HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory

Short comment. I have just read this paper: Transmission Between Archaic and Modern Human Ancestors During the Evolution of the Oncogenic Human Papillomavirus 16 by Ville N. Pimenoff, Cristina Mendes de Oliveira and Ignacio G. Bravo. Mol Biol Evol (2016), doi: 10.1093/molbev/msw214, First published online: October 7, 2016.

I am trying to see how it fits in with a non African origin of mankind because the authors are trying to fit their finding that the oldest and most diverse haplogroups of HPV 16 are not found in Africa, but out of it (the African variants of HPV are newer and less diverse) within the Out of Africa theory. And it may not be the case.

Above a map showing distribution of the main clades and below. Some quotes from the paper:

"HVP16A (fig. 2) (is), the most basal HPV16 lineage, in all continents and in all indigenous populations, except in sub-Saharan Africa"

"Moreover, for indigenous populations in South America, for instance, the increased presence of HPV16A lineage variants has been proposed to reflect the influence of recent European occupation (Picconi et al. 2003). However, such a rapid selective sweep of the putative pre-Columbian HPV16 genetic diversity would require strong selection forces for the viral dynamics in very short time scale, which are not compatible with our current understanding of PV evolution"

These Amerindians always have some oddity regarding their genetics, don't they?

"...most common HPV16A lineage haplotypes were observed mostly in Eurasian populations while most common HPV16B, C and D lineage haplotypes were observed mainly in African populations...
Neanderthals/Denisovans may have carried essentially the ancestral HPV16A. Evolution of HPV16 genomes in ancestral Hominin populations remaining in Africa, instead, would have lead to HPV16B and CD lineages (fig 4). The virtual absence of HPV16B outside Sub-Saharan Africa is parsimoniously explained if in the last out-of-Africa expansion, the modern human ancestors that left Africa probably lost the ancestral HPV16B lineage by a lineage sorting event ..."

And the above is the theory put forth by the authors to explain the anomaly of less diverse HPV in Africa vs. the Rest of the World.

"After the modern human dispersal, the HPV16CD ancestor generated in allopatry the HPV16C lineage in the populations remaining in Africa, and the HPV16D lineage in the populations outside Africa (fig. 4). During their expansion in Europe and in Asia, modern human ancestors experienced limited admixture with Neanderthal and Denisovan populations, and were exposed to the HPV16A lineage, most likely through sexual contact..."

But this is all conjectures, there is no physical evidence of HPV in Denisovans or Neanderthals:

"... there is hitherto no evidence of the presence of any PV sequences from ancient human samples. Indeed, we analysed the currently available Neanderthal and Denisovan pre-assembly sequence data, and we could not find any significant traces of any known HPVs in these data sets"

"... that the HPV16A1-3 lineage predominated in Europe, South Asia and Central/South America, and was also present in all other continental subgroups, albeit with very low prevalence in sub-Saharan Africa (fig. 2). HPV16A4 was the most prevalent lineage in East Asia and was also present in North America, but was virtually absent elsewhere. Variants B and C were largely restricted to Africa and were especially prevalent in Sub-Saharan Africa, although they were also observed in North America. Variant D was present in all continents, displaying low prevalence in Sub-Saharan Africa, and the highest frequency in Central/South America.·"

Why is "D" highest in the Americas if it is supposed to have originated in Africa (see further up)... slave trade by Europeans? We'd need to see Karitiana or Coya, Pima haplogroups...

Then we have the time frame!! (rather wide): "Depending on substitution rate priors, divergence times of extant HPV16 lineages showed to be between 260 kya and 4.8 Mya"... early enough to be older than our oldest relatives. It may also leave the window open for an Homo Erectus migartory event into Asia carrying the ancestral HPV16A root. And the diversity issue also seems odd: "Although HPV16A was thus always the basal clade, divergence within HPV16A showed to be lower than within HPV16BCD" So the oldest group with A type haplos are less diverse among them than the BCD are.. maybe some ancient bottleneck in the A groups?.

And the diversity again: " East Asian and Central American HPV16 isolates showed higher average number of pairwise differences compared with sub-Saharan African isolates, even after accounting for intralineage diversity.", what? something in America more diverse than in Sub-Saharan Africa... why?

