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 © 

Neutral Theory of Genetic Evolution and Out Of Africa

The main backing for the Out of Africa theory is the Genetic Neutrality Theory.

The arguments of an African origin of modern humans and our dispersal across the globe is supported by the high genetic diversity found in modern African populations, with lower diversity elsewhere, and a gradient or cline in diversity that reflects less diversity as distance to the African homeland increases. Both of these factors are expected according to the Neutrality Theory.

Starting with a highly diverse population, if a small group from that population migrates (into Eurasia), it can only feasibly carry with it a sub-sample of the original diversity. This is known as a Founder Effect, the founders of a new population carry fewer genes than the population from which they split from.

This happened time and time again, as sub-sub-groups split from the main population and moved into Europe, Eastern, Northern, and Southern Asia, Melanesia, Australia, Polynesia, and across North America, and then, into South America.

The Neutral Theory states that each split reduces genetic diversity.

Genetic Heterozygosity

Heterozygosity is a measure of diversity. Each person receives genes from their parents, that code for different proteins and produce traits. Those who have two different varriants (alleles) of a specific gene, one inherited from each parent are heterozygous. If the alleles are identical, they are homozygous.

The image below shows two parents (both are heterozygous) each carrying two different variants A and a. The probability for passing them on to the next generation is simple there are four possible combinations, each has a 25% probability of occurring:

Hetero and Homozygosity. Copyright © 2026 by Austin Whittall

The chances are that two of the offspring will carry Aa alleles, and will therefore be heterozygous, while the other two will receive the same allele from each parent and be either AA or aa, carrying two identical copies. This makes them homozygous.

As we can see, a population that is 100% heterozygous as become 50% homozygous and 50% heterozygous. All the possible combinations of those homozygous and heterozygous genes are shown below:

Combinations of alleles. Copyright © 2026 by Austin Whittall

As you can see 25% of each variant (AA, aa, Aa, and aA). So why would heterozygosity decrease? Suppose only aa homozygous couples mate, the chance of this happening is 1 in 16, or AA mate, again, 1 in 16. So 2:16 or, 1:8 chance of only homozygous mating and offspring. But... if these offspring meet and mate aa with AA, they would have a 100% heterozygous descent. This is true for large populations, but for smaller groups the founder effects and bottlenecks can reduce the allele diversity.

Genetic Bottlenecks

The argument of loss of heterozygosity, or its equivalent, increase in homozygosity is based on genetic bottlenecks, where a small sub-population splits and carries with it the homozygous variant, say only aa or only AA. Losing the possibility of reintroducing the lost allelle. This is a 1 in 16 chance.

Other causes of heterozygosity loss are natural catastrophes, war, and disease. But, why would such events affect the heterozygous individuals more than the homozygous. Wouldn't they be random, and therefore have an equal chance of impacting on hetero- and homozygous individuals?

Regarding the root population. There is the chance that the root from which a population split off from suffered some event that eliminated a large swath of it, while the migrating sub-population in another geographic location was not affected by it. Wouldn't that lower the heterozygosity of the basal group and make the sub-population appear as "enriched"?

Genetic Drift

Both Founder effect and Bottlenecks are part of process called Genetic Drift. As we saw, genetic drift takes place when random events, by chance modify which alleles passed on by parents to their offspring. They also include not only non-reproduction of certain individuals due to war, disease, natural catastrophes, but also loss of genetic variation due to people who don't reproduce because they die before mating, choose not to do so, etc. Genetic Drift isn't driven by evolution. The random changes may or may nor provide adaptations to a changing environment, so they may or not be acted upon by the forces of natural selection.

A sub-population may lose certain alleles, or others may become Fixed reaching a 100% frequency in the population due to chance events.

Mutations and Natural Selection

Random mutations take place, and modify the alleles, natural selection may also work, favoring the survival of individuals with alleles that provide adaptative benefits.

But, what about mutations, that happen by chance, that have a deleterious effect? Some mutations may have harmful consequences. The Neutral theory says that some deleterious mutations may rise to high frequencies in small populations due to fixation promoted by genetic drift. But, why wouldn't people carrying unfavorable genes be affected by natural selection, causing them and their descent to die out?

The Neutral Theory of Molecular Evolution

It was the creation of Motoo Kimura, who in 1968 proposed that at a molecular level, mutations are caused by random genetic drift. These mutations are neutral from a selective point of view. They aren't affected by natural selection.

Kimura has been criticized, for instance Kern and Hahn (2018), argue that modern, genome-scale data demonstrates far more evidence of adaptive evolution than the neutral theory allows, suggesting that natural selection (both positive and negative) shapes much of the genome.

As mutations take place by chance, the probability of them being neutral, deleterious, or beneficial would seem equivalent. So, why assume they are neutral? A beneficial mutation even if it is rare would confer an evolutionary advantage for those carrying it, and modify the population beyond what neutral models suggest.

Linked Selection. The loci (or addresses) that mark the location (locus) of a gene in our DNA isn't independent and isolated. Some genes or DNA sequences located close together on the same chromosome are inherited together, as a unit, during meiosis (linked chromosomes).

Selective Sweep is when an allele that improves the fitness of its carrier increases in frequency due to natural selection, is accompanied (hitchhiking) by other genes linked to it by physical proximity on the DNA strand are also increased in frequency even though they may be neutral. Finally, Background Selection is similar and has the opposite effect: deleterious alleles are removed by natural selection and neighboring neutral alleles are lost too, due to physical proximity to the harmful variants.

These examples show that "neutrality" is not necessarily true.

Molecular Clock

Kimura's theory states that neutral mutations took place at a constant speed, accumulating over time at the same pace. However, this is not true.

However mutations don't appear in a uniform manner in all loci along the genome, they arise unequally, and the probability of fixation depends on where they arise in the genome. This modifies how the clock ticks (Source). Furthermore, substitutions depend on population size, and generation overlap (Source).

Generation time is also an important factor: is it 20 or 30 years? 25? or 18? Over 10,000 generations this means a time scale that can vary from 180,000 to 300,000 years!

Back-Mutations and Recurrence Not Allowed

Kimura's theory, at least when applied in practice, has three axioms that are not true:

1. Infinite sites, it assumes that each mutation takes place at a site that has never mutated before.
2. No back-mutations, changes happen in one direction A → G. Which will never again flip back G → A
3. No Recurrence, in practice there are multiple mutations that take place at the same site. The neutral theory does not accept it, there can't be multiple mutations at identical loci in different lineages.

A paper gives a great example of why and how a back-mutation can have positive effects (here showing how a base C = Cytosine mutates to T = Thymine and back):

"...simple back-mutation is expected to generate slightly advantageous mutations. For example, let us imagine that a site is fixed for C, and that a new T mutation occurs that is slightly deleterious with a disadvantage of −s. Let us imagine that this T mutation spreads through the population and becomes fixed. If a new C mutation then occurs at this site, it will be slightly advantageous with an advantage of +s, unless the relative fitnesses of the C and T alleles have changed. Such a change in fitness could occur because of a change in the environment or the fixation of mutations at other sites which have epistatic interactions with the alleles at a site of interest."

Americas: Great Dying

Regarding Amerindian diversity, we know that up to 90%, or more, of the Native Americans died during the century that followed European "discovery". Disease, war, famine, social disruption, force labor, etc. killed tens of millions of Amerindians. Lineages died out, massively. This is the unique and most massive genocide (albeit unplanned) in the history of humanity. How can we know the number of unique, diverse, divergent alleles that were wiped out during this event? In 1491, America probably presented a far more diverse genetic structure than it does now.

And this brings us to the other point: African "diversity".

African Diversity... is it real?

Finally, and this will be the subject of a future post, do modern Africans reflect the genetic makeup of ancient Africa 100,000 or 75,000 years ago? Is a modern Nigerian, Gambian, Angolan African representative of the ancient population from which the Out of Africa migrants split? Have other events taken place within Africa, isolated from the sub-population that migrated into Eurasia? Admixture with archaic hominins after the OOA event, admixture between many separate and formerly isolated hunter gatherer sub-populations could have led to a modern highly diverse African population, while the original OOA root was far less diverse.

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

Heterozygosity for dummies

Heterozygosity is lower in all non-Africans when compared to Africans.

What does this mean?

First of all what is Hetrerozygosity?

Heterozygosity

We all have two copies of each gene. That is because we got half of our chromosomes (with their respective genes) from each of our parents), making one copy from each of them.

Genes come in different variants, known as alleles.

So if there are two possible alleles: "b" and "B" (one per gene) you may have any of the following combinations arising from the mixing of your parent's genes

• bb
• bB
• Bb
• BB

That is four options, two in which each gene has the same allele (bb, BB) and therefore you are Homozygous and two in which you have different alleles (bB, Bb) which makes you Heterozygous.

It is evident that homozygosity implies less genetic variability (being BB you lack the "b" allele or if you are bb, you will lack the "B" allele). And this may have consequences regarding your health and surviveability.

Populations.

We must also take into account that the proportion of "b" and "B" in can be different, in other words they are present at different frequencies: "p" and "q" respectively which are not necessarily the same.

In other words the frequency of each genotype (bb, Bb, or BB) in a given population (known as "allele frequency") will depend on the frequencies of each allele:

In a very large (infinte) population where individuals mate at random, we can calculate the allele frequency using the Hardy-Weinberg Theorem using this formula to calculate the frequencies (f) of each of the three genotypes (bb, BB, Bb):

• f(bb) = p²
• f(bB) = 2pq
• f(BB) = q²

And since they are "all" the genotypes, their sum must add up to 100% of the populaton:

100% = p² + 2(pq) +q²

Say b is present at p = 30% and B has a frequency of q= 70% (both frequencies must aldo add up to 100%), then:

100% = (30%)² + 2(30% x 70%) + 70%²

100% = 9% + 42% + 49%

So the frequency of bb alleles is only 9% meaning that 9% of the population is homozygous for b. 42% is heterozygous and 49% is homozygous for B.

But in a real world, humans don't mate randomly: they choose partners for different reasons, or, due to cultural rules may marry within their group (endogamy).

Also some homozygous alleles may cause genetic diseases such as cystic fibrosis, Tay-Sachs or phenylketonuria which may kill individuals before they become adults and reproduce, here selection is actively working to modify zygosity.

As populations are not infinte but finite, there is not an endless genetic pool, but a discrete one so in smaller or isolated populations, heterozygosity will fall due to random events (imagine adults that have no offspring, eliminating their alleles from the genetic pool).

The opposite effect is when two isolated populations admix, adding new alleles to the gene pool, increasing heterozygosity.

So, the factors that provoke homozygosity are:

• Inbreeding
• Geographic isolation
• Genetic Drift
• Cultural practices -i.e. consanguineous marriage or endogamy
• Positive evolutionary selection

It can fall, on the other hand if there is an isolation-breaking event such as the mixing of two previously isolated populations.

Let's take a look at each of these factors:

1. Interbreeding

The taboos that forbid marrying your next of kin have a genetic basis: those closely related to you will carry many genes identical to yours. Since relatives share alleles, inbreeding will bring together identical copies of an allele more frequently than breeding between unrelated mates, and this increases homozygosity:

"F", the Inbreeding coefficient is the probability that two alleles are identical copies of an allele from a common ancestor. It is also, the proportion of the population that is inbred (having two alleles identical by descent).

We can take the expression used above and adapt it to calculate the frequencies of alleles in an inbred population:

• f(bb) = p²+2Fpq
• f(bB) = 2pq (1-F)
• f(BB) = q²+Fpq

All must add up to 100% of the population.

So if inbreeding coefficient is 20%, the relative frequencies of bb, BB and Bb would be (we will use the same frequencies as in the original example: b is present at p = 30% and B has a frequency of q= 70%):

100% = (30%)² +2 x 20% x 30% x 70% + 2(30% x 70%)(1-20%) + 70%² +2 x 20% x 30% x 70%

100% = 13,2% + 33,6% + 53,3%

So the comparison is:

• bb increases from 9% to 13.2% of the population
• BB increases from 49% to 53.3% of the population
• Bb falls from 42% to 33.6% of the individuals

Heterozygosity drops due to inbreeding even though the same alleles are present.

Since some genetic traits are recessive, and manifest themselves only when the two alleles are present, that is, homozygosity for those alleles is present, inbreeding increases the frequency of these recessive traits, which could be as benign as blue vs. dark eyes or nasty as congenital diseases.

Genetic drift

Imagine a population which starts off with p = q = 50%. In other words, the proportion of B and b is identical. Applying Hardy-Weinberg Theorem we can calculate the genotype frequencies:

100% = (50%)² + 2(50% x 50%) + 50%²

100% = 25% + 50% + 25%

So50% are heterozygous (Bb) while the other half is equally homozygous: 25% are BB and 25% are bb.

But this is in an infinte population and also, the frequencies p and q are probabilities.

Real life may reflect these probabilities in a different way. Look at it this way: when you flip a fair coin there is an equal chance (p=50%) of getting heads and or tails (q=50%). But in practice we all know that you could throw 3 heads in a row and get only 2 tails in a series of five tosses. Which is not a 50 ⁄ 50 proportion. it is 66% ⁄ 40%. You may even get 3 heads in a row in a series of 3 tosses (100 ⁄ 0).

So in small series it is unlikely that the actual real frequency is close to the theoretical probability (p or q).

However, when you use larger series, for instance if you tossed the coin 1,000 times, the ratio would be closer to 50 ⁄ 50 (say 494 tails and 506 heads).

This same effect applies to the probability frequencies in small populations: two heterozygous parents (bB) could have all four offspring that are homozygous (bb) just by chance.

So, in small populations this phenomenon known as "Genetic drift" just by random forces -not by natural selection or deliberate interbreeding- can change the frequency of some alleles in very short time, making them extremely common ("Fixing them") or making them disappear.

Founder Effect

Founder events take place when a small sub-population of a larger one migrates and establishes a new settlement (hence "founder" population). It is obvious that not all the alleles present in the original population will be present in this smaller group. Those left behind will not appear in the new one, this reduces the total quantity or "allele richness" of the new subpopulation.

Liken it to randomly taking 4 M&M's from a bag holding 500 candies, it is probable that you will not pick all the available colors. So if the M&Ms in the bag are red, yellow, green, blue and brown in equal proportions, you could very well have picked: 2 yellow, 1 green, 1 red and no brown or blue candies. So this does in effect reduce the "diversity" or "richness" in the subpopulation but, it may not impact on heterozygosity:

Imagine the population we mentioned befor where 9% were homozygous for b (bb), 42% were heterozygous (Bb) and 49% were homozygous for B (BB). Now lets imagine that a small group from this original one forms a colony elsewhere, and just by chance, 60% of the individuals carry the Bb heterozygosity, while the remaining 40% are BB homozygous.

This new subpopulation will therefore have a higher heterozygosity than the original population (60% vs. 49%), but it will surely be less rich or diverse due to the alleles left behind (M&M analogy).

Founder effect impacts on the "allelic richness" by reducing it but it may no have much effect on hetrerozygosity. This is because the richness is based on the presence of the alleles and not on the internal diversity within them. A rare allele lost during a founder effect reduces the diversity but will probably have little impact on heterozygosity.

Bottleneck

This is a drastic reduction in a population. It could be caused by disease or a natural catastrophe (drought, volcanic eruption, fire, Ice Age, global warming).

Those that survive will carry only part of the genetic diversity of the original population, as those lineages that perished, are gone forever. But this does not mean that heterozygosity drops. Actually, allelic richness falls faster than heterozygosity because bottlenecks usually wipe out ,any low-frequency alleles and this causes an excess of heterozygosity in selectively neutral loci compared to normal populations subjected to genetic drift.

Leberg (1992) investigated loss of heterozygosity and allelic variation experimenting with mosquitofish and found that a decrease in heterozygosity only happens when the bottleneck is extreme and prolonged.

Selection

After the population reduction in founder effects or Bottlenecks & Geographic Isolation (which may also lead to inbreeding due to the smaller population), diversity will increase again due to chance mutations.

Another factor that may modify the genetic patterns is Natural Selection: the bottleneck may have caused the fittest to survive -imagine a disease that those equipped with some genetic advantage manage to survive while the others perish- and therefore selection increases the frequency of certain genes in the new population, when compared to the pre-bottleneck one.

Geographic Isolation

Similar to Bottlenecks, it is the separation of one group from the main population, as when there is a founder event.

Heterozygosity and Human Evolution

So when defenders of the "Out of Africa" theory use heterozygosity to support an African origin for Mankind, they point out that Africans have the highest heterozygosity of all human populations: the others (non-Africans) have lost it as they migrated out of Africa in small bands (founder effect), separated widely (geographic isolation), were more prone to fall prey to natural catastrophe (bottle necks), inbred more frequently as they were smaller populations and in doing so lost heterozygosity which the original basal population in Africa retained.

An example of this is shown in the image below which charts "heterozygosity vs. distance from Africa (Addis Ababa)" (from [1]):

This chart from [5] show more or less the same information:

Allelic Diversity

Having said this, we must point out that "Genetic Diversity" is not only measured by heterozygosity but also by the "number of alleles" present in a given population, that is "allele richness" or "allelic diversity" which is calculated as the average number of alleles per locus.

In other words a population may have a high heterozygosity compared to another and supposedly be "more diverse" but, overall have a lower number of alleles which makes it definitively "less diverse".

An example of this paradox is shown in this paper (Begoña Martínez-Cruz et al., In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations [1]) which has interesting data in its Table 2 which shows the "Average AR" - allelic richness- and "expected heterozygosity He" for each of the 26 Central Asian populations and other nearby regions:

AR He   Population
12.66 0.819 Central/South Asia
 8.60 0.820 Central Asia - TJK
 8.50 0.812 Central Asia - TJT
 8.50 0.774 Central Asia - UZB

The first two have the same He (heterozygosity) of around 0.82 but notably different allelic diversity (12.66 vs 8.60). The last two have the same allelic diversity (8.5) but different He (0.812 vs. 0.774).

Populations can have a richer genome despite having a lower heterozygosity, of course they could have mutated faster than another population and therefore increased the diversity in their genome adding new variants.

Does this mean higher heterozygosity in Africa mean that it is the cradle of humanity?

It means that heterozygosity is higher there. Just look at the archaic hominins, Neanderthals and Denisovans. Their heterozygosity is far lower than that of any extant human group, but we know that they predate Homo sapiens by several hundreds of thousands of years. They are less heterozygous but older and ancestral:

Prüfer et al. paper on Neanderthals [3] confirms this (highlighted in bold):

"The Neanderthal autosomal genome carries 1.7–1.8 heterozygous sites per 10,000?bp (Supplementary Information section 9). This is 84% of the number of heterozygous sites in the Denisovan genome, 22–30% of that in present-day non-African genomes, and 16–18% of that in present-day African genomes (Extended Data Fig. 1). When regions of homozygosity longer than 2.5?cM stemming from recent as well as long-term inbreeding in the Neanderthal are removed, 2.1–2.2 sites per 10,000 are heterozygous, similar to what is observed in the Denisovan genome. Thus, heterozygosity in Neanderthals as well as Denisovans appears to have been lower than in present-day humans and is among the lowest measured for any organism" [3]

Another paper by Meyer et al. on Denisovans [4] found the same diminshed heterozygosity:

"Denisovan genetic diversity. The high quality of the Denisovan genome allowed us to measure its heterozygosity, i.e., the fraction of nucleotide sites that are different between a person's maternal and paternal genomes (Fig. 5A). Several methods indicate that the Denisovan heterozygosity is about 0.022%. This is ~20% of the heterozygosity seen in the Africans, ~26 to 33% of that in the Eurasians, and 36% of that in the Karitiana, a South American population with extremely low heterozygosity. Because we find no evidence for unusually long stretches of homozygosity in the Denisovan genome, this is not due to inbreeding among the immediate ancestors of the Denisovan individual. We thus conclude that the genetic diversity of the population to which the Denisovan individual belonged was very low compared with that of present-day humans." [4]

This leads me to ask, what if African heterozygosity was enriched by recent admixture with other hominins in Africa? an inflow of different relic alleles elevated African diversity above that of non-Africans. Could current lower Amerindian heterozygosity reflect an ancient population just like that of Denisovans or Neanderthals?

We will look into these questions in my next post when we go over some recent papers on the possibility of an ancient Out of Africa event whose genes ended up in contemporary Papuans and Australians.

Sources

[1] Begoña Martínez-Cruz, Renaud Vitalis, Laure Ségurel, Frédéric Austerlitz, Myriam Georges, Sylvain Théry, Lluis Quintana-Murci, Tatyana Hegay, Almaz Aldashev, Firuza Nasyrova and Evelyne Heyer, In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations, European Journal of Human Genetics (2011) 19, 216–223; doi:10.1038/ejhg.2010.153; published online 8 September 2010.
[2] Paul Verdu, Trevor J. Pemberton, Romain Laurent, Brian M. Kemp, Angelica Gonzalez-Oliver, Clara Gorodezky, Cris E. Hughes, Milena R. Shattuck, Barbara Petzelt, Joycelynn Mitchell, Harold Harry, Theresa William, Rosita Worl, Ripan S. Malhi Patterns of Admixture and Population Structure in Native Populations of Northwest North America, PLOS Published: August 14, 2014 http://dx.doi.org/10.1371/journal.pgen.1004530
[3] Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H. Sudmant, Cesare de Filippo, Heng Li, Swapan Mallick, Michael Dannemann, Qiaomei Fu, Martin Kircher, Martin Kuhlwilm, Michael Lachmann, Matthias Meyer, Matthias Ongyerth, Michael Siebauer, Christoph Theunert, Arti Tandon, Priya Moorjani, Joseph Pickrell, James C. Mullikin et al., The complete genome sequence of a Neanderthal from the Altai Mountains, Nature 505, 43–49 (02 January 2014) doi:10.1038/nature12886
[4] Matthias Meyer et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual, www.sciencemag.org SCIENCE VOL 338 12 Oct 2012
[5] Keith Hunley, Claire Bowern, Meghan Healy, Rejection of a serial founder effects model of genetic and linguistic coevolution, Published 1 February 2012.DOI: 10.1098/rspb.2011.2296

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