scholarly journals Assortative mating on ancestry-variant traits in admixed Latin American populations

2017 ◽  
Author(s):  
Emily T. Norris ◽  
Lavanya Rishishwar ◽  
Lu Wang ◽  
Andrew B. Conley ◽  
Aroon T. Chande ◽  
...  
Keyword(s):  
Native American ◽  
Assortative Mating ◽  
Latin American ◽  
African Ancestry ◽  
Ethnically Diverse ◽  
Continental Population Groups ◽  
Continental Population ◽  
Novel Approach ◽  
Genome Wide ◽  
Facial Development

AbstractBackgroundAssortative mating is a universal feature of human societies, and individuals from ethnically diverse populations are known to mate assortatively based on similarities in genetic ancestry. However, little is currently known regarding the exact phenotypic cues, or their underlying genetic architecture, which inform ancestry-based assortative mating.ResultsWe developed a novel approach, using genome-wide analysis of ancestry-specific haplotypes, to evaluate ancestry-based assortative mating on traits whose expression varies among the three continental population groups – African, European, and Native American – that admixed to form modern Latin American populations. Application of this method to genome sequences sampled from Colombia, Mexico, Peru, and Puerto Rico revealed widespread ancestry-based assortative mating. We discovered a number of anthropometric traits (body mass, height, facial development and waist-hip ratio) and neurological attributes (educational attainment and schizophrenia) that serve as phenotypic cues for ancestry-based assortative mating. Major histocompatibility complex (MHC) loci show population-specific patterns of both assortative and disassortative mating in Latin America. Ancestry-based assortative mating in the populations analyzed here appears to be driven primarily by African ancestry.ConclusionsThis study serves as an example of how population genomic analyses can yield novel insights into human behavior.

scholarly journals Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations

2015 ◽  
Vol 112 (28) ◽  
pp. 8696-8701 ◽  
Author(s):  
Fernanda S. G. Kehdy ◽  
Mateus H. Gouveia ◽  
Moara Machado ◽  
Wagner C. S. Magalhães ◽  
Andrea R. Horimoto ◽  
...  
Keyword(s):  
Native American ◽  
Latin American ◽  
Middle Eastern ◽  
Classical Model ◽  
African Ancestry ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
European Ancestry ◽  
Eastern Region ◽  
Whole Genome Analysis

While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture. We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genome-wide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6–8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes.

scholarly journals Genetic admixture patterns in Argentinian Patagonia

2019 ◽  
Author(s):  
María Laura Parolin ◽  
Ulises F Toscanini ◽  
Irina F Velázquez ◽  
Cintia Llull ◽  
Gabriela L Berardi ◽  
...  
Keyword(s):  
Native American ◽  
Latin American ◽  
African Ancestry ◽  
Geographic Origin ◽  
Sub Saharan Africa ◽  
European Ancestry ◽  
Genetic Admixture ◽  
The North ◽  
Sub Saharan ◽  
Different Origins

AbstractAs for other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan Africa. However, it is known that the admixture processes did not occur homogeneously throughout the country. Therefore, considering the importance for anthropological, medical and forensic researches, this study aimed to investigate the population genetic structure of the Argentinian Patagonia, through the analysis of 46 ancestry informative markers, in 433 individuals from five different localities. Overall, in the Patagonian sample, the average individual ancestry was estimated as 35.8% Native American (95% CI: 32.2-39.4%), 62.1% European (58.5-65.7%) and 2.1% African (1.7-2.4%). Comparing the five localities studied, statistically significant differences were observed for the Native American and European contributions, but not for the African ancestry. The admixture results combined with the genealogical information revealed intra-regional variations that are consistent with the different geographic origin of the participants and their ancestors. As expected, a high European ancestry was observed for donors with four grandparents born in Europe (96.8%) or in the Central region of Argentina (85%). In contrast, the Native American ancestry increased when the four grandparents were born in the North (71%) or in the South (61.9%) regions of the country, or even in Chile (60.5%). In summary, our results showed that differences on continental ancestry contribution have different origins in each region in Patagonia, and even in each locality, highlighting the importance of knowing the origin of the participants and their ancestors for the correct interpretation and contextualization of the genetic information.

scholarly journals Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers

BMJ Open ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. e025530 ◽  
Author(s):  
Annina B Schmid ◽  
Kaustubh Adhikari ◽  
Luis Miguel Ramirez-Aristeguieta ◽  
Juan-Camilo Chacón-Duque ◽  
Giovanni Poletti ◽  
...  
Keyword(s):  
Latin American ◽  
Pain Sensitivity ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Healthy Individuals ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
The University ◽  
Genetic Contributions

