Human Genetic Diversity: Some Maps

The global human diversity map that I included in my previous post came without any reference to source or scientific backing, so it isn't reliable. I decided to search for something better and came across the three maps shown below.

They come from Figure 2, in the 2009 paper by Romero, I., Manica, A., Goudet, J. et al. How accurate is the current picture of human genetic variation?. Heredity 102, 120–126 (2009). https://doi.org/10.1038/hdy.2008.89

Interpolation of estimates of genetic diversity (HS) for short tandem repeats (STRs) (a), indels (b) and single nucleotide polymorphisms (SNPs) (c). The intensity of the red colour represents the genetic diversity obtained with an inverse distance-weighted (IDW) interpolation on landmasses. Blue dots represent the 54 populations from the H971 subset of the HGDP-CEPH data set. (d) The difference in genetic diversity between African and European populations for the three classes of markers. Error bars report standard deviation.. Fig. 2 in Romero, Manica, Goudet et al.

The map does not include data for Australia, South America appears with the lowest diversity for all three indicators, SNPs, indels, and SNPs, however, Africa has a low scoer in indels as you can see in (b).

I also found the source of the original map, it was published by Luca Pagani, as his thesis (online here, Through the layers of the Ethiopian genome: a survey of human genetic variation based on genome-wide genotyping and re-sequencing data. July 2013, DOI:10.17863/CAM.13969, Thesis for: PhDAdvisor: Toomas Kivisild). The map (shown again, below) is captioned "Pattern of genetic diversity in worldwide human populations. The distribution of STR diversity in worldwide human populations, adapted from the literature (Colonna et al. 2011), shows a higher diversity in African populations and a decline with the distance from Africa (each black dot represents a sampled population). The observed pattern fits with the proposed single African origin with subsequent migrations out of Africa proposed by Stringer and Andrews in 1988."

Colonna et al, (2011), cited by Pagani has several maps in his paper as Fig. 1 (Colonna, V., Pagani, L., Xue, Y. et al. A world in a grain of sand: human history from genetic data. Genome Biol 12, 234 (2011). https://doi.org/10.1186/gb-2011-12-11-234), where Pagani was a co-author.

I wonder what the plesiosaur in the Pacific stands for (?) it appears in the four maps of the 2011 paper.

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

Diversity in Africa. Some explanations on why it is so diverse

The contemporary San people in South Africa are usuallyt mentioned as the most basal group of humans, and the most diverse one, that split from all others ~150 ky ago (or more) and are the living proof of the richness in genetic diversity that was lost by those who trekked out of Africa.

By the way, this is the real post 1,000 ♥.

Human genetic diversity map (not sure how it was made). Source

About the image above. Interesting to see how Eastern China, Manchuria, Japan, Korea, Indochina, and Peru in South America are the least diverse! Also how African slave trade extended diversity into Brazil and European colonization into Eastern North America and parts of South America. The map is from reddit, though, so it has no references, source or hard data to back it. May be a fabrication.

However, a very recent paper published on line in Dec. 2025, in Nature, by Mattias Jakobsson et al., note that the alleles found in the modern San people are not only due to a large and stable population (large Ne), they also had an introgression from some other, unknown, group of genetically differentiated humans. The authors state that (yellow-bold highlighting is mine):

"Cumulatively, the genomes of the ancient southern Africans show that this group displays many Homo sapiens-specific variants (and variable positions) at amino acid-altering sites, also reflected among the modern-day San people. This observation cannot be explained solely by a large, stable southern African population, which retained derived variants to a greater extent compared with other groups. The ancient southern Africans were probably also isolated from other African groups for long periods. The derived variants unique to southern Africans may also signal low-to-modest gene flow from an unknown/unsampled group of genetically differentiated humans.
Genetic, anthropological and archaeological studies support an African origin of Homo sapiens, but the evolutionary process is debated based on fossils, archaeology and genetics, with Africa harbouring the greatest human genetic diversity, and southern and central African hunter-gatherer groups displaying some of the deepest diverging Homo sapiens lineages. Population stratification between southern Africa (the region south of the Zambezi River) and the rest of Africa probably existed for at least 300 thousand years (kyr), perhaps up to a million years. Such deep stratification may result from admixture with an unknown archaic African group predating the divergence of Homo sapiens from Neandertals and Denisovans, and/or from isolation from other groups.
Average population divergences between individuals representing the ancient southern African group (7 individuals with >7.2-fold genome coverage) to any other individual (ancient and modern-day western, eastern, central, northern Africans and non-Africans) were estimated to around 310–240 ka using a two-by-two site-frequency spectra approach (Supplementary Information 2.17 and Supplementary Data 15–31). Although the exact calibration of chronological population divergence-time estimates depends on model assumptions, mutation-rate assumptions and generation time, these estimates recapitulate findings in which the divergence between ancient southern Africans and all other groups captures the deepest population split-time at around 300 ka (see also Supplementary Fig. 11 for a comparison to modern-day Khoe-San individuals). This approximately 300 ka population-divergence-time estimate is not caused by a deeper partial archaic admixture event per se, but it does not negate such an event either (Supplementary Information 3.11 and Supplementary Figs. 12 and 13)."

