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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


Thursday, December 31, 2015

Ending the year with three Jokes! Happy New Year


Wishing you all a very Happy New Year and my best wishes for the new year. May it be a year full of new discoveries, fantastic revelations about our origins, and even more important, let us all have a peaceful, successful, lucky, joyful and healthy year. With love, prosperity and success in all our endeavours, personal or professional. And, as a closure for this great 2015, a silly joke!



Religious Cowboy
The devout cowboy lost his favorite Bible while he was mending fences out on the range. Three weeks later, a unicorn walked up to him carrying the Bible in its mouth.
The cowboy couldn't believe his eyes. He took the precious book out of the unicorn's mouth, raised his eyes heavenward and exclaimed, "It's a miracle!"
"Not really," said the unicorn. "Your name is written inside the cover."


Why was the Narwahl depressed?

Because it had no porpoise


Enough for today! Happy new year


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

Sunday, December 27, 2015

SLITRK1 and the peopling of America


I was reading a recent and yet unfinished paper (K H Ko, 2015 [1]) about the admixting history of humans (H. sapiens, Neandertal and Denisovans) with a rather different point of view to what one usually finds in this kind of paper. One thing that caught my eye was the following sentence: "Genetic studies have shown that the ADSL, GLDC, and SLITRK1 genes, which are linked to hyperactivity and aggressive behavior in modern humans, are not found in Neanderthals (Castellano et al., 2014)" [1].


Of course, I checked Castellano et al. (link) and found that they had actually written the following, regarding those three genes: "Thus, it is possible that the mutations in these genes may have affected some component of behavior unique to modern humans. However, we note that even if they did, the way in which they occurred is unknown. For example, if they affected activity or aggression levels, it is unclear whether they increased or decreased such traits. In any event, these changes clearly warrant further investigation."


So maybe the Neanderthals were the violent ones and we were - are the peaceful ones.


But I decided to check the global frequency of this SLITRK1 gene which is linked to Gilles de la Tourette syndrome (GTS), a neuropsychiatric disease which causes involuntary and repetitive movements and vocalizations (i.e. "tics").


And I came across a paper by Speed et al., (2008) [2] which describes a section of this gene and its different haplotypes. They found twelve haplotypes all of which derive from an ancestral haplotype which they inferred from genotyping non-human primates. However this ancestral form was not seen in any population. They found that the existing ones can be arranged into two separate branches from the ancestral one and they show in Fig. 1 in [2], the frequency of the most common haplotypes among different populations:



Fig 1 and Fig 2 in [2] SLITRK1 haplotypes

The interesting thing in that figure is the high frequency of Haplotype #3 among South Americans, Pacific Islanders and North Americans. Obviously these are Native people. In black, above. These are found at much lower frequencies elsewhere. Among South Americans Haplotype #1 which has the highest global frequencies of all Halpotypes, is lowest.

Now Haplo. #1 is in the same branch as Haplotypes #8, 12, 9, 4, 5 and 10. And is highest in Africa and Europe. While Haplotype #3 (more frequent among Amerindians and Pacific Islanders) is on the other branch with Haplos. 6, 7, 2 and 11.


Haplo 4 is most common in Africa and absent in the other regions. It is also 4 mutations away from the Ancestral type. Haplo 6 is highest in Africa and found at similar frequencies in the Americas. It is only 1 mutation away from the Ancestral form. And Haplo 3 is derived from #6 by one mutation. So it is 2 mutations away from the Ancestral type. Placing it at the same distance as haplos #12 (very rare) and the most prevalent #1.


Once again we have an unusual American frequency distribution. And including a type (#3) close to the ancestral one... does this imply it is an "old" type?. It is also on the same branch as #6 (from which it derives), found mainly in Africa and... the Americas. Could this imply some archaic population? Common to Africa and the Americas?


One could argue with the typical "Bottleneck" explanation that America was peopled by people carrying those specific haplos. and that they then diverged and expanded due to this founder effect beyond the original frequencies. But note how East Asians and Pacific Islanders have even less diversity than Amerindians! (3 haplotypes vs. 4 among Americans).


Haplo. #7 is two mutations away from #6 (so it is further away - ergo younger- than Haplo #3) and found at very low frequencies in Africa but... it is highest in SW Asia, followed by Europe and N.E. Siberia.


We could surmise that #3 is the oldest variant (the equivalent one, #8 on the other branch, is found at very low frequencies so it does not appear in Fig. 1), and it follows the migration of H. erectus out of Africa, and survived among Africans and Amerindians, lost elsewhere. The next branch of the tree #7 derives from #6 (Neanderthals) follows their distribution Europe, SW Asia and, the backflow into Africa; followed by N.E. Asia. #3 also derives from #6 and may reflect the Denisovans? found among Pacific Islanders and Amerindians and, to a lesser degree in the other human populations (maybe via Neanderthal admixture?).


The other variants are on the "other" branch which represent "modern" H. sapiens and their late migration out of Africa (Haplo #1).


So we see a high frequency of an "old" (Haplo 3- in black) and a lower proportion (hence more recent admixture) of Haplo. #1 among Americans.


Sources
[1] K.H. Ko, (2015). Evolution of Intelligence and History of Interbreeding, researchgate.net
[2] William C. Speed, Brian J. O’Roak, Zsanett Ta' rnok, Csaba Barta, Andrew J. Pakstis, Matthew W. State and Kenneth K. Kidd, (2008). Haplotype Evolution of SLITRK1, a Candidate Gene for Gilles de la Tourette Syndrome, American Journal of Medical Genetics Part B (Neuropsychiatric Genetics) 147B:463–466



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

Monday, December 21, 2015

Could Maludong remains belong to Denisovans?


A paper by Curnoe, Liu, Bao, Tacon and Ren published on Dec. 17, 2015, describes the unusal morphology of the remains found in Maludong (Yunnan), Southwest China.


They analyzed a femur found among other hominin remains and found that "...the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora" but, this person lived only 14,000 years ago, so they were contemporaneous with modern Homo sapiens in that part of Asia. Something akin to the Flores hominin.


Are they Denisovan remains?


This is the best part (bold highlight is mine):


"It is intriguing that such a plesiomorphic hominin could have survived at Maludong until near the end of the Pleistocene. Yet, this finding applies also to H. floresiensis, with its apparent minimum geological age only slightly older than MLDG 1678. Homo floresiensis has only been found on the island of Flores in eastern Indonesia though, and its occurrence has been explained by island biogeography. Moreover, the Maludong femur is distinct from the highly unusual femora of this species, with its unique mosaic of traits including resemblances to Australopithecus taxa. One possible explanation is that the Maludong femur samples the population presently known only from Denisova Cave in the Altai region and dubbed the “Denisovans”. Another candidate is the presently unnamed taxon represented by the Xujiayao fossils. However, the absence of femora from both of these groups makes these scenarios impossible to test at present...
...the Maludong femur might represent a relic, tropically adapted, archaic population that survived relatively late in the biogeographically complex region of Southwest China. " [1]


Sources


[1] Curnoe D, Ji X, Liu W, Bao Z, Taçon PSC, Ren L (2015) A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS ONE 10(12): e0143332. doi:10.1371/journal.pone.0143332



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

Sunday, December 20, 2015

An old paper with Amerindians as ancestral to Europeans and Asians


Just a very short post. I came across an old paper (A view of modern human origins from Y chromosome microsatellite variation, Ibrahim, Muntaser E.; Seielstad, Mark), which gave an "old" origin date for African Y chromosomes, which by the way were the "most diverse". The funny part are Fig. 1 and 2. Shown below:


human origins
Trees showing the relationship of Y chromosome among humans. Americans seem to be the oldest after Africa.. From Ibrahim and Seielstad.

These figures have Asians and Europeans further from the root than Amerindians...



