Syphillis and the Early Peopling of America

A A spring-shaped bacteria belonging to the genus Treponema causes several diseases in humans, one of them is well known for the devastating effects it produced in humans until the advent of antibiotics: syphilis. It is also the only venereal treponemal disease, because the other three (yaws, bejel and pinta) are transmitted via oral and⁄or skin contact.

Today's post will look into the treponemal diseases to see if it can help us gauge when America was peopled and if any of our more distant ancestors made it to the New World before Homo sapiens did.

Treponemal disease

There are four different varieties of the spirochete Treponema bacteria, and each one causes a different disease: T. carateum provokes pinta, T. pallidum subsp. endemicum causes bejel, also known as endemic or non-venereal syphilis, T. pallidum subsp. pertenue leads to yaws and T. pallidum subsp. pallidum is the cause of venereal syphilis (it is pictured above).

The interesting part is that they are morphologically and serologically identical and the genetic variability between them is very small (0.2% between yaws and syphillis) so this makes it very hard to distinguish between them (there are no specific serological tests to pinpoint the type of infection affecting individuals) [3].

The genetic sequencing of all the subspecies of T pallidum (except one, the vector of Pinta, T. carateum -more on this below) shows that ther are five genogroups which do not identify "discrete organisms for each treponemal disease [instead] there may in fact be a genetic continuum of the pathogenic Treponema, individual components of which affect pathogenesis in an individual host in concert with social or environmental factors that influence routes of transmission and disease manifestations." [3].

In other words, they are virtually identical but are assumed to be different "subspecies" because they appear in different geographical areas around the world and produce manifest themselves in different manners and virulence.

The range of each "subspecies" is the following: Pinta is quite rare and was found in Central and South America. Yaws appears across Central and Western Africa, Southeast Asia, New Guinea, Northern Australia, Indonesia and the coastal regions of tropical Central and South America. Endemic Syphilis is found in the Middle East, the Balkans, South Central Asia, North Africa and central Australia. Venereal Syphilis, is global.

A genetic analysis

The controversy over the origin of these diseases continues: Is venereal syphillis an American disease or did it originate in the Old World?, how are the different subspecies related? The modern tools of genetics will be able to settle these issues once more information is obtained and analysed. However initial studies by Harper et al, 2008 [5](which regrettably do not include the analysis of Pinta) have reached some interesting conclusions:

• A maximum likelihood tree placed all of the T. pallidum subspecies (strains) within a single clade showing their very close relationship in comparison to other Treponemes which infect primates.
• Two of the subspecies subsp. pallidum (venereal syphillis) and subsp. endemicum (endemic or non-venereal syphillis) grouped seprately from the subsp. pertenue (yaws).
• The different strains within subsp. pertenue are closer to the root of the tree, meaning that it is the "oldest" lineage in the family, the ancestral population to all other subspecies.
• pertenue (yaws) and endemicum (non-venereal syphillis or bejel) are genetically closer to each other than to the venereal strain subsp. pallidum. The paper [5] obviously interprets this as meaning that venereal syphillis is caused by the youngest strain (the one that "diverged most recently" [5])

The geographic distribution of the diseases is used together with the Treponemal gdp gene sequences for each subspecies to try to elucidate the realtionship and origin of each strain. The following map which I have adapted from figure 4 in [5] shows the reasonable proposal of Harper et al., (2008) [5]:

Global distribution of Treponemal diseases and their origin. Adapted from [5]

The map is based on the assumption that the Old World yaws is the ancestral form, and that the gdp gene's GATG sequence is the basal one. As the map above shows (red shaded regions are those with different varieties of yaws), this ancestral form is found in Southeast Asia and Africa. I added the Pinta strain, in pink, in America, absent in the original map because it is relevant as we will see below.

This strain mutates into another variety of yaws, only found in Africa, with the GATA sequence (in other word the final "G" mutates to "A").

It also mutates by switching the second "A" for a "G", becoming GGTG in Eurasia and North Africa, becoming the vector for Endemic Syphillis (shaded green on the map).

This ties in with the close genetic distance between the endemicum and pertenue subspecies mentioned further up.

The interesting part is that the American variety of yaws has a very distinct sequence, removed by three mutations from the Eurasian GGTG or the African GATA, the Amerindian yaws sequence is: AGGA which is also the same sequence found in the pallidum subspecies!, the one that causes venereal syphillis. In other words it seems to prove that this disease appeared in America as a more virulent strain of yaws.

It is a pity that the agent causing Pinta was not sequenced, it probably lies somewhere in between the Eurasian strain (for endemic syphillis) and the Amerindian yaws strain.

The paper proposes that this three mutation gap between New World yaws (and venereal syphillis sequence) and the Old World sequences is split into two steps: they place a hypothetical intermediate strain one mutation away from either the African or the Eurasian strains (GGTA) and this strain with two mutations becomes the AGGA Amerindian one:

"The pattern of substitutions suggest that a hypothetical intermediate strain, arising from either the group II subsp. pertenue strains [African yaws] or endemicum strains [Eurasian endemic syphillis], once existed and was a progenitor to both New World subsp. pertenue[yaws] and to all subsp. pallidum [venereal syphillis] strains. This data also suggests that the New World subsp. pertenue strains belong to a group distinct from the Old World subsp. pertenue strains, occupying a phylogenetic position somewhere between Old World non-venereal strains and modern subsp. pallidum strains." [5]

The authors conclude that " a T. pallidum strain from the Americas was introduced back into the Old World, probably as a result of the European exploration of the Americas, becoming the progenitor of modern syphilis-causing strains. Third, modern subsp. pallidum [venereal syphillis causing] strains disseminated from Europe to the rest of the world." [5].

I do believe that the tree is coherent and the sequence propsed is also adequate, I also agree that the venereal syphillis is the most recent strain to appear, my doubts are, as always, on the issue of the dates assigned to these events. The paper does not make any conjectures regarding dates it merely indicates that the Amerindian strains "diverged most recently, indicating that they emerged relatively recently in human history" [5], which if in line with mainstream science means any time between the discovery of America in 1492 AD and 16,000 ya -the date that Asians are supposed to have entered America from Beringia.

These findings are supported by another paper (Melo et al., 2010) [1] which statistically tests three scenarios and concluded:

1. A recent emergence of venereal syphilis. This rececent (500 years ago) origin is found "utterly unlikely, be it in the New or the Old World". [1] This time span was chosen because the first reports of the epidemic of syphilis which quickly spanned Europe, are from 1495. By the way, this epidemic reached India in Portuguese ships (1498) and Japan (1510), killing thousands. The disease seemed to mutate to a more benign and slower-killing strain.
2. An Homo erectus origin. Treponematoses have been plaguing our ancestors at least since the days of H. erectus. But it is not likely that the strain that caused it is one of the contemporary ones. It is probably due to "ancestral forms still unknown". [1] I differ, but we will go into that later.
3. If it emerged in the Americas between 16,500 and 5,000 years ago. They find it the most likely alternative. We will discuss it below.

The dates. As usual the paper is based on the orthodox dates for the "time of the first colonization of the Americas", which is set at 16,500 years. The other date of 5 kya is based on "the oldest probable evidence of venereal syphilis in the world." [1].

What would they have concluded if instead of 16.5 kya they had used 75 kya or 100 kya? Later we will try to work it out.

Melo et al., using this 16.5 - 5 ky time range conclude that they could not reject the hypothesis based on the mutation rates of treponemes, which is "compatible with those observed in other bacteria" (see my comments below). They are cautious however because there are "claims of precolumbian venereal syphilis outside the Americas [to be] taken into account", so they conclude that "the place of origin remains unsolved." [1].

In other words, it could have originated in Asia and moved from there into America and also remained in Asia or, originated in Asia and only moved into America or, finally, appeared exclusively in the New World and reached the Old World after the voyages of Columbus in 1492.

What do ancient remains tell us?

Since Pinta leaves no skeletal marks, we cannot say much about its prevalence in the past. The other forms of treponemal diseases do leave very distinct marks on the bones and can be identified (though as usual, there is always some disagreement between experts).

The paelopahtological studies. Amerindian remains dating back to 7,000 years ago [5] show that treponemal disease afflicted the natives. There are some disputed and isolated cases of pre-Columbian treponemal disease in the Old World [5].

