Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens

Abstract Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10−7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.

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Limited evidence for selection at the FADS locus in Native American populations

10.1101/2019.12.11.873356 ◽

2019 ◽

Author(s):

Iain Mathieson

Keyword(s):

Native American ◽

Native Americans ◽

Direct Evidence ◽

Northern Eurasia ◽

Ancestral State ◽

Limited Evidence ◽

Asian Populations ◽

Parsimonious Explanation ◽

Selection Signal ◽

Long Chain

AbstractThe FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA). This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of LC-PUFA varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals of selection are confounded by the presence of parallel adaptation–postdating their split from Native Americans–in the European and East Asian populations used in the population branch statistic (PBS) test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. A more parsimonious explanation for the present-day distribution of the haplotype is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.

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The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire

10.1101/219808 ◽

2017 ◽

Cited By ~ 1

Author(s):

Daniel N. Harris ◽

Wei Song ◽

Amol C. Shetty ◽

Kelly Lavano ◽

Omar Cáceres ◽

...

Keyword(s):

Native American ◽

Native Americans ◽

Evolutionary Dynamics ◽

Demographic History ◽

High Coverage ◽

Detailed Model ◽

Demographic Modeling ◽

Inca Empire ◽

Genomic Architecture ◽

Evolutionary Genomic

AbstractNative Americans from the Amazon, Andes, and coast regions of South America have a rich cultural heritage, but have been genetically understudied leading to gaps in our knowledge of their genomic architecture and demographic history. Here, we sequenced 150 high-coverage and genotyped 130 genomes from Native American and mestizo populations in Peru. A majority of our samples possess greater than 90% Native American ancestry and demographic modeling reveals, consistent with a rapid peopling model of the Americas, that most of Peru was peopled approximately 12,000 years ago. While the Native American populations possessed distinct ancestral divisions, the mestizo groups were admixtures of multiple Native American communities which occurred before and during the Inca Empire. The mestizo communities also show Spanish introgression only after Peruvian Independence. Thus, we present a detailed model of the evolutionary dynamics which impacted the genomes of modern day Peruvians.

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Abstract 3476: Factors Affecting The Incidence of Spontaneous Intracerebral Hemorrhage in a Multiracial Community in Northern California.

Stroke ◽

10.1161/str.43.suppl_1.a3476 ◽

2012 ◽

Vol 43 (suppl_1) ◽

Author(s):

Raul Guisado ◽

Linda Catalli ◽

Karen de la Cuesta

Keyword(s):

Diabetes Mellitus ◽

Native American ◽

Native Americans ◽

Intracerebral Hemorrhage ◽

White Women ◽

Geographic Origin ◽

Epidemiological Studies ◽

Asian Populations ◽

Santa Clara County ◽

Hispanic Patients

INTRODUCTION: Santa Clara County, California is a multi-racial community with a large Asian and Hispanic representation (30.6% Asian, 31.8% White and 31.9% Hispanics). The annual incidence of non-traumatic intracerebral hemorrhage (ICH) in our population is higher than the national average (29.2% vs. 13%) and the proportion of Asian patients with ICH is higher than expected (46.5% vs. 30.6% ). The reasons for the higher incidence of ICH in Asian populations are not known. We conducted a retrospective review of all cases of ICH in two Primary Stroke Centers in Santa Clara County, California to test the hypothesis that certain co-morbidities may explain the higher incidence of ICH in our community. METHODS: All cases of ICH admitted to two PSCs were abstracted from the Get With The Guidelines database. Data abstracted included racial and ethnic distribution (White, African American, Asian, Pacific Islander, Native American and Hispanic), age, sex, and selected co-morbidities (diabetes mellitus, hypertension and warfarin use. FINDINGS: There were a total of 260 patients. The total number of Pacific Islanders (4), Native Americans (1) and African Americans (13) was too small for further analysis and was not included. The age and sex distribution was similar between White, Asian and Hispanic patients but White women were significantly older (p = 0.018) than males. The rate of warfarin use was similar in all three groups. There was a higher incidence of hypertension and diabetes mellitus in Asian and Hispanics compared to White subjects ( Table ). Asian and Hispanic patients with hypertension and/or diabetes mellitus were at higher risk for ICH compared to White ( Table ). CONCLUSION: In our population, the incidence of ICH is disproportionately high in Asian subjects compared to Whites and Hispanics. This increase is only partially explained by higher incidence of hypertension and diabetes mellitus in Asians. Other factors, not included in the available databases, may include the geographic origin of Asian and Hispanic subjects (East vs. South Asian, North, Central or South American) and a generational effect on co-morbidities. Future epidemiological studies should include geographic and generational, as well as racial and ethnic data.

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Limited Evidence for Selection at the FADS Locus in Native American Populations

Molecular Biology and Evolution ◽

10.1093/molbev/msaa064 ◽

2020 ◽

Vol 37 (7) ◽

pp. 2029-2033 ◽

Cited By ~ 2

Author(s):

Iain Mathieson

Keyword(s):

Fatty Acids ◽

Native American ◽

Native Americans ◽

Polyunsaturated Fatty Acids ◽

Direct Evidence ◽

Northern Eurasia ◽

Ancestral State ◽

Asian Populations ◽

Selection Signal ◽

Long Chain

Abstract The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection—postdating the split from Native Americans—in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.

