Denisovan admixture within America?

Last may I published a brief post about a paper by Castro e Silva et al., (2026). The evolutionary history and unique genetic diversity of Indigenous Americans. Nature. https://doi.org/10.1038/s41586-026-10406-w. The paper is an in-depth study of South American natives' genetics, the three waves that peopled the subcontinent, and the "remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years." It attributes this permanence across ten millennia because this admixture was positively selected for due to benefits these alleles provided to those carrying them.

Archaic Introgression

I re-read the article and took note of the part that says that the Australasian signal is not the result of an archaic introgression, which means that Denisovans didn't share these same genes with Oceanian and American natives, there were different groups admixing with each population. The paper states: "Furthermore, we identified candidate regions of adaptive archaic introgression from Neanderthals and Denisovans that contribute to functions related to immunity, metabolism and epidermal integrity, thereby reinforcing the role of archaic alleles in shaping the evolutionary trajectory of non-African populations. Importantly, our data indicate minimal overlap between genomic regions with Australasian affinity and those introgressed from archaic hominins, supporting the interpretation that these signals represent distinct evolutionary phenomena."

Australasian signal

The Australasian signal in Amerindians is very very peculiar, it has a high prevalence in some groups that live in the Southwestern Amazon region and Chaco (these groups are the Awajún, Ayoreo, Guarani, Karitiana, Sirionó, Suruí, and Tsimané). This is known as the introgression from a "Y" population, or Ypykuéra (a Tupi word meaning "ancestor") which is a "ghost lineage" of ancient Amerindians with a high Australasian genetic content.

The paper confirms that the distribution of Australasian "alleles" is not uniform, it shows a "partially discontinuous spatiotemporal pattern" which suggests, according to the authors that "this ancestry was present during the initial peopling of America." It is also very ancient because the paper finds that Amerindians "diverged from other continental groups between about 70,000 and 15,000 years ago."

The paper states that isolation of these Amazonian groups that carry the highest frequencies of these introgressed alleles and their inbreeding and small population sizes are all factors that led them to have such a high prevalence of them. However, I wonder if another factor was at play: Denisovans lived in that region and encountered humans there, admixing in that area with them. After all it is a kind of cul-de-sac in the Amazonian rainforest nowadays, why wouldn't it have been one for the Denisovans? They also seem to have thrived in the jungles of Indonesia, and the Philippines in Southeast Asia.

The comparison between different groups within America, outside of America, and archaics, didn't detect any "correlation... between Australasian and Neanderthal... or Denisovan affinity... By contrast, Neanderthal and Denisovan affinities were strongly correlated... consistent with homogeneous archaic ancestry in the founding populations."

This is interesting because the Australasian signal is independent from the two archaic introgressions. This suggests that the Denisovans and Neanderthals that admixed with the first Amerindians were different from those who admixed with Australasians (including the Onge people and the Hòabìnhian people from Laos).

The authors wondered if the Australasian-Amerindian similarity was due to "shared archaic ancestry" but when the checked the introgression from Denisovans and Neanderthals in both groups, they found a "minimal overlap of 0.4%, corresponding to 11 genes/genomic regions... This minimal overlap indicates that the Ypykuéra ancestry is unlikely to have been derived from a known archaic hominin." (This is not clear, what do they mean by "a known archaic hominin"?)

The paper did find a "shared ancestry component between Indigenous Americans and Australasians that extends deep into the past." So this shared ancestry probably came from a similar modern human group, yet, as mentioned further up, the ancestors of the Amerindians split from other H. sapiens 15 to 70,000 years ago. I favor the older date. But, intriguingly, these people did not admix with the same Denisovans or Neanderthals that the Australasians bred with!

This could be explained by a split in this basal Homo sapiens: one group went into Australasia and admixed there with a group of Denisovans, the other headed north into East Asia mixing with other Denisovans, and eventually reached America. However, why is there no presence of other East Asian signals in Amerindians? This leads to a second alternative: the admixture event between Denisovans and the modern human ancestors of Amerindians took place inside America?

The map below outlines this possibility, with the Denisovans splitting from the Neanderthals somewhere in the South Caucasus, and moving into East Asia along different routes, a northern one to Altai, and then Tibet and East Asia, another along South Asia, and South East Asia into the Philippines and Papua New Guinea. Another hypothetical route could have led them across Siberia into America. Their last stand was in the Tropical Amazon region. They seemed to thrive in all types of climate, from icy siberia and Altai, to the highlands of Tibet, and the jungles of Sundaland and Sahul. America offers all of them: Cold Alaska, Canada and Northern USA, Patagonia, high mountains and plateaus in Bolivia and Peru, as well as along the Andes in Chile and Argentina, and of course the Jungles east of the Andes from Colombia, Venezuela and Bolivia to Brazil, Paraguay and Argentina.

---

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

Euphemus and the Satyrs (Amerindians?)

Ancient Navigators Series

Continuing with my series on ancient transatlantic voyagers, today's post looks into the story recorded by Pausanias, (143-176 AD), a Greek Geographer and traveler; in his book, Description of Greece.

He mentions a journey by Euphemus of Caria (Caria was a Greek city on the coast of Anatolia, now part of Turkey) who navigated into the Atlantic. Again, like with Sertorius, it is the wind that drives the ships into the Atlantic. It was an accident, not a planned voyage.

Pausanias' text is quoted below (Source, online):

"1.23.5 ... Wishing to know better than most people who the Satyrs are I have inquired from many about this very point. Euphemus the Carian said that on a voyage to Italy he was driven out of his course by winds and was carried into the outer sea, beyond the course of seamen [This Outer Sea is the Atlantic Ocean]. He affirmed that there were many uninhabited islands, while in others lived wild men. The sailors did not wish to put in at the latter,
1.23.6 because, having put in before, they had some experience of the inhabitants, but on this occasion they had no choice in the matter. The islands were called Satyrides by the sailors, and the inhabitants were red haired, and had upon their flanks tails not much smaller than those of horses. As soon as they caught sight of their visitors, they ran down to the ship without uttering a cry and assaulted the women in the ship. At last the sailors in fear cast a foreign woman onto the island. So the Satyrs outraged this woman not only in the usual place but her whole body similarly."

Greek vases c.450 BC with satyrs chasing women

The tailed mentioned in the story, remind me of the "tailed men of Patagonia" and Father Beauvoir's explanation that the natives wore furs of animals whose tails waving as they ran, gave the impression of them having tails. The "red hair" is an interesting fact. Probably these "satyrs" daubed their hair with red ochre making them appear red haired.

The way the satyrs stormed Euphemus' vessel is similar to the descriptions given by those who navigated the Strait of Magellan when they came across the natives. Some examples can be found online. For example (here (see p. 14), an incident took place in 1875 : "Only a short time ago a tribe of Fish Indians, without the least provocation, attacked, when on shore, the master and crew of an American sealing schooner. Fortunately the master was armed with a breach loader with which he fought his way through crowds of natives to the beach, losing, however, two of his men", and (on p. 18), a boarding in 1880 with several sailors killed by the natives.

Captain FitzRoy also tells about the Fuegians mood and behavior in the 1820s-30s: "they appear to be friendly when meeting strangers, but that their subsequent conduct depends entirely upon their relative numbers. They ought never to be trusted, however, as they have hasty tempers, and are extremely revengeful." (Online, see p. 188). He also tells of how they stoned Low's ship, the Adeona, when ordered to leave it (p. 196).

Amerindians or Guanches?

Could these satyrs have been a tribe of Native Americans? The only inhabited land west of Europe was America.

But, as the text mentions islands, there were many unhinhabited islands (Cabo Verde, Bermuda, Azores, Madeira, and some of the Canary Islands, but there were people living on the Canary Islands.

They had a native population originated in Northern Africa, the Guanches, later absorbed by the Spanish influx in the 1400s. I have found an old reference aobut the Guanche mummies with "red hair", but a recent paper published in Nature that analyzed the DNA from Guanches between 200 and 1500 AD suggest a North African genetic root for the Guanches and a colonization date of AD 200. The latter date means that when Euphemus sailed c.1300 BC the islands were uninhabited.

---

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

MUC19, Denisovans, and Amerindians.

Denisovans seem to have provided Native Americans with genes that protected them from disease.

A paper published last August (Fernando A. Villanea et al. ,The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science 389, eadl0882 (2025). DOI:10.1126/science.adl0882), suggests that Denisovans supplied Amerindians with genetic material that helped them adapt to their new environment when they reached America.

The authors report an introgression in some non-Africans, of "a mosaic region of archaic ancestry: a small Denisovan-like haplotype (72-kb) embedded in a larger Neanderthal haplotype (742-kb), that was inherited through Neanderthals who themselves acquired Denisovan ancestry from an earlier introgression event...
the [importance of the] gene MUC19... as a candidate to study adaptive introgression; one of the haplotypes that span this gene in modern humans is of archaic origin, as modern humans inherited this haplotype from Neanderthals who in turn inherited it from Denisovans, and the haplotype introduced nine missense mutations that are at high frequency in both Indigenous and admixed American populations. Individuals with the archaic haplotype carry a massive coding VNTR expansion relative to the nonarchaic haplotype and their functional differences may help explain how mainland Indigenous Americans adapted to their environments."

The authors explain that a 72-kb "Denisovan-like haplotype" was found in Neanderthals and modern humans (excluding Africans who didn't admix with Neanderthals as these never lived in that continent) and that it was nested within a "larger Neanderthal haplotype". So the Denisovans provided their bit of genetic materials to Neanderthals, and we inherited it, and also Neanderthal genetic material from the latter.

The interesting part is that the Altai Neanderthal (from central Asia) which is around 120,000 years old, "does not harbor the Denisovan-like haplotpe" (the 72-kb region) but those from Europe, the Chagyrskaya and Vindija Neanderthals carry it. These are younger (44 to 59,000 years old).

The lack of this haplotype in Neanderthals from Altai, led the authors to conclude that the Denisovans who carried this 72 kb-region "may not be closely related to Altai Denisovan" group. It was some other Densiovan population.

The study also found that within the "...in the core 72-kb region... some modern humans carry two Denisovan-specific synonymous mutations and nine Denisovan-specific nonsynonymous mutations." The nine Denisovan-specific missense variants are found in pre-Hispanic remains at frequencies that vary between 31.6% and 40.6%. That is, before Europeans (and their African slaves) reached America.

As expected, they are also found in admixed American populations (Amerindian plus other human groups) at frequencies that range between 6.9% and 30.5%, which is logical since the influx of Old World people into America must have diluted this ancient genetic component.

And, yes, it is much lower: 0.5% to 15.7% among modern European and South and East Asians.

Within the Mexican (MXL) group these nine mutations of Denisovan origin reach a 30.5% frequency! It is around 22% among Peruvians (PEL), 7% among Colombians (CLM), and 9% in Puerto Rico (PUR).

The paper also looked into Africans, analyzing 44 samples and only one of them turned up with the nine Denisovan mutations (a frequency below 1.1%). Clearly the Denisovans didn't admix inside Africa. Since this single case was a Khomani San individual, supposedly carrying ancient genes, and belonging to a population which diverged from the rest of mankind over 100,000 years ago (according to the Out of Africa theory) it is something that has to be explained.

This single San person carried all of the nine Denisovan missense variants. The authors explain this as follows "The sequence divergence between this San haplotype and the archaic MXL haplotype at the 72-kb region is high (0.001342), further supporting the origin of the archaic haplotype in non-Africans as introgressed... Finding a divergent haplotype in the San is consistent with a previous study, as ~1% of their ancestry can be attributed to lineages that diverged from the main human lineage more than 1 million years ago... Furthermore, we cannot determine whether this variant found its way into the San through modern admixture of non-African ancestry into Sub-Saharan populations." In other words, they got it from some ancestor of Denisovans or, through recent admixture with modern non-Africans. I tend to choose the latter.

Could it be possible that a band of Neanderthals reached America long ago, after trysting with Denisovans, and the later waves of Homo sapiens mingled with them, picked up their mutations?

It is also likely that after the "Great Dying" that wiped out 80 to 90% of Amerindians (European-borne diseases like flu, measles, smallpox, etc. in the early 1500s) those who survived were the ones carrying multiple VNTRs, that provided them with higher immunity.

The "Great Dying" is unique in modern history, and always ignored when studying Native American populations. It caused millions to die, and their genetic history is lost. Modern Americans with Amerindian genes don't carry those of the people who died then. It killed almost all of the Native Americans, altering the genetic makeup of those who survived. But this is, as I said above, ignored.

See my March 2026 series of posts on MUC19

I revisited this post and looked into the MUC19 allele and its implications regarding the peopling of America, and the interactions of Denisovans, Neanderthals, and Humans, in three additional posts:

• Part 1 of the MUC19 posts
• Part 2 of the MUC19 posts
• Part 3 of the MUC19 posts

---

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

Ancient Australasian signal found in South American natives

A paper published earlier this year (Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry. Marcos Araújo Castro e Silva, et al. PNAS April 6, 2021 118 (14) e2025739118; https://doi.org/10.1073/pnas.2025739118), suggest that the very early or even the earliest people to reach South America carried a genetic component that is not found in North or Central America, and that is linked to a "Y Population" the genetic signal inherited from this group (called "Y" after "Ypikuéra" or "ancestral" in Tupi language") is only found among Australasian people.

The paper reports that the Y-population signal originally found among Amazonian Amerindians is also found in natives from other parts of Brazil, and also in the Pacific coastal population of South America.

The authors write: "The best-fitted model showed that the Pacific coast is a mixed group of South American ancestry and a small non-American contribution associated with a sister branch of Onge, as also observed for Karitiana and Suruí. They suggest that the presence of this signal on the Pacific coast suggests that the original population reached the area following a coastal route.

The Onge are people that live in the Andaman islands, in the Bay of Bengal, dark skinned isolated people... and they are linked to South American natives.

Did they land in North America and Mesoamerica and die out? Did they bypass the northern part of the Americas and settle in the South?. The lack of this signal in the northern part of the continent is not explained in the paper.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2021 by Austin Whittall © 

The diversity of Amerindians - Purepecha from Michoacan

I have read a paper (Complex Nature of Hominin Dispersals: Ecogeographical and Climatic Evidence for Pre-Contact Craniofacial Variation, Ann H. Ross and Douglas H. Ubelaker Scientific Reportsvolume 9, Article number: 11743, 2019) that explored the differences in skull size and shape among Pre-Hispanic Amerindians from 0 CE to 1500 CE, so they are not very ancient.

One would expect cranial morphology to be influenced by inheritance (members of a group would have similar shaped skulls and faces when compared to other groups), but it is not so simple: the authors found "multifactorial forces from spatial/geographic distribution, altitude, and climate, as well as demic diffusion and drift" moulding the shape of skulls.

We'd expect many similarities among Native Americans, and differences too. The interesting find is that: "The sample from Michoacán is the most dissimilar from all of the samples", and that "The Mexican sample from Chihuahua is significantly different from all other samples" the two figures reproduced below show that this is quite true for the Michoacan natives but it does not seem so clear cut for the Chihuahuans.

From the paper.

What didn't surprise me was that the authors are aware of the "short" time allowed by current prevailing theories for these morphologic differences to develop. Not more than 15Ky. So they state: " It has been proposed that significant levels of craniofacial diversification that occurred in a relatively short time span observed in southern South America cannot be fully explained by drift alone and it was concluded that random factors such as directional selection and phenotypic plasticity should also be considered".

But, what if... these changes took place over longer periods of time? I will leave this question open.

The present inhabitants of Michoacan in Mexico are known as Purepechas or Tarascas. They are a Native American group, with a curious history.

In Geographical Origins of the Tarascans, Vincent H. Malström, Geographical Review Vol. 85, No. 1, January 1995, the American Geographical Society of New York, we find out that "only after the conquest of Michoacán was completed did the Spanish begin to perceive how different the people were from their neighbors to the east. In some ways the former were far more primitive than the Aztecs. They depended on hunting and fishing to the degree that the Aztec term for the region, Michoacán, meant "place of the fishermen." Their religion centered on the worship of fire and of the moon, and they had a rudimentary counting system based on five. Their calendar was a simplistic copy of that used by their neighbors. The temples they constructed looked like nothing else in Mesoamerica; their language was unrelated to that of any people in the region; and their manner of dress differed markedly from all other indigenous peoples in Mexico."

This paper adds that " the Spanish learned that the Tarascans called themselves Purepecha, which in their tongue meant "the latecomers" or "the recent arrivals." The term piqued the Spaniards' curiosity, and they immediately set about questioning the elders of the tribe as to where they had come from and when. As a preliterate people totally dependent on oral tradition, the Purépecha had no way to record their history in written form, except by drawing pictures. Consequently the Spanish had them summarize the legend of their migration on a piece of linen called the Lienzo de Jucutácato, which was not rediscovered until the 1870s (Craine and Reindorp 1970, x). It purports to explain how the Purépecha journeyed from a homeland far to the south to their current abode in Michoacán. Though historically the Lienzo is considered a priceless document, geographically it has to be one of the most farfetched reconstructions."

So they are "latecomers" with different culture, traditions and language; that came from somewhere else. This paper proposes a South American origin: "A primary assumption is that the Purépecha language is related to Quechua, the native tongue of the Incas (Adams 1991, 324). The obvious implication is that the Purépecha did come from South America, though not necessarily from Cuzco and certainly not by way of the Orinoco delta and Veracruz. Although a recent classification of Mesoamerican Ianguages relates Purépecha to Chibcha in Colombia rather than to Quechua (Greenberg 1987), the point remains the same - the closest antecedents of the Purépecha language are found in South America.".

But if this was the case, these Purepechas would be more similar to the Peruvian skulls and they are very different.

Other authors state that the links to Quechua, Mayan or Chibcha are tenuous (see Raina Heaton in Language Isolates).

I have not been able to find clear genetic information on the Purepecha, but when I do I will post it here.

To be continued...

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

A trait shared by East Asians and Denisovans: three rooted molar

As you can see, by checking my most recent posts, I have been reading recent articles and papers about Homo sapiens in Eurasia. Another one caught my eye: Rare dental trait provides morphological evidence of archaic introgression in Asian fossil record, Shara E. Bailey, Jean-Jacques Hublin, and Susan C. Antón, PNAS first published July 8, 2019 https://doi.org/10.1073/pnas.1907557116.

Bailey, Hublin and Antón found a dental trait in modern humans that is quite rare outside of Eastern Asia and the Americas and yet was found in the jawbones of two Denisovans. This suggests that modern Asians inherited this trait from an ancestral population that lived in Asia.

Let me quote the paper's Abstract to summarize its findings:

"The recently described Denisovan hemimandible from Xiahe, China [F. Chen et al., (2019) Nature 569, 409–412], possesses an unusual dental feature: a 3-rooted lower second molar. A survey of the clinical and bioarchaeological literature demonstrates that the 3-rooted lower molar is rare (less than 3.5% occurrence) in non-Asian Homo sapiens. In contrast, its presence in Asian-derived populations can exceed 40% in China and the New World. It has long been thought that the prevalence of 3-rooted lower molars in Asia is a relatively late acquisition occurring well after the origin and dispersal of H. sapiens. However, the presence of a 3-rooted lower second molar in this 160,000-y-old fossil hominin suggests greater antiquity for the trait. Importantly, it also provides morphological evidence of a strong link between archaic and recent Asian H. sapiens populations. This link provides compelling evidence that modern Asian lineages acquired the 3-rooted lower molar via introgression from Denisovans."

So the three-rooted second molar (3RM2) is unusal outside of Asia and it was found in the Xiahe Denisovan fossil which is 160,000 years old.

The paper also tells us that: "he recently described Penghu 1 mandible from Taiwan (190 to 10 ka) also exhibits a 3RM2 ... The Penghu mandible retains 'archaic' features, including a receding symphysis that lacks a chin, a thick mandibular corpus, and large molar crowns similar in size to Denisovans. Like Xiahe, these exceptionally large molars are coupled with agenesis of the third molar. For these reasons, Chen et al.suggest that Penghu 1 may also be closely related to Denisovans. Both mandibles show that the 3RM anomaly existed in archaic Asian hominins before H. sapiens in the region.".

The authors conclude: " the presence of “archaic features” in recent Asians that were once used to suggest continuity from Pleistocene Asian H. erectus may also have been obtained by introgression from Denisovans."

Some interesting facts they report are that " the 3RM has not been reported in the earliest H. sapiens from Asia, nor have we observed the trait in early H. sapiens from Africa or Homo erectus in Asia.* We note, however, that the lack of radiography of many specimens and the absence of the original Zhoukoudian remains make this conclusion preliminary."

The global prevalecy of the 3RM is highest in Asians (this paper cites a 25% prevalence rate for Nepal) and Esquimos. See the table in this other paper for more info on 3RM prevalence data.

The Homo luzonensis, which lived 67 kya in the Philippines (see post), had teeth that shared features of both modern H. sapiens and ancient H. erectus, yet they were far smaller than those of modern humans and... they also had three rooted molars.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

HPV Neanderthals, Africans and the early peopling of America

Almost two years ago I posted about HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory, and asked an open question about some oddities in the global distribution of HPV lineages: "Why is "D" highest in the Americas if it is supposed to have originated in Africa (see further up)... slave trade by Europeans? We'd need to see Karitiana or Coya, Pima haplogroups...".

I also made a comment and aked a second question because it turned out that the American HPV was more diverse than the Old World variants... which is unusual, considering that Amerindians are always considered as the least diverse humans (the famous Beringian bottleneck!). My comment and question was:

"And the diversity again: "East Asian and Central American HPV16 isolates showed higher average number of pairwise differences compared with sub-Saharan African isolates, even after accounting for intralineage diversity.", what? something in America more diverse than in Sub-Saharan Africa... why?"

A paper published two days ago (Nov. 1, 2018) has revisited HPV and provided answers and more data on these issues. (Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, et al. (2018) Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 14(11): e1007352. https://doi.org/10.1371/journal.ppat.1007352).

The paper suggests that HPV originated in Africa and that some 618,000 years ago (roughly at the time that Neanderthals and our Homo sapiens ancestors were splitting apart) an ancient HPV variant "A" split from the variant that would become lineages "B", "C" and "D".

Neanderthals left Africa with HPV A, which over the next few hundreds of thousands of years evolved into sublineages A1, A2, A3 and A4, all found in Eurasia, and in America, but very very rare in Africa.

Modern H. sapiens then left Africa 120-60 Kya and had sex with Neanderthals, picking up the HPV virus in its A variant sublineages. The African "B" and "C" variants are preponderant in that continent, with very small proprotion in Eurasia (5.6% among Caucasians and 1.8% among Asians) and America (2.3%). And the American "D" variant, according to this paper, originated in Africa, passed through Eurasia where it is found in extremely small amounts among Caucasians (11%) and Asians (6.3%). It entered America where it represents 48.3% of the HPV lineages.

Surprisingly the A4 variant that is 29.9% prevalent in Asia and 0.4% among Eurasian Caucasians, does not appear among Americans.

The authors sampled 212 complete genomes and built a phylogenetic tree of the different HPV16 variants based on this data. This tree shows two separate clades which coincides with previous findings, which had identified an Eurasian and an African lineage. They identified four lineages and named them A, B, C and D. These in turn were subdivided into four sublineages (A1 to 4, B 1 to 4, etc.). The breakdown of lineages is the following, where the percentages indicate their proportion in each population:

• A1 to A3: Eurasia (83% among Caucasians, 62% among Asians)and America (49.5%), only 2.4% prevalence in Africa.
• A4: As mentioned above prevalent in Asia (29.9%) and very little of it found elsewhere (0.4% among Caucasians) and nill in America and Africa.
• B: African (54.2%), 4% in European Caucasians, 0.2% in Asians and 0.5% among South and Central Americans.
• C: African (36.1%), 1.6% among European Caucasians and 1.6% among Asians. 1.7% in South and Central Americans
• D: America (48.3%), 7.2% in Africa, 11% in Europe, 6.3% in Asia.

Distribution of HPV16 lineages. From Schiffman M, Herrero R, Wood CE, Ruiz JC, et al.

The paper reports that there was more diversity in the African variants with an intragroup mean difference of 0.77% ± 0.04% compared to the Eurasian variants (0.32% ± 0.02%).

However the maximum divergence between sublineages was between the Eurasian A1 and the American D3 (2.23%) as can be seen in the Heatmap of pairwise diversity, which shows all of the 212 sequenced HPV16 genomes the maximum 2.23 difference is shown in red, and the minimum diferences are shown in blue. Amerindian D is therefore the most diverse.

So, summing up BCD and A split 618 thousand years ago, "indicative of an ancient divergence of HPV16 variants prior to the emergence of modern human ancestors".

The authors state: "The estimated divergence times between HPV16 A and BCD variants largely predated that of the out-of-Africa migration of modern human populations, consistent with a previously reported archaic hominin-host-switch scenario [19, 20]. One interpretation of the data implies that the present-day Eurasian HPV16 A variants were probably the products of multiple interactions between Neanderthals/Denisovans and modern Homo sapiens established during sexual contact after a long period of separation (e.g., 400–600 kya)"

The odd situation of the "D" variant (so diverse yet almost unique to America) is explained as follows (bold face is mine):

"Following a relatively recent out-of-Africa migration, the modern humans acquired the A variant from sex with archaic hominins and possibly carried D variants into Eurasia under conditions of a small population size. The ancestors of East Asian people crossed the Bering Strait and were early populators of the Americas (based on historical records and genetic relatedness). Surprisingly, the D lineage is phylogenetically rooted in the African clade, but we did not find a major reservoir of the D lineage in the present-day African populations. This interesting observation suggests either an advantage of niche ` colonization and expansion of HPV16 D variants in Native Americans or a bottleneck of HPV16 variants present in people populating the Americans. Alternatively, the lack of A4 and the high proportion of D lineages in the Americans could be the result of an early colonization of the Americas by an unknown group from Africa. More data is needed to sort out the evolutionary history of the HPV16 D lineage and might provide clues to new features of the populating of the Americas."

The idea of an "unknown group from Africa" colonizing America at an early date is very interesting. And the authors realize that this D lineage is special because in their closing comments they add: "Lastly, we provide new interpretations and questions on the HPV16 D lineage that is part of the African clade, but is highly prevalent in South/Central America.".

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

America peopled 130,000 years ago

Some very good news: atlastsome scientific evidence supporting an early =(130000 years ago) peopling of America; read more read more·

This is the link to the paper in Nature: Link to paper. And this is the abstract (I highlighted the Bold text):

"The earliest dispersal of humans into North America is a contentious subject, and proposed early sites are required to meet the following criteria for acceptance: (1) archaeological evidence is found in a clearly defined and undisturbed geologic context; (2) age is determined by reliable radiometric dating; (3) multiple lines of evidence from interdisciplinary studies provide consistent results; and (4) unquestionable artefacts are found in primary context1, 2. Here we describe the Cerutti Mastodon (CM) site, an archaeological site from the early late Pleistocene epoch, where in situ hammerstones and stone anvils occur in spatio-temporal association with fragmentary remains of a single mastodon (Mammut americanum). The CM site contains spiral-fractured bone and molar fragments, indicating that breakage occured while fresh. Several of these fragments also preserve evidence of percussion. The occurrence and distribution of bone, molar and stone refits suggest that breakage occurred at the site of burial. Five large cobbles (hammerstones and anvils) in the CM bone bed display use-wear and impact marks, and are hydraulically anomalous relative to the low-energy context of the enclosing sandy silt stratum. 230Th/U radiometric analysis of multiple bone specimens using diffusion–adsorption–decay dating models indicates a burial date of 130.7 ± 9.4 thousand years ago. These findings confirm the presence of an unidentified species of Homo at the CM site during the last interglacial period (MIS 5e; early late Pleistocene), indicating that humans with manual dexterity and the experiential knowledge to use hammerstones and anvils processed mastodon limb bones for marrow extraction and/or raw material for tool production. Systematic proboscidean bone reduction, evident at the CM site, fits within a broader pattern of Palaeolithic bone percussion technology in Africa3, 4, 5, 6, Eurasia7, 8, 9 and North America10, 11, 12. The CM site is, to our knowledge, the oldest in situ, well-documented archaeological site in North America and, as such, substantially revises the timing of arrival of Homo into the Americas."

Source
A 130,000-year-old archaeological site in southern California, USA Steven R. Holen Thomas A. Deméré Daniel C. Fisher Richard Fullagar James B. Paces George T. Jefferson Jared M. Beeton Richard A. Cerutti Adam N. Rountrey Lawrence Vescera Kathleen A. Holen. Nature 544, 479–483 (27 April 2017) doi:10.1038/nature22065

---

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

Denisovans, Inuit and Native Americans

An article, which you can read here Arctic Inuit, Native American cold adaptations may originate from extinct hominids from Dec. 2016, tells us something about the Inuit, Amerindians and Denisovans or some other now extinct archaic hominid... (the original paper is here).

Two genes, TBX15 and WARS2 seem to be critical in how the body deals with fat in cold climates to generat heat. The article points out the following:

" The Inuit DNA sequence in this region matches very well with the Denisovan genome, and it is highly differentiated from other present-day human sequences, though we can't discard the possibility that the variant was introduced from another archaic group whose genomes we haven't sampled yet," said Fernando Racimo, lead author of the study.
The authors found that the variant is present at low-to-intermediate frequencies throughout Eurasia, and at especially high frequencies in the Inuits and Native American populations, but almost absent in Africa. TBX15 is a gene known to affect the human body's response to cold, and is associated with a number of traits related to body fat distribution. The authors speculate that the archaic variant may have been beneficial to modern humans during their expansion throughout Siberia and across Beringia, into the Americas."

Allow me to suggest another option: the archaic variant evolved in Homo erectus in high latitude Asia, they had reached this part of the world at least 1 million years ago. They hunted big game (mammoths and hairy rhino lived there and did so for millions of years). What would stop them from following the heards into America? Thanks to this adaptation they could. And this is why, their descent, the Amerindians carry it. Later after Homo sapiens evolved in America, it back migrated into Siberia and Eurasia and reached -though diluted- Africa when it was peopled by modern H. sapiens from Asia and America.

This explains the cline from a peak in America to a low in Africa. As you moved into hotter regions it became less of an advantadge (actualy a fatty layer in a hot climate is a disadvantage).

Sources
Archaic Adaptive Introgression in TBX15/WARS2 Fernando Racimo David Gokhman Matteo Fumagalli Amy Ko Torben Hansen Ida Moltke Anders Albrechtsen Liran Carmel Emilia Huerta-Sánchez Rasmus Nielsen Mol Biol Evol (2017) 34 (3): 509-524. DOI: https://doi.org/10.1093/molbev/msw283 Published: 22 December 2016

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall © 

More on language diversity

I came across the map shown below, and I found it very similar to the map that I included in my previous post on Language diversity: it has the same clusters in Papua New Guinea, Amazonia and northern South America, South East Asia and Equatorial Africa. But! it depicted another thing, "Tone diversity".

The website that published that map has a very interesting post: Phonemic diversity decays "out of Africa"? (April 16, 2011)

Yes, the red dots are higher in Africa, S.E. Asia and PNG, but none in north Asia or Europe, and quite a few in America. Regarding the pink dots, America has more than the putative cradle od Amerindians (Siberia) or Europe.

The blog is very good as it makes fun of the paper it is criticizing.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Language diversity and the peopling of America

For years I have wondered why do Native American people speak so many languages? They supposedly reached the New World recently (i.e. 15,000 years ago) yet evolved over 40% of the global languages! A figure higher than that found in Africa, the "cradle of Mankind".

Africans have had the time (they are supposedly the oldest humans) and the advantage of not going through bottlenecks (I do imagine that bottleneck that wipes out genetic diversity does the same to languages... kill the speakers and the language dies), so they should have evolved most languages than any other group of humans. But they have not.

The diversity of Languages: highest in America. From [1]

Then we have the island of divesity in New Guinea has the highest language diversity in the whole world! 820 languages out of a global total of around 7,000. That is 1 language every 820 Papuans.

I found that quite reasonable, the island is a jungle, with many mountain ranges that isolate populations and keep them from mixinng. New Guinea has been considered as one of the first places reached by mankind during our epic trek out of Africa.

But America is different, we are newcomers. The Papuans had 50 ky to develop their languages, the Amerindians less than 15 ky. So how do we explain this?

To make matters worse, America's native population fell to half or even less during the period of discovery and conquest. How many languages were wiped out before even being discovered? Even so, it has the highest global language diversity.

The origin of languages

Human beings speak, and we are all aware that Chinese and English sound different, that Spanish, Italian and French may seem similar but are also different. We are humans and speak different languages despite having a common origin.

An early attempt to explain this can be found in the Bible (Genesis 11: 1- 9): "... But the Lord came down to see the city and the tower the people were building. 6 The Lord said, 'If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them. 7 Come, let us go down and confuse their language so they will not understand each other.'" So God made us all speak different languages by an act of his almighty power. Neat and simple.

But we now know that humans originated longe before any ziggurats were built in Mesopotamia. Language is something that arose tens of thousands of years ago. According to Chomsky, Tattersall, Bolhuis and Berwick (2014), "The faculty of language is likely to have emerged quite recently in evolutionary terms, some 70,000–100,000 years ago" [3]. Of course (I have posted on this before) that date range is not inferred from language studies, it is taken from the date suggested by anthropologists as the date of emergence of Modern Homo sapiens. So if that date was not correct, then the date given for the origin of languages is also incorrect.

In fact, our next of kin, the Neanderthals, could and did speak: "From the consilience of evidence from anatomy, archeology, and DNA, one can conclude that some language abilities, if not necessarily full modern syntactic language, were present in Neanderthals" so perhaps the ability to speak in Neanderthals predates that in humans. [4]

Daniel Nettle [2] suggests that people living near the Equator live easier lives regarding food supply and can split into smaller groups, which favours creation of new languages: "Where the climate allows continuous food production throughout the year, small groups of people can be reliably self-sufficient and so populations fragment into many small languages. Where the variability of the climate is greater, the size of social network necessary for reliable subsistence is larger, and so languages tend to be more widespread."

And this makes sense, as you can see in the map below, language diversity is highest close to the warm equatorial areas:

The diversity of Languages: location of highest densities. A. Whittall

Interesting, but this explains the evolution of languages during the last 11,000 years after the discovery of agriculture. I cannot imagine a large society of hunter-gatherers all speaking the same language, but one of farmers and tax collectors does make more sense.

But how fast do languages evolve? Take Australian English and English English or American English. They Aussies and Americans split from the mother tongue between 250 and 400 years ago, and did keep in touch with the distant British Metropolis yet evolved distinct stress and intonation for the same words. Something similar has happened with Spanish in the different Latin American countries and Spain over the past 500 years. But change has been small perhaps due to the lack of isolation.

The image above, from L. Luca Cavalli-Sforza & Marcus W. Feldman clearly shows that American languages are different to those in Asia, the "source" of the Native Americans' ancestors. This is surely conveniently explained by the "Beringian standstill" (how convenient) which allowed the future Amerindians to differentiate from those remaining behind in Asia.

Last but not least, I usually read that all indicators of genetic diversity fall as you move away from Africa, a clear indication of an African origin for all human beings. But, this is not seen in the case of human language diversity. Why?

I do believe that we should look into language diversity as an indicator of an older origin for mankind as a whole and for an earlier date for the peopling of America.

For those interesting in reading about this subject in depth, German Dziebel has written about linguistic diversity in support of his Out of America theory. Read More, and see an analysis of it here.

Sources

[1] Mobility and Ancient Society in Asia and the Americas, pp 117-126, chapter " How America Was Colonized: Linguistic Evidence. Johanna Nichols
[2] Explaining Global Patterns of Language Diversity, Daniel Nettle, journal of anthropological archaeology 17, 354–374 (1998) article no. AA98032
[3] Bolhuis JJ, Tattersall I, Chomsky N, Berwick RC (2014) >How Could Language Have Evolved? PLoS Biol 12(8): e1001934. doi:10.1371/journal.pbio.1001934
[4] Language Abilities in Neanderthals By:Johansson, S (Johansson, Sverker) ANNUAL REVIEW OF LINGUISTICS, VOL 1 Book Series: Annual Review of Linguistics Volume: 1 Pages: 311-332 DOI: 10.1146/annurev-linguist-030514-124945 Published: 2015

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Mandan & Arikara: Neandertal retromolar gap in Amerindians

The Neanderthal had a feature which was unique to them (they ALL had it) and is found in some modern humans: the retromolar gap or retromolar space.

A paper published in March 2015, "The Retromolar Space: A Morphological Curiosity Observed Amongst the Protohistoric Arikara and Mandan" by C. de la Cova DOI: 10.1002/oa.2451 International Journal of Osteoarchaeology, noted that it is quite frequent among two American Native groups, the Arikara and the Mandan peoples:

Abstract
The retromolar space (RMS), defined in paleoanthropology as a space posterior to the third molar, between the distal edge of the tooth and the anterior margin of the ascending ramus when the mandible is held in lateral view, has been described as an autapomorphic trait unique to Neandertals despite its presence in anatomically modern humans (AMHs). This study examined RMS prevalence in a sample of Protohistoric Arikara and Mandan Amerindians to determine what craniofacial morphology is correlated with the RMS. It was hypothesized that the feature would be present in the Amerindians studied and associated with a long cranial length, a large nasal height, midfacial prognathism, a broad mandible, and dental wear. The results indicated that RMSs were present in the Arikara and Mandan and significantly correlated with cranial length, cranial breadth, nasal height, bizygomatic breadth, basion-nasion length, basion-nasiospinale, mandible length, gonial angle, bigonial breadth, and dental wear. Thus, RMSs are associated with a dolichocephalic skull, wide cranial and facial breadth, a prognathic face, large nose, and a corresponding wide and long mandible with a reduced gonial angle. This suggests that the RMS is the result of these features merging together in the craniofacial complex and should not be considered a Neandertal autapomorph.

Of course, the conclusion that Ms. Cova reaches is that it is not an exclusive Neandertal feature but that it is related to a certain skull morphology that these natives have...

How about testing another hypothesis: the natives have it because they have a high admixture with Neandertals and got the genes that produce the retromolar gap from the Neandertals themselves... maybe even admixing in America and not in Asia before migrating to the New World.

Both Mandan and Arikara live in North Dakota, and some websites and some books too, suggest that they have some link to the Welsh! example below:

Several explorers claimed that the Mandans were white people; that the skin on their bodies was white and that the copper color was applied to the exposed parts. Verendrye even claimed that they were a mixture of white and black races. Volney, who was among them at a very early date, says that the children are born white like the Europeans and that the women were white upon the thighs, hips and lower parts of the body and says that it is wholly erroneous to suppose that the copper color is natural to them.
These travelers all make mention of many of the Mandans having blue eyes and red hair. Maximillion of Wied, a German traveler-scientist and linguist, and who lived with the Fort Clark Mandan villagers during the winter of 1833-34, tabulated a list of Mandan words and called attention to a very marked resemblance to the Welsh tongue...

Below: A Neandrtal skull and the "gap" behind the last molar.

The text above is from a very interesting site on the Mandans, based on the work of A.B. Welch which was written in the 1920s. Was the "white" "red hair" a Neandertal trait and not a Welsh one?

also tells about a Mandan who retold the ancient story of his people: An Indian tells Welch a story about meeting a "white man" who lived in the ground (cave dweller?) when they migrated to their current territory...

The text on these Indians, from "Travels in the Interior of North America" (1843) by Maximilian Wied (Prinz von) can be read here: (Link).

I definitively do not support the idea of a Welsh migration to America, or even the possibility that these were Vikings who admixed with the natives. Probably from time to time a group of Vikings or even cod fishermen from Medieval Europe were castaways on the coasts of America, but they could have never been enough of them to have such an impact as the one hinted at by Welch or Wied. A stable pre-existing population of Neandertal people would be another story and admixture would have had interesting consequences.

Further reading: Footprints of the Welsh Indians: Settlers in North America Before 1492, William L. Traxel Algora Publishing, 2004.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Loss of Amerindian genetic diversity post 1492

In a reply to a comment posted by a reader yesterday, I ratified my belief that the impact of the contact between Europeans and Native Americans was devastating for the latter. I have posted about this in the past:

"These studies overlook a unique situation which did not occur in other parts of the Old World: European discovery and conquest after 1492 AD provoked a massive eradication of native populations. This decreased the Amerindian gene pools dramatically (to between 33% and 4% of their original sizes). Over 80 M people died due to war and, mostly, microbia (measles, influenza, smallpox). Selective pressure acted to favor those better equipped to face the new environment.
It was this combination of disease and war-caused bottleneck plus natural selection that distorted the pre-Hispanic gene-frequency distribution obliterating genetic lineages, and obscuring ancestral frequency patterns. The pre-Hispanic genetic map of America was different and may have been much richer (i.e. similar to that of Asia or Austronesia). Studies that analyze gene frequencies in the New World do not seem to bear this in mind"

Of course, I never actually did some deeper research into the matter or looked into its genetic implications from a solid scientific point of view, although in other posts I have mentioned time and time again that the real bottleneck in Amerindian popultions took place after the discovery of America, and that it wiped out complete lineages.

Today's post will substantiate my claims that the diseases and war between natives and European conquerors led to a vast loss of genetic diversity in the Americas.

Massive death toll

Here in Argentina, during our school days they teach us about the Pre-Hispanic period in detail. We learn about the native cultures of Argentina and the Peruvian and Mesoamerican civilizations. We are later taught about Columbus and his voyages of discovery and the later conquest of America by Cortez, Pizarro, Valdivia and similar individuals. We learn about the Colonial institutions, the Viceroyalties, and the political and social aspects of colonial life. The gory details of death and the atrocities of conquest and subjugation are not mentioned.

But those students eager to read more about this period learn about the wars that took place between Spaniards and natives between 1492 and 1810. The use of cavalry, gunpowder, fire arms and war dogs gave the Spaniards a great advantage over the native troops who ony had bows and arrows, darts, spears and maces to fight the Europeans.

To make matters worse, the Spanish were aided by disease (flu and smallpox) which ran wild among the natives, decimating them.

Contemporary engraving of smallpox among Mexican Natives in the XV^th century.

The image above shows native Mexicans infected with smallpox, an Old World disease for which Americans had no immunity. The image is from the Florentine Codex prepared by a Franciscan friar, Bernardo de Sahagún during the 1500s. Its original title was "La Historia Universal de las Cosas de Nueva España", that is: "the Universal History of the Things of New Spain" (Mexico).

A little known fact is that Hern´ Cortez defeatied the Mexican Aztecs at their capital city of Tenochtitlan in 1520 while the natives were dying by the thousands, infected with smallpox they had caught from the Spaniards!

The Spanish knew the devastating effects of smallpox on the Indians. It had destroyed the natives in the Caribbean islands during the first phases of discovery. For instance the epidemic of 1518 in the Caribbean was terrible: "There occurred an epidemic of smallpox so virulent that it left Hispaniola, Puerto Rico, Jamaica and cuba desolated of Indians" [3]. This actually was the reason that slaves were brought from Africa to work in the fields, there were no more natives available: The local Taino aboriginals declined from over 1 million to less than 1,000 individuals by 1550.

War against the Aztec or Inca was, however quite limited. The other native societies offered more resistance. The Maya had no central government which if taken would lead to a total surrender as happened in Mexico or Peru. They had to be taken a village at a time. They were subdued by 1697.

Even minor civilizations were problematic: for instance, the Mapuche in Chile. They engaged the Spaniards and, in 1536, just after they arrived, torching the recently founded town of Santiago (which nowadays is the capital city of Chile). The Spaniards held firmly on and pushed the Mapuche south, into the Chilean Lake District. War raged on for years but the Spaniards managed to settle the Lake District in the 1560s, after defeating the native chief Caupolicán (1558) and impaling him.

The Araucanian or Arauco wars simmered on and the towns of Villarica, Osorno, Angol, La Imperial, were razed in 1598. The Spanish government retreated north and consolidated their frontier along the Bío Bío River. Native raids and uprisings led to a negotiation in the mid 1640s which concluded in an uneasy truce that lasted from 1665 to the 1860s.

War with the Mapuches. Ancient engraving [1].

In northwestern Argentina, the Kakán natives or Diaguita that lived in the fertile river valleys of the Andean foothills resisted Spanish occupation for over a century: the "Calchaquí Wars".

The area nowadays is a tourist attraction traversed by Argentina's National Highway Ruta 40, with cacti, arid mountains towering over 6,000 m (19,700 ft.) and the highest vineyards in the whole world, but the hundreds of "antigales" or ruins of native villages attest to a violent past.

Among the ruins is the settlement of the Kilmes or Quilmes natives. They lived by the Calchaqui River valley in Tucuman province, Argentina and firmly resisted the Spanish invaders. They held out in their mountain fortress against the Spaniards for decades during the Calchaqui Wars (1560 - 1666) but were defeated in an unexpected mid-winter raid in which the Spanish were aided by a traitorous group of neighboring natives.

Their village was destroyed, and the natives were transplanted en masse to Buenos Aires and forced to walk there (1,200 km or 746 mi.). Hundreds died on the way. They were "reducido" (restrained) in what is now a suburb of Buenos Aires, that adopted their name: the town of Quilmes. Finally, in 1812 the remaining three descendants of the Kilmes were set free.

The Kakan or Diaguita language is lost, nobody speaks it, it survives in place names recorded by the Spaniards in the 1500s, but the meaning is mostly unknown.

Other regions were left untouched by Spanish troops, but the European disease reached them (Amazon, Chacoans, Patagonian natives).

The European presence weakened the locals in many ways: the domestic animals that they introduced brought new diseases with them that infected the natives (tapeworm for instance). The natives were forced to leave their traditional villages and were gathered in other more densely and unhealthy towns built by the Spaniards. Lack of hygene and overcrowding soon promoted the spread of diseases (cholera and TB). Even the quality of the food intake fell. Less animal protein and more carbohydrates were ingested by the natives. Children were undernourished and tooth decay increased.

American Colonies and British bio-warfare in the 1700s

Even the North American colonies used terrible weapons against the natives. The English Commander officer during the French and Indian War (1754-1763), Lord Jeffrey Amherst, considered the natives' lives worthless and believed that they should be exterminated. He arranged for blankets infected with smallpox be sent to the natives to spread disease among them [2]. He was a pioneer in bio-warfare, using lethal (for the Indians) germs as a weapon.

After the Independence wars, the young American nations advanced their frontiers and soon the whole continent was under the control of Western people. I will not delve in the US opening the West or the Chaco and Patagonian wars of Argentina and Chile. Those were military campaigns with clear goals, and they did not intend to deliberately destroy civilians, only subdue them to the central governments.

Post-Colonial Genocide 1850 - 1900

Devastation continued once the colonial period had finished. The well intended Anglican Missionaries in Tierra del Fuego set out to civilize the Yamana (or Yaghan) canoe people living there. The natives had managed to adapt to the harsh Fuegian environment for over 6,000 years, but the American and European whalers of the mid 1800s wiped out the sea mammals that they hunted. Starvation began the process of extinction.

Mingling with the whalers put these formerly isolated natives in contact with tuberculosis, smallpox, tifus, whooping cough and measles. From a population of over 3,000 in 1850, the natives which had gathered at the Mission in Ushuaia (known by the natives as "welapatux-waia" or "Bay of death"), dropped dramatically. By 1900 their culture had vanished. By 1995 only 74 persons state that they have a Yamana ancestry.

The consequences from a genetic perspective

The dreadful impact of discovery and conquest can be imagined just by looking at the death toll: "the American Indians were at least seventy million or maybe more when the foreigners showed up on the horizon. One and a half centuries later, they were reduced to only three and half million". [4]

That is one incredibly big bottleneck: only 1 out of 20 natives survived. This means that 95% of the genetic diversity of America died out. Perhaps the real figure is not 95% (below we will see a paper mentioning a 50% drop) [7], but still, it is clear that what is left today is just a pale shadow of the diversity that once existed in America.

Death and decreasing diversity

Disease and War cause extreme reduction in population sizes and this impacts noticeably on its genetic diversity [6]. In Europe, the Black Death or plague in 1347-1351 caused a very high death toll (between 30 and 50% of the population died) [5], and the effects of this disease-caused bottleneck are even visible in the current genetic diversity of Britons: [5]

A paper [5] shows a dramatic decrease in Diversity as measured by haplotypes ⁄ sampled individuals:

• 0.84: Saxon Britain
• 0.75: Ancient Britain
• 0.45: Modern England

In other words currently 53% (0.45⁄0.84) of the former genetic diversity survives, 47% was lost.

See Table 1 in [5] for a full set of data showing a considerable drop in genetic diversity. The finding surprised the authors: "Based on the assumption that modern England is more cosmopolitan, higher geneitc diversity in the ancient sample was unexpected" [5]. And the reason for this was the bottleneck caused by the Black Death and the Great Plague of 1665 - 1666 (which wiped out 20% of the population of London).

The paper's comments regarding the impact of a disease on diversity are also valid for America, though we can imagine an even more drastic effect among the Amerindians due to the severity of their bottleneck:

"Because most human haplotypes are rare, lineages could have been forced to extinction even without a severe population bottleneck (millions remained). This is especially true if related families were lost when whole villages perished (either through shared susceptibility or environment). Furthermore, during the plagues some families were apparently more resistant than others, which could have led to high variance in the number of daughters surviving among different families and a consequent loss of mtDNA diversity at the population level. [5]

The upheaval caused by disease also favored some haplotypes more than others: an ancient haploytpe known as the Cambridge reference sequence (CRS) was found at 6.3% frequencies in the ancients but subsequently grew to almost 22% among modern Britons. [5]

A Native American study

So if this is what a mere 33 - 50% reduction in population caused in Europe, imagine Amerindians, whose population fell by 50 - 95%!

A very interesting paper by Brendan D. O'Fallon and Lars Fehren-Schmitz, (2011) [7] addresses the genetic impact of European contact in Native Americans. They are more cautious in their population decrease figures, but even so the value they estimate is very high: "Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ~50%" from the maximum it had reached about 5 ky BP. [7]

The authors compared ancient (3,000 BC to 1,200 C.E.) mtDNA and modern samples from North and South America to study how the population bottleneck impacted on diversity. They found that it "affected haplogroups C and D disproportionately" (D1 was hit worse than C or A2, B2 and X2a), and that "the depopulation was not localized to particular regions or communities, and instead, was likely to have been widespread... [and] had an especially severe impact on the most populous regions." [7]

Figure 4. in the paper, shown below clearly marks the "lost" haplotypes: "blue" in South America, "red" in North America, while gray represents the extant lineages.

It is interesting to see that most of the "lost" branches don't have any descent today they simply disappeared (it is not the case of a four pronged fork where 3 prongs died but one survived, in these lineages all prongs went extinct9.

The ancient samples they used came from 16 sites which is quite a lot, but they originated in only three geographic locations: SW Ontario, Canada; Fulton County, Illinois US and Palpa, Peru. Imagine if more locations from across America are added, will new haplogroups be found? I believe so.

For instance, take haplogroup M, which has not been found in any contemporary Native American group but has been reported at least twice in ancient remains (see my post on Ancient migrants into America with Hg M) and another recent study (Carpenter et al., 212) [8] which found mtDNA belonging halpogroup in pre-Columbian Chachapoyan and Chachapoya-Inca remains dated at 1,000 and 1,500 AD. They came from the Laguna de ls Cóndores site in Peru.

So, having said this and looking at the tree above I imagine that much more diversity was much more ample than we can imagine and that haplogroups other than M may have also existed in America and got lost in the discovery debacle.

Sources

[1] From Gerónimo de Bibar Crónica y relación copiosa y verdadera de los reynos de Chile
[2] Lord Jeffrey1 Amherst's letters discussing germ warfare against American Indians. www.nativeweb.org.
[3] Oviedo y Valdes G. F. (1851-1855), Historia General y Natuarl de las Indias..., Vol 1. 105.
[4] Bernardo Veksler, Una Visión Crítica de la conquista de America [5] A.L Töpf, M.T.P Gilbert, R.C Fleischer and A.R Hoelzel, (2007). Ancient human mtDNA genotypes from England reveal lost variation over the last millennium. Biol Lett. Oct 22, 2007; 3(5): 550–553. doi: 10.1098/rsbl.2007.0269
[6] Montgomery Slatkin, (2004). A Population-Genetic Test of Founder Effects and Implications for Ashkenazi Jewish Diseases. Am J Hum Genet. Aug 2004; 75(2): 282–293. doi: 10.1086/423146
[7] Brendan D. O'Fallon and Lars Fehren-Schmitz, (2011). Native Americans experienced a strong population bottleneck coincident with European contact. Pnas 20444–20448, doi: 10.1073/pnas.1112563108
[8] Meredith L. Carpenter, et al., (2013). Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. Am J Hum Genet. Nov 7, 2013; 93(5): 852–864. Table S1. doi: 10.1016/j.ajhg.2013.10.002

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Micro post on the Amerindians and their uniqueness

Micro post! I am just reading old papers on Amerindians and came across this one (Mesa et al., 2000) [1]. Which shows the very interesting tree pictured below:

Fig. 2. Mesa et al., 2000

See how Europeans and Asians cluster together on the left while Amerindians are on the right, in a branch splitting from the junction of Eurasia and Africa... Not the usual East Asia branching into Amerindians is it?

Source

[1] Natalia Mesa et al., (2000). Autosomal, mtDNA, and Y-Chromosome Diversity in Amerinds: Pre- and Post-Columbian Patterns of Gene Flow in South America.Am J Hum Genet. Nov 2000; 67(5): 1277–1286. Published online Oct 13, 2000. doi: 10.1016/S0002-9297(07)62955-3

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Out of America (into Asia)? Part 2

On the Y-Chromosome Q haplogroup

 

TThis is the second part (See First Part here) of my ramblings on a possible Out of America migration back into Asia.

I will carry on from where I left off: (Summary) some Asian (specifically Northern, Central and Northeastern Asians - from Siberia, NE China and Mongolia) have a small but noticeable content of specific genes of Amerindian content. Mainstream science has it that these Asians descend from the people that were also the ancestors of Amerindians therefore they do carry some of the same genes.

I posted that the Turkic people moved out from the Altai spreading West towards Europe and North, Northeast into Siberia (Sakha or Yakuts, Kets and Selkups) and that they probably admixed there with aboriginal Siberians who in turn had an American admixture due to an Out of America gene flow.

I pointed out tha the Kets have the highest frequency of Y chromosome haplogroup Q (Q hg) in all of Asia (93.7%), which is only found among Amerindians; The Selkups have the second-highest frequency of haplogroup Q (Q hg) in Asia (66.4%).

Other groups, Tuvans, Oroqen, Mongols, Hadza and Daur carry a much lower Amerindian content and is very likely due to admixing with the other Siberian peoples.

The Y-chromosome Q haplogroup (Q hg) mentioned above is very interesting due to its strong preponderance in the Americas. Could it be a signal of an Out of America back-migration into Asia?

The Y-Chromosome haplogroups in America

Global distribution of Q Y-Chromosome haplogroups

A paper analyzing American and Asian lineages of Y-Chromosome (Battaglia V., et al., 2013) [2] notes that of the two founding lineages of Y-chromosome found in America, (C and Q), Q is the oldest and most widespread (with 75% frequency), while C, is limited to North America and found at a lower frequency . This means that Q haplogroup (Q hg) reached America first and spread from Alaska to Tierra del Fuego, C hg is a later arrival.

Q haplogroup is found in two main lineages in America: Q1a3a1a-M3 (76.8%) and Q1a3a1-L54* (16.7%). It is however interesting to point out the great diversity of Q hg in America: another 8 haplotypes have been discovered, mainly found among Peruvians and Mexicans, and they add up to 6.4% frequency, much greater than the diversity found in Siberia. [2]

The M3 part of Q1a3a1a stands for the M3 marker which is believed by mainstream geneticists to have arisen in Beringia, except for some extant Far Eastern Siberians (it appears among Koryaks at a frequency of 40%) [2] it is only found among Native Americans. Its presence among Koriaks (see image below for Q1a3a1a* red and blue square) is believed to be "... the result of a back migration rather than be direct M3 Beringian descendants... [and] could also be due to recent contacts (gene flows) with modern northern Native Americans." [2] .

An alternative explanation could be that M3 originated in Asia and those that took it into America survived, while the Siberians that carried it, passed away without descent.

The other marker L54, is definitively American (with a higher frequency in Mexico and Central America and lower elsewhere), none were found in the "populations living along the entry route to the Americas" [2] , and "only a potential Q-L54* has been observed in one Chukchi from Northern Siberia" [2], the paper cautiously points out that "any interpretation of this result (new Asian lineage, remnant of an ancestral state, trace of forward or back-migration) is premature..." [2].

Eastern and Southern Siberian peoples, Mongolians from the Altai Region in Western Mongolia and southern Ataians are definded by the Q1a3a1c sub-clade defined by the L330 marker. Asian upstream intermediate is L53* is found in Northern-Altai and Mongolia, at very low frequencies.

The paper concludes that the Altai Mountains were the southern barrier for these people who carried an ancestral form of L54, which "in prehistoric times and long before the peopling of the New Continent, moved eastwards during the Beringian standstill." [2]

This is reasonable, but the dating of the different branches is very strange:

The Odd phylogenetic tree

What I find perplexing are the dates of the branches of Battaglia et al.'s Phylogenetic tree of Y-chromosome Q hg; where some branches are older than their roots!:

Below is my adaptation of Battaglia et al.'s figure 1; in red I shaded the American haplogroups (M3), and in blue the Asian ones. The number on the right is the age of each haplogroup, (kya). The branches that are "American" are shaded red. All other branches are fully Asian.

Phylogenetic tree of Y-chromosome haplogroup Q. From [2]
The ages are on the right. Blue= Asian, Red= Amerindian

We see an incongruity in the "main" branch MEH2 whose branches M120, MEH2* and M25 (with ages that range from 2.7 to 15.4 kya) are all younger than the offshoots of branch M346 which is at their same level.

Furthermore, M346 (dated by Zhong et al., [3] at 17.77 +⁄- 4.4 ky, then branches succesively into branch L53 which then branches into L54 and this one then branches into M3 which is the oldest in the tree with maximum ages between 21 and 23.6 kya.

Lets look at the details:

Dates (I round off the dates from Tables 2 and 3, in [2]):

• America
  
  • Q1a3a1a-M3*. Most (from 66 to 100%) Amerindians belong to it: 22 kya for Central and Southern Americans, 3.4 kya for Na-Denes and 7.4 kya for Eskimo-Aleuts. Which is reasonable since the last two populations belong to a more recent migratory wave into Northern North America.
  • Q1a3a-L54*. The remaining American Natives belong to it: 23.6 kya old, except Na-Dene which, again, are younger: 5.6 kya.
• Asia
  
  • Q1a1-M120 and Q1a2 - M25. Mongols were not dated in [2], however Table 1 in [3] gives 15.4 and 2.7 ky respectively.
  • Q1a*-MEH2. Koryaks = 3.5 kya and also the remains of the "Saqqaq" man from Greenland (Morten Rasmussen et al., 2009) [1] which are about 4,000 years old but belong to a later wave into America.

  • Q1a3a1c-L330. Mongols = 6.5 kya and Altaians: 2.9 kya.
  • Q1a3a*-M346, is dated at 17.77 +⁄- 4.41 kya [3]

Below I reproduce the data from Table 3 [2], showing the "average" ages for all Q haplogroups:

Average age Q lineages. From [2]

Once more, American Q hg are between 21.1 and 23.4 ky old. The Asian ones range from 10.3 to 22.4 ky with a decreasing age cline as you move East to West from America into Siberia.

This would suggest that these Asian Q lineages originated in America and dispersed West, diversifying (mutating) along the way since the youngest are deeper in central Asia.

But that assumption is apparently wrong, because the markers follow the opposite order (that is, Americans have markers that Asians don't, implying that these markers appeared later, in Americans).

I guess I am going to have to do some deeper research into specific Haplogroup markers, but first, let's look into the Siberian Q haplogroups.

Siberian ancestors (?)

The presence of haplogroup Q (Q hg) among Siberians was pointed out in 2002 (Karafet et al., 2002) [4] at relatively low frequencies of 18.8% (when compared to Native Americans). Two populations concentrate 79.5% of the ocurrences: the frequency reached 93.8% among Kets and 66.4% among Selkups. The age of haplogroup Q was estimated at 17,700 +⁄- 4,800 years [4], in tune with the mainstream theory (it is just a bit older than the 15 kya date for entry into America).

These high frequencies were due to "intergenerational genetic drift coupled with founder effects... supported by very low levels of Y-STR diversity associated with haplogroup Q in both populations (0.149 and 0.159, respectively)..." [4]

In other words it was not natural selection, but chance that acted upon the small population sizes and their high mobility allowing Q hg to become predominant; therefore its frequency grew (intergenerational genetic drift), add to this the fact that small groups with Q hg survived while other haplogroups just died out (bottleneck); outcome: Thus the Q hg became the prevailing line among these people.

Different to Americans and different to each other

But, as we have already seen, these haplotypes are not the same as those found in Native Americans; a Russian language paper (Volkov, 2013) [5] provides an interesting phylogenetic tree, reproduced below:

Phylogenetic tree of haplogroup Q1a3. From [5]

At the split between Americans and Asians (Q1a3a-L53), two branches appear, one leading to all Siberian groups in blue. Another one, in orange one leads to American Natives (red branch M3) while another (yellow) leads to the Q haplogroup found in certain Europeans: Q1a2a2 L804, L805 (Sweden, Norway and via Vikings: UK) - this is worth looking into! [6]

The Q frequency (L330) among Siberians is in agreement with Karafet et al: Kets: 84%, Northern Selkups: 66.4% (and drops to: Evens: 4.2%, Nenets: 1,4%, Kanthy: 1%). [5]

But they are not the same Q haplotypes: Selkups, who originally lived in the Urals, share the same haplotype with the Chechens of the Caucasus (which is close by). On the other hand, the remaining Siberian populations and among them the Kets belong to another haplotype, with other downstream mutations: DYS347=14, and DYS437=13, DYS390=23 ("DYS" stands for DNA Y chromosome Short Tandem Repeat, with a lenght of "n").

Considering that Altai was the source of Amerindian Q haplogroup, Dulik at al., (2012) [7] explored the differences between the Q hg of Southern and Northern Altaian's (this is also reflected in the image above). They found that the latter were quite recent (Bronze Age) the former older -early Bronze Age or late Neolithic.

Then they calculated the divergence times between Southern Altaians and Native Americans, but their TMRCA ages fluctuate widely; from a too recent 7.74 kya (Pedigree Based) to a more reasonable 21.96 ky (Evolutionary-Based); the Split Time values were 4.95 and 13.42 kya for Pedigree based and Evolutionary based, respectively.

Seeing this 3 fold difference between the ages and taking into account that America was peopled more than 8 kya, the authors dismissed the Pedigree based values arguing ("that the evolutionary rate provided a more reasonable estimate.... making the use of the pedigree-based mutation rate questionable." [7]).

These "average" values are to young (even more recent than the 23 kya age estimated further up for the M3 and L54 haplotypes found in America. And, in my opinion it is due to the fact that the 95% confidence intervals for the Bayesian analyses are extremely broad: they range from 12,260 to 42,690 ya. for TMRCA and 5,220 to 30,430 ya. for Splilt Time.

Taking the oldest figures would mean that the ancestors of Americans could have shared a common ancestor with Altaians 42,690 years ago, which is really much more reasonable and consistent with the earliest dated Upper Paleolithic industries from Altai: 43.3 kya [4].

Dating and TMRCA values: Are they reliable?

Looking at these disparities it seems that a key issue is the dating, the timeline, the estimation on when groups split or when they shared a common ancestor.

As seen above, Pedigree estimations differ substantially from those based on evolutionary estimations. And these depend on the mutation rates adopted.

When reading the papers that deal with this subject, my doubts intensify. For instance, a paper by Poznik et al., (2013) [8] estimates mutation rates by adopting, as a "calibration point, the initial migration into and expansion throughout the Americas", based on the dates of known archaeological sites (Paisley Cave and Buttermilk Creek in the US and Monte Verde in Chile) they find Goebel et al. estimation that " humans colonized the Americas around 15 kya” acceptable, and use it for calibration purposes. [8]

But what if instead of 15 kya the date was really 30 kya or 45 kya? This would introduce a strong bias in their estimations. Once again we see how a "recent date" for the peopling of America impacts upon other branches of formal science.

The authors then use the Y haplogroup Q for their calibrations and assume that M3 arose "shortly subsequent to initial entry to the Americas", and in doing so, underestimate the impact that an earlier divergence (Between L54 and M3) in Siberia, prior to the entry into the New world could have had on their calibration. [8]

The strange dates produced by these estimations are higlighted by the case I mentioned in a Previous post on the useless mtDNA clock, where the dating of a novel Y-chromosome haplogroup (Mendez et al, 2013) named A00, gave a very old age: " 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils..." [9], strangely old date indeed. The clocks need to be checked.

Another example can be found in a paper on a Q hg sublineage (Q5) detected in India (Sharma et al., 2007) [10]; the ate estimated for it was 47.1 kya (34.2 – 75.6 ky), but the authors believe that it is "an over estimate than the age of haplogroup Q (15,000–18,000 Years Before Present)" and try to explain the distorted "old" age they calculated as caused by "enhanced diversity, probably as an effect of population expansions and severe bottlenecks or might be due to later migrations and admixture" [10], they then recalculate it as 14.4 ky old! (fitting it nicely into the assumed age range).

Summary

Y chromosome Q hg predominates in America, most of it belongs to the M3 subtype, the rest is L54. There is a very small presence of these two subtypes in East Beringia (Asia), most likely due to a back migration into Siberia from America.

Greater diversity within Q hg is found in America than in North East and central Siberia, this hints at a deeper and more ancient origin for the American lineages.

However the ages of the oldest Amerindian haplotypes are quite recent and have been calculated as being 22 -23 kya. Asian strains contrary to what would be expected from the theory of a trans-Beringian peopling of America appear to be much younger. Suggesting instead a migration Out of America and into Asia, carrying Q hg. We will see in a future post that there is additional proof from mtDNA and language of a migration from America into Eastern Siberia.

Despite doubts regarding age calculations, the oldest mainstream date of 43 kya for a split between the ancestors of Altaians and Americans seems to allow for an early peopling of America.

There is something with the ages that I find strange. But that will be the subject of another post, where I will deal with the dating methods (in particular after reading how Anzic-1 remains from Montana US were dated. By the way, he was a Q-L54*(xM3) 12,600 years old.

I will review the markers that indicate splits in Q hg, because a radiation out of America seems highly probable. I will also take a look at those odd Q hg found in Europe which some attribute to the Huns, but may have more ancient roots, the same ancient roots that Amerindian Q hg has... (I am thinking about Neanderthal here... however Neanderthal Y chromosome would be even older than the A00 haplogroup mentioned above, and quite different from the current Q hg that descends from A00).

Sources

[1] Morten Rasmussen et al., (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835
[2] Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, et al., (2013). The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q.. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390
[3] Hua Zhong et al., (2010). Extended Y-chromosome investigation suggests post-Glacial migrations of modern humans into East Asia via the northern route. Oxford Journals.
[4] Tatiana Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life, Human Biology, December 2002, v. 74, no. 6, pp. 761–789.
[5] VG Volkov, (2013). Ancient Samoyeds of Yenisey, and migration in light of Genetic Data. Tomsk magazine Ling. and Antropo. 2013. 1 (1) 79-96
[6] International Society of Genetic Genealogy
[7] Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
[8] G. David Poznik et al., (2013). Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science 2 August 2013: vol. 341 no. 6145 pp. 562-565 S. Inf. page 13. DOI: 10.1126/science.1237619
[9] Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
[10] Swarkar Sharma et al., (2007). A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India. BMC Evol Biol. 2007; 7: 232. doi: 10.1186/1471-2148-7-2327
[11] Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©