Population genetics | Mexico | Latin America

How Indigenous Are Mexicans?

Mexico calls itself a mestizo nation, but the mix is not the same in Sonora, in Mexico City and in Oaxaca. Twenty years of genome studies, a national biobank and ancient DNA from Chichen Itza now allow an answer region by region.

93%of the maternal lineages of Mexican mestizos are Indigenous, against about 31% of their paternal lineages
36 to 66%average Indigenous ancestry of mestizos from Sonora in the north to Guerrero in the south, in the first genome-wide survey (2009)
47%Indigenous share of the average Mexican mestizo in Global25 in our analysis, between 46 and 48% whatever the reference populations

Hero image: AI generated illustration of a tianguis market on the main square of Mexico City around 1650, below the towers of the cathedral under construction and the snow-capped volcanoes. Nahua women sell maize, chiles, tomatoes, avocados and cacao beans, a Nahua porter carries a load with a tumpline, Spanish merchants inspect cloth, and Franciscan friars, a young mestizo couple and an Afro-Mexican woman with a basket of fruit cross the market beside the canoes of a canal. Clothing, buildings and the scene are approximations, and it is not a reconstruction of the individuals whose genomes are discussed here.

Ask how Indigenous Mexicans are and you will get two opposite answers. One says that Mexicans are a mestizo people, Spanish and Indigenous in equal parts. The other says that most Mexicans are simply Indigenous people who speak Spanish. Genetics gives a more precise answer, and it is not a single number: the average Mexican genome is a little over half Indigenous, but that average hides a gradient from the deserts of the north to the mountains of Oaxaca and the Maya lowlands, and a sharp difference between what Mexicans inherited from their mothers and from their fathers.

In this article we review the large genome studies of Mexico, from the first survey of six states in 2009 to the Mexican Biobank of 2023, and we model Mexican averages ourselves in Global25. We ask three questions: how much of the Mexican genome is Indigenous, which Indigenous peoples it comes from, and how far back that continuity goes.

Five centuries in the Mexican genomeFrom the conquest to the genome studies of the last twenty years1519 to 1521Conquest of the Aztec empireCortes lands on the Gulf coast in 1519; Tenochtitlan falls in August 15211520 to 1600Epidemics and collapseSmallpox, then the cocoliztli epidemics of 1545 and 1576; the Indigenous populationof central Mexico falls by perhaps 80 to 90% within a century1520s to 1700sAfricans in New SpainEnslaved Africans arrive through Veracruz, most of them before 1650;estimates for the whole colonial period run to the low hundreds of thousands1565 to 1815The Manila galleonShips link Manila and Acapulco; tens of thousands of Asians,mostly Filipinos, settle in New Spain1925The "cosmic race"Jose Vasconcelos makes mestizaje the core of national identity2009 to 2014The first genome mapsMestizos from six states (2009), then 20 Indigenous and 11 mestizopopulations (2014): a gradient from northwest to southeast2023 to 2024Biobank and ancient DNAThe Mexican Biobank genotypes 6,057 people from all 32 states;ancient genomes show continuity from Chichen Itza to the present Maya
Key dates for the peoples who built the Mexican population and for the genetic studies that measured it. Dates and estimates are approximate.

A mestizo nation, and what the census counts

Mexico does not ask its citizens whether they are mestizo. Its census records two other things. In 2020, 23.2 million people aged three and over, 19.4% of that population, said they considered themselves Indigenous, and 7.4 million, 6.1%, spoke an Indigenous language. For the first time, the 2020 census also counted Afro-Mexicans: 2.58 million people, about 2% of the population. Everyone else is, by default, the mestizo majority, which geneticists usually put at around 93% of Mexicans.

The word itself carries a political history. After the revolution, the philosopher Jose Vasconcelos described Mexicans as a "cosmic race" born from the fusion of peoples, and mestizaje became the core of national identity. That story is not wrong, but it is vague. It says nothing about proportions, and nothing about which Spaniards, which Africans and which of the dozens of Indigenous peoples of Mexico took part in the mixture. This is exactly what genomes can measure.

What the big studies found

The first genome-wide survey of Mexican mestizos, published in 2009 by Silva-Zolezzi and colleagues at Mexico's National Institute of Genomic Medicine, genotyped 300 mestizos from six states: Sonora and Zacatecas in the north, Guanajuato in the centre, Guerrero on the southern Pacific coast, Veracruz on the Gulf and Yucatan in the southeast. On average they were 55.2% Indigenous, 41.8% European and 1.8% African. But the averages ran from 36.2% Indigenous and 61.6% European in Sonora to 66.0% Indigenous and 28.5% European in Guerrero, and individuals within each state varied widely around these values.

