Cryptic Native American ancestry recapitulates population-specific migration and settlement of the continental United States

Mapping Intimacies ◽

10.1101/333609 ◽

2018 ◽

Cited By ~ 1

Author(s):

I. King Jordan ◽

Lavanya Rishishwar ◽

Andrew B. Conley

Keyword(s):

African American ◽

Native American ◽

Mexican American ◽

African Ancestry ◽

Westward Expansion ◽

Native American Ancestry ◽

Southeastern Us ◽

Jewish Ancestry ◽

The Us ◽

African Descendants

AbstractEuropean and African descendants settled the continental US during the 17th-19th centuries, coming into contact with established Native American populations. The resulting admixture among these groups yielded a significant reservoir of cryptic Native American ancestry in the modern US population. We analyzed the patterns of Native American admixture seen for the three largest genetic ancestry groups in the US population: African American, European American, and Hispanic/Latino. The three groups show distinct Native American ancestry profiles, which are indicative of their historical patterns of migration and settlement across the country. Native American ancestry in the modern African American population does not coincide with local geography, instead forming a monophyletic group with origins in the southeastern US, consistent with the Great Migration of the early 20th century. European Americans show Native American ancestry that tracks their geographic origins across the US, indicative of ongoing contact during westward expansion, and Native American ancestry can resolve Hispanic/Latino individuals into distinct local groups formed by more recent migration from Mexico and Puerto Rico. We found an anomalous pattern of Native American ancestry from the US southwest, which most likely corresponds to the Nuevomexicano descendants of early Spanish settlers to the region. We addressed a number of controversies surrounding this population, including the extent of Sephardic Jewish ancestry. Nuevomexicanos are less admixed than nearby Mexican-American individuals, with more European and less Native American and African ancestry, and while they do show demonstrable Sephardic Jewish ancestry, the fraction is no greater than seen for other Hispanic/Latino populations.

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Ancestry-dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

10.1101/382721 ◽

2018 ◽

Author(s):

Zachary A. Szpiech ◽

Angel C.Y. Mak ◽

Marquitta J. White ◽

Donglei Hu ◽

Celeste Eng ◽

...

Keyword(s):

Native American ◽

Mexican American ◽

Complex Disease ◽

Disease Risk ◽

African Ancestry ◽

Population History ◽

Whole Genome Sequencing Data ◽

Runs Of Homozygosity ◽

Sequencing Data ◽

Local Ancestry

AbstractRuns of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical-by-descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole genome sequencing data from 1,441 individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.

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Relevance of the ancestry for the variability of the Drug-Metabolizing Enzymes CYP2C9, CYP2C19 and CYP2D6 polymorphisms in a multiethnic Costa Rican population

Revista de Biología Tropical ◽

10.15517/rbt.v64i3.20901 ◽

2016 ◽

Vol 64 (3) ◽

Cited By ~ 7

Author(s):

Carolina Céspedes-Garro ◽

Fernanda Rodrigues-Soares ◽

Gerardo Jiménez-Arce ◽

María-Eugenia G. Naranjo ◽

Eduardo Tarazona-Santos ◽

...

Keyword(s):

Native American ◽

African Ancestry ◽

Geographic Location ◽

Central Valley ◽

Costa Rican ◽

The Self ◽

Native American Ancestry ◽

Admixed Population ◽

Increased Activity ◽

Cyp2d6 Polymorphisms

CYP2C9, CYP2C19 and CYP2D6 metabolize around 40% of drugs and their genes vary across populations. The Costa Rican population has a trihybrid ancestry and its key geographic location turns it into a suitable scenario to evaluate interethnic differences across populations. This study aims to describe the diversity of CYP2C9, CYP2C19 and CYP2D6 polymorphisms in Costa Rican populations in the context of their ancestry. A total of 448 healthy individuals were included in the study: Bribri (n= 47), Cabécar (n= 27), Maleku (n= 16), Guaymí (n= 30), Huetar (n= 48), Chorotega (n= 41), Admixed/Mestizos from the Central Valley/Guanacaste (n= 189), and Afro-Caribbeans (n= 50) from Limón. CYP2C9 (alleles *2, *3, *6) and CYP2C19 (*2, *3, *4, *5, *17) genotypes were determined by Real-Time PCR. African, European and Native American ancestry were inferred using 87 ancestry informative markers. The frequency of the decreased activity allele CYP2C9*2 is lower in the self-reported Amerindian groups compared to the admixed population, and the highest frequencies of CYP2C19*2 (null activity) and the CYP2C19*17 (increased activity) were found in the self-reported Afro-Caribbean population. Moreover, a frequency of 0.7 % CYP2C9 gPMs in the Admixed population and a variable frequency of CYP2C19 gUMs (0.0-32.6 %, more prevalent in Afro-Caribbeans) in Costa Rican populations, was found. Finally, the following alleles were positively correlated with genomic African ancestry and negatively correlated with genomic Native American ancestry: CYP2D6*5 (null activity), CYP2D6*17 (decreased activity), CYP2D6*29 (decreased activity) and CYP2C19*17 (increased activity). No correlation for CYP2C9 polymorphisms and genomic ancestry was found. Further studies assessing the CYP2C9 and CYP2C19 sequence in these populations, preferentially by sequencing these genes, are warranted.

