scholarly journals Whole genome sequence of Mapuche-Huilliche Native Americans

2018 ◽  
Author(s):  
Elena A. Vidal ◽  
Tomás C. Moyano ◽  
Bernabé I. Bustos ◽  
Eduardo Pérez-Palma ◽  
Carol Moraga ◽  
...  
Keyword(s):  
Native American ◽  
Native Americans ◽  
Latin American ◽  
Genome Sequence ◽  
Large Scale ◽  
Genomic Structure ◽  
Southern Cone ◽  
Population History ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants

AbstractBackgroundWhole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant.ResultsHere we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96–97% high confidence calls. We found approximately 3.1×106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes.ConclusionsMapuche-Huilliche genomes contain a unique set of small– and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

scholarly journals Genomic insights into the recent population history of Mapuche Native Americans

2021 ◽  
Author(s):  
Lucas Vicuña ◽  
Anastasia Mikhailova ◽  
Tomás Norambuena ◽  
Anna Ilina ◽  
Olga Klimenkova ◽  
...  
Keyword(s):  
Native American ◽  
Native Americans ◽  
Amazon Basin ◽  
Genomic Data ◽  
Population History ◽  
Ancestral Population ◽  
Effective Population ◽  
Southern Patagonia ◽  
History Of ◽  
Demographic Shifts

The last few years have witnessed an explosive generation of genomic data from ancient and modern Native American populations. These data shed light on key demographic shifts that occurred in geographically diverse territories of South America, such as the Andean highlands, Southern Patagonia and the Amazon basin. We used genomic data to study the recent population history of the Mapuche, who are the major Native population from the Southern Cone (Chile and Argentina). We found evidence of specific shared genetic ancestry between the Mapuche and ancient populations from Southern Patagonia, Central Chile and the Argentine Pampas. Despite previous evidence of cultural influence of Inca and Tiwanaku polities over the Mapuche, we did not find evidence of specific shared ancestry between them, nor with Amazonian groups. We estimated the effective population size dynamics of the Mapuche ancestral population during the last millennia, identifying a population bottleneck around 1650 AD, coinciding with a period of Spaniards invasions into the territory inhabited by the Mapuche. Finally, we show that admixed Chileans underwent post-admixture adaptation in their Mapuche subancestry component in genes related with lipid metabolism, suggesting adaptation to scarce food availability.

Native Americans and Cities

2015 ◽  
Author(s):  
Nicolas G. Rosenthal
Keyword(s):  
Native American ◽  
Native Americans ◽  
American Indians ◽  
21St Century ◽  
Large Scale ◽  
Monumental Architecture ◽  
Early 21St Century ◽  
Indian Country ◽  
Important Relationship ◽  
The Early 21St Century

An important relationship has existed between Native Americans and cities from pre-Columbian times to the early 21st century. Long before Europeans arrived in the Americas, indigenous peoples developed societies characterized by dense populations, large-scale agriculture, monumental architecture, and complex social hierarchies. Following European and American conquest and colonization, Native Americans played a crucial role in the development of towns and cities throughout North America, often on the site of former indigenous settlements. Beginning in the early 20th century, Native Americans began migrating from reservations to U.S. cities in large numbers and formed new intertribal communities. By 1970, the majority of the Native American population lived in cities and the numbers of urban American Indians have been growing ever since. Indian Country in the early 21st century continues to be influenced by the complex and evolving ties between Native Americans and cities.

Unpacking the Mascot Debate: Native American Identification Predicts Opposition to Native Mascots

2020 ◽  
Author(s):  
Stephanie A. Fryberg ◽  
Arianne E. Eason ◽  
Laura Brady ◽  
Nadia Jessop ◽  
Julisa Lopez
Keyword(s):  
Native American ◽  
Native Americans ◽  
American Indians ◽  
Large Scale ◽  
Political Orientation ◽  
Native People ◽  
Sports Teams ◽  
Identity Centrality ◽  
People’S Attitudes ◽  
Racial Ethnic

While major organizations representing Native Americans (e.g., National Congress of American Indians, n.d.) contend that Native mascots are stereotypical and dehumanizing, sports teams with Native mascots cite polls claiming their mascots are not offensive to Native people (Vargas, 2019). We conducted a large-scale, empirical study to provide a valid and generalizable understanding of Native Americans’ (N=1021) attitudes toward Native mascots. Building on the identity centrality literature, we examined how multiple aspects of Native identification uniquely shaped attitudes towards mascots. While Native Americans in our sample generally opposed Native mascots, especially the Redskins, attitudes varied according to demographic characteristics (e.g., age, political orientation, education) and the strength of participants’ racial-ethnic identification. Specifically, stronger Native identification (behavioral engagement and identity centrality) predicted greater opposition. Results highlight the importance of considering the unique and multifaceted aspects of identity, particularly when seeking to understand Native people’s attitudes and experiences.

scholarly journals Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21

2019 ◽  
Author(s):  
Nandita Mukhopadhyay ◽  
Madison Bishop ◽  
Michael Mortillo ◽  
Pankaj Chopra ◽  
Jacqueline B. Hetmanski ◽  
...  
Keyword(s):  
Birth Defects ◽  
Large Scale ◽  
Pediatric Research ◽  
Chromosome 21 ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Family Based ◽  
Kids First

AbstractOrofacial clefts (OFCs) are one of the most common birth defects worldwide and create a significant health burden. The majority of OFCs are non-syndromic, and the genetic component has been only partially determined. Here, we analyze whole genome sequence (WGS) data for association with risk of OFCs in European and Colombian families selected from a multicenter family-based OFC study. Part of the Gabriella Miller Kids First Pediatric Research Program, this is the first large-scale WGS study of OFC in parent-offspring trios. WGS provides deeper and more specific genetic data than currently available using imputation on single nucleotide polymorphic (SNP) marker panels. Here, association analysis of genome-wide single nucleotide variants (SNV) and short insertions and deletions (indels) identified a new locus on chromosome 21 in Colombian families, within a region known to be expressed during craniofacial development. This study reinforces the ancestry differences seen in the genetic etiology of OFCs, and the need for larger samples when for studying OFCs and other birth defects in admixed populations.

scholarly journals The population history of northeastern Siberia since the Pleistocene

2018 ◽  
Author(s):  
Martin Sikora ◽  
Vladimir V. Pitulko ◽  
Vitor C. Sousa ◽  
Morten E. Allentoft ◽  
Lasse Vinner ◽  
...  
Keyword(s):  
Native Americans ◽  
Large Scale ◽  
Human Remains ◽  
Population History ◽  
Northern Eurasia ◽  
Bering Strait ◽  
East Asians ◽  
Northeastern Siberia ◽  
History Of ◽  
Milk Teeth

ABSTRACTFar northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

scholarly journals Disentangling signatures of selection before and after European colonization in Latin Americans

2021 ◽  
Author(s):  
Javier Mendoza-Revilla ◽  
Camilo Chacon-Duque ◽  
Macarena Fuentes-Guajardo ◽  
Louise Ormond ◽  
Ke Wang ◽  
...  
Keyword(s):  
Native American ◽  
Latin American ◽  
Large Scale ◽  
Latin Americans ◽  
European Contact ◽  
Snp Data ◽  
Before And After ◽  
European Colonization ◽  
Source Populations ◽  
Genomic Regions

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. While classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ~4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico and Peru. Our approach replicates previous reports of selection in the HLA region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly-used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

scholarly journals Assessing Runs of Homozygosity: A comparison of SNP Array and Whole Genome Sequence low coverage data

2017 ◽  
Author(s):  
Francisco C. Ceballos ◽  
Scott Hazelhurst ◽  
Michèle Ramsay
Keyword(s):  
Genome Sequence ◽  
Complex Traits ◽  
Genetic Basis ◽  
Snp Array ◽  
Population History ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Technological Advances ◽  
Low Coverage

AbstractRuns of Homozygosity (ROH) are sequences that arise when identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. Using the PLINK Homozygosity functions, we found that by allowing 3 heterozygous SNPs per window when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using the two technologies.

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