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Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals
Open accessAbstract
The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.
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“They assessed genetic ancestry with 15,000 SNPs, making their index highly-reliable [56].”
From Global Ancestry and Cognitive Ability (2019) · cites this paper as [56]
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“%) and Middle Eastern (5.26%), reflecting a strong sex bias in the admixture process during and after the colonial period, as has been previously described in other Latin American populations 60–63 .”
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InfluentialGenetic ancestry and population structure in the All of Us Research Program cohort
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“…instance, while the proportion of Amerindian alleles in certain regions of South America is substantial (Wang et al., 2008; Galanter et al., 2012; Ruiz-Linares et al., 2014; Salzano and Sans, 2014; Homburger et al., 2015; SalazarFlores et al., 2015), there is little evidence of Amerindian…”
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The HABP2 G534E polymorphism does not increase nonmedullary thyroid cancer risk in Hispanics
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“Recent 64 work has begun to assess the implications of these patterns, including effects on common 65 demographic inference strategies and on genetic/phenotypic variation (7,14,24).”
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“This is somewhat expected as the Colombians have on average 60% European (Spanish) ancestry.(26) Having a well spread out distribution of allele frequencies is important in a GWAS as low-frequency alleles have lower power for a given sample and effect size.”
BackgroundSelf-citationA vitamin D pathway gene–gene interaction affects low-density lipoprotein cholesterol levels
Grave, N., Tovo‐Rodrigues, L., da Silveira, J., Rovaris, D. L., Bosco, S. M. D., Contini, V., & Genro, J. P. (2016) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2016.08.002 · Cited by 18
Assortative Mating on Ancestry-Variant Traits in Admixed Latin American Populations
Norris, E. T., Rishishwar, L., Wang, L., Conley, A. B., Chande, A. T., Dąbrowski, A., Valderrama-Aguirre, A., & Jordan, I. K. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00359 · Cited by 20
“The confluence of African, European and Native American populations that marked the conquest and colonization of the New World yielded modern Latin American populations that are characterized by three-way genetic admixture (Wang et al., 2008; Bryc et al., 2010; Ruiz-Linares et al., 2014; Montinaro et al., 2015; Rishis…”
BackgroundBiogeographic Ancestry and Socioeconomic Outcomes in the Americas: A Meta-Analysis
Kirkegaard, E. O. W., Wang, M., & Fuerst, J. G. R. (2017) · Mankind Quarterly · doi:10.46469/mq.2017.57.3.10 · Cited by 17
Boquett, J. A., Schüler‐Faccini, L., Jobim, L. F., Jobim, M., Fagundes, N. J. R., & Hünemeier, T. (2015) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2015.02.019 · Cited by 17
Santos, F. J. D. A., da Silva, L. S., Santo, J. D. E., de Mesquita, T. G. R., de Souza, M. L. G., Júnior, M. C. D. A., Talhari, S., & Ramasawmy, R. (2019) · PLoS ONE · doi:10.1371/journal.pone.0220572 · Cited by 17
Ongaro, L., Molinaro, L., Flores, R., Marnetto, D., Capodiferro, M. R., Alarcón-Riquelme, M. E., Moreno‐Estrada, A., Mabunda, N. J., Ventura, M., Tambets, K., et al. (2021) · Genes · doi:10.3390/genes12101580 · Cited by 17
Analysis of the LRRK2 p.G2019S mutation in Colombian Parkinson’s Disease Patients
Duque, A. F., López, J. C., Hernandez, H., Benítez, B. A., Yunis, J. J., Fernández, W., Arboleda, H., & Arboleda, G. (2015) · Colombia medica · doi:10.25100/cm.v46i3.1553 · Cited by 17
The Columbian Exchange as a source of adaptive introgression in human populations
Jordan, I. K. (2016) · Biology Direct · doi:10.1186/s13062-016-0121-x · Cited by 16
“Introgression on the scale seen for the three-way population mixing that characterized the Columbian Exchange [7–10] could have provided multiple adaptive alleles as standing genetic variation at intermediate to high population frequencies.”