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Transamerican Sentimentalism and Nineteenth-Century US Literary History

10.1093/oso/9780198862338.001.0001 ◽

2020 ◽

Author(s):

Maria A. Windell

Keyword(s):

Nineteenth Century ◽

African American ◽

Native American ◽

Literary History ◽

Sentimental Novel ◽

American Women Writers ◽

Cultural Violence ◽

The Us ◽

Anglo American ◽

Marginal Characters

Transamerican Sentimentalism and Nineteenth-Century US Literary History argues that African American, Native American, Latinx, and Anglo-American women writers use genre to negotiate hemispheric encounters amidst the gendered, racialized, and cultural violence of the nineteenth-century Americas. Although US literary sentimentalism is often framed in national and transatlantic terms, this book argues that the mode was deeply transamerican. Given the popularity of the nineteenth-century sentimental novel, the appearance of its central motifs—tearful embraces, fainting heroines, angelic children—in transamerican US texts is unsurprising. What is remarkable is how texts not generally considered sentimental deploy seemingly insignificant affective episodes to navigate gendered and racialized experiences of conflict throughout the Caribbean and the US–Mexico borderlands. Throughout Transamerican Sentimentalism, marginal characters, momentary gestures, offhand remarks, and narrative commentaries serve to disrupt plots, potentially connecting characters across cultural, racial, national, and linguistic borders. Transamerican sentimentalism cannot unseat the violence of the nineteenth-century Americas, but it does dislocate familiar figures such as the coquette and the mulatta to produce other potential outcomes—including new paradigms for understanding the coquette, a locally successful informal diplomacy, and motivations for violent slave revolt. Transamerican sentimentalism is a fleeting, mercurial, and marginal mode. Frequently overwhelmed by the violence pervading the hemisphere, it could be categorized as a failed venture. Yet it is also persistent; as it recurs throughout the nineteenth century, it opens into alternative African American, Native American, and Latinx avenues for navigating and comprehending US–Americas relations.

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Native American Ancestry and Air Pollution Interact to Impact Bronchodilator Response in Puerto Rican Children with Asthma

Ethnicity & Disease ◽

10.18865/ed.31.1.77 ◽

2021 ◽

Vol 31 (1) ◽

pp. 77-88

Author(s):

Maria Contreras ◽

Kevin Keys ◽

Joaquin Magana ◽

Page Goddard ◽

Oona Risse-Adams ◽

...

Keyword(s):