"... although HPV16A is the oldest lineage, the tmrca for the HPV16BCD variants (197kya, 95% 121-291kya) was older than the tmrca for the HPV16A lineage (88kya, 95% HPD 50 – 134kya), and the HPV16A lineage encompasses less genetic diversity than the sister HPV16BCD lineages." This is odd, again the diversity issue (bottleneck) but the split is younger in the "oldest" lineage?? That sounds odd.

I will keep on trying to make sense of this, and post later on this finding.

New 03 Nov. 2018, following a recent paper published two days ago, I have added a new post on this subject: HPV Neanderthals, Africans and the early peopling of America

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

Heterozygosity for dummies

Heterozygosity is lower in all non-Africans when compared to Africans.

What does this mean?

First of all what is Hetrerozygosity?

Heterozygosity

We all have two copies of each gene. That is because we got half of our chromosomes (with their respective genes) from each of our parents), making one copy from each of them.

Genes come in different variants, known as alleles.

So if there are two possible alleles: "b" and "B" (one per gene) you may have any of the following combinations arising from the mixing of your parent's genes

• bb
• bB
• Bb
• BB

That is four options, two in which each gene has the same allele (bb, BB) and therefore you are Homozygous and two in which you have different alleles (bB, Bb) which makes you Heterozygous.

It is evident that homozygosity implies less genetic variability (being BB you lack the "b" allele or if you are bb, you will lack the "B" allele). And this may have consequences regarding your health and surviveability.

Populations.

We must also take into account that the proportion of "b" and "B" in can be different, in other words they are present at different frequencies: "p" and "q" respectively which are not necessarily the same.

In other words the frequency of each genotype (bb, Bb, or BB) in a given population (known as "allele frequency") will depend on the frequencies of each allele:

In a very large (infinte) population where individuals mate at random, we can calculate the allele frequency using the Hardy-Weinberg Theorem using this formula to calculate the frequencies (f) of each of the three genotypes (bb, BB, Bb):

• f(bb) = p²
• f(bB) = 2pq
• f(BB) = q²

And since they are "all" the genotypes, their sum must add up to 100% of the populaton:

100% = p² + 2(pq) +q²

Say b is present at p = 30% and B has a frequency of q= 70% (both frequencies must aldo add up to 100%), then:

100% = (30%)² + 2(30% x 70%) + 70%²

100% = 9% + 42% + 49%

So the frequency of bb alleles is only 9% meaning that 9% of the population is homozygous for b. 42% is heterozygous and 49% is homozygous for B.

But in a real world, humans don't mate randomly: they choose partners for different reasons, or, due to cultural rules may marry within their group (endogamy).

Also some homozygous alleles may cause genetic diseases such as cystic fibrosis, Tay-Sachs or phenylketonuria which may kill individuals before they become adults and reproduce, here selection is actively working to modify zygosity.

As populations are not infinte but finite, there is not an endless genetic pool, but a discrete one so in smaller or isolated populations, heterozygosity will fall due to random events (imagine adults that have no offspring, eliminating their alleles from the genetic pool).

The opposite effect is when two isolated populations admix, adding new alleles to the gene pool, increasing heterozygosity.

So, the factors that provoke homozygosity are:

• Inbreeding
• Geographic isolation
• Genetic Drift
• Cultural practices -i.e. consanguineous marriage or endogamy
• Positive evolutionary selection

It can fall, on the other hand if there is an isolation-breaking event such as the mixing of two previously isolated populations.

Let's take a look at each of these factors:

1. Interbreeding

The taboos that forbid marrying your next of kin have a genetic basis: those closely related to you will carry many genes identical to yours. Since relatives share alleles, inbreeding will bring together identical copies of an allele more frequently than breeding between unrelated mates, and this increases homozygosity:

"F", the Inbreeding coefficient is the probability that two alleles are identical copies of an allele from a common ancestor. It is also, the proportion of the population that is inbred (having two alleles identical by descent).

We can take the expression used above and adapt it to calculate the frequencies of alleles in an inbred population:

• f(bb) = p²+2Fpq
• f(bB) = 2pq (1-F)
• f(BB) = q²+Fpq

All must add up to 100% of the population.

