First Asians were not Homo erectus revisited

Back in 2011 I posted The first Asians were not Homo erectus, and proposed some migration routes including one (shown in green in the map included in the post) leading to Flores Island, home of the Hobbit.

Today after reading the article on the 709,000 year-old evidence of hominins in the Philippines (see my previous post), I checked some recent papers on the Flores Island "pigmy" hominin, and found a paper suggesting that they descended from Homo habilis: The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters by Debbie Arguea, Colin P.Groves, Michael S.Y.Lee, William L.Jungersde. Journal of Human Evolution Volume 107, June 2017, Pages 107-133 Journal of Human Evolution. https://doi.org/10.1016/j.jhevol.2017.02.006. Below I quote from the abstract (paper behind a pay wall): note, I highlighted the bold text.

"Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens."

So, the Flores hominin was not afflicted with Down syndrome, instead it was a relict of an ancient (1,750,000 year old) migration out of Africa, which as you can see above is most likely Homo habilis.

Could these "primitive" relatives have moved across the sea into the Philippines... or across Asia and into America, long before Homo erectus appeared on the face of Earth?.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Hominins in the Philippines 709,000 years ago: watercraft?

This paper published in Nature a few weeks ago: Earliest known hominin activity in the Philippines by 709 thousand years ago, by T. Ingicco et al. (Nature volume 557, pages 233–237 (2018) doi:10.1038/s41586-018-0072-8) is amazing: the authors find stone tools and the remains of butchered megafauna several hundreds of thousands of years older than expected. These hominins were not Homo sapiens, and the Philippines was separated from the rest of Sundaland by open sea. So how did they get there? Did they use boats?

The paper says the folowing:

• The remains are between 631 and 777 Ky old. So this is +600 ky older than the alleged Out of Africa event of modern humans.
• They found dozens of stone tools, rather primitive, lacking retouching.
• They also found rhinoceros bones with cut marks and percussion marks (to break the bones), a clear indication of hominin activities.

The authors write: "Our excavations at Kalinga and the numeric dating results clearly provide securely dated evidence for human colonization of the Philippines by the early Middle Pleistocene epoch, and long before the appearance of modern humans in both the local context and wider Island South East Asia region. Although the identity of these archaic toolmakers remains unknown, it is likely that they dispersed over at least one sea barrier to reach Luzon Island. The most likely points of origin are Borneo through Palawan to the west, or China through Taiwan to the north, this latter island was connected to mainland Asia during periods with low sea levels..."

Then they wonder if these hominins are related to more recent remains found at Callao Cave, those of a small adult human:

"...a question clearly linked to our discovery is the origin of the Callao Cave hominin that has been dated to 66.7 ± 1 ka. This diminutive Callao hominin may represent a direct descendent from a Pleistocene migration stock related to these early Kalinga toolmakers—similar to what happened on Flores Island—or may be derived from a more recent migration wave of anatomically modern humans..."

The Callao Cave hominin was reported (New evidence for a 67,000-year-old human presence at Callao Cave, Luzon, Philippines,Armand Salvador Mijares et al. Journal of Human Evolution Volume 59, Issue 1, July 2010, Pages 123-132 https://doi.org/10.1016/j.jhevol.2010.04.008) after the discovery of a metatarsal bone (foot bone) of a diminutive hominin, which may have been or not a modern human:

"[The] metatarsal definitely belongs to the genus Homo. Morphometric analysis of the Callao metatarsal indicates that it has a gracile structure, close to that observed in other small-bodied Homo sapiens. Interestingly, the Callao metatarsal also falls within the morphological and size ranges of Homo habilis and H. floresiensis. Identifying whether the metatarsal represents the earliest record of H. sapiens so far recorded anywhere east of Wallace’s Line".

So it may have been a Homo habilis or even a Flores hominin! or, as the authors of the most recent find suggest, a migration of Homo erectus (see below) that became tinier due to insular dwarfism, see what Ingicco et al say about the rhino slayers:

"Despite the current evidence, it still seems too farfetched to suggest that H. erectus, or another unknown Pleistocene ancestral candidate for the Kalinga toolmakers (for example, Denisovans), were able to construct some sort of simple watercraft and deliberately cross sea barriers to reach these islands. However, considering evidence of overseas dispersal during the Middle Pleistocene stage is increasing in number, such a hypothesis cannot currently be rejected."

For me the important thing is precisely that: they crossed open sea to reach the Philippines. This means they dominated the art of building and sailing watercraft long before humans appeared, at the time that Neanderthals were splitting from the ancestors of H. sapiens (if the Out of Africa theory is correct). But do note how hesitant the authors are, to admit this (they write "too farfetched" instead of admitting that they did build a boat...)

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Sub Saharan Africans admixed with archaic hominins and that gave them more diverse genes

And yes, another post on archaic hominin introgression into modern humans in Africa: Yorubans have admixed with an unknown hominin and this gave them archaic genes. So much for the "diversity" of Sub Saharan Africans as proof of them being ancestral to the rest of human beings.

This paper: Recovering signals of ghost archaic admixture in the genomes of present-day Africans, by Arun Durvasula and Sriram Sankararaman - doi: https://doi.org/10.1101/285734 - says that:

"Yoruban individuals trace about 7.9% of their genomes to an as yet unidentified archaic population."

An eight percent of their genes are archaic far more than the Neanderthal admixture in Eurasians or the Denisovan introgression into non-Africans... This is really a "Big" introgression and that explains why they, the Africans are so different and "diverse" from non-Africans. They mixed with diverse ancient genes of some unknown hominin. So they aren't older than us, they simply "admixed" with archaic hominins.

The authors add:

"suggesting that there was a rich diversity of hominin species within Africa and that introgression was commonplace. Using our inferred segments of archaic ancestry in the Yoruba, we find that there are regions of the genome that are under higher selective constraint have reduced archaic ancestry on average indicating that the archaic alleles were deleterious in the hybrid population. More data is needed for a complete picture of these ghost populations. For example, it is unclear whether the archaic signatures found here are from the same as those found in other African populations"
....
"...Taken together, these results suggest that introgression from one or more deeply diverged populations 278 has shaped the genomes of a modern human population in Africa."

And no, these ancient genes didn't come from mixing with Pygmies. The authors found evidence "...suggesting that the Biaka are not the source of admixture"

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Archaic hominins admixed with Pygmies in Africa

Continuing with the theme of "archaic hominins admixed with modern humans in Africa leading to their current genetic diversity", I read this paper: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies, by PingHsun Hsieh, August E. Woerner, Jeffrey D. Wall, Joseph Lachance, Sarah A. Tishkoff, Ryan N. Gutenkunst and Michael F. Hammer. February 17, 2016, doi: 10.1101/gr.196634.115 Genome Res. 2016. 26: 291-300.

Spoiler alert: the Pygmies, often touted as being diverse, isolated from the rest of H. sapiens, according to this paper, are part of the "...complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.".

An admixture 30 Kya, after the alleged Out of Africa event means that some archaic group with very diverged genes mixed with modern Humans in Africa and gave them "old" and "diverse" genes, which would, in my opinion, make them seem "more diverse" than the rest of non-African Homo sapiens.

Below I quote from this paper:

" Plagnol and Wall (2006) and Wall et al. (2009) inferred a 5% genetic contribution from a now-extinct taxon to the Niger-Kordofanian Yoruba farmers or their ancestors. Hammer et al. (2011) analyzed DNA sequence data from 61 noncoding loci in three contemporary sub-Saharan African populations. They found that hunter-gatherer African populations, including the Biaka Pygmy, Mbuti Pygmy, and San, contain ∼2% genetic material likely introgressed ∼35 kya from an archaic population that split from the ancestors of modern humans ∼700 kya." (This last citation, Hammer et al, is what I mentioned in my previous post).

"...our inferences suggest recurrent archaic admixture in AMH evolution in Africa, with evidence that at least one such event occurred as recently as ∼9000 yr ago."

"...our results imply that frequent but low-level interbreeding between archaic and modern humans or their ancestors might have occurred in the past in Africa."

Of course the dates are uncertain: "... we found evidence of at least one African archaic admixture event within the last ∼150,000 yr. From our simulation study, this inferred admixture date of ∼9000 (95% C.I.: 1305–28,275) yr ago should be treated as a lower bound".

"However, it is important to point out that archaic introgression need not have been directly into the ancestors of modern Pygmies; rather, it may have resulted from recent gene flow from one or more modern human populations that themselves were recently admixed or that shared recent common ancestry with some unknown archaic hominin(s). The date of the inferred admixture is coincident with the development of agriculture in Africa ∼5–10 kya (Phillipson 2005) and the estimated time of agriculture expansion for Niger-Kodorfanian-speaking farmers ∼7 kya (95% C.I.: 5.7–9.6 kya) (Li et al. 2014). African Pygmies have undergone extensive gene flow with neighboring farmers (Patin et al. 2009; Tishkoff et al. 2009; Jarvis et al. 2012; Hsieh et al. 2016), and recent studies suggest that some Western African populations, including the Niger-Kodorfanian Yoruba farmers from Nigeria, show strong signals of ancient admixture (Plagnol and Wall 2006; Wall et al. 2009). Thus, it is plausible that archaic lineages associated with this inferred admixture event introgressed recently into one or more non-Pygmy African populations, such as the ancestors of African farmers, and subsequently entered the Pygmy population through recent gene flow from these non-Pygmy neighboring groups."

So much for the ancient roots of Pygmies and their archaic Y chromosome and mtDNA... could these have been an introgression from these "ghost" archaic hominins?

Interested in archaic introgression within Africa? Check this post: Archaic MUC7 Haplotype introgression in Africa.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

More on archaic introgression into H. sapiens in Africa: the source of African's genetic diversity

In a recent post titled African diversity is the result of admixture with archaic hominids I once again supported the notion that African genetic "diversity" is probably due to admixture between modern humans and archaic hominids in Africa and not the result of Homo sapiens having originated in Africa long ago, and all the rest of non-Africans having less "diversity" due to founder effects & bottle-necks.

Today I came across this paper: Genetic evidence for archaic admixture in Africa by Michael F. Hammer, August E. Woerner, Fernando L. Mendez, Joseph C. Watkins, and Jeffrey D. Wall. PNAS September 6, 2011. 201109300; published ahead of print September 6, 2011. https://doi.org/10.1073/pnas.1109300108.

The paper puts forth proof of an archaic hominin admixing with Homo sapiens during a "recent interbreeding event". The abstract says (I highlighted relevant parts in bold font):

"A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. 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. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.

The authors add "... central Africa may have been the homeland of a now extinct archaic form that hybridized with modern humans".

This is an extremely interesting step in the right direction!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On the genes that regulate teeth, archaic hominins and Africans

A paragraph in this paper: Neanderthal and Denisova tooth protein variants in present-day humans) by Clément Zanolli , Mathilde Hourset, Rémi Esclassan, Catherine Mollereau (Published: September 13, 2017https://doi.org/10.1371/journal.pone.0183802) caught my eye. It pointed out an anomaly: Africans sharing a trait with Neanderthals and Denisovans!

This is what it says:

"The finding in living Africans of rare derived polymorphisms that were present in Neanderthals (Fig 2: ENAM G389S, 5%) or Denisova (Fig 3: CEMP1 R80H, 0.5%) is difficult to reconcile with the fact that interbreeding of AMH with Neanderthals occurred out of Africa [75, 76]. However, as mentioned above, this could be explained by the inside Africa admixture between the ancestors of AMH and archaic hominins, or by the possible back migration of Neanderthal gene flux. Further genome analysis of the Neanderthal and Denisova polymorphisms in AMBN, ENAM, and CEMP1 certainly deserves attention as they could trace back an African ancestor common to Neanderthals, Denisova and early anatomically modern humans."

Well, it is not "difficult to reconcile" if the fact is wrong and AMH interbred with Neanderthals inside Africa...

The ENAM G389S variant is found not only in Africa at 5% but also at very low frequencies in the Americas 0.3% (maybe imported by African slaves or perhaps a genuine Amerindian-Neanderthal admixture). Its global prevalence is only 1.3% and is virtually absent in Asia and Europe. Denisovans carried the ancestral "G" type, found in chimps and gorillas. Neanderthals and modern humans carry the derived "S" type.

They also found a some proteins in Denisovans (K55 E variant) that appear at 26% frequency among Africans and 7% globally (the highest outside of Africa being in America at 2% and far lower elsewhere). This is the ancestral type, found in Denisovans, chimpanzees and modern humans, but it was not found in Neanderthals.

The paper also hints at an admixture in Africa between H. Sapiens and some archaic homo 35,000 years ago:

"Most of the amino acid changes are found in the dentin and enamel proteins that are encoded by genes located in two close clusters on the chromosome 4 (Fig 4) and supposed to derive from an ancestral gene encoding a secretory calcium-binding protein [68]. These clusters fall apart from known haplotypes on chromosome 4 and do not correspond to candidate Neanderthal or Denisovan gene flow regions in non-African living humans [69, 70]. However, a signal of archaic introgression in the locus 4qMB179 on chromosome 4 has been evidenced in Central African populations, and is supposed to result from admixture with an archaic Homo some 35 kya [71]."

Admixture with archaic hominins in Africa would "enrich" the diversity of African DNA and therefore contradict the prevailing theory that Africans are more diverse and therefore they are the "original" source of humanity.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Haplogroups of Humans and Neanderthals and Denisovans: mtDNA and Y chromosomes)

I have just read a paper that refutes my closing comments of this 2014 post: A shared Y chromosome lineage Neanderthals and Modern Humans but it does support the image I posted in it, pictured below:

Hypothetical Y chromosome phylogenetic tree for humans and Neanderthal. Copyright © 2014 by Austin Whittall

I explained the image as follows: "the ancestral population of both humans and Neanderthals, split into two groups: one that would later evolve into modern humans, and another that would evolve into Neanderthals. Each would carry, in the beginning, the "original" archaic Y chromosome of the ancestral population, which, as each lineage accumulated mutations due to chance and positive selection would begin to grow in different directions, forming two distinct branches, which then in turn would continue branching as more mutations appeared."

And that is what the paper states (Reconstructing the genetic history of late Neanderthals by Mateja Hajdinjak et al., 652 NATURE VOL 555 29 march 2018, doi:10.1038/nature26151.) Figure 2 in the article is shown below, and it agrees with the Y chromosome tree that I proposed back in 2014:

Phylogenetic trees for mtDNA, autosomal DNA and Y-chromosome of humans, Neanderthals, Denisovans and Sima de los Huesos hominin. From Hajdinjak et al.

The Human haplogroups are on distinct branches, well away from those of the older hominins.

See this Sept. 2020 update.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On human and Neanderthal - Denisovan mtDNA

There is no evidence at all of extant Neanderthal mtDNA in modern humans. This seems quite surprising, and many explanations have been offered. But the most simple and clear cut one is, in my opinion, the lack of enough samples of Neanderthal mtDNA tested to date. And this is precisely what this paper says: No Evidence of Neandertal mtDNA Contribution to Early Modern Humans, by David Serre, Andre Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, Michael Hofreiter, Göran Possnert, Svante Pääbo (Published: March 16, 2004https://doi.org/10.1371/journal.pbio.0020057)

They clearly state the following:

"..Under the model of a constant human effective population size (Tavare 1984; Nordborg 1998) of 10,000 over time (Figure 4A), any contribution of Neandertal mtDNA to modern humans 30,000 years ago larger than 25% can be excluded at the 5% level (Figure S3). A more realistic scenario may be that the spread of modern humans was accompanied by an increase in population size before and during their migration out of Africa and subsequent colonization of western Eurasia (see Figure 4B). In that case, the Neandertal contribution that can be excluded is smaller (i.e., less gene flow could have taken place)...
It is noteworthy that under the model of constant population size, about 50 early modern human remains would need to be studied to exclude a Neandertal mtDNA contribution of 10%. To exclude a 5% contribution, one would need to study more early modern human remains than have been discovered to date. Thus, definitive knowledge of the extent of a putative contribution of Neandertals to the modern human gene pool will not be possible... ."

The authors indicate that the Neandertal fossil remains carry "closely related mtDNAs that are not found among current humans", in fact all reads are very similar to each other and, different to the standard modern human reference.

They mention the possible causes for this lack of Neanderthal mtDNA in H sapiens: "...such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils.".

Both causes seem very reasonable and the authors fin that this "... excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution."

So, after all, there may have been a small introgression of Neanderthal mtDNA into us.

An intersting point to ponder is that "Although mitochondria retain their own genome, the vast majority of the >1000 proteins that function in mitochondria are encoded in the nucleus" (from The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Joel Sharbrough Justin C. Havird Gregory R. Noe Jessica M. Warren Daniel B. Sloan. Genome Biology and Evolution, Volume 9, Issue 6, 1 June 2017, Pages 1567–1581, https://doi.org/10.1093/gbe/evx114).

This means that the mitochondrial genes and the nuclear genes that encode these proteins (known as N-mt genes), proteins used by the mitochondria, have to adapt to each other during episodes of introgression in order to function correctly and not cause the death of the hybrid individual.

Sharbrough et al then apply this concept to Neanderthal ⁄ Denisovan admixture with H. sapiens:

"The potential for mitonuclear interactions among hominins is of interest because, unlike in the nuclear genome, there has not been any detectable mtDNA introgression from Neanderthals or Denisovans into modern human populations (Krings et al. 1997; Serre et al. 2004). Regardless of what has caused this lack of mtDNA introgression, one consequence is that all introgressed Neanderthal and Denisovan nuclear alleles must function on a modern-human mitochondrial background..."

In other words if there is no Neanderthal or Denisovan mtDNA in humans, our modern mtDNA however must have had to adapt to the N-mt genes that did introgress from our older relatives (Neanderthals and Denisovans). And their paper looks into this.

They concluded that "... genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes."

In other words there wasn't much incompatibility between the mtDNA and the N-mt genes after all! And this was because our and their mtDNA and nuclear genes were, or are, very similar. Which is what you'd expect anyway, we all branched off from the same tree not that long ago (say 750 Ky).

I do look forward to mtDNA sequences more complete in nature, from more individuals (archaic H. sapiens and Neanderthal & Denisovans), who knows, we may actually find one with a shared mtDNA Haplogroup...

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

Neanderthal and Denisovans split around 750 Kya

This paper: Early history of Neanderthals and Denisovans, by Alan R. Rogers, Ryan J. Bohlender, and Chad D. Huff (PNAS September 12, 2017. 114 (37) 9859-9863; published ahead of print August 7, 2017. https://doi.org/10.1073/pnas.1706426114), has some interesting insights into Neanderthal diversity and population size. Below we quote from this paper

"Discussion
These results contradict current views about Neanderthal population history. For example, Prüfer et al. estimate that the Neanderthal population was very small—declining toward extinction. This view receives additional support from research showing elevated frequencies of nonsynonymous (and presumably deleterious) mutations among Neanderthals. This abundance of deleterious alleles implies that drift was strong and thus that population size was small. Yet our estimate of Neanderthal population size is large—in the tens of thousands."