Studies with other markers found the same gradient. In 2009, Rubi-Castellanos and colleagues analysed 1,984 mestizos from ten populations and found Indigenous ancestry rising from north to south. Their key observation was historical: the gradient roughly follows the density of Indigenous populations before the conquest. Where Mesoamerica had dense farming populations, mestizos today carry more Indigenous ancestry; in the thinly populated north, Spaniards and their descendants made up a larger share of the founders. Averages also depend on who is sampled: 100 mestizos from northeastern Mexico, studied the same year, averaged 56% Native American ancestry, with individuals ranging from 27 to 81%, and a sample of 561 people from Mexico City averaged 65% Native American, 30% European and 5% West African.

In 2014, Moreno-Estrada and colleagues turned to the Indigenous peoples themselves, with more than 1,000 individuals from 20 Indigenous and 11 mestizo populations. They found that the Indigenous peoples of Mexico are genetically very different from one another. The Seri of the Sonoran coast and the Lacandon Maya of the Chiapas rainforest differ by an FST of 0.136, more than Europeans differ from East Asians (0.11). Small, isolated groups such as the Huichol, the Lacandon and the Seri carry more than 10% of their genome in long runs of homozygosity. And the Indigenous segments in mestizos mirror the Indigenous peoples who live nearby: Mexicans carry not a generic Native American ancestry, but the ancestry of their own region.

The Mexican Biobank, published in Nature in 2023 by Sohail, Moreno-Estrada and colleagues, extended this to the whole country: 6,057 people from all 32 states and 898 localities, about 70% of them rural and deliberately enriched for speakers of Indigenous languages. It confirmed the north to south gradient, found West African ancestry in every state, and detected East Asian ancestry at state averages of up to 2.3%, highest in Guerrero. A 2026 follow-up on 6,011 of these genomes found the highest average Indigenous ancestry in Oaxaca and the lowest in the northern states, with most individuals carrying between 1 and 5% African ancestry, and showed that the Indigenous component itself changes from region to region: Nahua in central Mexico, Zapotec in the south, Maya in the Yucatan peninsula.

Region by region

Putting these studies together gives a portrait of Mexico by region. The regions below follow the broad divisions used by archaeologists and by the Mexican Biobank; the states are examples, not exact boundaries.

RegionMain Indigenous peoplesWhat the genetic studies show
North
Sonora, Chihuahua, Nuevo Leon, Coahuila
Arido-American peoples: Pima, Raramuri (Tarahumara), Yaqui, SeriLowest Indigenous and highest European ancestry. Sonora: 36% Indigenous and 62% European on average (2009). The northeast is more mixed than its reputation, at 56% Native American in one sample. Ancient genomes from Sonora cluster with the present-day Pima in our analysis.
West
Jalisco, Nayarit, Michoacan
Huichol (Wixarika), Cora, PurepechaIntermediate. The Huichol are one of the most isolated peoples of Mexico, with more than 10% of the genome in long runs of homozygosity.
North of Mesoamerica
Guanajuato, Queretaro, Zacatecas
Otomi, PameTogether with the centre, the region where the Mexican Biobank sees the steepest fall in population size after the conquest. Ancient genomes from the Sierra Gorda of Queretaro show local continuity through the megadroughts of about 1,100 years ago.
Centre
Mexico City, Puebla, Tlaxcala, Hidalgo
Nahua, OtomiIntermediate to high Indigenous ancestry: 65% Native American in one Mexico City sample. The Indigenous component of local mestizos is Nahua-like.
Gulf
Veracruz, Tabasco
Totonac, Nahua, Teenek (Huastec)More African ancestry than in the north: Veracruz was the main port of the slave trade, and some individuals sampled there carry up to a third sub-Saharan ancestry.
Southern Pacific
Guerrero
Nahua, Mixtec, Me'phaa (Tlapanec), AmuzgoThe most Indigenous state of the 2009 survey, at 66%. Also the highest East Asian ancestry in Mexico, a legacy of the Manila galleon at Acapulco, and the Afro-Mexican communities of the Costa Chica.
OaxacaZapotec, Mixtec, Mixe and a dozen other peoplesThe highest average Indigenous ancestry of any state in the Mexican Biobank. 31% of the population speaks an Indigenous language. European ancestry there descends from very few founders.
Maya region
Yucatan, Campeche, Quintana Roo, Chiapas
Yucatec Maya, Tzotzil, Tzeltal, LacandonHigh Indigenous ancestry with a distinct Maya signal: in 2009, Yucatan was the only state with a recognisably Maya component. Ancient genomes from Chichen Itza match the present-day Maya.

Sources: Silva-Zolezzi et al. 2009, Martinez-Fierro et al. 2009, Martinez-Marignac et al. 2007, Moreno-Estrada et al. 2014, Villa-Islas et al. 2023, Sohail et al. 2023, Barberena-Jonas et al. 2026, Rodriguez-Rodriguez et al. 2022, INEGI census 2020, and our Global25 analysis.

Indigenous mothers, European fathers

The single most striking fact about the Mexican genome is not an average but an asymmetry. Mitochondrial DNA, inherited from mothers, was studied in 742 mestizos from ten populations by Martinez-Cortes and colleagues in 2013: 92.9% of the lineages were Native American, 5.3% European and 1.9% African. The Y chromosome, inherited from fathers, tells the opposite story: in a study by the same team, 64.9% of the paternal lineages were European, 30.8% Native American and 4.2% African.

Indigenous mothers, European fathersAverage ancestry of Mexican mestizos through the maternal line, the whole genome and the paternal line (published studies)0%25%50%75%100%Maternal linesmtDNA, 742 mestizos (2013)935Whole genome300 mestizos, six states (2009)5542Paternal linesY chromosome (2012)31654IndigenousEuropeanAfricanEast Asian
Average continental ancestry of Mexican mestizos in maternal lineages (Martinez-Cortes et al. 2013), the whole genome (Silva-Zolezzi et al. 2009) and paternal lineages (Martinez-Cortes et al. 2012). The East Asian component was estimated only in the genome-wide study.

The meaning is plain. The Mexican population was founded mostly by unions between European men and Indigenous women, at a time when Spanish women were few in New Spain. The same pattern appears across Latin America, as we showed for Peru and Bolivia and for Paraguay. European maternal lineages are most frequent in the northwest, and African lineages are rare but spread across the whole country.

Our Global25 analysis: the national average

Global25 contains an average of 131 Mexican mestizos, together with smaller groups labelled Euro-mestizo and Indo-mestizo, admixed Maya, Mixtec and Totonac, and nine Indigenous populations from Sonora to Chiapas. Where these samples were collected is not documented, so they cannot stand for any state. What they can do is show how a typical Mexican genome is built. We modelled each sample as a mixture of four sources: an Indigenous Mexican pool (the average of the nine Indigenous groups), Spaniards from Andalusia, West Africans (Yoruba) and East Asians (Filipinos).

How Indigenous are Mexicans in Global25?Each sample modelled as Indigenous Mexican (pooled), Iberian (Andalusia), West African (Yoruba) and East Asian (Filipino); our analysis0%25%50%75%100%fitEuro-mestizosGlobal25 average of 7148514Mexican mestizosGlobal25 average of 131474848Indo-mestizosGlobal25 average of 881177Maya, admixedaverage of 6851414Totonac, admixedaverage of 4, low resolution92820Mixtec, admixedaverage of 294512ZapotecOaxaca, average of 12988MayaYucatan, average of 1010014PimaSonora, average of 129810IndigenousIberianWest AfricanEast AsianFit: distance between the sample and the model, in Global25 units x 1000 (lower is better). Labels under 4% are not shown.
Global25 averages of Mexican mestizos, Euro- and Indo-mestizos, admixed and unadmixed Indigenous groups modelled with four sources. The Indigenous source is the average of nine Indigenous Mexican populations from Sonora to Chiapas (our analysis).

The average Mexican mestizo comes out 47% Indigenous, 48% Iberian, 4% West African and 0.5% East Asian, with a good fit. This is lower than the 55% of the 2009 survey, which suggests that the Global25 sample leans towards the north or towards cities, but it is well within the range of the published studies. The result is remarkably stable. We repeated the model with every combination of four Iberian sources (Andalusia, Extremadura, Castile and Leon, and a Spaniard buried in Mexico around 1610), four African sources (Yoruba, Esan, Mandenka and Kongo), three East Asian sources (Filipino, Javanese, Han from Fujian) and four Indigenous sources (the pool, Zapotec, Pima or Maya alone). Across all 192 models, the Indigenous share stays between 46.3 and 48.1%, the Iberian share between 47.1 and 49.0%, and the African share between 3.8 and 4.4%.

The labels Euro-mestizo and Indo-mestizo cover a wide range: 85% Iberian for the first, 81% Indigenous for the second. The admixed Indigenous groups carry between 5 and 14% Iberian ancestry, and the unadmixed Zapotec, Maya and Pima come out at 98 to 100% Indigenous, as they should. Mestizo, in other words, is not a genetic category. It is a cultural and historical one that spans almost the whole range from European to Indigenous.

Which Indigenous Mexico?

An Indigenous share of 47% says nothing about which Indigenous peoples Mexicans descend from. To see that, we first placed the nine Indigenous populations of Global25 on a map of their own, using only the variation among them. The second axis of this map is geography: it runs from the Huichol and the Pima in the north, through the Nahua and the Totonac, down to the Zapotec, the Mixtec and the Yucatec Maya. The first axis isolates the Mixe of Oaxaca and the Tzotzil of the Chiapas highlands, two peoples marked by long isolation and strong genetic drift.

The Indigenous map of Mexico in Global25Present-day Indigenous groups (dots), ancient genomes (rings) and the estimated Indigenous part of mestizos (diamonds); our analysisNORTHSOUTHPC1 (42% of the variation among these groups): drift of the Mixe and highland MayaPC2 (22%): north to southPima (Sonora)Huichol (Jalisco)Nahua (centre)Totonac (Veracruz)Mixe (Oaxaca)Mixtec (Oaxaca)Zapotec (Oaxaca)Maya (Yucatan)Tzotzil (Chiapas)Chichen Itza, Classic MayaTayopa, northwest, precolonialLa Playa and Trincheras, SonoraToluquilla, Queretaro, PostclassicSierra Tarahumara, PostclassicMexican mestizos (131)Indo-mestizosAdmixed MayaNorth and westCentre and GulfOaxacaMaya region
Principal component analysis of nine present-day Indigenous Mexican populations in Global25. Ancient genomes are projected onto it, as is the Indigenous part of three admixed samples, estimated by removing their Iberian, African and East Asian parts (our analysis). The Huichol and Nahua are each represented by one individual.

We then estimated the Indigenous part of each admixed sample by subtracting its Iberian, African and East Asian parts, and placed it on the same map. The method works: the Indigenous part of the admixed Maya falls right on the Yucatec Maya. The Indigenous part of the Indo-mestizos falls near Oaxaca, closest to the Zapotec. And the Indigenous part of the average Mexican mestizo falls in the middle of the map, between the Nahua, the Totonac and the Pima, which is where one would expect central and western Mexico to be.

A second approach models each sample directly with the nine Indigenous groups as separate sources. We first tested it on simulated mestizos built from 50% Spaniards, 45% of one Indigenous group and 5% West Africans. It recovered a Maya source perfectly, a northern source at 80%, a Gulf source at 74% and an Oaxacan source at 69%, with the remainder always leaking towards the Maya. With random noise added, the right region still came first in all runs for the Maya, in 80% of runs for the north and in only about half for Oaxaca. Fine regional origin is therefore readable, but blurry.

Where does the Indigenous part come from?Indigenous share split among regional sources (Iberian and African parts removed). Top: simulated mestizos with a known source; our analysis0%25%50%75%100%Test: northerntrue source: Pima8018Test: Gulftrue source: Totonac7426Test: Oaxacantrue source: Zapotec6931Test: Mayatrue source: Yucatec Maya100Mexican mestizosGlobal25 average of 131621919Indo-mestizosaverage of 826766Maya, admixedaverage of 62575Totonac, admixedaverage of 4116524NorthWestCentre and GulfOaxacaMayaEach bar is rescaled to the Indigenous share only. Simulations: 50% Spanish, 45% one Indigenous group, 5% West African.
Indigenous part of simulated and real samples split among regional Indigenous sources. Real samples were modelled with Iberian, West African and nine Indigenous sources. The split for the mestizo average is unstable: without the Pima as a source, it becomes mostly Nahua and Zapotec (our analysis).

On the real samples, the admixed Maya are 75% Maya and 25% Gulf in their Indigenous part, and the Indo-mestizos are two thirds Oaxacan. The average Mexican mestizo comes out as a mixture of northern, central and Maya sources, with nothing from Oaxaca. That split should not be read literally: if the Pima are removed from the sources, the same Indigenous part becomes Nahua and Zapotec instead. The robust result is the position on the map: the Indigenous ancestry of the typical Mexican mestizo in Global25 is central Mexican, not Oaxacan and not Maya.

From Chichen Itza to today's Maya

How old is this regional structure? Ancient DNA now gives a direct answer. In 2023, Villa-Islas and colleagues sequenced pre-Hispanic individuals from eight sites across Mexico and found that the genetic structure that separates northern and central Indigenous peoples today has been preserved for at least 2,300 years, including at Toluquilla, in the Sierra Gorda of Queretaro, where archaeologists had expected a population replacement during the megadroughts. In our analysis, the ancient genomes from the northwest, from Tayopa and from La Playa and Cerro de Trincheras in Sonora, and the individual from the Sierra Tarahumara are all closest to the present-day Pima.

The most famous case is Chichen Itza. In 2024, Barquera and colleagues sequenced 64 children buried around AD 500 to 900 in a chultun, an underground chamber near the Sacred Cenote. All were boys aged roughly three to six, many of them close relatives, including two pairs of identical twins, which suggests they were chosen for rituals that echo the Maya story of the Hero Twins. Compared with 68 present-day Maya from the village of Tixcacaltuyub, they showed clear genetic continuity, and the modern Maya carried signals of selection in immune genes that the authors link to the epidemics of the colonial period, including one caused by Salmonella.

Global25 includes an average of 32 of these boys. In our analysis, the present-day Yucatec Maya are modelled as 96% Chichen Itza and 4% Iberian, and the Tzotzil of Chiapas as 99.5% Chichen Itza, with the best fits of any Indigenous group (8.7 and 7.8). The Zapotec (12.5), the Mixe (15.7) and the Pima (19.9) fit much worse. On the map, Chichen Itza sits next to the Tzotzil, its closest present-day population in Global25 (distance 8.5). After a thousand years, a conquest and the epidemics, the Maya are still the descendants of the people of Chichen Itza. We covered the wider ancient DNA record of the region in our article on Mesoamerican and Maya genetics.

Africa and Asia in the Mexican genome

African ancestry is small in the average Mexican genome but present everywhere. Our 4% for the Global25 mestizo average falls within the 1 to 5% that the Mexican Biobank finds in most individuals, and our simulations show that the model recovers small additions precisely: adding 2% of Yoruba ancestry to the mestizo average raised the estimate from 4.2 to 6.1%, exactly as expected. The first Africans of Mexico City have been traced directly: three men buried in a 16th-century hospital were born in Africa, as we described in our article on the first Africans of Mexico City.

East Asian ancestry is the smallest and most surprising component. Between 1565 and 1815, the Manila galleon linked the Philippines to Acapulco, and an estimated 40,000 to 120,000 Asians, most of them from the Philippines, reached New Spain. In 2022, Rodriguez-Rodriguez and colleagues found Southeast Asian ancestry related to western Indonesians and Filipinos in present-day Mexicans, dated it to about 13 generations ago, around 1620, and found the highest levels in Acapulco, where one individual carried more than 14%. In the Global25 mestizo average, the East Asian share is only 0.5%, and depending on the reference it ranges from 0 to 2.1% (median 0.4%). Our simulations show that an addition of 1% is detectable in clean data, so the average Mexican carries at most a trace of this ancestry, concentrated in a few places on the Pacific coast.

What the averages hide

All of these figures are averages, and averages hide most of the story. Within a single state, individual mestizos range from mostly European to mostly Indigenous; in the 2009 survey, the standard deviation of Indigenous ancestry was about 15 points. Samples also differ: the Mexican Biobank deliberately oversampled rural and Indigenous-speaking communities, while the Global25 averages are of unknown origin and probably lean towards the north or the cities. And our regional decompositions depend on nine Indigenous reference groups, two of them represented by a single person, for a country with 68 Indigenous languages.

Finally, genetics and identity measure different things. Many people who speak an Indigenous language carry European ancestry, and many mestizos who have never considered themselves Indigenous carry mostly Indigenous ancestry. Being Indigenous in Mexico is a matter of language, community and self-identification, not of a percentage. What genetics adds is a historical record: of who survived the epidemics, who married whom, and how much of the ancient population of each region is still there.

The answer to the title question, then, is about half on average, a third in Sonora, two thirds in Guerrero, and more in Oaxaca and the Maya region. And in every region, the Indigenous part of the Mexican genome is local: it comes from the peoples who were already there, and in the Maya region, from the people who built Chichen Itza.

Key points

  • The average Mexican mestizo genome is a little over half Indigenous: 55% in the 2009 national survey, 47% in the Global25 average, with 4% African and a trace of East Asian ancestry.
  • Indigenous ancestry rises from north to south, from about 36% in Sonora to 66% in Guerrero and higher still in Oaxaca and the Maya region, roughly following the density of pre-Hispanic populations.
  • About 93% of the maternal lineages of mestizos are Indigenous, but only about 31% of the paternal lineages: Mexico was founded mostly by European men and Indigenous women.
  • The Indigenous ancestry of mestizos is local: Nahua-like in the centre, Zapotec-like in Oaxaca, Maya in the Yucatan. In Global25, the average mestizo's Indigenous part is central Mexican.
  • Ancient genomes show that this regional structure is at least 2,300 years old, and that today's Maya descend from the people of Chichen Itza.
  • Mestizo is a cultural category, not a genetic one: individuals range from mostly European to mostly Indigenous within every state.

Global25 coordinates used in this article

The Mexican averages, the Indigenous and ancient Mexican populations, and the Iberian, African and East Asian sources used in the models. They can be pasted directly into the Vahaduo tool.

Mexican_Mestizo_avg131,0.051548,-0.073043,0.068416,0.038728,-0.032123,-0.009457,-0.131665,-0.152065,0.004000,0.008156,-0.001431,0.001710,-0.003367,0.002372,0.000866,0.003190,0.001191,0.000118,-0.000686,-0.000387,-0.000769,-0.000229,-0.001156,-0.000201,0.000993
Mexican_Euro-Mestizo_avg7,0.092847,0.083418,0.041053,0.008859,0.017717,-0.006893,-0.042335,-0.043053,0.014580,0.025201,-0.001902,0.004667,-0.004969,-0.008906,0.008221,0.004603,-0.002142,-0.000815,-0.004543,-0.002698,-0.000838,-0.002879,-0.001778,-0.000964,0.000650
Mexican_Indo-Mestizo_avg8,0.053639,-0.225701,0.096307,0.071585,-0.079092,-0.014328,-0.223054,-0.263787,-0.006954,-0.008133,-0.002943,-0.000731,0.001487,0.013487,-0.004699,0.001293,0.002233,-0.000586,0.001226,-0.001876,-0.002371,-0.000016,-0.000385,-0.000362,-0.000733
Maya_admixed_avg6,0.058619,-0.235095,0.102514,0.072029,-0.084169,-0.012457,-0.238262,-0.282142,-0.008828,-0.006652,-0.002382,0.000250,-0.000917,0.011813,-0.003370,0.004862,0.010344,-0.002534,-0.002640,-0.000438,-0.001269,0.005276,-0.000452,-0.000643,-0.001716
Mixtec_admixed_avg2,0.053497,-0.276732,0.112005,0.086564,-0.099403,-0.015757,-0.260862,-0.308179,-0.011760,-0.015672,-0.003167,-0.005320,-0.000446,0.023464,-0.008008,0.003116,0.002217,0.004877,0.000189,-0.002376,-0.001123,0.004142,-0.001911,-0.001687,-0.001138
Totonac_admixed_lowres_avg4,0.058049,-0.269369,0.116153,0.083092,-0.091171,-0.014712,-0.259334,-0.301084,-0.006647,-0.010387,-0.005602,0.002286,0.001412,0.023568,-0.006447,0.001690,0.006421,-0.001900,-0.001163,-0.005503,0.000593,-0.006059,-0.003944,0.000904,0.005478
Pima_avg12,0.052264,-0.309059,0.109994,0.091221,-0.107533,-0.015362,-0.268049,-0.322429,-0.011573,-0.016174,0.000000,-0.003634,0.005154,0.019061,-0.006684,0.008408,0.005020,0.003695,0.004274,-0.003637,-0.002142,0.005070,-0.004180,0.002711,0.000958
Huichol,0.053497,-0.311768,0.115776,0.102068,-0.110482,-0.010877,-0.270497,-0.324217,-0.012476,-0.020593,-0.002111,-0.000300,0.003122,0.022432,-0.011129,0.000265,0.008084,0.000760,0.005656,-0.001876,0.000873,0.003462,-0.004437,0.004699,0.008143
Nahua,0.056912,-0.304659,0.109742,0.089471,-0.106789,-0.012271,-0.272377,-0.320756,-0.013703,-0.016037,-0.007632,-0.000899,-0.000297,0.018029,-0.004479,0.012994,0.003129,0.001647,0.003142,-0.003377,-0.005989,0.004822,-0.004190,0.002530,0.004910
Totonac_avg9,0.059820,-0.303305,0.116405,0.089579,-0.103267,-0.014471,-0.270941,-0.326063,-0.006340,-0.014660,-0.007253,-0.002298,0.000694,0.022142,-0.005776,0.004317,0.010981,-0.002126,0.001410,-0.002265,-0.003660,0.001896,0.000945,-0.004351,0.003965
Mixe_avg12,0.055204,-0.318538,0.121213,0.094747,-0.108482,-0.015083,-0.278488,-0.334909,-0.012800,-0.014290,-0.006076,-0.004658,0.001214,0.019003,-0.007499,0.004342,0.004020,0.000507,0.000848,-0.001501,0.000520,0.005770,0.003122,-0.001948,-0.001048
Mixtec_avg9,0.047932,-0.299017,0.110287,0.093993,-0.102344,-0.016764,-0.269897,-0.325602,-0.012817,-0.013911,-0.006153,-0.004862,0.002461,0.016622,-0.009199,0.003536,0.006447,0.000225,0.002472,0.000639,-0.003882,0.005221,0.000739,0.000977,0.000373
Zapotec_avg12,0.055394,-0.298566,0.112508,0.090252,-0.103635,-0.018825,-0.267462,-0.322448,-0.010925,-0.015718,-0.004763,-0.003534,0.002341,0.019164,-0.006786,0.001580,0.002966,-0.002059,0.001823,0.000677,-0.002496,0.002597,-0.000657,-0.000281,-0.002395
Maya_Yucatan_avg10,0.054521,-0.296636,0.111779,0.092217,-0.106605,-0.017542,-0.279240,-0.332455,-0.012885,-0.015454,-0.000828,-0.000989,0.001397,0.018538,-0.009052,0.004389,0.006962,-0.001204,-0.001043,-0.002038,-0.001959,0.006381,0.001849,-0.000867,-0.000922
Maya_Tzotzil_avg17,0.053765,-0.314575,0.115399,0.093024,-0.109776,-0.017406,-0.287349,-0.339787,-0.013126,-0.016380,-0.004165,-0.001922,0.003673,0.020992,-0.010435,0.001919,0.005975,-0.000604,-0.000229,-0.001457,-0.002554,0.007448,-0.001131,0.001864,-0.001219
Mexico_ClassicMaya_ChichenItza_avg32,0.052181,-0.315544,0.116436,0.094397,-0.111021,-0.018041,-0.289276,-0.342318,-0.012502,-0.016316,-0.003826,-0.001026,0.001319,0.020992,-0.006621,0.005432,0.005097,-0.000265,0.001092,-0.000871,-0.000472,0.004641,-0.001883,0.000139,-0.000086
Mexico_Classic-Postclassic_Tayopa_avg9,0.052612,-0.310413,0.114728,0.093383,-0.111747,-0.016052,-0.268095,-0.316679,-0.013953,-0.018406,0.002273,-0.000067,0.003221,0.018625,-0.007133,0.005245,0.005317,-0.002252,0.006034,0.000737,-0.004534,0.000344,-0.005272,0.001861,-0.001370
Mexico_Precolonial_LaPlaya_CerroDeTrincheras_avg7,0.050733,-0.315830,0.111089,0.092563,-0.112504,-0.018487,-0.265428,-0.316767,-0.010840,-0.017807,-0.000696,-0.000707,0.005585,0.018756,-0.004769,0.005588,0.002887,-0.003837,0.002999,-0.000268,-0.001016,0.002862,-0.000088,-0.000465,-0.004345
Mexico_Postclassic_Toluquilla_avg2,0.051790,-0.315830,0.116342,0.095123,-0.107713,-0.013387,-0.277430,-0.324333,-0.006953,-0.018132,0.002923,0.000599,0.000744,0.019336,-0.005090,0.004243,0.005607,0.002154,0.007039,-0.000500,-0.000999,0.006863,0.001294,0.001084,-0.004850
Mexico_Postclassic_SierraTarahumara,0.050082,-0.311768,0.110496,0.093670,-0.109251,-0.014502,-0.264387,-0.314295,-0.011044,-0.017677,0.002436,-0.002997,0.002825,0.019680,-0.003664,0.009414,0.006258,0.001900,0.005279,0.003252,-0.002121,-0.005935,-0.006409,0.006145,0.000120
Spanish_Andalucia,0.108132,0.146076,0.035707,-0.003434,0.045256,-0.005857,-0.001930,0.002660,0.024715,0.031162,-0.002154,0.007272,-0.013207,-0.011408,0.010243,-0.002498,-0.006176,-0.001100,-0.004261,-0.002133,0.002929,-0.001302,-0.001972,-0.005334,0.001885
Spanish_Extremadura,0.105096,0.149960,0.033061,-0.001184,0.040931,-0.002789,-0.003995,-0.001000,0.024679,0.031223,-0.001299,0.005046,-0.010604,-0.012248,0.007555,0.002608,-0.002347,-0.003294,-0.006411,0.000417,0.002121,-0.004740,-0.001479,-0.002771,0.001437
Spanish_Castilla_Y_Leon,0.107753,0.143867,0.040477,-0.002153,0.043803,0.001859,-0.001723,0.004615,0.028429,0.029218,-0.002328,0.007843,-0.012091,-0.012019,0.012260,-0.006541,-0.006780,-0.001731,-0.004525,-0.002293,0.000291,-0.000907,0.001315,-0.002571,-0.002754
Mexico_Colonial_European_I8558_AD1610,0.104717,0.142174,0.039221,-0.010336,0.038469,-0.005857,-0.005640,0.001385,0.013703,0.021139,-0.009743,0.008093,-0.010109,-0.008120,0.009500,-0.002784,0.006519,-0.005701,-0.006285,0.002501,-0.004118,-0.005935,-0.002958,0.000241,-0.004910
Yoruba_Nigeria_avg38,-0.630071,0.063791,0.021674,0.016422,0.000462,0.013159,-0.044732,0.047597,-0.048806,0.033464,0.005316,0.001850,0.024443,0.001351,0.012854,-0.010502,0.007229,0.000570,0.006086,-0.003097,0.001080,0.002372,-0.001314,-0.000701,0.000076
Esan_avg99,-0.631086,0.064071,0.021332,0.016636,-0.000096,0.013336,-0.041953,0.045331,-0.050290,0.034428,0.006435,0.000404,0.023164,0.002181,0.010836,-0.008499,0.006349,0.001396,0.005325,-0.001510,0.001153,0.002662,-0.001516,0.000072,-0.000360
Mandenka,-0.607499,0.063866,0.018269,0.010695,-0.000222,0.009048,-0.037954,0.038562,-0.030804,0.025857,0.005079,-0.001224,0.019499,-0.000994,0.016535,-0.012125,0.010916,-0.000267,-0.001941,-0.002202,-0.001795,-0.005647,0.000596,-0.001004,0.001497
Kongo,-0.628304,0.064994,0.020365,0.017442,-0.000615,0.016176,-0.016451,0.020076,-0.033746,0.020228,0.008607,-0.003147,-0.001933,0.001514,-0.006786,0.007690,-0.009648,0.001140,0.001257,0.003502,-0.002496,-0.000989,0.001109,-0.001084,-0.006826
Filipino_avg82,0.012410,-0.414757,-0.056242,-0.044456,0.131180,0.046326,-0.003643,-0.011355,-0.019365,-0.016137,0.042269,0.004213,-0.004828,-0.002472,0.009535,0.005651,-0.002859,0.004372,0.006659,-0.010252,0.003509,-0.023156,-0.003573,-0.006934,-0.045690
Javanese_avg29,0.011539,-0.404426,-0.079871,-0.034806,0.142191,0.066164,-0.004392,-0.012708,-0.011087,-0.018733,0.083384,0.007411,-0.010165,0.007004,0.005635,0.002789,-0.000629,-0.001284,0.000386,0.011488,-0.014199,0.002170,-0.012992,0.001471,0.020291
Han_Fujian,0.018895,-0.452114,-0.014557,-0.067895,0.086478,0.039547,0.002068,-0.001892,-0.014685,-0.001677,-0.051055,-0.004736,0.005768,-0.009386,-0.005619,-0.001538,0.002243,0.001596,-0.001986,-0.013607,0.017270,0.004773,0.016663,0.003856,-0.006706

References

  1. Genomics Silva-Zolezzi I, Hidalgo-Miranda A, Estrada-Gil J, Fernandez-Lopez JC, Uribe-Figueroa L, et al., Jimenez-Sanchez G (2009). Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico. PNAS 106: 8611 to 8616. doi.org/10.1073/pnas.0903045106
  2. Genomics Moreno-Estrada A, Gignoux CR, Fernandez-Lopez JC, Zakharia F, Sikora M, et al., Bustamante CD (2014). The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 344: 1280 to 1285. doi.org/10.1126/science.1251688
  3. Genomics Sohail M, Palma-Martinez MJ, Chong AY, Quinto-Cortes CD, Barberena-Jonas C, et al., Moreno-Estrada A (2023). Mexican Biobank advances population and medical genomics of diverse ancestries. Nature 622: 775 to 783. doi.org/10.1038/s41586-023-06560-0
  4. Genomics Barberena-Jonas C, et al., Moreno-Estrada A (2026). Clinical genetic variation across Hispanic populations in the Mexican Biobank. Nature Medicine 32: 725 to 735. doi.org/10.1038/s41591-025-04100-z
  5. Genetics Rubi-Castellanos R, Martinez-Cortes G, Munoz-Valle JF, Gonzalez-Martin A, Cerda-Flores RM, et al., Rangel-Villalobos H (2009). Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of Mexico. American Journal of Physical Anthropology 139: 284 to 294.
  6. Genetics Martinez-Fierro ML, Beuten J, Leach RJ, Parra EJ, Cruz-Lopez M, et al., Rojas-Martinez A (2009). Ancestry informative markers and admixture proportions in northeastern Mexico. Journal of Human Genetics 54: 504 to 509. doi.org/10.1038/jhg.2009.65
  7. Genetics Martinez-Marignac VL, Valladares A, Cameron E, Chan A, Perera A, et al. (2007). Admixture in Mexico City: implications for admixture mapping of type 2 diabetes genetic risk factors. Human Genetics 120: 807 to 819.
  8. mtDNA Martinez-Cortes G, Salazar-Flores J, Haro-Guerrero J, Rubi-Castellanos R, Velarde-Felix JS, et al., Rangel-Villalobos H (2013). Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups. American Journal of Physical Anthropology 151: 526 to 537.
  9. Y-DNA Martinez-Cortes G, Salazar-Flores J, Fernandez-Rodriguez LG, Rubi-Castellanos R, et al., Rangel-Villalobos H (2012). Admixture and population structure in Mexican-Mestizos based on paternal lineages. Journal of Human Genetics 57: 568 to 574. doi.org/10.1038/jhg.2012.67
  10. Genomics Rodriguez-Rodriguez JE, Ioannidis AG, Medina-Munoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortes CD, Moreno-Estrada A (2022). The genetic legacy of the Manila galleon trade in Mexico. Philosophical Transactions of the Royal Society B 377: 20200419. doi.org/10.1098/rstb.2020.0419
  11. Ancient DNA Villa-Islas V, Izarraras-Gomez A, Larena M, Mejia Perez Campos E, Sandoval-Velasco M, et al., Avila-Arcos MC (2023). Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 380: eadd6142. doi.org/10.1126/science.add6142
  12. Ancient DNA Barquera R, Del Castillo-Chavez O, Nagele K, Perez-Ramallo P, Hernandez-Zaragoza DI, et al., Krause J (2024). Ancient genomes reveal insights into ritual life at Chichen Itza. Nature 630: 912 to 919. doi.org/10.1038/s41586-024-07509-7
  13. Ancient DNA Barquera R, Lamnidis TC, Lankapalli AK, Kocher A, Hernandez-Zaragoza DI, et al., Krause J (2020). Origin and health status of first-generation Africans from early colonial Mexico. Current Biology 30: 2078 to 2091. doi.org/10.1016/j.cub.2020.04.002
  14. Census INEGI (2021). Censo de Poblacion y Vivienda 2020: resultados complementarios. Instituto Nacional de Estadistica y Geografia, Mexico.
  15. History Vasconcelos J (1925). La raza cosmica. Agencia Mundial de Libreria, Barcelona.
  16. Data Global25 coordinates by Davidski (Eurogenes), and the Moriopoulos Collection 2026 of averages and ancient individuals. Models, simulations and figures: ExploreYourDNA.