Air Pollution ◽

Native American ◽

Puerto Rican ◽

Mexican American ◽

Morbidity And Mortality ◽

Common Chronic Disease ◽

Asthma Morbidity ◽

Native American Ancestry ◽

Children With Asthma ◽

American Children

Objective: Asthma is the most common chronic disease in children. Short-acting bronchodilator medications are the most commonly prescribed asthma treatment worldwide, regardless of disease severity. Puerto Rican children display the highest asthma morbidity and mortality of any US population. Alarmingly, Puerto Rican children with asthma display poor bronchodilator drug response (BDR). Reduced BDR may explain, in part, the increased asthma morbidity and mortality observed in Puerto Rican children with asthma. Gene-environment interactions may explain a portion of the heritability of BDR. We aimed to identify gene-environment interactions associated with BDR in Puerto Rican children with asthma.Setting: Genetic, environmental, and psycho-social data from the Genes-environments and Admixture in Latino Americans (GALA II) case-control study.Participants: Our discovery dataset consisted of 658 Puerto Rican children with asthma; our replication dataset consisted of 514 Mexican American children with asthma.Main Outcomes Measures: We assessed the association of pairwise interaction models with BDR using ViSEN (Visualization of Statistical Epistasis Networks).Results: We identified a non-linear interaction between Native American genetic ancestry and air pollution significantly associated with BDR in Puerto Rican children with asthma. This interaction was robust to adjustment for age and sex but was not significantly associated with BDR in our replication population.Conclusions: Decreased Native American ancestry coupled with increased air pollution exposure was associated with increased BDR in Puerto Rican children with asthma. Our study acknowledges BDR’s phenotypic complexity, and emphasizes the importance of integrating social, environmental, and biological data to further our understanding of complex disease.Ethn Dis. 2021;31(1):77- 88; doi:10.18865/ed.31.1.77

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Genetic Ancestry and Skeletal Toxicities Among Childhood Acute Lymphoblastic Leukemia Patients in the DFCI 05-001 Cohort

Blood ◽

10.1182/blood-2019-126814 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 3811-3811

Author(s):

Qianqian Zhu ◽

Song Yao ◽

Peter D Cole ◽

Justine M. Kahn ◽

Marian H. Harris ◽

...

Keyword(s):

Native American ◽

Lower Risk ◽

Lymphoblastic Leukemia ◽

African Ancestry ◽

Genetic Ancestry ◽

Risk Of Fracture ◽

Native American Ancestry ◽

Hispanic Patients ◽

Race Ethnicity ◽

Hispanic White

Background: Despite outstanding cure rates of pediatric acute lymphoblastic leukemia (ALL), Blacks and Hispanics have inferior survival than Whites. We recently reported that among 794 children from DFCI ALL Consortium Protocol 05-001 trial, Hispanic patients had significantly lower rates of fracture and osteonecrosis, but higher risk of relapse and death compared with non-Hispanic Whites (PMID: 29090520). Studies from other groups have reported inferior ALL outcomes in children with Native American ancestry, however the association between genetic ancestry and skeletal toxicities has not been explored. We examined whether genetic inheritance could provide an explanation for the reduced incidence of skeletal toxicities in Hispanic patients in DFCI 05-001. Methods: A total of 576 DNA samples extracted from bone marrow samples or blood samples obtained during remission, including 2% blind duplicates, were genotyped using the Illumina OmniExpress Beadchip array. After data QC and cleaning, 449 ALL patients were retained in the final analysis. Estimates of global genetic ancestry were derived from STRUCTURE program, which was used to re-classify individuals with discordant clinical race/ethnicity as reported by study site, and to assign individuals with unknown race/ethnicity information to an ethnic group when possible. Regression model for the subdistribution hazard of the cumulative incidence function was used to relate clinical race/ethnicity, genetically reclassified race/ethnicity, and genetic ancestry respectively with risk of fracture and osteonecrosis, with death and recurrence as competing risk factors while controlling for age, gender and baseline clinical factors. Cox proportional regression models were used to test race/ethnicity and ancestry with overall survival (OS) and event-free survival (EFS). Results: Among the 449 patients analyzed, average age was 6.7 years; 26% of patients were ≥10 years and 44% were female. The demographic and clinical characteristics of patients with genotype data were similar to those of the overall cohort, although the proportion of Hispanics was slightly lower in the genotyped sub-cohort (17% vs. 21%), whereas the rates of fracture and osteonecrosis were higher (fracture: 25% vs. 18%; osteonecrosis: 10% vs. 8%). Based on clinical race/ethnicity, 66% of patients were non-Hispanic White, 17% were Hispanic, 5% were non-Hispanic Black, 3% were Asian, and 10% were reported as Other. Genetic ancestry analyses revealed that non-Hispanic White patients had a median of 96% European ancestry, non-Hispanic Black patients had a median of 76% African ancestry, and Asian patients had a median of 58% Asian ancestry. The genetic make-up of Hispanic patients in the 05-001 cohort was more admixed, with 23% Native American and 17% African ancestry, higher than the national average (18% and 6%, respectively). After genetic reassignment, racial/ethnic groups were as follows: 68% non-Hispanic White, 17% Hispanic, 9% non-Hispanic Black, 6% Asian, and 1% unassigned. In analysis of genetically reassigned race/ethnicity with skeletal toxicities, Hispanic and Black patients had significantly lower risk of fracture compared with white patients (Hispanic: subdistribution hazard ratio [SHR]=0.42, 95% confidence interval [CI]=0.22, 0.81; Black: HR=0.28, 95%CI=0.10, 0.75). These groups also had significantly less osteonecrosis (Hispanic: SHR=0.24, 95%CI=0.08, 0.78; Black: SHR=0.12, 95%CI=0.02, 0.93). Similar results were observed when using clinical race/ethnicity. Further analyses revealed that African genetic ancestry, but not Native American ancestry was associated with lower risk of fracture and osteonecrosis in a dose-dependent manner (Table 1). In analysis of death and recurrence, those with higher proportion of Native American ancestry had significantly higher risk of death/recurrence after adjustment (OS: hazard ratio [HR]=4.00, 95%CI=1.45, 11.02; EFS: HR=2.07, 95%CI=1.13, 3.79). Analysis of single variants and polygenic risk scores with skeletal toxicities and survival outcomes is ongoing. Conclusion: Hispanic children and adolescents from the DFCI 05-001 cohort, had highly heterogenous genetic ancestral make-up. Among Hispanic patients, the observed lower risk of skeletal toxicities might be driven by African ancestry, whereas poorer survival observed might be driven by Native American ancestry. Disclosures Silverman: Servier: Consultancy, Research Funding; Takeda: Consultancy.

