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81 results for “Genealogy”
The Jalakeli Project: House of Narasingh Genealogy Tree
<p>The <strong>House of Narasingh Genealogy Tree</strong> is a component of The Jalakeli Project, a web-based, women’s oral histories initiative in Manipur, India. </p> <p>As only women of the House of Narasingh are admitted into the two choirs of the Shree Shree Govinda Jiu Jalakeli Pala, the House of Narasingh Genealogy Tree is designed to help the Pala members keep track of familial relations in the lineage of the king. It seeks to preserve their oral genealogical information as data.</p> <p>The House of Narasingh Genealogy Tree uses the digital commons provided by Wikitree. It can be searched in www.wikitree.org under Ningthemcha Genealogy.</p> <p>The House of Narasingh Genealogical Tree is a conservation complement of the women’s oral histories of the of the Jalakeli Project.</p>
The genealogical divergence index across a speciation continuum in Hercules beetles
<p>The genealogical divergence index (<i>gdi</i>) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies used meta-analyses to show that <i>gdi </i>can be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different <i>gdi</i> values have yet to be studied. I showed that an increase in the calculated <i>gdi</i> value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a <i>gdi </i>value of 0.7 or higher was associated with divergences between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that could conventionally be treated as subspecific differences, such as geographic taxa that may or may not be morphologically divergent and whose reproductive isolation is likely incomplete, had <i>gdi</i> values that fell within the species delimitation ambiguous zone (0.2 < <i>gdi </i>< 0.7). Although exceptions did exist, different <i>gdi</i> values may prove to be biologically and evolutionarily informative should additional speciation continuums from different empirical systems be investigated, and the results obtained herein can help with objectively delimiting species in the era of integrative taxonomy.</p>
FIGURE 8 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 8. Comparative of head scales of Calyptommatus species from dorsal view (left) and lateral view (right). (A) C. sinebrachiatus (MTR39001); (B) C. confusionibus (MTR24343); (C) C. frontalis sp. nov. (MZUSP 106738); (D) C. leiolepis (MTR39096); (E) C. nicterus (ACG44). Scale bars correspond to 2 mm.
FIGURE 6 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 6. Habitat where Calyptommatus frontalis sp. nov. was collected, showing the typical deciduous caatinga vegetation over sandy soils present in the region during A) wet season and B) dry season.
FIGURE 9 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 9. Comparative of dorsal scales in Calyptommatus. (A) C. sinebrachiatus (MTR39001); (B) C. confusionibus (MTR24343); (C) C. frontalis sp. nov. (MZUSP 106753; MTR38962); (D) C. sp.2 (MTR18055); (E) C. leiolepis (MTR39096); (F) C. nicterus (ACG44). Scale bar corresponds to 2 mm.
FIGURE 5 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 5. Paratype of Calyptommatus frontalis sp. nov. in life from Brejo do Poção, Buritirama, state of Bahia, northeast Brazil.
FIGURE 4 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 4. Details of body scalation of the holotype of Calyptommatus frontalis sp. nov. (MZUSP 106738, field number MTR 38950): A) dorsal view at midbody; B) ventral view at midbody; C) lateral view at midbody; D) precloacal region and hindlimbs. Scale bars correspond to 2 mm.
FIGURE 3 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 3. Calyptommatus frontalis sp. nov., adult female holotype: Dorsal, lateral and ventral views of head (MZUSP 106738, field number MTR 38950).
FIGURE 2 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 2. Satellite image of the Xique-Xique dune field region showing the variation in frontal scales in Calyptommatus. Aerial image from Google Earth Pro 2021 DigitalGlobe Image Landsat/Copernicus.
FIGURE 1. A in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE 1. A) Bayesian inference phylogenetic tree for Calyptommatus and outgroups based on the mtDNA data set (16S + cytb + nd4; 1,918 bp). Values on nodes refer to Bayesian posterior probabilities (pp); values above 0.95 are considered high
FIGURE S2 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE S2. Bayesian inference phylogenetic tree for Calyptommatus and outgroups based on the five loci concatenated data set (16S + cytb + nd4 + c-mos + ntf3; 2,942 bp). Values on nodes refer to Bayesian posterior probabilities (pp); values above 0.95 are considered high statistical support for clades
FIGURE S1 in Morphological variation and genealogical discordance in Caatinga sand lizards Calyptommatus Rodrigues 1991 (Squamata: Gymnophthalmidae) with the description of a new species
FIGURE S1. Bayesian inference phylogenetic tree for Calyptommatus and outgroups based on the nuDNA data set (c-mos + ntf3; 1,024 bp). Values on nodes refer to Bayesian posterior probabilities (pp); values above 0.95 are considered high statistical support for clades.
Tree Sequence and Genealogical Forest Files for a Simulated Human Chromosome 20
<p>Dataset containing 640000 samples simulated using <a href="https://github.com/popsim-consortium/stdpopsim">stdpopsim</a> 0.2.0 and the <code>HapMapII_GRCh38</code> genetic map.<br>The tree sequence was converted to a genealogical forest files via <a href="https://github.com/lukashuebner/gfkit">gfkit</a> version <code>fbd2740</code>.</p>
Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes
<p>Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes.</p> <p>The genomes are the samples used in Wlodzimierz et al. 2023 (https://doi.org/10.1038/s41586-023-06062-z). </p> <p>longread-trees.tar.gz contains the output of Relate's estimate population size command (<a href="https://myersgroup.github.io/relate/modules.html#CoalescenceRate">https://myersgroup.github.io/relate/</a>modules.html#CoalescenceRate), including an anc/mut/dist/coal file for every chromosome. It also constains a tskit tree sequence (https://tskit.dev/) for each chromosome, converted from anc/mut.</p> <p>Thal_ref_Boec_Lyra_Malc_outgroups_nodupes_orthoonly.maf is the multi-species alignment (kindly provided by Tyler Kent, Adrian Platts, and the Brassicales Map Alignment Project (DOE-JGI, http://bmap.jgi.doe.gov/)) that we used to polarize the alleles.</p> <p>Snakefile is the code we used to generate the genealogies.</p>
Relate-inferred genealogies for 1552 Arabidopsis thaliana samples
<p>Relate-inferred genealogies for 1552 Arabidopsis thaliana samples.</p> <p>The genealogies for each of the 5 autosomes are given as .anc.gz and .mut.gz files.</p> <p>Each chromosome also has a .dist and .coal file, giving the space between mutations (accounting for genomic mask) and the inferred coalescence rates (inferred from trees on that chromosome only for the sake of computation time).</p> <p>keep.poplabels gives the IDs of the samples, in the order given to Relate. Since we filter out heterozygous sites, there is only one sample for each diploid individual.</p> <p>Pipeline given in Snakefile with Python environment given in requirements.txt.</p> <p>Genetic data from Durvasula et al 2017 (https://www.pnas.org/doi/abs/10.1073/pnas.1616736114), https://www.ebi.ac.uk/ena/browser/view/PRJEB44201?show=analyses.</p> <p>The .maf file is the multi-species alignment (kindly provided by Tyler Kent, Adrian Platts, and the Brassicales Map Alignment Project (DOE-JGI, http://bmap.jgi.doe.gov/)) that we used to polarize the alleles.</p> <p>Please don't hesitate to get in touch with questions.</p> <p>Matt</p>
FIGURE 1 in A multiple gene genealogy reveals the phylogenetic placement of Iodosphaeria tongrenensis sp. nov. in Iodosphaeriaceae (Xylariales)
FIGURE 1. MP tree based on dataset of LSU, ITS and SSU sequences. Bootstrap support values for maximum parsimony (MP) greater than 50% are given above the nodes. The strains numbers are given after the species names. The tree is rooted to Botryosphaeria ribis. All sequences from type strains are shown in bold face.
FIGURE 2 in A multiple gene genealogy reveals the phylogenetic placement of Iodosphaeria tongrenensis sp. nov. in Iodosphaeriaceae (Xylariales)
FIGURE 2. Iodosphaeria tongrenensis (holotype). A. Herbarium material. B, C. Ascomata on the surface of host. D. Section of ascoma. E. Peridium. F,G. Ascus apical apparatus (stained in Melzer´s reagent). H–J. Mature asci with ascospores. K. Ceratosporium -like conidia. L–O. Ascospores (N, O stained in India ink). Scale bars: B=1 mm, C=300 μm, D=50 μm, E=10 μm, F, G=5 μm, H–K=10 μm, L–O=5 μm.
FIGURE 3 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 3. Rhopalostroma lekae in OA after 2 weeks (MFLUCC 13-0123). A: Averse showing melanized pigments and central mycelia. B: Reverse side of culture. C: Development of stromatal primordia in the culture. D: Melanized mycelia at the centre. E–G: Conidiophores from simple to more complex structure. H–J: Development of conidia and conidiogenesis cells. K: Conidia. Bars: c–d 1mm; e–k 50 µm.
FIGURE 2 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 2. Rhopalostroma lekae (MFLU 13-0440). A: Habit on bark. B: Separated mature stromata. C: Stromata with dark purplish pigments in head part. D: Longitudinal section of stroma showing perithecial alignment in the periphery of stroma. E: Cross section of the stroma (head) showing perithecia. F and G: Mature ascus in water. H: Ascus in Melzer's reagent, Note the lack of an apical apparatus. I: KOH extractable pigments of stroma (left-head, right–stipe). J–l: Mature ascospores in water. Bars: a–b 5 mm; c–d 1 mm; e 2 mm; f–l 10 µm.
Naigama genealogy
<p>Figure 6 in</p> <p><em>To engrave his virtues on the disc of the moon… Inscriptions of the Aulikaras and Their Associates</em></p> <p>Dániel Balogh, 2019</p> <p>Possible genealogies of the Naigama family</p> <p>Approximate dates shown in CE on left and ME on right. The tree to the left of the Later Aulikara line shows my proposed reconstruction; the tree on the right shows a conventional reconstruction. Persons described as rājasthānīya or amātya in inscriptions are shown in shaded fields. Dates of the ancestors of Doṣa/Bhagavaddoṣa are estimated assuming 20 years per generation. Solid vertical lines indicate father-to-son descent, dotted lines show uncertain relations.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.