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 © 

Colombian Natives and their Transpacific origin (2025 paper)

Ijust came across a paper published nearly one year ago (February 2025) with a suggestive title: The Origin of Amerindians: A Case Study of Secluded Colombian Chimila, Wiwa, and Wayúu Ethnic Groups and Their Trans-Pacific Gene Flow by Arnaiz-Villena A, Lledo T, Silvera-Redondo C, Juarez I, Vaquero-Yuste C, Martin-Villa JM, Suarez-Trujillo F.. published in Genes. 2025; 16(3):286. https://doi.org/10.3390/genes16030286)

I have mentioned the Wayúu, in a post many years ago which dealt with Y-chromosome haplogroup C, and a probable transpacific origin of these natives! The 2025 paper looks at their HLA.

Arnaiz-Villena et al. wrote the following (I underlined the relevant text to highlight it):

"Results: The results obtained place the Chimila, Wayúu, and Wiwa populations phylogenetically close to the other North and South Amerindian populations included in this study. Amerindians are genetically separated from the rest of the world’s populations. Chimila, Wayúu, and Wiwa present unique extended HLA haplotypes and specific alleles, such as HLA-B*48 or HLA-A*24:01, shared with Oceanian populations. Conclusions: These genetic results and anthropological data support prehistorical trans-Pacific (bidirectional) contacts that contributed to the settlement of America and also suggest that the effects of ancient European gene flow cannot be discarded"

The paper mentions the HLA peculiarities and its similarity with Polynesian variants:

"The Chimila, Wayúu, and Wiwa samples studied in the present work revealed the presence of HLA-A*24 (A*24:02) and - B*48 alleles in their genetic profile at varying frequencies. Noteworthily, these alleles are characteristic of populations inhabiting Southeast Asia and the Asian and Pacific islands; they are found in Polynesian and Easter Islander genetic profiles, even in some sites located over 4000 km from the Pacific coast of South America...
If these alleles had been introduced via the Beringian migration route, they would likely be more evenly distributed across the continent rather than being concentrated along or near the Pacific coastline. This suggests the existence of direct genetic and population exchanges between Pacific Islanders and the indigenous peoples of the Americas, though it remains unclear whether these interactions were bidirectional or one-way.... [transpacific contact] could explain why the HLA-A*24(:02) and -B*48 alleles are in the Amerindian populations studied in the present work and also in others distributed along or close to the Pacific coast of America, such as Quechua (Peru and Bolivia, Aymara (Peru and Bolivia), Mayo (Mexico), and Mapuche (Chile), among others. This distribution supports the hypothesis that the settlement of America did not occur only from Asia (through the Bering Strait) but that the peoples of the continent had Pacific transoceanic contacts with other populations.

I am surprised at the remark about HLA-B*48, because in a recent post I included data about the global distribution of this variant and it was not high among Polynesians.

For HLA-A*24 the situation is different, it has a clear distribution that is trans-pacific: Japan, Taiwan, Melanesia, Polynesia, and some spots in America, as you can see in the following map (red circles mark higher frequency in the population, blue is lowest).

HLA-A*24 distribution map. Source

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

Australopiths and Homo may have coexisted in Dmanisi 1.8 My ago

The Dmanisi site in Georgia, in the Caucasus region has produced many fossil remains whose exact position in our ancestral tree is still being debated. These are the oldest hominin remains discovered out of Africa, and reveal that our ancestors left Africa as soon as they could.

A paper published on Dec. 3, 2025 (Nery V, Neves W, Valota L, Hubbe M (2025) Testing the taxonomy of Dmanisi hominin fossils through dental crown area. PLoS One 20(12): e0336484. https://doi.org/10.1371/journal.pone.0336484) studied the teeth of the Dmanisi hominin remains (H. Georgicus), and suggests that more than one species of hominins lived in Dmanisi, Georgia.

After analyzing teeth shapes the authors found that one specimen (D4500-D2600) shows strong affinities with australopiths, while others (D2282-D211 and D2700-D2735) are associated to Homo species. Based on this the paper suggests that "two distinct taxa coexist[ed] at the Dmanisi site, previously proposed to be Homo georgicus and Homo caucasi."

