Petralona: Neanderthals and Homo heidelbergensis coexisted 300 ky ago

The famous skull found in Petralona, close to Thessaloniki, Greece in a cave now known as "the Mausoleum", back in 1960. It was encrusted and cemented to the cave's wall with calcite, a mineral that precipitates from mineral-rich water in caves; it is known for shaping stalactites and stalagmites. Its age was unknown. But it was dated by C. Falguerès et al., (2025) who published a paper on it last September.

The paper reports how the team managed to date the skull: "the Petralona cranium has a minimum age of 286 ± 9 ka." This research also places it in our ancestral tree: "From a morphological point of view, the Petralona hominin forms part of a distinct and more primitive group than Homo sapiens and Neanderthals, and the new age estimate provides further support for the coexistence of this population alongside the evolving Neanderthal lineage in the later Middle Pleistocene of Europe."

The skull belongs to a more primitive group of hominins, older than Neanderthals and our species. The age of the sample shows that it coexisted with Neanderthals in Europe, alongside Neanderthals well into the Mid Pleistocene Period.

Petralona Skull.

This finding is important because it shows that human evolution is more complex than imagined. There were different kinds of of humans alive, coexisting, across the globe 300 ky ago: Denisovans, Anatomically Modern Humans, Neanderthals, and now, Homo heidelbergensis, and probably more. They surely met, exchanged sex, and know-how, shaping our evolution.

Linar trees with a single Neanderthal - Human split in Africa 600 ky ago, and simple models with unique, singular admixture events as proposed by certain models don't seem to accurately reflect the population dynamics that was going on in the Old World (and who knows, perhaps also in America), 300,000 years ago.

In a future post we will look into the validity of these trees and their shortcomings according to statistician and geneticist Alan R. Templeton.

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

Back Mutations are common & more frequent than previously stated

Reversions, also known as back mutations are considered rare in biology. Basically, what it means is an initial mutation in the geneome, reverses back to its original (wild-type) form through a second mutation that restores the base in the DNA sequence.

For example, a "chunk" of DNA could contain the following bases: ACGCTG and, a random, chance mutation replaces the cytosine (C) for an adenine (A) ACGATG and a second mutation restores (reverses) the original situation ACGCTG.

This has important consequences, first of all, if we look at the ancient sample and the most recent one, there is no way we will ever know that it mutated and reverse by back-mutating, (both have the same sequence: ACGATG so how can we know if there was a back and forth flip in between both samples?)... unless we find an sample of someone in the same line, or a parallel lineage with the first (derived) mutation, but not the reversion,which seems a very unlikely situation.

Assuming that all mutations are forward oriented and never reverse, may overlook mutations that were reversed. Since coalescence time and dates of lineage splits are based on mutations, if we overlook the reversions, we will miss out on the actual mutations (to and fro), counting zero when in fact there were two mutations.

So we will assume that mutation rates are lower than they really are by missing out these back-and-forth mutations.

If we overlook reversions we will assume there were only n mutations per a given amount of years, while there were actually m mutations: "n" that we see (for instance, there is a G instead of an A at a certain locus), and "p" mutations that flipped forth and another "p" that flipped back. n is therefore smaller than m; m = n+2p. So the mutation rate is higher than assumed.

However, the Neutral Theory of genetic evolution does not consider this alternative, it requires No back-mutations. Changes can only happen in one direction A → G. Which will never again flip back G → A, and No Recurrence there can't be multiple mutations at identical loci in different lineages.

Are they Common?

William Amos (2020) suggests that "back-mutations are far commoner than has been previously assumed" he adds that "Back-mutations are ‘silent' because they create the original ancestral allele, but can reasonably be assumed to occur about twice as often as triallelic SNPs are generated (two transitions are approximately twice as likely as one transition and one transversion). Triallelic SNPs are coded ‘MULTI-ALLELIC' rather than ‘SNP' in the 1000 genome data and are often ignored, but I counted 257,827 occurrences across all autosomes, implying over half a million sites carrying back-mutations. Moreover, this is probably an underestimate because the 1000 genomes data are low coverage and rely on extensive imputation which will often cause rare third alleles to go undetected. Equally, conservative curation will tend to remove third alleles that lack strong support. Note, triallelic sites are unlikely to be generated mainly by sequencing errors because only 1% of these sites carry a singleton as the rarest allele. This analysis is not intended to provide an accurate estimate of the back-mutation rate, but instead simply to demonstrate that large numbers of back-mutations do exist to the extent that models of evolution that rely on back-mutations occurring in appreciable numbers should not be dismissed a priori."

Research by Anke Fähnrich et al., (2023) on the North and Eastern African mtDNA shows that some mutations that serve as markers appear time and time again, the authors consider some as "Shared back mutations", others are simply repeat mutations. The paper shows them in a tree for "L0a1 and (b) L2a1" and clarifies that "We highlight with magenta, gray and turquoise boxes those variants that indicate that a different phylogenetic tree may better explain the samples from North and East Africa." These trees can be seen in the image below. The paper adds that "Shared back mutations (magenta) denote that parental haplotypes may be missing in PhyloTree. Mutations repeatedly observed in a subtree (gray) suggest that child haplogroups are missing. Variants that occur in multiple samples and differ from variants defining a parental haplogroup (turquoise) suggest that different variant combinations and haplogroup specifications may better explain North and East African mtDNA sequences". It also marks them with an "@" as "assumed back mutation or missing mutation". This goes to show that markers are shared across different haplogroups.

Figure 10, haplo tree mtDNA L. Source

A similar situation was reported by Neil Howell, Joanna L Elson, D M Turnbull, and Corinna Herrnstadt (2004) who were investigating the oldest mtDNA haplogroups L0 and L2. Besides finding oddities in the trees, ages, etc., they noted multiple reversions: "The L0a outgroup sequence carries C alleles at nucleotides 16189 and 16192, whereas the L2a ancestral sequence is predicted to carry C and T, respectively, at these sites. The 16189 site subsequently undergoes mutation on four occasions (three forward and one reverse relative to the outgroup sequence), whereas the 16192 site undergoes reversion on five occasions. Thus, both sites appear to have relatively high rates of mutation, a result that has been observed in previous studies (Excoffier and Yang 1999; Meyer, Weiss, and von Haeseler 1999; Howelland Bogolin Smejkal 2000) and in the L2a networks of Salas et al. (2002)... The ancestral L2a sequence carries a C:T transitional nucleotide 16519, which undergoes reversion on three occasions. These results are not surprising and this site has long been recognized to have a high mutation rate."

This seems to define a "mutation hotspot", that I mentioned in a previous post (Laguna de los Pampas 10,000 BP remains in Argentina).

