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8 results for “clustering analyses”
Figs. 5 and 6. Results from cluster and linkage tree analyses. Fig. 5 in Myrmecofauna (Hymenoptera: Formicidae) response to habitat characteristics of tropical montane cloud forests in central Veracruz, Mexico
Figs. 5 and 6. Results from cluster and linkage tree analyses. Fig. 5. Dendrogram of hierarchical standardized clustering based on the SØrensen similarity index of the studied fragments. The cophenetic correlation coefficient of the cluster is 0.89. The dendrogram displays with continuous lines the divisions for which the SIMPROF test rejects the null hypothesis (where assemblages in that group have no further structure to explore) and with dashed lines the groups of assemblages not separated (at P <0.05) by SIMPROF. Fig. 6. Linkage tree analysis (LINKTREE) showing divisive clustering of fragments (F1–F5) from species compositions constrained by inequalities on one or more environmental variables. Only binary partitions of uncorrelated environmental variables are shown in the cluster. The dendrogram displays with continuous lines the divisions for which the SIMPROF test rejects the null hypothesis (where assemblages in that group have no further structure to explore) and with dashed lines the groups of assemblages not separated (at P <0.05) by SIMPROF.
Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii
Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison to the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based in Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.
Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes
Bayesian clustering methods have been widely used for studying species delimitation and genetic introgression. In order to test the effect of phylogenetic relationships and sampling scheme on the inferred clustering solution and on the performance of Bayesian clustering analysis, I simulated genotypes of the interfertile oak species Quercus robur, Quercus petraea, and Quercus pubescens and I run analyses using two popular software programs, STRUCTURE and BAPS. First, based on purebred simulations, I compared clustering solutions resulting from different sample size configurations. While clustering solution generally reflected the taxonomic relationships when equal samples of each species were included, spurious partition was inferred by STRUCTURE when some species were represented by larger and others by smaller samples. In very unbalanced configurations, STRUCTURE failed to identify the three species, even if three subpopulations were assumed. By contrast, BAPS could properly identify the three species under any sampling scheme. Second, based on simulations of purebreds and hybrids, I tested the performance of individual assignments with variable number of loci. This analysis showed that STRUCTURE can detect introgressed individuals more efficiently than BAPS. However, BAPS could assign purebreds more efficiently with a lower number of loci. Method performance also depended on phylogenetic relationships. In the case of Q. petraea, Q. pubescens, and their hybrids, method performance was lower due to their phylogenetic affinity. Inclusion of three instead of two species into the analysis led to reduction of performance, and to misclassification of hybrids, which often reflected the phylogenetic affinity between Q. petraea and Q. pubescens.
Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii
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Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes
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Prediction of prognosis for small cell lung cancer based on genome-wide methylation analyses with surgical materials and robust clustering methods
GEO Series GSE62021. Homo sapiens. 25 samples. Type: Expression profiling by array.
Festem: Directly selecting differentially expressed genes for single-cell clustering analyses.
<p>Datasets related to article "Directly selecting differentially expressed genes for single-cell clustering analyses". Codes are available at <a href="http://github.com/XiDsLab/Festem_paper">https://github.com/XiDsLab/Festem_paper</a>.</p>
Comparative Physiological, Metabolomic, and Transcriptomic Analyses Reveal Developmental Stage-Dependent Effects of Cluster Bagging on Phenolic Metabolism in Cabernet Sauvignon Grape Berries
GEO Series GSE129916. Vitis vinifera. 42 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.