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193 results for “parsimony”
Data from: Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes
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Data from: Parsimonious inference of hybridization in the presence of incomplete lineage sorting
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Figure 126. Parsimony phylogeny. Part B in Erratum to Blahnik and Holzenthal (2017): Revision of the northern South American species of Mortoniella Ulmer, 1906 (Trichoptera: Glossosomatidae: Protoptilinae)
Figure 126. Parsimony phylogeny. Part B (above).
Figure 126. Parsimony phylogeny. Part A in Erratum to Blahnik and Holzenthal (2017): Revision of the northern South American species of Mortoniella Ulmer, 1906 (Trichoptera: Glossosomatidae: Protoptilinae)
Figure 126. Parsimony phylogeny. Part A (above). Part B continues on the next page.
Data from: Spatially explicit assessment of estuarine fish after Deepwater Horizon oil spill: tradeoffs in complexity and parsimony
Evaluating long-term contaminant effects on wildlife populations depends on spatial information about habitat quality, heterogeneity in contaminant exposure, and sensitivities and distributions of species integrated into a systems modeling approach. Rarely is this information readily available, making it difficult to determine the applicability of realistic models to quantify population-level risks. To evaluate the trade-offs between data demands and increased specificity of spatially explicit models for population-level risk assessments, we developed a model for a standard toxicity test species, the sheepshead minnow (Cyprinodon variegatus) exposed to oil contamination following the Deepwater Horizon oil spill and compared the output with various levels of model complexity to a standard risk quotient approach. The model uses habitat and fish occupancy data collected over five sampling periods throughout 2008-2010 in Pensacola and Choctawhatchee Bays, Florida, to predict species distribution, field-collected and publically available data on oil distribution and concentration, and chronic toxicity data from laboratory assays applied to a matrix population model. The habitat suitability model established distribution of fish within Barataria Bay, Louisiana, and the population model projected the dynamics of the species in the study area over a five-year period (October 2009 – September 2014). Vital rates were modified according to estimated contaminant concentrations to simulate oil exposure effects. To evaluate the differences in levels of model complexity, simulations varied from temporally and spatially explicit, including seasonal variation and location-specific oiling, to simple interpretations of a risk quotient derived for the study area. The results of this study indicate that species distribution, as well as spatially and temporally variable contaminant concentrations, can provide a more ecologically relevant evaluation of species recovery from catastrophic environmental impacts but might not be cost-effective or efficient for rapid assessment needs.
Distance matrices for parsimonious phylogeography
<p>This dataset includes distance matrices created for the publication "Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic". It includes geographic distances and effective distances, both between airports (stated via their IATA code) and countries (stated via their 2-letter country code).</p>
Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony
Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that have moved chromosomes within the phylogeny of 10 Drosophila species, including 87 gene families with multiple independent movements on different branches of the phylogeny. Using this large catalog of transposed genes, we detected accelerated sequence evolution in duplicated genes that transposed when compared to the parental copy at the original locus. We also observed a more refined picture of the biased movement of genes from the X chromosome to the autosomes. The bias of X-to-autosome movement was significantly stronger for RNA-based movements than for DNA-based movements, and among DNA-based movements there was an excess of genes moving onto the X chromosome as well. Genes involved in female-specific functions moved onto the X chromosome while genes with male-specific functions moved off the X. There was a significant overrepresentation of proteins involving chromosomal function among transposed genes, suggesting that genetic conflict between sexes and among chromosomes may be a driving force behind gene transposition in Drosophila.
Data from: Spatially explicit assessment of estuarine fish after Deepwater Horizon oil spill: tradeoffs in complexity and parsimony
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Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony
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Figure 1. Maximum parsimony rooted phylogenetic tree for a in A Coronavirus Detected in the Vampire Bat Desmodus rotundus
Figure 1. Maximum parsimony rooted phylogenetic tree for a segment of the ORF1b of the Coronavirus genus, showing each of the three groups in the genus and in bold and underlined the strain BatCoV DR/2007 detected in the enteric content of a Desmodus rotundus bat. Numbers at each node are 1,000 replicates bootstrap values.
Fig. Sa/b: (a) Strict consensus of 2 most parsimonious trees generated by exact analysis of sequence data. Numbers on branches represent bootstrap node confidence values from 100 replications. (b) Jac support tree. Numbers on branches represent confidence frequencies in nodes as quantified by parsimony jacknifing with Jac (Farris 1995). in Morphological and mitochondrial-DNA variation in Rhinolophus rouxii (Chiroptera)
Fig. Sa/b: (a) Strict consensus of 2 most parsimonious trees generated by exact analysis of sequence data. Numbers on branches represent bootstrap node confidence values from 100 replications. (b) Jac support tree. Numbers on branches represent confidence frequencies in nodes as quantified by parsimony jacknifing with Jac (Farris 1995).
Figure 24. Most parsimonious tree recovered from a in The skull of the Upper Cretaceous snake Dinilysia patagonica Smith-Woodward, 1901, and its phylogenetic position revisited
Figure 24. Most parsimonious tree recovered from a parsimony analysis of a data matrix containing 154 characters coded for 22 terminal taxa including the fossils Dinilysia patagonica, Eupodophis descouensi, Haasiophis terrasanctus, Najash rionegrina, Pachyrhachis problematicus, Sanajeh indicus, Wonambi naracoortensis, and Yurlunggur sp. Bremer support and bootstrap percentages are given at the nodes. Names have been added for nodes that represent broadly used clade names. Unambiguous synapomorphies for the labelled nodes are (see also Appendix 3): Node 1: 84 (1), 106 (1), 119 (1), 132 (1). Node 2: 10 (0), 34 (1), 63 (1), 76 (1), 99 (1), 144 (1), 148 (1), 149 (1), 154 (1). Node 3: 15 (2), 20 (1), 31 (1), 55 (1), 65 (1), 95 (1), 100 (1), 109 (1), 152 (1). Node 4: 23 (1). Node 5: 48 (2), 53 (1), 62 (1), 69 (1), 70 (1), 90 (1), 104 (1). Node 6: 83 (1), 85 (1), 98 (1), 99 (0), 125 (0), 126 (1), 128 (1), 132 (0). Node 7: 39 (1), 52 (1). Node 8: 43 (1), 56 (1), 68 (1), 79 (1), 102 (0). Node 9: 47 (1), 49 (1), 133 (1), 138 (0). Node 10: 72 (1), 125 (0). Node 11: 23 (1), 24 (1), 46 (1), 67 (1), 112 (1). Node 12: 10 (1), 41 (1), 51 (1), 78 (0), 91 (1). Node 13: 29 (1), 38 (1), 47 (1), 60 (1), 64 (2), 77 (0), 80 (2), 108 (1), 125 (0), 126 (1). Node 14: 17(1), 21 (1), 27 (2), 50 (0), 61 (1). Node 15: 99 (0). Node 16: 52 (1), 81 (1). Node 17: 13 (1), 65 (0), 122 (1), 143 (1). Node 18: 8 (1), 30 (1), 56 (0), 86 (1), 87 (1), 113 (2), 117 (1), 151 (1). Node 19: 15(1), 19(1), 20 (2), 21 (1), 22 (1), 26 (2), 71 (1), 73 (2), 111 (1).
FIGURE 1. Most parsimonious tree obtained using TNT under implied weighting and a k in Stevenia gilasiani sp. nov. (Diptera: Rhinophoridae): the first woodlouse fly with male sexual-patches
FIGURE 1. Most parsimonious tree obtained using TNT under implied weighting and a k-value of 8.594.
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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.