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

mtDNA variants and Natural Selection

The chance mutations that are fixed in the DNA of our mitochondria and accumulate there have been used to trace the spread of human beings across the globe. Passed on in a matrilineal form, we all receive the mtDNA from our mother's ovum. Our father's sperm does not carry any mitochondria. Randmo mutations gradually accumulate so they serve as markers in the mtDNA and specific markers define haplogroups.

A paper suggests that these random mutations are then shaped by the forces of Natural Selection. (D. Mishmar, E. Ruiz-Pesini, P. Golik, V. Macaulay, A.G. Clark, S. Hosseini,M. Brandon, K. Easley, E. Chen, M.D. Brown, R.I. Sukernik, A. Olckers, & D.C. Wallace, /2003) Natural selection shaped regional mtDNA variation in humans, Proc. Natl. Acad. Sci. U.S.A. 100 (1) 171-176, https://doi.org/10.1073/pnas.0136972100).

They note that although mutations arise in a random way in the mtDNA, as they have an effect on the mitochondria which produce the body's cells energy and regulate cellular metabolism by producing the energy-rich molecule adenosine triphosphate (ATP), they may be a target of natural selection. They state that "Natural selection shaped regional mtDNA variation in humans."

Mitochondria the body's powerhouse. Copyright © 2026 by Austin Whittall

Molecular clock affected

The fact that mutations are not neutral, and are acted upon by natural selection, implies that the assumptions on which the mtDNA molecular clock are based, are flawed. The paper warns: "If selection has played an important role in the radiation of human mtDNA lineages, then the rate of mtDNA molecular clock may not have been constant throughout human history. If this is the case, then conjectures about the timing of human migrations may need to be reassessed."

The molecular clock based on mtDNA is based on an axiom: genes accumulate new mutations in a clock-like manner, so knowing the rate at which mutations take place (i.e. 3 mutations per 10,000 years), and measuring the average amount of mutations that have appeared since a particular node on a phylogenetic tree (9 mutations), allows us to date the node: 30,000 years. And from there date other nodes based on the number of mutations and the mutation rate.

This is reasonable as long as the mutation rate is constant. But if it varies, then it will provide incorrect dates.

Positive selection could affect the mutation pattern similar and cause an acceleration in the mutation speed. (Further reading on the mtDNA clock: Eva-Liis Loogväi, Toomas Kivisild, Tõnu Margus, Richard Villems (2009))

mtDNA and Selection

After a long stasis in Africa where the L haplogroup is found, humans moved into Eurasia and two branches, or clades, M and N formed outside of Africa and comprise all the mtDNA diversity in the rest of the world. M and N are derived from the African haplogroup L3. And the split is supposed to have taken place around 55-70 kya, during the Out of Africa Event.

Interestingly, M is basically absent in the Middle East, yet it is found in Ethiopia, Southern Arabia and in India and East Asia, suggesting to some a Southern route of migration out of the Horn of Africa across Bab el Mandeb and Hormuz straits. However, a paper published in 2018 by Vicente M Cabrera, Patricia Marrero, Khaled K Abu-Amero, and Jose M Larruga, suggests that both M and N originated in Southeast Asia and migrated westwards. In the case of N haplogroup, it was believed to have formed in the area that links the Levant and Africa and that it appeared in humans taking a northern route out of Africa into Eurasia. But this paper suggests that N originated in Southeast Asia, and moved west across Asia towards Africa. The authors argue that "If one accepts that basal L3 lineages (M, N) evolved independently in southeastern Asia and not in Africa or near the borders of the African continent where the remaining L3 lineages expanded, one is confronted with the question of where the basal trunk of L3 evolved. A gravitating midpoint between eastern Africa and southeastern Asia would situate the origin of L3 in inner Asia."

The paper then states:

"L3 exited from Africa as a pre-L3 lineage that evolved as basal L3 in inner Asia. From there, it expanded, returning to Africa as well as expanding to southeastern Asia, giving rise to the African L3 branches in eastern Africa and the M and N L3 Eurasian branches in southeastern Asia, respectively. This model, which implies an earlier exit of modern humans out of Africa, has been tested against independent results from other disciplines...."

The paper includes the following maps as its Figure 1, and the caption reads: "Geographic origin and dispersion of mtDNA L haplogroups: a Sequential expansion of L haplogroups inside Africa and exit of the L3 precursor to Eurasia. b Return to Africa and expansion to Asia of basal L3 lineages with subsequent differentiation in both continents. The geographic ranges of Neanderthals, Denisovans and Erectus are estimates only."

The paper adds that the "early return and subsequent expansion inside Africa of carriers of L3... haplogroup might help explain, the Neanderthal introgression detected in the western African Yoruba and in northern African Tunisian Berbers." (see my recent post on Neanderthals in Africa).

The authors assume anatomically modern humans left Africa in an early migration 125 kya , met with Neanderthals in south-central Asia, admixed and as the climate worsened ~75kya, the humans moved west and returned to Africa (with the L3 variant with them and it diversified there), and they also moved east reaching SE Asia and China.

Selection and Diversification

Getting back to Mishmar et al., they argue that in Eurasia the M and N lineages spread across the continent in different lineages: A, C, D, and G. Which have a "striking regional variation, traditionally attributed to genetic drift. However, it is not easy to account for the fact that [these lineages] show a 5-fold enrichment from central Asia to Siberia". They argue that this enrichment is the result of natural selection acting as people left their traditional environment (warm, tropical, or temperate climates) and advanced into harsher and colder continental climates in Central and Northern Asia.

The researchers analyzed 104 complete mtDNA sequences from across the world and found that the African haplogroups more or less followed the neutral model, but American, European, Siberian and Asians didn't, they deviated from it. They found that the ATP6 gene, which is a "conserved" mtDNA protein had the highest variation in its amino acid sequences. "Conserved" means that it has remained mostly unchanged over the ages and among individuals and species because it has a low tolerance for mutations, because it is critical for cellular function. So, why would it present so many mutations?

To find out why, they compared the ratios of mutations for the ATP6 gene in different climate zones (arctic, tropical, and temperate) and found that it was highly variable in mtDNAs from the Arctic. Another mtDNA protein called cytochrome b which helps move electrons and create a proton gradient, essential for cellular energy production, was particularly variable in the temperate zones. Another protein, cytochrome oxidase I (or COX1), which also plays a vital role in electron transport, was more variable in the tropical areas. The authors concluded that "selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate."