This is something that I have mentioned several times in different posts: diversity in contemporary Africans is due to an introgression of highly divergent genes from super archaic hominins that took place recently.

The paper also attributes diversity to isolation and small subpopulations (more on this below).

Cecilia Padilla-Iglesias et al., (2025) in a paper published last May (Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution), explores the possibility of introgression and also how isolation, natural selection (adapting to local environmental challenges) and modest gene flow between separated populations shaped the contemporary highly diverse genetic makeup of Africans:

"Our results are consistent with findings that despite deep genetic divergences, there is evidence for intermittent episodes of gene-flow between all hunter-gatherer lineages. These episodes would have allowed on the one hand the emergence of adaptive cultural and phenotypic variants for local environments during periods of isolation, and on the other, the exchange of such variants during periods of connectivity. Crucially, our model highlights the vast diversity of environments in which the members of our species thrived throughout our evolutionary history, and thus, the adaptive potential of the human foraging niche.
The maintenance of viable population sizes and interconnectedness in the majority of African regions, following their initial settlement by hunter-gatherers, explains the evidence for low levels of historical inbreeding and high genetic diversity indicated by very few short runs homozygosity observed among contemporary and ancient African hunter-gatherers."

So isolation, selection, concentration of diverse alleles, and then exchange between groups shaped the current diversity, but what about archaic introgression? The paper addresses this issue too (MSA is Middle Stone Age):

"Our model reveals that West Africa, and in particular, the area around the Gulf of Guinea as well as Senegal is the region with the highest reconstructed population turnover in the continent and remains isolated for large periods of time throughout our evolutionary history, until the present. This is consistent with the finding of fossils showing very archaic features (and outside of contemporary human variation) as late as 11.2 kya (or 13 kya calibrated) in Iho Eleru, Nigeria, as well as the late persistence of MSA technologies in Saxomununya, Senegal, until a similar time well beyond their disappearance in Southern Africa, Eastern Africa and the Maghreb.
Genetic studies have shown that Southern African Stone Age hunter-gatherers (including those from our sample) despite representing the most diverged human genetic lineages, still share significantly more alleles with eastern Africans (including the present-day Dinka and Mota) than they do with present-day Western Africans (as represented by the Yoruba). These findings have been used alongside findings of some “archaic” morphological features and continued MSA industries in Western Africa in the Holocene to the presence of archaic lineages in the region that have left no direct descendants."

Survival of very old lithic technology from the MSA coupled to archaic cranial features until very recently (11-13 kya) suggests the presence of archaic hominins who surely mated with, and left their genetic imprint in, modern humans in Africa. However, the need to downplay archaic introgression as a source of diversity (God knows why!) leads the researchers to suggest another mechanism (which I didn't quite grasp), yet, they must include the admixture option (highlight, by me):

"However, another possibility leading to this pattern is that the cline of connected groups across the Eastern part of the continent (connecting Eastern and Southern Africa) was not nearly as connected to Western Africa. Our demographic reconstructions show reduced levels of East-West migration compared with East-South migration for the vast majority of evolutionary history. This, together with the fact that we were able to predict the morphological distance between the Iho Eleru specimen and the rest of cranial specimens in our sample, shows that the second scenario is sufficient to explain the observed patterns, though we do not exclude the possibility of small amounts of introgression."