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Native American sports mascots activate negative stereotypes about contemporary Native Americans

PsycEXTRA Dataset ◽

10.1037/e527772014-414 ◽

2011 ◽

Author(s):

Elizabeth Focella ◽

Jessica Whitehead ◽

Jeff Stone ◽

Stephanie Fryberg ◽

Rebecca Covarrubias

Keyword(s):

Native American ◽

Native Americans ◽

Negative Stereotypes

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Native Americans and the Third World Strike at UC Berkeley

Explorations in Ethnic Studies ◽

10.1525/esr.2019.42.2.32 ◽

2019 ◽

Vol 42 (2) ◽

pp. 32-39

Author(s):

LaNada War Jack

Keyword(s):

Native American ◽

Native Americans ◽

Personal Experience ◽

Third World ◽

Leadership Roles ◽

The Third ◽

The Creation ◽

The 1960S ◽

The Third World ◽

The University

The author reflects on her personal experience as a Native American at UC Berkeley in the 1960s as well as on her activism and important leadership roles in the 1969 Third World Liberation Front student strike, which had as its goal the creation of an interdisciplinary Third World College at the university.

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Indian Genocide – A Study Through The Works of Elizabeth Cook-Lynn

SMART MOVES JOURNAL IJELLH ◽

10.24113/ijellh.v6i9.9855 ◽

2018 ◽

Vol 6 (9) ◽

pp. 5

Author(s):

Poonam Chourey

Keyword(s):

Native American ◽

Native Americans ◽

South Dakota ◽

Native People ◽

The South ◽

The People ◽

Freedom Fighters ◽

Purpose Of Business ◽

Wounded Knee ◽

Shed Light

The research expounded the turmoil, uproar, anguish, pain, and agony faced by native Indians and Native Americans in the South Dakota region. To explain the grief, pain and lamentation, this research studies the works of Elizabeth Cook-Lyn. She laments for the people who died and also survived in the Wounded Knee Massacre. The people at that time went through huge exploitation and tolerated the cruelty of American Federal government. This research brings out the unchangeable scenario of the Native Americans and Native Indians. Mr. Padmanaban shed light on the works of Elizabeth Cook-Lynn who was activist. Mr. Padmanaban is very influenced with Elizabeth Cook-Lynn’s thoughts and works. She hails from Sioux Community, a Native American. She was an outstanding and exceptional scholar. She experienced the agony and pain faced by the native people. The researcher, Mr. Padmanaban is concerned the sufferings, agony, pain faced by the South Dakota people at that time. The researcher also is acknowledging the Indian freedom fighters who got India independence after over 200 years of sufferings. The foreign nationals entered our country with the sole purpose of business. Slowly and steadily the took over the reign of the country and ruled us for years, made all of us suffer a lot.

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A genome-wide map of regulatory elements in zebrafish

Lab Animal ◽

10.1038/s41684-020-00695-7 ◽

2020 ◽

Vol 50 (1) ◽

pp. 17-17

Author(s):

Alexandra Le Bras

Keyword(s):

Regulatory Elements ◽

Genome Wide ◽

A Genome

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Mapping CRISPR-Cas9 public and commercial innovation using The Lens institutional toolkit

Transgenic Research ◽

10.1007/s11248-021-00237-y ◽

2021 ◽

Author(s):

Osmat Azzam Jefferson ◽

Simon Lang ◽

Kenny Williams ◽

Deniz Koellhofer ◽

Aaron Ballagh ◽

...

Keyword(s):

Public Investment ◽

Open Data ◽

Regulatory Elements ◽

Policy Makers ◽

Base Editing ◽

The Public ◽

Homology Directed Repair ◽

A Genome ◽

Institutional Capability ◽

Cellular Dna

AbstractCRISPR-Cas9 is a revolutionary technology because it is precise, fast and easy to implement, cheap and components are readily accessible. This versatility means that the technology can deliver a timely end product and can be used by many stakeholders. In plant cells, the technology can be applied to knockout genes by using CRISPR–Cas nucleases that can alter coding gene regions or regulatory elements, alter precisely a genome by base editing to delete or regulate gene expression, edit precisely a genome by homology-directed repair mechanism (cellular DNA), or regulate transcriptional machinery by using dead Cas proteins to recruit regulators to the promoter region of a gene. All these applications can be for: 1) Research use (Non commercial), 2) Uses related product components for the technology itself (reagents, equipment, toolkits, vectors etc), and 3) Uses related to the development and sale of derived end products based on this technology. In this contribution, we present a prototype report that can engage the community in open, inclusive and collaborative innovation mapping. Using the open data at the Lens.org platform and other relevant sources, we tracked, analyzed, organized, and assembled contextual and bridged patent and scholarly knowledge about CRISPR-Cas9 and with the assistance of a new Lens institutional capability, The Lens Report Builder, currently in beta release, mapped the public and commercial innovation pathways of the technology. When scaled, this capability will also enable coordinated editing and curation by credentialed experts to inform policy makers, businesses and private or public investment.

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A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽

10.3390/genes12071007 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1007

Author(s):

Divya Kattupalli ◽

Asha Sreenivasan ◽

Eppurathu Vasudevan Soniya

Keyword(s):

Phytophthora Capsici ◽

Regulatory Elements ◽

Piper Nigrum ◽

Binding Motif ◽

Altered Expression ◽

Genome Wide ◽

A Genome ◽

Pathogenesis Related Protein ◽

Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

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