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

Tuesday, December 15, 2015

The mite on your face and the early peopling of America


Earlier this year I wrote a post about some tiny, minute mites that live inside the hair follicles of humans (and almost all mammals), the Demodex; in my post I suggested that they would be a useful tool to trace human migrations and the links between extant human populations. Yesterday I came across a very recent paper (M. Palopoli et al., 2001 [1]), whose findings I want to share with you in today's post.


The repulsive Demodex folliculorum mites


These mites are microscopic eight-legged creatures that are symbionts. They live on us, and we carry them with us and, as this pape [1] shows, the mites live for years on their hosts without moving. People get them from their immediate family environment (parents) or they may move between mates. As African Americans born in America carry the "A" clade which is mostly African and not found in Europe instead of the "D" clade which is very common in Europeans and white Americans, it is clear that these people still carry the mites that their ancestors brought with them from Africa to America when they were enslaved many generations ago.


Demodex and human migrations


The paper [1] detected "four deeply divergent lineages", which they named A, B, C and D. Each of these had a very high level of diversity, which implies that they have colonized their human hosts long ago, in other words "D. folliculorum has had a long association with humans."


Almost all Europeans belong to clade D clade (D is also found in all other regions and all other populations). A and B are common in Asia and Latin America. C is found in Africa and America, with a small share in Europe


An unexpected finding is that the high diversity found "suggest that D. folliculorum has not been through a severe population bottleneck in the recent past, despite evidence for a recent bottleneck among human populations...". This is interesting, as one of the typical arguments is that Amerindians and all non-Africans have gone through bottlenecks that reduced their genetic diversity, how could we go through a bottleneck and our symbionts remained unscathed? No explanation is given.


The genetic variability among Demodex is also interesting as shown in the paper's Table 1. Guess where diversity among Demodex is higest? Africa? No, actually it is lowest there. Asia? No. It is highest in America!:

  • "h" Haplotype Diversity, that is the proportion of individuals carrying unique hapotypes, is highest in America and its value is 1 (i.e. 100% which means each individual sampled had a unique haplotype!).
  • "π" Nucleotide Diveristy is highest in Asia and America with 0.06. This measures the differences between sequences. Africa's value is a bit lower 0.05.

So Demodex,unlike the usual Out of Africa theory, is different, it is more diverse out of Africa...


Nevertheless, the authors report that: "the observed patterns of mite diversity are consistent with an out-of-Africa model of human migration. As predicted by this model, the hosts of African descent harbored a very diverse sample of mite haplotypes..." [1]. They add in proof that as Africans have all clades present while "Only a subset of this variation was present on hosts of either Asian or European descent", these derive from an African origin. The revealing part is that Latin Americans have all four subsets too.


The authors put it this way: "One complexity that is not well accounted for by the out-of-Africa diversity model is that hosts from Latin America harbored a broad diversity of mites from all four divergent clades...". They attribute it to the slave trade that brought Africans to the New World, plus the European admixture with Native Americans.


Age


By using the average arthropod molecular clock, they estimate the duration of the mite relationship with humans: "... the time back to the most recent common ancestor of mitochondrial clades A, B, and C is more than 3 Mya, with a 95% highest posterior density (HPD) interval of 2.4–3.8 Mya. This date roughly corresponds with the origin of the genus Homo...".


They also consider that the clock may not be applicable to Demodex and add: "If such were the case for D. folliculorum, then the actual divergence times between lineages could be much more recent than found here. However, a rate 10 times as fast would still place D. folliculorum lineage divergences more than 200,000 y ago, before the estimated origin of modern H. sapiens."


This is a very interesting suggestion hinting at a pre-sapiens relationship. Could Demodex have arisen among our Homo erectus relatives? Let's look at the information in their Table S2 (supplemental information in [2]):


Table S2. Time to common ancestry of mitochondrial clades in D. folliculorum based on divergence in COIII

  • D: 3.2 Mya CI 2.4 - 3.8 Mya
  • B: 2.2 Mya CI 1.6 - 2.7 Mya
  • C: 1.1 Mya CI 0.7 - 1.4 Mya
  • A: 0.8 Mya CI 0.4 - 1.2 Mya

The oldest clade, D, is found all over the world, followed by B unique to Africa, Asia and Latin America. The next oldest clade C is found in Africa America and Europe but not in Asia. While the youngest clade A is unique to Africa, Asia and Latin America.


Of course the confidence intervals overlap but not entirely. Interestingly A and B have together, have a TCA of 3.2 Mya while A and B together have 2.8 Mya.


Can we make sense of this?


Let's take a look at the unrooted tree from Fig S.2 in [1]. It is quite clear that these clades are very distinct from each other.



Clade D has many branches, perhaps due to a bias in the sampling (most people sampled had a European origin) the second largest sample, Asians also had a large share of D followed by B, hence the quantity of branches on B is larger than that of A or C, which are mostly Africans and Latin Americans. So the branching cannot tell us much.


However the root of the tree as per Fig S.1. in [1], shown below, is located between A & B on one side and C & D on the other:



Looking at the outer circle (origin of the host's ancestors) and not the dots (place of birth of the hosts), a pattern emerges:

  • A is roughly 1/3 each, African, Asian, Latin American
  • B is mostly Asian, actually the "African" case has a Kenyan father and an Indian mother, who probably passed the mite to her child.
  • C is mostly African
  • D is mostly European

And when whe check the origin of the Asian populations (in the supplemental information), another pattern arises


Clade D Asians are roughly 50% Chinese and the others are Taiwanese (25%), and the balance from Nepal and Phillipines.


Clade B Asians are from Thailand 60% and India 40%. This does not include the "Kenyan" whose mother was Indian. In America it was found in a Colombian.


Clade A Asians are Indian and non-specified Asian 50 ⁄50.


The Latin Americans belonging to Clade A include a Brazilian,a Colombian, a Costa Rican and a Mayan. The first two may have African slave genes but the Mayan? Surely not.


A Hypothesis


Could A clade represent a very first ancient migration into America? It is not found among modern Europeans, only in Africa, America and Asia (Indians). As the Afro sample is actually Afro-American the data is scarce! But one could imagine Homo erectus carrying pre-Clade A mites into Asia from Africa.(Those that remained behind would evolve into Clade C in Africa). And their trek through Southern Asia (what will PNG mites tell us when they are sequenced?) and north into China (where they left no trace) and onwards into the New World.


Clade A then branched into Clade B in Asia in the southeastern region from India to Thailand, and it did not backflow into Europe or Africa but did find its way into America.


The C clade evolved in Africa and spread into Europe and (slave trade?) America. In Europe it was found in a Belgian (probable Congo admixture?).


D clade, the global one, found all over the world,in Asia a clearly Sino-Himalayan (Nepal, Taiwan, China), insular Asean (Phillipines) trait, and then in Africa, Europe and America. Could it represent the dispersal of Homo sapiens in Eurasia and later, white Europeans in America? It appears there in Peru and Mexico (Spanish conquest?) in Africa one is from Morocco.


A sampling including the mtDNA and Y Hg of the hosts plus a Papua New Guinea - Australia and Siberia sample would give a much better picture.


Source
[1] Michael F. Palopoli, et al., (2015), Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages doi: 10.1073/pnas.1512609112, doi: 10.1073/pnas.1512609112



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

Saturday, December 12, 2015

Pre-Wisconsin stone tool in Kansas (a 1984 paper)


A short and quick post, an old paper: Richard A. Rogers, (1984), The Donahue Locality: Evidence Suggesting a Pre-Wisconsin human presence in North America. Current Research in the Pleistocene Vol. 1, 1984. pp. 19. www.centerfirstamericans.com/crp/crp_pdf/1984_v1.pdf, tells of a stone tool that dates back to the Pre-Wisconsin period, that is, prior to the Wisconsin glacial event. It was dated by thermoluminiscence to an age of around 319,000 years, but it may be younger.


