruits. We characterize these traits in 148 date palms representing 135 varieties using headspace solid-phase microextraction gas chromatography. We discovered new volatile compounds unknown in date palm including 2-methoxy-4-vinylphenol, an attractant of the red palm weevil (<em>Rhynchophorus ferrugineus </em>Olivier), a key pest that threatens the date palm crop. Associations between volatile composition and sugar and moisture content suggest that differences among fruits in these traits may be characterized by system-wide differences in fruit metabolism. Correlations between volatiles indicate medium chain and long chain fatty acid ester volatiles are regulated independently, possibly reflecting differences in the biochemistry of fatty acid precursors. Finally, we took advantage of date palm clones in our analysis to estimate broad-sense heritabilities of volatiles and demonstrate that at least some of volatile diversity has a genetic basis.</p>
FIGURE 1 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 1. Geographical distribution of the studied Lolium rigidum populations.
FIGURE 1 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers
FIGURE 1. Distribution map of the studied populations.
Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats
<p><span>In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, </span><span>elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. </span><span>Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB.</span> <span>Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation</span><span>, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination</span><span> to investigate the causality of a number of</span><span> tested variants across different breed backgrounds</span><span>. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds.</span></p> <p><span>This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.</span></p>
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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)
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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.