So if inbreeding coefficient is 20%, the relative frequencies of bb, BB and Bb would be (we will use the same frequencies as in the original example: b is present at p = 30% and B has a frequency of q= 70%):

100% = (30%)² +2 x 20% x 30% x 70% + 2(30% x 70%)(1-20%) + 70%² +2 x 20% x 30% x 70%

100% = 13,2% + 33,6% + 53,3%

So the comparison is:

• bb increases from 9% to 13.2% of the population
• BB increases from 49% to 53.3% of the population
• Bb falls from 42% to 33.6% of the individuals

Heterozygosity drops due to inbreeding even though the same alleles are present.

Since some genetic traits are recessive, and manifest themselves only when the two alleles are present, that is, homozygosity for those alleles is present, inbreeding increases the frequency of these recessive traits, which could be as benign as blue vs. dark eyes or nasty as congenital diseases.

Genetic drift

Imagine a population which starts off with p = q = 50%. In other words, the proportion of B and b is identical. Applying Hardy-Weinberg Theorem we can calculate the genotype frequencies:

100% = (50%)² + 2(50% x 50%) + 50%²

100% = 25% + 50% + 25%

So50% are heterozygous (Bb) while the other half is equally homozygous: 25% are BB and 25% are bb.

But this is in an infinte population and also, the frequencies p and q are probabilities.

Real life may reflect these probabilities in a different way. Look at it this way: when you flip a fair coin there is an equal chance (p=50%) of getting heads and or tails (q=50%). But in practice we all know that you could throw 3 heads in a row and get only 2 tails in a series of five tosses. Which is not a 50 ⁄ 50 proportion. it is 66% ⁄ 40%. You may even get 3 heads in a row in a series of 3 tosses (100 ⁄ 0).

So in small series it is unlikely that the actual real frequency is close to the theoretical probability (p or q).

However, when you use larger series, for instance if you tossed the coin 1,000 times, the ratio would be closer to 50 ⁄ 50 (say 494 tails and 506 heads).

This same effect applies to the probability frequencies in small populations: two heterozygous parents (bB) could have all four offspring that are homozygous (bb) just by chance.

So, in small populations this phenomenon known as "Genetic drift" just by random forces -not by natural selection or deliberate interbreeding- can change the frequency of some alleles in very short time, making them extremely common ("Fixing them") or making them disappear.

Founder Effect

Founder events take place when a small sub-population of a larger one migrates and establishes a new settlement (hence "founder" population). It is obvious that not all the alleles present in the original population will be present in this smaller group. Those left behind will not appear in the new one, this reduces the total quantity or "allele richness" of the new subpopulation.

Liken it to randomly taking 4 M&M's from a bag holding 500 candies, it is probable that you will not pick all the available colors. So if the M&Ms in the bag are red, yellow, green, blue and brown in equal proportions, you could very well have picked: 2 yellow, 1 green, 1 red and no brown or blue candies. So this does in effect reduce the "diversity" or "richness" in the subpopulation but, it may not impact on heterozygosity:

Imagine the population we mentioned befor where 9% were homozygous for b (bb), 42% were heterozygous (Bb) and 49% were homozygous for B (BB). Now lets imagine that a small group from this original one forms a colony elsewhere, and just by chance, 60% of the individuals carry the Bb heterozygosity, while the remaining 40% are BB homozygous.

This new subpopulation will therefore have a higher heterozygosity than the original population (60% vs. 49%), but it will surely be less rich or diverse due to the alleles left behind (M&M analogy).

Founder effect impacts on the "allelic richness" by reducing it but it may no have much effect on hetrerozygosity. This is because the richness is based on the presence of the alleles and not on the internal diversity within them. A rare allele lost during a founder effect reduces the diversity but will probably have little impact on heterozygosity.

Bottleneck

This is a drastic reduction in a population. It could be caused by disease or a natural catastrophe (drought, volcanic eruption, fire, Ice Age, global warming).

Those that survive will carry only part of the genetic diversity of the original population, as those lineages that perished, are gone forever. But this does not mean that heterozygosity drops. Actually, allelic richness falls faster than heterozygosity because bottlenecks usually wipe out ,any low-frequency alleles and this causes an excess of heterozygosity in selectively neutral loci compared to normal populations subjected to genetic drift.

Leberg (1992) investigated loss of heterozygosity and allelic variation experimenting with mosquitofish and found that a decrease in heterozygosity only happens when the bottleneck is extreme and prolonged.

