4 results on '"Byrnes, Jake"'
Search Results
2. Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data
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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
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- 2013
3. Role of positive selection in the retention of duplicate genes in mammalian genomes.
- Author
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Shin-Han Shiu, Byrnes, Jake K., Pan, Runsun, Peng Zhang, and Wen-Hsiung Li
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GENES , *COMPLEMENTATION (Genetics) , *POPULATION genetics , *HUMAN genome , *BIOLOGICAL divergence , *GENOMICS - Abstract
The question of how duplicate genes are retained in a population remains controversial. The duplication-degeneration-complementation model, which involves no positive selection, stipulates a higher retention rate of duplicate genes in a small population than in a large one. This model has been accepted by many evolutionists. However, we found considerably more retentions and fewer losses of duplicate genes in the mouse genome than in the human genome, although the population size of rodents is in general larger than that of primates. Indeed, in nearly every interval of synonymous divergence between duplicate genes, the number of gene retentions in mouse is larger than that in human. Our findings suggest a more important role of positive selection in duplicate retention than duplication-degeneration-complementation. In addition, certain functional categories show a higher tendency of lineage-specific expansion than expected, suggesting lineage-specific selection or functional bias in retained duplicates. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
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4. Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation
- Author
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Kidd, Jeffrey M., Gravel, Simon, Byrnes, Jake, Moreno-Estrada, Andres, Musharoff, Shaila, Bryc, Katarzyna, Degenhardt, Jeremiah D., Brisbin, Abra, Sheth, Vrunda, Chen, Rong, McLaughlin, Stephen F., Peckham, Heather E., Omberg, Larsson, Bormann Chung, Christina A., Stanley, Sarah, Pearlstein, Kevin, Levandowsky, Elizabeth, Acevedo-Acevedo, Suehelay, Auton, Adam, and Keinan, Alon
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POPULATION genetics , *HUMAN genome , *HUMAN genetic variation , *GENE flow , *HETEROZYGOSITY , *DIPLOIDY , *SINGLE nucleotide polymorphisms - Abstract
Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas—70% of the European ancestry in today’s African Americans dates back to European gene flow happening only 7–8 generations ago. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
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