4 results on '"Muzzio, Marina"'
Search Results
2. Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data
- Author
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Gravel, Simon, Zakharia, Fouad, Moreno Estrada, Andrés, Byrnes, Jake K., Muzzio, Marina, Rodriguez Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K., Ruiz Linares, Andrés, Burchard, Esteban G., Martinez Cruzado, Juan Carlos, Bustamante, Carlos D., The 1000 Genomes Project, and Universitat de Barcelona
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Cancer Research ,Population genetics ,Amèrica ,Genoma humà ,92D25 ,purl.org/becyt/ford/1 [https] ,Effective population size ,Gene Frequency ,Models ,Human Genome Project ,Mexican Americans ,Sequencing ,Exome ,Aborígens ,Genetics (clinical) ,Native American Migrations ,Genetics ,0303 health sciences ,education.field_of_study ,Human migration ,Population size ,030305 genetics & heredity ,Chromosome Mapping ,Hispanic or Latino ,Bioquímica y Biología Molecular ,Full Genomes ,CIENCIAS NATURALES Y EXACTAS ,Research Article ,lcsh:QH426-470 ,Human Migration ,Population ,Black People ,America ,Biology ,White People ,Ciencias Biológicas ,03 medical and health sciences ,Pobles indígenes ,Migració de pobles ,Humans ,Ciencias Naturales ,Quantitative Biology - Genomics ,1000 Genomes Project ,purl.org/becyt/ford/1.6 [https] ,education ,Quantitative Biology - Populations and Evolution ,Molecular Biology ,Genotyping ,Allele frequency ,Mexico ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Genomics (q-bio.GN) ,Human genome ,business.industry ,Genome, Human ,Puerto Rico ,Racial Groups ,Native American ,Populations and Evolution (q-bio.PE) ,15. Life on land ,Migrations of nations ,lcsh:Genetics ,Genetics, Population ,Evolutionary biology ,FOS: Biological sciences ,Indians, North American ,Indigenous peoples ,business - Abstract
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations., Facultad de Ciencias Naturales y Museo, Instituto Multidisciplinario de Biología Celular
- Published
- 2013
3. Population structure in Argentina.
- Author
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Muzzio, Marina, Motti, Josefina M. B., Paz Sepulveda, Paula B., Yee, Muh-ching, Cooke, Thomas, Santos, María R., Ramallo, Virginia, Alfaro, Emma L., Dipierri, Jose E., Bailliet, Graciela, Bravi, Claudio M., Bustamante, Carlos D., and Kenny, Eimear E.
- Subjects
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POPULATION biology , *HUMAN geography , *BIOLOGICAL evolution , *PRINCIPAL components analysis - Abstract
We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
4. GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data.
- Author
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Cooke, Thomas F., Yee, Muh-Ching, Muzzio, Marina, Sockell, Alexandra, Bell, Ryan, Cornejo, Omar E., Kelley, Joanna L., Bailliet, Graciela, Bravi, Claudio M., Bustamante, Carlos D., and Kenny, Eimear E.
- Subjects
HUMAN genetic variation ,GENOMES ,MEDICAL statistics ,GENETIC polymorphisms ,ERROR rates ,POPULATION genetics ,HARDY-Weinberg formula - Abstract
Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
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