Pontus Skoglund et al., (2017) note the archaic admixture, they found: "... Evidence for a divergent human lineage contributing to western Africans... The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. "

The authors then mention the hypothesis: "there has been ancient structure in the ancestry of present-day Africans... One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages" This means, archaic, or super-archaic hominins liv

Yet, when confronted with taking a stance, the authors opt for a conventional explanation: "Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals." Meaning they mixed with more recent humans, not those that predate our split with Neanderthals some 600 ky ago.

J. H. Relethford (mentioned in a recent post), wrote an article, published in Nature back in 2008, in which he discussed the "regional diversity" issue very rationally, and offering explanations for the diversity in Africa and how it is a demographic rather than a phylogenetic matter:

"The genetic evidence: regional differences in genetic diversity
Not all living human populations show the same average level of genetic variability, and these differences in present-day diversity can provide us with inferences about our evolutionary history. DNA markers typically show higher levels of genetic diversity (heterozygosity and nucleotide diversity) in sub-Saharan African populations. This observation has been made for mtDNA (Cann et al., 1987), nuclear microsatellite DNA (Relethford and Jorde, 1999) and Alu insertion markers (Watkins et al., 2001). The same observation has been made on measures of variation from phenotypic traits; within-group variances are highest in sub-Saharan African populations for both craniometric measures (Relethford and Harpending, 1994; Manica et al., 2007) and skin color (Relethford, 2000).
Why would one geographic region consistently show higher levels of genetic and phenotypic diversity? One possibility is greater time depth for the accumulation of mutations. The longer a population has been in existence, the greater the number of mutations that will accumulate. Under an African origin model, mutations would accumulate longer in Africa, as any populations dispersing out of Africa would likely be small, and the subsequent founder effect would effectively ‘reset’ the accumulation of mutations in the non-African populations. Thus, a model of an initial African origin followed by dispersals out of Africa at a later point in time would generate the regional differences in genetic and phenotypic diversity that we see today. If correct, the observation of higher African diversity supports the other genetic (and fossil) evidence for an African origin for modern humans, but does not distinguish between an African origin with replacement and an African origin with admixture outside of Africa except to say that if there was any admixture it was not of sufficient magnitude to erase the genetic signature of an African origin.
Furthermore, the fact that the model of accumulated mutations is compatible with the observed genetic data does not mean that it is correct if there are other reasonable interpretations that are also compatible. In the case of genetic diversity, another possible explanation is regional differences in population size, because expected diversity is proportionally related to effective population size. Smaller populations experience more genetic drift and are therefore lower levels of diversity. If the long-term effective population size of Africa were larger throughout most of recent human evolution, then diversity would be greater in Africa than elsewhere, again consistent with our observations of present-day variation. Analyses of craniometric data and microsatellite DNA support this hypothesis (Relethford and Harpending, 1994; Relethford and Jorde, 1999). A larger African population is also consistent with archeological and ecological inferences (Relethford, 2001b; Eller et al., 2004). If higher levels of genetic diversity in sub-Saharan Africa are due to a larger long-term effective population size, then the observation of higher diversity does not provide any resolution about the modern human origins debate. All of the models proposed to date can easily accommodate a larger African population. In this case, genetic data may be telling us more about the demographic, rather than phylogenetic, history of our species."

Again, the higher Ne size and its impact on diversity. If we add introgression and, as mentioned further up, and also isolation in separate groups that evolve due to natural selection, and then admix with each other, it is easy to see what has shaped the diversity of modern Africans.

Nevertheless, Mark Lipson et al., (2022) published in Nature about the effect of many subpopulations: "Furthermore, small subpopulations with limited gene flow could result in low ancestral effective population sizes even if the region’s total population is high. Preservation of genetic diversity through the existence of many subpopulations over long time scales could also be a contributor to the high levels of genetic diversity observed in most present-day sub-Saharan African groups." This questions the need for a high Ne!

Fred W Allendorf, Ola Hössjer, and Nils Ryman (2025) expressed it as follows: "Fragmentation into many, small subpopulations with periods of infrequent gene flow, preserves allelic variation at the expense of heterozygosity. In contrast, fragmentation into a few, large populations maintains heterozygosity at the expense of allelic variation."

The original African pre-Homo sapiens populations were small groups of hominins with little admixing which meant that they had their own unique alleles, but, being small, had lower heterozygosity. When they came together, the outcome was a larger population with higher allele diversity and the sum of all the separate heterozygosities resulting in the current African high diversity.

