Why Does Hispanic Genetic Variation Occur?

While medical researchers and census-takers tend to lump Latinos or Hispanics into one group, new genetic data shows they’re diverse. For example, Mexicans from the dry north are genetically as different from those in the Yucatan as Europeans are from East Asians. Self-identified continental ancestry proportions in HCHS/SOL participants reflect recent gene flow from Latin America to the US. These findings suggest future genetic association studies may need to account for admixture at a geographic scale.

Cross-Cultural Admixture

Geneticists can tease out the complex admixture that gave rise to most Hispanics by analyzing the non-recombining region of their male Y chromosome, establishing haplogroups linked to specific geographical origins. For this study, researchers analyzed 18 Y-SNPs in individuals from 10 Mexican-Mestizo populations nationwide. Paternal European ancestry predominated, but there was also evidence of African and Native American ancestry. Other research, based on the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), has shown that the majority of the self-identified Hispanic population have at least some Native American ancestry, which reflects the fact that many of these ancestral lines were lost as indigenous communities were reduced or eradicated by Spanish colonizers. 


Researchers studying the genetics of Hispanic populations find a mix of indigenous and European ancestry. This admixture can complicate research, particularly in terms of understanding how certain genes might interact with each other. Latinos whose self-report as Puerto Rican or Dominican have higher levels of Native American ancestry than those who identify only as Mexican or Central American; those who additionally identify as white, Cuban, or South American report the highest level of European ancestry. However, this admixture is not random, and it reflects the long history of colonialism and slavery in the Americas, along with migration across geopolitical borders.

This complexity extends to the individual’s autosomal DNA, which recombines with each new generation, obscuring signals of ancient population structure. But the study of Y and mtDNA, which do not recombine, has revealed some striking admixture patterns in Hispanics.

Y-DNA analysis showed that paternal European ancestry varied by region, clustering in three areas:

  • North and West (now including the states of Chihuahua, Sinaloa-Durango, and Aguascalientes)
  • Center-south (including Veracruz, Guerrero-Oaxaca, and Jalisco)
  • Southeast (including Yucatan)

Similarly, mtDNA variation identified distinct regions: those with haplogroups R and I tended to come from indigenous groups; those with subclades of haplogroups E and J pointed to an African or Middle Eastern origin.

In addition, mtDNA analysis confirmed that a significant proportion of the Hispanic population contains markers common in Sephardic Jews. It suggests that the admixture with non-Hispanics is broader than previously thought, including some Spanish-speaking communities in the United States.


In the most comprehensive genetic analysis of Latinos, they used Y and mtDNA to tease out the origins of Mexican-Mestizo participants. They found that a significant proportion of paternal ancestry was from the eastern Mediterranean and North Africa, and a smaller fraction came from varying regions of Europe. However, most ancestral origins were within Latin America, including specific Native American and Amerindian genomic segments. The research also revealed that male and female Latinos of a predominantly low level of acculturation hold different beliefs and attitudes about genetic testing, with women expressing more anxiety than men. Participants also stated they needed more information on how a genetic test’s results can impact health outcomes. They also cited various barriers to genetic testing, including costs (including the cost of the test and the necessary follow-up medical care) and lack of access to affordable insurance coverage. In addition, participants discussed their preferred information sources about genetic testing, with a strong preference for seeking information from a trusted source. This discovery could point to opportunities for focused outreach to meet the needs of this underrepresented demographic. Moreover, it indicates that accounting for complex Hispanic admixture and genetic diversity will help to improve the accuracy of association studies of gene-environment interactions in this group.


The genetic analysis revealed a pattern of Hispanic genetic diversity consistent with Latin America’s history of intercontinental migration and colonization. Hispanics carry admixed genomes with three predominant continental ancestries, American Indian, European, and African, and these proportions vary across Latin America. Pairwise comparisons and genetic distances based on the Y chromosome’s non-recombining region indicated demographic clumping. In multidimensional genetic PC space, Mexicans and Central Americans were separated from Puerto Ricans and Cubans and Dominicans. This pattern is also evident from the clustering pattern depicted by the MDS plot and the NJ tree. Jalisco stood out as a distinct cluster in the MDS quadrant, probably because of the higher frequency of African haplogroups in this western state (8.7%).

In addition, the analysis reveals a large amount of Sephardic (Jewish) ancestry in Mexican-Mestizos. It is likely a legacy of conversos, or Jews who converted to Catholicism under the Spanish Inquisition, as well as the subsequent spread of Spanish-speaking Jews throughout the world, including Latin America. It demonstrates the importance of accounting for Hispanic diversity in genetic risk factors studies. It will require considering cultural and environmental diversity and the complex admixture that characterizes Hispanic populations. In the future, such an approach could allow researchers to identify more precise genomic determinants of disease.

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