More on the useless Mitochondrial DNA Clock

I wrote my previous post (The mtDNA clock ticks out of time) on the reliability of the mitochondrial DNA "clock" after doing my research on the D4h3 haplogroup (hg) in America for my post on it [mtDNA D4h3a (Continued)].

At the time, the variability in the amount of mutations along each lineage drew my attention. How could all these living people who came from a common root have differing amounts of mutations? After all, if there was a clock ticking of mutations at a steady rate, then all these people would have the same quantity of mutations. Well they don't. So, I suspected the clock was not reliable.

The smoking gun

The following image shows part of the tree that drew my attention:

D4 to Dh43 haplogroup (hg)tree, with mutations. From [1]

I will just take a part of the whole tree to make my point:

• Between the root at D4 and D1 there are 2 mutations (marked in red on the image as 2 m), and the time that has passed is 23.5 - 17.8 ky. That is: one mutation every 11.72 - 8.9 ky.
• Between root D4 and D4h3 there are 7 mutations (7 m), so you would expect them to be 77 to 63 ky apart, but no, surprisinglythis branch is between 500 and 2,500 years YOUNGER than its root. What sort of a tree is this? branches are born before the root?
• Between D4h3 and some extant humans which I have chosen and marked with violet, we have:
  
  • 10 mutations to individual #01
  •  9 mutations to individual #26
  • 18 mutations to individual #17
  You could argue that #26 and #10 had accumulated mutations at almost the same speed (barely 10% difference between them) but #17 lineage has mutated twice as fast as the other two did.
• Between D4h3a (in blue) and the extant humans on the bottom row, the amount of mutations varies between 3 and 12. A Four fold difference. The average is 6.95 mutations. I made a graph with these mutations and, surprise, it has a roughly bimodal distribution (the type I mentioned in my previous post). See below:
• Finally, the D4h3a haplogroup is dated at 18 - 14.3 kya, so based on the maximum and minimum mutations mentioned above (12 and 3) the clock can tick anywhere between: 1,191 and 6,000 years per mutation! (compare that to the 11,720 to 8,900 years calculated further up and you can see why the clock is pointless).

Bimodal distribution of mutations in D4h3a haplogroup. Copyright © 20154 by Austin Whittall

Implications of mtDNA clock violations

Despite these blatant violations of a mtDNA clock I thought that somehow I had misinterpreted the data or not understood how the mechanism works, so I did some research into the "clock" issue. The outcome was yesterday's post which substantiates (based on scholarly papers) that the clock ticks with variable rates.

The sad part is that time and time again, paper after paper I see dates defined for our Most Recent Common Ancestors (MRCA) and entry dates into America based on this non-existent clock.

Take the following example (Behar et al, 2014): “As the clock violation was observed only in a restricted number of specified cases, we applied the best available tools for estimating the ages of ancestral nodes.” [4].

The "best available tools" may surely be the orthodox point of view: A very long (>100 ky) incubation period in Africa, a small failed entry into the Middle East where modern humans briefly occupied the region some 90 kya. A sudden migration "out of Africa" some 50 kya followed by a quick expansion across southern Asia, Europe and Australia. A slower march north across East Asia and Siberia and a very late (<25 ky) entry into America.

I now believe that the mtDNA clock is irrelevant, it is guesswork and adjusted "by hand" to fit the dates defined by the orthodox point of view.

With this in mind, I believe that it is very likely that a group of humans could have left Africa with L3 haplogroup (hg). anytime between the 200 - 80 kya (yes the "failed" migration that took place 90 kya, could have been earlier), and then mutated along the M hg and D hg branches in say, 20 ky, allowing an entry into America of Modern Humans anytimg between 180 and 60 kya.

And I specifically give a very ancient date of 200 kya for the appearance of modern humans based on a Y chromosome haplogroup (Mendez et al, 2013) named A00 which was dated to: "338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. [5]"

This early date is resisted by orthodoxy arguing that mtDNA and skeletal remains give more recent dates and therefore argue that the mutation rate used to estimate the TMRCA for the Y chromosome was simply too low [6]. (I don't trus the mtDNA clock, and regarding bones... maybe the oldest human fossils have not yet been found.)

An early and rapid dispersion across Central and Eastern Asia could account for ancient Humans such as those found at Zhirendong, China with a minimum age of 100 - 113 kya (Wu et al, 2010). Fossils which prove that the "90 kya" migration into Asia was not a failure, the migrating humans settled in China.

These fossils have a mosaic of modern and archaic features (like a chin) that:

" any “dispersal” involved substantial admixture between dispersing early modern human populations
[...]
It therefore indicates a prolonged (>50,000 y) coexistence of late archaic and early modern humans across portions of Eurasia, and not just between Africa and Eurasia. Those late archaic humans include the Neandertals in western Eurasia until mid-MIS 3. They also encompass MIS 3 archaic humans in central Asia and Siberia and into at least MIS 5 in northern China..." [2]

Here we have a good explanation for the high proportion of Neanderthal genome in modern East Asians (Vernot and Akay, 2014) who have +20% more Neanderthal genes than Europeans.

It is a pity that Amerindians were not included in the study, it is likely that they have even more Neander genome than East Asians (based on other traits that they have inherited in a higher proportion than East Asians).

Have you noticed that Native Americans are rarely included in these studies?

Apparently 30% of Neanderthal's genome ended up in humans, of course no individual has more than 1 to 3%, but combine all those bits and pieces and it is one third of H. sapiens genome.

But getting to the point. Vernot and Akay suggest that Asians have more Neanderthal genes because there were two admixture events. One just after modern Humans left Africa and before they split into the Asian and European populations. And another, between Asians and Neanderthals after they split from the forebearers of modern Europeans. This double admixture gave them a higher dosage of Neanderthal DNA.

Sources

[1] Fig. S1. From Ugo Perego et al, Current Biology, Volume 19 1. Supplemental Data Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups
[2] Wu Liua et al., (2010). Human remains from Zhirendong, South China, and modern human emergence in East Asia www.pnas.org/cgi/doi/10.1073/pnas.1014386107
[3] Vernot, B. and Akay, J., (2014). Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science, DOI: 10.1126/science.1245938
[4] Behar, D., et al., (2014). A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012 doi:10.1016/j.ajhg.2012.03.002
[5] Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
[6] Wilson Sayres, Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al. http://arxiv.org/ftp/arxiv/papers/1304/1304.6098.pdf

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

The mtDNA clock ticks out of time

Each of our cells carries within it several Mitochondria. These are remarkable organelles which are essential for cellular metabolism. They are even more remarkable because they carry their own DNA, which are independent from our other DNA, the nuclear one, which codes our other proteins.

The fact that Mitochondria have their own DNA supports the notion that long ago, before eukaryotic cells formed, they were independent organisms. Somehow they formed a symbiotic relationship within eukaryotic cells, generating energy for them in exchange for protection and “food”.

mtDNA is inherited in an uniparental manner –from mother to offspring. Male mtDNA in sperm does not enter the fertilized egg. This means that it can be used to track matrilineal lineages back in time.

Eve theory

Since it is inherited on a matrilineal basis, your mtDNA is identical to your mother’s and, also to her mother’s (your maternal grandmother) and so on, backwards generation after generation, until we reach the group of families that make up the the first Homo sapiens clan. One of the women among them is the source of your mtDNA.

That would be true if mtDNA did not mutate, but it does, at higher than nuclear DNA mutates. As they lack enzymes to repair mutations mutations accumulate.

The Mitochondrial DNA (mtDNA) is much smaller than the nuclear DNA, but is critical because the genes it encodes are fundamental: they control cellular metabolism, and if they mutate in a negative way, the organism dies or suffers diseases.

A comparison of all modern human mtDNA shows that extant and fossil humans display a wide range of mtDNA sequences.

But all come from the original group of Homo sapiens. Actually all mtDNA of living humans can be traced to one woman. That does not mean she was the only woman alive at that time. It means that the other women had sons instead of daughters (a dead end for mtDNA), or died without issue, or their offspring died without having children.

Along the line, long ago, a mutation that was “neutral” (remember, wacky mutations lead to death or illness) appeared among the “original” lineage and the daughter who carried it, passed it on to the future generations through her female offspring. The original lineage carried on until another different “neutral” mutation split it from the “original” lineage, and was passed on to the next generation.

