Population genetics | South America | Language and DNA
Paraguay: the nation that speaks its mothers' language
Most Paraguayans are not Indigenous, yet two in three speak Guarani every day. Their DNA explains why: almost nine in ten maternal lines are Native American, while almost all paternal lines came from Europe.
Hero image: AI generated illustration of a Guarani mother and her mestizo child on the bank of the Paraguay River near early colonial Asunci?n. It is not a reconstruction of real individuals.
Across Latin America, the languages of the conquerors won. Spanish and Portuguese replaced hundreds of Indigenous tongues, and where Indigenous languages survive, from Quechua in the Andes to Maya in Yucat?n, they are spoken mainly by Indigenous communities. Paraguay is the exception. Indigenous peoples make up only around 2 percent of its 6 million inhabitants, yet Guarani is the everyday language of the majority, spoken in kitchens, markets, football stadiums and parliament by people who would describe themselves as mestizo or simply Paraguayan.
Bolivia and Peru also give Indigenous languages official status, but in those countries the speakers are largely Indigenous. In Paraguay a non-Indigenous majority adopted, kept and passed on a Native American language for almost five centuries. How did that happen? The history points to the household, and the genomes point to the women who ran it.
Before the Spanish: the Guarani world
Guarani belongs to the Tupi-Guarani branch of the Tupian family, one of the great language expansions of South America. Its speakers were farmers who grew maize, manioc and beans in forest clearings, made distinctive painted and corrugated pottery, and lived in large communal houses. Archaeologists have long argued that the Tupi-Guarani spread out of the Amazon roughly 2,000 years ago, one branch running along the Atlantic coast and another moving south into the Paran? and Paraguay river basins.
Genetics has confirmed the outline. In 2020, Castro e Silva and colleagues compared genomes of the coastal Tupiniquim with those of Guarani Mby? and other groups and found that both share ancestors who lived in southwestern Amazonia around 3,000 years ago, followed by two almost simultaneous migrations out of the same homeland. The Tupi expansion, they concluded, was a movement of people and not just of pottery styles or words.
Ancient DNA from the region is still sparse. The only ancient genome from Paraguay itself in our datasets is a single individual from the Pantanal wetlands on the upper Paraguay River, dated to about AD 350. In the lower Paran?, a large 2026 study of Argentine ancient genomes by Maravall-L?pez and colleagues reports that an individual from around 400 years ago with a Guarani archaeological association clusters with Brazilian groups, consistent with a Guarani presence that came from the north. When the Spanish arrived, Guarani villages occupied a vast arc from the Atlantic coast of southern Brazil to the Paraguay River.
1537: brothers-in-law of the Guarani
The Spanish expedition that founded Asunci?n in 1537 had come up the river looking for a route to the silver of Peru. It found instead a fertile land with no gold, a long way from any port, and a population of Guarani farmers who were willing to become allies against the hunting peoples of the Chaco. The colony survived because of that alliance, and the alliance ran through women.
Guarani society was built on kinship. A man who received a wife from a Guarani family became a tovaja, a brother-in-law, with obligations of labour and loyalty owed in both directions. The Spaniards adopted the system so enthusiastically that it got a name of its own, cu?adazgo, from the Spanish cu?ado (brother-in-law). Guarani leaders gave daughters and sisters to the newcomers; the Spaniards gained food, labour and warriors. Some conquistadors had dozens of Guarani women in their households, and contemporaries mockingly called Asunci?n the "paradise of Mahomet".
Very few Spanish women made the journey. The children of these unions, known as mancebos de la tierra (young men of the land), were raised in their mothers' households, by their mothers, grandmothers and aunts, in their mothers' language. They grew up to become the backbone of the colony, its soldiers and settlers, and many were recognised by their fathers as Spaniards. Legally Spanish, they spoke Guarani as their first language. Within a generation or two, the "Spanish" population of Paraguay was largely mestizo, and its mother tongue was Guarani.
If Guarani survived because it was the language of the mothers, Paraguayan genomes should carry a clear signature: Native American maternal lineages and European paternal lineages, far more lopsided than the overall ancestry would suggest.
Missionaries, a dictator and two catastrophic wars
Several later events reinforced what the household had started. From 1609 to their expulsion in 1767, the Jesuits ran a network of missions, the reducciones, where tens of thousands of Guarani lived under missionary rule. The Jesuits chose to work in Guarani rather than Spanish. Antonio Ruiz de Montoya published a great dictionary of the language in 1639 and a grammar in 1640, and the missions printed books in Guarani, turning it into a written language with a standard spelling and a Christian vocabulary.