Melo et al., 2010 [1] review these studies and finds that "treponemal diseases in general were well established in pre-Columbian times all over the world. The oldest dates we are aware of refer to bejel in Sudan 15,000 yBP, yaws in Florida some 7,900 yBP, and treponematosis in Peru more than 8,000 yBP" as well as those from Indian Knoll in the U.S. (5,300 yBP) and Colombia (5,000 yBP) with osseous evidences of venereal syphilis in the whole World, and in my opinion support an Amerindian origin of this disease. [1]

Checking the calculations

Melo et al., [1] assumed that the venereal syphillis subspecies split from the others, in America between 16.5 and 5 kya, and then calculated that the most recent common ancestor for the human treponeme group lived 77.4 kya (this is their 95%HPD), which means that H. erectus did not have a "modern" human kind of treponeme. This time frame allows for Old World dispersal of yaws and endemic syphillis as well as an American or Asian origin of venereal syphillis.

Which is very neat and tidy. But why did they dismiss the appearance of treponematosis in H. erectus? Well, I have gone over their Table 2 several times and believe that there is a mistake in the table: the other two tables give the MRCA for venereal syphilis as younger than the whole group, but this table has syphilis as older than the yaws - bejel subspecies, which contradicts the conclusions of Harper et al., [5] mentioned above, where yaws mutated into venereal syphilis. The text itself mentions 175,000 years as the MRCA for one of the subspecies but the table says 1.75 My... it is confusing! What is clear is that the age of these bacteria would be similar to that of H. erectus and the authors conclude that the microbial mutation rate would be too slow, so this hypothesis is discarded.

I am inclined to believe that the date may be in fact older than 16 kya. Looking at Table 4, the oldest date of 77.4 ky for all human treponemes is linked to a 12.5 ky date for the subsp. pallidum. Roughly 6.2 times greater than the MRCA for venereal syphilis.

If we assume that human treponematosis appeared 300 kya, the venereal strain would have appeared: 300/6.2 = 48 kya in America, which is in line with some of the oldest (not accepted by orthodoxy) sites in the Americas. This would imply a Neanderthal origin for these diseases. Extrapolating further, if it appeared 1.6 Mya among Homoe erectus, then syphilis would have appeared 258 kya, also, among Neanderthals. Or maybe among East Asian H. erectus.

Looking at the map and the temporal sequence suggested by Harper et al. the following scenario seems plausible and maybe even probable:

• Since the oldest genetic sequence is found in Africa and Southeast Asia, we can assume an African origin and an out of Africa Migration of this oldest sequnce, with the first OoA migrants: H. erectus.
  The coastal route along the Indian Ocean towards Indonesia is actually where this subspecies prevails and it is identical to the territories once occupied by Homo erectus. It also coincides with the Y chromosome haplogroup C range, which I have suggested mirrors the OoA migration of H. erectus.
• Those who remained in Africa mutated into a second clade of yaws, and it is still found there, and only there.
• The Asian variant carried by H. erectus mutated into the bejel or endemic syphilis kind, found only in Eurasia and North Africa (maybe due to a back-migration). When did this take place? Was it among H. erectus? Denisovans? Neanderthals? Surprisingly this green area is very similar to the range occupied by Neanderthals. The Australian patch may reflect a Denisovan admixture.
• Then these people moved into America, where the mutations leading to the American pinta (whose sequence is not known, but I bet will be found to be intermediate between the Eurasian bejel and the Amerindian yaws) arose. Very likely the Neanderthals took it into America and there it mutated again, into the Amerindian yaws - venereal syphilis kind.
• Perhaps it was quite lethal in America, maybe Neanderthal carried the benign kind. Absent in the Old World, when Columbus' crew took it back to Europe, it spawned a colossal epidemic.

See Second part and conclusion of this post.

Pinta

Pinta which is said to be caused by Treponema carateum is quite unique among all the Treponemal diseases because it is the least aggressive one and only causes changes in the color of the skin of those afflicted with it. [5]

It is also unique because it is an exclusively American disease. But it has become rare: at one time it was endemic in the Caribbean, Central America and Northern South America, now it is hard to find. [5]

I included it in the map above (pink shaded region), because it is quite interesting in its distribution: it is in the region where haplogroup C (Y chromosome) is found in America, Colombia, Ecuador, Mexico.

Paleopathological studies of Pinta are not possible because it leaves no visible lesions on the bones (like the other treponemal diseases do), so it is quite elusive!

The problem is that there is no pinta available for study: "no strains of this organism are available" [3], so it could not be sequenced. Additionally, "Treponema carateum is the etiological agent of pinta, although no isolates of this organism are known to exist" [4], the actual bacteria has not been collected and stored in any lab!

It was "Once found in Central and South America, this mild disease is characterized solely by alterations in skin color.[...] no strains or samples of T. carateum survive. Furthermore, it is uncertain whether the disease pinta still exists. No cases have been reported to the World Health Organization from the former endemic countries Mexico or Colombia since 1979." [5].

The issue of mutation rates is controversial: allow me to quote "Our data suggest that the T. pallidum genome is evolving in a largely clonal manner amenable to phylogenetic analysis" [5]. This is interesting because clonal evolution stabilizes favorable multilocus associations, "restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure" [2]

Actually scholars recognize that "A limitation on comparative studies has been the small amount of variation present in the T. pallidum genome [...] the level of polymorphism found between T. pallidum strains is quite low [...] for this reason, the level of resolution in the phylogenetic tree is relatively poor."[5]

The authors of one paper conclude that "it is unlikely that these SNPs have accumulated in a clockwork manner." [5].

I have expressed my reservations regarding "clocks", and in the case of T. pallidum, with a small genome, clonal evolution and limited variation between the different subspecies, it is in my opinion difficult to consider if a mutation rate is slow, fast or correct (as Melo et al. do). Perhaps it is a slow evolving bacteria, 10 or even 100 times slower than other bacteria. The dates calculated on bacterial mutation rates may be well off mark.

Sources

[1] de Melo FL, de Mello JCM, Fraga AM, Nunes K, Eggers S, (2010). Syphilis at the Crossroad of Phylogenetics and Paleopathology. PLoS Negl Trop Dis 4(1): e575. doi:10.1371/journal.pntd.0000575
[2] Michel Tibayrenc and Francisco J. Ayala, (2012 Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. PNAS (2012) www.pnas.org/cgi/doi/10.1073/pnas.1212452109
[3] Arturo Centurion-Lara et al., (2013). Fine Analysis of Genetic Diversity of the tpr Gene Family among Treponemal Species, Subspecies and Strains. PLoS Negl Trop Dis. May 2013; 7(5): e2222. Published online May 16, 2013. doi: 10.1371/journal.pntd.0002222
[4] RR Gray et al., (2006). Molecular Evolution of the tprC, D, I, K, G, and J Genes in the Pathogenic Genus Treponema. Mol Biol Evol (2006) 23 (11): 2220-2233. doi: 10.1093/molbev/msl092. First published online: August 22, 2006
[5] Harper KN, Ocampo PS, Steiner BM, George RW, Silverman MS, et al., (2008). On the Origin of the Treponematoses: A Phylogenetic Approach. PLoS Negl Trop Dis 2(1): e148. doi:10.1371/journal.pntd.0000148

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

A special Y chromosome marker

The Y chromosome has a "male-specific region" or MSY; it is the sector of the Y chromosome that differentiates sexes (females and males). It spans roughly 95% of the chromosome's length and is is made up of different sequences, one of which is known as "X-degenerate".

Despite its name, its sequences are the relicts of the ancient autosomes which later evolved into our current X and Y human sexual chromosomes.

A paper (Rozen et al., 2009)[1] analysed the human MSY region and reached some interesting conclusions.

An interesting mutation

The researchers sequenced a global sample of Y chromomes (belonging to haplogroups: A, B, C, D, E, G, H, I, J, T, L, M, N, O, P, Q and R) and found that they were all extremely similar in the X-degenerate protein sequences: any two chromosomes selected in a random draw only differ in one aminoacid; and in 50% of the cases, the differences are due to one particular mutation.

This special mutation switched Aspartic Acid for Glutamic Acid at a certain spot of the MSY region ( mim400005). It happened quite some time ago: the authors calculate that this mutation took place roughly 50 kya - 95% CI 37.7 - 55.7 kya (my comments on this date can be seen below).

They also found out that natural selection seems to be operating as a factor that preserves amino acid sequences in this part of the Y chromosome therefore raising doubts about the assumed "neutrality" of mutations taking place in the Y chromosome: they are assumed to be random but apparently are not.

The image below, (from [1]) shows the Y chromosome's haplogroups that were tested. The red dots mark nonsynonymous nucleotide substitutions, the other dots (blue and gray) mark other kinds of substitutions. The arrow indicates the particular mutation mentioned in the text above. I added a red sector indicating those haplogroups that do not carry this mutation, the "oldest" haplogroups A, B, C, D and E.

Y chromosome tree hgs. and mutations.. From [1]

Its location, at the root of branches leading to all the other haplogroups from G to R, makes it the oldest of the twelve mutations that the study found, as well as the closest one to the root of MSY genealogy.

The African haplogroups A and B, plus the most ancient Eurasian ones C and D as well as the East African E hg., do not carry this mutation, all other sampled haplogroups do. So this suggests that it originated in Asia After the Out of Africa migration of modern Humans.

The issue of the dates

The date assigned to this ancient mutation (37.7 to 55.7 ky) was not calculated directly. Instead the paper is based on another study (Karafet et al., 2008) [2], which provides the usual mainstream accepted dates for an OoA event of 50 to 60 kya.

I have already given my critical opinion on these dates and the assumptions on which they are based on, so I will not repeat them again here, but one of the objections is that mutations used to time the "molecular clocks" used to date human events (either using mtDNA or Y chromosome substitutions) may not be random, due to pure chance (or neutral), but may be selected for by evolutionary forces.

And, as mentioned above, this very paper [1] includes a comment which impacts directly on one of the basic assumptions of the "genetic clock": since Natural Selection is acting, then "the assumption that all MSY SNPs—as well as any structural polymorphisms in the Y chromosomes marked by these SNPs— are selectively neutral." is false. The paper adds (bold mine):

" [our] data contradict this simplifying assumption. The MSY does not undergo sexual recombination with a homologous chromosome, so it is subject to natural selection as an indivisible unit. Even if the particular MSY SNPs employed in a population study are functionally inconsequential, they may have been coupled to detrimental or beneficial SNPs or structural variants elsewhere in the MSY... Taken together, these studies of structural polymorphism and coding sequence variation in the MSY highlight the role of natural selection in human MSY lineages. This new awareness means that we can no longer assume selective neutrality in the MSY when drawing conclusions from population genetic studies." [1]

This mutation is selected for in a positive manner, it appeared and was conserved intact in the MSY region. It may have appeared a long time ago, 80 ky or 100 ky or even 300 ky ago. Which brings me to the reason for my post.

An ancient Eurasian mutation

If it appeared and was not obliterated by natural selection and it is not neutral, then it must provide an advantage to its carriers. The paper [1] points out that the substitution of Asp. for Glu. "may be of little functional consequence", and that 11 out of 12 mammals and birds studied have glutamic acid in this locus like men belonging to hgs. G to R.

The only one with aspartic acid instead of glutamic acid is the mouse and of course the "ancestral sequence of humans" found only among those men belonging to haplogroups A to D.

In other words it is absent among contemporary Africans (hg. A, B) and the oldest haplogroups (C, D, E), so it evidently originated in Eurasia. Since I distrust the 50 ky age, and believe the mutation to be much older, I ask: Was it a Neanderthal Trait? Did it admix back into H. sapiens from the Neanderthal?

Or if the date is correct, it may even be a Homo sapiens mutation that is not found in older Y chromosome lineages that, as I have suggested in other posts, date back even further than Neanderthals.

A closer look at the tree above shows that the mutation took place just after the split of C and the ancestor of all the other groups G to R. Perhaps the mutation marks the spread of Modern Humans out of Africa and even more interestingly, it spreads overlying the more ancient non-mutated haplogroups, which in turn reflect those of archaic humans. Which as I have suggested in previous posts (i.e. C hg.) mark the presence of H. erectus in Eurasia.

Sources

[1] Steve Rozen, Janet D. Marszalek, Raaji K. Alagappan, Helen Skaletsky, David C. Page, (2009). Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. Am J Hum Genet. 2009 December 11; 85(6): 923–928. doi: 10.1016/j.ajhg.2009.11.011
[2] Karafet TM1, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF, (2008). New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008 May;18(5):830-8. doi: 10.1101/gr.7172008. Epub 2008 Apr 2.

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

Mapinguari (continued)

Continuing with yesterday's post, I checked out the website of the TV series (Nightmare of the Amazon, National Geographic Channel, 2011) [7] in 2011 which has a photograph of David Oren, who did some scientific research on the Mapinguary, with a cast of a track left by the beast in the jungle. Below is the photograph: (from [7])

The image is not all that sharp, but it looks like two parallel depressions with a roughly ovoidal shape. And that brought to my memory a description of a similar paw print, which I quoted in my book.[1]

An American, Ned Chace, lived in southern Patagonia for a long period of time (1898 till 1929), and travelled extensively from the Pacific to the Atlantic and visited many mountain lakes in the region. He met plenty of people and must have heard many yarns during those long winter Patagonian nights. Below is one of them, related in third person by the authors the book that narrates his adventures: (bold text is mine)

"A friend of his had followed a track like that of a wooden shoe with two cleats across the sole, until he caught sight of what he took for a hairy pig as big as a bull. Just a glimpse he had. Once or twice, long afterwards, on a still night in a forest, beside a glacier, Chace himself heard a trumpeting, something like a steamboat whistle. That was long before there was a whistle on any Cordilleran lake." [3][1]

This text has two intersting bits of information:

1. The sloth yell. The one issued by the Mapinguary is described as "The horrible soul-wrenching humanlike cry" and when it is reproduced it sounds "loud high cry travels down the scale, ending as a low rumble" [9], could this be similar to the yells of the Patagonian animal, a "trumpeting ... steamboat whistle" heard in Patagonia? A shrill scream?

2. The Cleats. "a wooden shoe with two cleats across the sole", which in my opinion are similar to the tracks of Mapinguari shown in the photograph above.

I decided to check out what could "cleats" mean to an early twentieth century person. My mental image of cleats are the studs on a pair of sports shoes, but what exactly does "Cleat" mean?

cleat. noun ⁄ 'klet⁄
: a piece of rubber, wood, or metal that is fastened to the bottom of a shoe or boot to prevent slipping [4]

And the image of two strips of wood fastened across the sole of a wooden shoe reminded me of those traditional Japanese sandals, a hybrid between sandals and clogs, the Geta. They consist of a wooden base which is separated from the ground by two transversal wooden strips, a cloth thong fastens it to the foot (like those of flip-flops). Below is an image of a Geta:

It is not difficult to see that the print of a Geta in soft soil would reproduce the print described by Chace's friend and that it would look like the plaster cast shown by Oren above.

But this does not mean that the animal is a sloth (either contemporary or extant megafaunal one). In fact, what does a giant sloth paw print look like?

Below is a track left by a giant sloth at Guaminí in the Buenos Aires Pampas, Argentina some 30 kya. The area was a soft muddy region and is full of animal tracks, among which are some decribed as "Tracks of a Giant Sloth" [2]

It looks like a human footprint, no cleats or dual depressions, just a big long print. This human-like appearance led to some interesting debate back in the 1880s, when similar human-looking prints were found in Nevada, at a sandstone quarry (the image below is very similar to the Guaminí prints, and it should be since it also shows a giant sloth paw print) [6]:

The sandstone is about one and a half million years old and the size of the tracks led some to belive that they were the footprints of giants! But science soon took a look at the tracks and concluded that they were Mylodon tracks (its bones had been found in the same quarry).

The reason for the shape of the tracks is that these gigantic sloths walked with a pedolateral foot posture: with the weight of their bodies place on the external part of their feet so the sole of their feet faced inwards and the long claws pointed inwards and upwards. That explains why no claws were imprinted in the soft sand.

Further reading on the Nevada tracks:
LeConte, J. 1883. Carson Footprints. Nature, Vol. 28, Pp. 101-102.
Davidson, Geo., 1883, The Carson Fossil Footprints, Mining and Scientific Press. Davis, Sam P. (Ed.), 1912, The History of Nevada (Vol. II), Ormsby County.
An Interesting website.

The point is that these paw prints belonging to extinct giant sloths do not look like cleat marks at all (however in yesterday's post some witnesses claim that its tracks are like those of human footprints).

But perhaps they represent the rear paws (feet) and not the "hand" prints or front paw marks, because the sloths walked on two feet, like us, bipedally. This was confirmed in 1986 with the tracks discovered at Pehuén Có,another site with fossil tracks, in Argentina, which showed that the Megatherium sloth could and did walk on its two legs at will, and only walked on all fours when the terrain required it.

Maybe front paw marks are rare.

The image below shows a giant sloth walking on its four limbs, the rear ones are turned inwards as we described above, the body rests on the outer part of the foot.

The key are the front paws

Now comes the interesting part, the front paws are resting on the long nails, so the body's weight would press these nails into the soil and leave their imprint on the ground. Would this track mark look like two parallel cleats? If so, this would mean two (2) nails, the image has three (3)... Some explanation is needed if we are to accept the "claws equal cleats" theory.

The hands of sloths

The extant South and Central American tree sloth, the Bradypus is a three-toed sloth and possesses only three digits II to IV on the hand. Extinct sloths have a wide range of hand shapes: [5] "among megatheriids, primitive species of Eremotherium were pentadactyl [five digits] (albeit it with a short thumb and a fifth digit with only one phalanx) while the advanced species E. laurillardi was tridactyl [three digits], possessing only digits III-V, and of these only digits III and IV had unguals" [claws]. [5]

Below are some sloth hands (from D. Naish Tetrapod-zoology [5]),

Some of the diversity present in sloth hands. L to r: Pleistocene mylodontid Glossotherium robustum, in which the hand is pentadactyl; Pleistocene megatheriid Eremotherium laurillardi, in which digits I and II have been lost; Pleistocene megatheriid Megatherium americanum, in which the thumb is absent. Not to scale. Drawings by Darren Naish, redrawn from various sources. From [5].

So it three fingered sloths with two claws did exist (i.e. Eremotheium laurillardi) as well as the megalonychid Choloepus which only has digits II and III. Sloth phylogenetic studies have shown that on a genetic basis, extant Bradypus (3 toes) are similar to megatherids while the two-toed Cholepus are closer to mylodontids. [8]

So two toed sloths were related to the Mylodons... which lived in South America and may be related to the Mapinguari, this could somehow explain the two claw marks of Mapinguari tracks.

But, would these sloths leave a two-claw-imprint on the ground? one that resembles the plaster cast shown at the beginning of this post? I have not been able to come across frontal paw prints of extinct giant sloths, but will keep on looking for them. If I do and they look like those of the Mapinguari cast, it would explain the odd shape of the cryptid's tracks.

Sources

[1] Austin Whittall (2012), Monsters of Patagonia, Buenos Aires: Zagier & Urruty
[2] Photograph by Sergio Bogan. (2013) Huella de la "Era del Hielo" Exploración y Ciencia. Universidad Maimónides. N°1 ISSN 2314-2855 pp. 24
[3] Le Moyne Barrett, R. and Barrett K., (1931). A Yankee in Patagonia, Edward Chace.. Boston: Houghton Mifflin. pp. 29-30.
[4] Merriam Webster, dictionary
[5] Darren Naish, (2012) The anatomy of sloths, August 30, 2012.
[6] Photograph from: W. M. Keck Museum University of Nevada Reno
[7] Nightmare of the Amazon, Nat. Geo. Channel. 2011.
[8] Greenwood et al Mol Phy Evol 2001 / See Poinar et al Current Biology 2003
[9] Marguerite Holloway, Discover Magazine, (1999). Beasts in the Mist. Sept. 01, 1999

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

Mapinguari the Amazonian mylodon

A comment by a reader (thanks Kyle), prompted me to get together the short notes and bits of information that I gathered (and keep on gathering) when I was researching for my book Monsters of Patagonia. At that time I read about an Amazonian sloth-like creature, the Mapinguary, and althoguh I did metion the "Mapinguari" in my book I did not give it too much importance because of its Amazonian habitat which was quite far from -and very different to- the Patagonian setting of my book (which deals exclusively with the mythical beings of Patagonia). However, I did include a short reference to the Mapinguari because it may be related to the Patagonian Mylodon to which I dedicated a whole chapter in my book.

Today's brief post will be about the Mapinguari.

Sloths. Image from [8]

First of all, (ehem), as an example of my humility and modesty I will quote my own text on it:

Mapinguari
Mapinguari also known as ‘fetid beast’ is a mythical creature said to inhabit the Amazon River basin. Though very far from Patagonia we mention it because it is believed to be a giant sloth related to the extinct mylodon, which at one time lived in Patagonia and may still be alive there (more on this in chapter 9).
Mapinguari has been described as red haired, 2.15 m [7 feet] tall, and having the claws of a giant armadillo, the face of a monkey, and a nauseating smell, like excrement or rotten meat. Extant sloths are often covered with algae that make their fur give off a foul musty odor. Perhaps they share this feature with Mapinguari and the Patagonian mylodons. [1]

In my book, I cited a scholarly reference (there is a lot on Mapinguary in forums and blogs, but not many academic papers) for those interested in reading more about it: Oren, D., (1993). Did ground sloths survive to recent times in the Amazon Region?. Goeldiana Zoologica, 19: 1-11.

David Oren is mentioned in an article published in Discover Magazine (Sept. 1999), see link below [6], in which the Mapinguary story is told and Oren's quest to find it. The outcome of his expeditions has not been published. I do not know why. But he does appear in a TV series (Nightmare of the Amazon, National Geographic Channel) [7] in 2011 discussing this mysterious being.

There is additional information and I believe that original language sources tend to be more reliable than those translated back and forth, so below are some links that may be of help to those wanting to find out more about it:

1. Brazilian site. This Brazilian site on local folklore says that not one single chronicle dating to the colonial or Imperial periods in Brazil mention its name; and therefore they believe it is recent, and that it originated from the "Curupira" myth. See my post on the Curupira.
2. Check out the Projeto Paleotocas, Toca News N° 30, a serious academic project which studies ancient tunnels -"toca" in Portuguese- dug by the megafaunal sloths (they are enormous). Their Journal Issue #30 looks into the possibility of extant sloths (i.e. Mapinguari).
3. Another source with an image (also about with Brazilian folkore) See text and image on its page 35.

A very complete review of the Mapinguary can be found in George M. Eberhart, (2002) MYSTERIOUS CREATURES. A Guide to Cryptozoology, ABC Clio. pp. 318-19, quoted below [4]:

Mapinguari
Mystery Primate or Sloth of South America. Variant names: Capé-lobo (“wolf’s cape”), Juma, Mão de pilão (“pestle hand”), Mapinguary, Ow-ow, Pé de Garrafa.
Physical description: Height, about 5–6 feet when standing upright. Weighs about 500 pounds. Long, reddish fur or hair. Monkeylike face. Manelike hair along its back. Said to have another mouth in its belly. Its feet are said to turn backward. [Patagonian Monsters blog note: a common feature in several South American myths]
Behavior: Nocturnal. Avoids water. Descends from the mountains in the autumn. Cry is either a deafening roar or like a human shout. Releases a foul-smelling stench when threatened. Kills cattle by pulling out their tongues. Eats bacaba palm hearts and berries. Twists palm trees to the ground to get the palm hearts. Travels with herds of White-lipped peccaries (Tayassu pecari ). Said to be followed by an army of beetles. Cannot be wounded by weapons except around its navel. [Patagonian Monsters note: in this it is very similar to several sloth like creatures from Patagonia. More on this navel below]
Tracks: Either humanlike or like the bottom of a bottle stuck into the ground. Length, 11–21 inches. Stride, 3–4 feet. Feces similar to a horse’s.
Distribution: The apelike variety is more often seen in Mato Grosso and Pará States, Brazil; the slothlike variety has been reported in Amazonas and Acre States, Brazil. Possible evidence also exists in Paraguay.
Significant sightings: An adventurer named Inocêncio was with ten friends on an expedition up the Rio Uatumã, Pará State, Brazil, in 1930 when he was separated from them and got lost. As he slept in a tree for the night, he heard loud cries coming from a thickset, black figure that stood upright like a man. He shot at it several times and apparently hit it, as there was a trail of blood below his tree. In 1975, mine worker Mário Pereira de Souza claims he encountered a Mapinguari at a mining camp along the Rio Jamauchím south of Itaituba, Pará State, Brazil. He heard a scream and saw the creature coming toward him on its hind legs. It seemed unsteady and emitted a terrible stench. In the 1980s and 1990s, David Oren conducted fifty interviews with Brazilian Indians, rubber planters, and miners who know about the animal. He interviewed seven hunters who claim to have shot specimens. One group of Kanamarí Indians living in the Rio Juruá Valley claimed to have raised two infant Mapinguaris on bananas and milk; after one or two years, the creatures’ stench became unbearable, and they were released. In the late 1990s, Dutch zoologist Marc van Roosmalen heard that people in one village along the Rio Purus, Amazonas State, Brazil, moved their homes across the river after Mapinguari tracks were found nearby.
Possible explanations:
(1) Unknown ape similar to De Loys ’s Ape or the Didi.
(2) A surviving man-sized Patagonian cavedwelling sloth of the genus Mylodon. All subfossil fur samples are red. Mylodon walked with its clawed feet curved toward the center of its body. Its dermal ossicles (except around the navel) might protect it from gunfire. The round tracks might be the impression of the heavy tail tip as the creature stands upright. David Oren suggests that the “second mouth” is a specialized, scent-secreting gland.
Sources: Paulo Saldanha Sobrinho, Fatos, histórias e lendas do Guaporé, as quoted at http://www.pakaas.com.br/lenda2.asp; Frank W. Lane, Nature Parade (London: Jarrolds, 1955), p. 241; Luís da Câmara Cascudo, Dicionário do folclore Brasileiro (Rio de Janeiro: Instituto Nacional do Livro, 1962), vol. 2, p. 456; David C. Oren, “Did Ground Sloths Survive to Recent Times in the Amazon Region?” Goeldiana Zoologia, no. 19 (August 20, 1993): 1–11; “The Mother of All Sloths,” Fortean Times, no. 77 (October–November 1994): 17; Laurie Goering, “Amazon Primatologist Shakes Family Tree for New Monkeys,” Chicago Tribune, July 11, 1999; Marguerite Holloway, “Beasts in the Mists,” Discover 20 (September 1999): 57–65. [4]

Regarding the vulnerable navel, it is a feature shared by the Ellengassen, a mythical creature of Patagonia (probably an extant glyptodon) was described as follows (Source my book): "The creature was 'covered with an enormous shell, very thick, similar to that of the current armadillos, probably a glyptodon […] according to some, it had a human face and according to others it was a man of gigantic size, with its back covered with a shield, so it could only be wounded on its belly'". The quote I cite is from: Moreno, E., (1979). Reminiscencias de Francisco P. Moreno. B. Aires: Eudeba. pp. 105 and 129.

The word "Mapinguari", is actually the contraction of several Tupi-Guarani words: "mbaé-pi-guari" and means: a thing that has a bent or crooked foot - paw. If the animal was a pan-Amazonian being, it would have its own particular names in the different native languages, and it does: The Karitiana natives, of the Amazon, call the Mapinguari "owojo", "kida so'emo" or "kida harara" the word "kida" means ugly creatures and is used to describe fierce mammals (jaguars), insects and reptiles and also, the monstruous Mapinguari and the devil. The "so'emo" part means: "black face", so Mapinguary = "black faced beast" [2][3]. See the location of the territory where Mapinguary lives [3].

Megafaunal sloths became extinct in America between 10 and 4.4 kya. [5]. It is possible that some have managed to survive in the Amazon until recent times and originated these myths among the natives. As a final piece of information, see my post on Patagonian Tapirs, where I quote Capt. Fitz-Roy on a "Tapir with talons", from the southern jungles in Paraguay and Brazil, perhaps another reference to the "Mapinguari".

Sources

[1] Austin Whittall (2012), Monsters of Patagonia, Zagier & Urruty
[2] Felipe Ferreira Vander Velden, (2009). Sobre caes e indios: domesticidade, classificacao zoologica e relacao humano-animal entre os Karitiana. Avá n.15 Posadas dez. 2009.
[3] Ibid. (2010). De volta para o passado: territorializacao e 'contraterritorializacao’ na historia karitiana. Soc. e Cult., Goiania, v. 13, n. 1, p. 55-65, jan./jun. 2010
[4] George M. Eberhart, (2002) MYSTERIOUS CREATURES. A Guide to Cryptozoology, ABC Clio. pp. 318-19
[5] David W. Steadman, (2005). Asynchronous extinction of late Quaternary sloths on continents and islands. www.pnas.org/cgi/doi/10.1073/pnas.0502777102. PNAS, August 16, 2005, vol. 102, no. 33, 11763–11768
[6] Marguerite Holloway, Discover Magazine, (1999). Beasts in the Mist. Sept. 01, 1999
[7] Nightmare of the Amazon, Nat. Geo. Channel. 2011.
[8] Darren Naish, The anatomy of sloths. Tetrapod zoology. August 30, 2012

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

The Chilean Abominable Snow Man

Some time ago I posted about the Patagonian Yeti. Fact and Fiction. While posting on the recent DNA analysis of hair that supposedly came from Bigfoot or Yeti, I remembered my post.

The "hair DNA" issue reminded me how difficult it is to come across reliable information regarding cryptids, either via photographs (always blurry!), videos (ditto) or eyewitness accounts. Below is the translation of some newspaper reports from late 1950s dealing with the Chilean Snow Man.

The Chilean Yeti

Paper clipping. Look at the Tarzan-like clothes of the Snow man. From [1]

Rough translation of the news printed at that time, quotes are shown textually.

An "ape-man" was reported on the slopes of Mount Palomo at an altitude of 4,850 m (16,000 ft.) in the interior of Rengo, close to the village of Popeta, Chile. See Map insert below.

Eyewitnesses described the creature as being 2 m tall (6.55 ft.), with "A protruding belly, thin and bony arms and dressed with hides". [1]

The location is known as Valle de los huesos (Bones Valley) because of the large amount of bones found in holes which most of the time are covered with snow.

Eyewitness accounts

It was spotted by a farmer named Absalon Valencia in summer (December) of 1957. They had gone hunting guanaco going up the Portillo River and after passing the Pan de Azucar and Alto de Hormigas reached the Valle de los huesos. One of the group spotted a hairy animal that seemed to be crouching, and shot at it. The animal stood up and surprised the party by running away on two feet. The hunters were shocked, they realized it was a man, "a kind of monkey of colossal height, with ling arms, hair that reached its waist, clothed in hides... I would say it measured more than two and a half meters (8.2 ft.)"[1]

Another sighting was reported on April 3, 1958 by a farm-hand named Pablo Espinoza, who was looking for some stray cattle. He went up the valley by the Claro River and at the "Hoyo de los Huesos" (hole of bones) saw some fruit trees, some were fig trees, hundreds of years old. Suddenly he saw "Something moving around by means of long jumps" and rode up to see it closer, but he was soon terrified when, instead of seeing one of his lost calfs, he saw the "gigantic man, covered with hides, with long arms and a protruding belly, a black and tangled beard and a mane that reached his waist", [1] the creature soon disappeared and the man fled back to his village.

Map of the zone, right next to the Andes, on the left of the map, Chile, on the right, Argentina

 

A local "cowboy", Carlos Soto also sighted the creature two years earlier, on May 12, 1956, at Cerro Palomo next to the steep valley where the Cipreses River is born. He described it in the same way as the others did. He saw the same creature and also ran away from it.

Hoax? Joke? The police at Rengo opted for the Joke theory [1].

It is intersting to point out that at that time Yeti Snow Man was in vogue, so it would be likely that even farmers in Chile knew about abominable snow men. See the Google Ngram Chart which shows a peak during that period (and the very lower frequency of Bigfoot). I think that this was due to the fact that Sir Edmund Hillary, one of the first two men to reach the summit of the highest mountain on Earth, Mount Everest, (with Sherpa Tenzing Norgay) on May 29, 1953, found Yeti hair and was an avid Yeti searcher. His fame made Yeti well known as from the mid 50's - see image below.

Also, in 1957 a movie on the subject (The Abominable Snow Man, with Peter Cushing) was screened... did it impress the Chilean audience in the Rengo area? Were people more susceptible to seeing Yetis in the frozen Andean heights?

Source

[1] EL EXTRAÑO CASO DEL ABOMINABLE HOMBRE DE LAS NIEVES DE RENGO

Play with Google Ngram yourself!, compare trends in books for different keywords or subjects

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

Neanderthal Rock Art and Patagonia. A link.

In February 2012, I posted about the similarity between stencilled hands painted on rocks in Patgonia, South America and in New Guinea. Of course some readers pointed out that these hands are common and humans have painted them on rocks around the World. So I forgot about it until this afternoon when I read about the following image:

Neanderthal Rock Art. From Nature

And the surprising fact is that these hands were stencilled onto the stone walls of a cave by Neanderthals!

They were painted on what is known as the "Panel of Hands" in El Castillo Cave, Spain. At the site there are hand stencils and red disks. The hands were painted by blowing paint over a hand and once the hand is removed, the outline remains on the wall.

This is excactly the same technique that was used at the Patagonian World Heritage Site of the UNESCO, "Hands Cave" or "Cueva de las Manos"! (see the google map here to see where it is).

The red disks have been dated to be older than 40.8 ky old. And this is the point: it is the oldest rock art in Europe and it is attributed to Neanderthals because it is far too old to have been made by Homo Sapiens. [1]

Compare it with the Patagonian paintings, the similarities are striking:

These Patagonian paintings are old, very old by American standards: 9,500 to 13,000 years old (read more about this UNESCO site). And they are quite different from later rock art by the "descendants" of the Paleoindians who painted them. Below is an example of later rock art from Patagonia:

The Spanish Neanderthal also painted red dots onto the walls of their cave (see below):

The Cueva de las Manos site also has red dots, in two places at least; I saw them when I visited this place and took the following photographs. One shows the the top of the outcrop, yes, on the ceiling, and in the second photograph there are many dots, next to a hand and an animal tortoise? armadillo? (the latter are common in Patagonia):

And, surprisingly, so did the Patagonians at the Cueva de las Manos site! I saw them myself, and below is the photgraph I took:

Comments

The different Patagonian natives had several myths about the rock art in the caves; below are some quotes from my book Monsters of Patagonia:

• "Anchimalleguen or midget walichus [evil genies] that live in the caves of the Nahuel-Huapi"
• Ellengassen: "These beings existed before, but now they are extinct. They were harmless and never attacked. But when one came near them—especially at dusk—they threw stones. These strange beings lived in caves"
• "‘Kollón’ (the stone masked devil to whom they attributed rock-art)"

Were Kollón, Ellengassen and the Anchimalleguen different manifestations of Human - Neanderthal contact in America? I have posted about this Gualicho & Kollon myths: based on Neanderthal?, so I will not repeat the argument here. The fact is that now that I know Neanderthals also painted their hands on the walls of caves just like those found in Patagonia, I wonder... who painted the Cueva de las Manos? Humans? Paleoindians? or Neanderthals?

Sources

[1] A. W. G. Pik, (2012). U-Series Dating of Paleolithic Art in 11 Caves in Spain. Science 15 June 2012: Vol. 336 no. 6087 pp. 1409-1413 DOI: 10.1126/science.1219957

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

Bigfoot a Fake according to an Oxford study

A recent paper published by Bryan C. Sykes, Rhettman A. Mullis, Christophe Hagenmuller, Terry W. Melton, and Michel Sartori (Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates Proc. R. Soc. B. 2014 281 1789 20140161; doi:10.1098/rspb.2014.0161 (published 2 July 2014) 1471-2954) indicates that the Bigfoot and Yeti hair samples that were studied do not belong to unknown hominins but to other extant mammals:

In the first ever systematic genetic survey, we have used rigorous decontamination followed by mitochondrial 12S RNA sequencing to identify the species origin of 30 hair samples attributed to anomalous primates. Two Himalayan samples, one from Ladakh, India, the other from Bhutan, had their closest genetic affinity with a Palaeolithic polar bear, Ursus maritimus. Otherwise the hairs were from a range of known extant mammals.

The team was part of the Oxford-Lausanne Collateral Hominid Project, a project that began in 2012 to study these "anomalous hominids".

The scientists worked through a set of 57 hair samples which they screened and classified (some were not even hairs: the "hairs" were plant fibre or glass fibre) and the remaining group was analysed. mtDNA was extracted and sequenced in a broad manner allowing the identifiaton of the genus but not the species (i.e. canid but not wolf, coyote or dog).

The mtDNA was compared against known databases and... all were clearly identified as belonging to well known mammals: American black bears, canids, cows, horses, deer, and odd creaturs such as Malaysian tapir, serow or North American porcupines!.

A human hair was identified and, amazing find: an American racoon which came from a sample gathered in Russia (far away from the racoon's territory), a clear sign of cross-contamination or a deliberate fake.

The extinct bear

Two of the samples (#25025 and #25191) matched the sequence of a now extinct Pleistocene polar bear (Ursus maritimus). The samples are modern but the bear lived 40 kya in the Arctic islands of Svalbard, Norway. Also, they were not found in the polar regions: sample #25025 came from Ladakh, India, from an animal that was shot over 40 years ago. The other sample came from Bhutan in a high altitude bamboo forest (11,500 ft. or 3,500 m). What do these locations have in common with extinct polar bears?

Please see my post On Yetis and Polar Bears (Dec. 2013), which now, I see, is an advance report on the findings that were finally published early July 2014.

Implications and comments

It is a pity that they did not manage to confirm the existence of our well known Yeti and bigfoot, but it is also nice to know that good science can counter the poor science of some other "scientists" such as the bigfoot DNA of Melba Ketchum; by the way Ketchum is asking the public to donate money so she can keep up with her great research. Not a joke, see for yourself, I'd call it sponsoring non-science.

On the other hand I am persuaded that the bigfoot - hominin myths and those of South American Patagonian giants are not related to unknown apes but to our closer relatives such as Neanderthals and Homo erectus which probably reached America long before H. sapiens did, and shared the New World with them until relatively recently. If the Flores hominin co-existed with modern humans in an insular setting c. 13 kya and originated the local myth of "Ebu-gogo", why wouldn't our more primitive human relatives cause a similar reaction among the Paleo Indians in the Americas?

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

The face of a 300 ky Chinese H. Erectus

A super brief post with an image I came across. It is supposed to be the reconstrucion of the face of a female Homo erectus from Nanjing, China dated to 300 kya.

Actually it is the "Nanjing man", which is roughly 500 to 600 ky old (more information and a photo of the skull).

The reconstruction was done by an "expert". You can read more here (see article). Below is the image, quite "manga" like with the big round eyes and definitively oriental looking:

Homo erectus woman facial reconstruction (ca. 300 kya).

Well, Hollywood did worse, look at how Rachel Welch depicted a Prehistoric woman in "1 million years B.C." (filmed in 1966). Which would be the time frame for a Homo erectus. (Blonde?).

I actually prefer the following reconstruction of a female Homo erectus which looks less amateurish and has a odd amalgam of Australian Aboriginal, African but with straight hair! Picture source: Smithsonian Museum Of Natural History.

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

The recurrent 9-bp deletion in mtDNA (more)

Today's post adds some more information to yesterday's post on the 9-bp deletion in human mtDNA's Coding Region.

More Europeans with the deletion

My previous post menitoned African, Asian, Amerindian and two Portuguese carriers of the 9-bp deletion, today I will add some more European data:

1. Haplogroup I, from Italy.[1] and Haplogroup I, from Spain [2]

2. Another paper (Thomas et al., 1998) reports two individuals from Glasgow (2 in N=115), Scotland (forgive my lazyness, but this paper was published in 1998 and does not specify the haplogroup it does mention the mutations, so those interested may classify these two persons). I will quote this paper extensively because it is intereresting:

The paper found these two persons who were unrelated and noticed that their mtDNA Control Regions were quite different, which lead them to conclude that the mutation was not recent and predated the arrival of H. sapiens to Europe:

"The sharing of these rare polymorphisms suggests that the 9-bp deletion in these two individuals stems from a single mutation event. The CR sequences of these individuals di¡er by eight nucleotides, suggesting that their common ancestor was not recent and probably lived before the arrival of modern humans in Europe."
[...]
"date their most common ancestor to about 50 000 years before present [...] it is interesting to note that the estimated date is earlier than the arrival of modern humans in Europe." [3]

The paper points out that such an ancient origin means that "this polymorphism should be present elsewhere in Europe and we suggest that it would be rewarding to do additional surveys for the deletion" [3], as mentioned above, it is found in Europe but at very low frequencies which supports its ancient origin.

The paper does not contemplate the possibility of the "one-repeat" sequence (that is, the 9-bp deletion) being the archaich ancestral state while all repeat sequences (2, 3 and 4 repeats plus insertions of partial segments of the 9-bp sequence) are the mutations. It considers the basal state as the "tandem repeat" and all mutations (the deletion) or multiple repeats as derived from the tandem sequence.

They do however note that "In this study, we have not addressed the effect of different repeat numbers on general fitness or replication efficiency." [3], which as I mentioned in yesterday's post is something to be considered since it appears that the 9-bp deletion is correlated to certain diseases.

The authors also found one female individual (1 in N=115) carrying not one, but several insertions of the CCCCCTCTA motif and studied her maternal lineage and concluded that the individual was heteroplasmic.

Heteroplasmy.
A heteroplasmic individual has more than one (hetero = "various", plasmy = "kinds") type of mtDNA in his or her cells.
Our cells have hundreds of mitochondria and they mutate in a random fashion. Since they cannot repair their mtDNA, these mutations accumulate over time in our cells which contain a mix of mutant and wild-type mtDNA. A woman carrying the heteroplasmy will transmit them in variable amounts to her offspring. The outcome can be healthy children or on the contrary, a child affected by a terrible disorder.

They studied this woman's mother, aunt and grandmother and found that the frequency of the different repeat values which was conserved from grandmother to daughters (her mother and aunt), changed in one generation (from her mother to hereself).

The Four repeats increased at the expense of the three repeat mutation, which is at odds with the population frequencies we mentioned in our previous post, where the 3 repeat is more frequent than the 4 repeat. Probably in heteroplasmic individuals some other factors such as natural selection are acting on the relative frequencies of repeats.

Comments

Detecting two Southern Mediterranean individuals belonging to Hg. I carrying the mutation while others do not carry it [2] (samples from Spain and North Africa) seem to point to a common origin of this mutation in a specific group of Hg. I individuals before their arrival to the region and their later spread to Spain and Italy.

In a similar manner, the two Scots with the deletion also suggest a pre-European origin for the mutation ~ 50 kya. [3]. This is indeed interesting as it supports my hunch that the deletion is indeed archaic and found in many haplogroups.

The heteroplasmic woman is also interesting since she shows that the mutations tend to an increase in repeat numbers and not a decrease (i.e. a deletion from tandem to one-repeat), which means that it may not have originated independently in different populations, but once, long ago in Africa and survives until now as a trans-haplogroup trait, which if carefully analysed would allow us to detect the inconsistencies in our current haplo-trees!

Sources

[1] Torroni A. Petrozzi M., Santolamazza P., Sellrro D., Cruciani F. and Scozzari R., (1995). About the "Asian"-Specific 9-bp Deletion of mtDNA. Am. J. Hum. Genet. 57:507-508, 1995
[2] GenealogiaMolecular.com. (2007), Linajes mayores del genoma mitocondrial trazan antiguas expansiones humanas (in Spanish)
[3] Mark G. Thomas, Charles E. Cook, Kevin W. P. Miller, Michael J. Waring and Erika Hagelberg, (1998). Phil.Trans. R. Soc. Lond. B 955-965

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

The recurrent 9-bp deletion in mtDNA

AAs you know, different markers (or SNP mutations) are used to identify the haplogroups into which we classify human mtDNA these markers are assumed to have arisen by chance in a purely random manner within a population, and that they are not lost as they are passed on from mother to daughter generation after generation. This allows us to trace the relationship between different populations by verifying which markers are present and which are not.

Markers are therefore mutations, and they can be found in different regions of the human mtDNA. Today's post will look at the mtDNA's "Coding Region" and in a very particular mutation which is actually a deletion (part of the sequence found in some populations is absent in those carrying the deletion), which was lost due to the random mutation: the 9-bp deletion (9-bp d).

The 9-bp d in different populations around the world

First we will define the 9-bp deletion as a "length variant in the intergenic region between cytocrome c oxidase subunit II and the mitochondrial tRNA for lysine (COII⁄tRNALys)" [3]. What this means in a physically sense is the loss (deletion) of one (1) of the two (2) tandem repeats of the sequence "CCCCCTCTA" between nps 8281 and 8289. It is known also as the polymorphic anthropological marker MIC9D.

On the 9-bp sequence
Most people carry two (2) copies of the 9-bp sequence "CCCCCTCTA". This is generally assumed by mainstream science to be the ancestral state.
State which can be modified by mutations such as insertions of one or two additional 9-bp sequences, or by repeats of additional cytosine (C) or deletions and also by the loss of one full sequence (the 9-bp deletion). [12]

It was first detected among Asians by Wrischnik et al. (1987) [4], but later it was found at high frequencies (77% to 100%) in other populations in Polynesia such as the Maori, Niuean, Samoan and Hawaiian as well as among Australian Aboriginals:

The Polynesian branch seems to be associated with the influx or people from Taiwan who migrated southwards across Indonesia and led to the peopling of Polynesia. [5]

Another region where it is found is in the Indian subcontinent and insular areas next to it, where it is carried by southern Indian populations at frequencies that range from 68% in Yandi and 44% in Irula to 24% in Nicobarese and 4% in Siddi, [3] and 21% in Koyas and 3% in Chenchus. [2]

The Asian variant is found at frequencies of 15.6% (Thailand), 40% (Taiwanese Han), 20% (Hong Kong and Shanghai), but 3.3% in Shandong and Uygur populations. [5] In China it averages 14.7% (ranging from 0% to 32% in different ethnic groups). [15]

In addition to these Asian groups, it is also found in Africa and the Americas (as I said, it is global)

Africa

Among sub-Saharan Africans it is found at a frequency of 8.8% (or 81 individuals out of n=919), who carried it in different haplotypes (41 haplotypes in total).

The African Khoisan do not carry it, and is not frequent or absent among the people of the Western and Southwestern Africa. Pygmies and other populations in Central Africa, Malawi and Southern Bantu-speakers do carry it, suggesting according to orthodoxy a Central African origin and a recent dispersal to other regions. [1]

America

In America it is found in those populations belonging to mitochondrial haplogroup B, where it serves as a marker. It is one of the four founding lineages of Native Americans, but also has the peculiarity of being the only mtDNA haplogroup to cover the Pacific: it is found on both shores of the Pacific Ocean, in North and South America, Polynesia, Indonesia, Thailand, the Philippines, China and Japan.

Global yet different at a regional level

This global range is quite unusual since it spans different haplogroups.

The African and Asian (East Asia and India) mtDNA haplotypes are distinct and separate (see Fig. 2 in [3]).

A later study by Kivisild et al., (2003) [2] covering certain Indian populations noted that their 9-bp d was different in its haplotypes to the other Asian and African deleted lineages.

To study the relationship between the different populations carrying the 9-bp d, the following tree (Fig. 4 in [5]) is very useful. It shows that Africans (both those with the deleted 9-bp and the non-deleted populations) cluster together away from the rest.

The Australian Aboriginals and Indians without the 9-bp d are also distinctly separated on the tree from Indians and Australians carrying it.

The Chinese "cluster I" is very close to the non-deleted Chinese, which suggests a recent local origin.

The Amerindians and deleted Amerindians are very far apart.

There is a distinct separation which has three branches: (a) with all of the 9-bp deleted Thai, Cambodian and Nicobarese, (2) the Taiwan aboriginal, Amerindians, PNG, Indonesians and Polynesians and (c) the Chinese "cluster II".

The tree which does not specify the Haplogroups of the different populations clearly shows thre clusters which display the proximity of Amerindians, Asians and Melanesians; of Africans and of Aboriginal Australians.

Diseases linked to the 9-bp locus deletion

The locus of this 9-bp segment seems to have some strong correlation with the individuals' health: A study by Yiqui Jin et al, (2012) [6], links it to a form of cancer (Hepatocellular carcinoma or HCC). This is a very common form of cancer worldwide. The scholars found that the presence of the 9-bp deletion increases the risk of cancer (they call the deletion "one repeat", which is technically correct since the normal form is a tandem repeat [two repeats], so a deletion menas a "one repeat"):

"carriage of 9-bp one repeat fragment was associated with a significantly increased risk of developing HCC
[...] the frequency of 9-bp one repeat [that is: deletion] in our control samples (16.0%) was similar to that of previous reports in Chinese (14.7%). However, this frequency was 22.1% in the HCC groups, indicating a significant association between the 9-bp one repeat and the incidence of HCC." [6]

The reason for this is somehow linked to microRNA (miR) -mediated regulation because the deletion lies in a binding site region for certain miRs.

The locus is also associated with several other diseases: ataxias, idiopathic disorders, polycystic ovary syndrome, dilated cardiomyopathy, etc. [7].

If there is disease risk associated to the presence of one repeat, it seems logical to assume that natural selection would act to eliminate this mutation whenever it appears. However this does not appear to be the case, it is found in old (> 50 ky old haplogroups) with a global range.

Why? The deletion must provide its carriers with a positive side effect. But I have not managed to find any paper mentioning it.

The deletion and its origin

We have seen above that it appears all across the World (though at very low frequencies in Europe) and is considered by orthodox science as a marker that appeared independently in different human populations, yet despite this mutability it is neverheless used as a marker to define mtDNA haplotypes!:

The 9-bp d as a haplotype marker. From [9].

It appears in several haplotypes as markers in some, as a mutation in others:

• B ^[9]
• B6 ^[9]
• T2b15 ^[9]
• T2f ^[9]
• L0a2 ^[10]
• W ^[11]
• H ^[15]

the fact that it has such a high recurrence, meaning that it is found in different populations and in different mtDNA haplogroups around the world is very odd for a marker, since we would expect it to be distinct and appear only once and remain immutable.

Furthermore, the 9-bp d appears in the Coding Region and "Coding-region SNPs, [are] used as reliable markers to define Hgs because they are considered stable evolutionary events" [8]. But as I pointed out above, it seems that they "are nevertheless not entirely stable" [8] and a paper (Behar et al., 2007 [8]) shows that this instability leads to "inconsistent" haplogroup typing in 3.2% of the samples:

The 9-bp deletion is the major contributor to these inconsistencies, with an overall frequency of 1.2%. Which is quite logical since as we have seen above it appears in at least 7 haplotypes, and if the sequencing does not cover many markers an incorrect haplo-typing is surely to occur. [8]

Origin

According to Sodyall, Vigilant, Hill, Stonekin and Jenkins, 1996, [1] it arose independently in different populations around the world: the "locations and frequencies of variant sites" in Africans and Asians are not the same (different haplotypes), which suggests that ir appeared independently in both regions, and perhaps more than once in Africa [1] and twice in Asia [12].

Behar et al., 2007, also interpret this 9-bp deletion as a Homoplasy (which combines the Greek words for "same" -homo- and "form, shape" -plasis), in other words the chance duplication of a feature with a similar shape, structure or function but with an independent origin and no shared ancestry.

Homoplasy is found in the shape of the fins of fish, dolphins and Ichthyosaurs or wings in bats, birds, pterodactyls; which arose independently in separate and separate lineages of different kinds of creatures (reptiles, fish, mammals and birds) by chance, yet the shape is similar because of their similar function.

The independent origin of the 9-bp d is supported by the fact that the "most likely mode of origin of the deletion, namely, slipped mispairing during replication, can occur (and recur) in every population..." [12].

However Kivisild et al., (2003) [2], apart from suggesting an independent origin of the deletion also consider the possibility of "an ancient common root" [2]. And this is indeed interesting, so we will look into it below.

Ancient relict state

Behar et al., [8] found that out of a total amount of mutations of 592, there were 343 transitions, 199 tranversions, 35 insertions and 15 deletions. So the most rare mutation is a deletion (2,5% frequency). Yet for mainstream science, the deletion is the most obvious cause for the presence of one instead of two "CCCCCTCTA" sequences. But insertions are over twice as frequent as deletions. And in fact the tandem repeat is more common than the one-repeat (or deletion). Furhtermore, as we will see below, triplicate, cuadruplicate and even intermediate (expansion and contraction of the tandem repeat by loss or addition of individual bases) are present. What does not exist is a total deletion of the segment implying that the trend is towards growth not contraction.

Its low frequencies may be due to its association with illness, but since it has not been selected to extinction, it must provide some benefit to those carrying it.

The fact that it is found repeatedly in several haplotpes and especially in the ancestral African L0a2 line is an indication of its ancient origin. The most parsimonious explanation is that it appeared in the African populations (in fact their placement on the tree above, away from most groups clearly shows a distinct origin) and was lost in some of the downstream haplogroups due to a "9-bp insertion" that erased the "one repeat" and created the now most common tandem repeat, found in most populations. It is likely that a small number of individuals conserved the archaic deleted state. Which, as we see above makes its carrier prone to certain diseases and therefore maintained a low frequency of this variant.

It moved with humans into Asia, generating the Indian - Australian cluster and then (this resembles the Y chromosome C hg. expansion!) into South East Asia, Eastern Asia, Siberia and America.

It grew among mtDNA haplogroup B in such a way as to become its marker. This must imply some yet unknown benefit in carrying the 9-bp deletion.

Mutations

The Sakha from Siberia have a high frequency of mutation associated to the 9-bp locus: 1.8% deletions, 1.2% triplications and 0.26% four repeats all others have the usual "tandem repeat". These mutations were found among different mtDNA haplogroups, where B, T and W were the most common for deletions. [11]

Interestingly "No neighboring populations have been reported to carry a non-haplogroup B deletion [...] suggesting that shared ancestry or admixture or both are unlikely explanations for the presence of these polymorphisms in the Sakha. The identification of high levels of variation may be a function of the large sample size [N = 779] and the in-depth analysis of all derived polymorphisms" [11].

The comment on sample size is a very positive one, in my opinion most studies are based on very small samples and their sequencing is not done thoroughly, so many differences go unnoticed.

The authors conclude that these mutations are due to "multiple recent events" [11], but in my opinion the lack of admixture or shared ancestry means that these are archaic or relict mutations that have been carried by the Sakha and their ancestors for many generations.

The "three repeat" is very infrequent globally, besides the Sakha with 1.2% frequency, the triplicate insertion has been found among Chuckchi (Siberia), Nepalese Tharu (in 1 out of N=127) [12][13], a Portuguese Brazilian belonging to hg. H (1 in N=245), and Portuguese in Europe (2 in N=96) [14]; it is also very rare among Chinese at 0.25% (3 in N=1218) [15].

The normal tandem (two repeat) is also found mutated in some Indian populations. It appears as "contracted" among the Caste populations (Brahmin and Jalari) at an average frequency of 1% and as an "expanded" two repeat mutation among tribal populations (Khonda Dora and Santal) with a 3% frequency. [3] The expansion is due to a T to C transition followed by a replication of the C component. The contractions have "length variant intermediate between 1 - 2 repeats in length". [3] They have also been detected in Borneo, the Philippines and Samoa. [3]

Selective pressure is surely acting on this ancient mutation maintaining it despite the current prevalence of the tandem sequence.

Closing comments

This is a trait found in the most ancient lineages in Africa and also among other populations at low frequency. Yet one of Amerindians founding mtDNA haplogroups is identified with this specific mutation and it is found at very high frequencies among native Americans.

It causes some propensity to certain diseases yet despite this fact it has not disappeared, this implies that it has some yet to be detected positive aspect for those carrying it.

Deletions are infrequent yet this one is global. It surely signals its ancient origin. Furthermore, its presence in seven different haplotypes indicates in my opinion that the basic axioms of the mtDNA clock and neutral mutations used to set it are not to be taken seriously.

Its dispersion across the globe mimics that of Y chromosome hg. C, which I have suggested may be an ancient (Homo erectus) lineage and much older than mainstream science suggests. Could the 9-bp deletion be an archaic hominin trait?

Clearly some more research is needed here. I will keep my eyes open for additional data.

Sources

[1] H Soodyall, L Vigilant, AV Hill, M Stoneking, T Jenkins, (1996). mtDNA control-region sequence variation suggests multiple independent origins of an “Asian-specific” 9-bp deletion in sub-Saharan Africans. Am J Hum Genet, 58 (1996), pp. 595–608
[2] Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, et al., (2003). The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72: 313–332. doi: 10.1086/346068
[3] Watkins W. S. et al., (1999). Multiple origins for the mtDNA 9-bp Deletion in Populations of South India. American Journal of Physical Anthropology 109:147-158
[4] Wrischnik LA, Higuchi RG, Stoneking M, Erlich HA, Arnheim N, Wilson AC., (1987). Length mutations in human mitochondrial DNA; direct sequencing of enzymatically amplified DNA. Nucleic Acids Res 15:529–542
[5] Yong-Gang Yao, W.S. Watkins and Ya-Ping Zhang, (2000). Evolutionary History of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia. Hum Geet (2000) 107:504-512 doi: 10.1007/s004390000403
[6] Jin Y., et al., (2012). The mitochondrial DNA 9-bp deletion polymorphism is a risk factor for hepatocellular carcinoma in the Chinese population. Genet Test Mol Biomarkers. 2012 May;16(5):330-4. doi: 10.1089/gtmb.2011.0208. Epub 2012 Jan 27
[7] Borgione E., et al., (2013). The 9-bp deletion in region V of mtDNA: a risk factor of hearing loss and encephalomyopathy in Caucasian populations?. Neurol Sci (2013) 3$:1223-1226 doi: 10.1007/s10072-013-1297-9.
[8] Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, et al., (2007). The Genographic Project Public Participation Mitochondrial DNA Database PLoS Genet 3(6): e104. doi:10.1371/journal.pgen.0030104
[9] www.phylotree.org
[10] www.dnahaplogroups.org
[11] L. Tarskaia, R. R. Gray, B. Burkley and C. J. Mulligan, (2006), Genetic variation at the mitochondrial DNA 9-bp repeat locus in the Sakha of Siberia. Human Biology 05/2006; 78(2):179-98. doi: 10.1353/hub.2006.0038
[12] Redd A. J., et al., (1995). Evolutionary History of the COII⁄tRNALys Intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol. Biol. Evol. 12(4):604-615.
[13] Passarino G1, Semino O, Modiano G, Santachiara-Benerecetti AS, (1993). COII/tRNA(Lys) intergenic 9-bp deletion and other mtDNA markers clearly reveal that the Tharus (southern Nepal) have Oriental affinities. Am J Hum Genet. 1993 Sep;53(3):609-18.
[14] Alves-Silva J., Guimaraes P., Rocha J., Pena S. and Prado V., (1998). Identification in Portugal and Brazil of a mtDNA Lineage containing a 9-bp triplication of the intergenic COII⁄tRNALys Region Hum Hered 1999,49:56-58
[15] Yao YG1, Watkins WS, Zhang YP, (2000). Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia. Hum Genet. 2000 Nov;107(5):504-12.

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