Laguna de los Pampas 10,000 BP remains in Argentina. Comments

A paper published in Nature (online) last November (Maravall-López J, Motti JMB, et al., (2025). Eight millennia of continuity of a previously unknown lineage in Argentina. Nature. 2026 Jan;649(8097):647-656. doi: 10.1038/s41586-025-09731-3. Epub 2025 Nov 5. PMID: 41193808; PMCID: PMC12747222.) describes, like its title says, a new Native American lineage that "persisted for thousands of years with no evidence of interregional migration."

The authors studied more than 200 prehistoric genomes from central Argentina, between the Andes, the Paraná River, Patagonia and Bolivia, and Paraguay in the North. They found that the people who lived there had their own, unique lineage that lasted for millennia. They didn't live in isolation, they admixed with others. This paper is a step in the right direction towards understanding how America was peopled.

The 10,000 BP Laguna de los Pampas remains

I found the paper interesting, but what I found more interesting was the oldest specimen used in the genetic study, an individual from a tiny lake in the Argentine Pampas region (see it in Google Maps), at that time a vast open grassland. The lake is called Laguna de los Pampas (after the Historic natives, the Pampas people). It forms part of the region that the paper calls Central Southern Cone (CSC) which lies east of the Andes and spans Northwestern Argentina highlands and Mountain ranges, the pampean hills in central Argentina, the plains of the Pampas, as well as the drier western Pampa region north of the Patagonia, and west of the Paraná River. It also includes the Chaco forests and savanna or the Jungles, marshes and fluvial areas of the Paraná basin.

The authors state that "To understand how the oldest individual, Argentina_Pampas_LagunadelosPampas_10000BP (hence, LagunadelosPampas_10000BP) relates to other Early/Middle Holocene South Americans, we computed 𝑓4-statistics... These statistics reveal shared drift among LagunadelosPampas_10000BP and Argentina_Central_JesusMaria_8500BP (henceforth, JesusMaria_8500BP), the individuals from Southern Patagonia (5100-7300BP) and those from the Argentinian Pampas (7700-6800BP), with respect to both early individuals from the Central-East of Brazil (10400-6800BP) and the Central Andes (9000-8600BP)."

Then they display the relationship in the paper's Figure 2. But, surprisingly, it does not include the Laguna de los pampas 10000BP individual!

They go on to say that "We found no evidence of mixture events fitting the data significantly better, although this could be a reflection of low statistical power. LagunadelosPampas_10000BP is absent from the tree because of its ambiguous positions across well-fitting models."

So they have the oldest sample in the region, 10,000 years BP, and they couldn't fit it into their phylogenetic tree because their "well-fitting models" couldn't fit it. How well fitting are they if they can't account for this critical specimen?

They continue by saying that "All pairs of JesusMaria_8500BP, Southern Patagonia (5100-7300BP), and Argentinian Pampas (7700-6800BP) are symmetrically related to LagunadelosPampas_10000BP, up to the limits of our resolution for statistics unaffected by biases due to using different sequencing technologies (Figure 2a)"

This is the figure that does not include the Laguna de los Pampas specimen. And continue: "The most plausible explanation is that LagunadelosPampas_10000BP belonged to an ancestral Southern Cone population that split from Central East Brazil and Central Andes groups by 10000BP and was geographically in the CSC by that time before differentiating into distinct components."

This makes sense, it is the oldest sample and must have come, either from Brazil (Amazon or Atlatic Coast) or perhaps from the Central Andes (Peru or Bolivia).

They continue: "Neither PeñasdelasTrampas1.1_8800BP, from Southern Puna in Northwest Argentina, nor LosRieles_5100BP from Central Chile, showed affinity to LagunadelosPampas_10000BP, so we could not make a definitive statement about their relationship to this individual."

Therefore the Northern and Western samples (Chile, and the border area of Argentina with Bolivia) were not related to the Laguna de los Pampas sample. So, one would imagine it is associated to the Brazilian samples. But the paper ignores this issue. No further refrence is made to a possible Brazilian origin. The paper immediately jumps to the Anzic sample, 12,500 years old, from the Rocky Mountains in Montana, USA.

The paper says:

"We evaluated the affinities of LagunadelosPampas_10000BP to Anzick, a 12500BP individual from present-day Montana, USA, with distinctive genetic affinities to early South Americans relative to later ones. Chile_LosRieles_12000BP showed the strongest affinity (∣Z∣ < 4.1), followed by weaker affinity with LagunadelosPampas_10000BP (∣Z∣ < 2.6). However, since these three individuals were positioned together as a clade in an outgroup-f3 neighbor-joining tree (Supplementary Figure 1), both probably harbored a distinct Anzick-related genetic component. Affinity with Anzick in early South America, and absence thereof, has been associated with at least two independent migration waves and population replacement. However, the fact that LagunadelosPampas_10000BP also exhibits excess allele-sharing with later Southern Cone individuals without a significant genetic affinity towards Anzick, suggests that this individual may have been admixed between a basal Southern Cone lineage and a basal Anzick-associated lineage, and thus these Anzick-related lineages may not have been completely replaced."

What does this really mean? The Chilean sample from Los Rieles, 12 ky old is closer to the 12.5 ky Anzic sample. The ∣Z∣ formula, is simple, it is a measure in modulus or absolute value (the magnitude of a real number without regard to its sign, so -4 and +4 have the same modulus) of Z. Z, is the "Z score", a statistical tool used to validate admixture. If the value is less than 2, it means there is no evidence of admixture. if it is larger than 3, it may suggesting genetic shareing and admixture.

They say that it is known that ancient South American Natives had affinity with Anzic, while later ones did not. And that this suggests two waves of people entering South America. An older one with Anzic affinity and a more recent one, that had a different genetic makeup. But then they say that the 10,000 BP Laguna de los Pampas sample didn't have "significant genetic affinity towards Anzic" despite being ancient, and also "exhibits excess allele-sharing with later Southern Cone individuals." They conclude that he was a mixture of a both groups.

But, then they did another modelling and found a quirk! "The placement of LagunadelosPampas_10000BP was more ambiguous, appearing as an isolated lineage (3 models) or grouped with the Central Argentina JesusMaria_8500BP (5 models), or the Middle Holocene Argentinian Pampas (7700-6800BP) (1 model), consistent with its basal position in CSC diversity." So his placement was "ambiguous" and "isolated"

I believe that there aren't enough "ancient" genomes from South American to clearly understand the tree, the roots, the flow of people. Until more remains are discovered and sequenced we will find papers like this one, with a lot of amgiguity and conjectures.

Laguna de los Pampas. More information

A previous paper by Roca-Rada et al. (2021) reported that the Laguna de los Pampas person lived 10,223–9,764 Cal BP, and carried the mtDNA D1j haplogroup. The authors suggested that "D1j mitogenome in Laguna de los Pampas is basal in the D1j phylogeny and supports the hypothesis that D1j spread from the Pampas. Interestingly, a cranial morphometric study showed some affinities between the Early Holocene sites of Laguna de los Pampas and Lagoa Santa (Brazil) (Menéndez et al., 2015)." At last! a link between the Brazilian Lagoa Santa people and Laguna de los Pampas. The 2025 paper ignored this fact, it never explores the Brazilian option.

D1j mtDNA

The 2021 paper continues: "Furthermore, the D1j haplotype from Laguna de los Pampas lacks the T152C substitution but has the characteristic C16242T and T16311C substitutions. García et al. (2012) argue that the mutations at T16311C and T152C co-occur in both D1j and other D1 haplotypes found in central Argentina and propose that the substitution at T152C preceded the one at C16242T. Again, the ancient mitogenome from Laguna de los Pampas does not support this hypothesis as our observations indicate that the substitution C16242T preceded T152C. Nevertheless, it should be noted that 152 and 16,311 are mutational hotspots as described by Soares et al. (2009), increasing the odds of a recurrent mutation event." In other words, "hotspots" mean that a mutation can happen time and time again.

Hotspot

Comment: Doesn't this "hotspot" concept make the basics of genetic mutations a flimsy structure on which to build bold claims? Time and time again we are told that specific substitutions (mutations), such as one at position XXX that defines a haplogroup is then passed on to ALL future generations, and then, by chance, a later YYY mutation is added to the genome defining another haplogroup passed on to all those who come from that woman and her lineage. So looking at someone carrying both XXX and YYY we can identify them and place them in the branching tree, and the one with only XXX belongs to another branch. Now I learned a new concept, "mutational hotspots" that means that these mutations not as invariant as I had imagined. I will look into this in future posts.

Note added 21-February-2026: I did post about mutations, reversions and a comment on "hotspots". Online here.

So, the Laguna de los Pampas person had an ancient D1j mtDNA, distinct from the Anzic (D4h3a); the Los Rieles mtDNA has not yet been informed. D1 is one of the founding lineages of Amerindian mtDNA and the D1j derives from the slightly older D1g haplo.

The D1j mtDNA haplo is ancient, de Saint Pierre (2017) gave it a very old divergence date from D1g: 16.7 ± 9.4 kya. We have already mentioned the paper by Roca-Rada et al. (2021); in it the team "confirms that the D1j mitogenome from Laguna de los Pampas (LLP.S2.E1) is basal to the entire D1j clade." and finds the "TMRCA estimates for D1g (95% highest posterior density interval: 20.9–11.7 kya) and D1j (20.8–11.5 kya)."

Future research and more data should clarify the origins of these people.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

D4h3a mtDNA revisited

Yu-Chun, lI et al. published a paper in 2023, that looked into the link between Native Americans (NAs) mitochondrial DNA (mtDNA) lineage D4h3a and the variant D4h3b which until now has been found only in East China and Thailand.

The authors noted that "D4h3 and its ancestor type D4h are relatively rare in contemporary populations (∼0.5%)" and estimated the age of the NA variant at 19,400 years (15.11 - 24.05 ky).

The interesting part is that they suggest that this haplogroup took a coastal route by sea from China to America, going through Japan's Islands. It didn't cross from Siberia and Beringia into America, walking.

"The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs."

The authors highlight that this is a genetic source that is outside of Siberia, which provided mtDNA (a matrilineal lineage) to Native Americans. They stress that it is an "additional ancestral source for the ancestors of NAs beyond Siberia", and that "although only contributed to a small proportion of the mtDNA gene pool of NAs (D4h3a) [it] would be important in complementing the whole picture of origination histories of early NAs."

Below is an image from this paper:

Given the location of the original D4h variant, on the coast of Northern China, the authors suggest that it could have dispersed along the Pacific coastal rim: "we speculate that D4h would have documented LGM and post-LGM dispersals along the eastern Pacific coast. This echoes well with the dispersal D4h3a along the Pacific coastal path when the ice-free corridor was closed. Similarly, Y chromosome C-L1373, which probably radiated in parallel with mtDNA D4h, has also been reported in South Koreans (http://koreangenome.org/) and the Nivkh, thus lending support to a coastal population expansion scenario initiated from northern coastal China. This, together with the Paleolithic cultural affinities along the Pacific, e.g., stemmed points, and the palaeoecological feasibility of maritime dispersals (e.g., kelp highway hypothesis) lends further support to the coastal route hypothesis of early NAs."

It is also found along the coastal people in South America. Stuart J. Fiedel (source) in 2017 wrote that "D4h3a is a relatively rare clade of haplogroup D... it was reported mainly from coastal peoples, including the Fuegians of southernmost Chile, the Chumash of southern California, and the Cayapa of Ecuador The 10,300-year–old skeletal remains from On Your Knees Cave in coastal Alaska belonged to a derived clade of D4h3a."

However, Fiedel says that "the recent distribution of this clade is “deceptive” and has nothing to do with a hypothetical coastal migration".