The biface is shown below:


Biface from Kansas

A mammoth molar found in the area but in a younger layer of sediments was dated at 39,900 years BP by radiocarbon dating. So this tool is at least 40 ky old.



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

Thursday, December 3, 2015

The Diego blood group and the peopling of America


The Diego Blood group system was discovered by chance in 1953. At that time, a woman who lived in Caracas, Venezuela gave birth to her second child. The newborn became ill with hemolytic jaundice which was caused by an incompatibility between baby and mother's blood. The samples were sent fot analysis and the outcome wwas a new private antigen which was named after the baby, Diego (he died shortly after).


Further studies identified two different variants Dia and Dib. The first was found to be quite frequent among Amerindians and some Asian populations but absent among Caucasians, Africans and Australian Aboriginals. The second variant was common around the world.


Dia was also found among Polish people, and it is conjectured that it reached Europe via the Tartar - Mongol invasions in the 1300s.


The two variants arise from a mutation in the SLC4A1 gene. Where an amino acid change provokes Dia. As it is not found in all Asian populations it may have arisen in a confined area of Asia and moved into America with part of these people when they migrated into the New World.


In America there are two variants Di(a-) common in South America and NW North America while the other one D(a+) is found elsewhere. This may be due to the fact that the Di(a-) people are the remnants of a first wave of migrants, later over ran by a Di(a+) population. This theory was proposed by M. Layrisse and J. Wilbert [1] who wrote:


"The Diego blood group is an exclusive Mongoloid gene marker, although it is not present in all Mongoloid populations. The absence of the gene in Waica Indians and its very low frequencies in Warrau and Yaruro Indians of South America suggest that it represents a genetic characteristic of Marginal American Indians. Since Marginal Indians are considered to be early comers to the New World, we suggest that Diego-negative t populations were the first to arrive and to extend throughout South America, while the Diego-positive tribes came later."


Interestingly this theory would be completed by a later third wave that peopled the Arctic region where the Dia type is absent.


A recent paper by Bégat C, Bailly P, Chiaroni J and Mazieres S [2] gives another explanation:


"...For this purpose we assumed that the geographic distribution of the DI*A allele coding for Dia is not random but rather coincided with cultural traits according to the gene-culture comigration concept.
[...]
High frequencies were observed in the Peruvian Andes, on the Guyanese Plateau, in the southeastern Amazonian Basin, in a region comprising the Brazilian state of Pará, and along the Tapajos, Xingu and Araguaia tributaries of the Amazon River. Low frequencies occurred mainly in North America, in Chaco and at southern tip of South America. The DI*A allele was totally absent in the Arctic (Eskimo and Tlingit), Panama Isthmus (Bribri and Teribe), Tierra de Fuego (Alacalufe), and a few pocket areas in North America (Cherokee), Northern Brazil/Southern Venezuela (Ninam and Yanomama), and the Chaco area (Ayoreo, Zamucoan).
[2]


They go on to explain that the Ayore suffered from a "severe founder effect", and this may explain the lack of DI*A in them. Then they explain its absence among the Panama Isthmus populatons because these Chibchan-speakers "predecessors have lived in isolation from Central and South Amerindians since the early Holocene" [2].


The Fuegians lack this allele because of "isolation by distance with ensuing drift" [2] and its void in Northern North America is due to a "Secondary migration ... of non-Amerind-speakers, i.e., Eskimo-Aleut and Na-Dene speakers, from Alaska to Greenland and Southwestern North America.", they back-migrated into Siberia too, and that explains the link between their language and the Yeniseian languages in Siberia where the Yeniseian speakers also lack the Di*A allele. Then came even more gene flow carrying the DI*B allelle into the boreal part of the New World.


Frequency


  • 5% Chinese
  • 12% Japanese
  • 54% South American Natives
  • 4% North India
  • 0.47% Polish
  • 0.01% Other Caucasians

I must admit that the Diego blood Group is an oddity, found in many non-African It has an exclusively Amerindian variant the Dia variant but, and this is interesting: An antibody of the Diego antigen, Anti-Di(a), is the cause of hemolytic transfusion reactions and also of hemolytic disease of the newborn (like happened to the baby, Diego). The presence of this antigen, or Dia alloimmunization has been observed among different Asian and South American Amerindian populations. A study by Baleotti et al., (2014) [3] found that:


"...HLA-DRB1*07:01 allele was overrepresented in Dia-alloimmunized patients compared to nonimmunized patients and to healthy donors.
... Individuals carrying the HLA-DRB1*07:01 allele present an increased risk for Dia alloimmunization...
"


This means that those with the lowest frequency of this type of HLA, which in the map below would mean those native to the areas shaded in blue or pale blue, would not have the Anti-Di(a) antigen, because they have Di(a). And the map is clear: The Americas and east Asia. But! why is Australia, Melanesia and Africa also blue?


Also the Altai region (i.e. Denisova-land) is blue. Could the Australia -Melanesia - Americas mean some Denisovan introgression? But what about Southern and Western Africa?.


Could this imply some introgression there, in Africa, of an archaic hominin? See my post an ancient Y chromosome lineage, which mentions a possible archaic-human admixture in a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.

The map below shows the global distribution of DRB1*07:01:01:01, (Source).



And this is the image from [2] showing the distribution of the Diego factor in America (black = none, dark blue= high)



I have the impression that Diego factor is archaic, not the result of a bottleneck.


Sources
[1] M. Layrisse, J. Wilbert, Science (1961). Absence of the Diego Antigen, a Genetic Characteristic of Early Immigrants to South America, 13 October 1961, Vol. 134 no. 3485 pp. 1077-1078 DOI: 10.1126/science.134.3485.1077
[2] Bégat C, Bailly P, Chiaroni J, Mazieres S (2015) Revisiting the Diego Blood Group System in Amerindians: Evidence for Gene-Culture Comigration. PLoS ONE 10(7): e0132211. doi:10.1371/journal.pone.0132211
[3] Baleotti, W., Ruiz, M. O., Fabron, A., Castilho, L., Giuliatti, S. and Donadi, E. A. (2014), HLA-DRB1*07:01 allele is primarily associated with the Diego a alloimmunization in a Brazilian population. Transfusion, 54: 2468–2476. doi: 10.1111/trf.12652


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

Thursday, November 26, 2015

More on the Amerindian - Australasian link: Denisovans?


I I have already posted about this The link between Negritos, Papuans and Amerindians!, but the paper by P. Skoglund et al., published online on July 21, 2015 [1], found a close relationship between the genetic makeup of some Amazonian Native Americans and a group of Oceanian or Austalasian people. Namely, the team found "genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".


Being beind a paywall, since that first posts I have read other online sources who have accessed the paper found some interesting points to share in this post:


Skoglund et al., found that the Amazonian Amerindians like the Suruí, the Xavante and Karitiana share around 1 or 2% of their genes with aboriginal Andamanese, Papuans and Australians. Furthermore, the 12,600 year-old remains from Anzic, Montana, US, don't have any links to these Australasians suggesting that the Anzic child and modern Amazonians have different origins.


Their explanation is the following:


A simple migration from Melanesia north to Bering and then south into America does not seem likely because there are no traces of Australasian genes along the route. It is improbable that they would have covered such a long route without dallying with the locals and spreading their genes.


Instead they suggest that an ancestral population which is now extinct (that is why their genes cannot be found in Asia), lived in eastern Asia and split into two groups, one that moved south into South East Asia, PNG and Australia and another that marched north across eastern Asia and entered America.


They named these mysterious people as "Population Y" (Y from the Tupi word "Ypykuéra", which means "ancestor").