After independence in 1811, Paraguay turned inward under Jos? Gaspar Rodr?guez de Francia, who ruled until 1840. On 1 March 1814 his government issued a striking decree: European men were forbidden to marry women "known as Spanish" and could only marry Indigenous, mestizo or Black women. The measure was aimed at breaking the colonial Spanish elite, but it also pushed the population further toward a single mixed society in which Guarani, not Spanish, was the common tongue.
Then came the War of the Triple Alliance (1864 to 1870), in which Paraguay fought Brazil, Argentina and Uruguay at once. The scale of the loss is still debated, but a widely cited study by Whigham and Potthast, based on a rediscovered 1870 census, estimated that 60 to 69 percent of the population died or disappeared. Lower estimates exist, yet all agree that adult men were destroyed disproportionately. Postwar Paraguay was rebuilt to a great extent by women, in women-led households, and once again Guarani was the language of the home. In the Chaco War against Bolivia (1932 to 1935), Paraguayan units are reported to have used Guarani for field communications, a language most Bolivian officers could not follow.
For most of the 20th century Guarani was the language of the countryside and the family, while Spanish ruled schools, courts and offices. The 1992 Constitution made Guarani co-official with Spanish, and a 2010 Languages Law extended its use in public life. According to the 2022 household survey, 34.3 percent of Paraguayans aged five and over speak mostly a mix of Guarani and Spanish at home, 32.6 percent speak mostly Guarani and 30.4 percent mostly Spanish.
What the uniparental markers say
The largest genetic study of Paraguayans to date, by Sim?o and colleagues in 2021, typed 548 people from 14 departments of eastern Paraguay, the region where almost all Paraguayans live. Because most participants were men, the study could read both the maternal line (mitochondrial DNA, passed from mother to all her children) and the paternal line (the Y chromosome, passed from father to son), as well as 46 autosomal markers that estimate overall ancestry.
The result is one of the most extreme sex-biased admixture signals recorded anywhere in the Americas. 87.2 percent of mitochondrial lineages are Native American. On the paternal side the proportions are reversed: 92.2 percent of Y chromosomes are European, and only 5.2 percent belong to Native American haplogroups. In between sits the autosomal genome, which records all ancestors equally, at 33.8 percent Native American.
The maternal lineages themselves are a cross-section of South American diversity. Among the native mtDNA lineages, haplogroup B accounts for about 31 percent, C for 29 percent, A for roughly 23 percent and D for 17 percent. An earlier pilot study from the same group found that C1 alone made up 31 percent of native lineages. The authors also note that haplogroup B reaches 63 percent of native lineages in Asunci?n, a hint that the capital's founding mothers came from a particular set of local Guarani families.
On the paternal side, the dominant lineage is R1b-M269, and in particular R1b-S116 (also called DF27), the branch that is most frequent in Iberia. Paraguayan fathers, in other words, were overwhelmingly Spanish, followed later by other European immigrants. The few Native American Y chromosomes that survive belong to haplogroup Q.
This is exactly the pattern the history predicts. The first Spanish settlers were men; the women of the colony were Guarani. A child inherited a European surname and Y chromosome from the father and a Guarani mitochondrial genome from the mother, and with it the language of the house.
Our analysis: how Native American are Paraguayans?
To put a number on the overall ancestry, we modelled Paraguayan samples in Global25 with non-negative least squares (NNLS). A word of caution first. Only one Paraguayan individual in our datasets has directly genotyped Global25 coordinates (Paraguayan_Mestizo, n=1, Moriopoulos 2026). The Moriopoulos 2026 collection also contains a "With Sims" release, which adds simulated group averages for populations without public genotype data, including a Paraguayan mestizo group (n=100) and a Paraguayan Euro-mestizo group (n=23). These are modelled coordinates, not genomes, so we treat them as secondary evidence and test them against the published data.