And, finally the backflow from Eurasia! It contributed genes that may later have been lost as humans marched across the Old World, but were reintroduced into Africa at an early date, enriching the diversity there. A paper by Christopher B. Cole, Sha Joe Zhu, Iain Mathieson, Kay Prüufer, Gerton Lunter in the Covid pandemic year of 2020, boldly stated that "We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated."

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

Mutation rate is Faster in Africa

Mutation rate, the speed at which mutations occur in the human genome plays an important role in generating diversity, and is also used as a way to calculate the dates on which different lineages split from a basal one. It also has its problems because mutations are random, and don't take place at a constant rate, which makes the molecular clock based on them, erratical and unreliable.

While researching about the diversity in African human populations, I came across research by William Amos published in 2020, with a very intriguing title: "Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in Africa", it questioned the validity of the admixture events with Neanderthals and Denisovans (I posted about this a few days ago, here), and considered it an artifact caused by the rapid rate of evoultion found in Africa:

"A model where Africans are unusually different from Neanderthals through accelerated divergence rather than non-Africans being unusually similar to Neanderthals though carrying introgressed fragments requires both a large number of back-mutations and variation mutation rate between human populations. Specifically, the mutation rate in Africa would have to have been higher than the mutation rate outside Africa since the out of Africa event, causing significantly more back-mutations in Africans. By counting triallelic sites, I show that very large numbers of back-mutations are indeed present, estimated at more than half a million...
In conclusion, I present a simple analysis that reveals an unexpected pattern in which non-zero human D statistics are unambiguously dominated by heterozygous African genotypes. These sites invariably cause the African to be less closely related to archaics and so appear to carry signatures of increased divergence from our common ancestor. More work is needed to reconcile these results with those of previous studies that conclude most non-African humans carry 1–2% archaic sequences.
Putting these elements together suggests a model where large D is driven by a higher mutation rate in Africans causing relatively greater divergence from Neanderthals. Individuals not carrying heterozygous African sites, or who carry fewer than the individual against whom they are being compared, therefore appear closer to the ancestral state and, hence, closer to related taxa such as Neanderthals."

Modern Africans have evolved since the Out of Africa event and done so at a faster rate than other Eurasian and American humans, this shows even greater "diversity" difference, and cline between Africa and the rest of the world.

Heterozygosity modulates Mutation Rates

Another paper by W. Amos (2013) suggests that heterozygosity increases mutation rates, the chart below shows how Africans with high heterozygosity in comparison to other populations, has a higher mutation rate:

Mutation rate and Heterozygosity. Fig. 1 in Source

Amos suggests that "The “heterozygote instability” (HI) hypothesis suggests that gene conversion events focused on heterozygous sites during meiosis locally increase the mutation rate... As humans left Africa they lost variability, which, if HI operates, should have reduced the mutation rate in non-Africans... For humans, HI implies a reduction in mutation rate as we left Africa with the counter-intuitive result that non-Africans will appear more closely related than Africans to other hominid lineages such as Neanderthals, a trend that has been observed and used as evidence of introgression."

Furthermore, Amos posits that HI promotes genetic diversity by favoring recombination and mutation hotspots: "Phenomena like mutation hotspots might also be seen in a different light, as should variation in recombination rate, since both are likely to some extent to be exaggerated or even caused by HI: the gene conversion-like events attracted by heterozygous sites likely in some cases to be resolved by recombination." Recombination has been shown to be linked with higher heterozygosity, and genetic diversity (Source). So, is this a self-reinforcing feedback loop with heterozygosity pushing up mutation rate which will create higher heterozygosity?

The matter had been brought up in the past by J. H. Relethford (1997), who pointed out that "Global studies of within-group genetic variation have revealed a tendency for some traits, but not all, to show higher heterozygosity in sub-Saharan African populations. Although excess African diversity has been interpreted as reflecting a greater "age" of sub-Saharan African populations, more recent research has shown that this excess is more likely a consequence of a larger African long-term effective population size... Here, I examine another possible factor: that excess African heterozygosity is in part a function of mutation rate...The results indicate that there is little excess African heterozygosity for traits with low mutation rates and greater excess heterozygosity for traits with moderate to high aggregate mutation rates."

Let's look into Relethford's suggestion:

The larger effective population or Ne is a clear driver of diversity because being large, there is risk of loss of heterozygous variants (more of them initially, and more chances of at least some carriers of them, having offspring). They also accumulate new allelles that arise due to chance mutations in the population, and there is less inbreeding.