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Home life and health among Native American, African American, and Latino adolescents.

Health Psychology ◽

10.1037/hea0000776 ◽

2019 ◽

Vol 38 (8) ◽

pp. 738-747 ◽

Cited By ~ 1

Author(s):

Robert H. Bradley

Keyword(s):

African American ◽

Native American ◽

Latino Adolescents ◽

Home Life

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Women, the Civil War, and Reconstruction

10.1093/oxfordhb/9780190222628.013.21 ◽

2018 ◽

Author(s):

Hannah Rosen

Keyword(s):

Native American ◽

Civil War ◽

Political Violence ◽

Postwar Period ◽

Native American Women ◽

Black And White ◽

The Us ◽

Women's Lives ◽

Class Hierarchies ◽

Us Civil War

The rapid transformations brought on by the US Civil War and its aftermath touched women’s lives in contradictory ways. The disruption caused by war and the destruction of slavery opened up space, and at times created the necessity, for radically new roles for women that challenged antebellum gender norms and racial and class hierarchies. This essay examines the wartime and postwar experiences primarily of black and white but also Native American women. In this period, many women faced new circumstances that inspired them to confront power in novel ways—by, for instance, fleeing slavery, petitioning governors, organizing bread riots, participating in political parades, or protesting segregation. The chapter also explores political violence in the postwar period that affected women differently across class, race, and region and that eventually helped to shut down the radical potential of the era.

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African American Unemployment and the Disparity in Periviable Births

Journal of Racial and Ethnic Health Disparities ◽

10.1007/s40615-021-01022-7 ◽

2021 ◽

Author(s):

Ralph Catalano ◽

Deborah Karasek ◽

Tim Bruckner ◽

Joan A. Casey ◽

Katherine Saxton ◽

...

Keyword(s):

African American ◽

African American Women ◽

Unemployment Rate ◽

Racial Disparity ◽

Live Births ◽

Percentage Point Increase ◽

Point Increase ◽

The Us ◽

Race Ethnicity ◽

Hispanic White

AbstractPeriviable infants (i.e., born before 26 complete weeks of gestation) represent fewer than .5% of births in the US but account for 40% of infant mortality and 20% of billed hospital obstetric costs. African American women contribute about 14% of live births in the US, but these include nearly a third of the country’s periviable births. Consistent with theory and with periviable births among other race/ethnicity groups, males predominate among African American periviable births in stressed populations. We test the hypothesis that the disparity in periviable male births among African American and non-Hispanic white populations responds to the African American unemployment rate because that indicator not only traces, but also contributes to, the prevalence of stress in the population. We use time-series methods that control for autocorrelation including secular trends, seasonality, and the tendency to remain elevated or depressed after high or low values. The racial disparity in male periviable birth increases by 4.45% for each percentage point increase in the unemployment rate of African Americans above its expected value. We infer that unemployment—a population stressor over which our institutions exercise considerable control—affects the disparity between African American and non-Hispanic white periviable births in the US.

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