Patagonian monsters: July 2017

Wednesday, July 26, 2017

Into Africa: sub-Saharan genetic diversity is due to introgression with archaics

Following up on my previous post, I want to share some more papers on the subject of the admixture of Homo sapiens and archaic hominins in Africa, which may be the cause of the "genetic diversity" which is the main evidence supporting an African origin of modern humans.

This paper (Genetic evidence for archaic admixture in Africa, by Michael F. Hammera, August E. Woernera, Fernando L. Mendezb, Joseph C. Watkinsc, and Jeffrey D. Walld) reached the following conclusions:

"Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary 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."
...
"Th[is] suggests that one such introgression event may have taken place in central Africa (where there is a very poor fossil record). Interestingly, recent studies attest to the existence of Late Stone Age human remains with archaic features in Nigeria (Iwo Eleru) and the Democratic Republic of Congo (Ishango)"

The authors cite This paper (Allsworth-Jones, P., Harvati, K. and Stringer, C. (2010) The archaeological context of the Iwo Eleru cranium from Nigeria and preliminary results of new morphometric studies. In: Allsworth-Jones, P., (ed.) West African Archaeology New developments, new perspectives. BAR, S2164 . Archaeopress , pp. 29-42. ISBN 978 1 4073 0708 4):

""... results highlighted apparent archaic aspects in the specimen in its long and rather low cranial shape, and although modern overall, it also resembled fossils such as Omo Kibish 2 and Ngandong in certain respects. New studies... establish the relatively archaic shape of the vault, and confirm that this Late Stone Age individual was markedly different from succeeding populations.".

So we have archaic humans living relatively recently, and, the recent studies on Homo naledi also show that it was contemporary to the earliest modern humans (but it did not live -as far as we know in Central or Western Africa, but in South Africa:

In This paper we see that Homo naledi, is quite primitive but also relatively recent (The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa. Paul HGM Dirks. https://doi.org/10.7554/eLife.24231.001):

""We... establish[ed] that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity ... interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested ...: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils... we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology."

In other words dating range from 139 to 414 ka but the authors selected intermediate dates. They too seem surprised by its archaic appearance at such a late date.

And it was indeed "archaic" as attested by this paper (Human Evolution: The many mysteries of Homo naledi, Chris Stringer) which says:

"...Berger et al. describe how the collection displays a unique combination of primitive and derived characteristics (Berger et al., 2015). For example, the small brain size, curved fingers and form of the shoulder, trunk and hip joint resemble the prehuman australopithecines and the early human species Homo habilis. Yet the wrist, hands, legs and feet look most like those of Neanderthals and modern humans. The teeth have some primitive features (such as increasing in size towards the back of the tooth row), but they are relatively small and simple, and set in lightly built jawbones. Overall, to my eye, the material looks most similar to the small-bodied examples of Homo erectus from Dmanisi in Georgia, which have been dated at ~1.8 million years old".

Interesting that H. naledi resembles more primitive Homo erectus with an age of 1.8 million years when it is only roughly 200 ka old!.

Another Paper (Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.196634.115 Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies, PingHsun Hsieh et al.) supports this idea of an archaic introgression, but this time, in Pygmies!:

"... our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing model-based whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH (anatomically modern humans), likely within the last 30,000 yr."

These findings plus that of an early presence of Homo sapiens in Morocco - In this paper (New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens, Jean-Jacques Hublin et al. Nature 546, 289–292, 2017):

"...We identified a mosaic of features including facial, mandibular and dental morphology that aligns the Jebel Irhoud material with early or recent anatomically modern humans and more primitive neurocranial and endocranial morphology. In combination with an age of 315?±?34 thousand years (as determined by thermoluminescence dating)3, this evidence makes Jebel Irhoud the oldest and richest African Middle Stone Age hominin site that documents early stages of the H. sapiens clade..."

An age which clearly overlaps that of H. naledi

These findings may lead to an overhaul of the Out Of Africa theory as it is not implausible that H. sapiens originated in Eurasia or even America from other Out Of Africa migrants that departed long ago (Neanderthal ancestors or even H. erectus), and then they peopled Africa recently from North to South and mixed during their Into Africa journey with archaics like Naledi or Iwo Eluru, picking up genetic diversity and carrying it into sub-Saharan Africa with them.

Maybe archaic DNA will be recovered from Naledi and clarify the situation.

Friday, July 21, 2017

On an Archaic hominin introgression in Africa and an earlier date for the peopling of Australia

Today I have come across two brand new and very interesting papers:

The first one tells us that modern Homo sapiens reached Australia much earlier than formerly believed: 65,000 years ago. (Chris Clarkson et al., "Human occupation of northern Australia by 65,000 years ago", Nature 547, 306–310, 20 July 2017, doi:10.1038/nature22968).

The authors point out that "This evidence sets a new minimum age for the arrival of humans in Australia, the dispersal of modern humans out of Africa, and the subsequent interactions of modern humans with Neanderthals and Denisovans.".

The other paper by Duo Xu et al ("Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation", Molecular Biology and Evolution, 2017; DOI: 10.1093/molbev/msx206.) tells us that an archaic hominin interbred with sub-Saharan Africans.

This is an extremely interesting conjecture which the authors state as follows "...we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans...".

This introgression could explain why there is so much diversity in sub-Saharan Africans: they got it from an archaic human (I posted this same idea Here, where I wrote: "This leads me to ask, what if African heterozygosity was enriched by recent admixture with other hominins in Africa? an inflow of different relic alleles elevated African diversity above that of non-Africans" and Here where I wrote: "These ancient African humans carried the A00 lineage in them, mated with AMH (within the last 195 ky)").

The second paper is interesting and I will post on it later because it has some "orthodoxy" influencing its hypothesis, see this for instance, where the authors look into the introgressed halpogroup, (E):

"However, introgression of haplogroup E from Neanderthals or Denisovans is unlikely, because haplogroup E is exclusively found in sub- Saharan African populations, whereas introgression events between Neanderthals or Denisovans with modern humans happened after modern humans migrated out of Africa (Vernot and Akey 2014) (Figure 5A, Figure S5). As such, we hypothesize that an archaic hominin, at that time still roaming in Africa, contributed haplogroup E to the ancestors of extant Africans."

They are assuming that H. sapiens originated in Africa and moved "Out" of Africa. If they had move "Into" Africa from Eurasia, then Neanderthals or Denisovans could have been the origin of the haplogroup...

Friday, July 7, 2017

An even older Out of Africa event (270kya)!!

A paper published in Nature, by Cosimo Posth et al, published in Nature looks into the odd discrepancy in the age of the split between Modern Human and Neanderthal genomes

The date of the split between humans and Neanderthals differs when you consider their nuclear or their mtDNA:

Nuclear DNA says that humans and Nearnderthals split some 765,000 to 550,000 years ago
Mitochondrial DNA or mtDNA says we split 365,000 to 400,000 years ago

I believe that discrepancies are what makes science leap forward (like the problems caused by the "ether" theory that led to relativity and quantum physics). And a gap like this of several hundreds of thousands of years is a big discrepancy. Either the dating is all wrong and has to be reviewed (ie. mutation rates and so forth), or the current ideas on the migration and origin of Homo sapiens are incorrect.

The paper looks into the mtDNA extracted a "complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago..."

This date of 270 kya is actualy the average, the real divergence date between HST and all other Neanderthals (95% HPD) is between 316 and 219 kya. The Altai Neanderthals split from the other Neanderthals some ∼160,000 years ago (95% HPD of 199 - 125 kya).

This paper tries to explain the genetic incongruence of Sima de los Huesos (see my post Sima de los Huesos remains, Neanderthals, Denisovans and their nuclear and mtDNA), the remains from Sima de los Huesos in Spain which are 430 ky old, have mtDNA that resembles that of Denisovans more closely than that of the Neanderthals. But, their nuclear DNA is more similar to that of Neanderthals than to Denisovan nuclear DNA.

The authors write (Bold is mine) that the nuclear DNA (nDNA) "... from the Sima de los Huesos site... confirmed their closer affinity to the Neanderthal lineage, suggesting that at least by ∼430 ka, Neanderthals and Denisovans had already diverged. However, in contrast to genome-wide data, the Sima de los Huesos mtDNA was found to branch off with the deeply divergent Denisovan mtDNA lineage. The phylogenetic discrepancies could be reconciled if the mtDNA of early Neanderthals was indeed Denisovan-like and was subsequently replaced by a more derived mtDNA lineage.".

This "derived mtDNA" got into the Neanderthals through " a genetic introgression event from African hominins into the early Neanderthal population that gave rise to the ‘Late Pleistocene’ Neanderthal mtDNA lineage".

This introgression took place long ago, and came from " an African source, which we constrain taking place more than ∼270 ka". In other words the paper suggests an Out of Africa event over 270,000 years ago which admixed human mtDNA into Neanderthals, mtDNA which replaced the older mtDNA -i.e. Denisovan and Sima de los Huesos hominin, with a new lineage, the "African mtDNA that evolved into the Late Pleistocene Neanderthal mtDNA type". And this "new" mtDNA spread from the HST Neanderthal in Germany to all others, including Sidron in Spain and eastwards all the way to Altai. Thousands of kilometers from the Atlantic to Siberia.

Furthermore, they estimate that "if Ne (effective population) was <5,000 units, a mean temporal interval of 300 ka is sufficient for an incoming mtDNA lineage below 0.1% in frequency to drift up to fixation." in other words, a very small initial input of "African genes".
But looking at this theory with a critical eye, we must point out that Neanderthals were spread out over a very wide area, which makes it very difficult for this replacement to take place in the whole population.

Furthermore a different explanation can be found: if modern humans were already outside of Africa i.e. in Asia, and they mixed with the Neanderthals outside of Africa -no Africans involved in the introgression. They would have had plenty of time to admix over a wide area, and this would also explain why there was an Ancient gene flow from early modern humans into Eastern Neanderthals 100,000 years ago as suggested by Martin Kuhlwilm et al, in Nature, Feb. 2016. DOI:10.1038/nature16544.

So instead of suggesting an earlier migration (it actually took place 1.8 Mya when Homo erectus left Africa for Asia) why not think about H. sapiens living in Eurasia and mixing with Neanderthals?

I wonder how this ties in with the Oldest Homo sapiens remains dating back to 315,000 years ago, found in Morocco?

Sources

(1) Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals, Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause. Nature Communications 8, Article number: 16046 (2017). doi:10.1038/ncomms16046.