This conclusion has interesting implications regarding the first Out Of Africa migrations which until now have been attributed to our ancient ancestor, Homo erectus. The authors of this paper state the following:

"Although our analyses did not formally test the phylogenetic history of the Pleistocene Georgian hominins, the proposal of more than one species in the Dmanisi fossil assemblage has implications for the dispersal of the genus Homo out of Africa in the beginning of the Pleistocene. It is traditionally accepted that the Homo erectus migration started in Kenya (Turkana) around 1.89 Ma, reached Georgia (Dmanisi) around 1.77 Ma, continued into eastern Eurasia (Yuanmou) around 1.7 Ma, and finally arrived to Indonesia (Sangiran) by ~1.57 Ma. However, the speciation events that led to the evolution of more than one species in Dmanisi requires that lineages were separated for long periods after leaving Africa, and were likely also evolving in response to different selective environments.
...
If the Dmanisi specimens cannot be taxonomically grouped with Homo erectus, it raises the possibility that early Homo evolution had multiple episodes of cladogenesis, where some of them may have started in Africa, and others outside Africa. Of particular interest to this discussion is the high similarity between the D4500-D2600 specimen and australopiths, which suggests either a retention of the ancestral dental proportions of australopiths in Dmanisi, or an evolutionary convergence after the initial differentiation of early Homo. With the evidence available, it is not possible to properly evaluate if Homo georgicus and Homo caucasi evolved from Homo erectus ancestors, or if they evolved from australopith-like ancestors, but alternative scenarios are worth exploring and considering as new early Homo fossils are discovered in Asia."

The paper also mentions evidence of an earlier expansion out of Africa, signalled by more primitive stone technology, the Oldowan, which is older than the Acheulean tool kit of the H. erectus: "Recent discoveries of Oldowan tools and associated cut marks in Jordan and Romania, respectively, predate the arrival of Homo erectus to these regions, offering further support for the presence of earlier hominin species in the north of or even outside of Africa [16,56,57]"

The citations 16, 56, and 57 are the following:

16.Neves W, Senger MH, Valota L, Hubbe M. Revisiting the cranial variability of the Dmanisi hominins. Anthropol Rev. 2024;87(2):113–25.

56.Parenti F, Varejao FG, Scardia G, Okumura M, Araujo A, Ferreira Guedes CC, et al. The Oldowan of Zarqa Valley, Northern Jordan. J Paleolit Archaeol. 2024;7(1):3.

57.Curran SC, Dragusin V, Pobiner B, Pante M, Hellstrom J, Woodhead J, et al. Hominin presence in Eurasia by at least 1.95 million years ago. Nat Commun. 2025;16(1):836. pmid:39833162

Consequences of Australopithecines in Georgia

An earlier presence of archaic Australopith hominins in Eurasia opens the door to the evolution (outside of Africa) of Homo erectus there from an earlier wave who peopled the area. H. erectus probably originated in Eurasia and later moved "into Africa", as well as moving "around Eurasia", possibly following the steps of these Australopithecines (why would they have only trekked to Georgia? They could have even reached East Asia or Sunda, Sahul... and America). If the Australopiths were part of the first migration out of Africa, maybe 2 Million years ago, it opens up many new, unexpected options for the peopling of the world, and the origin of "Homo".

My previous posts on Dmanisi and H. Georgicus:

The First Asians were not H. erectus

Homo habilis left Africa 2.4 million years ago

H. erectus in Georgia 1.8 Ma (Kvemo Orozmani site). Aug. 2025 discovery

Homo georgicus revisited: An ancient peopling of Eurasia

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

Prehispanic Leprosy back in the 1890s

In yesterday's post I mentioned some studies that investigated the "American" strain of leprosy, which dates back to pre-Columbian times. It is caused by a bacteria called Mycobacterium lepromatosis. Today's post shows that over 135 years ago, some scientists suspected that there had been cases of pre-Columbian leprosy in America.

Muñiz and Ashmead

According to Máximo Farro and Irina Podgorni (2015) ("Pre-Columbian Moulages" Huacos, mummies and photograps in the International controversy over precolumbian diseases 1894-1910a Medicine nei secoli arte e scienza, 27/2 (2015) 631-654), it was Manuel Antonio Muñiz (1861-1897), a physician who had studied medicine in the San Marcos University in Lima, who in 1886 published the first article on pre-Hispanic leprosy. He mentioned that the Spanish conquistador, Gonzalo Jiménez de Quesada (1509-1579), who had founded Bogotáa (now the capital of Colombia) in 1538, had become infected with leprosy in America.

Muñiz also collected native artifacts and skeletal remains, some of which he interpreted showed signs of the deformation caused by leprosy. He shared his collection with during different international medical and anthropological meetings, and in 1895 published a formal paper on his findings about leprosy in America.

Muñiz startled the scientific world, if there was leprosy in America before the arrival of Europeans, it meant that either it was taken there by previous, unknown voyagers to the New World, or, it had an independent origin there.

At that same time, an American physician who had specialized in leprology, Albert Sydney Ashmead (1850-1911), also published on this subject. Ashmead was one of the founders of the International Leprosy Congress, and defended these ancient American cases of leprosy againts the critics who suggested that the lesions were not leprous, but syphilitic or caused by leishmaniasis .

Latcham's paper.

The image above shows the title of the paper by Robert Lehmann-Nitsche (1899) "Lepra Precolombina ensayo crítico" (Pre-Columbian Leprosy, critical essay) Revsta Museo de La Plata Vol. 9, p.337. In it, he reviews the history and evidence supporting or disproving an endemic leprosy in america. The author concludes that there was a disease that caused the lesions reported by Ashmead and Muñiz, but that he didn't believe it was leprosy.

The outcome of endless scholarly discussions was that there had been no leprosy in America before the Europeans brought the Old World strain of leprosy to the continent after 1492.

As we now know, Muñiz and Ashmead were right. There was an American strain that caused leprosy, an ancient one, distinct from the Old World variety.

Further Reading

Pre-Columbian leprosy, Albert S. Ashmead. American Medical Association, 1895.

Pre-Columbian Leprosy. Albert S. Ashmead, M.D., JAMA, February 10, 1900 1900;XXXIV;(6):379. doi:10.1001/jama.1900.02460060063020

Regarding Pre Columbian Leprosy, Dr. H. Polakowsky, Berlin p.260 May 1900. The St. Louis Medican and Surgical Journal. 78.

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

Leprosy in America - Revisited

There are two microbes that produce leprosy in humans, one is Mycobacterium leprae, with a global dispersion, the other is Mycobacterium lepromatosis, the latter was first found in humans in America, suggesting a New World origin.

The M. lepromatosis is also found among the red squirrels found in Britain, which seems odd, but has an interesting explanation.

Red Squirrels and Leprosy

Charlotte Avanzi et al., (2016) (Red squirrels in the British Isles are infected with leprosy bacilli. Science 354, 744-747 DOI:10.1126/science.aah3783) investigated the matter.

Red squirrels (Sciurus vulgaris) is a Eurasian species, and spans the vast land mass from Ireland to Eastern Siberia, as shown in the map below.

Red squirrel distribution map.

They also lived in the United Kingdom, where they became extinct in the 1700s. They were reintroduced from surviving popualtions in Ireland. Now, in England, Scotland, and Wales they are protected as an endangered species because humans have been putting pressure on their habitat and also, the gray squirrel, imported from North America, (Sciurus carolinensis) has invaded their territory adapting to it and competing with them. To make matters worse, they are infected with a poxvirus and leprosy of the M. leprae variant and, surprisingly, the "American" M. lepromatosis.

The authors analyzed the DNA of the bacteria and calculated the date when these strains originated. The M. leprae variant seems to have passed from humans to squirrels in the Middle Ages, when it was prevalent among people, who also interacted with them, as pets and also bred them for food.

The other (M. lepromatosis) strain diverged from the strain currently found in human beings in America (Mexico), a long time ago. Their phylogenetic tree shows that 26,859 years ago the human and squirrel variants shared their last common ancestor. The paper states that:

"we estimated that the British Isles and Mexican strains diverged from their most recent common ancestor around 27,000 years ago, whereas the Irish and British strains diverged as recently as 200 years ago (Fig. 3A). The latter estimate is consistent with the date of the first campaign to reintroduce the red squirrel into Ireland from England between 1820 and 1856, following its extinction in the 17th century. This suggests that these animals may already have been infected with M. lepromatosis when they were reintroduced."

But where did these Irish red squirrels catch their infection?

They didn't get it from the mainland, a paper published in 2019 analyzed red squirrels captured in Belgium and the Netherlands, and did not find traces of leprosy in them. The source of the bacteria does not seem to have originated in NW Europe. They confirmed that the squirrels in the British Isles are the only known rodents carrying leprosy bacilli.

Did they arrive in infected gray squirrels brought from America?

M. lepromatosis in Ancient Native Americans

Ramirez et al, (2025) found genetic traces in the remains of two adult men who lived 4,000 years ago in Chile, close to what is now the city of Coquimbo (Ramirez, D.A., Sitter, T.L., Översti, S. et al. 4,000-year-old Mycobacterium lepromatosis genomes from Chile reveal long establishment of Hansen’s disease in the Americas. Nat Ecol Evol 9, 1685–1693 (2025). https://doi.org/10.1038/s41559-025-02771-y June 2025).

They built a phylogenetic tree and also used the British red squirrel genetic data. Their tree shows the red squirrels on a separate branch from the human one, which split from it 26,794 years ago. Within the human branch, the ancient Chilean remains sit on a fork, and the modern human cases from North America sit on another, see Fig. 3 d in the paper, shown below.

M. lepromatosis phylo tree. Ramirez et al., (2025)

The paper found a similar split date between the human and red squirrel variants: "we estimate the median time for the most recent common ancestor (tMRCA) of M. lepromatosis to be ~26,800 years ago (95% HPDI range of 4,206 to 115,340 yr bp). Genomes obtained from human hosts yield a divergence estimate of ~12,600 years (95% HPDI: 5,304 to 49,659 yr bp), while the tMRCA for the red squirrel clade is ~440 years (95% HPDI: 73 to 2,063 yr bp)."

This is interesting, however the confidence intervals are very large: the haplotype found in ancient Chileans and the one found in contemporary leprosy patients in Mexico split between ~5,300 and ~50,000 years ago! (mean of ~12,600). The latter number makes me wonder if it was adopted because it falls neatly within the acceptable dates for human presence in America. Nevertheless, if we take the 50,000 year date for a split between the bacteria living in South American paleoindinans and those that remained in Mexico (causing the modern infections), we would have a very old date for people migrating across America.

The same could be said about the split between squirrel and human variants: ~4,200 to ~115,000 years bp. The older figure would imply Neanderthals or even Denisovans passing it on to squirrels or getting it from them!

Regarding the British squirrels, the dates are ~73 to ~2.000 years. The older date could suggest an ancient transatlantic contact c. 1AD, Romans, or navigators fishing cod in Terranova brought some gray squirrel infected with this American leprosy?

Gray squirrels, imported into Britain in the 1870s, are originally an East Coast creature (see map below). Did they harbor the infection? If so, why aren't any gray squirrels reported as carriers in these studies?

Gray squirrel distribution map.

Ramirez et al suggests that "finding of two M. lepromatosis infections in South America, before the periods of known contact with either Oceanian or European populations, implies either movement of the pathogen within human groups during an early peopling event or its previously established endemicity in the continent in a separate reservoir species eventually acquired by humans. The latter would imply that its current distribution arises from a postcolonial dissemination, and would make it one of the few global diseases known to have emerged in the Americas." In other words: the first Americans c.12,600 y BP brought it with them, or the got infected from a local "reservoir species" and, the North American (Mexican) variants were due to its spread during the Spanish Colonial period.

Another paper published last year by Maria Lopopolo et al., (2025) (Pre-European contact leprosy in the Americas and its current persistence. Science 389, eadu7144 .DOI:10.1126/science.adu7144) reported that the M. lepromatosis cases have been "mostly reported in the Americas, with a few sporadic cases in Asia..." (two cases in Singapore, and two in Myanmar). I guess that the Asian cases are post-Discovery dispersal due to transpacific trade from America.

Lopopolo found more ancient samples in America, one from Canada and two from Argentina, their dates are 1,310 to 860 BP.

The phylo tree built by this team (see below) finds five clades: two of them contain the ancient variants (North America, South America), another has the red squirrel variant, and there are two more that hold the modern cases in North America (not only Mexico, but also, Costa Rica, and the U.S.). Interestingly one of these contemporary branches "represented by two present-day US strains, forms a basal clade that diverged from all others around 10 millennia ago." This basal clade 10 ky old, is, again, in my opinion someting forced into the data to coincide with the accepted dates for the peopling of America ~15 ky. How could they justify a date of 50 ky? They'd have to explain how human beings in Siberia or East Asia carried this leprosy strain into America but, at the same time, leave no trace of it in Asia.

Lopopolo also suggests that the other modern clade is recent, dating from the postcontact (after 1492) period. They also found that the split between the two varieties of leprosy Mycobacterium leprae and Mycobacterium lepromatosis took place later than previously estimated, 2 million to 700 ka vs. ~14 million years ago.

Since armadillos and humans are the carriers of the Old World leprosy, and armadillos only live in the Americas, the split between both types of leprosy requires hominins 2,000,0000 to 700,000 years ago carrying both variants. It also requires an explanation on why there are no traces of the "American" leprosy in Eurasia or Africa.

This, in my opinion, allows for an archaic hominid to have been the vector carrying the old world strain in Eurasia, Africa and Oceania, and some other group within that population, carrying the New World strain. This period spans manhy ancient hominins H. erectus, H. antecessor, H. heidelbergensis, Neanderhtals, and Denisovans! Could one of these groups have carried the strain into America. Where it jumped species to the squirrels?

M. lepromatosis phylo tree. Fig 2 A. in Lopopolo et al., (2025)

There is one final, and very recent paper by S. Souguel, T. Oueslati, G. Grine, M. Drancourt published in December ( The role of red squirrels in leprosy dynamics in the United Kingdom: a critical review, One Health, Vol 21, 101114 https://doi.org/10.1016/j.onehlt.2025.101114).

The authors propose that "M. lepromatosis was imported into the United Kingdom following the progressive expansion of the British Empire, starting from the 16th century expansion into Canada through to the 19th century expansion" of the Empire that were "most probably imported from British colonies for their fur."

The authors indicate but do not provide a bibliographic reference that "lepromatosis has been further reported in red squirrels in a geographical belt limited by the 55th parallel north (in Scotland) and the 25th parallel south (in Paraguay), indicating the geographical source of its introduction." There are other species of squirrels in the Amazon, in Ecuador, Peru, Brazil, and Paraguay. But they are not red squirrels. There are also native squirrels in Argentina in the Yungas jungles in the Northwest, also in Bolivia. But, as I mentioned, the authors don't provide a source for this information (M. lepromatosis in squirrels outside of the UK). I searched online for references, and didn't find any.

The paper concludes with a teaser, "The predominance of M. lepromatosis—until recently undocumented in medieval human remains but frequently found in contemporary red squirrels— challenged the notion of direct historical zoonotic transmission. However, forthcoming research suggesting the presence of M. lepromatosis in human remains from the medieval era may significantly alter this narrative and restore plausibility to a broader zoonotic hypothesis."

Are the authors preparing a paper on European M. lepromatosis from the Middle Ages?

We will wait for it!

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

HHV6 - Human betaherpesviruses and the peopling of America

Human herpesvirus (HHV-6) has to haplotypes, A-6 and B-6, interestingly the virus can merge into human genes, blending into our DNA (the scientific term is that it "can integrate into the germline"). Roughly 1% of the global population (around 80 million people) carry the DNA of this virus inside one of their chromosomes, in each of the cells of their bodies. Scientists have asked themselves if this "integration" is ancient, or recent, and if it is still happening as people get infected with the virus.

Roughly 90% of humans are seropositive to HHV-6B, because as infants we are exposed to the virus (Roseola Infantum, also known as the Sixth Disease).

Research by Aswad A, et al. (2021) (Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol. 2021 Jan 4;38(1):96-107. doi: 10.1093/molbev/msaa190. PMID: 32722766; PMCID: PMC7782865.) explored the history of the virus and its "integration".

The "integrated" virus, which forms part of the chromosome, is passed on to the offspring of carriers, and this inherited chromosomally integrated HHV-6 (iciHHV-6). If the integration was ancient, it was passed down along thousands of generations in a parents-to-children line.

The inherited-integrated iciHHV-6 has been found in several chromosomes like number 17 and 22.

Aswad et al., built a phylogenetic tree of the circulating HHV-6 variants A and B (that cause Roseola) and the integrated virus snips inside human chromosomes. The authors state that "the ancestral circulating strains that resulted in these particular independent integration events are not among the known currently circulating strains sampled here. Similarly, the integrated HHV-6A is not acting as a reservoir for ongoing production of circulating strains... In contrast to HHV-6A, the tree for HHV-6B revealed a more entangled topology between circulating and endogenous genomes..."

They found that some clades mirror geographic origin: "among the iciHHV-6A sequences, we observed that individuals from clades A2 and A4 are exclusively European or North American... HHV-6B clades B3–6 and B8 are similarly homogenous and likely represent orthologous integrations in white Europeans and North Americans (and one Australian). This suggests that for each of these clades, those now carrying the virus share a common ancestor who was also European, and thus the virus integration event occurred prior to the diaspora of ancestors of these individuals; the virus thus likely integrated before the colonial era."

"our analysis also revealed a previously unidentified Native American carrier of iciHHV-6B, who possesses an HHV-6B sequence distinct from the other North American samples. Instead, this sequence is almost identical to the iciHHV-6B genome of a Maasai Kenyan sequence uncovered through our SRA mining, and a previously identified Pakistani sample (Zhang et al. 2017) (figs. 2 and 4)."

They then explain how this rare shared variant appeared in America, Asia, and Africa, a Native American who shares "integrated" sequence with a Kenyan and a Pakistani!:

"Unlike the ancestral European integrations, the last common ancestor of these individuals would have been before humans migrated out of Africa (50–100,000 years ago). The observation that they also resolve near the base of the tree further supports this interpretation, as does the fact that the most closely related sequence outside this clade is a circulating strain isolated from a Ugandan patient..."

By "resolve near the base of the tree" they mean that this specific branch is close to the root, and therefold, older than the other branches. As it is similar to the strain of an African (Ugandan), the Out of Africa logic suggests that the root of the tree is based in Africa. Below is the tree and this branch is highlighted.

HHV-6B phylogenetic tree (detail). Fig 2. in Aswad et al.

However, as you can see in the image, not only is a "similar African" strain located at the root, there are three other Ugandan and three D.R.Congo subjects there too, all black-Africans but... one, closest to the root, is a WHITE NY U.S.A. sample!

The authors propose that an ancient ancestor in the distant past (~100 ky ago) before humans left Africa, underwent this "integration" of the virus into one of his or her chromosomes, and this bit of DNA passed on, unscathed, through countless generations, ending up in a Native American, a Pakistani, and a Kenyan Maasai. The tree below is Fig. 4 B, in their paper:

The age of this "integration" was estimated "to be ∼85,000–342,000 years old (depending on the mutation rate used)." Then it says "The Native American is a reference individual used in a South American study on the influences on physical appearance (Chacon-Duque et al. 2018)" Chacón-Duque's paper says that they "examined data for over 500,000 autosomal SNPs typed in more than 6,500 individuals born in Brazil, Chile, Colombia, Mexico and Peru." So, it does include Mexicans, from North America, and the rest of the samples are from South America. Notice that there was only one (1) sample in 6,500 who carried this integrated variant of HHV-6B. A very low frequency indeed!

The data used by Chacon-Duque also noted a high prevalence of African genes (slave trade) in Latin Americans: "~22% of the individuals studied show more than 5% sub-Saharan African ancestry." Which backs my suggestion of African introgression in the Native American sample of "integrated" HHV-6B .

Discussion

The Native American sample's origin isnt' clear in the paper, in one part it says that this sample differs from "the other North American samples", implying that it is North American.

The idea is interesting. However, considering all the bottlenecks that Amerindians have gone through including the founding effect of Beringia, and the loss of 90% of the Native American DNA due to disease, and strife during the conquest and discovery period 1492-1700s, it is difficult to believe that a trait that is now only found in 1% of human beings, managed to survive among Native Americans.

That it is shared by Old World people like the Maasai and the Pakistani could be possible, but the Amerindian carrying this genetic material seems to stretch the odds. Furthermore, no signs of this unique integration is found in Europe or the rest of Asia. What happened to those who carried the gene into Pakistan, and across Asia into America? They left no descent?

Could it be possible that an escaped African slave brought by the Portuguese or Spaniards to South America admixed with natives and passed on this chunk of HHV "integrated" into one of his genes?

It seems a more reasonable explanation.

The tree branch that holds all three samples shows that the closest to the root is the Pakistani, followed by the Amerindian and then, the Kenyan. Shouldn't the Kenyan be closer to the African root?

What is interesting is how the data is "adapted" to the preconceptions of an OOA move some 50-100 kya. Shouldn't the data independently show if that date is correct? Notice the wide window they calculated, a four-fould spread between lower and upper limits" ∼85,000–342,000 years old (depending on the mutation rate used).

It could have originated outside of Africa: We could also imagine a scenario where a Homo antecessor living in Eurasia 700,000 years ago, picked up the virus and it "integrated" into one of its chromosomes, his descent spread Denisovans and Neanderthals, and from there admixing with a modern humans ended up in Pakistan and America, and others crossing Gibraltar (see this post) reintroduced it into Africa. Somehow it didn't survive among those who would later become Europeans, and if these migrants took a northern route, it could have also avoided Eastern and Southern Asians, leaving no trace there.

It could have originated earlier among H. erectus and spread back into Africa with them, and possibly into America in an ancient peopling wave 500,000 years ago. Much later, once modern humans left Africa they could have intermixed in Pakistan, and (no need for them to carry it across Beringia), mated with H. erectus who carried the "integrated" virus, in America.

There are no records of "integrated" virus in ancient Amerindian (or Old World) samples. These would be important as they could help clarify the migration patterns of the virus inside our ancestors' chromosomes.

Let's see what future research discovers.

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