Selection

After the population reduction in founder effects or Bottlenecks & Geographic Isolation (which may also lead to inbreeding due to the smaller population), diversity will increase again due to chance mutations.

Another factor that may modify the genetic patterns is Natural Selection: the bottleneck may have caused the fittest to survive -imagine a disease that those equipped with some genetic advantage manage to survive while the others perish- and therefore selection increases the frequency of certain genes in the new population, when compared to the pre-bottleneck one.

Geographic Isolation

Similar to Bottlenecks, it is the separation of one group from the main population, as when there is a founder event.

Heterozygosity and Human Evolution

So when defenders of the "Out of Africa" theory use heterozygosity to support an African origin for Mankind, they point out that Africans have the highest heterozygosity of all human populations: the others (non-Africans) have lost it as they migrated out of Africa in small bands (founder effect), separated widely (geographic isolation), were more prone to fall prey to natural catastrophe (bottle necks), inbred more frequently as they were smaller populations and in doing so lost heterozygosity which the original basal population in Africa retained.

An example of this is shown in the image below which charts "heterozygosity vs. distance from Africa (Addis Ababa)" (from [1]):

This chart from [5] show more or less the same information:

Allelic Diversity

Having said this, we must point out that "Genetic Diversity" is not only measured by heterozygosity but also by the "number of alleles" present in a given population, that is "allele richness" or "allelic diversity" which is calculated as the average number of alleles per locus.

In other words a population may have a high heterozygosity compared to another and supposedly be "more diverse" but, overall have a lower number of alleles which makes it definitively "less diverse".

An example of this paradox is shown in this paper (Begoña Martínez-Cruz et al., In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations [1]) which has interesting data in its Table 2 which shows the "Average AR" - allelic richness- and "expected heterozygosity He" for each of the 26 Central Asian populations and other nearby regions:

AR He   Population
12.66 0.819 Central/South Asia
 8.60 0.820 Central Asia - TJK
 8.50 0.812 Central Asia - TJT
 8.50 0.774 Central Asia - UZB

The first two have the same He (heterozygosity) of around 0.82 but notably different allelic diversity (12.66 vs 8.60). The last two have the same allelic diversity (8.5) but different He (0.812 vs. 0.774).

Populations can have a richer genome despite having a lower heterozygosity, of course they could have mutated faster than another population and therefore increased the diversity in their genome adding new variants.

Does this mean higher heterozygosity in Africa mean that it is the cradle of humanity?

It means that heterozygosity is higher there. Just look at the archaic hominins, Neanderthals and Denisovans. Their heterozygosity is far lower than that of any extant human group, but we know that they predate Homo sapiens by several hundreds of thousands of years. They are less heterozygous but older and ancestral:

Prüfer et al. paper on Neanderthals [3] confirms this (highlighted in bold):

"The Neanderthal autosomal genome carries 1.7–1.8 heterozygous sites per 10,000?bp (Supplementary Information section 9). This is 84% of the number of heterozygous sites in the Denisovan genome, 22–30% of that in present-day non-African genomes, and 16–18% of that in present-day African genomes (Extended Data Fig. 1). When regions of homozygosity longer than 2.5?cM stemming from recent as well as long-term inbreeding in the Neanderthal are removed, 2.1–2.2 sites per 10,000 are heterozygous, similar to what is observed in the Denisovan genome. Thus, heterozygosity in Neanderthals as well as Denisovans appears to have been lower than in present-day humans and is among the lowest measured for any organism" [3]

Another paper by Meyer et al. on Denisovans [4] found the same diminshed heterozygosity:

"Denisovan genetic diversity. The high quality of the Denisovan genome allowed us to measure its heterozygosity, i.e., the fraction of nucleotide sites that are different between a person's maternal and paternal genomes (Fig. 5A). Several methods indicate that the Denisovan heterozygosity is about 0.022%. This is ~20% of the heterozygosity seen in the Africans, ~26 to 33% of that in the Eurasians, and 36% of that in the Karitiana, a South American population with extremely low heterozygosity. Because we find no evidence for unusually long stretches of homozygosity in the Denisovan genome, this is not due to inbreeding among the immediate ancestors of the Denisovan individual. We thus conclude that the genetic diversity of the population to which the Denisovan individual belonged was very low compared with that of present-day humans." [4]

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. Could current lower Amerindian heterozygosity reflect an ancient population just like that of Denisovans or Neanderthals?

We will look into these questions in my next post when we go over some recent papers on the possibility of an ancient Out of Africa event whose genes ended up in contemporary Papuans and Australians.

Sources

[1] Begoña Martínez-Cruz, Renaud Vitalis, Laure Ségurel, Frédéric Austerlitz, Myriam Georges, Sylvain Théry, Lluis Quintana-Murci, Tatyana Hegay, Almaz Aldashev, Firuza Nasyrova and Evelyne Heyer, In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations, European Journal of Human Genetics (2011) 19, 216–223; doi:10.1038/ejhg.2010.153; published online 8 September 2010.
[2] Paul Verdu, Trevor J. Pemberton, Romain Laurent, Brian M. Kemp, Angelica Gonzalez-Oliver, Clara Gorodezky, Cris E. Hughes, Milena R. Shattuck, Barbara Petzelt, Joycelynn Mitchell, Harold Harry, Theresa William, Rosita Worl, Ripan S. Malhi Patterns of Admixture and Population Structure in Native Populations of Northwest North America, PLOS Published: August 14, 2014 http://dx.doi.org/10.1371/journal.pgen.1004530
[3] Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H. Sudmant, Cesare de Filippo, Heng Li, Swapan Mallick, Michael Dannemann, Qiaomei Fu, Martin Kircher, Martin Kuhlwilm, Michael Lachmann, Matthias Meyer, Matthias Ongyerth, Michael Siebauer, Christoph Theunert, Arti Tandon, Priya Moorjani, Joseph Pickrell, James C. Mullikin et al., The complete genome sequence of a Neanderthal from the Altai Mountains, Nature 505, 43–49 (02 January 2014) doi:10.1038/nature12886
[4] Matthias Meyer et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual, www.sciencemag.org SCIENCE VOL 338 12 Oct 2012
[5] Keith Hunley, Claire Bowern, Meghan Healy, Rejection of a serial founder effects model of genetic and linguistic coevolution, Published 1 February 2012.DOI: 10.1098/rspb.2011.2296

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

The folly of creationism in the guise of science

While serious people try to explain the origin of mankind and use sophisticated scientific tools, publishing their findings so that all can go over them, criticise them, add further proof or improve them, some guys who call themselves "religious scholars" publish fancy fairy tales and try to pass them off as science!

This is a clear example of the latter: New genetic research suggests dawn of human ethnic groups occurred after Tower of Babel event in Bible.

An excerpt: "... Though Genesis 5 indicates that ten paternal generations passed from Adam to Shem, more maternal generations might have passed from Eve to the Flood.8 Using a variety of generation times, a 6–22 nucleotide difference could easily have been produced in the ~1660 years from Creation to the Flood (Supplemental Table 4), which easily encompasses the 2–8 nucleotide pre-Flood branch length....". from the "paper" On the Origin of Human Mitochondrial DNA Differences, New Generation Time Data Both Suggest a Unified Young-Earth Creation Model and Challenge the Evolutionary Out-of-Africa Model by Dr. Nathaniel T. Jeanson on April 27, 2016. Read its "hard facts here".

As usual, I must say that (Mark 12:17) leave to scientists what is for scientists to do and let those who believe in religion as set down in the Bible, do their thing with their god.

Religion has given us a lot of trouble when meddling with other human affairs (burning witches, infidels, jews, muslims, not openly condemning slave trade or slavery, etc.).

Religion lies in a different realm, apart from science, its role is to comfort those who fear death and the uncertainty of death. So they should stick to their guns and provide solace to believers. But to try to pretend that the Bible explains the origin of mankind is, to put it bluntly, plain stupid.

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

More on the loss of genetic diversity in the Americas after European discovery

A post that I wrote in July 2014 regarding the Loss of Amerindian genetic diversity post 1492, has now more evidence to support it, as shown by a paper by Bastien Llama et al., Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas Science Advances 01 Apr 2016:Vol. 2, no. 4, e1501385, DOI: 10.1126/sciadv.1501385.

The paper states that "As a result, our ancient mitochondrial data suggest that European colonization was followed by local mass mortality and extinction of lineages associated with major population centers of the pre-Columbian past. Our results contrast with previous observations that Native American genetic diversity has been temporally and geographically stable for at least the past 2000 years".

And has some interesting graphs showing the loss of lineages.

I disagree with the timeline and the Beringian standstill notion, but I must admit it is an interesting paper.

The following image, from the paper, shows the magnitude of this loss of diversity, but the magnitude is surely bigger as the sampling of archaic genomes is quite small: the paper only includes one (1) sample from the US and Canada, one from Northern Mexico (none from Yucatan or Central America, Venezuela, Guyanas, Colombia, Ecuador,Brazil, Southern Chile, Paraguay or Uruguay, and only 2 from Argentina, excluding Patagonia... (see Fig. S1 in the paper)

Fig. S6 in the Supplementary Materials of the paper. The Red lineages are extinct, the blue ones have survived. (this is one of 3 simulations in the Fig. all three are very similar.

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

The Award for idiotic ideas goes to this Creationist

Our April 2016 Award for Stupid theories goes to this Creationist, proclaimed "researcher", Emmanuel Fortes.

The Institute of Creationist Biology (if such a thing can exist), located in Barcelona, Spain has claimed that our ancestor, Homo erectus had gay inclinations which led it to extinction.

They state that "new archeological evidence emerging from the Palau Pe Dang site in Indonesia [shows that] these ancestors of modern humans possibly favored interbreeding with their own gender, leading to a steep decline of their population".

What led these "scientists" to come to such ridiculous conclusions is still being debated. Perhaps they found the remains of coupling Homo erectus, or was it the "homo" part of their scientific name that led them to conclude they were "homosexual"?.

Of course we are interested in the creationist biology, how do they explain the origin of the "creator"? What proof do they have to uphold such "scientific" theories?. Did they find erectus remains in the ruins of Sodom and Gomorrah

Hint Genesis 1:

11 And God said, Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit after his kind, whose seed is in itself, upon the earth: and it was so.

12 And the earth brought forth grass, and herb yielding seed after his kind, and the tree yielding fruit, whose seed was in itself, after his kind: and God saw that it was good.

Of course plants appeared on day three before day and night were created on day four and the sun too. How is this explained by "Creationist science", perhaps a miracle kept the plants alive before sunlight began fuelling their clorophyl production....

The article I have read says that "DNA studies done on LGBT community members worldwide clearly show the remnants of the Homo erectus DNA in much stronger percentiles than in heterosexual groups, a fact mainstream scientists dismiss as pseudo-science, but the numbers are there for everyone to see" this was said by the Assistant Director of the Creation Science Museum, in Salt Lake City, Utah, a Mormon community.

Maybe the May 2016 award will be given to this Assistant Director...

How can such silly ideas survive in the XXIst century?

Paraphrasing Jesus, (Luke 20:25), "Then give back to Science what belongs to Science, and to God what is God's." In other words religion is nice and soothes people's anxieties when facing difficult situations and the uncertainty of death, but leave it to science to explain how the universe works.

Read the article here

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

Sima de los Huesos remains, Neanderthals, Denisovans and their nuclear and mtDNA

A very interesting paper published in Nature (Matthias Meyer et al.) has confirmed that the Sima de los Huesos remains, that 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.

Since the Sima de los Huesos hominins are supposed to be the ancestors of Neanderthals it is reasonable that their nuclear DNA is similar to that of Neanderthals and different from Denisovans. But why is the relationship regarding mtDNA exactly the opposite?

The paper offers three explanations:

1. The Sima de los Huesos people had two very diverging mtDNA types, one leading to Neanderthals the other to Denisovans, and these samples are of the first kind.
2. Some "other" hominin contributed its mtDNA to both Denisovans and Sima de los Huesos people
3. The original proto Neanderthal mtDNA was inherited by their Neanderthal descent but was completely diluted by later inflow of Neanderthal mtDNA from Africa, which we find in more recent Neanderthals.

In science, the breakthroughs come from finding the correct answer to discrepancies like these. So it is very exciting and who knows what will eventually be learned from this!.

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

An even earlier Out Of Africa 2.6 MyA.

A very early out of Africa may have taken place if the paper by Anne Dambricourt Malassé et al., Anthropic activities in the fossiliferous Quranwala Zone, 2.6 Ma, Siwaliks of Northwest India, historical context of the discovery and scientific investigations (Comptes Rendus Palevol, doi.org/bb7c) is correct.

Though it is behind a paywall, the abstract clearly states that: "This paper presents the historical context and the rigorous scientific process, which has led to the acknowledgment that some bones, dating back to the Latest Pliocene, present intentional and precise cut marks made by sharp edges in quartzite and an intelligence, which knew the anatomy of the bovid carcasses. Our pluridisciplinary works support anthropic activities 2.6 Ma ago in the sub-Himalayan floodplain and the probability of finding hominin fossils in the Quranwala Zone. ".

Now 2.6 million years ago is long before any Homo erectus moved out of Africa (their oldest Asian remains have been dated at 1.8 Ma). Or perhaps they did migrate but much earlier. Or were their predecessors, the Homo habilis the first to leave Africa. Perhaps the H. habilis evolved into H. erectus in Asia and these back migrated into Africa...

The point is that this site in Siwalik hills is about 300 kilometres north of New Delhi, India, well in the heart of Southern Asia, and it is a clear indication that human origins are much more complicated than we once believed.

Also, it gives us about 1 million additional years for those archaic people, to reach America...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

Humans in Siberia 10,000 years earlier than formerly believed,

Seems like human beings have been on the move for much longer than formerly believed. A paper published in Science (Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains Vladimir V. Pitulko, Alexei N. Tikhonov, Elena Y. Pavlova Pavel A. Nikolskiy, Konstantin E. Kuper, Roman N. Polozov, Science 15 Jan 2016:Vol. 351, Issue 6270, pp. 260-263 DOI: 10.1126/science.aad0554), mentions their discovery of a butchered mammoth, with clear signs of pre and post-mortem wounds caused by intelligent beings. The date is 45000 years ago, and pushes back the presence of humans in the area some 10,000 years.

The free-access text says:

"Earliest human Arctic occupation
Paleolithic records of humans in the Eurasian Arctic (above 66°N) are scarce, stretching back to 30,000 to 35,000 years ago at most. Pitulko et al. have found evidence of human occupation 45,000 years ago at 72°N, well within the Siberian Arctic. The evidence is in the form of a frozen mammoth carcass bearing many signs of weapon-inflicted injuries, both pre- and postmortem. The remains of a hunted wolf from a widely separate location of similar age indicate that humans may have spread widely across northern Siberia at least 10 millennia earlier than previously thought.
Abstract
Archaeological evidence for human dispersal through northern Eurasia before 40,000 years ago is rare. In west Siberia, the northernmost find of that age is located at 57°N. Elsewhere, the earliest presence of humans in the Arctic is commonly thought to be circa 35,000 to 30,000 years before the present. A mammoth kill site in the central Siberian Arctic, dated to 45,000 years before the present, expands the populated area to almost 72°N. The advancement of mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia."

The place is well north of the Arctic Circle, at 72° north. Location map.

So they were there longer ago than expected which means they were equipped to reach America via the Arctic earlier than expected too. or Move out of America into Asia at an early date... After all, who said they were Homo sapiens? They could be Denisovans, archaic Asian or even archaic American hominins.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

More evidence of archaic humans in Asia ca. 100-200 kya.

A paper published in Nature, two days ago: Earliest hominin occupation of Sulawesi, Indonesia by Gerrit D. van den Bergh et al., Nature 529, 208–211 (14 January 2016) doi:10.1038/nature16448, reports an interesting finding in Indonesia:

"Sulawesi is the largest and oldest island within Wallacea, a vast zone of oceanic islands separating continental Asia from the Pleistocene landmass of Australia and Papua (Sahul). By one million years ago an unknown hominin lineage had colonized Flores immediately to the south1, and by about 50 thousand years ago, modern humans (Homo sapiens) had crossed to Sahul. On the basis of position, oceanic currents and biogeographical context, Sulawesi probably played a pivotal part in these dispersals. Uranium-series dating of speleothem deposits associated with rock art in the limestone karst region of Maros in southwest Sulawesi has revealed that humans were living on the island at least 40 thousand years ago. Here we report new excavations at Talepu in the Walanae Basin northeast of Maros, where in situ stone artefacts associated with fossil remains of megafauna (Bubalus sp., Stegodon and Celebochoerus) have been recovered from stratified deposits that accumulated from before 200 thousand years ago until about 100 thousand years ago. Our findings suggest that Sulawesi, like Flores, was host to a long-established population of archaic hominins, the ancestral origins and taxonomic status of which remain elusive.

The Bold, part that I highlighted above is very clear: archaic humans lived in this part of Sulawesi between 200 and 100 thousand years ago. They were not Homo sapiens, who arrived there about 50,000 years ago. So what are these "elusive" people?

The evidence of a non-African ancestral human group is growing. Could they be Denisovans? Homo erectus? We will just have to wait and see.

Did they move further north, into China, Eastern Siberia and, maybe the Americas? Or did they come from there in an Out-Of-America dispersal?

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

Helicobacter pylori and the Out of Africa theory

A paper published in Science (F. Maixner, 2016 [1]) reported that they studied the DNA of the Helicobacter pylori recovered from Ötzi, the iceman, whose mummified body was discovered in an Alpine glacier melt in 1991. They body is 5,300 years old and they expected to find the typical European variety of H. pylori in the remains of his stomach. Instead they found the Asian variety. Casting a shadow on the current Out of Africa theory of the peopling of Europe.

Their abstract says: (bold is mine) "The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years."

I wrote about this some time ago, that the different H. pylori variants are not necessary of an African origin. These findinngs by Maixner and his team seem to support this idea.

According to the paper (it is free access), the Iceman's variant of H.pylori is closer to the South Asian one! (India, Malaysia, Bangladesh, Thailand, Philippines) and is furthest from the N.E. Africa and W. Africa variant (from Nigeria to Ethiopia)... See this graph with the different variants and Ötzi's position closest to Asian types.

So this is no man from the steppes or a Middle Eastern H. pylori variant. This copper age man has a H. pylori found in SE Asia. The route taken by humans out of Africa, and long before them, by Homo erectus to... South East Asia. Are we seeing some signal of an old variant of H. pylori here? One that predates European H. pylori and also the African one?

What is odd is that a paper by A. Keller et al., (2012) [2] found the Iceman was closely related to the population of the two islands of Corsica and Sardinia in the NW Mediterranean Sea: "Sequence analysis showed genetic distance from modern mainland European populations, but proximity to the extant populations of Sardinia. Interestingly, the Iceman's Y-haplogroup G2a4 has hitherto only been found at appreciable frequencies in Mediterranean islands of the Tyrrhenian Sea (Sardinia and Corsica). Although admixture and demographic history cannot be reconstructed from one individual alone, the Iceman's Y-chromosomal data document the presence of haplogroup G in Italy by the end of the Neolithic and lends further support to the demic diffusion model. The affinity of the Iceman's genome to modern Sardinian groups may reflect relatively recent common ancestry between the ancient Sardinian and Alpine populations, possibly due to the diffusion of Neolithic peoples." [2]

What do Sardinians and South Asians have in Common? Perhaps Keller et al. are right and it just reflects a group that survived from the days of Ötzi in isolation in those two islands, and ths same DNA is found at very low levels (less than 1%) across Europe.

The paper states that: "Furthermore, our co-ancestry results indicate that the Iceman’s strain belonged to a prehistoric European branch of hpAsia2 that is different from the modern hpAsia2 population from northern India" [1]. Which is very interesting. It is a really ancestral branch. (Neanderthal ?)

Figure 4 in the paper shows the tree, with two big branches, one is N.E.Asia and America, the other has Africa, Europe, South Asia and Oceania. That is indeed striking.

The First branch, splits into Africa and Europe, and another which holds the Iceman and also includes to India, Papua New Guinea and Sahul.

The other main branch with N. E. Asians (Korea, China and Japan) also hash the Amerindians (Peru: Puno and Cuzco variants and Venezuela) with many smaller branches. Does that imply a longer time for their diversification vs. the other human groups?

The best part is that over the last few months a series of discoveries have cast some doubt on the Out Of Africa theory: Neanderthal backflow into Africa, and the 80- 120 kya old teeth found in China. What new findings will 2016 bring with it?

Source

[1] Frank Maixner, et al., 8 January 2016: The 5300-year-old Helicobacter pylori genome of the Iceman Vol. 351 no. 6269 pp. 162-165 DOI: 10.1126/science.aad2545
[2] A Keller et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing, Nature Communications 3, Article number: 698 doi:10.1038/ncomms1701

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall ©