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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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“Moreover, the variant was found in 69, 8.4, and 7.3% of unselected subjects diagnosed with choroid plexus carcinoma, neuroblastoma and osteosarcoma, respectively (Seidinger et al., 2011, 2015).”
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“Its work focused on urban populations from Mexico, Colombia, Peru, Chile, and Brazil, to characterize their physical appearance, examine their gene pool and social environment, and assess their perception and attitudes towards themselves and others (Ruiz-Linares et al. 2014).”
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Automatic Ear Detection and Segmentation over Partially Occluded Profile Face Images
Cintas, C., Delrieux, C. A., Navarro, P., Quinto‐Sánchez, M., Pazos, B., & González‐José, R. (2019) · Journal of Computer Science and Technology · doi:10.24215/16666038.19.e08 · Cited by 6
Galvez, A. S., Ramírez, H., Placencia, P., Rojas, C. R., Urzúa, X., Kalergis, A. M., Salazar, L. A., & Escobar‐Vera, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.640956 · Cited by 7
“6%), while European ancestry contribution is higher in the central region and Native-American ancestry prevails in the southern region (Fuentes et al., 2014; Ruiz-Linares et al., 2014; Eyheramendy et al., 2015).”
BackgroundMaldonado, B. L., Piqué, D. G., Kaplan, R. C., Claw, K. G., & Gignoux, C. R. (2023) · Journal of Community Genetics · doi:10.1007/s12687-023-00686-4 · Cited by 7
“…consor-tium-based and national initiatives occurring across Latin America, including novel, large studies coming online such as the Mexico City Prospective Study (Ziyatdinov et al. 2023), the Mexican Biobank (Sohail et al. 2023), and the trait-focused consortia Candela (Ruiz-Linares et al. 2014).”
BackgroundWatanabe, A., Neves, P. D. M. D. M., Nunes, K., Lerário, A. M., Watanabe, E. H., Ferreira, F. M., Malheiros, D. M. A. C., Narcizo, A. D. M., Guaragna, M. S., Araújo, S. D. A., et al. (2024) · Kidney International Reports · doi:10.1016/j.ekir.2024.09.005 · Cited by 6
“Variants of uncertain signi fi cance identi fi ed, respective genes, mode of inheritance, segregation, ACMG criteria, gnomAD frequency, classi fi cation of pathogenicity, age of NS onset, kidney histology, immunosuppression, time to kidney failure, and follow-up time.”
Quiñones, L. A., Martínez, M. F., Vargas, R., Cerpa, L. C., López‐Cortés, A., Martínez, F. D. G., Fonseca, D. J., Duconge-Soler, J., Varela, N., Lares-Asseff, I., et al. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1721828 · Cited by 6
Santo, J. D. E., de Souza, J. L., da Silva, L. S., da Silva, C. C., do Nascimento, T. A., de Souza, M. L. G., da Cunha, A. F., Batista, J. D. S., Neto, J. P. D. M., Guerra, M. V. D. F., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1232488 · Cited by 6
Mardini, A. C., Pereira, F. D. S., Schüler‐Faccini, L., & Matte, Ú. D. S. (2017) · Twin Research and Human Genetics · doi:10.1017/thg.2017.2 · Cited by 6
“Nevertheless, data on genetic admixture of Latin American populations (Ruiz-Linares et al., 2014) showed a marked genetic homogeneity in the southernmost part of Brazil — the same origin of samples for the present study.”
BackgroundRe-thinking race and geography in multiple sclerosis
Ontaneda, D., & Amezcua, L. (2023) · Multiple Sclerosis Journal · doi:10.1177/13524585231205969 · Cited by 6
“Hispanic ancestry is a genetic admixture of mainly Native American/American Indian, European, and African ancestries 17 with differing proportions as a consequence of complex political, social, and migratory histories to regions.”
BackgroundBurguete-Argueta, N., Cruz, B. M. D. L., Camacho-Mejorado, R., Santana, C., Noris, G., López‐Bayghen, E., Arellano‐Galindo, J., Majluf‐Cruz, A., Meraz‐Ríos, M. A., & Gómez, R. (2015) · Annals of Human Biology · doi:10.3109/03014460.2015.1127424 · Cited by 6
“Toluca, Estado de M exico), which absorb immigrants with different genetic backgrounds (Ruiz-Linares et al., 2014).”
