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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