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MIDutch

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#1
Aug 30, 2012
 
http://www.sciencedaily.com/releases/2012/08/...

ScienceDaily (Aug. 28, 2012) Max Planck researchers have described the Denisovan genome, illuminating the relationships between Denisovans and present-day humans.

The analyses of an international team of researchers led by Svante Pbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, show that the genetic variation of Denisovans was extremely low, suggesting that although they were present in large parts of Asia, their population was never large for long periods of time. In addition, a comprehensive list documents the genetic changes that set apart modern humans from their archaic relatives. Some of these changes concern genes that are associated with brain function or nervous system development.

In 2010 Svante Pbo and his colleagues sequenced DNA that they isolated from a finger bone fragment discovered in the Denisova Cave in southern Siberia. They found that it belonged to a young girl of a previously unknown group of archaic humans that they called "Denisovans." Thanks to a novel technique which splits the DNA double helix so that each of its two strands can be used for sequencing, the team was able to sequence every position in the Denisovan genome about 30 times over. The thus generated genome sequence shows a quality similar to genomes that have been determined from present-day humans.

In a new study, which is published in this week's issue of the journal Science, Svante Pbo and his colleagues compare the Denisovan genome with those of the Neandertals and eleven modern humans from around the world. Their findings confirm a previous study according to which modern populations from the islands of southeastern Asia share genes with the Denisovans. In addition, the genomes of people from East Asia, and South America include slightly more genes from Neandertals than those of people in Europe: "The excess archaic material in East Asia is more closely related to Neandertals than to Denisovans, so we estimate that the proportion of Neandertal ancestry in Europe is lower than in eastern Asia," the Leipzig researchers report.

"This is an extinct genome sequence of unprecedented accuracy," says Matthias Meyer, the lead author of the study. "For most of the genome we can even determine the differences between the two sets of chromosomes that the Deniosovan girl inherited from her mother and father." From this the researchers can tell that genetic variation of the Denisovans was lower than in present-day humans. This is likely due to that an initially small Denisovan population that grew quickly while spreading over a wide geographic range. "If future research of the Neandertal genome shows that their population size changed over time in similar ways, it may well be that a single population expanding out of Africa gave rise to both the Denisovans and the Neandertals," says Svante Pbo, who led the study.

The researchers furthermore generated a list of about 100,000 recent changes in the human genome that occurred after the split from the Denisovans. Some of these changes affect genes that are associated with brain function and nervous system development. Others possibly affect the skin, the eye and dental morphology. "This research will help determining how it was that modern human populations came to expand dramatically in size as well as cultural complexity while archaic humans eventually dwindled in numbers and became physically extinct," says Svante Pbo.

Earlier this year, the Leipzig researchers had already made the entire Denisovan genome sequence available to the broader public by publishing it online.

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REAL science doing REAL research.

And demonstrating that only one side of the SCIENCE vs. bronze age FAIRY TALES "debate" has any scientific research and empirical evidence in support.

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#2
Aug 30, 2012
 
http://www.topix.com/forum/us/T9QUH2OMJGJK10D...
Various posts address a later connection with homo-sapiens.
Besides Sumer/melanesian austrasians moving to south-america initially, for Denizovan genes are also found in those populations.

The article woud suggest either a very ast evolving genome in Denizovans, or a very early split from humans.
Genome changge went faster in humans once they had the last split from apes. 25 genomes per 100,000 years.(or was it 1 M year, makes a huge difference. We are different by 154 genomes?)
I'm not sure whether that can be used one on one so to say.
grin redo or rather reread everything sofar on the topic.

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#3
Aug 30, 2012
 
MAAT wrote:
I was frankly looking for genetic links:
The usefullness of haplogroups to study migration
What ancient KIN-EN-GIR (Sumerians=exoname) have in common with f.i. Melanesians (and Denisovans) Japanese and some other groups, plus and alternative route that bypassed China and an added sea-route.
http://www.fossilsscience.com/research/Feces_ ...
Which can be linked to the changed or missing allele for aldehyde dehydrogenase.(see further on for the working link.)
-The article i read was a bit vague, too vague on what happened or had happened to the allele, apperently is was missing, so people get more diabetes and addiction to alcohol, but can easier shift to use of lipids instead of glucose.
Common traits as we shall see.
Ancient Sumer skeletons were dug up and assessed showing afro-australasian traits.
Links with New-Guinea and Melanesia established.
Those again turned out to have Denizovan (Altai area) genes. So i took it from there.
http://asiapacificuniverse.com/pkm/austro.htm
http://users.on.net/~mkfenn/page8.htm
http://www.biomedcentral.com/1741-7015/10/40
http://www.thefreelibrary.com/The+genetics+of ...
Well i have to type them in so let's hope it went allright.
http://www.fossilscience.com/research/Feces_f ...
Since i wondered whether they would also be more prone to diabetes given the effect of ALDH2.
But in short: we can link Altai Denizovans (Altai the origin of appels)with Sumerians - that traveled back and forth it seems, Malai Moken and Uruk Lawoi,Java, New Guinea Japanese, Mariana , Melanesia and Polynesia, Uru and Aborigines from Australia and Tasmania with Native Americans of the South and Baja Californa in customs.
We have depictions of boats with 30 people.
it seems that a viable population needs at least 38 individuals.

Homo sapience did have an earlier migration and then a later one.
They found a skeleton in Kenia of yet another hominid in Africa, so that would make two that could have combined with African genes.
Provisional list:
Neanderthal with Denizovans
Both might be of the same genus with just smal but teling differences.
They again might have had contact with homo-erectus.
That were apparently also widespread and overlapped our timeline.
So contact might also have been possible.
Denizovan with Sumerians (link worked out in above post)
HS with Homonids.
Neanderthal in Europe.
Pekingman in China (though some studis suggest that slanted eyes is a comparatively recent developement)
Homo Erectus in Austro-aborigines.

They also found evidence of Giganthropus.
A 750.000 y.o. homonid found near the Murrimbidgee river, that lived till as recently as 10,000 y.a. in Australia. They found an axehead of 25 kg!
Also a conclusion that we had two different peoples in Australia: former aborigines and the later URU.
And we have Flores people that where thought to be a smaller version of local pygmees or New Guinea highlanders of 120,000 y.a. I can't recall whether they ended up being classed as a seperate genus.

DNA of Austro-aborigines was found in skeletons in Panama, California and Tierra del Fuego, some 40,000 y.o. part of a then widespread expansion.
The Sumerians KI-EN-GIR are thought to have invaded/migrated to Sumer as part of Uru expansion. A traveling bunch.
Uru of the Kimberlies (I'm now comparing cultural traits such as f.i.engravings of the huge man in rock-art and matrix- art.)depict ing dancing maidens est. 17,000-80,000 y.a.
To sumer they brought stories of lord Anu and Melanesian Tutuwa (all life force mother) So Gilgamesh allegorically killes tattood TuTuwa-life in the time of the flood. Comet in the Iraqi marches ~2300 BC

Lately skeletons were found in israel of modern humans dated ~200,000 y.o.
So out of Africa migration seems to have had several waves.
Arbil was f.i. continously inhabited since 150,000 years ago.

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#4
Aug 30, 2012
 
Homo sapience did have an earlier migration and then a later one.
They found a skeleton in Kenia of yet another hominid in Africa, so that would make two that could have combined with African genes.
Provisional list:
Neanderthal with Denizovans
Both might be of the same genus with just smal but teling differences.
They again might have had contact with homo-erectus.
That were apparently also widespread and overlapped our timeline.
So contact might also have been possible.
Denizovan with Sumerians (link worked out in above post)
HS with Homonids.
Neanderthal in Europe.
Pekingman in China (though some studis suggest that slanted eyes is a comparatively recent developement)
Homo Erectus in Austro-aborigines.

They also found evidence of Giganthropus.
A 750.000 y.o. homonid found near the Murrimbidgee river, that lived till as recently as 10,000 y.a. in Australia. They found an axehead of 25 kg!
Also a conclusion that we had two different peoples in Australia: former aborigines and the later URU.
And we have Flores people that where thought to be a smaller version of local pygmees or New Guinea highlanders of 120,000 y.a. I can't recall whether they ended up being classed as a seperate genus.

DNA of Austro-aborigines was found in skeletons in Panama, California and Tierra del Fuego, some 40,000 y.o. part of a then widespread expansion.
The Sumerians KI-EN-GIR are thought to have invaded/migrated to Sumer as part of Uru expansion. A traveling bunch.
Uru of the Kimberlies (I'm now comparing cultural traits such as f.i.engravings of the huge man in rock-art and matrix- art.)depict ing dancing maidens est. 17,000-80,000 y.a.
To sumer they brought stories of lord Anu and Melanesian Tutuwa (all life force mother) So Gilgamesh allegorically killes tattood TuTuwa-life in the time of the flood. Comet in the Iraqi marches ~2300 BC

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#5
Aug 30, 2012
 
sorry, the forum reacts a bit slow this morning.

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#6
Aug 31, 2012
 

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#7
Aug 31, 2012
 
Also by Svante Paabo the Neanderthal genome.
99,5% similarity with modern humans.
http://www.msnbc.msn.com/id/29171854/ns/techn...

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#8
Aug 31, 2012
 
http://arstechnica.com/science/2010/05/neande...
Most significant similarities and differences in protein-coding.

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#9
Sep 1, 2012
 

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#10
Sep 1, 2012
 
Ha..no challenge.
Quote:
Lying at the intersection of what is today Russia, Mongolia, China and Kazakhstan, the region known as the Altai "is a key area because it's a place that people have been coming and going for thousands and thousands of years," said Theodore Schurr, an associate professor in Penn's Department of Anthropology. Schurr, together with doctoral student Matthew Dulik and a team of graduate students and postdoctoral researchers, collaborated on the work with Ludmila Osipova of the Institute of Cytology and Genetics in Novosibirsk, Russia.

Among the people who may have emerged from the Altai region are the predecessors of the first Native Americans. Roughly 20-25,000 years ago, these prehistoric humans carried their Asian genetic lineages up into the far reaches of Siberia and eventually across the then-exposed Bering land mass into the Americas.

"Our goal in working in this area was to better define what those founding lineages or sister lineages are to Native American populations," Schurr said.

The team's study, published in the American Journal of Human Genetics, analyzed the genetics of individuals living in Russia's Altai Republic to identify markers that might link them to Native Americans. Prior ethnographic studies had found distinctions between tribes in the northern and southern Altai, with the northern tribes apparently linked linguistically and culturally to ethnic groups farther to the north, such as the Uralic or Samoyedic populations, and the southern groups showing a stronger connection to Mongols, Uighurs and Buryats.

Schurr and colleagues assessed the Altai samples for markers in mitochondrial DNA, which is maternally inherited, and in Y chromosome DNA, which is passed from fathers to sons. They also compared the samples to ones previously collected from individuals in southern Siberia, Central Asia, Mongolia, East Asia and a variety of American indigenous groups. Because of the large number of gene markers examined, the findings have a high degree of precision.

"At this level of resolution we can see the connections more clearly," Schurr said.

Looking at the Y chromosome DNA, the researchers found a unique mutation shared by Native Americans and southern Altaians in the lineage known as Q.

"This is also true from the mitochondrial side," Schurr said. "We find forms of haplogroups C and D in southern Altaians and D in northern Altaians that look like some of the founder types that arose in North America, although the northern Altaians appeared more distantly related to Native Americans."

Calculating how long the mutations they noted took to arise, Schurr's team estimated that the southern Altaian lineage diverged genetically from the Native American lineage 13,000 to 14,000 years ago, a timing scenario that aligns with the idea of people moving into the Americas from Siberia between 15,000 and 20,000 years ago.

Though it's possible, even likely, that more than one wave of people crossed the land bridge, Schurr said that other researchers have not yet been able to identify a similar geographic focal point from which Native Americans can trace their heritage.

End quote---
northern altai, though that could include Denizovans.
In any case worth keeping a sharp eye on, lest my theory be challenged.
Sofar no Denizovan has been found in Northern native -Americans.
The rest of the site also provides interesting information.

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#11
Sep 1, 2012
 
Svante Paabo's research was published 30 August 2012 in Science. Scientific American provided that information. Nature also had an article.
In the meantime i googled for: H17 and Denizovan genes. A lot of hits.
http://forwhattheywereweare.wordpress.com/201...
Interesting blog, up to date. F.i. basques are nothing special, just culturally more secluded.
This blog has material gathered for easy reading.
Denizovan had black skin, brown eyes and hair.
Split of 700,000 y.a.
Some have suggested for new names Homo Sapiens Neanderthalens and Homo Sapiens Denizovans given that so little seperates us.

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#12
Sep 1, 2012
 
http://www.scientificamerican.com/article.cfm...
http://www.lifescience.com/16171-denisovans-h...
Florensies might get a revisit to undo the botch job, so as to finally provide us with an answer.

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#13
Sep 1, 2012
 
https://docs.google.com/viewer...
An overview and list of literature on what used to be called 'The Sumerian problem'.
Ineresting: in north-western Iraq neanderthalens used to live.
Arbil has been a continous habitat for 150,000 years. If any admixture this should be rich grazing ground.

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#14
Sep 1, 2012
 
An article from 2007 still hinting at the blackhaired interpreted translation by Armenians and for some weird reason also dragging Aryans and Tibetans in the mix.(Found an article on a russian site. About the city of Airkaim -if my recall is correct- that the Aryans abandoned 4000 ya or 4000 BC. Quite unclear what a group of mountain people from what we could loosely call Elam/Iran that consisted of cow herders with a superiority complex, who relatively late, say 150 BC made their way into India, might have to do with that dig. Sanskrit is not all that old as it is claimed to be.
Aryans as far as i could find is quite a blown-up title ented upon the liguistic roots so to say of Europe, before other inter-cultural theories came into play.
The distinction is not made regarding the skeletons, or rather so broad that it could cover any and all.
http://www.armeniapedia.org/index.php...

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#15
Sep 1, 2012
 
Inter-cultural:
Ancient tablets in Romania predating Sumer but with similar inscriptions. Decent pics to make a comparison.
http://www.abovetopsecret.com/forum/thread668...
It does pay to visit these conspiracy- and ufo fora occasionally.

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#16
Sep 1, 2012
 
Sigh...swamped in giants.
But there is always Dienekes Anthropology blog.
Googling: Sumer Melanesia DNA...we get:
http://dienekes.blogspot.nl/
Starts with Denizovans.
26 august 2012 world9
And a bit later we see Anatolia as the homeland of the socalled indo-european language-family.

There are stronger cultural clues in tribal archeological and recent customs, nevertheless;
Some intriguing pottery found in the south-america's first dealt with as a hoax.
http://jszostak.webs.com/View%20The%20Evidenc...

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#17
Sep 1, 2012
 
Ethnoepidemiology of HTLV1 related diseases Ethnic determinants of HTLV1 susceptibility and its worldwide dispersal hsc_journal01.pdf
https://docs.google.com/viewer ?...
In case the link does not work.

problem.
A )We either interbred with our 'cousins'...
1) We thus got HLA antibody genes in one go, that are used to determine where we more or less originated and belonged.
The negative option supposes several big changes.
B )We did not interbreed but got HLA allele from concestors:
2) We acquired and developed HLA irrespective of place of origin.
3)We split earlier for chimpanzees
4)We then had a Neanderthalens split.
5)We later had a Denizovan split.
With maybe more hominids somewhere in between that as concestors provided the HLA.

Furthermore not all tribes in South-America and ancient bones have been charted.

Why are HLA alleles important?
https://docs.google.com/viewer... *11+found+in+South-America &hl=nl&gl=nl&pid=b l&srcid=ADGEESjzd7zQaJm282 cxZ__GgAxhR0UfJjAEHQBtRhu8GMeR XKxaqLi5xSoaZXILT0y5-3V34qA3F0 2XEToGd2GpLAGn8t6QM0fGNP1EZdhv 6tLq87MM5t-4aeuID7_zUhbsrFKAYU TF&sig=AHIEtbSepJ3yqArBCpO WBnqYfPFKSKjCMg

The funny, in the sense of remarkable, fact is however that specificly also those with high linkage to Neanderthaelens and Denizovans are involved (65% S.E Asian and 90% Melanesian f.i. HLA-A*11) as well as an Andean mummie found in the Atacama.
Further Reading to get an overview:
http://www.sciencemag.org/content/334/6052/89...
http://austhrutime.com/australian_aboriginal_...
See bottom link 5 to a.o.
http://www.cosmosmagazine.com/news/4670/ancie...
http://www.cosmosmagazine.com/news/3943/finge...
You will find that other news items are referenced and accessable.
One will state that we did not interbreed and a later one that our bodyshapes where well suited to do so, suggesting we did.

A lot hinges on this, though if i recall properly the oncogenic study had found a different way to determine 'familiarity' and proper timeframes.

Also interesting for perusing:
http://www.sciencedaily.com/releases/2012/01/...

HTLV1 is linked unusually to two diseases, dependent on what HLA one has.
Another ERV.
Krause or Kreis (Not sure whether they are the same person or two people) goes al the way for option A, Svante Paabo given what it all entails ditters but still supposes B.
There must be a way to figure who is right.
Maybe it is convenience that decides this choice for now, but it might turn out to be a half-truth.

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#18
Sep 2, 2012
 
Class I discovered since 1993 and studied ever since.
HLA-A
six families A2/28, A1/3/11, A9, A10, A80 and A19.
A19 does not form one closely related clade.
The Allele devided into two divergent groups, in support of Kato et al.findings (A29, A31, A32,Aw33 probably not A30) suggesting a more complex evoutionary history.
On the whole however we get a consistent phylogenetic tree.

HLA-B
High levels of inter allelic recombination for over 5 million years.
Lack of comprehensively identifiable evolutionary relationships.

HLA-C (also saw it caled pseudogenes)
The most modern and more closely related to HLA-B by duplication, Homologues identitifiable in chimp and gorilla but not in Asian Old World Monkeys.
It either points to a recent ancestor or more likely a cell specific role: NK cell regulation.

Serological connections are also different.
Phylogenetic trees are provided.
The markedly high levels of polymorphism present in classical class I loci of the human major histocompatibility complex
have been implicated in infectious and immune disease recognition. The large numbers of alleles present at these loci
have, however, limited efforts to verify associations between individual alleles and specific diseases. As an approach to
reduce allele diversity to hierarchical evolutionarily related groups, we performed phylogenetic analyses of available HLA-
A, B and C allele complete sequences (n = 216 alleles) using different approaches (maximum parsimony, distance-based
minimum evolution and maximum likelihood). Full nucleotide and amino acid sequences were considered as well as
abridged sequences from the hypervariable peptide binding region, known to interact in vivo, with HLA presented foreign
peptide. The consensus analyses revealed robust clusters of 36 HLA-C alleles concordant for full and PBR sequence
analyses. HLA-A alleles (n = 60) assorted into 12 groups based on full nucleotide and amino acid sequence which with
few exceptions recapitulated serological groupings, however the patterns were largely discordant with clusters prescribed
by PBR sequences. HLA-B which has the most alleles (n = 120) and which unlike HLA-A and -C is thought to be subject
to frequent recombinational exchange, showed limited phylogenetic structure consistent with recent selection driven
retention of maximum heterozygosity and population diversity. Those allele categories recognized offer an explicit
phylogenetic criterion for grouping alleles potentially relevant for epidemiologic associations, for inferring the origin of MHC
genome organization, and for comparing functional constraints in peptide presentation of HLA alleles.

Keywords: evolution; HLA; phylogenetic; peptide binding region
MS395_McKenzie.pdf
https://docs.google.com/viewer ?...
7hugh.pdf
Cytotoxic T-Lymphocyte Escape Mutation Identified by HLA Association Favor Those Which Escape and Revert Rapidly
http://jvi.asm.org/content/86/16/8568.figures...

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#19
Sep 2, 2012
 

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#20
Sep 2, 2012
 
https://docs.google.com/viewer...
Hughes: origen and evolution of class 1 pseudogenes.
So we learn that they are all called pseudogenes.

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