Homo erectus left Africa earlier than thought (New 2026 paper)

As mentioned in yesterday's post, there have been some recent discoveries that are changing what we knew about the spread of our ancestors out of Africa and across Eurasia.

A new paper has disclosed that the site of Ubeidiya, in the Valley of the Jordan river has been dated to an age older than 1.9 million years. This is relevant because Acheulean tools, typical of Homo erectus have been found in those sediments, and this date is much older than previous estimates, pushing the first Out Of Africa event further back in time.

The paper: A. Matmon, et al., (2026). Complex exposure-burial history and Pleistocene sediment recycling in the dead sea rift with implications for the age of the Acheulean site of ‘Ubeidiya. Quaternary Science Reviews, Volume 378, 2026, 109871, ISSN 0277-3791, https://doi.org/10.1016/j.quascirev.2026.109871. 🔒

The Abstract reads as follows: "We present early Pleistocene burial ages of the ‘Ubeidiya Formation sediments in the Jordan Valley, a segment of the Dead Sea Rift Valley. A minimum age of ∼1.1 Ma is constrained both by paleomagnetic analysis and U-Pb dating of Melanopsis shells. Simple cosmogenic burial ages (i.e., one very long exposure period followed by one period of burial) calculated from the ratios of 26Al to 10Be and 10Be concentrations indicate ages of ∼3 Ma, contradicting the geological and paleomagnetic constraints as well as a reasonable age of the ‘Ubeidiya archeological site, as it contains human remains. A more sophisticated way of treating the results, by combining numerical modeling of cosmogenic nuclide build up during repeated burial-exposure cycles, paleomagnetic analysis (indicating reverse polarity) and a minimum burial age of 1.1 Ma set by U-Pb dating of Melanopsis shells, suggests two most probable time slots (1.19-1.77 and 1.93- 2.14 Ma) for the absolute age of the ‘Ubeidiya Formation. However, the skewed distribution of cosmogenic isotope burial ages, with a median age of 2.05 Ma, indicates a much higher probability of the older ages, most likely >1.9 Ma. The exposure-burial history that emerges from the model implies recycling of sediments previously deposited and buried in the rift valley, between 4.5 and 3.2 Ma, and subsequently exhumed, eroded, transported and then redeposited along the ‘Ubeidiya paleo lake shoreline."

Previous research had provided inconclusive dates, and used obscure methods. The consensus dates for the tools found there were between 1.2 and 1.6 million years. So this discovery pushes the first Out Of Africa migration back at least 300,000 years.

Furthermore, some previous dating of 3 Ma was due to the "recycling", that is the erosion of old strata, the transport and reburying of older sediment further down the valley making the sites seem older than they really are. However, the burial of sediments also preserved the information of magnetic field reversals which is a useful tool to date old strata ( magnetostratigraphy), the team also used radioactive decay of isotopes formed by cosmic rays in chert and quartz, and dating of snail shells using radioactive decay of Uranium to Lead. These three methods helped define the dating.

These dates make sense, because the earliest homo found in Eurasia, at Dmanisi, Georgia is slightly younger. This earlier presence of erectus in Israel, suggests that these erectus could have moved north towards Georgia, and also east, across Asia, reaching Eastern Asia (Indonesia and China) much earlier than previously expected (as we will see in my next post), and also, a possible continuation of their journey into America. They had almost 2 million years to do so before the arrival of Modern Humans in Eurasia.

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

China is redefining hominin evolution

A paywalled paper published three days ago (Feb. 24, 2026) in Nature (Yang, SX., Martinón-Torres, M. & Petraglia, M. Palaeoanthropological evidence from China is changing the picture of hominin evolutionary history. Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-026-02983-w) reports on the recent research, datings and findings in China that have upended conventional beliefs about the evolution of our species.

"Abstract
Recent palaeoanthropological discoveries in China indicate that eastern Asia had an important role in the evolutionary history of the genus Homo over the past 2 million years. New taxonomic proposals have been made to re-group archaic human fossils, including those considered to be Denisovans, as Homo juluensis and Homo longi. The hypothesis that the affinities of Yunxian 2, dated to about 1 million years ago, also infer an early divergence of the Homo sapiens lineage further underscores China’s pivotal role in global evolutionary narratives. Here we explore key biological and cultural evidence emerging from the Chinese record and its evolutionary implications, raising questions about the relationships between ‘transitional’ clades and their differing adaptive capabilities. Rather than an evolutionary cul-de-sac, China now appears as a dynamic evolutionary crossroad where multiple Homo lineages may have arisen, interacted and adapted to shifting environments. The growing fossil and genetic evidence point to a diversity of populations whose demographic history and gene flow exchange helped to shape the broader mosaic of our species."

In my next two posts I will look into two very papers that report two remarkable findings: an earlier age for the first Out Of Africa event that saw Homo erectus enter Asia (or possibly, even an australopithecine) leave Africa 1.95 million years ago, and also a much older date for erectus' arrival in China. Plus two other papers mentioning sites that are possibly over 2 million years old in China.

I am not a Sinophile, and not because I dislike the Chinese people or their culture, quite the opposite. I have visited China many times before I retired as I worked for several years with companies there, visited customers, traveled the country extensively. I spent vacations there, with my wife, and I also have Chinese friends. I enjoy the food, the rich history, the diverse culture, and its natural sights. I am reluctant to embrace China because I am at odds with the system that governs that great nation. The Chinese Communist party, allied with the People's Liberation Army, is a one-party system that perpetuates a caste, an elite, living in luxury, backed by force that has, for the past 77 years destroyed and ignored the human rights (as we see them with our Western eyes) of its people, jailed opposition, suppressed free press, and supported dictators (like the ones who govern Iran, North Korea, and Russia). Then there are the territorial claims in the South China Sea (Spratly Islands), and its heavy handed attitude with South Korea, and Japan. Add to that the official silence over the origin of the Covid-19 pandemic, and how it has gradually eroded the rights agreed upon with Britain for Hong Kong ("One country, two systems", for 50 years) and is slowly but surely imposing its totalitarian views and police-state grip there. The increasingly aggressive stance with Taiwan, the Republic of China, a thriving democracy, is also troubling.

Nevertheless, I am glad that research is uncovering new findings in China. This will help us understand how our ancestors peopled Asia, America, and the interplay between the different branches of hominins.

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

Human Genetic Diversity: Some Maps

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

My 1000th post!

This is my post number one thousand!

It has been over sixteen and a half years since my first post on August 19, 2009!

I am quite proud of having come so far, and I thank you for your support, and patience. I know that some posts may be boring, others may also be outside of the scope of this blog, and others may sound like pseudoscience, or pure BS, but I try my best to provide engaging content and share interesting information with all of you.

I will do my best to keep on posting quality content.

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

Templeton's critique (Admixture, Statistical Tools)

American geneticist and statistician Alan R. Tempeleton (b. 1947), at Washington University in St. Louis, U.S., has been an outspoken and vocal critic of the use of Bayesian statitstics to support the Out Of African theory, and the replacement of ancient humans in Asia by our more recent African ancestors.

He holds a master's degree in statistics, so he is an expert in that field, unlike most geneticists (by the way, he also holds a doctorate in human genetics). This places him in the unique position to understand the genetics underlying the black-box algorithms used by researchers. He knows the statistical tools.

Templeton has criticized the incorrect use of Bayesian calculations and the mathematical and formal errors reproduced in different research publications.

His arguments sound solid, and professional. He disputes the missuse of specific statistical tools, as only an expert can. Below are some excerpts from his work.

One paper published in 2023 (Templeton A. The importance of gene flow in human evolution. Hum Popul Genet Genom 2023; 3(3):0005. https://doi.org/10.47248/hpgg2303030005) states the following:

"By the 1980’s CE, the paleontological record had convinced most scientists that the ancestors of humans had first evolved in Africa and then spread out into Eurasia in the early Pleistocene as Homo erectus. However, there was no consensus on what happened next. Three major models emerged by the latter half of the 20th century: the out-of-Africa replacement (OAR) model [1], the candelabra model of racial isolates [2], and the multiregional model [3,4]. Both the OAR and candelabra models posit that the expansion of Homo erectus into Eurasia results in independently evolving populations with no or extremely little genetic interchange. The OAR model in addition assumes a more modern form of humans, Homo sapiens, first evolved in Africa followed by an expansion into Eurasia, where the more modern humans completely replaced the archaic inhabitants of Eurasia. In both of these models, human evolution is dominated by splits into isolated lineages, followed by mostly independent evolution within the isolates. The OAR model in addition posits that the African isolate evolved into a form that expanded into Eurasia where it drove to extinction all the archaic Eurasians without genetic interchange with them. There is no or little role for gene flow in human evolution under these two models: rather, human evolution is dominated by splits, isolation, and extinction of lineages. Weidenreich’s multiregional model takes an opposite position on the importance of these evolutionary forces. There are no splits or isolates in his model because all human populations are interconnected by gene flow.
...
Despite the extensive evidence for gene flow and the lack of evidence of highly isolated evolutionary lineages, much of the human evolutionary literature is still full of “splits’, “divergence times of populations”, and pictures of human evolutionary trees showing separate branches leading to modern day Europeans, Asians, and Africans. These “splits”, “divergence times”, and “trees” are typically estimated with computer programs that will automatically yield a population tree regardless of whether or not the underlying data has a tree-like structure."

This is a clear description of the OOA hypothesis, and the expansion of hominins from Africa into Eurasia. Then he mentions the artifacts and models created with computer programs (trees, splits and dats for the forks of the branches of those trees). This is a novel point of view. It shows how we frame our ideas in models that then restrict how our thoughts can evolve in the future. A generation of geneticists thinks in terms of trees, splits, divergences, and coalescence dates.

In 1995, Templeton developed a statistical method called Nested Clade Phylogeographic Analysis or (NCPA) which uses genetic and geographic data to study how a population evolved (more about it in this paper). He mentions this method in his 2023 article, which continues below:

"... aDNA studies have confirmed the most controversial conclusion from NCPA that there was limited genetic interchange between the expanding out-of-Africa population with Eurasian populations. Moreover, genomic studies have revealed much genetic interchange and movement of human populations over the last 100,000 years, as reviewed in. One common method for achieving such inferences is to assume an evolutionary tree for the populations being sampled, and then calculate from the sequence data various statistical tests such as ABBA/BABA or several other alternatives... These statistics are tests of the null hypothesis that the underlying data do indeed come from a tree of populations. Rejection of this null hypothesis indicates that genetic interchange occurred that violated the assumed tree-like structure. When these tests reject a tree-like structure, often an admixture event of genetic interchange is assumed to have occurred to explain the rejection of the null hypothesis of a tree. For example, Figure 4... presents a typical visualization of this type of analysis."

Figure 4 is reproduced below.

Regarding the term "null hypothesis" used by Templeton, it is a statistical term used when one analyzes if the difference between two features of a population are due to chance, sampling errors, or some unknown real variable. To do so, one defines a null hypothesis (in this case, the differences between populations are due to a tree-like structure) and then performs rigorous statistical tests to compare the samples to see if chance or a real effect is responsible for any differences (usually a Student's t-test, created by English statistician William Sealy Gosset (1876–1937), aka Student), one also specifies a probability (the significance level or p), usually 5%, which sets the rejection threshold. If the calculated probability value from the t-test is lower than the significance level, one can reject the null hypothesis and accept that the results are not caused by random chance alone. In Templeton's example the null hypothesis was that tree populations explain human populations' genetics. But statistical analysis rejects this hypothesis meaning that some other genetic factors have intervened that are not tree-like. To save the day, geneticists have concocted admixture events into their trees to explain away the null hypothesis rejection.

Fig. 4 in Templeton
Figure 4. A simplified version of Figure 8 from [51] that shows the estimated gene flow between populations of modern humans and various archaic populations. Gene flow from modern humans into archaic hominins was not estimated.
Source

Tempelton rejects these admixture patches and the concept itself:

"There are two serious problems with this analytical approach. First, these test statistics have an identifiability problem as they cannot distinguish between a single, virtually instantaneous admixture event, versus multiple, recurring admixture events, versus continuous gene flow, or versus gene flow with isolation by distance.
Hence, figures such as Figure 4 are visually misleading as they imply a degree of knowledge that is not truly available from the test results. Drawing a trellis between populations with gene flow would have been equally justified for Figure 4. Other workers have used fossils from different time periods and/or analytical techniques that make use of the length of introgressed genomic segments to infer recurrent and frequent genetic interchange between Neanderthals and modern humans in Eurasia from 100,000 ybp to 37,000 ybp, and perhaps as far back as 270,000 ybp.
Hence, Figure 4 is not only visually misleading, it displays a false narrative for Neanderthals and modern humans. The only conclusion that is justifiable from these ABBA/BABA and similar analyses is the falsification of the null hypothesis that these populations are interrelated through an evolutionary tree. The null hypothesis of human population evolutionary trees has been falsified again and again since the mid-Pleistocene (as reviewed in Chapter 7 in [19]), and this is not surprising as NCPA already indicated that since the mid-Pleistocene human population structure has been dominated by population movements and/or individual dispersal coupled with interbreeding, with no significant role for splits and isolation"

Then he attacks the statistical logic behind the analysis that leads to these trees, and points out how researchers use computing tools to suit the outcome they are searching for, and don't quite grasp the meaning of the output of these programs:

"The second and more serious reason why figures such as Figure 4 are misleading is that the analytical method of starting with a tree and then adding connections to reflect gene flow is that this approach is statistically inconsistent when the actual relationship of the populations is a more complicated network than a simple tree.
Statistical inconsistency means that the estimators do not converge to the true answer with increasing amounts of data; indeed, the more data you have, the more likely you will have the wrong answer. Patently, inconsistency, just like incoherence, is a highly undesirable statistical property. This inconsistency is illustrated by the work of Pugach et al. They analyzed genomic data from Siberian populations for which some prior demographic historical information was available. Using the TreeMix program that starts with an evolutionary tree of the populations followed by adding on admixture events as needed, they found that the “TreeMix results were not easy to interpret and seem to contradict well-accepted aspects of human population history.” They then analyzed the same data with SpaceMix, a program that does not assume an underlying evolutionary tree. In contrast to TreeMix, the SpaceMix results fit the genomic data better and without contradictions to well-accepted aspects of the population history. SpaceMix indicated a history that included isolation by distance, long-distance dispersals, and multiple admixture events – all of which violate the assumption of a population evolutionary tree. Because of inconsistency, the credibility of figures such as Figure 4 is highly questionable in human evolutionary studies."

Templeton then attacks the use of trees and the lack statistical knowledge or interpretation by scholars:

"Despite the almost universal rejection of tree-like structures in human evolution since the mid-Pleistocene, some workers in this area still construct population trees using programs that will always generate a tree no matter how bad the fit is to a tree, treating each human population as an isolate on its own branch of the tree without any indication of any genetic interchange between branches... These population trees are typically presented without any statistical assessment of how well the tree fits the underlying genetic data. I tested the tree given in [63], and rejected a tree-like structure with a p-value < 10-200. To say the least, this is an abysmal fit, and the utility of such poor-fitting trees to gain insight into human evolution and population structure is highly questionable."

I agree with Templeton, and in the past posted on these tools (Some thoughts about the tools used in genetic admixture analysis), remarking that a craftsman is only as good as his tools.

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

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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