Regarding mutation rate (μ) is seems reasonable that a population with a higher mutation rate will produce new variants. A reason for this seems to be that heterozygous loci cause Heterozygote instability during meiosis (the process during which the chromosomes split and sparate, halving their number in the gametes -sperm in men and ovum in women), this instability reduces the effectiveness of DNA repair mechanisms. Also, if mutations are related to adaptative benefits, selection will promote them.

In a population that is in equilibrium there is a formula that calculates the average expected heterozygosity "H". It involves the following terms: the neutral mutation rate or μ, and the effective population size or Ne (Source).

H = 4Ne μ / (4⁢Ne μ +1)

I calculated values of heterozygosity (y-axis) for different Ne sizes (x-axis) for two mutation rates, 10^-5 and twice that value (2*10^-5), the graph below shows the outcomes:

H as a function of Ne for two different μ values. Copyright © 2026 by Austin Whittall

As Ne increases, so does heterozygosity. But, with a same effective population size and a higher mutation rate, H increases too! Africans with a higher mutation rate (μ) would have increased their heterozygosity due to that effect alone, compared to slower mutating Eurasians.

Finally, a very interesting paper by Amos, Flint, and Xu (2008). states that "our analysis suggests that a feedback loop can operate causing heterozygosity to increase over time, each increase also increasing the mutation rate which in turn raises heterozygosity." Could this have happened, and still ocurr in Africa?

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

On the diversity of Native American genes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Comments

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

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

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

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

Not he usual "Out of Africa" cline

A paper (Hai et al., 2012) [1] analized a very special and unconventional gene, miR-941, it immediately drew my attention because it goes against the usual decreasing gradient of variability from Africa outwards, which shows lower variability in the fringe regions that are further away from our purported Eden in Africa. This post will look into this oddity and its implications.

microRNAs or miRNA

Genes usually are in charge of producing proteins or RNA strands (i.e. tRNA) that in turn interact with gene expression pathways. But this is not the case with micro RNAs (miRNAs) which have very important roles in gene expression. miRNAs are short single-strands of RNA (20 to 24 nucleotides long), hence the name "micro".

The appearance of a new miRNA can impact on the expression of hundreds of genes, so for this reason, the the authors of the paper [1] set out to detect a human-specific miRNA and then tried to figure out its evolution and impact on modern humans. They sought microRNAs (miRNAs) specific to the human genome.

The older (archaic or more ancient) miRNAs tend to have higher expression levels than those that have appeared more recently, and a survey of several human-specific miRNA showed just that: low expression levels, a sure signal that they are quite recent. But there was an exception: miR-941 which was found in the human brain at very high expression levels, higher than other miRNAs found in humans and primates.

miR-941

More interesting was the fact that its expression was absent in macaques and chimpanzees showing that it evolved in the hominid line after we split from the chimps some 6 million years ago (Mya). Its upper limit is given by Denisovans, who do also carried it, and this split took place about 1 Mya. So the miR-941 evolved in our hominin ancestrors between 6 and 1 Mya.

What is exciting is the fact that it interacts with our brains, and the human intellect began to evolve during that time span: the "Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling." [1] it is active in the cerebellum and the prefrontal cortex, which are two processing regions within our brains.

The media hyped up this paper based on its role as "making us human" and its impact on our brain-power, but, as we will see below its role is much deeper than that.

The paper suggests that our extended life span and a higher tendency to developing cancer (compared to chimpanzees and macaques) is probably due to this microRNA. So we should thank miR-941 not only our higher reasoning abilities but also our unusually long life span (yes, cancer is a terrible collateral effect). The authors put it this way:

"It is, therefore, appealing to speculate that emergence of miR-941 enhanced the maintenance of adult stem cell populations, thus supporting longer human lifespan, but rendering human cells more prone to malignant transformation. The role of miR-941 in the regulation of insulin signaling adds support to this notion. The insulin-signaling pathway was consistently implicated in lifespan regulation in many species, including humans. Notably, experimentally verified targets of miR-941 within this pathway include genes directly shown to be involved in lifespan extension in model organisms: IRS1, PPARGC1A and FOXO140 (ref. 40). Furthermore, FOXO1 was linked to extended human longevity." [1]

Not the usual cline though

Unlike many genetic markers which show a high diversity in Africa and then a decreasing gradient as you move away from our purported homeland, miR-941 shows quite a different picture:

Although it is found in all humans, the number of precursor copy-number, or repeats is quite variable: it ranges from 2 to 11 copies. This variaton is linked to geographical location too. Although there is a clear indication that the usual decreasing cline is not present in miR-941, orthodoxy compels the authors to affirm that there is a higher African variability and a West to East cline!:

"The average pre-miR-941 copy number decreased from the west to the east: from eight copies in sub-Saharan Africans to six copies in Eastern Asians. miR-941 precursor copy number variation was also significantly higher in sub-Saharan Africans compared with 'out of Africa' populations, with the exception of Oceanians and native Americans
[modern human carry] 2–11 copies of miR-941 precursor, with an average of 8 copies found in sub-Saharian Africa, an average of 7 copies in Europe, America, Oceania and most of Asia, and an average of 6 copies in East Asia." [1]

Look at the figure below (from [1]) and make up your own mind; it shows miR-941 precursor copy repeats in different populations:

The upper part of the image (c) shows that the variability is highest among South American Karitiana (5 to 9 counts), Papuans and Palestinians (4 to 7) folllowed by San (6 to 9). In other words, it is not higest among Sub-Saharan Aficans!

In the case of the Amerindians, it is a surprising find since they are, according to orthodoxy, supposedly a bottleneck population "lacking the diversity of the Africans" , the other Eurasian people -purported ancestors of the American Natives have less variability than Amerindians.

Part d reflects this, showing the average of each region with the highest count numbers in Oceania, Africa and among Native Americans. All other populations have a lower count.

The Variance (in part e) clearly shows the highest variances in Africans and Native Americans. This does not depict a west - east cline, actually it drops off in the middle and grows again as you move on east.

This is clearly at odds with the accepted notion that diversity drops off with distance to Africa, with the New World populations being the less diverse! The authors actually state this mainstream notion in their abstract: "... shows a trend for decreasing copy-number with migration out of Africa" [1] which is not what the facts in their paper shows. (preconceptions are so hard to erase aren't they?).

So even though the main text shows that diversity drops in Eurasia but increases in Oceania and America the authors overlook it and don't even try to seek an explanation for it.

Speculations and Copy-number variation (CNV)

The paper points avoids controversy and does not analyse the significanse of the different Copy-numbers, it merely points out that a different amount of repeats "is not unexpected, given general instability of genomic regions formed by tandem repeats" [1].

But it is not chance that is at play here but natural selection the authors point out tha when a new miRNA appears (obviously its initial appearance is due to chance), it may wreak havoc in the established network due to negative changes in gene expression. So the forces in natural selection would quickly get rid of it or modify the binding sites that produce negative effects. In the case of miR-941, since it was not eliminated, what changed were its binding sites, which were lost.

So if Amerindians have a higher Copy-number variation (CNV), there must be a selective pressure at work. Actually this is the case:

"The "high-degree of copy-number variation (CNV) ... among contemporary human ethnic populations, suggest[s] a high degree of functional variability even among humans. New cell biological funcions acquired because of the appearance of mR-941, for example, new controls over sonic hedgehog and insulin-signaling pathways (Hu et al., 2012), are likely to be important as CNV-dependent determinants of human-specific adaptations to the environment and to disease." [2]

In other words, CNV is important and should not be overlooked.

It is clear that Amerindians and Papuans have a wide range of CNV than Europeans or Asians, and comparable to those of Africans. Yet they are always depicted a population that originated from a founder effect and later went through a bottle neck which reduced its genetic diversity even further. Why is CNV higher among them?

I am at a loss to explain this, but it the high CNV in Oceanians and American natives is a well known phenomenon, and is an incongruity that is explained away as a sampling bias! [3]:

"higher-frequency CNVs were more common especially in Oceania and the Americas... in contrast with their usual reduced variation, populations from Oceania and the Americas had more CNV loci and more previously unobserved loci than most other populations." [3]

The authors try to explain this anomaly as due to "some bias may exist in CNV detection" and go into an elaborate explanation on sampling. Then they simply ignore this large variability in CNVs compared to the usual Out of Africa cline of decreasing diversity and conclude that: [3]

"despite a difference from SNPs in the frequency spectrum of the copy-number-variants (CNVs) detected - including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas- the global distribution of CNVs largely accords with population analyses for SNP data sets of similar size..." [3]

The image below, from [3] actually shows the opposite (peaks in America, Oceania and the Kalash -from Pakistan):

Since African CNV is low, it shows that the high CNV in the Americas is not due to admixture with Africans brought to the New World as slaves. It is due to another cause.

