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9 results for “Ancestry inference”
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
It is now clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. Together, mixnmatch and ancestryinfer are powerful tools for predicting the performance of local ancestry inference methods on real data.
Inferred ancestry of scytonemin biosynthesis proteins in cyanobacteria indicates a response to Paleoproterozoic oxygenation
<p>Protection from radiation damage is an important adaptation for phototrophic microbes. In the case of cyanobacteria, surface, shallow water, and peritidal environments are especially exposed to long- wavelength ultraviolet (UVA) radiation. Several groups of cyanobacteria within these environments are protected from UVA damage by the production of the pigment scytonemin. Paleontological evidence of cyanobacteria in UVA-exposed environments from the Proterozoic, and possibly as early as the Archaean, suggests a long evolutionary history of radiation protection within this group. We show that phylogenetic analyses of enzymes in the scytonemin biosynthesis pathway support this hypothesis, and reveal a deep history of vertical inheritance of this pathway within extant cyanobacterial diversity. Referencing this phylogeny to cyanobacterial molecular clocks suggests that scytonemin production likely appeared during the early Proterozoic, soon after the Great Oxygenation Event. This timing is consistent with an adaptive scenario for the evolution of scytonemin production, wherein the threat of UVA-generated reactive oxygen species becomes significantly greater once molecular oxygen was more pervasive across photosynthetic environments.</p>
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
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Inferred ancestry of scytonemin biosynthesis proteins in cyanobacteria indicates a response to Paleoproterozoic oxygenation
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Fig. 2 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 2. Population tree inferred by TreeMix using all 42 sampling sites across the mountain pine beetle range. Terminal branches are labeled using locality information (see Supp Fig. 1 [online only] for further detail) and migration arrows are colored according to migration weight.
Fig. 3. Scenario 9 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 3. Scenario 9 was identified as the 'best' from 11 competing phylogeographic scenarios. This scenario represents an east-to-west colonization route with stable population sizes in which cluster 4 is derived from clusters 1 and 3 through admixture. Terminal branch labels are consistent with the five STRUCTURE clusters identified (Fig. 1). T = time expressed as number of generations assuming one generation per year; R = inferred migration rate.
Fig. 1 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 1. Map of mountain pine beetle sites throughout western North America. Each site is represented by a pie chart depicting the average assignment (Q values) of individuals to one of five STRUCTURE clusters (K = 5).
The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers
<p>Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received infuences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds difer considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African infuence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confrm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.</p>
The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers
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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.