mtDNA Haplogroup M in America - 2007 paper revisited

Back in 2014 I posted about Ancient migrants into America carrying mtDNA M haplogroup 5,000 years ago. In it, I mentioned the only study published, in 2007*, on the analysis of remains from a site in British Columbia, Canada (China Lake) and reported finding mtDNA haplogroup M, and suggested, due to the age of the reamains, that it was, together with haplogroups A (A2), B (B2), C (C1b, Cc, C1d9), X (X2a), and D (D1) one of the founding maternal lineages in America.

This groundbreaking paper reported the following:

"We analyzed two mid-Holocene (∼5000 years before present) individuals from North America that belong to mitochondrial DNA (mtDNA) haplogroup M, a common type found in East Asia, but one that has never before been reported in ancient or living indigenous populations in the Americas. This study provides evidence that the founding migrants of the Americas exhibited greater genetic diversity than previously recognized, prompting us to reconsider the widely accepted five-founder model that posits that the Americas were colonized by only five founding mtDNA lineages."

* Malhi, Ripian et al. (2007), Mitochondrial haplogroup M discovered in prehistoric North Americans. Journal of Archaeological Science 34, 642-648. doi:10.1016/j.jas.2006.07.004

Nineteen years of Silence

I find it surprising, that in almost 19 years after the publication of the original paper there haven't been andy new studies, research, publications, or confirmation (or refutation) of this finding... What is going on?

Citations

But Malhi's paper was noticed. I checked Google Scholar and saw that there were 85 papers that cited Mahli et al. Yet, none of them seem to deal with this new founding haplogroup.

Mahli's paper specifically thanks the support provided by the "Canoe Creek, Soda Creek, and Dog Creek Bands who allowed the DNA testing of their ancestors". A similar paper, also published in 2007, reported the presence of haplogroup A in 5,000 year-old remains from Big Bar Lake, British Columbia, In this case the haplogroup is one of the recognized founding lineages and the authors stated that "Testing for mitochondrial DNA indicated haplogroup A, which is widespread in living Native Americans. Comparative mtDNA data suggest long-standing genetic continuity in the Pacific Northwest, but with evidence for a genetically diverse population in existence at 5000 BP."

This scientific ratificaton is what Native American communities are looking for, and what they like: continuity and "original people" confirmation. The paper also notes the support from the first people: "Collaboration between anthropologists and the Canoe Creek and High Bar First Nations"

I did find a publication ( Ancient DNA In Canada Reveals New Founding Lineage of Native Americans, Mammoth Trumpet, April 2007, Vol 22 No. 2 p.18), that mentions Malhi's paper and gives advances of his findings. It says, among other things: "These remains are 5,000 years old, and mtDNA recovered from the bones belong to haplogroup M. Like the other five Native American haplogroups, M has its roots in Asia, so it is consistent with the accepted model of the peopling of the Americas that has Asian groups migrating across Beringia, or along the Pacific rim, and into North America. This discovery, however, calls into serious question other aspects of the traditional model. Dr. Malhi and his co-authors write, “Our discovery demonstrates that a more genetically diverse group of migrants colonized the Americas than previously thought and supports the hypothesis that significant undocumented genetic diversity likely still remains in the Americas.” In other words, the discovery of a previously unknown haplogroup not only demonstrates that ancient America was more genetically diverse than modern native America, it also increases the likelihood that more undiscovered haplogroups remain to be revealed by additional research." It also informs that the native tribes and the scientists agreed to rebury the remains after the studies. So, maybe that is why no further research was conducted on them.

A 2015 symposium included a paper by Alexa Walker, Brian Egan and George Nicholas (DNA & Indigeneity Proceedings, p. 5. The Changing Role of Genetics in Indigenous Rights, Tribal Belonging, and Repatriation. Oct. 22, 2015, Vancouover, BC, Canada) which gives a very brief summary of the discovery: "China Lake Ancestors In 1982, two individuals dated to over 6,000 years ago were found in a single burial site near China Lake, British Columbia. Genetic results found that both individuals belong to haplogroup M. Prior to this study, haplogroup M had not been found in any ancient or living North American populations. The results indicate that we still have much to learn about human expansion into the Americas. Further reading: Malhi et al. 2007."

Mahli also attended the symposium and his presentation can be read on page 49 (Partnerships with First Nations of British Columbia on Studies that include DNA Analysis). He again mentions the finding: "However, the China Lake individuals were found to possess a mitochondrial genome not currently found in sampled Indigenous individuals from the Americas. This lineage may either be in very low frequency or it may not exist anymore, possibly as a result of European contact and colonization."

Another paper published in Science (Victor Moreno-Mayar, 2018), in its Supplementary material (see p. 3), gives more details when it mentions the Big Bar Lake mtDNA results adding that "the two individuals recovered from the roughly contemporaneous, nearby China Lake site (the two sites are separated by just ~25 km), which could only be identified to mtDNA superhaplogroup M but excluding haplogroups C and D, a lineage common in East Asia, but otherwise unknown in the Americas. But, once again, it is citing the original, and for now, only paper on this subject, Malhi's 2007 work."

mtDNA M Haplogroup

I will summarize an interesting paper on this haplogroup by Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol. 2016 Nov 10;16(1):246. doi: 10.1186/s12862-016-0816-8. PMID: 27832758; PMCID: PMC5105315.

There are no "ancient and autochthonous mtDNA M lineages in western Eurasia", which is strange because the Out of Africa migration had to pass through this area in its initial dispersal, and the M haplogroup is ancient, splitting from the basal African L haplogroup at the time of the Out of Africa migration. The mtDNA M haplogroup is found in Australia, South East Asia, India, China, Arabia, Central Asia, Siberia. It is also found in some parts of North Africa and Europe (due to a back-mirgration from Asia).

The authors support a northern route for its dispersal and not a southern one that followed the coast of the Indian Ocean.

There are M1 lineages in the Mediterranean regions of Europe and the Middle East, and are believed to have arrived there from North Africa during the Paleolithic. And reached Africa from Southern Asia. The M haplogroup curently found among the Finno-Ugaric people in Lapland, the Urals, Northern Russia and Hungary is very recent, and due to a migration originating in East Asia (the Huns settled in Hungary, and we have the Mongols of Gengis Khan too!). There are also historic mixtures of Indian M variants in Mesopotamia and in the Roma (gypsy) people in Europe.

The Expansion route out of Africa: across the Middle East. the authors consider the archaich "fossils of early modern humans at Skhul and Qafzeh" as the first to successfully leave Africa, carrying the L3 haplo with them. They marched with a Northeastern course, and are associated with the early modern humans found in China ~100 ka. The authors propose an older age than generally accepted for the M haplogroup and say: "...we opine that the geneticists should resynchronize the mtDNA molecular clock with the Levant and East Asia fossil records instead of consider them as result of unsuccessful migrations."

These early migrants went north, reaching the Altai Mountains, admixed with Neanderthals and Denisovans there and then headed south due to the harsh weather there, crossing China into Southeast Asia, across Sunda, into Papua New Guinea, the Philippines, and Australia. From SE Asia they headed towards the NW, into India. Later "...in subsequent mild climatic windows, demographic growth dispersed macrohaplogroup M... northwards, most probably from overlapping areas that in time colonized northern Asia and the New World."

The maps below (fig. 2 in the paper) show the original dispersal (a) and the later one (b) including the backflow of M1 into Africa (dashed line).

Could these archaics, with Denisovan and Neanderthal admixture have continued their trek from Altai towards Beringia and then into America, 100,000 years ago? Did they carry the M haplogroup to America? Are the remains from China Lake in Canada the last of a long lineage that was stamped out by later arrivals c. 20 kya?

Considering also that the M haplo is also found in Melanesia... could it suggest an ancient +5ky old transpacific contact between Melanesia and British Columbia?

Continues in my next post.

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

Malaria and the Peopling of America

Today's post will explore the pathogens that cause Malaria, and how they reached America.

A paper published in April 2021 (Population genomic evidence of a Southeast Asian origin of Plasmodium vivax J. Daron, A. Boissière, L. Boundenga, B. Ngoubangoye, S. Houze, C. Arnathau, C. Sidobre, J.-F. Trape, P. Durant, F. Renaud, M.C. Fontaine, F. Prugnolle, V. Rougeron. bioRxiv 2020.04.29.067439; doi: https://doi.org/10.1101/2020.04.29.067439 Now published in Science Advances doi: 10.1126/sciadv.abc3713) proposed a Southeast Asian origin (below we will see two other papers, one, suggesting an African origin, the other an Asian one.)

The paper includes the following phylogenetic tree. Notice how America forms one of the three branches, with two separate clades, and the other two branches are: Most Asian countries, and India, Madagascar and Africa (perhaps linked by trade across the Indian Ocean).

P. vivax phylogenetic tree. Fig. 3 in Daron et al.

For America the authors suggest two possible explanations: "Across the Americas, P. vivax strains were structured in two distinct ancestral populations (Fig. 3, B to D). This is consistent with two putative evolutionary scenarios of the parasite in America. The first scenario hypothesizes that both ancestral populations originated from the isolation between Amazonian and non-Amazonian populations, after a single introduction during the European colonization in the 15th century. In the second scenario, two distinct waves of introduction occurred from the same or from different sources. Disentangling these two hypotheses will require more samples and statistical population genetic modeling."

The original online publication in Bioarxiv included text that was ommitted in the Science publication:

"Across the Americas, P. vivax strains were structured into two distinct ancestral populations. This is consistent with recent findings suggesting two successive migratory waves responsible for the introduction of P. vivax in America (37). The first wave has been suggested to occur following a reverse Kon-Tiki route, with a long-range oceanic crossing from the Western Pacific to the Americas. The second wave, has been recently attributed to an introduction by the European colonization of the Americas during the 15th century, and represents the major genetic contributors to the New World P. vivax lineages."

The paper cited as (37) is the following: Rodrigues, P. T., Valdivia, H. O., De Oliveira, T. C., Alves, J. M. P., Duarte, A. M. R., Cerutti-Junior, C., ... & Ferreira, M. U. (2018). Human migration and the spread of malaria parasites to the New World. Scientific reports, 8(1), 1993.🔓

The paper analyzes the genetics and relationship between the different lineages of malaria-causing parasites. It says it originated in Africa ("Plasmodium falciparum is currently hypothesized to have originated from a lateral transfer from gorillas to humans in Western Africa between 10,000 and 100,000 years ago" and spread globally.

In the case of American variants it notes that: "The TMRCA estimates for SAM populations of P. falciparum (37,002 years; 95% HPD interval, 21,385–56,606 years before present) and P. vivax (52,149 years; 95% HPD interval, 29,896–60,659 years before present) indicate that the hypothetical most recent common ancestor of New World malaria parasites largely predates the first human migrations to the continent."

Ah! the question of the arrival in America makes them say that being 37 or 52 ky old means that they "predate the first human migration" into America. Why not accept the facts, and suppose that there were humans in America 37-52 ky ago and that these parasites evolved there, in America?

They continue the analysis looking at the African variant (AFR) and point out that "Moreover, these estimates are rather similar to those obtained for populations of AFR P. falciparum (35,384 years; 95% HPD interval, 21,101–54,974 years before present) and P. vivax (41,685 years; 95% HPD interval, 28,630-57,563 years before present). Therefore, skyline analysis and TMRCA estimates argue against a severe population bottleneck associated with the recent malaria parasite migration to the Americas; to the contrary, SAM lineages appear to have retained much of the diversity that preexisted in their ancestral populations." Which is interesting: the parasite didn't have a bottleneck like the one that is always argued, happened to the humans that peopled America -and carried it there. And also, that the American variant is as old as the Old World African clade.

The paper concludes that slave trade and European navigation brought malaria parasites from Africa to America, and from India and Asia via Madagascar, and South Africa. There may have been a transpacific route from Asia to Central America. They also note that Melanesian variants could have also reached America in pre-Hispanic times: "We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans... While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax."

However, the great diversity observed in America surprises them and they try to explain it as sampling errors or, the successive waves from different places: "The lack of an apparent bottleneck in South American populations of P. falciparum is somewhat surprising. Not only parasite migration events, but also selective sweeps induced by large-scale antimalarial use in more recent years could have drastically reduced parasite diversity in this continent. We argue, however, that the current diversity levels have originated from the very many introductions of this parasite into the continent over centuries, from several different source populations in Africa. The substantial differentiation between present-day SAM and AFR lineages of P. falciparum likely results from the fact that we have not sampled all potential AFR source populations (Supplementary Fig. 15) or all P. falciparum subpopulations currently found in the Americas."

But looking at the phylogenetic tree from this paper, below, we see that the American (and the Atlantic rainforest simian variety) clades clearly are nested within the SE Asian and Melanesian clades, while the African and some other Asian clades form a different branch (with some -few- American samples, these surely came with the Slave Trade.

Global Malaria phlogenetic tree. Adapted from Fig. 2 in Rodrigues et al.

Polynesian - Melanesian migration?

As mentioned above, this paper also mentions the transpacific route and also adds: "Carter has speculated that a relapsing parasite such as P. vivax might have survived long-range, pre-Columbian oceanic crossings from the Western Pacific to the Americas through a reverse Kon-Tiki route." citing: Carter, R. Speculations on the origins of Plasmodium vivax malaria. Trends Parasitol. 19, 214–219 (2003).🔒

Carter suggests a South Asian origin for P. vivax" from where it moved aroun 1 million years ago into Europe and Africa, surviving in warm, humid places until humans were infected some 10 to 20 ky ago.

Closing Comments

There are three separate clusters, or branches on the malaria pathogen tree: Africa, Asia, and America. If the parasites originated in Asia and moved to Africa 20-50,000 years ago (or vice versa) and originated a seprate branch there, it took 20 to 50 ky to acquire its present diversity. So, why are we expected to imagine that these same pathogens came to America barely 400 years ago and suddenly evolved into another separate branch with equally enormous diversity?