IntroductionPain constitutes a major component of the global burden of diseases. Recent studies suggest a strong genetic contribution to pain susceptibility and severity. Whereas most of the available evidence relies on candidate gene association or linkage studies, research on the genetic basis of pain sensitivity using genome-wide association studies (GWAS) is still in its infancy. This protocol describes a proposed GWAS on genetic contributions to baseline pain sensitivity and nociceptive sensitisation in a sample of unrelated healthy individuals of mixed Latin American ancestry.Methods and analysisA GWAS on genetic contributions to pain sensitivity in the naïve state and following nociceptive sensitisation will be conducted in unrelated healthy individuals of mixed ancestry. Mechanical and thermal pain sensitivity will be evaluated with a battery of quantitative sensory tests evaluating pain thresholds. In addition, variation in mechanical and thermal sensitisation following topical application of mustard oil to the skin will be evaluated.Ethics and disseminationThis study received ethical approval from the University College London research ethics committee (3352/001) and from the bioethics committee of the Odontology Faculty at the University of Antioquia (CONCEPTO 01–2013). Findings will be disseminated to commissioners, clinicians and service users via papers and presentations at international conferences.

scholarly journals Eyes of Africa: The Genetics of Blindness: Study Design and Methodology

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olusola Olawoye ◽  
Chimdi Chuka-Okosa ◽  
Onoja Akpa ◽  
Tony Realini ◽  
Michael Hauser ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Case Control Study ◽  
African Ancestry ◽  
Collaborative Study ◽  
Data Set ◽  
Human Heredity ◽  
Genome Wide ◽  
A Genome ◽  
Multiplex Families ◽  
Control Study

Abstract Background This report describes the design and methodology of the “Eyes of Africa: The Genetics of Blindness,” a collaborative study funded through the Human Heredity and Health in Africa (H3Africa) program of the National Institute of Health. Methods This is a case control study that is collecting a large well phenotyped data set among glaucoma patients and controls for a genome wide association study. (GWAS). Multiplex families segregating Mendelian forms of early-onset glaucoma will also be collected for exome sequencing. Discussion A total of 4500 cases/controls have been recruited into the study at the end of the 3rd funded year of the study. All these participants have been appropriately phenotyped and blood samples have been received from these participants. Recent GWAS of POAG in African individuals demonstrated genome-wide significant association with the APBB2 locus which is an association that is unique to individuals of African ancestry. This study will add to the existing knowledge and understanding of POAG in the African population.

Methods for Using Ecological Momentary Assessment to Assess Weight-related Behaviors in the Home Environment of Children from Low-Income, Racially/Ethnically Diverse and Immigrant Households (Preprint)

2021 ◽  
Author(s):  
Amanda Trofholz ◽  
Allan Tate ◽  
Mark Janowiec ◽  
Angela Fertig ◽  
Katie Loth ◽  
...  
Keyword(s):  
Native American ◽  
Phase I ◽  
Home Environment ◽  
Low Income ◽  
Ecological Momentary Assessment ◽  
Ethnically Diverse ◽  
Conducting Phase ◽  
The Family ◽  
Ecological Momentary ◽  
Momentary Assessment

BACKGROUND Ecological momentary assessment (EMA) is an innovative tool to capture in-the-moment health behaviors as people go about their regular lives. EMA is an ideal tool to measure weight-related behaviors, such as parent feeding practices, stress, and dietary intake, as these occur on a daily basis and vary across time and context. A recent systematic review recommended standardized reporting of EMA design for studies that address weight-related behaviors. OBJECTIVE This manuscript describes in detail the EMA design of the Family Matters study. METHODS Family Matters is an incremental, two-phased, mixed-methods study conducted with a racially/ethnically diverse and immigrant/refugee sample from largely low-income households designed to examine the risk and protective factors for childhood obesity in the home environment. The Family Matters study intentionally recruited White, Black, Hmong, Latino, Native American, and Somali parents with young children. Parents in Phase I of the study completed eight days of EMA on their smart phones, which included 1) signal-contingent surveys (e.g., asking about the parent’s stress at the time of the survey); 2) event-contingent surveys (e.g., descriptions of the meal the child ate); 3) end-of-day surveys (e.g., overall assessment of the child’s day).cribes in detail the EMA design of the Family Matters study. RESULTS A detailed description of EMA strategies, protocols, and methods used in Phase I of the Family Matters study is provided. Compliance with EMA surveys and participant time spent completing EMA surveys is presented, stratified by race/ethnicity. Additionally, lessons learned while conducting Phase I EMA are shared to document how EMA methods were improved and expanded upon for Phase II. CONCLUSIONS Results from this study provide an important next step in identifying best practices for EMA use in assessing weight-related behaviors in the home environment.

Impact of depression and stress on placental DNA methylation in ethnically diverse pregnant women

Epigenomics ◽  
2021 ◽  
Author(s):  
Markos Tesfaye ◽  
Suvo Chatterjee ◽  
Xuehuo Zeng ◽  
Paule Joseph ◽  
Fasil Tekola-Ayele
Keyword(s):  
Dna Methylation ◽  
Fetal Brain ◽  
Ethnically Diverse ◽  
Antenatal Depression ◽  
Epigenetic Changes ◽  
Clinical Trial Registration ◽  
False Discovery ◽  
Genome Wide ◽  
Neuropsychiatric Diseases ◽  
Registration Number

Aim: To investigate the association between placental genome-wide methylation at birth and antenatal depression and stress during pregnancy. Methods: We examined the association between placental genome-wide DNA methylation (n = 301) and maternal depression and stress assessed at six gestation periods during pregnancy. Correlation between DNA methylation at the significantly associated CpGs and expression of nearby genes in the placenta was tested. Results: Depression and stress were associated with methylation of 16 CpGs and two CpGs, respectively, at a 5% false discovery rate. Methylation levels at two of the CpGs associated with depression were significantly associated with expression of ADAM23 and CTDP1, genes implicated in neurodevelopment and neuropsychiatric diseases. Conclusion: Placental epigenetic changes linked to antenatal depression suggest potential fetal brain programming. Clinical trial registration number: NCT00912132 (ClinicalTrials.gov)

“Borderland” as a way of preserving and asserting identity. The historical experience of the Native American cultures of Latin America in a universal context

2021 ◽  
pp. 83
Author(s):  
Yakov Shemyakin
Keyword(s):  
Latin America ◽  
Native American ◽  
Latin American ◽  
Historical Experience ◽  
Cultural System ◽  
Relationship Of ◽  
The Relationship ◽  
Linguistic Reality

The article substantiates the thesis that modern Native American cultures of Latin America reveal all the main features of "borderland" as a special state of the socio-cultural system (the dominant of diversity while preserving the unity sui generis, embodied in the very process of interaction of heterogeneous traditions, structuring linguistic reality in accordance with this dominant, the predominance of localism in the framework of the relationship between the universal and local dimensions of the life of Latin American societies, the key role of archaism in the system of interaction with the heritage of the 1st "axial time», first of all, with Christianity, and with the realities of the "second axial time" - the era of modernization. The author concludes that modern Indian cultures are isomorphic in their structure to the "borderline" Latin American civilization, considered as a "coalition of cultures" (K. Levi-Strauss), which differ significantly from each other, but are united at the deepest level by an extremely contradictory relationship of its participants.

Application of the Optimized Summed Score Attributes Method for Sex Estimation

2021 ◽  
Author(s):  
Holly Long ◽  
Alexandra Klales
Keyword(s):  
Sexual Dimorphism ◽  
African Ancestry ◽  
European Ancestry ◽  
Sex Bias ◽  
Sex Estimation ◽  
Black African ◽  
Asian Populations ◽  
Novel Approach ◽  
Calibration Sample ◽  
Accuracy Rates

The optimized summed scored attributes (OSSA) method was first developed for cranial ancestry estimation (Hefner & Ousley 2014). Tallman and Go (2018) adapted this method for sex estimation with the five skull traits described by Buikstra and Ubelaker (1994) and Walker (2008). Using an Asian sample, Tallman and Go (2018) achieved moderate accuracy rates (83.7% calibration; 81.9% validation) but also high sex bias (29.1% calibration; 34.5% validation), possibly due to lower levels of sexual dimorphism in Asian populations. To further explore this novel approach to sex estimation, the OSSA method was applied to a U.S. Black/African ancestry and White/European ancestry calibration sample (N = 700). Accuracy rates were 77.4% in Black individuals and 77.2% in White individuals. Despite generally higher levels of sexual dimorphism in these groups, a high sex bias still occurred (15.4% Black individuals; –20.5% White individuals) using OSSA. The method was tested in a separate validation sample (N = 200) with accuracy of 78.0% in Black individuals (8.0% sex bias) and 70.0% in White individuals (–56.0% sex bias). When these same traits were tested with Walker’s (2008) logistic regression and in the MorphoPASSE Program (Klales 2018) using random forest modeling, accuracy rates varied ,with OSSA (77.3% correct), performing slightly better than Walker’s (2008) method (75.6% correct) but worse than MorphoPASSE (85.3% correct). The higher accuracy and lower sex bias in MorphoPASSE suggests that the Walker (2008) traits can be used to accurately estimate sex with statistical approaches more appropriate and robust than OSSA.

scholarly journals Ancestry-dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

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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