So the authors find that the neanderthal population was large!. They then try to find common ground with other authors, adding:

"To reconcile these views, we suggest that the Neanderthal population consisted of many small subpopulations, which exchanged mates only rarely. In such a population, the effective size of the global population can be large, even if each local population is small. A sample from a single subpopulation would show a misleading signal of gradual population decline, even if the true population were constant. Furthermore, there is direct evidence of large genetic differences among Neanderthal populations. Finally, the rich and widespread fossil record of Neanderthals is hard to reconcile with the view that their global population was tiny. We suggest that previous research has documented the small size of local Neanderthal populations, whereas our own findings document the large effective size of the metapopulation that contributed genes to modern humans."

All of which makes perfect sense. They then address the timing of Neanderthal-Denisovan split:

"...As discussed above, our results also disagree with previous estimates of the Neanderthal–Denisovan separation time. On the other hand, Meyer et al. show that 430 ky-old fossils from Sima de los Huesos, Spain are more closely related to Neanderthals than to Denisovans. This implies an early separation of the two archaic lineages. Our own estimate—25,660 generations, or 744 ky—is earlier still. It is consistent with the results of Meyer et al. but not with those of Prüfer et al., as discussed above. The cause of this discrepancy is unclear. Prüfer et al. use the pairwise sequentially Markovian coalescent (PSMC) method, which may give biased estimates of separation times in subdivided populations..."

So they find a rather old (almost 750,000 years ago) split between Neanderthals and Denisovans.

In their introductory comments they mentioned some competing theories

"Around 600 kya, Europe was invaded by large-brained hominins using Acheulean stone tools. They were probably African immigrants, because similar fossils and tools occur earlier in Africa. They have been called archaic Homo sapiens, Homo heidelbergensis, and early Neanderthals, yet they remain mysterious. They may have been ancestors of Neanderthals and modern humans, or ancestors of Neanderthals only, or an evolutionary dead end. According to this last hypothesis, they were replaced later in the Middle Pleistocene by a wave of African immigrants that separated Neanderthals from modern humans and introduced the Levallois stone tool tradition to Europe."

Regarding the above, the authors write:

"Our results shed light on the large-brained hominins who appear in Europe early in the Middle Pleistocene. Various authors have suggested that these were African immigrants. This story is consistent with genetic estimates of the separation time of archaics and moderns. Our own results imply that, by the time these hominins show up in European archaeological sites, they had already separated from Denisovans. This agrees with Meyer et al., who show that the hominins at Sima de los Huesos were genetically more similar to Neanderthals than to Denisovans. It also agrees with Hublin, who argues that Neanderthal features emerged gradually in Europe, over an interval that began 500–600 kya."

And, they conclude:

"It appears that Neanderthals and Denisovans separated only a few hundred generations after their ancestors left the modern lineage. During the intervening interval, the Neanderthal–Denisovan lineage was small. After separating from Denisovans, the Neanderthal population grew large and fragmented into largely isolated local groups. The Neanderthal metapopulation that contributed genes to modern humans was much larger than the local population of the Altai Neanderthal fossil."

Denisovans admixed with Africans

Among their findings is corroboration of what we already know: "...yn is more common than xn —Neanderthals share more derived alleles with Europeans than with Africans. This suggests gene flow from Neanderthals into Europeans", and then, a startling finding: "More surprisingly, xd is more common than yd. The same pattern appears in all four combinations (YRI.CEU, YRI.CHB, LWK.CEU, and LWK.CHB) of African and Eurasian populations in our analysis. This pattern suggests gene flow from Denisovans into Africans..." (bold mine). This is unexpected: Denisovan admixture into Africans! Maybe it reflects an Out of Asia episode into Africa...

The fact that the Neanderthals were a large population split into sub-groups is very interesting because it is the opposite to what has been widely proclaimed until now: that they were a small, inbred group on the verge of vanishing when they mingled with modern humans...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall ©