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 © 

Out of America (into Asia)? Part 1

A paper (Morten Rasmussen et al., 2009) [1] reports the sequencing of the genome of a male from Greenland; it was obtained froma a hair (about 4,000 years old) that was found in the permafrost. The man belonged to a wave that peopled the New World long after the original and older migration of modern Amerindians.

The interesting part (from my perspective) is the information regarding Native Americans and how different they are from their purported Siberian ancestors.

The following image (Adapted from Fig. 3 in [1]) and, just by looking at it you can see some intriguing trends:

Figure 3. From [1]

Part (b) of the figure (upper right corner of the image) shows a clear distribution where Siberians and East Asians are found on the upper branch, Europeans on the Right tip, where upper and lower branches meet, and Southern and Meso-American Natives are found on the bottom left tip of the lower branch.

It is very evident by the distance between them, the vector orientation and their placement in different branches, that current Siberians and Asians are not related to modern Amerindians.

Part (c) shows a plot generated by the ADMIXTURE39 algorithm with K = 5. It shows individuals from 35 extant Eurasian and American populations which are represented by stacked columns with five ancestry proportions (y axis indicates the fraction of each of the five inferred ancestral groups).

We can see that:

1. (Blue color). There is an important western Eurasian component admixed into Siberians, Northernmost North Americans and Greenlanders. This drops off sharply with a North to South cline for the other Amerindian populations.
2. (Brown or Burgundy color). The Amerindian component is prevalent with a decreasing South - North Cline, among all Native American groups. And is also found in minimum fractions among Chuckchis, Tuvinians, Altai, Selkups and Kets. (We will look into this further down)
3. (Pale Yellow). Found in minimum frequencies in Eastern Siberia, it incrases to nearly 90% among West Beringian Koryaks and Chukchis, with a strong prevalence among Arctic Americans and Na-Dene natives. It drops off with a north to south cline from around 40% in Na-Dene to a <10% fraction among Southern Amerindians.
4. The other components are absent among South American Natives.Orange, which is prevalent among Chinese, Japanese and East Asians, drops off towards Eastern Siberia. Dark Yellow, which grows with a West to East cline and is maximum in Central and Northern Siberia.

The Amerindian signature in Asia

The "brown component" found in small frequencies in Asia is quite interesting and exactly the same pattern appears in another paper (Li et al., 208) [2]; In this case the sample includes populations from African, Southern Asian, PNG and the Middle East. Below is its Figure 1 A:

Figure 1A. From [2]

The image indicates the ancestry of different populations at K = 7 (seven inferred ancestral groups). [2]

We see that the pattern is repeated and that the Amerindian component (Violet) appears predominantly (>90%) in South America (with a slight admixture of European and even less components from other regions).

The Amerindian "violet color" reappears in East Asia among the Yakut, but with extremely small frequencies among the: Oroquen of Heilongjiang (China), the neighboring Daur of Mongolia, Hazara (Afghanistan) and Mongols. It reappears again at relatively higher frequencies among the Russians.

Why do all these Eurasian people have a tiny proportion of Amerindian in them?

Orthodox view

The accepted theory is the following:

Modern Humans reached Siberia relatively late, the rest of the Old World was already peopled. The icy Siberian regions had effectively formed a barrier to all hominins until the superior skills of modern Homo sapiens (invention of needles to sew fur clothes and the mastery of glacial-condition survival skills) breached that last barrier.

This enabled Siberians from Central Asia to trek out on a Northeastern course, reach Beringia and stay there about 5,000 years during the peak of the last Ice Age, hunting mammoths and other tundra herbivores. During this time they became quite distinct from a genetic point of view from the relatives that stayed behind in Siberia. Then during deglaciation they packed their tents and gear and rapidly marched on into the vast and empty New World occupying it in less than 2,000 years.

A second wave of migrants admixed with the first, bringing some more recent Siberian alleles which are found among Na-Dene, Innuit and other North American natives. South America remained free from this admixture.

So, any similarity between Siberians and Amerindians is due to their common ancestry. There are differences of course, but these are due to the long sojourn in Beringia which gave time for unique Native American alleles to appear and also for founder effect (only a few clans of Siberians reached Beringia, so their set of genes was rather limited) and bottleneck (some clans died out and their lineages with them, further depleting Amerindian genetic diversity) to act and further separate Americans from Asians.

By the way, these people expanded into America in small isolated groups that did not mix frequently with their neighbors, so they developed in a very short period of time, hundreds of unique languages and their genomes took disparate courses which due to drift made them appear different, but actually all sharing the same recent Asian origin.

Last of all, enslaved Africans and Europeans admixed after 1492 C.E. as a consequence of the discovery of America by Europeans so any odd European or African genes found among Amerindians (even the most isolated groups) are due to this recent admxiture.

Another unorthodox view

The model outlined above does not even consider the possibility of a pre-sapiens peopling of America. The H. habilis from Dmanisi in Georgia, the H. erectus from China or even Neanderthals and Denisovans from Altai, could have continued onwards into America, but archaic sites with Acheulean or Mousterian tools are lightly dismissed by mainstream science as geofacts or of recent manufacture.

The recency in the peopling in America is taken as a proven fact and the data are used by other branches of science (i.e. genetics) when calibrating their methods. As seen in previous posts, the late peopling of America and Siberia is accepted without questioning. This in turn implies that Old World populations have "deeper evolutionary histories", and Amerindians, in contrast are "recent".

The bottleneck and founder effects are generally assumed to have taken place prior to or during the Beringian Standstill, thus restricting the gene pool that entered America. I have not seen papers that explicitly recognize that America was peopled by a popuation with a wide spectrum of alleles and that they became extinct due to the negative impact of mass deaths caused by disease, war and over exploitation of natives after the Discovery and Conquest of America. This overlooked event was an exceptionally strong force even as recently as the late 1800s, and early 1900s.

As an example, the population of Yaghans or Yamana, canoe people living in the fjords of Southern Tierra del Fuego and the Selknam hunter gatherers of the Fuegian mainland, dropped dramatically after contact with Europeans:

The Yaghans passed from 3,000 to 100 people between 1850 and 1916; in 1995 only 75 people of admixed Yaghan origin survived. The Selknam decreased from 3,500 to 800 during the same period, today only 696 persons of mixed Selknam descent survive. Whooping cough, tuberculosis, small pox and VD wiped them out.

These were the real bottlenecks that wiped out people who had lived in isolation from Old World illnesses for milennia. But let's get back to our main subject. The alternative theory for the peopling of America.

What to Yakuts, Oroquen, Daur, Hazara, Mongols, Russians, Chuckchis, Tuvinians, Altai, Selkups and Kets have in common that allows them to have minute quantities of Amerindian ancestry?

The map I prepared (see below) shows their approximate geographic location and the figure inside each oval is the rough percentage of Amerindian ancestry in each group (it indicates the average value within each population):

Amerindian ancestry in different Asian populations. Copyright © 2014 by Austin Whittall

We see a high frequency of Amerindian ancestry among Chukchis, Kets and Selkups. And a drop towards the south: Altai, China, Mongolia and the Hadzas. Russians: it is hard to define a location for them since we do not have the data about where the samples were taken. But the value is high and uniformly distributed among them.

I believe that there was a back-migration from America into Eastern Siberia. This accounts for the high content among Chukchis (red arrow A in map).

The dispersal advanced further into East Asia along a northern corridor since to the south mountain ranges (Cherskiy and Kolyma) along the coast blocked the way. The route then crossed the Verkhoyansk Range and reached the Lena River Basin, and, further West, the Yenisei River Basin where it admixed with the aboriginal people living there. (red arrows B in map). To the south, the Iablonovy and Stanovoy Mountains blocked their advance into Manchuria, Mongolia and China. This was the maximum advance of these "Out-Of-America" migrants. (shaded pale red in map).

Much later, the current populations of Selkups, Yakuts and Kets moved north and east into these regions and admixed with these aboriginals, incorporating the Amerindian alleles into their genome (blue arrows in map).

And then, much more recently, further mixing towards the South along the Amur and then West through Mongolia incorporated these genes into the Oroqen, Daur and Mongols. Additional dispersal towards Altai and into Russia took place along the Northernmost Silk Road (Euasian Steppe Road); similar dispersal incorporated them into the Hadza in Afghanistan. (green arrows in map).

But who are these Selkups, Yakuts and Kets?

The Turkic people

The homeland of the Turkic people and their language is in the Altai region, where proto Turkic appeared ca. 400 BC. It expanded from there: the Tuvans and Sakha (or Yakut) moving East and Northwards, and others moving west around Aral, the Caspian and into Asia Minor (finally settling in Turkey).[3]

Let's take a look at the Asians who carry these American components:

The Sakha or Yakut left their Altai homeland forced by their neighbors. They advanced along the Lena River towards the northeastern forests of Siberia. They admixed with the local natives (some of which carried the ancient Amerindian component) and also with mongol people, which have left a strong Mongol - East Asian component in them.

The Kets, also from the Altai, and also forced north due to conflict with belicose neighbors. They have a very strong Amerindian component and also, the highest frequency of Y chromosome haplogroup Q in all of Asia (93.7%), which is only found among Amerindians. Currently they are a small population (<1,500 people) yet many name places in Siberia are Ket. They are linked to the later wave that peopled America through the Na-Dene - Yeniseian languages.

The Selkups (currently about 4,300 people) have the second-highest frequency of haplogroup Q in Asia (66.4%). They were not originally from Siberia, they migrated East from the Urals and mixed with Turkic elements in the Altai area and also with the aboriginal peoples of the Yeniseian region (Siberia) who carried the Amerindian alleles. [4][5]

The Y-chromosome Q haplogroup mentioned above is very interesting and worthy of the second Part of this post.

Continues in Part 2.

Sources

[1] Morten Rasmussen et al., (2009). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835.
[2] Li JZ, Absher DM, Tang H et al., (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 319: 1100–1104
[3] The Turkic Languages in a Nutshell
[4] The Red Book of the Peoples of the Russian Empire
[5] Tatiana M. 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.

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