They then downplay the effects of founder effects arguing as follows:

"..there are striking differences in the nature of the mtDNAs found in different geographic regions. Previously, these marked differences in mtDNA haplogroup distribution were attributed to founder effects, specifically the colonizing of new geographic regions by only a few immigrants that contributed a limited number of mtDNAs.
However, this model is difficult to reconcile with the fact that northeastern Africa harbors all of the African-specific mtDNA lineages as well as the progenitors of the Eurasia radiation, yet only two mtDNA lineages (macrohaplogroups M and N) left northeastern Africa to colonize all of Eurasia and also that there is a striking discontinuity in the frequency of haplogroups A, C, D, and G between central Asia and Siberia, regions that are contiguous over thousands of kilometers.
Rather than Eurasia and Siberia being colonized by a limited number of founders, it seems more likely that environmental factors enriched for certain mtDNA lineages as humans moved to the more northern latitudes.
Natural selection has been hypothesized to explain anomalies in the branch lengths of certain European and African mtDNA lineages."

However, a paper by Taku Amu and Martin Brand (2007), disagrees with this concept, and states that there were no differences between the mitochondrial energy management in Arctic or Tropical populations, and that the mutations which were expected to lower coupling efficiency leading to more heat generation in colder climates wasn't detected, and in fact, "Contrary to the predictions of this hypothesis, mitochondria from Arctic haplogroups had similar or even greater coupling efficiency than mitochondria from tropical haplogroups."

More recent research by Jukka Kiiskilä et al (2021) also notes that mtDNA variants are under natural selection and that different mtDNA haplogroups exert a different effect on the physical performance in athletes! the paper looked at Finnish military conscripts and reported that "Following a standard-dose training period, excellence in endurance performance was less frequent among subjects with haplogroups J or K than among subjects with non-JK haplogroups."

Takayuki Nishimura and Shigeki Watanuki (2014) studied mtDNA haplogroup D vs. non-D groups regarding body warmth, and found that "[Non shivering thermogenesis] NST was greater in winter, and that the D group exhibited greater NST than the non-D group during winter...no significant differences in rectal and skin temperatures were found between groups in either season. Therefore, it was supposed that mitochondrial DNA haplogroups had a greater effect on variation in energy expenditure involving NST than they had on insulative responses... individuals from the D group exhibited greater winter values of ΔVO2 than individuals from the non-D group." So, mtDNA haplogroup D subjects had higher oxygen uptake (ΔVO2), meaning their body was "burning" more oxygen but not shivering or increasing the temperature. This suggests an efficient use of energy to heat the core only, and it has a clear mtDNA haplogroup component to it.

Interestingly, Haplogroup D seems to enhance energy burn (without shivering), and without increasing external temperature. From an engineering point of view this is great, since the ΔT or temperature differential between a body and its surroundings impacts directly on the energy loss (Q) the body experiences: Q = U · A · ΔT (where "A" is the area that transfers heat loss, and "U" is a heat transfer coefficient). So this is why the study didn't notice differences in skin or rectal temperatures.

Closing Comments

If random mtDNA mutations somehow provide an adaptative advantage (efficient energy use to keep warm in cold climates), and natural selection acts upon it, then the "neutral" theory is mistaken, and the molecular clock used to calculate dates is also wrong.

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

The Three Out Of Africa Migrations

I came across research by J. H. Relethford, who in a paper published in Nature in 2008 cites Templeton's work about the different expansions of our ancestors out of their African homeland.

The Archaeological Evidence

The fossil evidence shows that H. georgicus and H. erectus lived in Eurasia roughly 1.7 million years ago, and that there were different hominins in that region since then. The remains of H. heidelbergensis, Neanderthals and Denisovans also show evolution and possibly other out of Africa events around 600 ky ago. Finally our own branch, H. sapiens left Africa possibly twice, an early, "failed" migration around 250-100 ky ago and the final move that established modern humans around the world ~60 ky ago. At least, that is the official account.

The Genetic Confirmation

What is interesting is that genetic analysis done by Templeton confirms these dates. Again, I wonder if this fit between the data in the genes and the bones and stones is real, or was somehow eased with the foreknowledge of what had to be confirmed...

Below Is what Relethford wrote, including his citation of Templeton:

"The most comprehensive of these analyses has been performed by Templeton (2005, 2007) who examined 25 DNA regions: mtDNA, Y chromosome DNA, 11 X-linked markers and 12 autosomal markers using a 6-Myr-old date for the human–chimpanzee divergence for calibration. Using a method known as nested-clade phylogeographic analysis, Templeton found that 15 of these markers showed evidence of geographic expansion. The estimated ages of range expansion vary significantly across these markers and do not fit a model of a single expansion, but instead cluster into three groups: (1) an expansion out of Africa 1.9 Myr ago (95% CI=0.99–3.10 Myr), (2) an expansion out of Africa 650 000 years ago (95% CI=390 000–970 000 years ago) and (3) an expansion out of Africa 130 000 years ago (95% CI=9600–169 000 years ago)."

These three events coincide with the H. georgicus and H. erectus, the Neanderthal, and the H. sapiens migrations! I find the confidence intervals rather large (0.9 to 3.1 million years for erectus, 390-970 ky for Neanderthals and 9.6 to 169 ky for us). Such large intervals reveal a high uncertainty in the statistical analysis.

Is this a Coincidence? or do genetics and hard archaeology agree with solid evidence?

Relethford warns that: "Given the large confidence intervals typical of coalescent analysis, this correspondence should be taken as suggestive and not conclusive, but the apparent congruence of the fossil and genetic records is interesting and deserves continued attention, particularly as data on more low-recombination DNA regions become available."

Note that word of caution about Templeton's findings. John Henry Relethford originally was a staunch supporter of the Multiregionalism theory (humans evolved in parallel in the Old World and intermingled) and rejected the initial Out of Africa theory which suggested a total replacement of other hominins by modern humans as they marched across Eurasia, wiping them out. He later shifted to a compromise theory (Mostly Out of Africa) where there was an interplay between African H. sapiens and the hominins in Eurasia. He was concerned with the fate of these Eurasian people.

Alan Templeton on the other hand adopted a rigid position against the replacement Out of Africa theory, criticizing it. His papers reflect this (see above), and he continued with another paper in 2013, and again in 2023, supporting his point of view.

Templeton wrote a very interesting critique about some statistical tools, and admixture trees, which will be the subject of a future post.

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

Neanderthals in Africa?

Continuing with my series of posts on the diversity and higher heterozygosity of contemporary Africans, which may be due to many factors: post-OOA admixture within Africa with diverse archaic hominins leading to a higher Ne. A higher mutation rate due to this higher Ne, and to adapting to the environmental challenges of Africa. Higher mutation rate driven by higher heterozygosity. All of which lead to a higher diversity in contemporary Africans (note that we have no ancient DNA sequences from H. sapiens in Africa as we do for Neanderthals in Eurasia, and H. sapiens in Eurasia, Oceania, and America.

There is also the question of Neanderthal admixture in Africans. I discussed this in a 2019 post and in a 2020 post but more papers have appeared on the subject as we will see below.

The generalized notion is that human beings admixed with Neanderthals, who lived in Eurasia, during the Out Of Africa migration. Since there were no Neanderthals in Africa, those humans who remained behind in Africa never mingled with the Neanderthals, and therefore have no genetic input from them. But, back in 2018 a paper reported a Neanderthal genes in East Africa, they were carried there by Eurasian humans who had admixed with the Neanderthals in Eurasia

In and Out of Africa. Copyright © 2026 by Austin Whittall

The map above shows the homeland of the OOA migrants, in the Horn of Africa (Ethiopia) and the red arrows mark the OOA migration across Eurasia and Oceania. In Europe and Western Asia they met the Neanderthals who lived there, mated, admixed, and some modern humans returned to Africa (blue arrows) carrying Neanderthal alleles with them.

The 2020 paper mentioned above suggests that "Back-Migration with Non-Africans and Pre-out-of-Africa Human-to-Neanderthal Gene Flow Contribute to Apparent Neanderthal Ancestry in Africans", two mechanisms, one, the backflow and second, an early gene flow from an early, failed OOA migration that introgressed human alleles in Neanderthals (100-250 ky ago), and which appear as shared between Neanderthals and humans when they are compared.

Below is an image from A. Ragsdale (2023), that shows these gene sharing events (early-OOA with Neanderthals, and Neanderthal-Later OOA admixture and backmigration of Eurasians to Africa).

Figure 1. A history of reciprocal introgression between humans and Neanderthals. (A) Population structure among the ancestors of modern humans extended deep in the past, though common ancestry of all present-day humans is more recent than the expansion of early Homo sapiens out of Africa that resulted in human-to-Neanderthal admixture. Arrows indicate major migration and admixture events.. Fig. 1A in Ragsdale (2023)

The Neanderthal admixture was present in samples obtained from LWK = Luhya in Webuye, Kenya, East Africa. GWD = Gambian in Western Division, Mandinka, in West Africa. MSL = A Mende population from Sierra Leone in West Africa. YRI = Yoruba in Ibadan, Nigeria, in West Africa. ESN = Esan in Nigeria, West Africa. This is a pan-African presence.

This paper found that "of the Neanderthal sequence identified in African samples, more than 94% was shared with non-Africans..." only a small part was uniquely African, as you can see in the following image, Fig. 2 B in that paper captioned: "Venn diagram showing the amount of overlap in identified Neanderthal sequence in non-African and African populations." Europeans have ~80% more unique Neanderthal alleles than Africans, yet they have their own unique alleles not shared with Eurasians, they seem to have been lost in Eurasia, or, did they come from introgressions with other archaics in Africa, carrying these alleles?

Then they "also performed extensive simulations and found that the signal of Neanderthal ancestry in Africans was unlikely to be explained by false positives due to shared ancestry." They therefore attribute the signal to admixture. But where? In Africa or due to a backflow?

The paper states that they considered both options: "studied models where non-African individuals, who carry Neanderthal sequences inherited from hybridization, migrated back to Africa and models of human-to-Neanderthal gene flow due to an early pre-out-of-Africa (pre-OOA) dispersal of modern humans." Note that they don't consider the inside-of-Africa mixing but, instead, admixing in an Early out of Africa mixing (more on this below).

Regarding backflow they found that "These data are consistent with the hypothesis that back-migration contributes to the signal of Neanderthal ancestry in Africans. Furthermore, the data indicate that this back-migration came after the split of Europeans and East Asians, from a population related to the European lineage."

Early Out Of Africa

The paper then finds that there is "strong evidence that human sequence in the Neanderthal genome also contributes to the signal of the Neanderthal ancestry we detect in Africans." The first out of Africa event which supposidly took place betewwn 100 and 150, or even 250 ky ago introgressed human genes into Neanderthals, a gene flow from H. sapiens of this first wave into Neanderthals. Previous studies have noted the genetic contribution of a pre-out-of-Africa gene-flow event from humans into Neanderthals. So, when comparing Neanderthals with current modern humans, we find that we share some alleles (of course, they were originally human genes).

West Africa

Both the 2020 paper mentioned above, and anothe paper by Anders Bergström (2020) found ancient admixture of Neanderthal genes in West Africa. West Africa! which is on the opposite side of Africa from which the OOA event ocurred. How could there be Neanderthal genes so far from East Africa?

Bergström assumes it is a backflow from Eurasia, but also adds that they may be relict alleles from the period that predates the OOA event, and that preserved these genes in Africa, which were lost elsewhere:

"We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa....
Alleles private to Africa, however, include a higher proportion of ancestral alleles, and this proportion increases with allele frequency, reflecting old variants that have been lost outside of Africa. For the same reason, many high frequency private African variants are also found in available Neanderthal or Denisovan genomes."

If Africans carry variants of Neanderthal and Denisovan genes not found elsewhere it means that these introgressed into Africans, within Africa, maybe from isolated populations of these ancient humans found inside of Africa.

When it comes to splits within African populations, Bergström's paper assumed "a mutation rate of 1.25 × 10−8 per base pair per generation and a generation time of 29 years" and calculated the splits between populations but found that "all of these curves are clearly inconsistent with clean splits, suggesting a picture where genetic separations within Africa were gradual and shaped by ongoing gene flow over tens of thousands of years. For example, there is evidence of gene flow between the San and the Biaka until at least 50 kya, and between the Mbuti, the Biaka, and the Yoruba until the present day." This is in line with an "enrichment" of modern Africandiversity by agglutination of the past diversity preserved in isolated African populations, as mentioned in my recent posts.

Ancient structure influenced modern diversity: "For the deepest splits, there is some evidence of genetic separation dating back to before 300 or even 500 kya... The implication of this is that there lived populations already at this time that contributed more to some present-day human ancestries than to others... but also a small fraction of present-day ancestries retaining traces of structure that is older than this, potentially by hundreds of thousands of years." Here, I ask, are these ancient alleles result of recent post OOA introgression of ultra-archaic hominins in Africans? or the common ancestors of humans and Neanderthal-Denisovans?

The presence of Neanderthal alleles in Africans was quantified by Bergström as follows: "The West African Yoruba also display a Neanderthal admixture signal that is similar in shape but much less pronounced than that in non-Africans (Fig. 6D and fig. S9). Other African populations do not clearly display the same behavior. These results provide evidence for low amounts of Neanderthal ancestry in West Africa, consistent with previous results that were based on other approaches, and we estimate this at 0.18 ± 0.06% in the Yoruba using an f4-ratio (assuming that the Mbuti have none). The most likely source for this is West Eurasian admixture and, assuming a simple linear relationship to Neanderthal ancestry, our estimate implies 8.6 ± 3% Eurasian ancestry in the Yoruba."

Sub Saharian Africa (SSA)

The people living in Africa south of the Sahara also carry Neanderthal alleles, a study by xvklñfjadsklñfjdskñl ------------------------- " As a percentage of the genome, therefore, Neanderthal ancestry in the 180 SSA dataset ranges from 0% to ~1.5%, with the highest levels observed in the Amhara and Fulani."

They favor the sequence: early migration of anatomically Moderh Humans (AMH) out of Africa ~250 ky ago, admixing with Neanderthals in Eurasia, leaving a ~6% AMH genetic trace in Neanderthals. Then, the final OOA event with modern humans, who mated with Neanderthals (~40 to 55 kya), receiving these AMH haplotypes from the Neanderthal (NIRs). Then, " Third, at least two subsequent recent migrations of non-sub-Saharan African AMHs into sub-Saharan Africa brought introgressed Neanderthal haplotypes (NIRs) to sub-Saharan African AMH populations with whom they admixed."

Perhaps the best theory is the one that suggests that the Neanderthal signal was acquired inside Africa, as we will see below.

An introgression within Africa

Arun Durvasula and Sriram Sankararaman (2020) on the other hand suggest that the Neanderthal genes came from a direct "within Africa" admixing event:

"We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans... Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."

They compared three different models in which part of the West African ancestry comes from, (A) people who split from their ancestors after modern humans and Neanderthals split; (B) people who derive from the ancestors of Neanderthals after they split from modern Humans, and (C) people who split from the ancestors of modern humans and Neanderthals before modern humans and Neanderthals split. They found that (C) was the best model:
"support for a contribution to the genetic ancestry of present-day West African populations from an archaic ghost population whose divergence from the ancestors of modern humans predates the split of Neanderthals and modern humans.
... We determined the posterior mean for the split time to be 625,000 years before the present (B.P.) [95% highest posterior density interval (HPD): 360,000 to 975,000], the admixture time to be 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction to be 0.11 (95% HPD: 0.045 to 0.19). Analyses of three other West African populations (ESN, GWD, and MSL) yielded concordant estimates for these parameters. Combining our results across the West African populations, we estimate that the archaic population split from the ancestor of Neanderthals and modern humans 360 thousand years (ka) to 1.02 million years (Ma) B.P. and subsequently introgressed into the ancestors of present-day Africans 0 to 124 ka B.P. contributing 2 to 19% of their ancestry."

This means that an ancient, relict population that split from the branch leading to Modern Humans and Neanderthals between 360 and 975 ky ago, on avg. 625,000 years ago, mated with Homo sapiens people in Western Africa, and this event ocurred after the OOA event that peopled the rest of the world, this admixture inside of Africa took place roughly 43,000 years ago (0 to 124 ky).

Maybe later there was backflow from Eurasia, but this introgression in Western Africa with an ultra archaic human is the one tha injected Neanderthal-like genes into this population. It must have surely contributed to the diversity of these populations, adding more heterozygosity to them.

This idea is supported by Nina Hollfelder, Gwenna Breton, Per Sjödin, and Mattias Jakobsson, (2021):

"Another possibility is that the large Ne is shaped by multiple introgression events from divergent lineages, which are hard to distinguish without archaic reference sequences. Unfortunately, many studies of archaic or ghost introgression in Africa focus on a few populations and/or use only one method for inference, so that the effect of the identified archaic or ghost introgression is not yet comparable across all major branches of modern humans in a systematic way.
Interestingly, many studies identified a fairly recent time for the introgression from extinct lineages in Africa, with introgression events even after the split from non-African populations, hinting at survival of archaic human populations until relatively recently in time."

Where Ne is the effective population, the large Ne of the African population is considered as one of the factors that created its diversity vs. the rest of the World, with lower Ne's due to bottlenecks and lower diversity. Here, we see that multiple introgression from diverse populations that merge can also lead to the effect of a high Ne!

I personally support the idea of super-archaics mixing with Africans after the OOA event, adding diversity and heterozygosity to their genetic makeup, and I don't exclude a backflow from Eurasia with Neanderthal genes.

No Neanderthals or Denisovans, but an archaic introgression

Last but not least, Lorente Galdos et al., (2019)" found no signals of Neanderthal or Denisovan introgression in the sub-Saharan individuals... We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.... Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans. "

The timeline given in this paper is the following: "the AMH lineage and the one from the archaic Eurasian populations diverged 603 kya (95% credible interval (CI) ranging from 495.85 to 796.86 kya). The ghost XAf archaic population and the AMH lineage split 528 kya (95% CI of 230.16 to 700.06 kya), whereas the Denisovan and Neanderthal lineages split 426 kya (95% CI from 332.77 to 538.37 kya). Archaic introgression estimates from XAf to African populations range from 3.8% (95% CI 1.7 to 4.8%) in Khoisan and 3.9% (95% CI 1.3 to 4.9%) in Mbuti to 5.8% (95% CI 0.7 to 0.97%) in West Africa. Our analyses also identified the archaic introgression from early AMHs into Neanderthal."

I wonder if the AMH introgression into Neanderthals (also mentioned further up) which is said to have taken place during the early OOA event 250-100 ky ago, isn't just the reflection of the common origin and relatedness between Neanderthals and these early AMHs. They split in Africa and had common genes. Seems a simple, straightforward explanation.

Regarding the ghost archaics XAf population, I have posted about them in the past (see this post, this post, this one, and this post among others), they are indeed a source of diversity, rare alleles, and heterosygosity for contemporary Africans.

Comments

As you can see, many research papers, authors, models, interpolations, algorithms, and softwares used and different interpretations from the same basic genetic samples!

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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 Africans

In a recent post I wrote about the Neutral Theory of molecular genetics, and its shortcomings. Today's post will explore the African genetic diversity, a foundation on which the Out Of Africa (OOA) theory is based.

There are several questions that should be answered: 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 in other populations that were isolated from the sub-population that was the root or base from which modern H. sapiens migrated into Eurasia?

Admixture with archaic hominins after the OOA event (such as H. naledi), admixture between many separate and formerly isolated hunter gatherer sub-populations due to migrations like the Bantu migration could have led to a modern highly diverse African population, while the original OOA root was far less diverse.

The image below is a crude attempt to reflect the isolated populations within Africa at the time modern Humans appeared. Each circle is a population. They all contain allelles (colored red, blue, yellow, etc.) some shared, others unique to each population. The black arrows show the migration Out of Africa, with humans dispersing across Eurasia towards Siberia, Europe and Oceania, and America. They lose diversity on the way due to Genetic Drift.

The dashed red arrows converging on a circle shows the internal migrations within Africa by which these formerly isolated sub-populations of humans admixed and the final, contemporary population has an even higher diversity than the original root of the Out of Africa migration (set in the horn of Africa).

It does not show any back-flow of humans from Eurasia into Africa, or archaic introgression either in Africa or in Eurasia (Neanderthals, Denisovans).

Genetic Drift out of Africa. Copyright © 2026 by Austin Whittall

Population structure in Africa

The humans in Africa were not a uniform population. A paper published in Nature suggested that there were "low levels of gene flow among archaic populations before the emergence of anatomically modern humans — that is, they imply the existence of ancestral population structure." It also hints at admixture with primitive, archaic, hominins in Africa: "There is also growing evidence that some highly divergent genetic lineages might have entered our genome through hybridization between an expanding anatomically modern human population and archaic forms of humans."

Another article published in Nature, questions the use of modern Africans to model the OOA event. While highlighting the high diversity within Africa, the paper also states that "we will need to establish whether selection has continued to operate effectively on complex traits, leading to unbiased estimates from these populations. If not, it may still be inappropriate to use a specific modern African population as a proxy for the ancestral population of modern humans."

Additional research (Source) looks into the effects of the structured population within ancient pre-OOA Africa: "Several studies have indicated that ancestral populations were geographically structured before modern humans migrated out of Africa. For example, it has been suggested that the deep coalescence times of mtDNA and X-chromosome lineages are consistent with a demographic scenario of ancient population structure in Africa. A recent analysis of cranial shape variability in anatomically modern human fossils (dating to 200–60 kya) from Africa and the Middle East also reported a high level of morphological divergence among these fossil hominids which was interpreted as evidence for ancestral population structure in Pleistocene Africa. Thus, arguably, a considerable amount of genetic and phenotypic diversity may have been present at an early stage of modern human evolution."

Indeed! And not all of this diversity was found in one population, each sub-population had their own alleles, later admixed into modern Africans (minus alleles lost due to genetic drift) and plus backflow from Eurasia with introgressed Neanderthal genes, and the mutations added by an additional 100 ky of evolution in Africa, subjected to natural selection and random mutations over that period of time.

This paper also mentions the backflow: "The reverse migration of non-Africans into Africa was also shown to contribute to the gene-pool of modern African populations"

The variations observed in skulls mentioned above was reported by a paper published in Nature. Different skull shapes mean that different sets of genes were working and they were not the same alleles in each sub-population.

"Late Middle Pleistocene (LMP, from 350 to 130 ka) African fossils [were highly variable]... Even when excluding the H. naledi material, African LMP fossils exhibit extremely variable morphologies. The Omo I22 and Herto specimens have a modern-like anatomy... and are generally considered the earliest undisputed remains of H. sapiens. All other LMP African fossils show a mosaic of derived and archaic characters. For instance, the Jebel Irhoud remains were originally described as showing strong similarities with Neandertals, while the study of the new Irhoud remains emphasises their affinities with H. sapiens, despite the absence of key modern humans apomorphies. The Guomde, Ngaloba, Eliye Springs and Florisbad specimens along with Omo II... have been mostly referred to as ‘archaic H. sapiens’, a category grouping isolated fossils with disparate morphologies. This situation challenges any attempt at identifying the evolutionary mechanisms that may explain the morphological pattern in the African LMP fossil record, as well as identifying the ancestral population, or populations, of modern humans"

The Admixture Within Africa

These different groups of humans must have later admixed into the base from which modern Africans come from. Possibly after the basal Homo sapiens left Africa in its OOA journey.

Yet another paper from Nature investigated contemporary African diversity. It looked at the genes and ancient migrations in different populations, including the Hunter gatherers (HG) and the supposedly most ancient group of humans, and the most diverse one, those living in sub-Saharan Africa (SSA), to define the current genome of Africans. It found an important effect from Eurasian admixture and a strong influence of natural selection modelling modern genes:

"Eurasian ancestry has a substantial impact on differentiation among SSA populations...
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA. Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ∼7,500–10,500 years ago), old admixture among Ethiopian populations (∼2,400–3,200 years ago) consistent with previous reports, and more recent complex admixture in some East African populations (∼150–1,500 years ago). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period.
We also find evidence for complex and regionally distinct HG admixture across SSA, with ancient gene flow (∼9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations.
Positive selection in SSA
We examined highly differentiated SNPs between European and African populations, as well as among African populations to gain insights into loci that may have undergone selection in response to local adaptive forces. To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry. On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift..."

So modern African diversity is the result of recent admixture across the continent and the forces of natural selection. These people are not the same people that saw the OOA migration depart.

Archaic introgression in Africa

Regarding introgression of archaic human in Africa, I had posted back in 2019 about it (See post: Archaic Ghost population admixed with Modern Humans in Africa) which quotes a paper by Lorente-Galdos et al. that reported that: "We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage."

Another paper form 2020, published in Science found the same effect in Western Africa: "We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."

This introgression took place in West Africa after the OOA: "the admixture time ... 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction ... 0.11 (95% HPD: 0.045 to 0.19).", that is 11% mean (4.5 to 19%). And then subject to selection as it was an adaptive introgression.

This surely contributed to the diversity of the alleles in these people compared to those who left Africa in the OOA migration.

Other confounders

Finally, there is the question of back-migrations from Eurasia into Africa. These people who returned "Into Africa" or "Out of Asia" back flow carried with them genes from people who had left Africa, plus admixture with Neanderthals (and maybe, Denisovan, ultra-archaics, first wave humans who left before the final OOA event). This surely contributed to the genetic diversity of Africa.

Another element to consider is the mutation speed or faster evolutionin Africa which could have fueled diversity starting even before the final OOA event 60-100 ky ago. But that is the subject of a future post.

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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 © 

Did Humans admix with Neanderthals? Paper in Nature says NO

Research published in Nature on Dec. 13, 2024 suggests, as its title says, that some models used by scientsts may lead to assume the existence of false introgressions. The word spurious used in the title means "based on false reasoning or information that is not true, and therefore not to be trusted". The paper can be found online: Tournebize, R., Chikhi, L. Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events. Nat Ecol Evol 9, 225–236 (2025). https://doi.org/10.1038/s41559-024-02591-6🔒

A preprint free version is available on line in Biorxiv 🔓

The paper's Abstract is quoted below:

"Abstract
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation."

Notice how the authors criticise the models used ("mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure [but, ignoring] population structure can lead to the inference of spurious demographic events ").

The authors assumed that there were two population groups. One named metapopulation M_A tht generated a second one, M_B between 9 Million years ago and 500 ky. This created two populations (Bipartite structure) within Africa. Then, some individuals from the M_B group left to colonize Europe and Asia splitting some 650 ky ago from the remaining populations that stayed in Africa. Those who went to Eurasia became the metapopulation M_N, originating the Neanderthals or Hn population. The African metapopulations M_A and M_B evolved into Homo sapiens (Hs). Later Hs left Africa and colonized Eurasia forming an M_C metapopulation there. The paper states that "the new Hs Eurasian metapopulation M_C with the African Hs metapopulation M_B (itself connected to the Hs metapopulation M_A). Note however that none of the Hs metapopulations (M_A, M_B and M_C) ever exchanged gene flow with the Hn metapopulation (M_N). In brief, our model does not allow admixture between Hs and Hn."

Therefore this study suggests that instead of actual mating between Homo sapiens and Neanderthals, as a means by which genetic material was shared by both groups, the common fragments of genetic material may have originated in ancestral populations that split and carried them with them through time with no need for admixtwure.

Below is Fig. 1 from the paper, and the original caption is the following: "Simplifed representation of the 1D structured model considered in this study. Time flows from top (past) to bottom (present), with an initial metapopulation M_A consisting of nA (=10) demes exchanging migrants with their neighbours. At some point in the past, the rightmost deme of M_A founds a new metapopulation M_B of nB (=10) demes, with which it will continue exchanging migrants till the present. Later, the rightmost deme of M_B founds the metapopulation M_N of nN (=10) demes which will become Neanderthals. The MN metapopulation will never exchange migrants with any other deme from the other metapopulations. Closer towards the present, the rightmost deme of M_B founds M_C which corresponds to the expansion of H. sapiens towards Eurasia. White feet represent the sampled populations (not the specific demes) for respective sampling times. The location of the sampled demes (within the corresponding metapopulations) is a random variable... Fifty individuals are sampled in M_A and in M_C to represent modern-day YRI and CEU samples respectively. For the Neanderthals (M_N), one individual is sampled at 50 kya."

Fig. 1 in the Biorxiv preprint. Source

Comments

Interesting indeed! Could these admixture events be mere artifacts of these black-box statistical models used by scholars? I have posted some critical comments on these models in the past (See: Some thoughts about the tools used in genetic admixture analysis, Biases in Genetic Models that are generally overlooked). I favor admixture, yet, I also consider that the software used by scientists may not accurately reflect the real population dynamics of our ancestors.

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

Inventio Fortunata

In this series of posts I have mentioned the Welsh prince Madoc and his mythical voyages to America, Legendary King Arthur (of Camelot and Knights of the Round Table fame) and his conquest of Iceland (plus a pre-Viking Celtic peopling of Iceland c.550 AD); I also mentioned David Ingram's 2,000 mile trek from Tampico, Mexico to Nova Scotia, Canada, where he saw elephants, gigantic eagles, strange beasts, horses, cattle, sheep, and also Indians that spoke Welsh. Today's post will look into the adventures of an English priest who sailed to the North Pole. All of these myths were used by John Dee to establish the precedence and rights of Elizabethan England over America.

The Franciscan Priest who visited the North Pole in 1360 AD

There is a lost book called Inventio Fortunata which recorded the Polar adventures of a priest in the Middle Ages. It was read by cartographers of the Modern Age who recorded its existence.

First Mention: 1508 AD

It was first mentioned in a marginal note by Johannes Ruysch in his map published in 1508: "It is written in the book of the 'Inventio Fortunata' that there is a very lofty rock of loadstone beneath the Arctic Pole, thirty-three German miles in circuit. Round this flows an indrawing sea, fluid like a vase, pouring water through openings below. About are islands, of which two are inhabited. Huge and broad mountain chains surround these islands, of which twenty-four will not allow of settlement by man." (Source). Loadstone is magnetite, a naturally magnetized mineral.

Second Mention: 1577 AD

This lofty magnetic island was known as Rupes Nigra, Latin words for "Rock" and "Black". As we will see below, Mercator showed it in his map. He also described it in a letter to John Deem written in 1577 (source). Mercator mentions the Franciscan friar and that he visited the Pole in the year 1360 AD.

1606 Mercator Hondius Map of the Arctic (First Map of the North Pole). Source - interactive map

Mercator begins his story describing the Circumpolar area and then he mentions King Arthur!:

"The islands adjacent to the North Pole were formerly called Ciliae (perhaps Thule), and now the Septentrionales
... Part of the army of King Arthur which conquered the Northern Islands and made them subject to him. And we read that nearly 4000 persons entered the indrawing seas who never returned. But in A.D. 1364 eight of these people came to the King’s Court in Norway. Among them were two priests, one of whom had an astrolabe, who was descended in the 5th generation from a Bruxellensis: One, I say: The eight (were sprung from?) those who had penetrated the Northern Regions in the first ships.
That great army of Arthur’s had lain all the winter (of 530 A.D.) in the northern islands of Scotland. And on May 3 a part of it crossed over into Iceland. Then four ships of the aforesaid land had come out of the North. And warned Arthur of the indrawing seas. So that Arthur did not proceed further, but peopled all the Islands between Scotland and Iceland, and - also peopled Grocland. (So it seems the Indrawing Sea only begins beyond Grocland). In this Grocland he found people 23 feet tall, that Is to say of the feet with which land is measured.
When those four ships returned, there were sailors who asserted that they knew where the magnetic lands (?) were."

So we have priests who descended from those who had settled the circumpolar areas during King Arthur's time. The Icelandic ships warned the king about the dangers and he didn't go on, but peopled the Orkneys, Shetlands, Faroe (between Scotland and Iceland) as well as Grocland (inhabited by giants).

The letter continues:

" [Arthur afterwards put on board a fleet of 12 ships about] 1800 men and about 400 women. They sailed north¬ wards on May 3 in the year following that in which the former ships had departed. And of these 12 ships, five were driven on the rocks in a storm, but the rest of them made their way between the high rocks on June 18, which was 44 days after they had set out. (More precisely, perhaps, some of them made their way.)
The priest who had the astrolabe related to the king of Norway that in A.D. 1360 there had come to these Northern Islands an English Minorite from Oxford, who was a good astronomer etc. Leaving the rest of the party, who had come to the Islands, he journeyed further through the whole of the North etc., and put into writing all the wonders of those, and gave the King of England this book, which he called in Latin Inventio Fortunatae, which book began at the last climate, that is to say latitude 54°, continuing to the Pole."

The letter then goes on to describe the islands, and seas, mountains, forests, short-statured people not more than 4 feet tall (1.2 m). Interestingly it tells of previous voyagers: "This Monk said that In two other places further inland he found a great piece of ship’s planking and other balks which had been used in big ships besides many trunks of trees which at some earlier date had been hewn down. So that he could say with certainty that there had formerly been habitation there but the people had now gone." and mentions Brazil trees: "All these four countries are high open lands (i.e. plateaus) except some mountains four fathom [sic] high. There are many trees of Brazil wood." A fathom is 1.8 meters or 6 ft. The text continues:

"In the midst of the four countries is a Whirl-pool... into which there empty these four Indrawing Seas which divide the North. And the water rushes round and descends into the earth just as if one were pouring it through a filter funnel. It is 4 degrees wide on every side of the Pole, that is to say eight degrees altogether. Except that right under the Pole there lies a bare rock in the midst of the Sea. Its circumference is almost 33 French miles*, and it is all of magnetic stone. And is as high as (the clouds?) so the Priest said, who had received the astrolabe from this Minorite in exchange for a Testament. And the Minorite himself had heard that one can see all round it from the Sea: and it is black and glistening. And nothing grows thereon, for there is not so much as a handful of soil on it. That was the writing and words of the Minorite, who has since journeyed to and fro five times for the King of England on business. They are to be found in a book called Inventio Fortunae, of which the Minorite himself was author."

* One French mile was known as a lieue or league, it varied according to the region (That is why the French, during the Revolution created the Metric system). It was equivalent to 2-3 miles or 3.6 to 4.8 km.

The four countries were islands that surrounded the Arctic region, they can be seen in the map below. The sea in this area was said to flow towards the pole (indrawing the water and ships into a vortex that flowed into the Earth). It was so strong, according to the letter, "that no wind can make a ship sail back against it." The Rupes Nigra island was made of magentic rock, a giant magnetic mountain that drew all of the compass needles towards the North (interesting explanation for the then unknown Earth's magnetic field). Minorite was the name given to a member of the Franciscan Order of friars, or Orders of Friors Minor, called so because minor means "lesser" in Latin and St. Francis of Assisi held that his followers should be frateres minores or "lesser brothers", living austere lives like he did.

Nicholas of Lynne

The misterious Minorite is believed to have been Nicholas of Lynne, a Franciscan friar. He was also an astronomer and mathematician who lectured in Oxford in the mid 1300s.

In this work, Hakluyt includes a chapter dedicated to Certaine testimonies concerning king Arthur and his Conquests of the North Regions and includes The voyage of Nicholas de Lynna, a Franciscan Frier, and an excellent Mathematician of Oxford, to all the Regions, situated vnder the North pole, in the yeere 1360 in the raigne of Edward the 3, king of England, the text is in Latin and also translated in the same text into English on p.249. Below is the English version:

"Touching the descriptions of the North parts, I have taken the same out of the voyage of James Cnoyen of Hartzevan Buske, which attegeth certain, conquests of Arthur king of Britaine, and the most part, and chiefest things among the rest he learned of a certain priest in the king of Norway’s court, in the year 1364. This priest was descended (In the fifth generation)’ from them which King Arthur had sent to inbabito these Islands, & he reported in the yeere 1360, a certaine English Frier, a Franciscan, and a Mathematician of Oxford, came into those Islands, who leaving them, & passing further by his magical Arte, described all those places that he sawe, & tooke the height of them with his astrolabe, according to the forme that I have set down in my map, and as I have taken it out of the aforesaid Jacob Cnoyen. He said that those foure Indraughts were drawne into an inwarde gulfe or whirlepoole, with so great a force, that the ships which once entered therin could by no means be driven backe againe, and that there is never in these partes so much wind blowing as might be sufficient to drive a cornmill. Geraldus Cambrensis hath certaine words altogether alike with these."

But John Dee seems to have believed the friar was another Franciscan known as Hugo of Ireland (Source), and Thomas Blundeville wrote in 1589 that he didn't believe that the friar had sailed to the Arctic. (Source): "Moreover the north side of the Promontorie Tabin hath 76 degrees of latitude, which place, whatsoever Plinie saith thereof in his fourth 'Booke of Histories', yet I beleeve that no Roman came ever there to describe the Promontorie. Neither doe I beleeve that the Frier of Oxford by vertue of his art of magike, ever came so nigh the Pole to measure with his astrolabe those cold parts, together with the foure floods, which Mercator and Barnardus doe describe both in the front and also in the nether end of their maps, unlesse he had some cold Deuill out of the middle region of the aire to be his guide. And therefore I take them in mine opinion to be meere fables."

Another option is that the information about the polar regions was collected by Ivar Bárdson who travelled to and from Greenland, starting in 1340, in charge of a see there. He must have had first hand information about the islands, seas, and neighboring Canada. He was in Norway around 1360 and could have met the Oxonian franciscan friar there, sharing his knowledge with him (Source).

Comments

The fantasy of the magnetic mountain island, the whirpools and subducting water at the pole make an amazing tale. The pygmies and giants also add to a story adapted to people who were transitioning from the Middle Ages to the Modern times of the Rennaisance and Humanism

The multiple islands, channels, icebergs and strong currents could portray a vision of North America: the tides along Canada's coast, the Estuary of St. Laurence River, Terranova, Nova Scotia and Newfoundland, and the dark forests peopled with strange Native Americans would have excited the imagination of Medieval voyagers and chroniclers.

Interestingly the Brazil tree wood used to dye and tint in Medieval Europe appears in these stories, probably sourced from Brazil in South America, but assigned to these unknown Arctic regions.

There may be an ancient true story hidden in these sagas. It is possible that there were voyages of Monks to these northern islands (Greenland, Iceland, Faroe, Shetland and Orkneys) which also originated the myth of Saint Brendan and his mysterious Island. Then there are the Arthurian folkore of conquests of the norther island which may evoke ancient Celtic voyages west towards America.

Further Reading

B. F DeCosta. Inventio Fortunata. ARCTIC EXPLORATION WITH AN ACCOUNT OF Nicholas of Lynn, Read before the American Geographical Society, Chickering Hall, May 15th, 1880. Reprinted from the Bulletin of the Society.

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