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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Showing posts with label Africa. Show all posts
Showing posts with label Africa. Show all posts

Saturday, November 8, 2025

Diab - The mysterious Island. Was it part of America?


Ancient Navigators Series


While rereading an old Argentine history book, part of a collection that my dad bought second hand back in the late 1960s, I came across the following text (in the chapter dedicated to the ancient voyages to America prior to Columbus' discovery):


"The map of fra Mauro of the year 1457... holds a mystery regarding Cape Diab, that is, the southern tip of Africa corresponding to the current Cape of Good Hope. There, it depicts a large southern land mass, and in an inscription it says that the strait that divides Cape Diab from that sourthern land it s flanked by tall mountains and thick jungles and the water has dangerous whirpools. There is no such narrows at the Cape of Good Hope. This fact has no other explanation than that of admitting that some unknown navigator who was thrown by the storms to the Strait of Magellan, on his return to Europe, and refer his adventures. As America's existence was not known, the goeographer situated this strait in the only spot in the world where it was possible to imagine it: on the tip of Africa, which had not yet been discovered, and due to this story, it was imagined as separated by a strait from a large southern land mass."

Source: See p. 233 in Historia de la Nación Argentina v.ii, chap.ix, 1939, Enrique de Gandia. Ricardo Levene, General Director.


The map below shows where the landmarks mentioned by de Gandia and this post.

maps of America and Africa
Africa and South America, Diab and other islands. © 2025 A. Whittall

Checking online, I found many interesting sites on fra Mauro's 1457 map, including a zoomable interactive copy of the map. The map, unlike modern ones, has the North on the bottom and the South on the top as you can see below:


fra Mauro 1457 map
Fra Mauro map, (1457), South is top, North, bottom.. Source

Below is a closeup of the Diab area, the text in ancient Venetian Italian in red can be read clearly:


Diab, Fra Mauro map

Fra (from Frater - brother in Latin) Mauro was a Venetian map-maker and monk (c.1400 - 1464) he compiled information from different sources and produced his map of the known world (notice it does not include America or Australia, Oceania or the Antarctic).


Since ancient Venetian Italian is not my forte, I found an online translated version of the map's text in English, but it is not very complete.


The inscription in red ink, upper right ("Circa di ani del signor 1402 una nave...") is translated as follows (I have added some text omitted in this translation):


"About the year of Our Lord 1420 a ship, what is called an Indian junk [çoncho d'India], on a Crossing of the Sea of India towards the Isle of Men and Women, was driven by a storm beyond the Cape of Diab, through the Green Isles [tra le isole verde] , out into the Sea of Darkness on their way west and Southwest, in the direction of Algarve for 40 days. Nothing but air and water was seen for forty days and by their reckoning they ran 2,000 miles and fortune deserted them. When the stress of the weather had subsided they made the return to the said Cavo de Diab in seventy days and drawing near to the shore to supply their wants the sailors saw the egg of a bird called roc, the egg being as big as a seven gallon cask, and the size of the bird is such that from the point of one wing to another was sixty paces and it can quite easily lift an elephant or any other large animal. It does great damage to the inhabitants and is very fast in its flight."


These "Green Isles" therefore seem to be west of Cape Diab (in the Atlantic or "Sea of Darkness"). Algarve is on the southern coast of Portugal. The roc bird with gigantic eggs found upon their return to Africa are surely eggs of the now extinct Elephant Birds of Madagascar, probably the largest birds in the world. They were wiped out after humans reached the island some 500 to 1000 years ago. Madagascar and the Roc is mentioned in "The Travels of Marco Polo" (Chap. XXVI p. 429)


Diab and the "channel"


On the lower side of the Diab "Strait" by a sailing ship is an inscription, that is not translated in the source mentioned further up ("Nota che questo cavo de Diab..."): "Note on this Diab Cape, it is separated from Abassia (Abbysina?) by a channel which is surrounded on one side and another by very high mountains and and trees so large that they protect the dark canal which in its depths creates a dangerous circle so that if a ship were to descend it would be in danger."


This is the text mentioned by de Gandia. But which is this channel, and Diab, the Green Men, the Men and Women isles?


The channel that separates Madagascar from Africa, or Mozambique Channel is over 420 km wide at its narrowest point (260 mi), it is very different to the narrow channel with whripools, dark and concealed by trees described by Fra Mauro.


To the left of Diab, the map shows two islands, Nebila and Magla. Above them is a scroll with an inscription "These two islands are inhabited by Christians, in one of them called Nebila, live the women, in the other called Mangla, live the men who pass only three months a year with the women". They are in the SW of the Indian Ocean east of Port Elizabeth, South Africa.


These islands are found in Marco Polo's Travels (Chap. XXIV p. 423) and they are 30 miles from each other (48 km.) Perhaps the women's Island is a mythical one related to the Amazon female tribe. The word Nebila is Arabic and means "beautiful" - nabilah (Source). The isle of Magla seems to be close to the Maldvies Island (source).


The Atlantic?


On the western or southern tip of Diab's channel is another scroll that reads "Just beyond these off-shore islands, shadows begin to appear, but within this cape they do not hinder navigators." There is a string of islands running along the coast. There are no islands along the eastern coast of South Africa, but if it were South America, these would be the islands along the Pacific coast of Chilean Patagonia, with storms, clouds, squalls and sleet. (possibly the "shadows"). See this timelapsed crossing of the Strait of Magellan.


Fra Mauro repeats the story of the voyagers swept westwards (the text can be seen in the 2 o'clock quadrant above the words "Ethyopia Occidetal" and "Garbi":


"What is more, I have spoken with a person worthy of trust, who says that he sailed in an Indian ship caught in the fury of a tempest for 40 days out in the Sea of India, beyond the Cape of Soffala and the Green Islands towards west-southwest; and according to the astrologers who act as their guides, they advanced 2,000 miles."


He mentions that Eudossus (see my post on Eudoxus) sailed from the Arabian Gulf to Gades around Africa.


Soffala is no other than the old port-city in Mozambique, Africa, on the Indian Ocean (see map). Pieter Derideaux, in his blog states that the Green Islands were known to the Arabs as Zanzibar and Pemba. The Kilwa Chronicle, reported by Barros in the 1550s (online) calls Pemba "the Green Island". Pemba is in Tanzania (see it in Google Maps).


I understand that the "Green Islands" were in the Atlantic, they are reached only after you enter the Atlantic Ocean. There are not many Islands in the South Atlantic: Tristan da Cunha, Ascencion, Saint Helena, and further north, in Guinea, Santo Tome, Falkland-Malvinas, South Georgias).


An article by Marco Vigiano states that "Diab means Gold, Dehab in Arabic, or Swahili" and suggests that it represents the Rift Valley in East Africa, it does not agree with it being identified with Madagascar.


The distance from South Africa to Brazil is 6000 km (3700 mi) and more or less the same to the Falklands-Malvinas Islands, far more than the 3200 km (2000 mi) that the Indian Junk sailed.


Nevertheless, de Gandia's theory of the Strait of Magellan is very interesting, and original.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

Monday, February 3, 2020

The complex Human tree in Africa...


A new paper published in Nature (Ancient West African foragers in the context of African population history, Mark Lipson, Isabelle Ribot, David Reich. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1) tells us about the admixture going on in Africa some thousands of years ago:


The paper's highlights are:

  • They sequenced the DNA of four children from Shum Laka in Cameroon buried on two separate occasions (two of the children were buried 8,000 years ago, the other two, 3,000 years ago).
  • One of them carried the oldest and most divergent Y chromosome haplogroup: A00
  • Their model implies that these children belong to the fourth group that originated modern human lineages. There were three more groups: (i) from which modern Khoisan people descend from. (ii) Ancestral group to the East Africans. (iii) An exinct "ghost" population. These groups are some 250 ky old.

Science tells us more about the extinct group (iii): "Another two-thirds of children’s DNA came from an ancient "basal" source in West Africa, including some from a "long lost ghost population of modern humans that we didn’t know about before" says population geneticist David Reich of Harvard University, leader of the study."


And even more interesting is that "...the Shum Laka individuals are most related to present day rainforest hunter-gatherers [pygmies] and not ancestors of Bantu-speakers is surprising given that Shum Laka was long considered by archeologist[s] as the site where Bantu-speaker culture [was] developing in situ" (from LiveScience).


These four children are therefore not related to the modern Africans living in Cameroon or to the Bantu speakers who spread out across Africa. Instead they are closer to the pygmies of Central Africa!



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Sunday, November 3, 2019

A human homeland in Botswana 200 kya? (unlikely)


A paper published last Monday in Nature (Human origins in a southern African palaeo-wetland and first migrations - Chan, E.K.F., Timmermann, A., Baldi, B.F. et al. Nature (2019) doi:10.1038/s41586-019-1714-1) reports that modern humans originated in what is now Botswana, in southern Africa "within the residual Makgadikgadi–Okavango palaeo-wetland of southern Africa, approximately 200 ka (95% confidence interval, 240–165 ka)".


These people carried the "oldest" mtDNA lineage, the L0 one. After 70,000 years of isolation in this former wetland, they finally moved out dispersing to the northeast and southwest between 110 and 130,000 years ago, eventually peopling the whole world.


This paper has received strong criticism for several reasons, such as:


  • It did not use Y chromosome data, which tell a different story.
  • Modern Human Fossils older than 200,000 years have been found in different parts of Africa, including NW Africa (i.e. Morocco 300 kya)
  • It assumes that people don't move: current carriers of L0 living in the area are assumed to have remained there over the last 200 kya! Maybe they moved there from somewhere else.
  • There has been no ancient DNA extracted from human fossils in Africa older than 15,000 years. So we cannot make assumptions on things that took place 200 kya based on contemporary populations.

This is a good criticism to the paper: No, a genetic study didn’t pinpoint the ancestral homeland of all humans

I strongly agree with the critics, and find the paper by Chan et al. unconvincing. Below is a map from the paper.


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Thursday, September 29, 2016

Heterozygosity for dummies


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


What does this mean?


First of all what is Hetrerozygosity?


Heterozygosity

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


Genes come in different variants, known as alleles.


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

  • bb
  • bB
  • Bb
  • BB

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


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


Populations.

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


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


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

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

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


100% = p2 + 2(pq) +q2


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


100% = (30%)2 + 2(30% x 70%) + 70%2


100% = 9% + 42% + 49%


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


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


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


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


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


So, the factors that provoke homozygosity are:

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

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


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


1. Interbreeding

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


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

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


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

All must add up to 100% of the population.


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


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


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


So the comparison is:


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

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


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


Genetic drift

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


100% = (50%)2 + 2(50% x 50%) + 50%2


100% = 25% + 50% + 25%


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


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


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


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


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


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


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


Founder Effect

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

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


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


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


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


Bottleneck

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


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


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


Selection

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


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


Geographic Isolation

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


Heterozygosity and Human Evolution

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


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



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



Allelic Diversity

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


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


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


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


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


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


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


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


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


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


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

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


This leads me to ask, what if African heterozygosity was enriched by recent admixture with other hominins in Africa? an inflow of different relic alleles elevated African diversity above that of non-Africans. Could current lower Amerindian heterozygosity reflect an ancient population just like that of Denisovans or Neanderthals?


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


Sources


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


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

Saturday, October 10, 2015

Into Africa gaining strength


A paper pubished in Science (Gallego Llorente et al., 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science DOI: 10.1126/science.aad2879 two days ago, reveals what has been suspected for some time: All Africans have a Eurasian component in their genes.


The abstract says so clearly:


Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.


As it is behind a pay wall, I checked the web and found the following additional data:

  • "the scientists believe up to 25% of the DNA of modern Africans can be traced back to this event."
  • "... if you go to the corners of Africa, all the way to West Africa or South Africa, even populations that we really thought were purely African have 5-6% of their genome that dates back to these western Eurasian farmers."
  • "...it is also interesting to discover now that even sub-Saharan Africans have a bit (0.3-0.7%) of Neanderthal ancestry."

Who knows, perhaps this is the first step into a serious analysis of the real roots of mankind, and may lead to a revision of the conclusions of another recent paper (L. Pagani, 2015, Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians Cell):


"... the Ethiopian and Egyptian genomes showed different patterns. In particular, the Egyptian0 genomes displayed a more recent split from both the West African (21,000 years ago) and the non-African (55,000 years ago) genomes than did the Ethiopian genomes (37,000 and 65,000 years ago, respectively). This suggests a higher similarity between non-African and Egyptian components than between non-African and Ethiopian components, which is consistent with the fact that Egypt is the last stop on the way out of Africa. Such split dates also hint at a recent interaction between Egyptians and West Africans..."


They too noticed a similarity between Egyptian and Eurasian genes, but their conclusions are different.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Thursday, May 21, 2015

As they were found in Africa they are tools...


A paper published in Nature describes the finding of the most ancient stone tools, and informs that they predate the genus "Homo". So it was not old Homo habilis who made the first tools. Instead it was made by some other hominin. The authors propose the name Lomekwian for this pre-Oldovan lithic technology.


Below are some photos, of the tools and the site (yes, like my previous post, this one too was inspired by news that I read today in bbc.com)


Lomekwian tools and the site. From BBC.com

The paper (can be read in full) is: Harmand, S. et al. 3.3 Million-Year-Old Stone Tools from Lomekwi 3, West Turkana, Kenya. Nature, published online May 21, 2015


It is an exciting find, pushing back the origin of tool making to the very first of our kin. But it also makes me wonder about the prejudice in science. Similar stones found in America, at the Calico site would be dismissed as geofacts, made by nature, flash floods knocking stones together in a desert environment. Nobody even suggests such an origin for African stones. After all, oldest hominin fossils come from Africa so any old chipped stone found in the area where these people lived must surely have been made by them.


Below are some stones from Calico (source)



They look man-made don't they? However they are considered as natural.


In America, on the other hand, we all know that Siberians migrated there some 15 kya after spending some time isolated in Beringia so anything found in America that does not resemble a modern Homo sapiens "advanced" tool is not even identified by those looking for stone tools (Mousterian, Acheulean or Oldovan tools are not considered when seeking stone tools in America).


We need scientists with an open mind, seeking the truth, not just seeing what they were taught to see...



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Saturday, April 4, 2015

On the African of the "Ape woman" Zana


I have just read some articles about a new book (The Nature of the Beast) by Bryan Sykes. Coming from an Oxford professor it is a daring subject and the conclusions that are mentioned online are indeed surprising.


The yellow press loves these controversial subjects and puts forth eye-catching headlines like "Russian Apewoman could have been a Yeti" or "apewoman was not human", but there is no substance behind those claims so, unless I buy the book or read the scientific papers that apparently will appear later on, I will remain in the dark!


Fortunately, The Times published some excerpts from the book, and I am sharing them below (the link is this here): in bold I have highlighted some strange points in the text


Excerpts from The Times

Published at 12:01AM, April 4 2015 Bryan Sykes, professor of human genetics at the University of Oxford, set out to investigate rumours that something almost human had been found lurking in remote woodland between Georgia and Russia. What he discovered could rewrite the history of humanity.
“In the early 1850s a merchant visiting the Ochamchir region of Abkhazia came across a young almasty [the Russian equivalent of the yeti] by a remote stretch of the Adzyubzha river. As soon as it caught sight of him the creature vanished into the forest. Some days later he returned with a group of hunters. When they saw it again, their dogs were unleashed, chased it into the forest and brought it down.
“After a fierce struggle it was eventually subdued and shackled to a log. It was clearly a female. She was held in a ditch surrounded by sharpened stakes, then sold on to a succession of “owners” until she was purchased by the Abkhaz nobleman Edgi Genaba and taken to his farming estate at Tkhina on the Mokva river.”
The wild humanoid was named Zana and tamed by Genaba until she came to serve him as a slave. About 6ft 6in, dark-skinned, covered with long, reddish-brown hair and extraordinarily muscular, she slept outdoors and ran naked around the estate until her death in 1890.
“In many ways Zana’s is a classic tale of a wild creature part-human, part-animal, captured and tamed. What has kept the story alive is that she had at least four children with local men. There are tales of drunken orgies and curious men being granted access to her in exchange for money.
“Two developments turned Zana’s story from an intriguing folk tale, albeit one substantiated by several witnesses, into a case with potential for scientific investigation. The first was that in 1971 Igor Burtsev [a Russian cryptozoologist] located the grave of Khwit, the younger of Zana’s two sons, in an overgrown graveyard in Tkhina and exhumed his body. The second was that Burtsev, and also lately Dmitri Pikulov, had managed to trace six of Zana’s living descendants.
“I could see a way of obtaining genetic information about Zana from her son’s skull. If I could recover mitochondrial DNA [passed down through the mother’s line], the strict matrilineal inheritance would mean that its sequence was identical to Zana’s. I could also see a way of discovering more about Zana’s genetic makeup through her living descendants.”
Professor Sykes sent one of the Russian enthusiasts to take DNA samples from Zana’s living relatives and set to work on analysing one of her son’s teeth. Their initial frustration at finding no matches with Neanderthal gene sequences quickly turned to astonishment.
“As soon as Khwit’s sequence came through I set about comparing it to the dozen or so Neanderthal sequences that have been published. It was very soon clear that Khwit’s, and thus Zana’s, mitochondrial DNA was not Neanderthal. The disappointment was temporary. Zana may not have been a Neanderthal but when I compared her detailed mitochondrial DNA sequence with my database of hundreds of thousands of records from all over the world, there was a major surprise. The sequence from Khwit’s tooth showed beyond doubt that his mitochondrial DNA, and therefore Zana’s, was from sub-Saharan Africa. I was stunned. How could it have happened that Zana, living wild in the forests of the Caucasus, had DNA from thousands of miles away on another continent?”
The DNA swabs from Zana’s descendants told the same story: she was pure African. But how did she get there?
“How was it that a full-blooded sub-Saharan African came to be living wild in the foothills of the Caucasus mountains in the middle of the 19th century? None of the explanations is straightforward. There had been a few African slaves in Abkhazia in earlier centuries when it was part of the Ottoman Empire and Zana could have been an escaped slave. The difficulty is that although the slave theory might explain her African DNA, it does not account for her appearance. She was nothing like a modern African in her looks or behaviour. Feral children and adults are rarely healthy and are usually discovered on the verge of starvation, yet Zana had superhuman strength and athleticism. Is it likely that an escaped slave could have sustained herself in the wild, and so well that she developed remarkable physical attributes? Almost certainly not.
“But if not a Neanderthal, was she fully human? Zana may have been in the genus Homo without being fully Homo sapiens. To begin to answer this intriguing question, I checked to see if there were any matches with Zana’s mitochondrial sequence in any of the available databases. There were none that matched exactly. I also had the scraps of her nuclear genome scattered among her descendants. Again, the African segments did not match any records. I hope to know soon whether Zana was indeed a survivor of an antique race of humans. If Zana’s people were in the Caucasus during the 19th century when she was captured, they might well still be there to this day, living as they have for millennia somewhere in the wild valleys that radiate from the eternal snows of Elbrus.”
• Extracted from The Nature of the Beast: The First Scientific Evidence of the Survival of Apemen into Modern Times by Bryan Sykes (Coronet £25). To order for £20 including postage visit thetimes.co.uk/ bookshop or call 0845 2712134.


So here we have a woman captured in the Caucasus, whose mtDNA was Sub-Saharan African yet it did not exactly match any of those existing in the database.


Vague to say the least. Most Sub-Saharan African mtDNA belong to L haplogroups. And there are many differences among them yet all are "L", we can imagine that Zana's mtDNA was "L", and that pinpoints her as African, the fact that it is has some additional mutations does not mean it is ancient.


However, to be fair (I actually thought it was all some wild idea of Sykes), I found this scientific paper "Reconstructing ancient mitochondrial DNA links between Africa and Europe" by María Cerezo et al. Published in Advance March 27, 2012, doi:10.1101/gr.134452.111 Genome Res. 2012. 22: 821-826, which had some interesting findings about L mtDNA Hg in Europe:


Abstract Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ∼65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.


So it seems that African L hg got into Europe around 11 kya and that accounts for more than one third of this Hg in Europe. The rest is modern, due to slave trade or migration.


Figure 5. Diagram showing the coalescence ages of L-European lineages and their 95% C.I. (see also Supplemental Table S2) and the estimated frequencies in Europe over the total number of existing L mitochondrial genomes from Europe..from Cerezo et al. (2012)

So maybe Sykes is on the right track, an African input (no Yeti or apemen) in the Caucasus, derived from an ancient migration OOA. We will have to see what hg his mtDNA belongs to. And compare it to those shown in the image above.


Let's not forget however that this area was home to the Homo Georgicus, as I posted in 2011. And they were "Africans" too, but about 1.8 million years older than any recent 11 ky old African migration into Europe. Could Zana have some relationship to those archaic hominins?



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

Wednesday, July 9, 2014

Not he usual "Out of Africa" cline


A paper (Hai et al., 2012) [1] analized a very special and unconventional gene, miR-941, it immediately drew my attention because it goes against the usual decreasing gradient of variability from Africa outwards, which shows lower variability in the fringe regions that are further away from our purported Eden in Africa. This post will look into this oddity and its implications.


microRNAs or miRNA


Genes usually are in charge of producing proteins or RNA strands (i.e. tRNA) that in turn interact with gene expression pathways. But this is not the case with micro RNAs (miRNAs) which have very important roles in gene expression. miRNAs are short single-strands of RNA (20 to 24 nucleotides long), hence the name "micro".


The appearance of a new miRNA can impact on the expression of hundreds of genes, so for this reason, the the authors of the paper [1] set out to detect a human-specific miRNA and then tried to figure out its evolution and impact on modern humans. They sought microRNAs (miRNAs) specific to the human genome.


The older (archaic or more ancient) miRNAs tend to have higher expression levels than those that have appeared more recently, and a survey of several human-specific miRNA showed just that: low expression levels, a sure signal that they are quite recent. But there was an exception: miR-941 which was found in the human brain at very high expression levels, higher than other miRNAs found in humans and primates.


miR-941


More interesting was the fact that its expression was absent in macaques and chimpanzees showing that it evolved in the hominid line after we split from the chimps some 6 million years ago (Mya). Its upper limit is given by Denisovans, who do also carried it, and this split took place about 1 Mya. So the miR-941 evolved in our hominin ancestrors between 6 and 1 Mya.


What is exciting is the fact that it interacts with our brains, and the human intellect began to evolve during that time span: the "Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling." [1] it is active in the cerebellum and the prefrontal cortex, which are two processing regions within our brains.


The media hyped up this paper based on its role as "making us human" and its impact on our brain-power, but, as we will see below its role is much deeper than that.


The paper suggests that our extended life span and a higher tendency to developing cancer (compared to chimpanzees and macaques) is probably due to this microRNA. So we should thank miR-941 not only our higher reasoning abilities but also our unusually long life span (yes, cancer is a terrible collateral effect). The authors put it this way:


"It is, therefore, appealing to speculate that emergence of miR-941 enhanced the maintenance of adult stem cell populations, thus supporting longer human lifespan, but rendering human cells more prone to malignant transformation. The role of miR-941 in the regulation of insulin signaling adds support to this notion. The insulin-signaling pathway was consistently implicated in lifespan regulation in many species, including humans. Notably, experimentally verified targets of miR-941 within this pathway include genes directly shown to be involved in lifespan extension in model organisms: IRS1, PPARGC1A and FOXO140 (ref. 40). Furthermore, FOXO1 was linked to extended human longevity." [1]


Not the usual cline though


Unlike many genetic markers which show a high diversity in Africa and then a decreasing gradient as you move away from our purported homeland, miR-941 shows quite a different picture:


Although it is found in all humans, the number of precursor copy-number, or repeats is quite variable: it ranges from 2 to 11 copies. This variaton is linked to geographical location too. Although there is a clear indication that the usual decreasing cline is not present in miR-941, orthodoxy compels the authors to affirm that there is a higher African variability and a West to East cline!:


"The average pre-miR-941 copy number decreased from the west to the east: from eight copies in sub-Saharan Africans to six copies in Eastern Asians. miR-941 precursor copy number variation was also significantly higher in sub-Saharan Africans compared with 'out of Africa' populations, with the exception of Oceanians and native Americans
[modern human carry] 2–11 copies of miR-941 precursor, with an average of 8 copies found in sub-Saharian Africa, an average of 7 copies in Europe, America, Oceania and most of Asia, and an average of 6 copies in East Asia." [1]


Look at the figure below (from [1]) and make up your own mind; it shows miR-941 precursor copy repeats in different populations:

miR-941 global repeat frequency

The upper part of the image (c) shows that the variability is highest among South American Karitiana (5 to 9 counts), Papuans and Palestinians (4 to 7) folllowed by San (6 to 9). In other words, it is not higest among Sub-Saharan Aficans!


In the case of the Amerindians, it is a surprising find since they are, according to orthodoxy, supposedly a bottleneck population "lacking the diversity of the Africans" , the other Eurasian people -purported ancestors of the American Natives have less variability than Amerindians.


Part d reflects this, showing the average of each region with the highest count numbers in Oceania, Africa and among Native Americans. All other populations have a lower count.


The Variance (in part e) clearly shows the highest variances in Africans and Native Americans. This does not depict a west - east cline, actually it drops off in the middle and grows again as you move on east.


This is clearly at odds with the accepted notion that diversity drops off with distance to Africa, with the New World populations being the less diverse! The authors actually state this mainstream notion in their abstract: "... shows a trend for decreasing copy-number with migration out of Africa" [1] which is not what the facts in their paper shows. (preconceptions are so hard to erase aren't they?).


So even though the main text shows that diversity drops in Eurasia but increases in Oceania and America the authors overlook it and don't even try to seek an explanation for it.


Speculations and Copy-number variation (CNV)


The paper points avoids controversy and does not analyse the significanse of the different Copy-numbers, it merely points out that a different amount of repeats "is not unexpected, given general instability of genomic regions formed by tandem repeats" [1].


But it is not chance that is at play here but natural selection the authors point out tha when a new miRNA appears (obviously its initial appearance is due to chance), it may wreak havoc in the established network due to negative changes in gene expression. So the forces in natural selection would quickly get rid of it or modify the binding sites that produce negative effects. In the case of miR-941, since it was not eliminated, what changed were its binding sites, which were lost.


So if Amerindians have a higher Copy-number variation (CNV), there must be a selective pressure at work. Actually this is the case:


"The "high-degree of copy-number variation (CNV) ... among contemporary human ethnic populations, suggest[s] a high degree of functional variability even among humans. New cell biological funcions acquired because of the appearance of mR-941, for example, new controls over sonic hedgehog and insulin-signaling pathways (Hu et al., 2012), are likely to be important as CNV-dependent determinants of human-specific adaptations to the environment and to disease." [2]


In other words, CNV is important and should not be overlooked.


It is clear that Amerindians and Papuans have a wide range of CNV than Europeans or Asians, and comparable to those of Africans. Yet they are always depicted a population that originated from a founder effect and later went through a bottle neck which reduced its genetic diversity even further. Why is CNV higher among them?


I am at a loss to explain this, but it the high CNV in Oceanians and American natives is a well known phenomenon, and is an incongruity that is explained away as a sampling bias! [3]:


"higher-frequency CNVs were more common especially in Oceania and the Americas... in contrast with their usual reduced variation, populations from Oceania and the Americas had more CNV loci and more previously unobserved loci than most other populations." [3]


The authors try to explain this anomaly as due to "some bias may exist in CNV detection" and go into an elaborate explanation on sampling. Then they simply ignore this large variability in CNVs compared to the usual Out of Africa cline of decreasing diversity and conclude that: [3]


"despite a difference from SNPs in the frequency spectrum of the copy-number-variants (CNVs) detected - including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas- the global distribution of CNVs largely accords with population analyses for SNP data sets of similar size..." [3]


The image below, from [3] actually shows the opposite (peaks in America, Oceania and the Kalash -from Pakistan):


higher CNV in America

Since African CNV is low, it shows that the high CNV in the Americas is not due to admixture with Africans brought to the New World as slaves. It is due to another cause.


So why do Papuans and Amerindians have a higer CNV diversity?


CNVs can have a negative effect on health and provoke diseases (these will tend to be selected against as the carriers will have a burden which may impede them from having children). Other CNVs have a positive effect and may protect the carrier against disease and "other copy number variants carried by healthy individuals that seem to have no function might actually be evolutionarily retained in populations if they provide a selective advantage." [5]


Could the American and Oceanian variety in CNVs be due to the forces of natural selection retaining CNVs that have been lost by other populations?


Or did they receive these variants from other archaic populations that lived in these areas and admixed with them, receiving these extra CNVs which conferred them a selective advantage?


If so, then the archaic people were already living in America and Sahul when humans reached those regions.


More on the decreasing diverstity myth


splitting populations and diversity

When a population with a given diversity (Population A in the image above; diversity is shown by the different colored circles) splits and a sub-population (Population B) moves away, -shown in stage 1- diversity will decrease. In this case we took B as having the same mix as A, but it could have been different, reducing diversity even further (see Population C for instance). The smaller population is more prone to genetic drift which reduces diversity and will also be less likely to evolve new mutations as its size is smaller. It will also be subject to the risk of extinction or loss due to natural calamities than a larger population spread out over a wider territory. So even if the migrating group grows at the same pace as the original population (stages 2 and 3), the outcome will be a reduced diversity.


The acepted theory suggests that variation within a population is proportional only to n (the effective population size) and μ (the mutation rate) which should be the same across all human groups (is it?). [4] So size influences variation: bigger sizes, more variation. Which makes me ask (as an explanation to the higher CNV observed in the New World and Sahul): Did America and Oceania have a larger population in the past which later became extinct? Well, we know that the Americas suffered a devastating impact after its discovery by Europeans in 1492: its population was decimated and its diversity plummeted. Did something simila happen in Oceania? Probably not, as an Old World population they were well adapted to Old World diseases.


Another factor is that, before mutation-drift equilibrium is reached, the age of a population influences its diversity: older populations accumulate more variations. So could the observed CNV diversity be due to an early peopling of America or Oceania by one of our ancestors (Homo erectus? Neanderthal? Denisovans?). This would extend the timeline well beyond the accepted 50 kya for the OoA event or the 15 kya for the peopling of America and allow for diversity to develop.


And, as a closing grand finale look at these two images from Seielstad et al., (1999) [4], which also depict a close relationship between Africans and Americans instead of the usual "decreasing gradient away from Africa":


Africa and America closest

Yes, the paper (which looks into Y chromosome STR diversity), dates back to 1999 and its figures are extremely unsual but the paper nevertheless echoes the well known mantra of orthodoxy:


"A recent African origin for all humans is supported by a robust corpus of evidence. This evidence takes three major tracks: (1) increased genetic diversity in Africa versus the rest of the world, (2) phylogenetic analyses placing the deepest branches between African and non-African populations, and (3) indications that the age of the “genetic most recent common ancestor” is very young. The Y chromosome, like mtDNA and the autosomes, appears to support a recent African origin." [4]


Sources


[1] Hai Yang Hu, et al., (2012). Evolution of the human-specific microRNA miR-941. Nature Communications 3, Article number: 1145 doi:10.1038/ncomms2146
[2] Antonio Noronha, Changhai Cui, Robert Adron Harris, John C. Crabbe, editors. (2014). Neurobiology of Alcohol Dependence. Elsevier, May 2, 2014. pp 500
[3] Mattias Jakobsson et al., (2008) Genotype, haplotype and copy-number variation in worldwide human populations. vol. 451 doi:10.1038/nature06742
[4] Mark Seielstad, Endashaw Bekele, Muntaser Ibrahim, Amadou Touré, and Mamadou Traoré, (1999). A View of Modern Human Origins from Y Chromosome Microsatellite Variation. Genome Res. Jun 1999; 9(6): 558–567.
[5] Lobo, I. (2008) Copy number variation and genetic disease. Nature Education 1(1):65


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

Sunday, May 6, 2012

HTLV-II and the peopling of America


HTLV-2 in Africa
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.


HTLV-2 strains
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]


HLTV-2 divergence times
PTLV evolution times Fig. 8.2 from [6].

HTLV2 divergence
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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