The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Brigitte Pakendorf - One of the best experts on this subject based on the ideXlab platform.
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high resolution mitochondrial dna analysis sheds light on Human Diversity cultural interactions and population mobility in northwestern amazonia
American Journal of Physical Anthropology, 2018Co-Authors: Leonardo Arias, Mark Stoneking, Chiara Barbieri, Guillermo Barreto, Brigitte PakendorfAbstract:Objectives Northwestern Amazonia (NWA) is a center of high linguistic and cultural Diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns, with some groups being foragers and others agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners are taken from different language groups. In this study, we use high-resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural Diversity on the genetic relationships and population structure of NWA groups. Methods We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1,030×. Results The mtDNA data revealed that NWA populations have high genetic Diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher genetic Diversity, while the foraging Nukak have lower genetic Diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Discussion Contrary to the view of NWA as a pristine area inhabited by small Human populations living in isolation, our data support a view of high Diversity and contact among different ethnolinguistic groups, with movement along rivers probably facilitating this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world.
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high resolution mitochondrial dna analysis sheds light on Human Diversity cultural interactions and population mobility in northwestern amazonia
bioRxiv, 2017Co-Authors: Leonardo Arias, Mark Stoneking, Chiara Barbieri, Guillermo Barreto, Brigitte PakendorfAbstract:Objectives: Northwestern Amazonia (NWA) is a center of high linguistic and cultural Diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns: some groups are foragers while others are agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners must come from different language groups. In this study, we use high resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural Diversity on the genetic relationships and structure of NWA groups. Methods: We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1030x. Results: The mtDNA data revealed that NWA populations have high genetic Diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher mtDNA Diversity, while the foraging Nukak have lower Diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Discussion: Contrary to the view of NWA as a pristine area inhabited by small Human populations living in isolation, our data support a view of high Diversity and contact among different ethnolinguistic groups; movement along rivers has probably facilitated this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world.
Leonardo Arias - One of the best experts on this subject based on the ideXlab platform.
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high resolution mitochondrial dna analysis sheds light on Human Diversity cultural interactions and population mobility in northwestern amazonia
American Journal of Physical Anthropology, 2018Co-Authors: Leonardo Arias, Mark Stoneking, Chiara Barbieri, Guillermo Barreto, Brigitte PakendorfAbstract:Objectives Northwestern Amazonia (NWA) is a center of high linguistic and cultural Diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns, with some groups being foragers and others agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners are taken from different language groups. In this study, we use high-resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural Diversity on the genetic relationships and population structure of NWA groups. Methods We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1,030×. Results The mtDNA data revealed that NWA populations have high genetic Diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher genetic Diversity, while the foraging Nukak have lower genetic Diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Discussion Contrary to the view of NWA as a pristine area inhabited by small Human populations living in isolation, our data support a view of high Diversity and contact among different ethnolinguistic groups, with movement along rivers probably facilitating this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world.
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high resolution mitochondrial dna analysis sheds light on Human Diversity cultural interactions and population mobility in northwestern amazonia
bioRxiv, 2017Co-Authors: Leonardo Arias, Mark Stoneking, Chiara Barbieri, Guillermo Barreto, Brigitte PakendorfAbstract:Objectives: Northwestern Amazonia (NWA) is a center of high linguistic and cultural Diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns: some groups are foragers while others are agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners must come from different language groups. In this study, we use high resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural Diversity on the genetic relationships and structure of NWA groups. Methods: We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1030x. Results: The mtDNA data revealed that NWA populations have high genetic Diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher mtDNA Diversity, while the foraging Nukak have lower Diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Discussion: Contrary to the view of NWA as a pristine area inhabited by small Human populations living in isolation, our data support a view of high Diversity and contact among different ethnolinguistic groups; movement along rivers has probably facilitated this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world.
Andrew Chess - One of the best experts on this subject based on the ideXlab platform.
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extensive sequence influenced dna methylation polymorphism in the Human genome
Epigenetics & Chromatin, 2010Co-Authors: Asaf Hellman, Andrew ChessAbstract:Background Epigenetic polymorphisms are a potential source of Human Diversity, but their frequency and relationship to genetic polymorphisms are unclear. DNA methylation, an epigenetic mark that is a covalent modification of the DNA itself, plays an important role in the regulation of gene expression. Most studies of DNA methylation in mammalian cells have focused on CpG methylation present in CpG islands (areas of concentrated CpGs often found near promoters), but there are also interesting patterns of CpG methylation found outside of CpG islands.
Heini M Natri - One of the best experts on this subject based on the ideXlab platform.
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genome wide dna methylation and gene expression patterns reflect genetic ancestry and environmental differences across the indonesian archipelago
PLOS Genetics, 2020Co-Authors: Georgi Hudjashov, Heini M Natri, Katalina S Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S Jacobs, Stephen J Lansing, Herawati SudoyoAbstract:Indonesia is the world's fourth most populous country, host to striking levels of Human Diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the Human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of Diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease Diversity and the strong selective pressures these diseases have exerted on Humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.
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genome wide dna methylation and gene expression patterns reflect genetic ancestry and environmental differences across the indonesian archipelago
bioRxiv, 2019Co-Authors: Georgi Hudjashov, Heini M Natri, Katalina S Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S Jacobs, Stephen J Lansing, Herawati SudoyoAbstract:Indonesia is the world9s fourth most populous country, host to striking levels of Human Diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the Human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of Diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10% of tested genes are differentially expressed between the islands of Mentawai (Sumatra) and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.7% of genes strongly correlating with nearby CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia tropical role as a source of infectious disease Diversity and the strong selective pressures these diseases have exerted on Humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by very local environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.
Jeffrey M Kidd - One of the best experts on this subject based on the ideXlab platform.
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population genetic properties of differentiated Human copy number polymorphisms
American Journal of Human Genetics, 2011Co-Authors: Catarina D Campbell, Jeffrey M Kidd, Nick Sampas, Anya Tsalenko, Peter H Sudmant, Maika Malig, Tiffany H Vu, Laura Vives, Peter TsangAbstract:Copy-number variants (CNVs) can reach appreciable frequencies in the Human population, and recent discoveries have shown that several of these copy-number polymorphisms (CNPs) are associated with Human diseases, including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. We developed a method based on single-channel intensity data and benchmarked against copy numbers determined from sequencing read depth to successfully obtain CNP genotypes for 1495 CNPs from 487 Human DNA samples of diverse ethnic backgrounds. This microarray contained CNPs in segmental duplication-rich regions and insertions of sequences not represented in the reference genome assembly or on standard SNP microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that biallelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although biallelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multicopy CNPs do not (40% with r > 0.8). We selected a subset of CNPs for further characterization in 1876 additional samples from 62 populations; this revealed striking population-differentiated structural variants in genes of clinical significance such as OCLN, a tight junction protein involved in hepatitis C viral entry. Our microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that cannot be imputed from SNP genotypes) might have contributed disproportionately to Human Diversity and selection.
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extensive copy number variation of the Human olfactory receptor gene family
American Journal of Human Genetics, 2008Co-Authors: Janet M Young, Rae Lynn M Endicott, Sean S Parghi, Megan Walker, Jeffrey M Kidd, Barbara J TraskAbstract:As much as a quarter of the Human genome has been reported to vary in copy number between individuals, including regions containing about half of the members of the olfactory receptor (OR) gene family. We have undertaken a detailed study of copy-number variation of ORs to elucidate the selective and mechanistic forces acting on this gene family and the true impact of copy-number variation on Human OR repertoires. We argue that the properties of copy-number variants (CNVs) and other sets of large genomic regions violate the assumptions of statistical methods that are commonly used in the assessment of gene enrichment. Using more appropriate methods, we provide evidence that OR enrichment in CNVs is not due to positive selection but is because of OR preponderance in segmentally duplicated regions, which are known to be frequently copy-number variable, and because purifying selection against CNVs is lower in OR-containing regions than in regions containing essential genes. We also combine multiplex ligation-dependent probe amplification (MLPA) and PCR to assay the copy numbers of 37 candidate CNV ORs in a panel of ∼50 Human individuals. We confirm copy-number variation of 18 ORs but find no variation in this Human-Diversity panel for 16 other ORs, highlighting the caveat that reported intervals often overrepresent true CNVs. The copy-number variation we describe is likely to underpin significant variation in olfactory abilities among Human individuals. Finally, we show that both homology-based and homology-independent processes have played a recent role in remodeling the OR family.
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population stratification of a common apobec gene deletion polymorphism
PLOS Genetics, 2007Co-Authors: Jeffrey M Kidd, Tera L Newman, Eray Tuzun, Rajinder Kaul, Evan E EichlerAbstract:The APOBEC3 gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a detailed sequence and population genetic analysis of a 29.5-kb common Human deletion polymorphism that removes the APOBEC3B gene. We developed a PCR-based genotyping assay, characterized 1,277 Human Diversity samples, and found that the frequency of the deletion allele varies significantly among major continental groups (global FST = 0.2843). The deletion is rare in Africans and Europeans (frequency of 0.9% and 6%), more common in East Asians and Amerindians (36.9% and 57.7%), and almost fixed in Oceanic populations (92.9%). Despite a worldwide frequency of 22.5%, analysis of data from the International HapMap Project reveals that no single existing tag single nucleotide polymorphism may serve as a surrogate for the deletion variant, emphasizing that without careful analysis its phenotypic impact may be overlooked in association studies. Application of haplotype-based tests for selection revealed potential pitfalls in the direct application of existing methods to the analysis of genomic structural variation. These data emphasize the importance of directly genotyping structural variation in association studies and of accurately resolving variant breakpoints before proceeding with more detailed population-genetic analysis.