BackgroundInfluentialDental genetics in Brazil: Where we are
Casado, P. L., Quinelato, V., Cordeiro, P. C. D. F., Prazeres, J. M. B., Campello, M., Bonato, L. L., & Aguiar, T. R. D. S. (2018) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.457 · Cited by 6
Pergolizzi, J. V., Taylor, R., LeQuang, J. A., Lara, A., Hernández-Ortiz, A., & Ibán, M. Á. R. (2019) · Pain and Therapy · doi:10.1007/s40122-019-0126-0 · Cited by 6
COVID-19 and gastrointestinal symptoms in Mexico, a systematic review: does location matter?
Pizuorno, A., Fierro, N. A., Copado-Villagrana, E. D., Herrera-Solís, M. E., Oskrochi, G., Brim, H., & Ashktorab, H. (2021) · BMC Infectious Diseases · doi:10.1186/s12879-021-06252-y · Cited by 6
“In this sense, as in most Latin American countries, the genetic structure of the Mexican population is an admixture of three paternal lineages consisting of Amerindian, European and African ancestry [7].”
BackgroundDemographic history differences between Hispanics and Brazilians imprint haplotype features
da Cruz, P. R. S., Ananina, G., Secolin, R., Gil‐da‐Silva‐Lopes, V. L., Lima, C. S. P., de França, P. H. C., Donatti, A., Lourenço, G. J., de Araujo, T. K., Simioni, M., et al. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac111 · Cited by 6
“These demographic events largely impact haplotype structure (Ruiz-Linares et al. 2014; Martin et al. 2017, 2018).”
BackgroundLazo‐Porras, M., Ruíz-Alejos, A., Miranda, J. J., Carrillo-Larco, R. M., Gilman, R. H., Smeeth, L. L., & Bernabé‐Ortiz, A. (2020) · Diabetic Medicine · doi:10.1111/dme.14298 · Cited by 6
Russo, M. G., Rocca, F. D. F., Doldan, P., Cardozo, D. G., Dejean, C. B., Seldes, V., & Avena, S. A. (2016) · Revista del Museo de Antropología · doi:10.31048/1852.4826.v9.n1.12579 · Cited by 7
Fuerst, J. G. R. (2015) · Open Behavioral Genetics · doi:10.26775/obg.2015.06.18 · Cited by 6
Castañeda-González, J. P., Parra-Medina, R. S., Riess, J. W., Gandara, D. R., & Carvajal‐Carmona, L. G. (2025) · Clinical Lung Cancer · doi:10.1016/j.cllc.2025.03.004 · Cited by 5
A genomic perspective on South American human history
Silva, M. A. C. E., Ferraz, T., & Hünemeier, T. (2022) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2022-0078 · Cited by 5
“to shift even more until reaching the current configuration (Ruiz-Linares et al., 2014; Montinaro et al., 2015; Adhikari et al., 2016; Chacón-Duque et al., 2018; Ongaro et al., 2019).”
Tracing human genetic histories and natural selection with precise local ancestry inference
Lerga-Jaso, J., Novković, B., Unnikrishnan, D., Bamunusinghe, V., Hatorangan, M. R., Manson, C., Pedersen, H., Osama, A., Terpolovsky, A., Bohn, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59936-3 · Cited by 9
“For example, the highest percentage of Native American ancestry (NAM) was found in Bolivia, Peru, Ecuador and Mexico, matching demographic and genetic reports from this region 24 – 26 .”
MHC2TA and FCRL3 genes are not associated with rheumatoid arthritis in Mexican patients
Mendoza-Rincón, J. F., Elias, A. K. R., Fragoso, J. M., Vargas‐Alarcón, G., Murillo, K. M., Jiménez, M. L. R., Cobos, R. E. B., Morales, S. J., Zamudio, G. L., Tovilla‐Zárate, C. A., et al. (2015) · Rheumatology International · doi:10.1007/s00296-015-3358-2 · Cited by 5
Juárez-Cortés, E. D., Contreras-Sieck, M. Á., Arriaga-Perea, A. J., Macías-Medrano, R. M., Jaime, A. B., Everardo, P., Zúñiga, J., Acuña-Alonzo, V., Granados, J., & Barquera, R. (2017) · Human Biology · doi:10.13110/humanbiology.89.3.02 · Cited by 5
Self-citationEvaluating DNA evidence in a genetically complex population
Hessab, T., Aranha, R. S., Moura-Neto, R. S., Balding, D. J., & Schrago, C. G. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.06.019 · Cited by 5
Self-citationKoenigstein, F., Boekstegers, F., Wilson, J. F., Fuentes‐Guajardo, M., González‐José, R., Bedoya, G., Bortolini, M. C., Acuña-Alonzo, V., Gallo, C., Ruiz‐Linares, A., et al. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab302 · Cited by 5
“Latin Americans are a highly heterogeneous ethnic group and the distribution of ancestry proportions varies greatly both between and within Latin American regions and countries (24).”
Self-citationGenetic and self‐perceived ancestries in Argentina: Beyond the three‐hybrid model
Ruderman, A., Luisi, P., Paschetta, C., Teodoroff, T., Perez, L., de Azevedo, S., Trujillo‐Jiménez, M. A., Navarro, P., Morales, L., Pazos, B., et al. (2023) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24702 · Cited by 6
Self-citationLima, M. O., Saraiva, L. C., Ramos, V. R., de Oliveira, M. C., Costa, D. L. C., Fernandez, T. V., Crowley, J. J., Storch, E. A., Shavitt, R. G., Miguel, E. C., et al. (2023) · Psychiatry Research · doi:10.1016/j.psychres.2023.115627 · Cited by 5
Rodríguez, C. A., Zuluaga, A. F., Neely, M. N., Sierra, Y., Morales-Gutierrez, J., Zapata, J., Serna, J. D. Z., Naranjo, T. W., & Agudelo, Y. (2019) · Therapeutic Drug Monitoring · doi:10.1097/ftd.0000000000000661 · Cited by 5
Ancestry dynamics in a South American population: The impact of gene flow and preferential mating
Hedrick, P. W. (2017) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23220 · Cited by 5
Asgari, S., Luo, Y., Belbin, G. M., Bartell, E., Calderon, R. I., Slowikowski, K., Contreras, C. C., Yataco, R. M., Galea, J. T., Jiménez, J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/561241 · Cited by 5
“reported that Native American ancestry is correlated with lower height (4).”
BackgroundFlores-López, B. A., López-Ceballos, A. G., López-Aguilar, C., Rico-Méndez, M. A., Acosta-Ramírez, K., Cano-Ravell, A., Gembe-Olivarez, G., López-Quintero, A., Aguilar-Velázquez, J., Ramírez-de-Arellano-Sánchez, J. A., et al. (2025) · Genes · doi:10.3390/genes16101227 · Cited by 4
“Moreover, if phenotypic predictions are interpreted without nuance, they may lead to overgeneralizations about biogeographic ancestry which are especially problematic in socially diverse societies like those in Latin America [18].”
Lewy Body Dementia Research in Latin America: A Scoping Review
Cano, C. A., Salazar‐Londoño, S., Rodríguez, F. B., Páez‐García, S., Giraldo, S., Escudero, J. M. S., Aarsland, D., Borda, M. G., & COL‐DLB (2025) · Movement Disorders Clinical Practice · doi:10.1002/mdc3.70059 · Cited by 5
Mueller, M., Blandino, A., Scherer, D., Zulantay, I., Apt, W., Varela, N., Llancaqueo, M., V, García, L., Ortiz, L., Nicastri, E., et al. (2025) · Journal of Infection · doi:10.1016/j.jinf.2025.106613 · Cited by 4
González‐José, R., Alfaro, E., Arencibia, V., Argüelles, C. F., Avena, S. A., Bailliet, G., Berenstein, M., Bravi, C. M., Cuello, M., Dipierri, J. E., et al. (2025) · Biopreservation and Biobanking · doi:10.1177/19475535251390754 · Cited by 4
Self-citationInvisibilidad Indígena en el Uruguay: Genética, Historia y Género
Sans, M. (2022) · RUNA archivo para las ciencias del hombre · doi:10.34096/runa.v43i2.10722 · Cited by 4
Zollner, L., Torres, D., Briceño, I., Gilbert, M. B., Torres-Mejı́a, G., Dennis, J., Bolla, M. K., Wang, Q., Hamann, U., & Bermejo, J. L. (2023) · Breast Cancer Research · doi:10.1186/s13058-023-01713-5 · Cited by 4
“In Colombia, Native American proportions are particularly high in the east and southwest of the country, central areas show generally high percentages of European ancestry, and proportions of African ancestry increase in coastal regions, especially along the Pacific [17].”
BackgroundGermline mutations in pediatric cancer cohort with mixed‐ancestry Mexicans
Alonso‐Luna, O., Mercado, G., Meléndez-Zajgla, J., Barquera, R., Zapata‐Tarrés, M., Juárez‐Villegas, L., Mendoza‐Caamal, E., Rey‐Helo, E., & Borges-Yáñez, S. A. (2023) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.2332 · Cited by 4
“We were able to detect five components in both the cases and the paired controls (Data S5) that were consistent with the demographic models assumed for present-day mixed-ancestry Mexicans (Barquera et al., 2020; Price et al., 2007; Ruiz-Linares et al., 2014; Wang et al., 2007; Zúñiga et al., 2013).”
ResultFlores, I., Torres-Reverón, A., Navarro, E., Nieves-Vázquez, C. I., Cotto-Vázquez, A. C., Alonso-Díaz, J. M., Bracero, N., & Vincent, K. (2024) · Pain · doi:10.1097/j.pain.0000000000003230 · Cited by 6
Treating the Latin American Aesthetic Patient: A Review
de Almeida, A. R. T., Garcia, P. E., Banegas, R., Zimbres, S., Martínez, C., Frolík, J., & Cazerta, C. (2024) · Clinical Cosmetic and Investigational Dermatology · doi:10.2147/ccid.s482551 · Cited by 4
Amyotrophic lateral sclerosis mortality rates in Latin America and the Caribbean: a meta-analysis
Erazo, D., Luna, J., Preux, P., Medina, M. T., Magné, J., Boumédiène, F., & Couratier, P. (2022) · Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration · doi:10.1080/21678421.2022.2048310 · Cited by 4
“In Brazil, a higher level of European ancestry has been evidence in the south, conversely a higher level of African ancestry has been described in the East (33).”
BackgroundInfluentialCanzian, F., Rizzato, C., Stein, A., Flores‐Luna, L., Camorlinga‐Ponce, M., Méndez-Tenorio, A., Chen, W., Kasamatsu, E., Bravo, M. M., Torres, J., et al. (2023) · European Journal of Cancer Prevention · doi:10.1097/cej.0000000000000779 · Cited by 4
Leveraging International Collaborations to Advance Genomic Medicine in Colombia
Cock-Rada, A. M., & Ossa, C. A. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811531-2.00009-6 · Cited by 4
Modeling Population Structure Under Hierarchical Dirichlet Processes
Elliott, L. T., Iorio, M. D., Favaro, S., Adhikari, K., & Teh, Y. W. (2018) · Bayesian Analysis · doi:10.1214/17-ba1093 · Cited by 4
“Latin American samples are uniquely advantageous for this purpose [50] because of their well-documented history of extensive mixing between Native Americans and people arriving from Europe and Africa.”
BackgroundSelf-citationMesa, K. G., Bermejo, J. L., Torres, D., Gilbert, M. B., Plass, C., & Hamann, U. (2020) · OncoTargets and Therapy · doi:10.2147/ott.s274431 · Cited by 4
Challenges in Genetic Testing and Treatment Outcomes Among Hispanics With Lung Cancer
Raez, L. E., Cardona, A. F., Lopes, G. D. L., Jr., & Arrieta, O. G. (2022) · JCO Oncology Practice · doi:10.1200/op.22.00096 · Cited by 4
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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