BackgroundFernández‐Rhodes, L., Graff, M., Buchanan, V. L., Justice, A. E., Highland, H. M., Guo, X., Zhu, W., Chen, H., Young, K. L., Adhikari, K., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.27.445969 · Cited by 17
Self-citationCraniofacial Growth Analysis of Individuals With and Without Cleft Lip and Palate in Colombia
Téllez-Conti, C., Mora, I., Díaz‐Báez, D., Ocampo-Arias, I. J., Jiménez-Luna, N. E., Niño-Paz, J. C., & González-Carrera, M. C. (2021) · The Cleft Palate-Craniofacial Journal · doi:10.1177/10556656211013690 · Cited by 16
“Obviously, these criteria have their limitations, given that certain body characteristics can skew the perception of the professional, resulting in a different clinical assessment from the genetic estimate (Ruiz-Linares et al., 2014; Ruderman et al., 2020).”
BackgroundUrbanization, mainly rurality, but not altitude is associated with dyslipidemia profiles
Lazo-Porras, M., Bernabé‐Ortiz, A., Quispe, R., Málaga, G., Smeeth, L. L., Gilman, R. H., Checkley, W., & Miranda, J. J. (2017) · Journal of clinical lipidology · doi:10.1016/j.jacl.2017.06.016 · Cited by 16
Quinto‐Sánchez, M., Muñoz‐Muñoz, F., Gómez‐Valdés, J., Cintas, C., Navarro, P., de Cerqueira, C. C. S., Paschetta, C., de Azevedo, S., Ramallo, V., Acuña-Alonzo, V., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-19324-y · Cited by 16
Self-citationRamstein, G. P., & Casler, M. D. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200969 · Cited by 18
Assortative mating by population of origin in a mechanistic model of admixture
Goldberg, A., Rastogi, A., & Rosenberg, N. A. (2020) · Theoretical Population Biology · doi:10.1016/j.tpb.2020.02.004 · Cited by 16
Mendoza-Rincón, J. F., López-Cano, D. J., Morales, S. J., Jiménez, M. L. R., Cobos, R. E. B., & Ramírez‐Bello, J. (2016) · Clinical Rheumatology · doi:10.1007/s10067-016-3223-z · Cited by 16
Ancestry analysis in rural Brazilian populations of African descent
Gontijo, C. C., Mendes, F. M., Santos, C., Klautau‐Guimarães, M. D. N., Lareu, M. V., Carracedo, Á., Phillips, C., & de Oliveira, S. F. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.06.018 · Cited by 17
Body shape: Implications in the study of obesity and related traits
Navarro, P., Ramallo, V., Cintas, C., Ruderman, A., de Azevedo, S., Paschetta, C., Pérez, O., Pazos, B., Delrieux, C. A., & González‐José, R. (2019) · American Journal of Human Biology · doi:10.1002/ajhb.23323 · Cited by 15
Self-citationGouveia, M. H., César, C. C., Santolalla, M. L., Sant’Anna, H. P., Scliar, M. O., Leal, T. P., Araujo, N. M., Soares‐Souza, G. B., Magalhães, W. C. S., Mata, I. F., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-53988-4 · Cited by 16
Ayele, F. T., Ouidir, M., Shrestha, D., Workalemahu, T., Rahman, M. L., Mendola, P., Grantz, K. L., Hinkle, S. N., Wu, J., & Zhang, C. (2021) · Human Genetics · doi:10.1007/s00439-021-02265-4 · Cited by 15
Ortega-Vega, E. L., Guzmán-Castañeda, S. J., Campo, O., Velásquez-Mejía, E. P., de la Cuesta‐Zuluaga, J., Bedoya, G., & Escobar, J. S. (2019) · Gut Microbes · doi:10.1080/19490976.2019.1619440 · Cited by 16
“The ancestral genetic composition of each subject served to adjust statistical models (see Statistical analysis below), limiting the detection of spurious associations due to hidden genetic structure produced by the recent admixture among Europeans, Native Americans and Africans of the Colombian population.(72)”
BackgroundSelf-citationAguinaga‐Ríos, M., Rezaei, M., Monroy-Muñoz, I. E., Mechtouf, N., Duran, J. P., Moreno, E., Valdespino, Y., Galaz, C., Razo, G., Medina, D., et al. (2021) · Journal of Assisted Reproduction and Genetics · doi:10.1007/s10815-021-02132-1 · Cited by 14
“[26] estimated individual ancestry proportions in different countries from Latin America and found that in the Mexican population, Native American ancestry is highest in the center/south of the country where the highest number of patients with L750V was observed.”
BackgroundThe genomic landscape of contemporary western Remote Oceanians
Arauna, L. R., Bergstedt, J., Choin, J., Mendoza‐Revilla, J., Harmant, C., Roux, M., Mas-Sandoval, À., Lemée, L., Colleran, H., François, A. R. J., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.055 · Cited by 17
Hernández-Sandoval, J. A., Angulo, M. G., Magaña‐Torres, M. T., Alvizo-Rodríguez, C. R., Ramírez-Plascencia, H. H. F., Flores-López, B. A., Valenzuela-Pérez, J. A., Peregrina-Sandoval, J., Moreno-Ortíz, J. M., Dominguez–Valentin, M., et al. (2020) · Journal of Investigative Medicine · doi:10.1136/jim-2020-001301 · Cited by 14
Frequency of CYP2D6*3 and *4 and metabolizer phenotypes in three mestizo Peruvian populations
Alvarado, Á. T., Ybañez‐Julca, R. O., Muñoz, A. M., Tejada-Bechi, C., Cerro, R., Quiñones, L. A., Varela, N., Alvarado, C. A., Alvarado, E. A., Bendezú, M. R., et al. (2021) · Pharmacia · doi:10.3897/pharmacia.68.e75165 · Cited by 14
Macromorphoscopic trait expression in a cranial sample from Medellín, Colombia
Monsalve, T., & Hefner, J. T. (2016) · Forensic Science International · doi:10.1016/j.forsciint.2016.07.014 · Cited by 14
Characterization of Alzheimer’s Disease and Mild Cognitive Impairment in Older Adults in Panama
Villarreal, A. E., Grajales, S. A., O’Bryant, S. E., Edwards, M., López, L., Montalván, A., & Britton, G. B. (2016) · Journal of Alzheimer s Disease · doi:10.3233/jad-160402 · Cited by 14
Alfaro, A., Juárez-Torres, E., Medina‐Martínez, I., Mateos-Guerrero, N., Bautista-Huerta, M., Román‐Bassaure, E., Villegas‐Sepúlveda, N., & Berumen-Campos, J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0169315 · Cited by 14
Montalva, N., Adhikari, K., Liebert, A., Mendoza‐Revilla, J., Flores-Carrasco, S. V., Mace, R. H., & Swallow, D. M. (2018) · Annals of Human Genetics · doi:10.1111/ahg.12277 · Cited by 14
“…were used to estimate proportions of European, African, and Amerindian ancestry for each individual, according to their similarity to a reference dataset of 876 individuals from three parental populations: 299 Europeans, 169 Africans, and 408 Amerindians (obtained by Ruiz-Linares et al., 2014).”
InfluentialSelf-citationTorres, D., Bermejo, J. L., Mesa, K. G., Gilbert, M. B., Briceño, I., Pohl‐Zeidler, S., Silos, R. G., Boekstegers, F., Plass, C., & Hamann, U. (2018) · International Journal of Cancer · doi:10.1002/ijc.32023 · Cited by 15
“Breast cancer (BC) is the most common cancer type and the most common cause of cancer death among Colombian women.1 Latin Americans and Hispanics/Latinos in other parts of the world are ethnically diverse.2–8 Their admixture proportions of Native American, European and African ancestry differ between and within countr…”
BackgroundNeanderthal introgression in SCN9A impacts mechanical pain sensitivity
Faux, P., Ding, L., Ramírez, L. M., Chacón-Duque, J. C., Comini, M., Mendoza‐Revilla, J., Fuentes‐Guajardo, M., Jaramillo, C., Arias, W. H., Hurtado, M., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05286-z · Cited by 15
Self-citationKim, J., Edge, M. D., Goldberg, A., & Rosenberg, N. A. (2021) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24261 · Cited by 16
The impact of socioeconomic and phenotypic traits on self-perception of ethnicity in Latin America
Paschetta, C., de Azevedo, S., Ramallo, V., Cintas, C., Pérez, O., Navarro, P., Bandieri, L. M., Quinto‐Sánchez, M., Adhikari, K., Bortolini, M. C., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-92061-x · Cited by 13
Self-citationSaeedi, R., Mojebi, A., Sandhu, S. K., Dubland, J. A., Ford, J., Yousefi, M., Pudek, M. R., Holmes, D. T., Erb, S. R., Kwan, W. C. P., et al. (2017) · Annals of Hepatology · doi:10.5604/16652681.1231580 · Cited by 13
Twin Peaks: A spatial and temporal study of twinning rates in Brazil
Cardoso‐dos‐Santos, A. C., Boquett, J. A., Zagonel-Oliveira, M., Callegari-Jacques, S. M., Barbian, M. H., Sanseverino, M. T. V., Matte, Ú. D. S., & Schüler‐Faccini, L. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200885 · Cited by 13
Schut, R. A. (2021) · International Migration Review · doi:10.1177/0197918321993100 · Cited by 13
“Individuals hailing from Latin America possess vastly heterogeneous ancestries due to centuries of mixing between indigenous, European, African, and Asian populations in the region (Ruiz-Linares et al., 2014).”
BackgroundInfluentialClinical differences between children with asthma and rhinitis in rural and urban areas
Sánchez, J., Sánchez, A., & Cardona, R. (2018) · Colombia medica · doi:10.25100/cm.v49i2.3015 · Cited by 13
Characterizing features affecting local ancestry inference performance in admixed populations
Mauer, J., Shah, N. N., Maihofer, A. X., Zai, C. C. H., Belangero, S. I., Nievergelt, C. M., Santoro, M. L., & Atkinson, E. G. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.12.005 · Cited by 15
Kappel, D. B., Schuch, J. B., Rovaris, D. L., da Silva, B. S., Cupertino, R. B., Winkler, C., Teche, S. P., Vitola, E. S., Karam, R. G., Rohde, L. A., et al. (2017) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2017.06.011 · Cited by 15
“Considering that even the general regional population has over 90% of European ancestry according to genomic estimates of interethnic admixture (Ruiz-Linares et al., 2014), the possibility of population stratification biases is negligible as previously reported (Zembrzuski et al., 2006).”
ResultPhotoanthropometry of the Face in the Young White Brazilian Population
Gonzales, P. S., Machado, C. E. P., & Michel‐Crosato, E. (2018) · Brazilian Dental Journal · doi:10.1590/0103-6440201802027 · Cited by 12
“Genetic markers of native Brazilians are predominantly found in the northern region (23).”
BackgroundUse of craniometric data to facilitate migrant identifications at the United States/Mexico border
Spradley, M. K. (2021) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24241 · Cited by 12
Silva, C. P., Castro, C. D. L. F., Zarzar, T. G., Raghavan, M., Tonko-Huenucoy, A., Martínez, F. I., & Montalva, N. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.817318 · Cited by 13
“Chilean genomic research has followed the international trends, prioritizing the genetic characterization of the national mestizo population (Ruiz-Linares et al., 2014; Berrios, 2016; Paschetta et al., 2021), but also articulating genetic ancestry and ethnic identity by exploring the “origins” (i.”
BackgroundLima‐Costa, M. F., Macinko, J. A., Mambrini, J. V. D. M., Peixoto, S. V., Pereira, A. C., Tarazona‐Santos, E., & Ribeiro, A. L. P. (2016) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0004724 · Cited by 12
“Latin America is one of the most ethnoracially heterogeneous regions of the world [12], and Brazil is the largest and the most populous ChD endemic country in the region.”
Backgroundda Silva, B. S., Rovaris, D. L., Schuch, J. B., Mota, N. R., Cupertino, R. B., Aroche, A. P., Bertuzzi, G. P., Karam, R. G., Vitola, E. S., Tovo‐Rodrigues, L., et al. (2016) · Journal of Affective Disorders · doi:10.1016/j.jad.2016.08.008 · Cited by 14
TGF-β Polymorphisms Are a Risk Factor for Chagas Disease
Ferreira, R. R., Madeira, F. S., Alves, G. F., Chambela, M. D. C., Curvo, E. O., Moreira, A. D. S., de Sá, R. A., Mendonça-Lima, L., Cabello, P. H., Bailly, S., et al. (2018) · Disease Markers · doi:10.1155/2018/4579198 · Cited by 12
“Still, it is important to understand if polymorphisms in the TGFB1 gene are also implicated in Chagas disease susceptibility in Brazil, as the Brazilian population presents a different genetic background from that of other Latin American countries [45].”
BackgroundAdmixture, Genetics and Complex Diseases in Latin Americans and US Hispanics
Soares‐Souza, G. B., Borda, V., Kehdy, F. S. G., & Tarazona‐Santos, E. (2018) · Current Genetic Medicine Reports · doi:10.1007/s40142-018-0151-z · Cited by 13
Silva, G., Ramasawmy, R., Boechat, A. L., Morais, A. C., Carvalho, B., Sousa, K., de Souza, V. C., Cunha, M. G. S., Barletta-Naveca, R. H., dos Santos, M. P. M., et al. (2015) · Human Immunology · doi:10.1016/j.humimm.2015.01.011 · Cited by 12
Population impact of pharmacogenetic tests in admixed populations across the Americas
Suarez‐Kurtz, G. (2020) · The Pharmacogenomics Journal · doi:10.1038/s41397-020-00200-w · Cited by 11
The genomic footprint of social stratification in admixing American populations
Mas-Sandoval, À., Mathieson, S., & Fumagalli, M. (2023) · eLife · doi:10.7554/elife.84429 · Cited by 14
Tracing the Distribution of European Lactase Persistence Genotypes Along the Americas
Alves, A. C. G., Sukow, N. M., Cipolla, G. A., de Aquino, M. M., Leal, T. P., Petzl‐Erler, M. L., de Souza, R. L. R., de Souza, I. R., Sánchez, C., Santolalla, M. L., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.671079 · Cited by 11
Metadata
- Authors
- Ruiz-Linares, A., Adhikari, K., Acuña-Alonzo, V., Quinto-Sanchez, M., Jaramillo, C., Arias, W., Fuentes, M., Pizarro, M., Everardo, P., de Avila, F., Gómez-Valdés, J., León-Mimila, P., Hunemeier, T., Ramallo, V., Silva de Cerqueira, C. C., Burley, M.-W., Konca, E., de Oliveira, M. Z., Veronez, M. R., Rubio-Codina, M., Attanasio, O., Gibbon, S., Ray, N., Gallo, C., Poletti, G., Rosique, J., Schuler-Faccini, L., Salzano, F. M., Bortolini, M.-C., Canizales-Quinteros, S., Rothhammer, F., Bedoya, G., Balding, D., & Gonzalez-José, R.
- Affiliations
- University College London (GB)
- Universidad de Antioquia (CO)
- University of Tarapacá (CL)
- National Institute of Anthropology and History (MX)
- Universidade Federal do Rio Grande do Sul (BR)
- Institute for Fiscal Studies (GB)
- University of Geneva (CH)
- Universidad Peruana Cayetano Heredia (PE)
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-09-25
- Volume
- 10
- Issue
- 9
- Pages
- e1004572
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC4177621
- OpenAlex
- W2112602049
- Cited by
- 442
- References
- 58
- Citations by year
- 2026: 24 · 2025: 39 · 2024: 25 · 2023: 40 · 2022: 27 · 2021: 45 · 2020: 41 · 2019: 46 · 2018: 41 · 2017: 38 · 2016: 45 · 2015: 28 · 2014: 2
- FWCI
- 24.74
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- Open Research Online (The Open University) (acceptedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-sa)
- Americanae (AECID Library) (submittedVersion, cc-by)
- Institutional Repository University of Antioquia (University of Antioquia) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Universidad de Chile (submittedVersion, cc-by-nc-nd)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Greater South Information System
- Funders
- Leverhulme Trust (F/07 134/DF)
- Biotechnology and Biological Sciences Research Council (BB/I021213/1)
- Economic and Social Research Council (ES/H021221/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Social Sciences › Anthropology › Race, Genetics, and Society
- Keywords
- admixture, genetic ancestry estimation, population structure, phenotypic diversity, demographic history, genetic diversity, self-perception bias
- MeSH terms
- Ethnicity, Biological Evolution, Female, Genetics, Population, Geography, Humans, Latin America, Male, Phenotype, Self Concept, Genetic Variation, Quantitative Trait, Heritable
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