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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