As I am not constrained by the rigidity of orthodox science, I can suggest that there is a Denisovan link involved in this process:


As Austronesians have a very high share of Denisovan genetic input, the hypothetical "Population Y" may well be the group that admixed with Denisovans, and therefore Denisovan genes in America could have this origin.


An alternative explanation however for the lack of "Population Y" traces in Asia could be that the Denisovans lived both in Asia and America, and admixed with the first wave of humans that went into America and also with the first wave through their Asian homeland: the ancestors of the modern Australasians. Later, they became extinct, but their genes lived on. Later still, Asians with a different genetic make up entered America and swept the first people away. Nowadays only 2% of the old genome survives in the Amazonian forests.


Since the very old hg M mtDNA was found in some ancient native remains in America, but is also found in parts of South East Asia, PNG, India and Tibet. Could this be a signal of the first people to reach America from South East Asia?


We have evidence of humans in Southern Asia aroung 120 kya, a very archaic population of humans; and they probably moved into America and mixed with Denisovans there or in Asia. What is the mtDNA of these people? If the hypothetical Out of Africa move took place earlier, then they could be Haplogroup M. We will have to wait for more evidence.


Source


[1] Pontus Skoglund, et al. (2015) Genetic evidence for two founding populations of the Americas, Nature 525, 104–108 (03 September 2015) doi:10.1038/nature14895.



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

Sunday, November 22, 2015

Into and across America... the timing factor


A very interesting post Did humans approach the southern tip of South America more than 18,000 years ago? (19 Nov 2015) at John Hawks blog (thank you Shane) looks into Dillehay et al. paper on the Monte Verde (Chile) site.


I found some very interesting pointers in the blog, and I want to share them with you:


On the rapid peopling of America once modern humans reached it: "There is a school of thought that population growth should have been rapid once humans entered the virgin landscape of the Americas"... "But there may be a problem with the assumption of rapid growth. It assumes that people could rapidly change their strategies to spread into the very different ecologies of inland North and South America.
Maybe it wasn’t so easy for them to develop the technical and organizational innovations necessary to move into those continental ecosystems.
"


This is a very interesting point. A coastal population living off the resources of the Pacific Ocean's coast, would have to devise new hunting - gathering techniques to tackle the Amazonian rainforest or the Argentine Puna or Patagonia (hunting guanaco and rhea).


An early peopling of America: "The earliest cranial remains we have from both North and South America are surprisingly variable in comparison to later peoples of the Americas. Those skulls suggest the possibility that they represent populations that had already experienced a lot of diversifying evolution by genetic drift. An earlier initial spread of humans across South America might explain that appearance.".


This is an interesting point. It is very clear that America was peopled in waves and not in "one go" from an isolated population in Beringia!.


John Hawks continues: "Could there have been an earlier habitation, now only present in living Native American peoples as traces of a “ghost population” that we haven’t yet identified?
If so, that scenario might explain the evidence for “deep divergence in Native American populations” that Rasmussen et al. (2014) found to predate the 12,600-year-old Clovis-associated Anzick-1 burial.
"


migration timing

I have already posted about the odd theory that has man take 50,000 years to reach Australia, 85,000 years to reach Beringia, but only a couple of millennia to span the whole American continent as contended by Bodner, Perego and Parson who asserted "... that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even < 2000 yr." Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes (Martin Bodner, Ugo A. Perego, [...], and Walther Parson).


More sites like Monte Verde will be discovered (funding is scarce in South America) and we will find that humans have been living in the New World for much more than 50 ky. And the recent finding that humans have been living in Southern China for around 120 ky make this even more likely.


This link to Dilleahy's book is quite interesting it has photos of the 33 ky old MV-1 Level (see Fig. 18)


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

Wednesday, November 18, 2015

The Inca Child from Argentina and a new haplogroup C1bi


The third and last post of the day deals with a novel mtDNA sub clade found in the mummified (due to the high dry altitude of the Andes) remains of a child sacrificed by the Inca people about 500 years ago. The child's mtDNA is similar to that found in some very old remains in Upward Sun River, Alaska.


The paper (see below [1]), reports that this new variety of C1b haplogroup and that it is very ancient: The authors believe it originated some 14,000 years ago along the Andes in South America. As it is rare nowadays they suggest that either (a) it is due to a bias in sampling -so it has not been detected in large frequencies, or (b) it has become extinct in many parts due to the mass deaths caused by the turmoil of European discovery and conquest during th 1500s. They write:


" the phylogenetic patterns of C1bi point to a geographic origin in the Andean side of the South American sub-continent approximately 14 kya. The haplotype found in the Inca child from the Cerro Aconcagua, interpreted in the light of present-day variation in South America and together with the different archaeological and anthropological findings, supports the existence of demographic movements along the Pacific coastline during the Inca period. The fact that C1bi is very uncommon in present-day populations from South America could be explained by insufficient sampling of modern populations (although the present-day haplotype databases of mitogenomes and partial mtDNA sequences are very large). Alternatively, this rarity could reflect important changes in the gene pool of South America since the period of the Inca civilization. Further research on modern and ancient South American populations" [1]


Regarding the age, those 14 kya are maybe even too recent, their confidence intervals are rather wide, from 5 to 23.6 kya. The child was sacrificed 500 years ago during an Inca rite on the highest mountain located outside of Asia, the Aconcagua.


They point out that " C1b most likely arose relatively early, either in Beringia or at a very initial stage of the Paleoindian southward migration [...] While some C1b sub-clades were exclusively observed in Mesoamerica or in South America, a few of them were found in both territories." The map published in the paper shows the distribution of C1b across America: it is strongly concentrated in Mexico, Peru and strangely, in Puerto Rico.


C1b haplogroup map in America
C1b distribution heat map. From [1]

The child has a new clade named C1bi (where "i" stands for "Inca") and is similar to the clade "C1b13. The TMRCA of this sub-clade is 11.8 (8.6–15.1) kya; it is virtually absent from North-Central America and its geographic location is mainly centered in Chile", which fits in the same geograpic area of C1bi.


The clade is very rare: "By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes)." [1]


I have already written about the loss of diversity in America not because of a Beringinan or Out of Asia bottleneck but due to the high death toll that virtually wiped out the Native Americans when they were contacted by the European navigators after 1492. Interestingly, my post cites a paper which points out that Hg C suffered a greater impact of lost diversity (with Hg D) than either haplogroups A or B.


In another post I tried to link mtDNA hg. C1 with the Neanderthals. In this post I mention that hg C1 spans Eurasia and America, closely following the Neanderthal homeland.


In [1], the authors found one sample "...that belongs to haplogroup C1b13b sampled in a Spanish individual, although born in Talagante (Chile); therefore we labeled it here as originating in America" [1], in other words a person of European origin born in America carried a European variant of C1. They assumed perhaps that this individual had some Amerindian admixture, I believe that it is just a coincidence that this man has C1 and by chance his ancestors migrated to America.


The hot spot in Puerto Rico is very interesting and requires some explanation. The local Carib - Taino natives were wiped out early during the discovery period. So where did the C1b found there come from?


Sources
[1] The complete mitogenome of a 500-year-old Inca child mummy Alberto Gomez-Carballa, Laura Catelli, Jacobo Pardo-Seco, Federico Martinon-Torres, Lutz Roewer, Carlos Vullo y Antonio Salas Scientific Reports 5, Article number: 16462 (2015). Nature, Nov. 12, 2015 doi:10.1038/srep16462


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

The Hobbits were a mix of human and Homo erectus.


A paper published today (Kaifu Y, Kono RT, Sutikna T, Saptomo EW, Jatmiko, Due Awe R (2015) Unique Dental Morphology of Homo floresiensis and Its Evolvotionary Implications. PLoS ONE 10(11): e0141614. doi:10.1371/journal.pone.0141614) refutes a previous paper [2] that suggested that the Hobbit of the Indonesian Flores Island was a microcephalic human. Instead it suggests that the Hobbit was a primitive human species that underwent insular dwarfism.


hobbit skull

Above: reproduction of a Hobbit skullby Javier Truebamsf


To settle the issue of "new species" vs. "degenerate human" they took a peek at the Hobbit's teeth. And found that "H. floresiensis had primitive canine-premolar and advanced molar morphologies, a combination of dental traits unknown in any other hominin species. The primitive aspects are comparable to H. erectus from the Early Pleistocene, whereas some of the molar morphologies are more progressive even compared to those of modern humans."


Their paper disproves an even older origin (i.e. Australopithecines or H. habilis) but, and this is interesting their results suggest that " H. floresiensis derived from an earlier Asian Homo erectus population and experienced substantial body and brain size dwarfism in an isolated insular setting.".


They studied many variables and concluded that " the dental morphology of H. floresiensis is derived relative to H. habilis s. l. and is comparable to post-habilis grade Early Pleistocene Homo or H. erectus s. l. ...[giving] strong support to the hypothesis that H. floresiensis evolved from an early Javanese H. erectus population or a related form from the ancient Sundaland with substantial body and brain size dwarfism... "


The dwarfism is considerable, since an average Homo erectus is about 5.4 ft (1.65 m) tall and has a brain with 860 cm3 and the Hobbit is only 3.6 feet (1.1 m) tall and its brain is only 426 cm3.


But such insular dwarfism is not uncommon among mammals: elephants and hippopotamus that became midgets in Cyprus and mammoths that shrunk in Crete and on Flores itself, the dwarf stegodon (a relative of elephants).


Further reading
[2] Argue D, Donlon D, Groves C, Wright R. Homo floresiensis: microcephalic, pygmoid, Australopithecus, or Homo? J Hum Evol. 2006; 51: 360–374. pmid:16919706 doi: 10.1016/j.jhevol.2006.04.013


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

Denisovans. More information on their genetics


A paper by S. Sawyer et al., Nuclear and mitochondrial DNA sequences from two Denisovan individuals, PNAS, doi: 10.1073/pnas.1519905112 Published Nov. 16, 2015 has sequenced the nuclear and mtDNA of two Denisovans. Their findings are the following:


Abstract
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.


Denisovan teeth
Take note of how large the Denisovan teeth are. From the paper

The paper notes that "Both Denisova 8 and Denisova 4 are very large compared with Neandertal and early modern human molars, and Denisova 8 is even larger than Denisova 4. Only two Late Pleistocene third molars are comparable in size: those of the inferred early Upper Paleolithic modern human Oase 2 in Romania and those of ObiRakhmat 1 in Uzbekistan"


The teeth though primitive looking also seem to differ from H. erectus teeth too. Which is quite interesting.


Denisova 8 is about 60,000 years older than Denisova 3 and Denisova 4 meaning that they are 110,000 years old. This is a long period of time in a same location.


The paper says the following about this long occupation: ", suggests Denisovans were present in the area at least twice, and possibly over a long time, perhaps interrupted by Neandertal occupation or occupations. Denisovans may therefore have been present in southern Siberia over an extended period. Alternatively, they may have been present in neighboring regions, from where they may have periodically extended their range to the Altai.".


The paper ends with an open question: " Given that the high-coverage genome from the Denisovan 3 phalanx carries a component derived from an unknown hominin who diverged 1–4 million years ago from the lineage leading to Neandertals, Denisovans, and present-day humans, it is possible that this component differs among the three Denisovan individuals. In particular, it may be that the older Denisovan population living in the cave carried a larger or different such component. It is also possible that the two diverged mtDNA lineages seen in Denisova 8 on the one hand and Denisova 3 and Denisova 4 on the other were both introduced into the Denisovans from this unknown hominin, as has been suggested for the mtDNA of Denisova 3. However, more nuclear DNA sequences from Denisovan specimens of ages similar to Denisova 4 and Denisova 8 are needed to address this question fully.".



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

Sunday, November 8, 2015

Homo erectus in America, the Malaria clue


My recent post Africans reached America ca. 1310 C.E.? led to a comment by Ron Quiroriano, in which he wrote "Sickle cell anemia, is not an African only disease, its a natural defense against malaria, and is found through out tropical populations, it just reaches its peak distributions in Africans.", and this made me think about Malaria and the peopling of America. The outcome is today's post.


I had always believed that Malaria originated in Africa and that the only defense against it was the mutation that caused sickle cell anemia among Africans. But I was mistaken. Actually there are several strains of Plasmodium that cause malaria in humans and, there are several mutations among humans to fend off the disease.


Malaria a brief overview


Malaria is caused by microorganisms (actually protozooans) of the genus Plasmodium they are transmitted by mosquito bites. The infected person will suffer from fever, vomiting, fatigue and may even become severely ill and die.


There are different strains of Malaria, the worst is P. falciparum, which causes most deaths. The others: P. vivax, P. ovale, and P. malariae are more benign and lead to a more mild illness. This, in my opinion indicates a more recent origin for P. falciparum, as it is too virulent. The other strains have surely lived with us for a long time and evolved not to kill us (which is the best gambit for a parasite, why kill your host?).


The evolutionary pressure has selected positively some genetic traits among humans which give the carrier a better chance to reach maturity, mate and pass on those genes to their offspring. These mutations are found among people living in areas where Malaria is endemic.


There are different mutations that give different resistence against the illness: sickle cell trait, thalassaemia traits, glucose-6-phosphate dehydrogenase deficiency, the lack of Duffy antigens on red blood cells and Ovalocytosis.


This wide range of mutations indicates that they have arisen in different groups of humans in different areas as a response to the pressure of this terrible disease.


malaria mutations in humans
map from (1) St George's University, 2007

So Sickle Cell is prevalent in Africa and some variants of Haemoglobin diseases (HbC, HbD and HbE) are found in Africa and Asia. The alpha and beta Thalassaemia are found in a wide swath from Western Europe to Melanesia. All of them overlap the area where Malaria is predominant in the Old World.


But what about America? We will get there later. Now lets look at South East Asia.


Egg shaped red blood cells


Amato and Booth, (2) found that the hereditary Ovalocytosis is found among 5 to 20% of Melanesians in the coastal (malaria prone) areas of Papua New Guinea. This is comparable to the frequency among Malaysian and Indonesians. The trait is also found in the Philippines.


It causes oval shaped blood cells, hence its name.


It is several hundred times more common than the sporadic type of oval shaped red blood cells (elliptocytosis) found in other populations (at a 0.02 - 0.05% frequency), a clear indication that it is being selected for positively.


And as Rosanas-Urgell at al (2012) have proven by three independent studies (3): "strong associations between Southeast Asian ovalocytosis (SAO) and protection against P. vivax malaria by a mechanism that is independent of the Duffy antigen. P. vivax malaria may have contributed to shaping the unique host genetic adaptations to malaria in Asian and Oceanic populations."


The mention of Duffy antigen is because it was believed that this trait common in Africa indicated that P. vivax resistence evolved there, in the cradle of mankind when our distant human ancestors encountered P. Vivax, but it seems that this was not an Out Of Africa case. Actually it is quite the opposite.


And this is what Oleksyk, Smith and O'Brien (4) have asserted: "Plasmodium vivax is closely related to Asian primate malaria vectors, and Mu et al. (2005) have speculated that the pathogen may have emerged from Macaca to humans 53,000–265,000 years ago, and entered Africa afterwards."


But, as we will see below, the date may actually be much older. Anyway, 54 - 265 kya in South East Asia is very old, and takes us beyond the accepted date of an Out Of Africa event (ca. 60-100 kya). This means that P. vivax infected Homo erectus, which had been living in Asia for at least 1.5 million years.


From monkeys to Homo erectus


The ancient origin for Malaria infection among Hominids mentioned above is in line with Neafsey et al. (5) who compared P. Falciparum with P. vivax noticed some interesting differences between them:


"Other departures in the global population history of these two species are indicated by the topology and branch lengths of their respective phylograms... The relatively large degree of divergence between the IQ07 Peruvian isolate and the Brazil I and Salvador I strains of P. vivax suggests a distinct history in the New World relative to P. falciparum, which exhibits low diversity in the New World and is thought to have been introduced within the last 500 years via the African slave trade." (5).


In other words, P. vivax has had more time to diversify and evolve in America than the more recently introduced P. Falciparum. And this is what they say (Bold is mine):


"The high New World diversity of P. vivax, combined with the closer phylogenetic affinity of the three New World P. vivax isolates with the east Asian (North Korean) rather than the African (Mauritania I) or south Asian (India VII) strains, could suggest the precolonial arrival of P. vivax in the New World accompanying human dispersal from Asia by sea or, less likely, by the Bering land bridge during the last glacial maximum." (5).


Or, may I add, perhaps an even older arrival (they are constrained by orthodoxy and a late peopling of America, I am not). Incidentally, they calculate for P. vivax, "we can estimate the TMRCA as 768,000 years" (5), much older than the appearance of the first H. sapiens, and in line with H. erectus living in Asia.


This same theory, that Macaca passed it on to Hominids in South East Asia is also supported by other scholars like Escalante et al., who point out that the range of both species "overlapped, especially, during the late Pliocene and middle Pleistocene (0.7–2.5 Myr), making possible the exchange of parasites in any direction" (6). This period, once again, predates the appearance of Homo sapiens.


They are cautious however and state that "this investigation points to P. vivax being derived from ancestral macaque parasites when hominoids colonized Southeast Asia." (6) and calculate a TMRCA "between 45,680 and 81,607 years ago, and possibly as old as "132,445" years, and they write "this time frame includes the accepted estimates for the introduction of H. sapiens in Southeast Asia; however, other hominoids were present such as H. erectus" (6).


Jongwutiwes et al., (2005) (7) take it up and give an even older age: "We estimated the age of the most recent common ancestor (MRCA) of the mitochondrial genomes of both P. vivax and P. falciparum at around 200,000–300,000 years ago. This is close to previous estimates of the time of the human mitochondrial MRCA and the origin of modern Homo sapiens, consistent with the hypothesis that both of these Plasmodium species were parasites of the hominid lineage before the origin of modern Homo sapiens and that their population expansion coincided with the population expansion of their host." (6).

They re-estimate Escalante's data and obtain "the age of the MRCA were 206,000–314,000 years (A.L. Hughes, unpublished), in good agreement with the present study" (7).


Which they conclude "P. vivax became a parasite of hominids – presumably in Asia – long before the origin of modern Homo sapiens. By about 1 Mya, Homo erectus is known to have inhabited both Africa and a wide geographic area of southern Asia (Anton 2003). We hypothesize that P. vivax transferred from a monkey host to H. erectus in Southeast Asia sometime before 1 Mya and subsequently spread across southern Asia into Africa through the H. erectus population. This model assumes that P. vivax reached Africa by dispersal through a H. erectus population that was distributed nearly continuously across Africa and southern Asia." (7)


So we have an ancient origin for P.vivax in South Asia, and evidence that it infected H. erectus over 300,000 years ago. Now lets look at its current endemicity:


Plasmodiium Vivax global Endemicity map, 2010
Plasmodiium Vivax global Endemicity map, 2010.(8)

It is evident that the areas where P. vivax are endemic are Papua New Guinea, South East Asia and India. Which was the homeland of H. erectus. In Africa it is present but at low rates, and... surprisingly, it is very prevalent in America, in eastern Central America and in the Amazon basin. So How did it reach America?


P. vivax in America


A very interesting thesis by Petr Triska (9) looks into the Plasmodiums in America and concludes that "P. falciparum has been endemic to Americas for more than 600 years." (9), it is a Precolombine infection with later events of colonization due to African slave trade.


Regarding P. vivax Triska writes: "that Plasmodium vivax was present in Americas prior European colonization and prior documented contacts with Polynesia.
Colonization of Americas from Africa is not supported in our network. Ancestral haplotype of Americas is not shared with Africa. Furthermore, majority of slaves dragged to Americas were embarked in West Africa, however, West Africans are highly resistant to P.vivax and P. vivax is not prevalent there.
" (9)


He finds no support for a recent (last 600 years) migration from Polynesia. Neither did he find any "suggestion that present day American population of malaria parasites emerged from African strains" (9). He finds "Population ages were in magnitude of tens of thousands years", a clear indication that it is very old.


The Homo erectus link


Another protection from Malaria is given by O blood group. Apparently (Cserti-Gazdewich et al. 2011) Heterozygotes 00 grants resistance against malaria while A0, B0 and AB probably have no resistance. Since Amerindians are almost exclusively O group ( 80-100%), we can suppose it is due to positive selection against Malaria. Curiously, another hot spot for high O blood group is in Northern Australia and Melanesia.


O blood group America and Melanesia
Global O Blood Group distribution. (10)

So, we have evidence that P. vivax infected Homo erectus in South East Asia. That it reached America long ago, that it did not come via Polynesia or Africa. So it reached the New World from Asia. That it is prevalent in the deep Amazon, meaning it got there long ago, when it was first inhabited. That South East Asians and Melanesians have a mutation (oval shaped red blood cells) that protects them against P. vivax Malaria.


And, incredibly, this strange "ovalocytosis" mutation found in South East Asia, has been detected in Mexico, in two patients with no ties with S.E. Asia! pure Native American Mexicans:


Lets quote Ramos-Kuri et al. (11): "We describe the finding of two Mexican patients with a specific 27-bp deletion in the solute carrier family 4 gene (SLC4A1Δ27) (also known as the band 3 gene found on chromosome 17q21–q22), characteristic of Southeast Asian ovalocytosis (SAO). The patients were asymptomatic, and the initial diagnosis was made by microscopic observation of the presence of typical stomatocytic ovalocytes. The gene deletion was confirmed by PCR and DNA sequencing. Both patients were heterozygous for the deletion. One patient is from Tabasco state, in southeastern Mexico, a malaria-endemic zone. The other patient is from Mexico City, which is not a malaria-endemic area. Their families have no non-Mexican ancestors and their previous generations were born in Mexico. Both patients carry the HLA-B*3501 subtype, characteristic of Amerindians and Asian populations. Familial and HLA data led us to conclude that these two patients are the first report of SLC4A1Δ27 in Amerindians. The nucleotide analysis showing a perfect match sequence between Southeast Asian and Mexican patients suggests, but does not prove, that the Mexican gene is not a de novo mutation. Instead, this gene might be the result of migration of individuals with Asian ancestry into the Mexican gene pool. We are looking for other families with the mutation to detect, by HLA analysis, the ancient ethnic origin of these patients." (11).


Does this imply that the mutation was carried to America by a common ancestor of both South East Asians and Amerindians? Or is it the outcome of an even older carrier that admixed with Native Americans in America? I am suggesting that Homo erectus reached America with this mutation and passed it on to Amerindians later, when modern H. sapiens reached the New World.


Sources


(1)Sickle Cell Anemia St George's University, 2007
(2) D. Amato and P.B. Booth, (2005), Hereditary Ovalocytosis in Melanesians PNG Med J 2005 Mar-Jun;48(1-2): 102-108.
(3) Rosanas-Urgell A, Lin E, Manning L, Rarau P, Laman M, Senn N, et al. (2012) Reduced Risk of Plasmodium vivax Malaria in Papua New Guinean Children with Southeast Asian Ovalocytosis in Two Cohorts and a Case-Control Study. PLoS Med 9(9): e1001305. doi:10.1371/journal.pmed.1001305
(4) Taras K. Oleksyk, Michael W. Smith, Stephen J. O'Brien, (2009) Genome-wide scans for footprints of natural selection 24 November 2009.DOI: 10.1098/rstb.2009.0219
(5) Daniel E Neafsey et al., (2012) The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nature Genetics 44, 1046–1050 (2012) doi:10.1038/ng.2373
(6) Ananias A. Escalante, Omar E. Cornejo, Denise E. Freeland, Amanda C. Poe, Ester Durrego, William E. Collins, and Altaf A. Lal (2004). A monkey's tale: The origin of Plasmodium vivax as a human malaria parasite vol. 102 no. 6 doi: 10.1073/pnas.0409652102
(7) Somchai Jongwutiwes et al., (2005) Mitochondrial Genome Sequences Support Ancient Population Expansion in Plasmodium vivax Mol Biol Evol. 2005 Aug; 22(8): 1733–1739. Published online 2005 May 18. doi: 10.1093/molbev/msi168
(8) Plasmodiium Vivax global Endemicity map, 2010
(9) Petr Triska, (2011), Master's Thesis Masaryk University, Brno. Assessing human history by investigating phylogeography of Plasmodium parasites
(10) O blood group map
(11) Manuel Ramos-Kuri, Joaquin Carrillo Farga, Joaquin Zuniga, Maria Teresa Amador Guerrero, Julio Granados, Francisco J. Estrada (2005). Molecular Demonstration of SLC4A1 Gene Deletion in Two Mexican Patients with Ovalocytosis Human Biology Volume 77, Number 3, June 2005 pp. 399-405 | 10.1353/hub.2005.0052



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

Sunday, November 1, 2015

Africans reached America ca. 1310 C.E.?


I have read several blogs posting about the Olmec "heads" as an example of an early presence of Africans in America (this is a typical example). I usually consider those theories a bit outlandish and shrug them off with little effort. But today I found something a bit more scientific; A paper by Dr. Clyde Winter who looks into the HLA variants to pinpoint an African expedition to Mesoamerica around 1310 AD.

olmec head

Read his article here: Winters C. Inference of Ancient Black Mexican Tribes and DNA. WebmedCentral GENETICS 2015;6(3):WMC004856 doi: 10.9754/journal.wmc.2015.004856.


Apparently Abubakari II, ruler of Mali in Africa sent an expedition to America in 1310 and that is the source of admixture in Mesoamerica (not the later slave trade that brought millions of unfortunate Africans to work and die in the New World; read more about this African king.


For a good explanation on African - Native American admixture, see this website. The first Africans to reach America did so in what is now Santo Domingo Island in 1502. Some escaped, met the local natives and that led to the first admixture.



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

Monday, October 26, 2015

The age of the mtDNA from Upward Sun River in Alaska


The paper by Justin C. Tackney et al., (2015) Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia, PNAS doi: 10.1073/pnas.1511903112, published today has found that the remains of a stillborn baby and a very young infant that were buried at the same time in a grave in Upward Sun River, Alaska 11,500 years ago, belong to Mitochondrial DNA types C1b and B2, and these "allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.".


Though it is behind a paywall, the information published online indicates the ages of "about 12,800 years ago for C1b and 12,000 years ago for B2" and that one of the paper's co-authors "O'Rourke suspects the real times were even earlier, but that nonetheless both 11,500-year-old infants were at or near the root of their respective genealogical trees".


Additionally, O'Rourke said "'You don't see any of these lineages that are distinctly Native American in Asia, even Siberia, so there had to be a period of isolation for these distinctive Native American lineages to have evolved away from their Asian ancestors. We believe that was in Beringia,'".


This value of 12 to 12.8 kya is interesting. Why not 20 or 25 kya? It is convenient that the these 12,000 years situate the origin of these haplotypes at the time of a purported Beringian standstill. Lets see how they were calculated.


The Supplemental information, on page 4 tells us that "... Mutational distances were converted into years using a corrected molecular clock proposed by ref. 27 or a whole-genome substitution rate of 2.67 × 10−8 sub per site per year".


And this is a critical point, because based on this mutation rate is that the authors have estimated the age of these mtDNA haplotypes.


However this mutation rate is questinable. For instance a value of 0.43 × 10−9 per site per year was reported for the 45,000 year old shin bone from Ust’-Ishim.


The difference between 0.43 x 10-9 and 2.67 x 10-8 (which I will express as 26.7 x 10-9) is 62 times!


I eliminated the previous paragraphs because I was using autosomal and mtDNA mutation rates and they are not comparable. (see the comment below dated 27/Oct.) However, the following is valid. Because as I mention in Comments below, the mtDNA mutation rates estimated by different authors vary and considerably, from 1.3 to 3.2 x 10-8. Even the range for a 95% Confidence Interval is too wide for my liking, so...


Fidgeting with mutation rates one can get a wide range of coalescence dates...and that means you can get mistaken ones too.


I posted in June 2014 about mtDNA C1 haplogroup and in that post, I cited a paper that gave the following age to C1b: 17.9 +⁄- 2.3kya. Which is at odds with the figure calculated by Tackney's team.


In that post, besides questioning the molecular clock (I always seem to be irked by this subject), I wrote: "Interesingly, C1 has a high values for nucleotide diversity indices, and show a South to North cline (with most variations in South America), indicating that it has deeper roots in the southern part of the New World or that bottlenecks reduced its diversity in the North. In my opinion in points at an older date of entry into America than those mentioned above.", which again seems to be at odds with such early (12 kya) dates and a late Beringian standstill.



 C1 mtDNA hg map
A Map showing the mtDNA C1 haplogroup current and probable archaic range
Copyright © 2015 by Austin Whittall

Let's wait and see if they can get a Y chromosome haplogroup from the remains (but it seems both were girls).



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

Wednesday, October 21, 2015

More on language diversity


I came across the map shown below, and I found it very similar to the map that I included in my previous post on Language diversity: it has the same clusters in Papua New Guinea, Amazonia and northern South America, South East Asia and Equatorial Africa. But! it depicted another thing, "Tone diversity".


The website that published that map has a very interesting post: Phonemic diversity decays "out of Africa"? (April 16, 2011)



Yes, the red dots are higher in Africa, S.E. Asia and PNG, but none in north Asia or Europe, and quite a few in America. Regarding the pink dots, America has more than the putative cradle od Amerindians (Siberia) or Europe.


The blog is very good as it makes fun of the paper it is criticizing.


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

Sunday, October 18, 2015

Language diversity and the peopling of America


For years I have wondered why do Native American people speak so many languages? They supposedly reached the New World recently (i.e. 15,000 years ago) yet evolved over 40% of the global languages! A figure higher than that found in Africa, the "cradle of Mankind".


Africans have had the time (they are supposedly the oldest humans) and the advantage of not going through bottlenecks (I do imagine that bottleneck that wipes out genetic diversity does the same to languages... kill the speakers and the language dies), so they should have evolved most languages than any other group of humans. But they have not.


The diversity of Languages: highest in America. From [1]

Then we have the island of divesity in New Guinea has the highest language diversity in the whole world! 820 languages out of a global total of around 7,000. That is 1 language every 820 Papuans.


I found that quite reasonable, the island is a jungle, with many mountain ranges that isolate populations and keep them from mixinng. New Guinea has been considered as one of the first places reached by mankind during our epic trek out of Africa.


But America is different, we are newcomers. The Papuans had 50 ky to develop their languages, the Amerindians less than 15 ky. So how do we explain this?


To make matters worse, America's native population fell to half or even less during the period of discovery and conquest. How many languages were wiped out before even being discovered? Even so, it has the highest global language diversity.


The origin of languages


Human beings speak, and we are all aware that Chinese and English sound different, that Spanish, Italian and French may seem similar but are also different. We are humans and speak different languages despite having a common origin.


An early attempt to explain this can be found in the Bible (Genesis 11: 1- 9): "... But the Lord came down to see the city and the tower the people were building. 6 The Lord said, 'If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them. 7 Come, let us go down and confuse their language so they will not understand each other.'" So God made us all speak different languages by an act of his almighty power. Neat and simple.


But we now know that humans originated longe before any ziggurats were built in Mesopotamia. Language is something that arose tens of thousands of years ago. According to Chomsky, Tattersall, Bolhuis and Berwick (2014), "The faculty of language is likely to have emerged quite recently in evolutionary terms, some 70,000–100,000 years ago" [3]. Of course (I have posted on this before) that date range is not inferred from language studies, it is taken from the date suggested by anthropologists as the date of emergence of Modern Homo sapiens. So if that date was not correct, then the date given for the origin of languages is also incorrect.


In fact, our next of kin, the Neanderthals, could and did speak: "From the consilience of evidence from anatomy, archeology, and DNA, one can conclude that some language abilities, if not necessarily full modern syntactic language, were present in Neanderthals" so perhaps the ability to speak in Neanderthals predates that in humans. [4]


Daniel Nettle [2] suggests that people living near the Equator live easier lives regarding food supply and can split into smaller groups, which favours creation of new languages: "Where the climate allows continuous food production throughout the year, small groups of people can be reliably self-sufficient and so populations fragment into many small languages. Where the variability of the climate is greater, the size of social network necessary for reliable subsistence is larger, and so languages tend to be more widespread."


And this makes sense, as you can see in the map below, language diversity is highest close to the warm equatorial areas:


The diversity of Languages: location of highest densities. A. Whittall

Interesting, but this explains the evolution of languages during the last 11,000 years after the discovery of agriculture. I cannot imagine a large society of hunter-gatherers all speaking the same language, but one of farmers and tax collectors does make more sense.


But how fast do languages evolve? Take Australian English and English English or American English. They Aussies and Americans split from the mother tongue between 250 and 400 years ago, and did keep in touch with the distant British Metropolis yet evolved distinct stress and intonation for the same words. Something similar has happened with Spanish in the different Latin American countries and Spain over the past 500 years. But change has been small perhaps due to the lack of isolation.



The image above, from L. Luca Cavalli-Sforza & Marcus W. Feldman clearly shows that American languages are different to those in Asia, the "source" of the Native Americans' ancestors. This is surely conveniently explained by the "Beringian standstill" (how convenient) which allowed the future Amerindians to differentiate from those remaining behind in Asia.


Last but not least, I usually read that all indicators of genetic diversity fall as you move away from Africa, a clear indication of an African origin for all human beings. But, this is not seen in the case of human language diversity. Why?


I do believe that we should look into language diversity as an indicator of an older origin for mankind as a whole and for an earlier date for the peopling of America.


For those interesting in reading about this subject in depth, German Dziebel has written about linguistic diversity in support of his Out of America theory. Read More, and see an analysis of it here.


Sources


[1] Mobility and Ancient Society in Asia and the Americas, pp 117-126, chapter " How America Was Colonized: Linguistic Evidence. Johanna Nichols
[2] Explaining Global Patterns of Language Diversity, Daniel Nettle, journal of anthropological archaeology 17, 354–374 (1998) article no. AA98032
[3] Bolhuis JJ, Tattersall I, Chomsky N, Berwick RC (2014) >How Could Language Have Evolved? PLoS Biol 12(8): e1001934. doi:10.1371/journal.pbio.1001934
[4] Language Abilities in Neanderthals By:Johansson, S (Johansson, Sverker) ANNUAL REVIEW OF LINGUISTICS, VOL 1 Book Series: Annual Review of Linguistics Volume: 1 Pages: 311-332 DOI: 10.1146/annurev-linguist-030514-124945 Published: 2015


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

Thursday, October 15, 2015

An earlier dispersal of Modern Humans or an Asian origin for mankind?


A very interesting paper by Liu, W. et al. in Nature The earliest unequivocally modern humans in southern China http://dx.doi.org/10.1038/nature15696 (2015) reports having found modern human teeth in Southern China that are at least 80,000 years old, and up to 120,000 years old. This is clearly at odds with other papers that suggest a much later "Out Of Africa" event.


The Abstract reads:


"The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started."


In the article (by some odd miracle I was granted Online access to the article by the nature.com content sharing initiative) it mentions that: "This evidence could support different origins and/or dispersal routes for modern humans across Asia". And indeed it does. Here we have humans in China 80 to 120 kya while they failed to reach Europe until 35 to 75 kya. The authors attribute this to the fact that: "... the possibility that H. Neanderthalensis was for a long time and additional barrier for modern human's expansion...".


An article by E. Callaway also in Nature includes this interesting comment: "Although Hublin says there is a good case that the Daoxian teeth are older than 80,000 years, he notes that several of the teeth have visible cavities, a feature uncommon in human teeth older than 50,000 years. “It could be that early modern humans had a peculiar diet in tropical Asia,” he says. “But I am pretty sure that this observation will raise some eyebrows." Martinon-Torres says her team plans to look more closely at the cavities and the diet of the Daoxian humans by examining patterns of tooth wear."


Dental cavities are much older than mankind. Cavities have been found in a distant relative, the Paranthropus robustus, that lived in Africa 2 million years ago. However the bacteria that causes tooth decay seems to have become more prevalent among humans after the invention of agriculture. Perhaps because it provided more carbohydrates in the diet, a good source of sugars for the tooth-decay bacteria. Nevertheless, a diet with plenty of fruit in subtropical China could also cause cavities.


The idea of an ancient dispersal out of Africa and admixture in Asia with even more archaic migrants is not new and has recently received support (see: Early modern human dispersal from Africa: genomic evidence for multiple waves of migration (2015), Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani. doi: http://dx.doi.org/10.1101/022889). However others have contended that dispersal took place only recently (See: Levantine cranium from Manot Cave (Israel) foreshadows the first European modern humans (2015), Israel Hershkovitz, et al., Nature 520, 216–219 (09 April 2015) doi:10.1038/nature14134) some 60 to 40 thousand years (kyr) before present (BP) as demonstrated by the former oldest remains of modern H. sapiens outside of Africa at Manot Cave (Western Galilee, Israel) dated to 54.7 +/- 5.5 kyr BP.


There has been another paper by Wu Liu et al., (2010). (Human remains from Zhirendong, South China, and modern human emergence in East Asia, PNAS 19201–19206, doi: 10.1073/pnas.1014386107) which clearly states that: "...The Zhiren Cave human remains, securely dated to at least 100 kya (early MIS 5), therefore represent the oldest evidence of derived modern human morphology in East Asia....The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia."


So, how did these modern humans reach China 80 to 120 Kya? Did they leave Africa even earlier? Did they originate outside of Africa?


Apparently the old peopling wave some 130 kya proposed by Hugo Reyes-Centeno, Silvia Ghirotto, Florent Détroit, Dominique Grimaud-Hervé, Guido Barbujani, and Katerina Harvati ( Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia. PNAS, April 21, 2014 DOI: 10.1073/pnas.1323666111) is a fact. The South Asian route could explain an early modern H. sapiens in south China.


But there was admixing with other archaic people in Asia, the Denisovans are one of those groups, and did mix into the ancestors of Melanesians.


An early 130 kya wave of humans may have also headed north and then west, into America, reaching the New World 100,000 years earlier than what is now currently accepte...



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