Our model offered six European sources (Castilian, Andalusian, Canarian, Portuguese, Venetian and German), two African sources (Yoruba and southwestern Bantu) and five Native American sources spanning the continent: Karitiana (a Tupian-speaking group from Rond?nia in the Amazon), Wich? (Gran Chaco), a Kaingang individual buried in southern Brazil around 1870, Peruvian Quechua and Mixe (Mexico). We then summed the sources into three continental totals.
| Target | European | Native American | African | Fit distance |
|---|---|---|---|---|
| Paraguayan mestizo (n=100, simulated) | 62.6% | 35.5% | 2.0% | 0.0070 |
| Paraguayan mestizo (n=1, genotyped) | 46.8% | 49.9% | 3.4% | 0.0211 |
| Paraguayan Euro-mestizo (n=23, simulated) | 82.7% | 16.8% | 0.5% | 0.0044 |
The continental totals are robust. Re-running the model with 108 alternative source combinations (nine different Native American proxies, four European configurations and three African configurations) moves the Native American share of the n=100 group only between 33.3 and 37.1 percent, and that of the genotyped individual between 45.9 and 51.0 percent. The condition number of the full model is high (about 290) because the European sources are close to each other (the closest pair, Andalusian and Portuguese, sit only 0.010 apart), so we do not interpret the split between individual European sources. The continental sums are unaffected by this collinearity.
The cross-validation is encouraging. The simulated Paraguayan group comes out at 35.5 percent Native American, within two points of the 33.8 percent measured with autosomal markers by Sim?o and colleagues. The single genotyped individual, at about 50 percent, is more Indigenous than the average, which is entirely plausible for one person: the published samples show substantial individual variation. The Euro-mestizo group, at 17 percent, represents the more European end of Paraguayan society, which absorbed large numbers of Italian, Spanish, German and other immigrants after 1870.
A typical South American genome with an atypical language
Here lies the real surprise. When we put Paraguay next to its neighbours, its overall ancestry is not unusual at all.
The Paraguayan mestizo profile sits close to mestizo groups in Argentina, Uruguay, Chile, Colombia and lowland Bolivia, all of which speak Spanish. Mexican mestizos carry more Native American ancestry than Paraguayans; Peruvian mestizos carry far more. The genetic distances agree: among the nearest populations to the Paraguayan n=100 group in the Moriopoulos collection are Argentine (0.017), Chilean (0.026) and Uruguayan (0.031) mestizo groups, themselves simulated averages.
This is precisely the conclusion Sim?o and colleagues reached in the title of their paper: "a typical South American profile with a unique pattern of admixture". Paraguayans are not exceptional because they have more Indigenous ancestry than other Latin Americans. They are exceptional because of how that ancestry arrived, almost entirely through women, and because the women's language won. The same genetic mixture produced Spanish-speaking nations elsewhere. What made the difference in Paraguay was who raised the children, how isolated the colony was, the Jesuit decision to write in Guarani, and two centuries of demographic shocks that repeatedly removed men and left households in the hands of women.
Which Indigenous people? Testing the limits
Can Global25 tell us which Native American population Paraguayans descend from? We would expect a Guarani-like source, but there is a problem: no Guarani individuals have public Global25 coordinates. We therefore let the five Native American sources compete.
| Target | Karitiana (Amazon, Tupian) | Wich? (Chaco) | Kaingang (south Brazil) | Quechua (Andes) | Mixe (Mexico) |
|---|---|---|---|---|---|
| Paraguayan mestizo (n=100, sim.) | 0.7% | 17.2% | 0% | 14.7% | 3.0% |
| Paraguayan mestizo (n=1) | 0% | 0% | 43.4% | 4.1% | 1.8% |
| Paraguayan Euro-mestizo (n=23, sim.) | 0% | 13.9% | 0% | 2.8% | 0% |
| Peruvian mestizo (control) | 0% | 0% | 0% | 66.5% | 0% |
| Mexican mestizo (control) | 0% | 0% | 4.1% | 4.3% | 37.8% |
The controls behave well. Peruvian mestizos take all of their Native American ancestry from Quechua, Mexican mestizos almost all of theirs from Mixe. For Paraguay the answer is clearly southern South American lowland ancestry: the model rejects a Mexican source and prefers the Chaco and southern Brazilian proxies. The genotyped Paraguayan takes almost all of their Native American share from the Kaingang individual, who lived in the Atlantic forest of southern Brazil, a region that bordered Guarani territory. The simulated groups prefer Wich?, the nearest Chaco population.
Two results, however, need to be handled with care.
The Andean signal is not stable. The 14.7 percent Quechua in the n=100 group collapses to 1.7 percent if we replace modern Quechua with an unadmixed Inca period genome from Peru, with Wich? rising to compensate. Modern Quechua carries about 8 percent European ancestry of its own, and in an admixed target it can absorb part of the European signal. We therefore do not claim any Andean ancestry in Paraguay from these data.
Karitiana is rejected, but the zero is only partly reliable. It is tempting to read the near zero for Karitiana as a striking result: the Karitiana speak a Tupian language, yet contribute nothing. Before accepting a zero, we ran spike-in tests, adding known amounts of Karitiana to each Paraguayan target and re-fitting.
For the n=100 group, the detection floor is about 2 percent: anything above that would have been seen, so the absence of Karitiana-like ancestry is real. For the single genotyped individual, the model fails to see Karitiana ancestry below about 4 to 5 percent, because Karitiana and Wich? sit only 0.027 apart and the other South American sources can absorb it. Here the honest statement is that a small Amazonian-like component cannot be excluded.
The deeper point is that a language family is not a genetic population. The Karitiana and Suru? of Rond?nia are small, isolated Tupian-speaking groups that have experienced extreme genetic drift, which makes them poor stand-ins for the large Guarani population that once spread across the Paran? basin. The Guarani carried a Tupian language south, but over two millennia their genomes also took in the ancestry of the peoples they met, and the Paraguayan Indigenous component accordingly looks closer to its Chaco and southern Brazilian neighbours than to Amazonian Tupi speakers. A true Guarani reference in Global25 would settle the question, and we will update this analysis if one becomes available.
The African thread
Paraguay's African heritage is often forgotten. Enslaved Africans were brought to the colony, and the Afro-Paraguayan community of Kamba Cu?, near Asunci?n, descends from Afro-Uruguayan soldiers who followed Jos? Artigas into exile in Paraguay in 1820. Sim?o and colleagues estimated 10.8 percent African ancestry with their autosomal marker panel, and 5 percent of maternal lines are African.
Our Global25 models give a lower figure: 2.0 percent for the simulated n=100 group and 3.4 percent for the genotyped individual. This is not a detection problem, because the spike-in test shows that added African ancestry is recovered almost exactly (Figure 5). The divergence more likely reflects the difference between a 46-marker panel, which estimates ancestry from a small number of loci with wide individual error, and genome-wide coordinates, as well as the different samples behind each estimate. We report both numbers and regard the true value as uncertain, probably between 2 and 10 percent depending on region and sample.
Conclusion: a language carried by mothers
The genetics of Paraguay reads like a summary of its history. The fathers were Spanish, the mothers Guarani. Their children were legally Spanish, genetically mixed and linguistically Guarani, because language is learned at home, and the home belonged to the women. The Jesuits gave the language a written form, Francia's marriage policy blended the colonial population further, and the wars of the 19th and 20th centuries repeatedly removed men and left women to rebuild the nation.
By overall ancestry, Paraguayans look like many other South American mestizo populations, around one third Native American on average. What they kept, and others lost, is the voice of their grandmothers. More than four centuries after the founding of Asunci?n, the Guarani women who married Spanish soldiers are still present in the mitochondria of almost nine in ten Paraguayans, and in the language that two thirds of them speak at home.
Global25 coordinates used in this article
Paraguayan and South American Indigenous references from the Moriopoulos 2026 collection of Global25 coordinates (Global25 by Davidski). The n=100 and n=23 Paraguayan groups are simulated averages from the "With Sims" release and should be used with that caveat. They can be pasted directly into the Vahaduo tool.
Paraguayan_Mestizo_(n=1),0.053497,-0.083273,0.069013,0.040052,-0.040007,-0.009203,-0.143827,-0.171685,0.003886,0.009659,-0.007957,0.004046,-0.010258,-0.001514,0.001493,0.005834,0.013821,-0.002154,-0.00176,0.003502,0.000624,0.008285,-0.002835,-0.002169,0.004431
Paraguayan_Mestizo_(n=100),0.07098362,-0.01696658,0.0644936,0.03220399,-0.0131793,-0.00680139,-0.10765346,-0.124969,0.00954096,0.01136371,0.00260661,0.00238888,-0.00529468,0.00065111,0.00114067,0.00052537,0.00053473,-0.00002927,-0.00032318,-0.00001633,0.00175713,-0.00123836,-0.00006091,0.00026717,0.0012324
Paraguayan_Euro-Mestizo_(n=23),0.095579087,0.068279957,0.052775087,0.016575304,0.013984609,-0.0024923913,-0.053031696,-0.05910187,0.013067435,0.017001913,0.00013078261,0.0035470435,-0.0071967826,-0.0028299565,0.0037832609,-0.00046578261,-0.001256087,-0.00048569565,-0.0014163478,-0.00051095652,0.0018278696,-0.0015513043,-0.00022978261,-0.0006686087,0.00096547826
Paraguay_Pantanal_1600BP_(n=1),0.045529,-0.311768,0.123696,0.107237,-0.108328,-0.01506,-0.308099,-0.368985,-0.021066,-0.019317,0,0.009292,0.002527,0.018166,-0.00095,0.008618,0.007693,0.003294,-0.009427,0.001251,-0.003244,0.01014,0.008627,-0.00964,0.005868
Wichi_(n=15),0.052282733,-0.31643913,0.1201758,0.098471933,-0.12059693,-0.019057533,-0.31143593,-0.3671692,-0.0125032,-0.018636667,-0.00082266667,-0.0003796,0.0007434,0.030359533,-0.010586133,0.0064172667,0.0081445333,-0.00030406667,0.0031675333,0.0022678,-0.0015720667,0.010460867,0.00057513333,-0.0025222667,-0.0025066667
Karitiana_(n=14),0.058049857,-0.32025443,0.117985,0.10709836,-0.11281221,-0.014004214,-0.32070557,-0.37908857,-0.014711143,-0.019226071,0.0014497857,-0.0020980714,-0.0013272143,0.027544214,-0.0055353571,0.0044322857,0.010514643,0.001466,-0.000826,-0.0013488571,-0.0062122143,0.011782357,-0.0041639286,-0.0021689286,-0.0071849286
Surui_(n=8),0.056911625,-0.3205265,0.1169545,0.1066715,-0.116214,-0.018895125,-0.33013112,-0.39537775,-0.01608075,-0.01977275,0.0022125,-0.003559375,0.00027875,0.036710875,-0.01450525,0.001823125,0.01105,-0.000285,-0.00011,0.00139125,-0.003868,0.0135245,-0.007625875,-0.008073125,-0.0093555
Brazil_Kaingang_100BP_(n=1),0.055773,-0.312783,0.118793,0.092701,-0.109251,-0.027052,-0.291178,-0.35237,-0.010635,-0.009659,-0.001786,0.001798,-0.004311,0.021882,-0.001764,0.005436,0.009779,-0.003167,-0.000503,0.008879,0.00861,0.011376,-0.002095,-0.00241,-0.006107
Methods in brief
Global25 scaled coordinates were merged with first occurrence priority from Davidski's population averages, modern averages, the Moriopoulos 2026 collection (all averages, no sims) and the dated individual ancients file; the Moriopoulos "With Sims" modern file was added last, only for populations absent from the other files. Scale compatibility was checked on shared populations (for example Surui and Yoruba agree to the third decimal across files). Distances are Euclidean over 25 dimensions. NNLS models use a sum to one constraint enforced by a heavily weighted extra equation, with results normalised. The main model uses 13 sources (condition number 291; closest pole pair Karitiana and Wich? at 0.027 among Native American sources, Andalusian and Portuguese at 0.010 among European sources). Robustness was tested on 108 alternative source sets. Spike-in tests add a known fraction of a source to the target and re-fit to determine the detection floor. G25 results are a proxy; where published marker-based results exist, we report them alongside and discuss divergences.
References
- Genetics Sim?o F, Ribeiro J, Vullo C, et al. (2021). The ancestry of eastern Paraguay: a typical South American profile with a unique pattern of admixture. Genes 12(11): 1788. doi.org/10.3390/genes12111788
- Genetics Sim?o F, et al. (2017). Paraguay: unveiling migration patterns with ancestry genetic markers. Forensic Science International: Genetics Supplement Series. sciencedirect.com
- Genomics Castro e Silva MA, Nunes K, Lemes RB, et al. (2020). Genomic insight into the origins and dispersal of the Brazilian coastal natives. Proceedings of the National Academy of Sciences 117(5): 2372 to 2377. pubmed.ncbi.nlm.nih.gov/31932419
- Ancient DNA Maravall-L?pez J, et al. (2026). Eight millennia of continuity of a previously unknown lineage in Argentina. Nature 649. doi.org/10.1038/s41586-025-09731-3
- History Whigham TL, Potthast B (1999). The Paraguayan Rosetta Stone: new insights into the demographics of the Paraguayan War, 1864 to 1870. Latin American Research Review 34(1): 174 to 186. bibliographic record
- History From Paraguay, a history lesson on racial equality (2016). The Conversation. theconversation.com
- Language Agencia IP (2023). M?s del 34% de la poblaci?n paraguaya habla con frecuencia el castellano y guaran? (INE household survey 2022). ip.gov.py
- Data Global25 PCA coordinates (Davidski) and the Moriopoulos 2026 collection of Global25 averages, including the "With Sims" release. eurogenes.blogspot.com