Almost two years ago I posted about HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory, and asked an open question about some oddities in the global distribution of HPV lineages: "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...".
I also made a comment and aked a second question because it turned out that the American HPV was more diverse than the Old World variants... which is unusual, considering that Amerindians are always considered as the least diverse humans (the famous Beringian bottleneck!). My comment and question was:
"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?"
A paper published two days ago (Nov. 1, 2018) has revisited HPV and provided answers and more data on these issues. (Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, et al. (2018) Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 14(11): e1007352. https://doi.org/10.1371/journal.ppat.1007352).
The paper suggests that HPV originated in Africa and that some 618,000 years ago (roughly at the time that Neanderthals and our Homo sapiens ancestors were splitting apart) an ancient HPV variant "A" split from the variant that would become lineages "B", "C" and "D".
Neanderthals left Africa with HPV A, which over the next few hundreds of thousands of years evolved into sublineages A1, A2, A3 and A4, all found in Eurasia, and in America, but very very rare in Africa.
Modern H. sapiens then left Africa 120-60 Kya and had sex with Neanderthals, picking up the HPV virus in its A variant sublineages. The African "B" and "C" variants are preponderant in that continent, with very small proprotion in Eurasia (5.6% among Caucasians and 1.8% among Asians) and America (2.3%). And the American "D" variant, according to this paper, originated in Africa, passed through Eurasia where it is found in extremely small amounts among Caucasians (11%) and Asians (6.3%). It entered America where it represents 48.3% of the HPV lineages.
Surprisingly the A4 variant that is 29.9% prevalent in Asia and 0.4% among Eurasian Caucasians, does not appear among Americans.
The authors sampled 212 complete genomes and built a phylogenetic tree of the different HPV16 variants based on this data. This tree shows two separate clades which coincides with previous findings, which had identified an Eurasian and an African lineage. They identified four lineages and named them A, B, C and D. These in turn were subdivided into four sublineages (A1 to 4, B 1 to 4, etc.). The breakdown of lineages is the following, where the percentages indicate their proportion in each population:
- A1 to A3: Eurasia (83% among Caucasians, 62% among Asians)and America (49.5%), only 2.4% prevalence in Africa.
- A4: As mentioned above prevalent in Asia (29.9%) and very little of it found elsewhere (0.4% among Caucasians) and nill in America and Africa.
- B: African (54.2%), 4% in European Caucasians, 0.2% in Asians and 0.5% among South and Central Americans.
- C: African (36.1%), 1.6% among European Caucasians and 1.6% among Asians. 1.7% in South and Central Americans
- D: America (48.3%), 7.2% in Africa, 11% in Europe, 6.3% in Asia.
The paper reports that there was more diversity in the African variants with an intragroup mean difference of 0.77% ± 0.04% compared to the Eurasian variants (0.32% ± 0.02%).
However the maximum divergence between sublineages was between the Eurasian A1 and the American D3 (2.23%) as can be seen in the Heatmap of pairwise diversity, which shows all of the 212 sequenced HPV16 genomes the maximum 2.23 difference is shown in red, and the minimum diferences are shown in blue. Amerindian D is therefore the most diverse.
So, summing up BCD and A split 618 thousand years ago, "indicative of an ancient divergence of HPV16 variants prior to the emergence of modern human ancestors".
The authors state: "The estimated divergence times between HPV16 A and BCD variants largely predated that of the out-of-Africa migration of modern human populations, consistent with a previously reported archaic hominin-host-switch scenario [19, 20]. One interpretation of the data implies that the present-day Eurasian HPV16 A variants were probably the products of multiple interactions between Neanderthals/Denisovans and modern Homo sapiens established during sexual contact after a long period of separation (e.g., 400–600 kya)"
The odd situation of the "D" variant (so diverse yet almost unique to America) is explained as follows (bold face is mine):
"Following a relatively recent out-of-Africa migration, the modern humans acquired the A variant from sex with archaic hominins and possibly carried D variants into Eurasia under conditions of a small population size. The ancestors of East Asian people crossed the Bering Strait and were early populators of the Americas (based on historical records and genetic relatedness). Surprisingly, the D lineage is phylogenetically rooted in the African clade, but we did not find a major reservoir of the D lineage in the present-day African populations. This interesting observation suggests either an advantage of niche ` colonization and expansion of HPV16 D variants in Native Americans or a bottleneck of HPV16 variants present in people populating the Americans. Alternatively, the lack of A4 and the high proportion of D lineages in the Americans could be the result of an early colonization of the Americas by an unknown group from Africa. More data is needed to sort out the evolutionary history of the HPV16 D lineage and might provide clues to new features of the populating of the Americas."
The idea of an "unknown group from Africa" colonizing America at an early date is very interesting. And the authors realize that this D lineage is special because in their closing comments they add: "Lastly, we provide new interpretations and questions on the HPV16 D lineage that is part of the African clade, but is highly prevalent in South/Central America.".
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These pieces of evidence can be explained by modern humans largely outcompeting archaic types on every continent, and spreading everywhere. Some of the older types are components to the modern races on each continent. For instance, in Europe, Neanderthal genes are 1% to 4%. Neanderthal can be found in Asia, along with Denisovan, which is not found in Europe. According to the Out of Africa theory, human lineages L0 (Bushmen), L1 (Central African Pygmy) and L2 (West African) are older than L3, which they believe originated in East Africa. OOA theory is clear that L3 is the primary ancestry for most of humanity, and I believe that to be true. However, the place of origin of L3 is still up for grabs, with the Middle East and India being as likely as East Africa. It's entirely plausible that L3 back-migrated into Africa. And if not, even the OOA proponents believe that L3 back-migrated onto L0, L1, and L2. So they do believe in back-migrating, except they believe (with no good reason) that L3 originated in East Africa.
ReplyDeleteAll of this backmigrating would account for the genetic diversity being the greatest in Africa, because the older types have maintained a significant genetic presence. There could also be an older type in the America's, and accounting for some of the evidence in this article. I do believe that to be the case, and I've done some research on Amerindian tribes in Mexico. There are some that are particular short in stature, with large and sometimes pointed ears, and very large noses compared to the face. I've seen some of them as immigrants living in my area, and some are barely 4 feet tall. They look nothing like Native Americans that I know, nor do they resemble native Ecuadorians or Peruvians, and if anything resemble the crypto-humanoid from the Eastern United States known as the Pukwudgie. There is something about these particular Mexican tribes. I believe they represent a very ancient lineage. Someone much more expert than me in these matters should investigate further.