The neutrality of mutations is something we will be going back to further down. Please remember it.

This branching from the original lineage has led to a diversity of lineages, each carrying the mutations that have accumulated across the millennia.

If these mutations happen at regular intervals we could time when they took place and find out when did the original group of Homo sapiens live. We could also compare the mtDNA of all mankind and find where they lived.

This was done, and according to this theory, the original woman (“Eve”) lived in Africa some 150 kya.

But… is this based on sound science? Does the mutational clock tick at a regular pace? Can we extrapolate backwards in time with confidence? In my previous post I expressed my doubts, today I will substantiate them with evidence.

The clock ticks at a variable pace

When I first looked at a haplogroup tree, which shows the mutations along each branch, I was surprised to see that the number of mutations differs along the branches.

An African, a European, an Asian and an Amerindian all living now and traceable back to the same woman would all have to have (if the clock ticks with a regular pace) the same number of mutations (i.e. 40 mutations) over those 150,000 years. They would not be the same mutations of course: we would share those that took place before the branching points and would have our particular ones along the tips of our different branches. Maybe some would repeat across branches due to chance. But we would all have the same amount of mutations.

Well, this is not the case. So the clock theory is not correct. That is my blunt conclusion, but let’s read some more subtle comments on the matter, because thera are some papers that point out that mutations occur at a variable rate, no clock here, just mutations happening in a haphazard manner:

Galtier, Nabholz, Glémin and Hurst. (2009)

“we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. […] The molecular clock, therefore, is certainly not a tenable assumption as far as mtDNA is concerned. Nonclock-like evolution is common, and the departure from homogeneous rates can be very strong. In mammals, the mitochondrial mutation rate appears more variable across lineages than the nuclear one” [3]

Nabholz, Glémin and Galtier. (2009)

“This study confirms and extends the message of caution […] about the usage of mtDNA as a molecular marker of biodiversity in vertebrates: (i) mtDNA diversity is not related to species abundance; (ii) mtDNA greatly departs the molecular clock hypothesis. The 2% per site per million year calibration (estimated from primate data) has no degree of generality, and should not be used for dating purposes in the absence of fossil data.” [4]

Yes, both were written by the same team, so not to cheat I will quote other papers:

The paper by Behar et al. [1] which reviewed the mtDNA tree and proposed some rational changes, also noted that there are some problems with the “clock”:

The accepted notion of a molecular clock means that contemporary mtDNA haplotypes should show statistically insignificant differences in the number of accumulated mutations from the RSRS.

Note: RSRS is the “ancestral Eve”. In other words all humans should have the same amount of mutations in their mtDNA when compared to “Eve”, but, we do not . Behar et al. add:

The range of substitution counts separating contemporary mitogenomes belonging to major haplogroups from the RSRS is shown in Figure S2. The mean distance is 57.1 substitutions, the median is 56 and the empirical standard deviation is 5.9. Widely different distances ranging from 41 substitutions in some L0d1a1 mitogenomes to 77 in some L2b1a mitogenomes are observed. [1]

This means that we don't have say 60 substitutions (mutations), no, we have between 41 and 77. The middle value is 56. A very oddly ticking clock indeed. But let’s read more from Behar et al.:

” Interestingly, the ranges of substitution counts within haplogroups M and N, which are hallmarks of the relatively recent out-of-Africa exodus of humans, are also very large. For example, within M there are two mitogenomes with 43 substitutions (in M30a and M44) and two mitogenomes with as many as 71 substitutions (in M2b1b and M7b3a). This is especially striking because the path from the RSRS to the root of M already contains 39 substitutions. Hence, the difference between the M root and its M44 descendant is only four substitutions (two in the coding region and two in the control region) as compared to 32 substitutions in the M2b1b and M7b3a mitogenomes.[…] Our results demonstrate violations of the molecular clock in M […] and give mixed results for the entire tree [...] and L2 […] and borderline results in N […] We are currently unable to offer well-founded explanations for these findings, which remain the scope of future studies. [1]

In other words haplogroups L, M and N violate the clock, but, despite these reservations, Behar et al ignore them and merrily go on to estimate lineage ages (Quote: "As the clock violation was observed only in a restricted number of specified cases, we applied the best available tools for estimating the ages of ancestral nodes" [1]).

The Figure S2 mentioned above in Behar et al. is interesting because one might expect the variability within a haplogroup to follow a Normal Distribution (Gauss bell-shaped frequency distribution), with a strong central mean value of substitutions and a dispersion to each side… but instead most of the frequency distributions are very clear Bimodal distributions.

Bimodal Distributions

As an engineer I am well acquainted with statistics, we use them every day to analyze how our industrial manufacturing processes are running. Take a look at the distributions shown in Figure S2 below (the red arrows show the “peaks” of the double humped Bimodal distribution):

Bimodal distributions, modes marked with red arrows. Adapted From [1]

For the layman: if a process is affected by some regular variation, on a chance basis, you will notice a bell-shaped distribution of frequencies. Such as height of people: Some will be very tall, others very short but most will fall close to a median height. This is a Normal distribution and looks more or less like the one adopted by M in the image above (a bell-shaped curve) .

Now a Bimodal Distribution has two “humps” or modes (a peak or local maxima): If you have a machine making bottles, the weight of the bottles should adopt a bell-shaped Normal distribution. Now imagine two different machines making bottles. Each will have its own bell shaped distribution: Machine A and Machine B, with their own mean values. Now mix all the bottles in a box and draw some samples at random from the mixture, if you graph the frequencies for these samples based on their weights: it will combine both bells into a double-hump distribution, a Bimodal one.

It is clear that something is altering the Normal Distributions in the L1, L2 and N haplogroups. L0 and L3’6 are not Normal either.

What process could skewer the Normal distribution in this manner?

Howell, Elson, Turnbull and Herrnstadt (2004) [2] also noticed this odd “clock-violating” behavior of the Ancient African L lineages and the bimodal distribution of substitutions:

“Based on the results presented here, such control region clocks are highly suspect[…] We have recently analyzed a set of 560 mtDNA coding region sequences (Herrnstadt et al. 2002) and shown that selection has influenced the evolution of the human mitochondrial genome. […] As a follow-up to those studies, we report here our tests ofclock-like evolution in African haplogroup L mtDNA sequences. The results are complex, and they argue against any simple mtDNA clock fortiming events during human evolution. ” [2]

Non Neutral mutations

In other words, the mutations in mtDNA are not neutral that happen by chance, they are influenced by natural selection, and it is this that alters the “ticking” of the clock. They note in their paper that: “the pairwise mismatch distributions are “jagged” (data not shown), the typical finding for sequences from African populations […] thus indicate selection, rather than recent population expansion.” [2]

They also took a larger sample of African mtDNA and found “ Marked violations of clock-like evolution were now observed both in the coding and control regions […] evidence that haplogroup L2 subclades evolve at different rates” [2]

Mishmar et al. (2003) looked into the natural selection issue: why would mtDNA “evolve” under selective pressure. They conclusions are very interesting: [6]

”Human mtDNA shows striking regional variation, traditionally attributed to genetic drift. However, it is not easy to account for the fact that only two mtDNA lineages (M and N) left Africa to colonize Eurasia and that lineages A, C, D, and G show a 5-fold enrichment from central Asia to Siberia. As an alternative to drift, natural selection might have enriched for certain mtDNA lineages as people migrated north into colder climates.” [6]

In other words, as humans moved across Asia their mtDNA mutated and a lot. They point out (below) that mitochondria encode certain molecules crucial for energy production within the cells and therefore impacting on the ability to produce heat and survive in cold climes:

“Natural selection has been hypothesized to explain anomalies in the branch lengths of certain European and African mtDNA lineages. […] the genes of the mtDNA are central to energy production, both to generate ATP to perform work and to generate heat to maintain body temperature.
We now hypothesize that natural selection may have influenced the regional differences between mtDNA lineages. This hypothesis is supported by our demonstration of striking differences in the ratio of nonsynonymous (nsyn)/synonymous (syn) nucleotide changes in mtDNA genes between geographic regions in different latitudes. We speculate that these differences may reflect the ancient adaptation of our ancestors to increasingly colder climates as Homo sapiens migrated out of Africa and into Europe and northeastern Asia.” [6]

Comments and Conclusions

Based on the above it seems pointless to calculate the dates of the branch splitting points and the date our ancestral “Eve” originated. Yet, as we saw (Behar et al.), even though the method is baseless, it is used just the same.

As I mentioned in previous posts, the mutation rates are “hand – adjusted” so that the calculated branching dates “fit” the “evidence” provided by the bones and stones archaeologists. If America is supposed to have been peopled not more than 30 kya then the haplogroups found in America must not be much older than that… and so on.

Science should corroborate findings using independent sources not circular ones.

But let’s go back to the bimodal distribution… Why would a group of haplogroup N people have a mode of 51 and others have a mode of 61 substitutions? Perhaps it could be interpreted as per Rogers and Harpending [8] (I don’t think so). I believe that it may be caused by a fusion of two groups of people (Murray-Macintosh, 1998 [5]) , one carrying a large amount of substitutions and another with much less. And that the mutations are due to selective pressure. So the more mutated population could be an older one and the less mutated one, a younger one. That is, two waves of people entering the same region from the same homeland in two separate waves.

The LM3 Lake Mungo mtDNA

And last, but not least, the Australian remains of a male, gracile Lake Mungo 3 (LM3), which is about 60 ky old, its mtDNA was tested. The outcome was startling (Adcock et al., 2001) [7]:

“His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations.
This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. […] This finding does not imply that all living people originated in Australia, any more than previously described deep lineages in Africa demand a recent origin of humans on that continent. Deep lineages in Africa and our finding of an even deeper lineage in Australia are consistent with a number of possible models of the demographic and evolutionary history of our species.” [7]

Where does this "ancient and different mtDNA" fit into the branches of the mtDNA tree built by orthodoxy? These remains are only 60 ky old, so are therefore younger than L haplogroup from Africa as reconstructed by Behar et al [1], see image below from their paper:

The scale at the top shows that the mutations happen (according to Behar and his team) at a regular pace!. To place LM3 before L0 would imply an age of 170 kya, but LM3 lived 6 0kya. Something is not quite right. And that is the reason that LM3 is ignored in all papers on the mtDNA timeline and haplogroups.

Sources

[1] Behar, D., et al. (2014). A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012 doi:10.1016/j.ajhg.2012.03.002
[2] Neil Howell, Joanna L. Elson, D. M. Turnbull and Corinna Herrnstadt, (2004). African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution. Mol Biol Evol (2004) 21 (10): 1843-1854. doi: 10.1093/molbev/msh184
[3] N. Galtier, B. Nabholz, S. Glemin, G.D.D. Hurst, (2009). Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology (2009) 18, 4541–4550 doi: 10.1111/j.1365-294X.2009.04380.x
[4] Benoit Nabholz, Sylvain Glémin and Nicolas Galtier, (2009). The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals Evolutionary Biology 2009, 9:54 doi:10.1186/1471-2148-9-54
[5] Rosalind P. Murray-McIntosh, Brian J. Scrimshaw, Peter J. Hatfield, and David Penny, (1998). Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences. Proceedings of the National Academy of Sciences www.pnas.org vol. 95 no. 15
[6] Dan Mishmar et al. Natural selection shaped regional mtDNA variation in humans. Proceedings of the National Academy of Sciences www.pnas.org vol 100. no.1, 171–176, doi: 10.1073/pnas.0136972100, doi: 10.1073/pnas.0136972100
[7] Gregory J. Adcock, et al. (2001). Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins. PNAS u January 16, 2001 u vol. 98 u no. 2 u 537–542
[8] Harpending H C, Sherry S T, Rogers A R, Stoneking M (1993). The genetic structure of ancient human populations, Curr Anthrol 34:483–496. http://content.lib.utah.edu/cdm/ref/collection/uspace/id/2702

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

Homo Erectus in America, a 1986 paper

Just a quick, short and to the point post.

I want to share a paper titled: Homo Erectus in America, Possibilities and Problems written in 1986 by by Frederick G. Dreier, which you can read online here

Enjoy!

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2013 by Austin Whittall © 

South African musings

Cape Agulhas, southernmost tip of Africa. Photo by Austin Whittall May 2012.
Copyright © 2012 by Austin Whittall

I visited South Africa. During the last two weeks my wife and I have taken a lovely vacation to that great country at the tip of the African continent. This is not the place to go into its turist attractions, the beauty of its landscape, the friendliness of its people, its wildlife, great food and wines, so please be assured that I won't bore you with my travel anecdotes. Instead I will post some thoughts on the peopling of South America starting out from the African Continent.

The nasty waters south of Africa

I had the opportunity to see the rough South Atlantic Ocean beating upon the rocky shores of the Cape of Good Hope, Hermanus and Cape Agulhas. I also experienced the Indian Ocean's surf roaring against beaches and cliffs along the south of South Africa between Port Elizabeth and Cape Agulhas. The sea is really rough.

The sight of these choppy waters has has made me reconsider the theory that I have mentioned in previous posts (The South African Out of Africa), which suggests that our ancient ancestor Homo erectus crossed these waters and skirted the Antarctic continent to reach America.

No man (or hominin) in his senses would dare venture into those roaring waves.

The photograph above was taken at the southernmost point of Africa, Cape Agulhas (34° 49' 58"S, 20° 00' 12"E), where the Indian Ocean and Atlantic Ocean waters meet.

Ancient record of humans in Southern Africa

I also had the chance to visit a caveat Mossel Bay, on the point, under the lighthouse.

Located at 22° 10' E and 34° 12' S the Cape of St. Blaize separates the rough Indian Ocean waters from those of Mossel Bay. The tip of the Cape was named after the Saint of the day Portuguese navigator Bartolomeu Dias spotted this part of the world, in February 1488. He named the place Aguada de Sao Bras (Watering place of St Blaize).

The cave is actually an overhang, is known as Bat Cave and is set on Cape St. Blaize. It was excavated partially by Leith in 1888 and again in 1932 by A. J. H. Goodwin and B. D. Malan, who reported their findings in 1935. [1] The stone tools were described as Middle Stone Age "Mossel Bay Industry" and record about 165,000 years of human presence in this area.

The cave itself is about 30 m (95 ft) above sea level and is about 90 ft wide by 40 ft deep (27 by 12 m). It faces towards the southeast and offers a lovely view of the surf below. The following photograph shows both cave under the lighthouse:

Bat Cave at Mossel Bay. Photo Austin Whittall Copyright © 2012 by Austin Whittall

So, modern humans have lived here for most of our existence as a distinct group of hominins. On the flight back to Buenos Aires, I read an interesting article [2] that made me wonder if other more ancient groups such as Australopithecus sediba may have lived at Mossel Bay or roamed the coasts of Southern Africa.

A. sediba may be the link between our homo genus and the more distant and primitive Australopithecines and has been proposed as an ancestor to H. erectus . These hominins lived about 2.3 Mya and their remains have been found at Johannesburg.

Could they be the ones that made it to Georgia? Was it they who left Africa before H. erectus? Since I am now discarding the South Atlantic route, could they have drifted across the more benign Equatorial route pushed by ocean currents? (see my post on the Trans Atlantic route) Or did they trek all the way into America across Asia and Beringia?

Further reading

[1] A. J. H. Goodwin and B. D. Malan, Archaeology of the Cape St. Blaize Cave and Raised Beach, Mossel Bay. Annals of the South African Museum, Vol. 24, part 3, S. 111-140

[2] Kate Wong, First of Our Kind: Could Australopithecus sediba Be Our Long Lost Ancestor?. Sensational fossils from South Africa spark debate over how we came to be human. Scientific American. March 20, 2012.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2012 by Austin Whittall © 

HTLV-II and the peopling of America

Map showing HTLV-II in Central Africa. Copyright © 2012 by Austin Whittall

Human T cell leukemia / lymphoma virus (HTLV) is found in four types numbered from one to four, they are closely linked to similar virus found among simians (STLV). Collectively, the HTLV groups and their STLV analogues are called “primate T-lymphotropic viruses” (PTLV).

In today’s post we will focus on the two main HTLVs (they are retrovirus that causes cancer and other disorders). The first of them is known as HTLV-I; it is closely related to a simian virus (STLV-I) and is considered an Old World virus, which has affected both humans and apes in Asia and Africa for milennia. [2]

The other type, HTLV-II is a cosmopolitan endemic illness among Intravenous Drug Users (IUD) all around the world. However, in 1990, it was unexpectedly discovered among an isolated group of American Indians, the Guaymi in Panama and a year later among other native Americans in the US. This came as quite a surprise which is difficult to explain how it could have appeared among separate Amerindian groups.

HTLV-II the American virus

Further research has established that HTLV-II is found among highly separated and often geographically isolated native American groups and this poses a problem because, highly influenced by the prevailing theories, nobody dates the arrival of HTLV-II type to America beyond the established 10,000 - 40,000 years ago that fits the orthodox temporal window for the Asian migration into the New World through Beringia.

As we mentioned above, HTLV-II, is prevalent all across the globe in intravenous-drug users (IUD), and the dispersal they caused is a very recent event. They surely picked up the infection sharing needles with Native Americans in the US, however the point of origin is not yed defined.

The interesting part is that prior to IUD dispersal, HTLV-II was only found in America, where two (actually three) subtypes can be found:

• HTLV-IIa is only found exclusively among some groups of American Indians such as the American Indian tribes of North, Central, and South America, including the Navajo and Pueblo in New Mexico and the Kayapo, Kraho, and Kaxuyana in Brazil. (this endemic Brazilian Amazonian subcluster is slightly different and have been designated as HTLV-IIc[1], it may differ due to a founder effect and is intimately linked to the original Paleo Indians who peopled the region.[10]
• HLTV-IIb is the other strain which is also found exclusively among Amerindians: Guaymi in Panama, the Wayu and Guahibo in Colombia, the Toba and Mataco in Argentina, and some Navajo and Pueblo in New Mexico. It is known as the “Paleo Indian strain” [7] [1]

As it was found among isolated Amerindian groups, and at high frequencies, initially the HTLV-II virus was thought to have originated in America. However, and this is another surprising fact, the virus is also present among Pygmies in Africa.

The fact that there are two reservoirs of HTLV-II, one in indigenous American populations and the other in African pygmies, groups which are as far apart within H. sapiens as one can find, is indeed a deep mystery.

The Pygmy connection: Africa

Besides infecting Pygmies, there is also an African simian virus very similar to HTLV-II that affects bonobos (a relative of the chimpanzees). This may indicate an African origin for the human virus, derived from the simian one. Furthermore, HTLV-IIb is found among Cameroonian Pygmy people but has very close phylogenetic relation with Amerindian HTLV-2b strains. [1].

The strains are “highly similar to each other (below 1% nucleotide divergence) , as well as to Amerindian HTLV-2b strains”[9]; a molecular clock analysis indicates that it has been endemic among the Bakola Pygmies for “a long time”.[9]

The HTLV-b strain has also been found in a non-Pygmy Gabonese family. If we cannot rule out some transoceanic contact with Paleoindians, then this virus must have originated in Africa [7]. We will look into this later (see below: Conclusions).

There is also another strain, HTLV-IId discovered among the Congolese Efe Pygmy (Bambuti Pygmies), a group which is not very admixed with other groups and are considered one of the oldest African people.[1]

So, we have two distinct groups of Pygmies infected with two different subtypes of HTLV-II, the Bambuti and the Bakola, each located at the extreme eastern and western points of the Pygmy territory. These are people which are completely different from their neighbors with whom they do not mix and have been separated from them for ten to twenty thousand years . Their isolation and lack of admixture means that they must be an ancient reservoir of the HTLV-II virus. [7]

The paper that deals with the Pygmy strain of HTLV-IId, [1], states that as the closest simian virus is found among the bonobos in Africa, the human strain must have originated there too, remained in Africa and, had the “longest independent evolution” among al HTLV-II strains. It goes on and says that the other two strains reached America on human hosts[1], in two different “waves” [7].

We will look into this assertion later (see below: Conclusions)

But, and this is an interesting question: How did HTLV-2 reach America? And why are there two varieties (“a” and “b”) found in America? There is no evidence of HTLV-II in Asia, the route upheld by orthodox science as the one taken by modern humans “Out Of Africa”, across Asia and through Beringia into America. I will try to answer both below.

To clarify the picture, the following figure, (from [10]) shows the different HTLV-II strains:

• HTLV-IIa (Amerindians) in Yellow
• HTLV-IIb (Amerindians) in Green. IUDs not shaded; cosmopolitan distribution
• HTLV-IIc (Amazonian strain) is shown in blue.

Pygmies are highlighted with an arrow, the “b” and “d” subtypes. And also an “a” type. Which I had not found mentioned in the bibliography.

From Fig 2 [10].

In America but not in Asia how can that be?

Assuming that the contemporary Asian descendants of the humans who peopled America had HTLV-II, a group of scientists [2] sampled 778 Siberians in 1993 at Tchoukotka and Sakhalin island and at other Northern Siberian populations. The sampling spanned a wide range of ethnic groups: Tchouktche, Nivkh, Evene, Yakoute, Eskimo, Russians, Dogen, Orok, Nganas, Evenke, Nenetse, and various other ethnic origins, surprisingly, not one of them was HTLV-II positive. A similar finding was reported by Neel et al. (1994) (sample n=473). [2]

Trying to explain this odd situation that defies the logic of the Beringian entry into America, the authors suggested several possible explanations:

• the sample did not cover groups that had the virus.
• A founder effect (population bottle neck that wiped out those carrying the original virus).
• The extant population contains only a small proportion of the ancient mongoloid group that peopled America (and had the virus).
• The virus disappeared due to a drop in transmission rate caused by (unexplained) cultural and / or environmental changes. [2]

The final and most likely probable cause given was that the current Siberians are not related to the group that peopled America and hence, don’t have the virus.[2]

In no other part of Asia has the HTLV-II virus been found with the exception of a single report of HTLV-IIa serological profiles in three Mongolian women, which was reported in a 1994 Annual Meeting of Virologists (W.W. Hall et al. 1994). [3]

However this finding was not printed later in any journal and, the author professor Hall, who is a world authority on HTLV-II, did not mention the issue again in the 18 years that have gone by since then.

Hall has recently studied HTLV infections in America and in Asia, his team was, of course, seeking the source of Amerindian HTLV, so knowing that Siberia showed no signs of the virus, “the researchers decided to go to Outer Mongolia” there “Hall's group found HTLV-I among remote peoples in Mongolia, but no HTLV-II. Not finding HTLV-II was significant, as it suggested an American origin [of the virus].” [4], a conclusion that is in contradiction with the Pygmy findings in Africa and the African origin of the virus.

Based on this evidence we can safely conclude that there is no clear proof available on the existence of HTLV-2-like viruses in modern Asian human and nonhuman primates.

So, how did the virus get to America without leaving any traces in modern Asian humans? Furthermore, HTLV-1 is present in Asia and also in America, so the human host who brought it into America managed to live on in Asia with it (in a future post we will take a look at HTLV-1 and the peopling of America). Why did HTLV-2 leave no traces in Asia?

Quick answer: it was not taken there by modern humans but by other now extinct hominids More below, see Conclusions.

It is a matter of Time and divergence

When comparing the different strains of virus, scientists look at the differences (nucleotidic divergence) and take it as an indication of how long they have evolved separately. The more differences, the longer they have been apart.

The divergence between HTLV-IIa and HTLV-IIb is about 4.8%. What can this tell us?

Since the internal divergence of HTLV-IIb between the different Amerindian groups varies from 0 to 0.4%, on an average 0.2%, and these people have been isolated for milennia, a very simple and straightforward calculation (and a very approximate one also) would allow us to calculate that the “a” and “b” strains have been apart for about (4.8/0.2 = 24) twenty four times longer. [7]

Of course, evolution rate may not be constant as time passes (accelerates, decelarates, stops and starts), it may vary along the nucelotide, quicker in some areas, slower in others. This is reflected in the range given for the evolutionary rate in the bibliography: evolutionary rate is estimated at 0.1 to 1% per 1000 years (a tenfold difference). Furthermore, it seems that it may even be lower in populations with predominantly vertical (mother-child) transmission such as Amerindians [8]

Virologists test their divergence estimates against “established” mileposts defined by anthropologists, take this example (from [11]):

”The relaxed molecular clock was calibrated with two independent molecular calibration points; 12,000 – 30,000 ya as confidence intervals for the origin of HTLV-2 as it migrated out of Africa and Asia and into the Americas via the Bering land bridge and 40,000 – 60,000 ya as confidence intervals for the origin of HTLV-1 in Melanesia as it became populated with people from Asia... The PTLV evolutionary rate assuming the global molecular clock model was estimated by using the divergence time of 40,000 – 60,000 years ago (ya) for the Melanesian HTLV-1 lineage (HTLV-1mel) and 12,000–30,000 ya for the most recent common ancestor of HTLV-2a/HTLV-2b native American strains..."[11]

But what if the clocks are based on incorrect temporal events? Say it was a pre-sapiens hominid who brought the HTLV-II into America long before the 12-30 Kya date? Or if HTLV-1 reached Melanesia in the blood of a H. erectus 1.8 million years ago?

Below are two different examples of the outcome of these divergence estimates and the dates of course differ

1. Divergence of the different HTLV and STLV virus [6]

This paper includes a Figure, shown below, in which the PTLV-1 and PTLV-3 human and simian viruses are intermingled, but the HTLV-2 and STLV-2 have lineages that are clearly separated from each other. [6] Does this reflect that there is no recurrent or repeated cross-infections between species in HTLV-2?

Note the split dates. The split between PTLV-3 and the other two happened between 947 and 632 Kya. HTLV-2 broke off from the simian STLV-2 some 192- 287 Kya, and it was about 579 to 867 Kya that PTLV-1 and PTLV-2 split apart.[6]

PTLV evolution times Fig. 8.2 from [6].

HTLV-II Divergence Tree. Fig 5 from [11].

2. Divergence of the different HTLV and STLV virus [13].

This paper includes several figures all similar (though the exact dates differed slightly) and we have taken one, shown above which depicts the different HTLV and STLV variants and their evolution. The branch lengths are proportional to “median divergence times” in years and the scale at the bottom shows 100,000 years.

It estimates the following dates in years BP: PTLV-4 split from PTLV-2 happened between 49,800 and 378,000 years ago. The PTLV-1 : 54,250 - 75,100 years, PTLV-2: 75,200 -128,600 years, and PTLV-3: 40,850 - 71,700 years.

The dates of examples 1 and 2 differ considerably, so it makes me wonder how reliable are these “clocks” and divergence times. Furthermore, since they are taking the entry date of modern humans into America (12- 30 Kya) as a benchmark to calibrate their clocks, I am even more doubtful about their reliability. As we will see below there is some discrepancy among specilists regarding the divergence dates.

Conclusions, Discussion and possible explanations

Having read all the facts and seen all the data we have to explain the following:

• A virus strain, HTLV-II with three subtypes “a”, “b” and “c” found basically in America (North and South)
• The same virus HTLV-II subtype “b” found among Gabonese and Bakola Pygmies.
• Another unique African strain “d” , apparently the most divergent and therefore ancient, among another group of Pygmies, the Efe or Bambuti.
• No virus (we exclude the recent dispersal by IUDs) anywhere else in the whole world.
• Similar virus in D.R. of Congo Bonobo simians in Africa suggesting an African origin.

First lets take a look at the African “b” Subtype “outliers” the Gabonese and the Bakola Pygmies.

Why are the IIb subtypes from America and the Pygmies so similar?

Long residence in isolated populations such as the Amerindians and the Pygmies should provoke a high level of genetic drift. But, the divergence within IDUs is higher than the one found among the reservoir populations! And “tree branch length of nearly all viral strains within the major groups are short, indicating only a few genetic differences are unique to each strain irrespective of origin.” [13].

This could be explained by “a recent origin of modern day HTLV-II with repeated episodes of intercontinental dissemination” [13] But this option can be discarded based on the unique diversity of subtype IId and STLV-II

But the extreme similarity between strains fouond in Colombia and Cameroon; and Chile and Gabon, show such a small divergence that [13] ”based on the rates of change from IVDU (Salemi et al. 1998a), yields a recent divergence time of 100–400 years ago for the transcontinental strains.”[13] (Below is a link to Salemi’s paper).

In an attempt to circumvent this contradiction some have proposed that coevolution between host and virus in isolated communities is different to the mutation rate of the virus when it enters a new host population such as IDUs (where it evolves faster). Thus mutation rate may be “mutation rate may be orders of magnitude different”[13] (slower) among Amerindians.

I think that the answer is much more simple and straightforward:

The Gabonese and Bakola HTLV-IIb source: Brazil

If we accept Salemi’s time frame of 100 – 500 years BP as the age of HTLV-IIb subtype, and ask ourselves if there is any link between Equatorial Africa and America through which the virus could have moved during that window, we can immediately answer: yes, there was a link: the Atlantic slave trade.

Of the 11 million Africans that were captured, enslaved and ferried across the Atlantic, about 3 to 5 million went to Brazil. This country held the largest slave population in the whole world. These Africans came from the Portuguese setlements in Africa: Mozambique, Angola, Cabinda, Guina Bissau, Cape Vert and other sites along the Gulf of Guinea. Gabon and Cameroon were providers of slaves too.

It is highly probable that the HTLV-IIb strain detected in Gabon, and virtually identical to the Amerindian strains may came from America: Gabon was a source of slaves for the Americas and a coastal settlement set up for this purpose in ths sixteenth century, taking slaves from deep inland and loading them on slave ships. Paradoxically it ended up as Libreville (Freetown), the current capital of Gabon, which housed freed slaves captured by the French navy in the 1840s and grew to become a settlement with freed slaves.[15]

The crew of slave ships could have easily become infected with Amerindian HTLV-II from prostitutes at the South American Ports (Brazil or elsewhere in Spanish America) where they unloaded their human cargo, and taken the virus back with them to Africa on their voyages to pick up more slaves or to trade with goods sent from Brazil to Africa. Similar horizontal transmission from sailors to African prostitutes at the Eastern African slave loading posts would have ensured transmission from one side to the other side of the Atlantic Ocean.

Could the infection have spread to the isolated Bakola Pygmies?

The Bakola Pygmies were not so isolated

The eastern Bakola Pygmies have interacted with the Bantu people along the coastal areas of Congo, Cameroon and Gabon for hundreds of years: ”In fact, unilateral marriage practicesin which Kwassio [ Bantu] men marry Bakola [Pygmy] women, and the children born from suchmarriage, have provided an opportunity for a spatial and temporal developmentof a long standing Bakola /Ngoumba relationship”. [16]

Marriage and the carnal relations it entails are a sure way for horizontal transmission of HTLV-II from coastal groups in touch with slave ship crews and inland Pygmy populations.

Wrap up: Therefore it is plausible therefore that American HTLV-II b subtype virus entred Gabon via slave ship crews and that prostitues in both America and Africa acted as infection routes: in America from Amerindians to sailors and in Africa from sailors to local population. These in turn through marriage infected the Bakola. The recent temporal window suggested for this virus subtype and the homogeinity among the viral strains in disparate locations are thus explained.

The Bambuti Pygmy “d” strain and bonobos

The “d” subtype is very interesting and there are two possible scenarios that can explain its great divergence from the Amerindian strains:

1. Recent origin: “it cannot be excluded that this yet unique HTLV-2 D strain could have been quite recently acquired from a a simian host, implying that its divergence does not reflect a long standing presence in the human host.”[12]. The text cited, speaks for itself. In other words, the apes infected the Bambuti pygmies recently

2. Ancient origin: it could be equally likely that the strain is very old among humans, as can be seen by its great divergence and is closer to the STLV-2 strains. This indicates an ancient origin in Africa.

What cannot be defined however is “whether the virus originated in the bonobo chimps and then infected humans, or if a common ancestor infected both humans and P. paniscus early within type II evolution”.[13]

This is interesting and we will look into it again below.

Why is it not found in Asia?

Quick answer: it was not taken there by modern humans but by other now extinct hominids. Lets elaborate on this:

The classic scenario for the dispersal of HTLV-II is the following: [13]

...type II viruses diverged from a common ancestor with other HTLV/STLV in Africa, and HTLV-II subsequently formed a minimum of three major lineages (IIa, IIb, IId) within Africa. With ancestral human migration events, subtypes IIa and IIb were carried into the New World and segregated among ethnic Amerindian tribes... [13]

This scenario requires two separate waves of ancestral humans taking the two different “a” and “b” varieties of HTLV-2 to America. Which, in my opinion is very complicated, especially since not one member of these waves remained in Asia with the HTLV-II virus in them.

The simple explanation is the following: PTLV-II originated in Africa and infected the bonobos and a group of hominids, perhaps Homo habilis, that preyed on them and got infected. The STLV-II adapted to these hominids and produced an ancestral HTLV strain.

Some of the infected H. habilis moved out of Africa and into Asia, taking the “proto IIC” (yes, “c”) with them. Others remained in Africa, and their HTLV-II would later evolve into the “IId” which died out elsewhere, but survived to infect the Bambuti humans. It is probable that H. habilis was preyed on by groups of H. erectus or other hominds, and that the last relict non “sapiens” hominids infected the Bambutis.

H. habilis bypassed Southern Asia and its simian inhabitants, which is why the Asian apes are not infected. They chose to live in the Caucasus. Their “Georgian” descendants must have pushed on, through an empty Siberia, across Beringia, into America, following their big megafaunal game. The few that remained behind disappeared without a trace and did not infect the hominids that would follow their steps. Or perhaps did, infecting Neanderthals, but since they passed away too, their HTLV-II is lost.

H. erectus who followed them later, chose a southern route (India, Indonesia, China and perhaps Australia), but they were not infected and did not take the virus with them. Perhaps they had HTLV-I, but we will look into that in another post.

Modern humans when they left Africa and entered Asia, were also free of HTLV-II, it remained in a backwater of Congo, tied up in the Bambuti Pygmies.

Modern humans lived in an HTLV-II free Asia!. That is why it has not been detected there.

The Georgians into America across Beringia 1.5 million years ago is a very ancient event, and it surely puts the “genetic clock” used to calculate divergence and evolution of viral strains in another setting. The dates divergence are very likely unreliable.

Highlight. There were no humans in Asia when H. habilis took a proto HTLV-IIa across Siberia and into America.

Cross-species transmission and the PTLV-II anomaly

STLV-1 strains have repeatedly infected human beings and this is the origin of the different subtypes of HTLV-1 found in Africa. The same can be said for the origin of HTLV-3. [11] The source of infection: hunting and eating monkeys, a horizontal prey-primate hunter transmission of a zoonotic infection, and intimate contact with the prey’s body fluids. [11]

Evidence of this is the more than 15 species of Asian and African apes are infected with HTLV-I, and 15 African ones with HTLV-III, your would expect a similar situation with HTLV-II, but no, it has not been detected in any wild apes in Africa, and has only been isolated in pygmy chimpanzees or bonobos (Pan pansicus) housed at the Yerkes National Primate Research Center in the USA but originally captured in the Democratic Republic of Congo [6] (where evidence of STLV-2 among wild bonobos has recently been sugested).[17]

So, beyond the bonobos, no STLV-II virus is found in Africa, this is very different to PTLV-I and III. Why?

The surprising thing is that STILV-II has been found in New World spider monkeys (Atles fusciceps) from Panama. [5] The authors of the paper that discoverd this, cautiously write: “There are several lines of evidence to suggest that the STLV-II isolate described here is a new simian retrovirus closely related to but distinct from HTLV-II...”. They continue and speculate: “New fossil evidence suggests that the time of origin of simian primates may be pushed back into the Paleocene period, which means that direct migration of simians between Africa and South America is more likely...”.

And finally: “HTLV-II infection may be endemic in certain New World aboriginal populations [...] since these Indian tribes are relatively isolated [the infection] may have arisen from close contact with primates....[5]

In other words: Ancient African apes had STLV-II, and that long ago,when South America and Africa were part of a Supercontinent, the virus was present in both groups. Later it evolved and infected Amerindian humans with HTLV-II. This is very unlikely (the similarity between African and American PTLV-II suggests one unique origin and dispersal out of Africa into America in more recent times than the Paleocene.

The more likely situation is that H. habilis entered America (which was free of PTLV-II), and that they infected the spider monkeys.

The Amazonian “IIc” anomaly: it is an ancient strain

We have mentioned at the beginning of this post that HTLV-IIc is included as a subcluster of IIa. What is interesting about “IIc” is that it has a very unusual feature, a protein encoded by its Tax gene (the virus contains this and other genes that modulate viral expression and play an important role in its pathogenesis) is similar to the one encoded by HTLV-IIb but is longer than that of type IIa. On the other hand its env (another gene) and LTR (gene expression control center) strongly resembles type IIa.

A possibility is that the long Tax gene is ancestral and was lost by the IIa subtype but was kept by IIc. Interestingly, the other “ancient” lineages of PTLV-II, the STLV-II and the “IId” variety also have long Tax genes. [13]

Point to remember The Amazonian “IIc” must therefore be older than “IIa” (which surely arose from it), and also older than “IIb”. It is probably as ancient as the “IId” found among the Bambuti Pygmies.

This is logical if you assume that H. habilis brought the proto HTLV-IIC with him into America. It evolved there isolated from the other “d” strain. And originated the “a” and “b” strains, the latter would then infect the newcomer H. sapiens when they reached America, and through them would later return to Africa in the blood of the slave ship crews to infect Gabonese and Bakola Pygmies.

Closing Comments

This has been a very long post, though I sincerely hope it was not a boring one!

What I tried to point out were two things: one, that a hominid other than us, modern humans could have brought HTLV-II into America long before the accepted date of entry (beyond 30 Kya) of humans into the New World. And two, that scientists take this date (30 Kya) as written in stone and calibrate their genetic clocks as well as build complicated theories to avoid going against it other, unconventional yet much more simple explanations such as the one mentioned above (early peopling of America by non-sapiens hominids.

Comments, suggestions, criticism is welcome

Sources

[1] Anne-Mieke Vandamme, et al. (1988). African Origin of Human T-Lymphotropic Virus Type 2 (HTLV-2) Supported by a Potential New HTLV-2d Subtype in Congolese Bambuti Efe Pygmies. J. Virol. May 1998 vol. 72 no. 54327-4340

[2] Gressain, Antoine, et al. (1996). Serological Evidence of HTLV-I But Not HTLV-II Infection in Ethnic Groups of Northern and Eastern Siberia. Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology: 1 April 1996 - Volume 11 - Issue 4 - pp 413,414. Letters to the Editor.

[3]Hall, W. W., S. W. Zhu, P. Horal, Y. Furuta, G. Zagaany, and A. Vahlne., (1994). HTLV-II infection in Mongolia. Abstracts of the Annual Meeting of the Laboratory of Tumor Cell Biology, National Cancer Institute, Bethesda,Md.

[4] Clarie O’ Connell, (2007). UCD virus hunter travels the world seeking answers. Science Spin - January 2007

[5] Chen, Y. M. A., Y. J. Jang, P. J. Kanki, Q. C. Yu, J. J. Wang, R. J. Montali, K. P. Samuel, and T. S. Papas, (1994).Isolation and characterization of simian T-cell leukemia virus type II from New World monkeys. J. Virol. 68:1149–1157

[6] Alexander Voedvodin, Preston Marx, (2009). Simian Virology, Wiley-Blackwell. pp. 197.

[7] Antoine Gessain et al. (1995). Isolation and molecular characterization of a human T-cell lymphotropic virus type II (HTLV-II), subtype B, from a healthy Pygmy living in a remote area of Cameroon: An ancient origin for HTLV-II in Africa. Proc. Natl. Acad. Sci. USA. Vol. 92, pp. 4041-4045, April 1995.

[8] Angus G. Dalgleish. HIV and the New World Viruses pp 308+

[9] Philippe Mauclère (2011). HTLV-2B Strains, Similar to Those Found in Several Amerindian Tribes, Are Endemic in Central African Bakola Pygmies. Journal of Infectious Diseases. Published on behalf of Infectious Diseases Society of America. Volume 203, issue 9, pages 1316-1323

[10] Ethienne Lobato dos Santos et al., (2009). Molecular characterization of HTLV-1/2 among blood donors in Belém, State of Pará: first description of HTLV-2b subtype in the Amazon region Rev. Soc. Bras. Med. Trop. vol.42 no.3 Uberaba May/June 2009

[11] William M Switzer, et al., (2009). Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology 2009, 6:9 doi:10.1186/1742-4690-6-9.

[12] Thomas Leitner, Ed. The Molecular Epidemiology of Human Viruses. Chapter 7. Gessain A, Meertens L and Mahieux R. Molecular Epidemiology of Human T cell leukemia / lymohoma viruses Type 1 and Type 2...”. pp. 149.

[13]Jill Pecon Slattery, Genoveffa Franchini, and Antoine Gessain, (1999). Genomic Evolution, Patterns of Global Dissemination, and Interspecies Transmission of Human and Simian T-cell Leukemia/Lymphotropic Viruses. Genome Res. 1999. 9: 525-540

[14] Salemi M., Vandamme A.-M., Gradozzi C., Van Laethem K., Cattaneo E., Taylor G., Casoli C., Goubau P., Desmyter J., Bertazzoni U.(1998a) Evolutionary rate and genetic heterogeneity of human t-cell lymphotropic virus type II using isolates from European injecting drug users. J. Mol. Evol. 46:602–611.

[15] P. Hinks, John R. McKivigan,R. Owen Williams. Encyclopedia of Antislavery and Abolition, Volumen 2. pp. 432,

[16] Ngima Mawounga. (2001), The relationship between the Bakola and the Bantu poples of the coastal regions of Cameroon ...". Study Monographs, Suppl.26: 209-235, March 2001 209. pp. 214

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2012 by Austin Whittall © 

Circling Antarctica and getting into America

 

Route from New Zealand to Tierra del Fuego. Copyright © 2012 by Austin Whittall

Yesterday's post mentioned the possibility that archaic humans may have crossed the Southern South Pacific Ocean from New Zealand or Australia to Southern South America or Tierra del Fuego. Lets take a critical look at this idea.

Why would a group of humans get into a boat and row 1,400 km (870 mi) south towards the South Pole (which they ignored was there in the first place) and then circle the continent eastwards until after another 7,100 km (4,412 mi) they reached the southernmost tip of South America?

The most obvious explanation is: Chance. They were cast adrift and the oceanic currents pushed them away all the way to America. But, is this possible?

Yes: a paper by Gastineau [2] "A northward displacement of the ACC and a relatively higher flux of lithogenic particles from Australian or New Zealand were found for the LGM." (the ACC is the Antarctic Circumpolar Current, an oceanic current that encircles the southern continent in a west to east direction. This AAC however is a deep ocean current, the surface ones also flowed from Australia an New Zealand towards South America. Below is Fig. 12 of Gastineau's paper:

LGM currents South Pacific. From [2]

The image shows the surface and deep oceanic current, Iceberg trajectories in the Pacific sector of the southern ocean as well as the ACC during LGM. Notice the green arrows (surface currents) going towards America (the red arrow which was added by me, shows the general direction of these currents).

Could H. erectus, Denisovans or Neanderthals get to America following this route? Perhaps they took other currents further north, but note that the circulation in the South Pacific is counter clockwise that is, in the Equatorial part it flows west, then turns south next to Melanesia and returns east above Antarctica.

Referring to modern humans, Wyatt (2004) [1] suggests, regarding the peopling of America:

... a transpacific route from the Old World to the New World via the islands of Oceania has been essentially ignored. Of the many factors involved in completing such a voyage, besides an adequate watercraft, landfall frequency and prevailing winds and currents were most important. A chain of islands in the landless eastern South Pacific, with its consequent and possibly favorable modifications of regional sea surface currents, would have been particularly beneficial to eastbound mariners. Comparing present-day bathymetry with estimated late Pleistocene glacially induced sea level fluctuations suggests that latent islands may actually exist, especially when the effects of other geological phenomena are also considered. If exposed during the last glacial maximum (LGM), such a chain of islands could have provided facilitating layover points for ancient eastbound seafaring explorers, thus making a transpacific journey more plausible.

And may I add, during any previus Glacial Maximum and not only H. Sapiens, but any of our ancestors who managed to master the art of building water crafts.

Just as a point to ponder upon regarding primitive water craft, taken from a very interesting book that I recently translated for Carlos Pedro Vairo:

According to the historian Samuel Bennett, the Australian bark canoes were the most primitive appliances ever used by mankind for the purpose of navigation. [3]

They were named Bark canoes because they were made from bark stripped off gum trees in one piece and sewn together. Furthermore:

A canoe found in Arnhem Land by the anthropologist Sir Baldwin Spencer, during his 1901-1902 expedition to northern Australia, is kept at Victoria’s National Museum of. It is 5 m long [16.4 ft.]. It was brought there by eight Aboriginals the Pellew Islands, who went up the Macarthur River about 8 km [5 mi.]. This trip is interesting because it shows that they had to navigate about 16 kilometers [10 mi.] across the sea.
There are differences in the life spans of these canoes. Those for a single passenger which in case of an emergency were put together quickly, lasted a few days; however, large canoes built by several men and used to carry cargo apart from being used for fishing, could last a couple of years.[3]

These canoes are found in different parts of the world, and yes, you guessed correctly: the Fuegian natives made bark canoes too!:

After discovering islands such as Navarino and Lennox, the expedition under Admiral Jacques L’Hermite (1624) came into contact with the Yamanas on the southern shores of Navarino. Aboard the Amsterdam, flagship of the Nassau fleet, was the Dutch Vice Admiral Geen Huygen Schapenham, to whom we owe the first description of the Yamana bark canoe. In his journal, translated by historian Pablo Gallez, he wrote: “...their canoes are worth admiring. In order to make them, they take the whole bark of a thick tree; they shape it and cut off certain parts and later sew them so that it acquires the shape of a Venetian gondola.” [3]

The Yamana canoes were made from the bark stripped off southern Beech or Nothofagus trees.

Sources
[1] Steve Wyatt, (2004) Ancient transpacific voyaging to the new world via Pleistocene South Pacific Islands. DOI: 10.1002/gea.20008. Geoarchaeology. Volume 19, Issue 6, pages 511–529, August 2004.
[2] G. Gastineau Provenance of the terrigenous sediments of the pacific sector of the southern ocean and variation during the LGM
[3] Carlos Pedro Vairo, (2001). The Yamana Canoe. Zagier & Urruty Publications. My translation for Vairo's next edition of this book (2011).

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia
Copyright 2009-2011 by Austin Whittall © 

Neanderthals in America some genetic proof

 
I have already written about the possible entry of Homo erectus into America and its colonization of the New World until the arrival of Modern humans some (45? to 15? thousand years ago [kya] - the actual date is still uncertain).

Today I will look into the possibility that our distant "relative", Neanderthal (or Neanderthal) colonized America long before modern humans appeared on scene. And it will back up a previous post on Neanderthals in America.

Neanderthals some background

Actually little is known about their origin. In fact, the human family tree is still being drawn. Each expert has his or her own theory and read the facts differently. After reading different articles and papers, I believe that we can outline the following "sketchy" timeline:

1. Homo erectus left Africa and settled in Asia about 1.8 Million years ago. Most of their fossils (and, by the way, very old ones) have been found in the Far East (China, Indonesia), but more recent ones (800,000 years old) have been unearthed in the Caucasus.
2. Europe's oldest fossils were found by Bermúdez de Castro in 1997, at Atapuerca, Spain, the Homo antecessor it is an "archaic" hominin, and differs from the mor primitive H. erectus. They date from 780 kya ago.
3. Then there is the Homo heidelbergensis found in Europe, where it lived 600 to 400 thousand years ago. This leads to some questions:

• Did they originate in Europe from H. antecessor, and later moved back into Africa?
• Did they originate in Africa and migrate to Europe, replacing H. antecessor?

4.In either case, we, modern humans (Homo Sapiens) and Neanderthal evolved from H. heidelbergensis .
5. The Neanderthal split about 300,000 years ago We do not know where they split. Modern Humans did so in Africa about 200,000 years ago.
6. Scientists do not know where Neanderthals evolved; there are several possibilities:
Did some African H. heidelbergensis migrate from Africa into Eurasia and evolve there into Neanderthal? or did the European H. heidelbergensis evolve there into Neanderthals?
The outcome was the same, Neanderthals lived outside of Africa and occupied a range which covered most of Southern Europe, the Middle East, Caucasus and the Iran, Afghanistan area. See map below.

Neanderthal homeland.

None lived in Africa. They were encountered by modern humans when our ancestors moved out of Africa and took over the world, condemning Neanderthals to extinction.

Did we mix with them?

Research published in early 2011 by Yotova et al. [1] which focused on a very small part of a gene which is found on the X chromosome and known as B006 haplotype has come up with some interesting conclusions:

We share B006 with Neanderthals. And it is clear from the map below (taken from [1]) that it is very common outside of Africa and, non-existent in Sub-Saharan Africa, which suggests that it comes from a non human gene pool. That is, some hominin living outside of Africa and that later passed on this haplotype to modern humans: Neanderthal.

Worldwide distribution of B006 haplotype based on a worldwide sample of 6092 X chromosomes. From [1]

Notice that America has the highest prevalence of B006 in the whole world! (centered on Canada's west coast).

Let me qute Yotova:

" the evidence for Neandertal origin of B006 appears very strong. [...] Outside Africa, B006 is found in all habitable continents including Australia, as determined from a remote community of isolated indigenous Australians living in Central Australia [...] The ubiquity of B006 lineage reflects a worldwide contribution of Neandertal lineages to non-African genomes. It indicates very early Neandertal admixture prior to successful range expansion of the population ancestral to virtually all contemporary non-African populations" [1]

A previous paper (Zietkiewicz, Yotova - 2003) [2] on B006, stated that "this lineage could have left Africa before the expansion (as early as 160,000 years ago) and admixed, outside of Africa, with the expanding [human] lineage".
The map included in that paper is interesting, and I include it below, and as you can see it repeats the same pattern as the map above but, adds some interesting data:

B006 distribution map. From [2]

"Different colors, if present, indicate different Tn alleles shared by the same B haplotype."[2]

The map shows that America and Europe share the same Tn allele (in green in the map), which according to Table 1 in [2], is T16 (out of the 74 cases of this T16 allele, 47 appeared in America, 14 in Europe, 10 in Asia and 3 in Africa. It is predominantly American. On the other hand, the other allele (T15) did not appear in America at all.

Notice how the "green" T allele in the Old World is concentrated in the Neanderthal homeland!

But, believing in the "out of Africa" theory and the relatively recent population of America, the authors of paper [2] however disregarded American data in their analysis: "(disregarding the exceptionally low S2 value of 0.2 in the Americas)." The formula they use in their calculations was:

E(s²) = g_e x μ

Where g_e is the number of generations (at approx. 25 years per generation) since the population began to expand rapidly and, μ is the rate of mutation, and s² is the standard deviation.

They took the mutation rate μ=2.3×10^-5 and "estimated the time of the non-African lineage expansion (ge from eq. [5]) to be 4,040–4,260 generations, or 101–107 kya." [2] . That is, the time since humans emerged from Africa.

The same formula, applied to America gives: 188 kya!! Nearly 190,000 years. In other words, The lineage had all that time to evolve in America.

Discussion no the meaning of this. Lets highlight the main points:

• The highest frequency of B006 occurrence is not in Neanderthal's homeland (Map 1) but in America : 25% approx. prevalence in America vs. 10% approx in Europe.
• B006 has two Tn alleles. One of them, T16 is found in America: almost exclusively there, with 64% of the world's T16. That is followed by 19% in Europe, and the rest in Asia (14%) and Africa (of American Origin or Arabe Slave trade). T15, the other allele is not found in America, it is mostly (88%) Asian.
• So there is clearly a Europe-America link and, as T15 is not found in America and it is very common in the supposed homeland of Amerindians (Asia), there is a clear Asia - America "gap" or disconnection.

Devil advocate: Orthodox science explains the loss of the predominant B haplotypes found in Eurasia and the increase of B006 as follows:

"However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians" [3]

In other words the cause is either :

• A "founder effect" is the cause: a small group of Asians entered America and so they had a limited "gene pool" to begin with, all other Amerindians derive from this small group.
• or "population bottleneck" : a large diversified population is drasticall reduced (illness, famine, etc.) and the few that survive, and repeople the region, have a limited or restricted gene pool

We side with an opposite point of view which can be supported with the previous data:

Neanderthal had the B006 T16 lineage, and wandered into Asia, well beyond his European-Levantine homeland. There, he crossed into America, perhaps finding Eastern Asia unfriendly or already peopled with H. erectus.
America was empty, unpeopled so they expanded into a new continent free from competing hominids.

But we have evidence from another source, Blood, Amerindians and Neanderthals have a very high frequency of O blood group:

Neanderthal blood groups.

The blood of two Neanderthal individuals has been analyzed and found to belong to the O blood group. So it dates back at least to their days, and it may even be much older: "The results however suggest the presence of the human O01 allele already in the common ancestor of Neandertals and modern humans and thereby confirming an emergence of the O01 allele more than 1 Mya predating the divergence of the modern human and Neandertal populations".

Furthermore, they concluded that there was " a potential selective advantage of the O allele" [4] within the Neanderthals, meaning that it was a very common blood group in that population.

Unsurprisingly, Amerindians belong, almost exclusively to the O group (85.5% in North America and 90.9% in South America vs. a global average of 69.2% ). A group of Neanderthals migrating to America would have taken their O group with them.

"All major ABO blood alleles are found in most populations worldwide, whereas the majority of Native Americans are nearly exclusively in the O group [...] in all American populations, the same set of haplotypes O1, O1v, and O1v(G542A) was present" [5]

The authors believe that this is due to a founding population effect and suggest that the O1v(G542A) mutation found only in Amerindians, "could have emerged in Beringia, probably during the differentiation process of Asian lineages that gave rise to the founding population of the [American] continent"[5]

Ahh, the out of Asia and into Americas theory is so ingrained! please le me point out that: (O1v(G542A)), have not been found in Asians, suggesting an Ameri can origin of the allele or, perhaps a Neanderthal (pre-h. sapiens) origin.
It is interesting to point out that O blood allele appears in a large quantity of variations, this must clearly indicate that it evolved selectively and diversified, lets read about this diversity:

"Far from being monomorphic, at the sequence levels Native Americans present a variety of O haplotypes, some isolated geographically (such as O05 and Ov7 in the Cayapa, O32 and O33 in the Aymara), some shared with other human populations (O1 and O1v), and one haplotype called “O1v542” which has been found in all Native American populations screened at this level (Nahua, Mazahua, Maya, Mexican Mestizo, Cayapa, Aymara) and may very well be unique to the Americas (Estrada-Mena et al., 2009). [6]

The alleged "cradle" of Amerindians, Asia, is the highest in the world for type B blood allele (America is the lowest - and mainly in Western Alaska). Furthermore it is the rarest blood allele (only 16% of mankind has it).

Closing comments
Perhaps more research and field activities will unearth Neanderthal remains in America or, as genetic studies advance, they will provide more evidence and let us settle this issue.

Sources

[1] Yotova et al., (2011). An X-linked haplotype of Neandertal origin is present among all non-African populations 25.01.11. You can read it here:
http://operatorchan.org/z/src/molbev.msr024.full.pdf
[2] Ewa Zietkiewicz, Vania Yotova, Dominik Gehl, et al. (2003), Haplotypes in the Dystrophin DNA Segment Point to a Mosaic Origin of Modern Human Diversity Am J Hum Genet. 2003 November; 73(5): 994–1015. Published online 2003 September 25.
[3] Bourgeois, S., Yotova, V., Wang, S., Bourtoumieu, S., Moreau, C., Michalski, R., Moisan, J.-P., Hill, K., Hurtado, A. M., Ruiz-Linares, A. and Labuda, D. (2009), X-chromosome lineages and the settlement of the Americas. American Journal of Physical Anthropology, 140: 417–428. doi: 10.1002/ajpa.2108
[4] Carles Lalueza-Fox, Elena Gigli, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Jaume Bertranpetit and Johannes Krause, (2008) Genetic characterization of the ABO blood group in Neandertals BMC Evolutionary Biology 2008, 8:342
[5] Benito Estrada-Mena, F. Javier Estrada, Raúl Ulloa-Arvizu, Miriam Guido, Rocío Méndez, Ramón Coral, Thelma Canto, Julio Granados, Rodrigo Rubí-Castellanos, Héctor Rangel-Villalobos, Alejandro García-Carrancá, (2009). Blood Group O Alleles In Native Americans: Implications In The Peopling Of The Americas. American Journal of Physical Anthropology; 142(1): 85 - 94
[6] Fernando Villasnea, (2010). Evolution of the ABO Blood group locus in Pre-Columbian Native Americans.

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