Perhaps the pathogens reached America 50 ky (or even 100, or 200 ky earlier, via a migration from Asia by infected Neanderthals, Denisovans, or even older hominins like H. erectus then they diversified there, in the New World, where they infected monkeys in the Brazilian rainforests.

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

Asian vs. African origin of Humans and the "inverted" phylogenetic tree of Shi Huang

I have mentioned Shi Huang in two previous posts (Out of China? in 2019 and On Neanderthals in America and the Out of China Hypothesis in 2025).

I love how he inverts the phylogenetic trees, from a root in Africa and youngest brances in East Asia, Europe, and America, to one rooted in Asia, with a youngest African branch, going against the consensus of the Out of Africa theory.

This posture is similar to what I suggested in a post nearly 8 years ago, "On the direction and root of phylogenetic trees" (April 2018): "When I see a phylogenetic tree (also known as an evolutionary tree), I always wonder why do we believe that those branches, trunk and the root which anchors it, are correct. I ask myself why is it assumed that the mutation took place in one direction and not the other. And this trivial question is fundamental because the branches open up from other branches based on the differences between the DNA as you move along them." (sorry for quoting myself). The post included the image below.

Two different trees built from the same genome samples. Copyright © 2018 by Austin Whittall

In today's post I mention another paper co-authored by Shi Huang: Ancient Y chromosomes confirm origin of modern human paternal lineages in Asia rather than Africa, Hongyao Chen, Ye Zhang, Shi Huang. bioRxiv 2020.03.10.986042; doi: https://doi.org/10.1101/2020.03.10.986042

The paper includes the following figure, which, as you can see, inverts the root of the Y-chromosome tree, from Africa to Asia, and places Africa in the newest branch.

Figure 1. Y chromosome phylogenetic trees of modern humans. Only major branches and representative SNPs are shown with branch lengths not to scale. The tree topology was built without making use of any ancient DNAs. A. The Out of East Asia model. B. The Out of Africa model.. Source

They argue in this paper that "The mutation pattern in the ancient Y chromosomes as revealed here confirms the expectation that ancient haplogroups should mutate in only a fraction of the sites that define a haplogroup they belonged to. Two observations here confirm the Asia model and invalidate the Africa model. First, only haplogroups specific to the Asia model showed the expected mutation pattern in ancient samples. Second, the genetic reality that a haplogroup, be it ancient or present, should not carry mutations found in basal haplogroups to which they do not belong is only met by the Asia model but not the Africa model."

Interesting and controversial, and also, not peer reviewed either.

By the way, Shi Huang expands this idea in a paper published one year ago: Examining models of modern human origins through the analysis of 43 fully sequenced human Y chromosomes, Shi Huang. bioRxiv 2023.11.09.566475; doi: https://doi.org/10.1101/2023.11.09.566475. In it he uses the same inverted trees to argue against the Out of Africa theory and support his Out of East Asia theory.

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

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.

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.

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 © 

Votan

Continuing with ths subject of my previous post, today I will share smore information on the demigod Votan.

French abbot, Brasseur de Bourbourg, mentions Votan in his work published in 1857-59, Histoire des nations civilisées du Mexique et de l'Amérique-Centrale : durant les siècles antérieurs a Christophe Colomb Vol. 1 chap. 3

Brasseur de Bourbourg disclosed his sources: "Having been unable to obtain the original documents in the Tzendale language, which record the history of Votan and his successors, we are reduced to collecting the short fragments found scattered in the manuscript works of Ordoùez and Cabrera, and in the Diocesan Constitutions of Nunez de la Vega, Bishop of Chiapas, etc. (see footnote 1 on p. 82).

Votan came by Sea

"In accordance with Yucatec traditions, Tzendal historians trace the origins of the famous Votan, whom their commentator believes to be on the island of Cuba, to Valum-Votan several centuries before the Christian era. After sailing along the coasts of the Peninsula, accompanied by other chiefs of his people, he advanced among the thousand islands of the Terminos Lagoon.
... Votan then traveled up the Uzumacinta River, and it is on the banks of one of the tributaries of this great river that the cradle of civilization is placed. His stay there gave birth to a city which, since then, has had the honor of being the metropolis of a great empire. It was situated at the foot of the Tumbala Mountains: the name Nachan, which is attributed to it, is less well known than that of Palenque, whose majestic ruins were revealed, barely a century ago, to the astonished eyes of travelers.
... The astonishment of the Tzendales was perhaps as great then as that which they felt, two thousand years later, at the sight of the Spaniards. For these foreigners had large boats, and wore long and loose clothing, which led to them being given the name "Tzequil", or men in women's skirts, which remained with them in this region; a tradition adds that they spoke the Nahuatl language, and that it was they who brought it to America.The Tzendales welcomed them as brothers, and Votan was rewarded with unique insights they imparted to him concerning divinity and the governance of men. Their settlement in the land was soon followed by an alliance with the Tzendale women. Enlightened and instructed by them, Votan wisely worked to organize the administration of his states; from this time truly dates the foundation of the Palenquean empire.
... Nevertheless, the circumstances of his first voyage, as Ordonez extracted them from the Tzendal histories, are too remarkable not to give them verbatim here: “Votan,” it is said, “wrote a collection on the origin of the Indians and their transmigration to these lands. The main argument of his work is reduced to proving that he descends from Imos, that he is of the race of Chan, the Serpent, and that he originates from Chivim. He was, he says, the first man whom God sent to this region to populate and divide the lands that we call America.” He describes the route he followed and adds that after founding his settlement he made several trips to Valum-Chivim. These trips numbered four: in the first, he recounts that, having left ValumVotan, he took his way towards the "Abode of the Thirteen Serpents." From there, he went to Valum-Chivim, from where he passed to the city where he saw the house of God, which was being built. He then went to the ruins of the ancient edifice, which men had erected, by the command of their common ancestor, so that they might, by this means, reach heaven. He adds that the men with whom he conversed assured him that this edifice was the place from which God had given each family a particular language. He affirms that upon his return from the house of God he went a second time to examine all the underground passages through which he had already passed, and the signs that were found there. He says that he was led through an underground path that went beneath the earth and ended at the root of the heavens: regarding this circumstance, he adds that this path was nothing other than a serpent's hole, into which he entered because he was the Son of the Serpent."

The story continues, with his actions (like introducing the tapir into the region), and travels. There is no hint of a European or Asian origin in this text. The arrival of Votan took place 2000 years before the Spaniards reached Mexico (which took place in the early 1500s) so this happened around 500 BC.

The nonsense of Votan, Babel, and Noah

Brasseur de Bourbourg also translated the Mayan book known as "Popol Vuh" and in his introduction, he mentions Votan once again: "Don Ramon de Ordoñez y Aguiar, canon and provost of the bishopric of Ciudad-Real, otherwise known as San-Cristobal de Chiapas, appears to have been the first to have had knowledge of Ximenez's historical works, and to have used the translation of the Quiche manuscript: he copied this document, altering it from beginning to end, in order to melt it into his indigestible work entitled Historia del cielo y de la tierra, etc., where he tends to establish that Votan, placed as the third sign of the tzendal calendar, was the descendant of the Hivites*, that is to say of the Canaanites, driven out of Palestine by Joshua, and who, having emigrated to the Canaries, would have passed from there to the Antilles. Its main objective was to prove that Quetzalcohuatl was the same as the apostle Saint Thomas, who was said to have been miraculously brought from India to America to preach the Gospel.

* Hivites are a nation mentioned in the Bible in Israel, in Joshua 11:3.

Interestingly Alexander von Humboldt also mentioned Votan and Odin (Vues des Cordilleres, published in 1810) as follows (page 72):

"In the kingdom of Guatimala (sic), the inhabitants of Teochiapan preserved traditions that dated back to the time of a great flood, after which their ancestors, led by a chief named Votan, had come from a land to the north. In the village of Teopixea, descendants of the family of Votan or Vodan (these two names are the same, as the Toltecs and Aztecs did not have the four consonants d, b, l, and s in their languages) still existed in the sixteenth century. Those who have studied the history of the Scandinavian peoples in heroic times must be struck by the discovery in Mexico of a name reminiscent of Vodan or Odin, who reigned among the Scythians, and whose lineage, according to Bede's remarkable assertion, "gave kings to a great number of peoples."
If it were true, as several scholars have supposed, that these same Toltecs, whom a plague combined with a great drought had driven from the Anahuac plateau around the middle of the eleventh century AD, reappeared in South America as founders of the Inca Empire, how could the Peruvians not have abandoned their script to adopt the Toltec hieroglyphic writing? Almost at the same time, at the beginning of the twelfth century, a Greenlandic bishop had brought, not to the continent of America, but to Newfoundland (Vinland), Latin books, perhaps the same ones that the Zeni brothers found there in 1580."

On page 148, von Humboldt again mentions Votan: "We have already drawn our readers' attention above to this Votan or Wodan, an American who appears to be related to the Wods or Odins of the Goths and peoples of Celtic origin. Since, according to the scholarly research of Sir William Jones, Odin and Buddha are probably the same person, it is curious to see the names Boud-var, Wodans-dag (Wednes-day), and Votan designate, in India, Scandinavia, and Mexico, the day of a short period. According to ancient traditions collected by Bishop François Nuñez de la Vega, "the Wodan of the Chiapas people was the grandson of that illustrious old man who, during the great flood in which most of humankind perished, was saved on a raft, he and his family." Then, he mentions the tower of Babel! "Wodan cooperated in the construction of the great edifice that the men undertook to reach heaven: the execution of this audacious project was interrupted; each family was henceforth given a different language, and the great spirit Teotl commanded Wodan to go and populate the land of Anahuac. This American tradition recalls the Menou of the Hindus, the Noah of the Hebrews, and the dispersion of the Cuscbites of Singar."

In his "Historia antigua de Mexico..." Francesco Saverio Clavigero (1731-1787) cites Nuñez de la Vega, bishop of Chiapas, who mentions Votan as moving on after the Babel tower incident (p. 136), and being the first to people Chiapas after the Noachian flood (p. 152).

Even the Mormons took advantage of an "Israelite" Votan to further their religion. You can read an interesting article online here, Votan, the culture hero of the Mayas published in the Juvenile Instructor, Vol. 14, No. 5 (1 March 1879), pp. 57–58.

However, the Middle East connection does not necessarily imply Israelites, it could also involve Phoenicians, which makes more sense.

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

Phoenicians Discovery of America (Book from 1892) and Votan

Thomas Crawford Johnson wrote a short essay titled "Did the Phoenicians Discover America?", published in 1892 by the Geographic Society of California.

This essay is a short read, and suggests among other things, that the Phoenicians knew how to navigate using the magnetic compass (p.14), that their voyages for the Jewish kings took 3 years, and this time would imply that they sailed to America's western coast (p. 22) via Melanesia and Easter Island to Peru, and the coast of Colombia, Ecuador, Panama, and Central America.

One would have expected them to sail across the Atlantic, from Gades (Cadiz) to Mexico, but they didn't they took the longer route, along the Red Sea, Arabian Sea, Gulf of Bengal, skirted Java and Sumatra, sailed between Australia and New Guinea, across Polynesia and the Pacific all the way to Northern Chile.

The image below from Crawford Johnson's work shows the route taken by the Phoenicians:

Route taken by the Phoenicians to America. Source

The book mentions a voyager recorded by the Native Americans called Votan (p.28): ""Votan, it seems, came from a foreign land, and found the whole country, from Darien to California, occupied by a barbarous people. Votan and his followers arrived in large ships, and wore long, flowing garments." According to one document by Ordonez this event is laid a thousand years before Christ. It is desirable to notice that this date corresponds exactly with the dates given in the Bible narrative of the historic voyages of Hiram and Solomon, and the building of the temple, which was about l000 B. C. " This journey to America from their native country was a long and painful one and indicates that seas and lands intervened between them. The tradition reports it to be in the far East, and that the first comers filled seven ships.""

This is a quote of someone named Ordonez (actually Ordoñez). This person was Father Ramon Ordonez de Aguilar, a Catholic priest who served in the Maya region and wrote a book called "Probanza de Votan" (more on him further down).

Crawford's text also suggests that the gold and silver brought to Israel came from Mesoamerica, the only possible source for such wealth. Finally it mentions the Aztec god Quetzalcoatl (p.30) "The native traditions held that Quetzalcoatl traversed the peninsula, from the Pacific to the Atlantic, and on reaching the last ocean, sent back his companions to tell the Cholulans that in a future age his brothers, white men and bearded like himself, would land there from the sea, where the sun rises, and come to rule the country." Suggesting that the Phoenicians would return from the East, crossing the Atlantic Ocean,

Votan - the Civilizing Gold

The Probanza de Votan was a native text, surely a codex, written in the native Tseltal language and it was illustrated. The Spanish authorities held it until the 18th Century when it mysteriously got lost. It seems that Votan was the Mayan equivalent of the Aztec Quetzalcoatl. He founded Palenque, navigated in a boat with his family during the Universal Flood, brought his people to settle Yucatan among the natives. There was even a day in the Maya calendar named after him.

There have been wild conjectures about Votan being Woden (similar sounding names) or Odin of the Scandinavians (see p. 81 in Historia Antigua de la Conquista de Mexico by Manuel Orozco y Berra, 1880) or even Buddha! (see chapter V in the same book).

A serious, scholarly paper on the subject was published in 2009 by a Historian, Díaz Perera, Miguel Angel (Tras las huellas de Palenque: las primeras exploraciones. LiminaR, 7(1), 104-134. http://www.scielo.org.mx/scielo.php?script=sci_arttext&pid=S1665-80272009000100007&lng=es&tlng=es). He mentions the Probanza de Votan text and that Ordoñez had written about "A white, bearded Christian priest named Votán, who arrived by sea and founded Nachán (Palenque) after having traveled through Spain, Rome and Jerusalem." In his paper, Diaz Perera mentions research by Frederic Waldeck, published in 1832 after he visited Palenque and interviewed the natives there:

"The traditions that have been communicated to me by the misanthrope of the ruins seem worth recording [...] The true name of the ruins of Palenque is Natchan, and not Otitoiun, which is a foreign word in the Chol language, and which would be more accurately described as Mayan, a language derived from it. Around ten centuries before the birth of Christ, three white, bearded individuals came from the place where the sun rises: the first, the sage Ymas; the second, Ik; and the third, Vot&aacut;en, the one who attained all the renown that tradition bestowed upon him. Although corn is indigenous, it was not as prevalent in the landscape as it was in his time, and it was Votán who brought them this marvel; he united it with civilization and the arts. The time of his death is a problem; tradition, if it is accurate, says he died violently, and nine kings succeeded him, each to reign for half a century, according to the custom he himself had prescribed. An ambitious one succeeded him, and his name was Chanan (5). Those who came after were Abaghu (6), Bem (7), Hix (8), Tzequin, Chabin, Chinax, Cahagh, and Akbal. It was under this last king that Natchan was destroyed by the nation of Tula, a city that had been founded by Votan and which later became an enemy of Natchan (referring to Tonina). Its ruins are near Ocosingo."

There is however a book by Ordoñz, published online where he mentions the "Probanzas de Votan" and its loss, and also provides more information on Votan on p.14.

I hadn't heard about Votan until now. He seems to be a civilizing demigod similar to Amalivaca, who brought civilization to the Orinoco River natives in Venezuela, Viracocha among the Incas and, of course, Quetzalcoatl.

In my next post I will comment on the details about Votan published by abbot Brasseur de Bourbourg in 1857-59, and some other comments, including von Humboldt on Votan from 1810.

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

Early Hominin presence in Sulawesi

An article published one month ago (Burhan B, Hakim B, Sumantri I, Suryatman, Saiful AM, Oktaviana AA, et al. (2025). A near-continuous archaeological record of Pleistocene human occupation at Leang Bulu Bettue, Sulawesi, Indonesia. PLoS One 20(12): e0337993. https://doi.org/10.1371/journal.pone.0337993. Dec. 23, 2025), reported that there was an archaic kind of hominin living in Sulawesi long before the arrival of modern humans to the island, and may have even coexisted there until they disappeared.

The study reported the presence of stone tools as old as 208,000 years ago, and surprisingly some of them were of a kind of tool known as "picks", which have appeared in some older sites in the region suggesting the presence of a well established culture of archaic hominins in this part of Asia long before H. sapiens arrived.

Below are some quotes from the paper

"Prior research has indicated that the Indonesian island of Sulawesi was host to archaic hominins of unknown taxonomic affinity from at least 1.04 million years ago (Ma), while members of our own species (Homo sapiens) were probably established on this Wallacean landmass from at least 51.2 thousand years ago (ka), and possibly as early as 65 ka.
... Here, we report the results of multiple seasons of deep-trench excavations at Leang Bulu Bettue, a limestone cave rock-shelter complex in the Maros-Pangkep karst region of South Sulawesi.
... Notably, there is evidence for animal butchery and stone artefact production including a stone ‘pick’ at around 132.3–208.4 ka followed by a major shift in human cultural activity during the Late Pleistocene. By around 40 ka, an earlier occupation phase (Phase I) characterised by a straightforward cobble-based core and flake technology ... had been replaced by an entirely new occupation phase (Phase II) with a markedly distinct archaeological signature, including the first evidence for artistic expression and symbolic culture. We consider the implications of this behavioural disconformity for our understanding of the history of humans on Sulawesi, including the possibility it reflects the replacement of archaic hominins by modern humans."

So the Phase I "cobble-based" core flake stone knapping technique and the "pick" cultural tradition vanished 40 ky ago, surely due to the replacement of the archaic people by modern humans.

The paper notes that stone tools were recently discovered in Sulawesi, not far from this site, at Talepyu (over 194 ky old) and at Calio (over 1 Million years old). They state that these archaic hominins are "of a yet unknwon taxonomy." These dates and those of this Leang Bulu Bettue site (132-208 ky ago) show that they were not made by modern humans.

The authors propose two scenarios to explain what took place here on Sulawesi:

1. "The entirety of Phase I reflects the last period of a long history of occupation by a group of archaic hominins–as already noted, likely those responsible for the early lithic artefacts recovered from the Walanae Basin (Talepu and Calio) ~80 km to the northeast – that was replaced by an incoming group of modern humans around 40ka, with the arrival of the latter being the cause of the change in the LBB record (i.e., the onset of Phase II). The archaic hominins, based on the present state of knowledge from the wider region, could have been H. erectus and/or a taxon closely related to H. floresiensis, Denisovans, or an as-yet undocumented hominin species that is now extinct."
2. ""The earliest H. sapiens in the region produced lithic technologies that more closely resembled the technology of the archaic hominins of the Walanae basin at least 200 ka to 1.04 Ma than those made by later H. sapiens, and that the technological disconnect cannot be described by a species-level replacement. The apparent technological continuity may be the result of contact between two groups, or simply a convergent response to the same resources and conditions. This situation is in keeping with the evidence for the behavioural flexibility of early modern humans as they spread out of Africa and began to colonise unfamiliar environments. The technological and faunal shift at around 40 ka, resulting in Phase II and the lithic Upper Industry, would therefore reflect an unknown local trigger, spontaneous innovation, and/or the arrival of a second wave of H. sapiens."

The Calio stone tools (Paper here, published in Aug. 2025) were dated to 1.04 million years, and "and possibly up to 1.48 Ma" this makes them as old, or even older than the stone tools found on Flores Island at Wolo Sege, which are 1.02 Ma. These are the oldest ones yet discovered in this region, and they mark a very early date for the presence of ancient hominins in this area. Much older than the previous date from Talepyu (paper here).

These ancient and now extinct hominins navigated open sea to cross the Wallace Line (an imaginary boundary that runs through the Lombok Strait in the Indonesian archipelago) and reach Sulawesi. Even during glacial maximums, with low sea levels, the shortest distance between Sulawesi and the closest continental Asian landmass was at least 50 km (31 miles).

An interesting paper modelled how these hominins could have crossed the sea: "Results indicate that crossings are facilitated by low sea level, but the possibility of crossings at high sea level cannot be discarded. All of the three analyzed departure areas could be considered feasible sources for arrivals at Sulawesi but, Borneo is by far the most likely source area and Mindanao departures more likely to arrive in Sulawesi than those from the Banda Arc. The shortest simulated period voyagers would have to survive at sea are 3–8 days, 14–19 days and 12–20 days for Borneo, Mindanao and Band Arc departures respectively...Our results suggest that Sulawesi could have been reached by accidental drift voyages and offer direct support to previous studies that inferred drift-based arrival at the island based on spatial distribution of fauna and hominin subsistence strategies over Wallacea. While successful drifts could have started from any of the three evaluated source areas, arrivals from Borneo are more likely than those from Mindanao and trips from Banda Arc."

So, these people drifted on a mat of vegetation from Borneo to Sulawesi, the same way that animals are supposed to have crossed the Wallace Line. They managed to survive the crossing which lasted between 3 and 14 days by chance and settled in Sulawesi.

We should consider the option that they made rafts, or canoes and carried their kits or gear with them, to fish or move along the coast. Perhaps they drifted to Sulawesi on these boats.

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

Ancient Treponema in Colombia and the peopling of America

Apaper published two days ago, on Jan 22, 2026, reported that the authors had detected and dated the genome of a bacteria belonging to the Treponema genus, which causes syphilis, yaws, bejel, and pinta. The pathogen that was found in human remains that are 5,500 years old, in Bogotá, Colombia.

The paper published in Science is the following: Davide Bozzi et al.(2026). A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia. Science 391, eadw3020. DOI:10.1126/science.adw3020

The microbe is a Treponema pallidum subspecies, but it is closer to the base of the tree, an older relative of the other branches, that carry subspecies that cause syphilis, yaws, pinta, and bejel.

The paper then tried to date how old this variant, named TE1-3, is. They estimated it split around 13,700 years ago from its sister lineatges: 6768 to 20,592 cal yr B.P. The authors noted that "This suggests that the divergence between TE1-3 and the modern, genomically characterized T. pallidum subspecies occurred during the Late Pleistocene to Early Holocene, closely following the peopling of the Americas, whereas the diversification of the known subspecies themselves took place more recently, within the Holocene ~6000 cal yr B.P. (3622 to 9452 cal yr B.P. 95% HPD)."

As mentioned in previous posts, I wonder if the date fit was "eased" into a recent window that coincides with the currently accepted date for the peopling of America. What would a date of 40,000 y BP have meant?. The Methods don't specify how this date was calculated. The methods describes the process:

"Given TE1-3 is several thousand years older than all ancient T. pallidum sequenced to date, it is an ideal tip calibration for molecular clock analyses. To assess temporal signal, we performed a root-to-tip regression using radiocarbon-dated ancient genomes and collection dates for modern genomes (table S9). This analysis confirmed a strong temporal structure (R2 = 0.67; fig. S17).
We then applied tip-dated Bayesian inference in BEAST2 (49), which yielded a mean substitution rate of 8.86 × 10−8 substitutions per site per year [95% Highest Posterior Density (HPD): 6.5 to 11.2 × 10−8]. The divergence of TE1-3 from the other T. pallidum lineages is estimated at 13,746 cal yr B.P. (95% HPD: 6768 to 20,592 cal yr B.P. )"

However, the root-to-tip regression used a lot of recent data points from the late 1900s, and 2010s a few from the 1700s, and 1500s, and then a few older ones from 1371 AD, 1329 AD, 3438 BP. These are given in their Table S9 (Supplementary table S9. Tip dates used in assessment of temporal signal and root-to-tip regression).

"Regression" is a statistical tool that helps see the trend in a series of scattared data points, assign a function to explain the data and use that function to calculate other data points. For instance, the black dots in the image below are data points and the red line is the best fitting curve (in this case it is a linear regression of the y= a + bx type, the equation for a line. Once the line is known, we can extrapolate the value of y for a given x value.

The fitting isn'd done manually, there is a mathematical-statistical tool to do so. The so called "correlation coefficient" or R squared (R2 mentioned above) its value ranges from 0 to 1, where 0 is no correlation and 1 is a 100% correlation. In this case they state the value is 0.67. But in my engineer point of view, it is heavily skewed by the data points in their Figure S17 shown below, where all the data points (upper left) are lined in vertical strips, and one solitary data point dated 3438 BP in the lower left is used to align the function.

Furthermore, in their Fig. 17, they report two lower values for R2, of 0.294 and 0.127!

Fig. S17 in this paper. Supplementry Figures

The authors caption for Fig. S17. "Root-to-tip regression. Inspection of the temporal signal of the dataset... the root-to-tip regression displaying the temporal signal of the dataset (black line) and of specific clades: TPA in dark green and TPE/TEN in light green. For the global clock rate we observe a rate of 1.336 x 10^-7 with an R2 of 0.667, while a weaker temporal signal (lower R2) but similar evolutionary rates were observed within the other two clades: 1.202 x 10^-7 for TPA (R2 = 0.127) and 1.190 x 10^-7 for TPE/TEN (R2 = 0.294). Plot generated with clockor2 (112)".

The authors also state that " We see that using the even more divergent Cuniculi A genome as a reference pushes the date back in time. Consequently, our estimate when using the Nichols reference genome is best viewed as a lower bound for divergence of TE1-3." It seems that the split between Old World human variants and the Amerindian one would have been older if they used the Treponema paraluisleporidarum Cuniculi A genes as a basal reference! The paper mentions how the "trimmed" genes to adapt it to their needs.

Comments

The paper is relevant because it gives an American origin, and an old date of over 13 ky, to a bacteria with high virulence: "All previously identified virulence factors common to Treponema pallidum are present in TE1-3, including immune evasion and tissue tropism tpr paralogs, suggesting that it possesses the same virulence potential as T. pallidum."

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

On the diversity of Native American genes

Native Americans are described as the least diverse human beings in the world, bottlenecks along the way depleted variation in their genetic stock, and the small founding population that reached America carried a tiny part of the originally diverse set of genes that they started out with.

However, it seems that there were different waves that reached America, and each one carried diversity, the Amerindians had plenty of varibility but this vanished when the Europeans reached America in 1492.

Eduardo Tarazona-Santos, Denise R. Carvalho-Silva, et al., (2001) in Genetic Differentiation in South Amerindians Is Related to Environmental and Cultural Diversity: Evidence from the Y Chromosome. AJHG, Vol 68:6, June 2001, Pages 1485-1496, https://doi.org/10.1086/320601, argues that it did not cause much difference, that diversity was lost in the distant past, not during European discovery and conquest:

They admit that the population reduction was more severe in Eastern South America than in the Andean region, yet argue that the reduced diversity was not caused by contact with Europeans, instead they suggest that "it has been shown that reduction of gene diversity (i.e., in average expected heterozygosity) began several generations later (Maruyama and Fuerst 1985; Cornuet and Luikart 1996). Therefore, the recent demographic depletion undergone by Amerindian populations 20–25 generations ago could not account for the differences in gene diversity evidenced in the present study, which are more likely to be related to more-ancient (i.e., pre-Columbian) demographic events."

I disagree. The current distribution of natives was also impacted by the European conquest, populations were displaced in the Andean region, from rural areas to cities, from farms to mines, from their homeland to "reducciones" (Spanish word for subduing by force and concentrating in one spot, for easier control an domination), some were over 1,600 km (1,000 mi) from the natives' original homeland, like the Quilmes people, who walked from the Andean foothills in Tucumán to what is now a suburb of Buenos Aires, named after them, Quilmes. See the image (the map is from my website -in Spanish- on Argentina's Ruta 40 highway).

Even the Incas moved people from one part of their empire to another, to settle the newly dominated regions (Mapuches in Chile received an influx of Andean settlers, also the Chachapoyas.) This altered the original genetic patterns and still distorts modern samplings.

Further proof on the drastic decline of Native American populations can be found in Arnaiz-Villena et al., (2025): "After Columbus’s arrival in 1492 AD, the Amerindian population from Alaska to South America (about 80 million) was drastically reduced by 1552 AD (8 million) because of new European-borne diseases (mainly influenza, smallpox, and measles) and war. This drastic population reduction likely caused a genetic bottleneck, which explains why modern Amerindian HLA profiles do not always follow strict geographic patterns. The loss of genetic diversity may be attributed to the selective survival of certain alleles in populations able to present peptides derived from newly introduced pathogens."

The interesting note is the natural selection effect, as the natives died out but some adapted to the new environment, and this promoted the selection of certain genes, resistant to the new diseases, starvation, and exertion of forced work for the conquerors. The real survival of the fittest. 72 million people out of 80 million died, 90% of them! A gigantic loss of genetic diversity.

A similar argument is put forward by Michael H. Crawford (1998) in his work "The Origins of Native Americans: Evidence from Anthropological Genetics" (Cambridge: Cambridge University Press, 49–51, 260–261), quoted below:

"The Conquest and its sequelae squeezed the entire Amerindian population through a genetic bottleneck. The reduction of Amerindian gene pools to from 1/3 to 1/25 of their previous sizes implies a considerable loss of genetic variabilty in New World populations. Who survived the epidemics? It is highly unlikely that survivorship was genetically random."

He then makes the point that those who survived didn't do so by chance, but by natural selection of fitter traits:

"If Amerindians of today are different from their pre-Conquest ancestors with respect to many genetic systems, most likely those genetic traits that confered some selective advantage under the conditions of the Conquest are more numerous among contemporary Amerindians. Thus, the present gene-frequency distributions of Amerindian populations may be distorted by a combination of effects stemming from genetic bottlenecks and natural selection."

An additional factor mentioned by Crawford is the inflow of African slaves and Europeans: "In addition, the gene frequencies of the native populations were further modified by the massive gene flow or admixture with Europeans and Africans, thus possibly obscuring the pre-Conquest patterns. As a result, great care should be exercised in the interpretation of sophisticated multivariate analyses of gene-frequency distributions among New World populations based upon samples collected by various researchers utilizing a diversity of sampling techniques."

Crawford then asks why were Amerindians more susceptible to the diseases brought by the Europeans. In fact, these diseases were also lethal in the Old World, and the African ones, like Yellow fever also wiped out Europans, just as it killed the Native Americans.

He suggestst that "...the death toll from measles was no different than what was observed in European populations that had not been repeatedly exposed to the same disease.... In Europe, epidemics caused by smallpox, yellow fever, and influenza were extremely severe with high mortality. The mortality was somewhat higher in the New World because the disease effects were further exacerbated by starvation, slavery and physical exhaustion. Thus, it has been argued that Amerindians did not have any special sensitivity or susceptibility to imported Old World diseases." This is a novel idea for me, as I had imagined that in Europe and Asia, perhaps those equipped with a fine-tuned immune system, inherited from those who survived epidemics, and through epigenetic changes, created a population that was less susceptible to these diseases. It seems that the situation is different.

So, nowadays, when we look at the genes of "Native Americans" we are looking at what was left of the original diversity, distorted by natural selection over the 433 years elapsed since European discovery, and also, certain admixture of European, African, and also, Asian genes.

A study (Jorge Lindo et al., (2018). Patterns of Genetic Coding Variation in a Native American Population before and after European Contact. The American Journal of Human Genetics, Vol 102:5, 3 May 2018, pp 806-815. https://doi.org/10.1016/j.ajhg.2018.03.008) took a look at current Amerindian genes and the ancestral genetics (from samples taken from pre-contact skeletal remains) belonging to a group of natives, the Coast Tsimshian people living in Prince Rupert Harbour, British Columbia, Canada.

These people have lived there at least for the past 6,000 years and suffered a drastic drop in population after contact with the Europeans which in this part of America was later than in others. In the 1800s they were struck by smallpox epidemics and roughly 175 years ago their population declined by 57%. Then they admixed with people who were not Tsimshian, mainly natives of other groups, and Europeans.

The authors noted that diversity (genetic variation) is the outcome of mutation, recombination, migration, genetic drift, and natural selection, all of these factors played a role among these people.

They found that the ancient natives, compared to the modern ones, had "higher levels of mean observed heterozygosity within coding regions (mean heterozygosity across modern 1.230 × 10⁻⁴ versus ancient 4.935 × 10⁻⁴ individuals)." This is a fourfold difference.

Unexpectedly, the authors expected genetic drift to increase the frequency of certain alleles. The genetic drift would be a consequence of the collapse and slow recovery. However, they found that this didn't happen. They attributed this to the "relatively short evolutionary timescale within which these events occurred; and, second, the recent admixture with both indigenous and non-indigenous populations, which may have increased genetic diversity and countered the deleterious effects of reduced population size"

Another study by O'Fallon BD and Fehren-Schmitz L., (2011) (Native Americans experienced a strong population bottleneck coincident with European contact. Proc Natl Acad Sci USA. 2011 Dec 20;108(51):20444-8. doi: 10.1073/pnas.1112563108. Epub 2011 Dec 5. PMID: 22143784; PMCID: PMC3251087) looked into the effects of European contact: "We find that indigenous Americans experienced a significant contraction in population size some 500 years before the present (ypb), during which female effective size was reduced by ∼50%, thus suggesting that the impact of European colonization was both widespread and severe... the scale of the contraction suggests that the depopulation was not localized to particular regions or communities, and instead, was likely to have been widespread or to have had an especially severe impact on the most populous regions."

Comments

For all of these reasons I am always skeptical on genetic conclusions that are based on admixed, heavily diluted, Native American genes such as those using data coming from CLM: Colombians from Medellín, Colombia, PUR: Puerto Ricans from Puerto Rico PEL: Peruvians from Lima, Peru, or MXL: Mexican Ancestry from Los Angeles, California.

And when a paper uses DNA collected from an Amazonian tribe, the data is usually considered inadequate due to genetic drift and founder effects!

Sampling of ancient, and therefore "pure" Native American genes could provide a real, clear view of the rich diversity lost after 1492.

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

Asian evolution of Hominins (2024 paper)

Today's post shares a paper on the dispersal and evolution of hominins in Eastern and Southeastern Asia. It has plenty of interesting insights on the time line and geographic dispersal of our ancient ancestors in Asia.

The paper is the following: Rikai Sawafuji, Takumi Tsutaya, Naoyuki Takahata, Mikkel Winther Pedersen, Hajime Ishida, (2024). East and Southeast Asian hominin dispersal and evolution: A review. Quaternary Science Reviews. Volume 333, 1 June 2024, 108669. https://doi.org/10.1016/j.quascirev.2024.108669.

It summarizes current knowledge, and theories, as well as suggesting some future research avenues. A very good paper!

I enjoyed the description of Homo erectus. This hominin has always fascinated me since I was a teen, when I read about it in my elder sister's highschool biology book (no internet in the 1970s). At that time there was the Peking Man, and the Java Man from Solo Rivr, and no African erectus. I also read about the Rhodesia Man, Neanderthals, Cro-Magnons, and the Australopithecines in Africa, more primitive and smaller. It seemed a complex mixture of different people. Now, over 50 years later, the panorama is still obscure!

"There are various views on the classification of H. erectus, e.g., H. erectus from Africa as a separate species called H. ergaster (Tattersall et al., 2015). In this review, we use the broader definition of H. erectus (H. erectus sensu lato) and consider the African H. erectus as part of the same taxon.
H. erectus is currently recognized as the first hominin to spread out of Africa and is thought to have migrated eastward across Eurasia and then southward into Southeast Asia. The fossil records are concentrated in Europe, China, and Java, with little data available for the intermediate areas.
Some of the earliest probable fossils of H. erectus are the ∼2.04 Ma cranium found at Drimolen, South Africa (Herries et al., 2020) and ∼2 Ma mandible at Melka Kunture, Ethiopia (Mussi et al., 2023), while the earliest generally accepted evidence of their presence out of Africa was discovered at Dmanisi, Georgia, and dated to ∼1.8 Ma (Ferring et al., 2011; Lordkipanidze et al., 2013).
In China, recent findings have suggested an earlier hominin presence although the evidence is scarce and primarily based on stone tools found at Shangchen, dated to ∼2.1 Ma (Zhu et al., 2018), and on hominin teeth dated between 2.42–1.8 Ma at Jianshi-Longgu Cave (Li et al., 2017a). These findings, which might predate the Dmanisi fossils, suggest the intriguing possibility that either H. erectus or another hominin arrived in China earlier than the time of Dmanisi (Cartmill and Smith, 2022). However, due to the scarcity of comprehensive fossil records, these conclusions must be approached with caution, as definitive identification of these early hominins in China remains challenging.
Fossils and lithics of likely H. erectus found in China include ∼1.66 Ma stone tools from Majuangou III in the Nihewan Basin (Zhu et al., 2004) and 1.7–1.6 Ma stone tools from Shangshazui (Ao et al., 2013), and a ∼1.63 Ma cranium from Lantian-Gongwangling, near Shang Chen (Zhu et al., 2015). Two ∼1.7 Ma incisors have also been found in Yuanmou, South China (Zhu et al., 2008), though their age determination remains questioned (Bae, 2010). Taken together with the fossil and lithic evidence, the conservative age of the emergence of H. erectus in China is about 1.7–1.6 Ma."

The interesting part is the suggrestion of hominin presence in China ~2.4 to 2.1 Ma, older than the earliest South African fossils (~2.04 Ma), also that they were not Homo erectus but "...another hominin arrived in China earlier than ... Dmanisi." This could imply the presence of Homo habilis or even Australopithecines in Asia.

The following image shows how the different lineages of hominins coexisted in Asia during the past 2 million years.

Chronology of the genus Homo in EA/SEA.. Source

The image below shows the distribution of hominins in Eastern and Southeastern Asia/p>.

The Story and Timeline of Hominins in Asia

The paper gives a brilliant description of the dispersal of hominins in East Asia and Southeast Asia.

"As more and more pieces are continuously added to our understanding of hominins, their geographical distribution and persistence, new questions arise, and details about how the different hominins dispersed and why they went extinct still remain unclear. From current fossil records and genetic evidence, one plausible and coherent scenario of hominin dispersal is the following: H. erectus emerged in Africa and expanded into the Eurasian continent around 2 Ma, later occupying Europe, East Asia (China) and Southeast Asia (Java).
Subsequently, the common ancestor of H. sapiens, Neanderthals and Denisovans split into two groups: one was in Africa (later leading to H. sapiens) and the other settled around the Middle East at some point. The latter interbred with a super-archaic hominin group (possibly H. erectus) around 700–600 ka.
The Eurasian hominin group then split into two groups. One settled in the West (Europe and Western Asia) leading to Neanderthals, while the other settled in Asia leading to Denisovans. Denisovans interbred with H. erectus in Eurasia, occupying their niche. At some point, Denisovans also expanded into East and Southeast Asia, where the groups diverged into different subgroups (D0, D1, D2, D3, the details are in the chapter of Denisovans). Meanwhile, H. erectus may have become extinct around 400 ka in East Asia and 100 ka in Southeast Asia. Denisovans reached the Altai region, eventually meeting and interbreeding with Neanderthals several times around 140–80 ka. Meanwhile, some H. sapiens left Africa before 200 ka. This initial migration was unsuccessful, but interbreeding with Neanderthals at this time left traces in their genome (Peyrégne et al., 2023). There were several subsequent out-of-Africa events, which might have reached Asia, but the populations that led to our ancestors left Africa around 55 ka. They interbred with Neanderthals in West Asia and with Denisovans in EA/SEA. Note that we consider the super-archaic hominin contributing to the Denisovan genome to be H. erectus. While there is a possibility that hominins other than H. erectus and Denisovans migrated into Asia or evolved from H. erectus, this is not considered here due to the lack of evidence."

The suggestion that (no date given for this event) the ancestor of modern humans, Neanderthals and Denisovans moved out of Africa, settled in the Middle East and some 700-600 ya mating there with H. erectus is very interesting!

The further admixing of Denisovans with erectus as they moved across Eurasia is not often mentioned. And the final comment that "... there is a possibility that hominins other than H. erectus... migrated into Asia or evolved from H. erectus," is worth exploring as there is no evidence to prove it happened. But, it is possible and likely.

The paper also has some interesting comments on the four lineages of Denisovans (with a neat map), and their history:

Denisovans

"The common ancestor of Denisovans and Neanderthals which occupied around the Middle East interbred with a super-archaic hominin, and afterwards the Denisovan ancestors diverged from the Neanderthal ancestral group and moved into Asia. Some of them spread towards Papua and settled in Island Southeast Asia (D1). Another group remained in South or Southeast Asia (D2), and from there, another group moved further north into East Asia (D0, D3). During the early phase of this migration, they encountered a super-archaic hominin population and interbred. The D0 group settled somewhere in East Asia. The D3 group reached the Altai in Siberia (D3), where they met and interbred with Neanderthals."

The section dedicated to small-sized hominins Homo floresiensis and Homo luzonensis is great, I learned that the latter's "finger and toe bones are elongated and curved, a feature similar to australopithecines". Nevertheless, evidence suggests both "tiny" hominins may descend from H. erectus.

Ancient Mariners

It is remarkable that these two groups of people (and a third responsible for stone tools found in Sulawesi) crossed open sea, settled in islands, and lived there in isolation until their demise when modern humans reachd the area. Navigating abilities is something seldom discussed in any paper, including this one, which only says "Although it is unclear how each hominin crossed the sea, they succeeded intentionally or accidently"

It is evident that even archaic forms of hominins like erectus crossed open sea. Could they have reached America? (See my post about their navigating skills, and this post on Neanderthal "sailors").

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