So why do Papuans and Amerindians have a higer CNV diversity?

CNVs can have a negative effect on health and provoke diseases (these will tend to be selected against as the carriers will have a burden which may impede them from having children). Other CNVs have a positive effect and may protect the carrier against disease and "other copy number variants carried by healthy individuals that seem to have no function might actually be evolutionarily retained in populations if they provide a selective advantage." [5]

Could the American and Oceanian variety in CNVs be due to the forces of natural selection retaining CNVs that have been lost by other populations?

Or did they receive these variants from other archaic populations that lived in these areas and admixed with them, receiving these extra CNVs which conferred them a selective advantage?

If so, then the archaic people were already living in America and Sahul when humans reached those regions.

More on the decreasing diverstity myth

When a population with a given diversity (Population A in the image above; diversity is shown by the different colored circles) splits and a sub-population (Population B) moves away, -shown in stage 1- diversity will decrease. In this case we took B as having the same mix as A, but it could have been different, reducing diversity even further (see Population C for instance). The smaller population is more prone to genetic drift which reduces diversity and will also be less likely to evolve new mutations as its size is smaller. It will also be subject to the risk of extinction or loss due to natural calamities than a larger population spread out over a wider territory. So even if the migrating group grows at the same pace as the original population (stages 2 and 3), the outcome will be a reduced diversity.

The acepted theory suggests that variation within a population is proportional only to n (the effective population size) and μ (the mutation rate) which should be the same across all human groups (is it?). [4] So size influences variation: bigger sizes, more variation. Which makes me ask (as an explanation to the higher CNV observed in the New World and Sahul): Did America and Oceania have a larger population in the past which later became extinct? Well, we know that the Americas suffered a devastating impact after its discovery by Europeans in 1492: its population was decimated and its diversity plummeted. Did something simila happen in Oceania? Probably not, as an Old World population they were well adapted to Old World diseases.

Another factor is that, before mutation-drift equilibrium is reached, the age of a population influences its diversity: older populations accumulate more variations. So could the observed CNV diversity be due to an early peopling of America or Oceania by one of our ancestors (Homo erectus? Neanderthal? Denisovans?). This would extend the timeline well beyond the accepted 50 kya for the OoA event or the 15 kya for the peopling of America and allow for diversity to develop.

And, as a closing grand finale look at these two images from Seielstad et al., (1999) [4], which also depict a close relationship between Africans and Americans instead of the usual "decreasing gradient away from Africa":

Yes, the paper (which looks into Y chromosome STR diversity), dates back to 1999 and its figures are extremely unsual but the paper nevertheless echoes the well known mantra of orthodoxy:

"A recent African origin for all humans is supported by a robust corpus of evidence. This evidence takes three major tracks: (1) increased genetic diversity in Africa versus the rest of the world, (2) phylogenetic analyses placing the deepest branches between African and non-African populations, and (3) indications that the age of the “genetic most recent common ancestor” is very young. The Y chromosome, like mtDNA and the autosomes, appears to support a recent African origin." [4]

Sources

[1] Hai Yang Hu, et al., (2012). Evolution of the human-specific microRNA miR-941. Nature Communications 3, Article number: 1145 doi:10.1038/ncomms2146
[2] Antonio Noronha, Changhai Cui, Robert Adron Harris, John C. Crabbe, editors. (2014). Neurobiology of Alcohol Dependence. Elsevier, May 2, 2014. pp 500
[3] Mattias Jakobsson et al., (2008) Genotype, haplotype and copy-number variation in worldwide human populations. vol. 451 doi:10.1038/nature06742
[4] Mark Seielstad, Endashaw Bekele, Muntaser Ibrahim, Amadou Touré, and Mamadou Traoré, (1999). A View of Modern Human Origins from Y Chromosome Microsatellite Variation. Genome Res. Jun 1999; 9(6): 558–567.
[5] Lobo, I. (2008) Copy number variation and genetic disease. Nature Education 1(1):65

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