He bases this argument on the fact that the Anzick baby had D4h3a mt DNA, and is roughly 12,900 years old, but it was found in south-central Montana, far from the Pacific coast, and that other remains are also from the interior of the continent like the Hopewell remains found in the Klunk Mounds in Illinois, and that this variant has been found in extant people of Native American origin in Peru, Bolivia, Brazil, and Mexico.

I had posted about D4h3a back in 2014 and pointed out the same idea:

"We see that the D4h3a tends to have a coastal distribution along the Pacific Ocean from Canada to Tierra del Fuego: Canada, California, Ecuador, Southern Chile and Argentina.
The Yaghan, Alakaluf, Chono, Cayapa, Chumash and the man from On Your Knees Cave, all had this haplogroup.
They all built sea-going craft: rafts, dugout canoes, bark canoes and "sewn plank" canoes.
Other groups also built canoes or rafts; the Changos in Northern Chile, the Pericú, and the Aleuts, though we cannot tell if they also carried this rare haplogroup.
But, as we will see in our next post, it is also found quite far from the Western Coast: as it was detected in ancient remains from the Klunk Mound (Illinois) and in Shandong, China.
Furthermore, the Ainu people of Japan also built "lashed-canoes" -like the Chono and the Chumash (as well as dugouts), and they may have a link with the Amerindians."

It pointed out the Chinese connection, the coastal route, and the original Japanese people, the Ainus. The second post in that 2014 series reported the Klunk Mound remains with this haplogroup variant and proposed that "This haplogroup was widespread across America (Pacific coast and well across the Rockies) and became extinct among all native groups being replaced by the other more common haplogroups now found in those groups (A, B, C, D). These surely migrated later into America." It also suggested a back-migration from America to Asia.

Let's see what future investigations find.

My nest post will be about the Cayapa people of Ecuador.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

Remains found in Colombia 6,000 years-old, unrelated to all South American natives old and current

A Paper (Kim-Louise Krettek et al., A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia. Sci. Adv.11,eads6284(2025).DOI:10.1126/sciadv.ads6284) published last June, reports that they analyzed the genes of people who lived 6,000 years ago in the highlands of Colombia, close to what is now Bogotá, and found that they are unrelated to all the rest of Amerindians that live in South America and are not similar to ancient North American natives. They were completely replaced around 2,000 years ago by other groups crossing through Panama.

The authors write:

"Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America."

This is interesting: we have people living in Colombia that are not related to Ancestral North American natives. We'd expect them to be linked to North Americans if the flow of peope into South America was north-to-south across Central America via Panama. But they differ from the 12,700 year-old Anzic-1 people!

They are not related to any known ancient or modern South American natives. But, surely they would have been part of a migration that spread across South America. They were replaced by later arrivals. This shows how the lower genetic diversity in extant Native Americans reflects loss due to whole populations becoming extinct.

The study shows that we have limited knowledge about how many waves of people reached America, when the arrived and when they died out. We also lack data regarding in-depth genetic coverage of ancient and contemporary native people.

Their analysis lead the authors to state that "these results suggest the positioning of Colombia_Checua_6000BP as an outgroup to virtually most Indigenous South Americans." in fact "this group is not more closely related to subsequent ancient Colombians than to any other South American population in our dataset..." These ancient people were replaced by other groups that reached the Colombian highlands: "Overall, the performed analyses provide robust evidence for a major genetic replacement on the Altiplano between 6000 and 2000 years ago"

The paper concludes that they are quite unique and unrelated to other native groups:

"We show that the hunter-gatherer population from the Altiplano dated to around 6000 yr B.P. lack the genetic ancestry related to the Clovis-associated Anzick-1 genome and to ancient California Channel Island individuals, suggesting their affiliation to the southern Native American lineage that became the primary source of ancestry of South Americans by 9000 yr B.P. However, unlike ancient genomes from the Andes and the Southern Cone that are associated with the same wave of ancestry, the analyzed Preceramic individuals from Colombia do not share distinct affinity with any ancient or modern-day population from Central and South America studied to date. Colombia_Checua_6000BP can thus be modeled as a previously undescribed distinct lineage deriving from the radiation event that gave rise to multiple populations across South America during its initial settlement."

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall ©