Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall

Tuesday, June 10, 2014

A critical post on the current methods of genetics when applied to human ancestry

If you have been reading my posts over the last couple of years, you will notice that time and time again I write about the "early peopling of America". The reason for this is, one one hand, because I believe that our ancestral relatives, either Homo habilis, Homo erectus or even the Neanderthals reached the New World long before the 30 - 15 kya window currently accepted by orthodox mainstream science as the date of arrival of modern humans to the Americas. I also believe that H. sapiens reached America much earlier than that date. However, proof in the shape of stones and bones is lacking, or if produced, is dismissed as geofacts (for the tools) or poorly dated. I have the hunch that Acheulian or Mousterian tools are not even found because nobody is on the look out for them as would be the case in the Old World.

Why do I investigate the early peopling of America?

My original objective for looking into archaic humans in America arose from the intriguing posibility that extant populations of these hominins could have survived until recently in the Americas and been the origin of Native American myths regarding wild men, ogres and bigfoots across the continent. The recent survival of the Flores Island hominin is proof that such an idea is not absurd. Unfortunately we have no proof yet, that any of those hominins ever reached the New World.

My dismay regarding research and a Critique

Being an amateur in this subject, I decided to look into the different findings, sites, dates, the pattern of human migrations, the current ideas regarding the evolution of our species and the hard, solid and factual evidence that is behind the current consensus among scholars that dedicate their lives to study these matters.

My research into these matters, with the open mindeness of a person well read in science, with a University degree in engineering and a sceptic but questioning mentality has opened my eyes to the methods of geneticists and archaeologists. Methods which are often surprising becaus they are unquestioning regarding the evidence they base research on. Some papers are based on educated guesses or cite papers which cite other papers that do the guessing and therefore appear well backed by research and proven by peer review.

Most papers on ancestry and haplogroup datings or admixture between modern and archaic humans are dense models based on computer run simulations with pages of statistical formulae and probabilistic assumptions (mutation rates, migratory events) and equations dredged from previous papers, cited again and again. Seldom are these basic axioms questioned or scrutinized with an impartial approach.

Taking all of the above into account it is very logical to assume that they will all produce similar scenarios supporting the currently prevailing Out of Africa theory.

The model of an Out of Africa migration of modern humans, after they evolved in that continent, and then dispersed across the globe, replacing previous migrants without leaving trace of them has evolved since its inception in the early 1990s, was based on weak premises. But it was acclaimed by all and has adapted: it now admits introgression and admixture with archaic hominins in both Africa and Eurasia (though their mtDNA and Y chromosome haplogroups have vanished without a trace but not so their autosomal DNA-funnily nobody really sees this as unusual...). The African origin theory goes mainly unquestioned.

A dissident Voice against "Out Of Africa"
By the way, there is an excellent paper criticising the Out of Africa theory focusing on many of the things that I have pointed out in some of my previous papers: self-fulfilling circular-logic papers where data is bent or tinkered with to prove something (i.e. calibrate a clock based on a date arising from archaeology and then, via complex genetic inferences and hand-picked data, reach that same date and wield it as proof.
It is a very interesting paper and I recommend reading it: Anatole A. Klyosov, (2014) Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof. Advances in Anthropology 2014. Vol.4, No.1, 18-37 February 2014

The Chinese view of the world OOC

I have also come across some Sino-centric papers written by Chinese scientists at Chinese Universities which seem to promote an Out-Of-China origin of modern humans (Well, after all, Chinese invented the compass, paper, the printing press and gunpowder so it is natural to assume that modern humans come from China too). The story goes something like this: [1]

Our darkest and deepest ancestors appeared in Africa, but soon dispersed: H. habilis moved into Asia (Georgia, Sundaland and Nihewan, China), followed later by H. erectus. The latter evolved in Lantian in China to produce H. yunxianensis which back-migrated to West Eurasia 600 kya and originated H. heidelbergensis and later, the Neanderthals. They also trekked back into Africa, where they were the ancestors of H. rhodesiensis and ultimately the Homo sapiens in Africa, replacing in the process the hominins that had evolved in Africa and Europe (H. leakeyi and H. antecessor respectively).

The hominins in China in the meantime kept on evolving, originating archaic humans in China (H. mapaensis in the South and H. daliensis in the North) some 400 kya. The modern H. sapiens left Africa 120 kya and intermixed with the archaic Eurasians in China and India. They were followed by modern H. sapiens 60 kya which kept on admixing and this "led to the emergence of fully modern Chinese hominans by approximately 35,000 ya." [1]. I rest my case.

Please don't misinterpret me; I have nothing against China or science in China, what is more, I do agree on a dynamic model of human evolution with migrations and introgressions, and even with an Eurasian origin of mankind.

The current one with isolated branches either evolving into other hominins or dying stunted is too linear for me. There is no doubt that the branches criss-cross and merge, but the OOC (out of China) theory is a bit too much for me, lacking as it does, solid proof.

An example of Sino-centrism is a recent paper on the sequencing of the DNA from the Tianyuan remains (allegedly 40 kya, but younger according to others). The bones, from a site close to Beijing, China, show a moisaic of modern and achaic features. However its DNA admixture with Neanderthals is similar to current-day populations in the region (and it has no Denisovan genes). The Sino-centric part comes when the paper claims that its mtDNA is "ancestral to present-day haplogroup B" [2], insinuating that it is the "root" of all Amerindian and South East Asian humans belonging to hg. B. Placing a Chinese origin to the dispersal of these people. But we know that this haplogroup arose in West Asia, in the Caucasus, 50 kya, and not in China 10 ky later.

The findings are interesting: admixture if it happened took place long before 40 kya (otherwise Tianyuan would have more Neander or Denisovan admixture since it had less time to dilute). The Phylo site indicates that the nucleotide mutations place it in the B6 haplotype within R11'B6 [3], which has a more regional distribution than the other B lineages spread across America and Asia:

  • R11'B6 (occasionally also in Japan and South Asia)
    • R11 (recorded in Hainan but not in Laos.)
    • B6 (Centred on South China. Recorded in Laos but not in Hainan. )

By the way, the paper explicitly mentions in the mtDNA sequence, a long deleted block at positions 8281-8289 (this is the famous 9bp deletion), which if you search for it in the Phylo Tree page above will turn up 4 times! Meaning it is not so uncommon or perhaps that it is ancestral and the haplogroups should be reviewed to accomodate it in a better way. This is an interesting marker and will be scrutinized in future posts.

Surviving Homo erectus

Despite my misgivings, I do find some papers very interesting, like the one that claims that Homo erectus survived until very recently in Northern China [4]:

The Lantian site, close to Xi'an (renown for its imperial tomb with hundreds human-sized terracota warriors) has unveiled stone artifacts of a clear Acheulean technology. The site is located on the terraces of the Bahie River and its toolage has been dated to the period between 70 and 30 kya. (Wang et al., 2014) [4].

This relatively modern dating (and the type of tools, which includes hand-axes), implies that Homo erectus was alive in the Lantian region "from the early and middle Pleistocene to the later period of the late Pleistocene" [4].

There is also a paper [5] (more below) that hints at a recent introgression, in Africa between archaic humans and modern ones some 37 kya. These archaics had split from our line between 700 and 2,100 kya, meaning they could be any hominin from H. erectus onwards.

But, except these two papers, Homo erectus is seldom mentioned in any of these papers concerning admixture; they are regarded as a dead end, perhaps extinct by the time modern humans reached East Asia. Not many follow up on the clues on the possible admixture from H. erectus into modern humans, as suggested by Prüfer et al., 2013 [6]: that Denisovans carried an introgression from an archaic hominin that split from our line over 1 Mya. (H. erectus perhaps?).

(Well, some do follow up, sort of, as you will see below in point 3 or 4)

And the possibility of H. erectus entering America, migrating across Northeastern Asia is, of course, completely ignored (excuses given: too dim witted to deal with the cold Arctic conditions, not able to navigate, etc.).

Competing Theories are good for Science

But, fortunately for Science, new ideas appear, and they are analysed from different points of view and with different tools; this is good for science and for the advancement of our knowledge.

It seems that almost everyone now agrees that there was admixture between Neanderthals and Modern Humans (While not too long ago -see Herrera et al., 2009 [7], there were serious doubts and scepticism regarding admixture). Then we have the mysterious Denisovans whose genome is found in high proportion of Melanesians and Papuans but not among South East Asians.

We are know asking: Who admixed with who? did Africans admix with Neanderthals? What is the degree of all this admixture?

And the answers differ and even have opposite points of view, as we can see below (from a very small sampling on the matter), and from these differences, Science will grow stronger:

  1. Neanderthal DNA Only in Europeans: 3.6% introgression in Europeans with a decreasing cline as you move away from Europe. Neanderthal genes in Africans' (as well as Denisovan presence in Melanesians and Papuans) is not due to admixture but to "the retention of ancient mutations in these populations" [8], that is, the archaic genes survived in them -but, may I ask, why did they disappear in Europeans?
  2. 40% More Neanderthal DNA in East Asians (9.6%) than Europeans (6.4%). The Maasai of East Africa have a small but significant fraction of Neanderthal DNA but not through direct contact with them, but with Eurasians humans carrying Neanderthal DNA in them; a "Back into Africa Migration".
    Admixture with Neanderthals happened at least twice or, over a long period of time 50,000 to 80,000 ya., with Europeans splitting off first and therefore being less exposed to Neanderthal genes. [11]
  3. Archaic admixture in Africa: "African populations contain a small proportion of genetic material (~2%) that introgressed ~35 kya from an archaic population that split from the ancestors of anatomically modern humans ~700 kya.... [which] introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa." [5]
    This study sets the split between our line and the "archaics" at 1.25 Mya (95% CI, 0.7–2.1 Mya) and an admixture time of 37 kya (95% CI, 1–137 kya). Note the very very large Confidence Intervals. [5]
    When CI are large, I begin to wonder about the soundness of the statistical tools used...
  4. Not one, but many introgressions. This one is interesting; it finds "introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes" [9]
    These episiodes of admixture are shown in the image below. The "E" hominin may be H. erectus or even "australopithecines, which inhabited Africa; it was proposed that those hominins might have migrated out of Africa at ~3 Mya" [9]. Note however that "E" does not admix with modern humans either in Africa or Asia, it is an indirect influx via Neanderthals or the unknown X hominin (EN + N or X arrows) or an admixture with the pre-OOA humans (EA arrow), which takes us to the case proposed in point 3 of an introgression in Africa.

admixture in humans from archaic hominins
Figure 3, from [9]

This last paper is interesting but we don't see an admixture between H. erectus and humans in Eurasia, only indirect introgression via Neanderthals or X hominin. In this context, the mtDNA extracted from the remains of Sima de los Huesos, Spain, belonging to a Mid Pleistocene H. heidelbergensis about 300 ky old. may give some clues:

It shows that these archaich Spaniards shared descent with the Denisovans, implying that the Denisovans of Altai and the Sima de los Huesos people formed a clade with a common ancestor some ~800 to 900 kya, which is not the same ancestor of Neanderthals and modern humans. [10]

Could this ancestor be H. erectus who had been in Eurasia for nearly 1 My at that time? or the descendants of Georgian H. habilis? Is there any other candidate from out of Africa at that time?

Interestingly we have the H. heidelbergensis in East Europe which must have extended its range or even migrated into Western and Central Asia to originate our mysterious Denisovans. Did this happen before the appearance of the Neanderthals in the Middle East? or did they overlap?

Now if Neanderthals did not originate from the European H. heidelbergensis as thought until now, where did they evolve? In the Levant, and migrated from there into Europe and West Asia?

Regarding the genesis of these clades, notice that we see very deep splits between mtDNAs not in Africa, but in Eurasia: so much for the OOA. But then, these are mtDNA lineages, what do the autosomal and the Y chromosomes have to say, we have no input yet. But it will be interesting when we do.

And these questions, the migrations and admixtures of our ancestors, take me back to a post (First Asians were not H. erectus) (Sept. 2011), where I mentioned the initial departure of H. habilis from Africa for Georgia in Asia. The image below is an update of the original one from that post.

human dispersal since H. habilis
Hypothetical routes of our ancestors out of Africa. Copyright © 2014 by Austin Whittall

The paths drawn above start with an Out of Africa event, long ago: H. habilis leaves Africa, reaches Asia where it evolves into H. erectus. Some H. habilis reach Indonesia the ancestors of Flores hominin, others may have reached America. The H. erectus cross Europe becoming the ancestors of the Sima de los Huesos people, and also re-enter Africa and they go East too, into South Asia and China. Some march on, into America. The Afro-European hominins evolve into Neanderthal, the Eurasians (now it seems that it is the H. heidelbergensis of Europe) into Denisovans.

They all admix as they criss cross their territories. Somewhere (Africa? Asia? or why not, America?) modern humans appear and also mix with the surviving archaics.

This possible story outlined above, is of course a wild conjecture, with no proof to back it. A fancy tale.

But who knows, maybe if I phrased it using formulae with Greek letters (θ, ρ and so on,) framed with obscure statistical phrases ("the likelihood function f(γ), describing the probability -p(x,y,n)- of the data under different parameter values; and f(z) is the total probability of the data summed and integrated over the parameter space considering a bias scatter ratio in the Bayesian inference based on the...") and ran a Computer program to validate it ("We then ran (n=1,000) simulations on GATACCA® using 150,000 ARGs for each parameter value, storing approximations of the summary statistic distribution, discarding outliers below conformed threshold ratios...")... would someone buy it?

Mind you I am an engineer with a solid foundation in statistics, advanced maths and am particularly fond of quantum mechanics but in all honesty, most genetics papers nowadays are based on statistical simulations.

And we should not forget that simulations are only as robust as the models they are based on, and models tend to oversimplify reality using assumptions that may or may not be correct. The ample confidence intervals informed in many papers is a clear indication of uncertainty in the models and the variability within the sample employed.

Other factors such as migrations influx, population sizes and growth, generation duration and mutation rates also impact on the models' predictions. Explaining anomalies away aducing bottlenecks, founder effects and genetic drifts is like invoking ether for light transmission in the pre-relativity days of modern physics. Predictions should be made and validated by the models to prove reliability.

Thanks for bearing me out!


[1] Dennis A. Etler, LI Tianyuan, A Multiple Dispersal Hypothesis for Interpreting the Pattern of Hominan Evolution in China
[2] Qiaomei Fu, et al., (2012). DNA analysis of an early modern human from Tianyuan Cave, China. PNAS vol. 110 no. 6 2223–2227, doi: 10.1073/pnas.1221359110
[3] van Oven M, Kayser M., (2009). Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. doi:10.1002/humu.20921.
[4] Shejiang Wang et al., (2014). Newly discovered Palaeolithic artefacts from loess deposits and their ages in Lantian, central China. Chinese Science Bulletin Jan- 2014. 10.1007/s11434-013-0105-5
[5] Michael F. Hammer et al., (2011). Genetic evidence for archaic admixture in Africa. PNAS. vol. 108 no. 37 15123–15128, doi: 10.1073/pnas.1109300108
[6] Prüfer K.,et al., (2013). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43-49.
[7] Kristian J. Herrera et al., (2009). To what extent did Neanderthals and modern humans interact?. Biol. Rev. (2009), 84, pp. 245–257. doi:10.1111/j.1469-185X.2008.00071.x
[8] Lowery RK et al., (2013). Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms. Gene. 2013 Nov 1;530(1):83-94. doi: 10.1016/j.gene.2013.06.005. Epub 2013 Jul 19
[9] Ya Hu, et al. (2014). Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History. arXiv preprint arXiv:1404.7766
[10] Matthias Meyer et al., (2013). A mitochondrial genome sequence of a hominin from Sima de los Huesos Nature (2013) doi:10.1038/nature12788
[11] Jeffrey D. Wall et al., (2013). Higher Levels of Neanderthal Ancestry in East Asians than in Europeans. Early Online February 14, 2013, doi: 10.1534/genetics.112.148213 Genetics May 1, 2013 vol. 194 no. 1 199-209

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