Denisovan's strike again

[Green Baron]

It does actually gloriously and happily confirm what Archaeology has suggested before. As it did in Sardinia (see above) or, for example, the picture of the migration of modern humans into Europe. As can be read on Wikipedia. Contradictions that without doubt exist will be solved [snip]

Edited March 25, 2018 by Vanamonde

[PB666]

8 hours ago, Green Baron said:

It does actually gloriously and happily confirm what Archaeology has suggested before. As it did in Sardinia (see above) or, for example, the picture of the migration of modern humans into Europe. As can be read on Wikipedia. Contradictions that without doubt exist will be solved

[snip]

When i point the finger at PA i am pointing the finger at their interpretation. not neccesarily at the data but this may include the comparative techniques that they use. When does one find impetus to redate a sample, is it often not done because of critiques. . . . . .remember LM3. Critique is good as long as you dont take it personally. Thirne may have not been right but he convinced Bowler to redate LM3 which resulted in an earlier dating of LM3.

If you want an abstract critique of the problem I can make the point like this. There is a progression of natural events and the interpretation of those events. What archaeology does is gather information that places data points. For example you go to Jamestown virginia and knowing the history you can provide further interpretation. 

In an example like Sardinia, you can interpret the first evidence of occupation, but this should not be interpreted as the first occupation. But unfortunately this is what archaeology does. For example pottery usage can be traced along the mediterranean, but the problem is that pottery use is associated with certain contexts, mostly cultivation and animal husbandry. What is the consideration of cultures that are purely coastal foragers?

So here in lies the problem, and its multifold. The First of the two problems is the stand. In Sardinia very old cultures will tend not to leave evidence if they were coastal foragers. The second problem is if they used largely soft tools for hunting and gathering they might also not leave much evidence. A third issue is how they buried the dead, if the dead were not intered, were cremated or dearticulated they may nit leave remains. If they buried their dead in acidic soils, the acids might dissolve and soften the bones into mush. It takes alot of things to go right to uncover the remains of ancient humans. 

Then there is the 'gee we didn't know' phenomena in which PA assumes a certain kind of progression, ans for instance in the New World finds multiple old skulls that have more adrican/melanesian features than Native American/siberian features. 

So what happened in Sardinia, the archaeology offers an North central and eastern mediterranean origin. Again, the key word is archaeology. When one looks at the immune genes, and particular 6p21.3 about 35% of the population carry DR3DQ2, which is not particularly an eastern European or Italian hap, as a matter of fact its under negative selection in the Eastern mediterranean for the last 8000 years. This frequency may not seem important, but its very high for a class II haplotype. And somthe question is, genetically, how did this come to be. The second problem is that DR3 splits DR17 (irish and norwegion are two mjor nodes in Europe) and DR18. Sardinians carry DR18, which tends to be found at highest frequencies in west africa. Then the next problem is more severe DR3DQ2 elongates with A30B18. The A30 is A*30:02. This is one of the highest/longest if not the highest geographically defined haplotype frequency in Europe possibly the world. This allele is in almost complete linkage disequilibrium in Europe, it is only found in the Basque and right along the italian/ french coasts at much lower frequencies and almost always in A30B18. It is not found in the greeks.  So then what is the origin of A3002; that is to say what place in the world has the highest observed recombination. That place is West Africa. Oddly despite the high frequency of the type there is scant evidence of other West Africa types in Sardinia, and only N. African types to the degree one expects with transmediterranean migration, a low smattering of haplotypes not of any particular remarkable frequencies. All the data can be found at www.allelefrequencies.net . . . . so no particular secrets there. For all to see. 

How does an allele from a cryptic source become so predominant relative to other haplotyes with such a long run of homozygosity. The answer any population geneticists knows, a regimen of inbredding or an acute population constriction can result in fixation, including immune gen fixation, over long enough time. How then does it become so cryptically predominant. . . . . .founder effect. So what does this say for the first occupation, either a complete replacement of a nascent founder effect. Again, this is a prediction that based on these long haplotypes that N.Mediterraneans  were not the first to settle Sardinian although they are the majority of the gene representation now, the contributor of the predominant 6p21.3 alleles for each locus are African. This represents the complexity of PA but not neccesarily visible the interpretation of physical anthropologist and archaeologist. 

There is a medical connotation to this also persistent chronic inflammatory diseases in Sardinia were some of the lowest in Europe, but as the modernization of Sardinia occurred these rates shot up very quickly, notably some of thr African DR3 effects seen in other populations that bear the varient. . . . .why i care about this issue, i used to study one of the 'caused' diseases. As I pointed out above when certain immune genes fix, people tend to get autoinflammatory disease when exposed to autoinflammatory agents (these are suprisingly ubiquitous and ignored in Western society), they may live absolutely happily eating fish and diving for clams, then overtime culture changes. 

Overtime i learned to not waste my time trying to figure out what archaeology got wrong; i assume its misinterpreted and then look for parsimony. In other instances people just asked me, you dont accept the ideas of Wolpoff or Brace, is there any reason you might believe in multiregionalism might exist. I have to remind people that i am not against admixture or multiregionalism. I am against interpretations that are not supported by a large perspective of supported facts. There were, even before N/H comparisons adequate evidence that admixture occurred, just not the way they said it occurred or to the degree they said it occurred.  So when i was asked I used they same available databases, allelefrequenies link. I went to the EBI databse, took every allele, took them apart and traced their origins back to africa. All alleles could be traced back to Africa, with general zero or one change. Afew could be explain by a couple synonous small changes or a major change. But there was a handful of types that did not easily fit a recent African model. I did not search these out to show anyone up, I was asked to look privately by friends who agreed with me about W&B but thought MR may still be acting in other specific areas. I looked, and i presented and then left the issue more than a decade ago. . . . my work in inflammation also done, left more than a year ago

Take these words or leave them, but similar  advanced interpretations of molecular anthropology will still march on indifferent of antiquated perspectives. The decision you have to make is whether you want to be up to date with evidence or live in some past era where physical anthropology went unchallenged to the point it could not correct serious errors in perspective (i.e. Eurocentrism, ladder-like evolution, ape theories)

[PB666]

[snip]

I am no longer following archaeology to any degre and haven't for a decade, I think i stated that. And you 'false claim' argument was neither explicit or clear. At that time the favored hypothesis is that it was settled from Greece. The post you made previous was so cluutered i missed the link, rather than have me go search through the garbage just repost it and state your argument clearly without the false claim perjorative. 

The modern human occupation of Iberia I considered unsettled science, so I am not bringing that into the debate, im only looking at a bit of evidence. My point was that humans could have and probably did overlap with N in Iberia, but they probably favored different areas. Does this constitute a geographic barrier, its hard to say. 

The point was this, [snip]The paper stated that 5 new European, plus the existing and i think two altai Neandertals have been sequenced not counting the Denisova type specimen. This is a body of evidence. While it is not comprehensive evidence for no evidence of directional mixing into Classical stg4 Neandertals it is a a very good running hypothesis that deserves at least tentative recognition. 

Secondarily, the point is that there is a meshing of African and European traits in Iberia that precede prehistory. One African trait is a genomic anomoly (its posseses the longest identifyable run of homozygosity in the human genome), and because of this its evolution can be dated and roughly placed in Iberia, that date was published to 20 ky and is highly identifyable as a Western European Haplotype. Even if you disregard the 70 to 150 kya date, there is a problem that arises in Iberia. Here is the genetic problem in total. 

The bits and pieces that form A1B8DR17DQ2 all appear to come from NW africa and these bits are strewn in the coastal population all the way down to the Bubi. IOW not only did this haplotype probably form in iberia, but the bits and pieces that formed it were in Iberia before it formed, probably 1000s of years before. 

So here we have a problem in that there is a relatively confined space, you have a gently declining backward probability that humans were present before 20 kya in iberia carrying classical SSA markers, and directly from Africa. The closest two points are Gibralter and the tip of Morooco on the other side. Then there is a gently falling with forward probability gradient that Neandertals survived starting around 26kya and sloping to zero at some unknown point before the end of the LGM. In that context we do not see any higher indication of admixture in peoples that carry the A1..Dq2 haplotype in higher frequencies. 

OK so no evidence of admixture specific to Iberia, what about elsewhere in Europe. Again looking at the evidence it is diificult to see any specific place in Europe or western Eurasia that is a mode of Neandertal introgression. Again one can draft an alternative hypothesis, but then one is bucking the genetics. So the best running hypothesis that it occurred at one place and time, with one type of Neandertal and not later with another type but that this does not rule out admixture at later times, in other places, with other types. Just the one type appears to be barred. Taken together, the lack of evidence, despite lots of data, of introgression either population into the other population the best running hypothesis is that a barrier should have existed.

Next we can move on to the last aDNA paper. This paper stipulates that around 20kya there were migrations across the southern mediterranean. This is not new, there is evidence as early as 8 kya ovids  were being move from SW Asia to Iberia via Africa, including evidence of one african bovid mtDNA. But this particular referenced genetic evidence is considerably before the Iberia mesolithic/neolithic boundary and before wavey-line poterry cultures in Africa. This indicates that human populations were in flux in North Africa. So what, this creates several contradictions, or do they. Here i present evidence of migrations into Europe from north Africa >20kya and later migration fro W. Africa into Sardinia, apparently much later, and in between we have migrations into the morroco from the middle east. So thats the North African complexity.

If we repeat these motions in N. Africa for long periods of time and admixture occurred in Africa between Neandertals (generic argument) could we later detect a node. From 70 kya, no, actually using immune genes its difficult to find cohesive modes that are even 20ky. So if it looks African or middle eastern admixture preference only depends on one thing, average flux. If the average flux is from Asia to Africa, the the mode sharpens in North or NW Africa assumming SSA is a barrier, if its from SSA to Asia, then later Iberia, then the mode dulls and disappears. This is why I postulate there are models of admixture in Africa that flush into Asia. 

This does not rule out that some early stage4 N went to Africa or middle east and mixed, but it does make it extremely unlikely that what mixed 70 to 150 kya was a 'full blooded' European Neandertal, and more likely a mixtures with hominimes that lived in the region. Oddly this probability has been roughly the same for since the  Tishkoff suggested the migration of low 100s of people back in the 90s. The current level of suggested admixture is roughly the tolerance limits of admixture into a migrating expanding population in which outcome mtDNA and Y are human and evidence of admixture is ambiguous (and thus controvertable between many studies). So that some of the 'bad' molecular studies werent bad, just recombination is a tempest when relative contributions are quantizable. The problem was that the number of sampled sites in any given study were two few to be conclusive. And that which was being sample was uncharacterized in terms of the form of evolution. 

So what is the global meaning in this? The meaning is this, 20 years ago there was mtDNA, Y, X-linked, autosomal, HLA studies . . . . as takahata concluded there was a certain inevitability to Out of Africa and he was right mostly. But there were also leaks in the bulwork, and potential leaks, if they exist, create significant contribution. But wait, thats a model.   its a kind of null hypothesis, we assumme that everything has the same origin (africa) and if in testing the hypothesis fails then we can test specific datasets (many local genomes sequenced and compared with others). If that then also fails the null hypothesis we have grounds for further analysis, including looking into aDNA comparisons of specific hominimes. Thats the way to approach the problem and avoid the errors of the past. 

Edited March 25, 2018 by Vanamonde

[Green Baron]

1 hour ago, PB666 said:

The modern human occupation of Iberia I considered unsettled science, so I am not bringing that into the debate, im only looking at a bit of evidence. My point was that humans could have and probably did overlap with N in Iberia, but they probably favored different areas. Does this constitute a geographic barrier, its hard to say. 

Last Neandertals (Chatelperronien) apparently retreated to the southwest of Iberia with a climatic deterioration after 30.000bp. I would say (and if you call for a proof i will try to find something) that it is improbable that there was no coexistence, as in southwestern France at that time we already have around 10.000 years of Aurignacien, which is the first cultural appearance strongly connected to modern humans.

Quote

Secondarily, the point is that there is a meshing of African and European traits in Iberia that precede prehistory.

Well, cough, nothing human related precedes prehistory per definition :-)

Quote

Even if you disregard the 70 to 150 kya date, there is a problem that arises in Iberia. Here is the genetic problem in total. 

I never did. I said the paper doesn't name a date for the mixture (nobody can at this time) but a group that separated from N before 70k. Which i will live with until it is corrected again :-)

Quote

The bits and pieces that form A1B8DR17DQ2 all appear to come from NW africa and these bits are strewn in the coastal population all the way down to the Bubi.

Sorry, i can't find anything about this ...

Quote

So here we have a problem in that there is a relatively confined space, you have a gently declining backward probability that humans were present before 20 kya in iberia carrying classical SSA markers, and directly from Africa. The closest two points are Gibralter and the tip of Morooco on the other side. Then there is a gently falling with forward probability gradient that Neandertals survived starting around 26kya and sloping to zero at some unknown point before the end of the LGM. In that context we do not see any higher indication of admixture in peoples that carry the A1..Dq2 haplotype in higher frequencies.

Modern humans (Aurignacien) in Cantabria date to 32.000bp. I must admit that it's 15 years since i last was deeper into that and will have to look up the find sites and their interpretation if asked. Early upper palaelithic in Portugal dates to at least 24.000bp (Lagar Velho). So that seems to be all on the same rail.

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 OK so no evidence of admixture specific to Iberia, what about elsewhere in Europe.

Well, that is not that clear. Lagar Velho 1 could be interpreted as a hybrid. It is still an open question.

Quote

Taken together, the lack of evidence, despite lots of data, of introgression either population into the other population the best running hypothesis is that a barrier should have existed.

Well, then that's a fro and to and one best awaits the future. My last stand is that the DNA evidence of interbreeding is solid, and that is just 2 years ago. Find sites almost leave no other interpretation. So, where is the work that says otherwise ? The above surely doesn't !

https://www.sciencemag.org/news/2016/02/humans-mated-neandertals-much-earlier-and-more-frequently-thought

https://www.sciencemag.org/news/2015/01/humans-and-neandertals-likely-interbred-middle-east

Hypothetically, could it be that poor preservation or preparation, contamination, handling and deterioration still might have a slight influence on some of the analyses ?

Quote

Here i present evidence of migrations into Europe from north Africa >20kya and later migration fro W. Africa into Sardinia, apparently much later, and in between we have migrations into the morroco from the middle east. So thats the North African complexity.

Where is it ? Am eager to read !

[rest snipped, i am having a problem finding a clear line ...]

Edited March 25, 2018 by Green Baron

[PB666]

2 hours ago, Green Baron said:

Well, that is not that clear. Lagar Velho 1 could be interpreted as a hybrid. It is still an open question.

Zilhoa tends to think so, but he is in the Trinkhaus camp.

2 hours ago, Green Baron said:

Well, then that's a fro and to and one best awaits the future. My last stand is that the DNA evidence of interbreeding is solid, and that is just 2 years ago. Find sites almost leave no other interpretation. So, where is the work that says otherwise ? The above surely doesn't !

https://www.sciencemag.org/news/2016/02/humans-mated-neandertals-much-earlier-and-more-frequently-thought

https://www.sciencemag.org/news/2015/01/humans-and-neandertals-likely-interbred-middle-east

Hypothetically, could it be that poor preservation or preparation, contamination, handling and deterioration still might have a slight influence on some of the analyses ?

[snip] we are talking specifically about European Neanderthals, [snip] My point was specifically made below that it was unlikely purely European Classic Neandertals and more likely what was called stage three or Levantine Neanderthals. What they refer to in the first article is Denisovan, which sophisticated molecular genetics handled separately, and BTW, given the reference that started this thread, more than one place with Denisovan.

Denisovans are a particularly early branch of Neanderthal, which you might compare with Arago or Early Sima de los heucos.

2 hours ago, Green Baron said:

Am eager to read !

http://blogs.discovermagazine.com/deadthings/2018/03/15/interbreeding-denisovans/#.WqsdGech2Ul

http://www.ox.ac.uk/news/2018-03-21-oldest-dna-africa-offers-clues-ancient-cultures

http://www.cell.com/cell/abstract/S0092-8674(18)30175-2

[snip]

There is a full article about the recent corroboration between Eastern Neandertals and human here.

You have to remember this tempers the argument why there is 4 to 6% Neandertal contribution in Koreans and Japanese and 2% in Iberia.

Quote

In the Japanese and Chinese (Dai, Beijing, and Southern Han) populations we see that the Denisovan cluster of segments has a wide and bimodal distribution of match rates to the Altai Denisovan genome (Figure 4). A test for two distinct components of Denisovan ancestry (see the STAR Methods) is statistically significant (p < 0.05 after adjusting for multiple testing) in each of these four populations (Table 2) but is not significant in the other 1000 Genomes populations -http://www.cell.com/cell/fulltext/S0092-8674(18)30175-2

Again this was predicted many years ago, not the beast, but that there was probably another beast out there and it goes now by the name Denisovan.
 

While you may not see it this is how actually the issue of admixture gets worked out. People make predictions and eventually the predictions are tested, it helps however if the prediction has a basis.

Quote

Lack of Evidence for Multiple Waves of Neanderthal Ancestry

The frequency of Neanderthal introgression is substantially higher (∼30%) in East Asians than in Europeans (Meyer et al., 2012, Wall et al., 2013). This difference cannot be explained by differential effects of selection, but could be due to an additional Neanderthal admixture event into the ancestors of East Asians after the Europe-Asia split (Kim and Lohmueller, 2015, Vernot and Akey, 2015). Another possible explanation would be dilution of Neanderthal admixture in Europe due to migration from a population without Neanderthal admixture (Meyer et al., 2012, Vernot and Akey, 2015). -http://www.cell.com/cell/fulltext/S0092-8674(18)30175-2

As I stated there is substantial evidence from Iberia from the second, gene flow that after the LGM spread into the rest of Europe.
 

Quote

There is also no clear difference between East Asians and Europeans in the similarity of their Neanderthal-introgressed segments to the Vindija 33.19 Neanderthal (Figure S4). Thus, if the ancestors of East Asians received a large pulse of Neanderthal admixture after splitting from Europeans, then the original (shared Eurasian) and additional (East Asian-specific) admixing populations must have been closely related. -http://www.cell.com/cell/fulltext/S0092-8674(18)30175-2

 In order to understand the problem you need to first read this paper.

https://www.ncbi.nlm.nih.gov/pubmed/24162011

This informs as well reducing the African genes that are also given by Non-African hominim contribution (excluding the pygmy contribution, which Tishkoff deals with in another paper).

From this again depending on where and how much the introgression could have been in Africa. Tishkoffs analysis is through, but she cannot model what cannot be seen and the flux in super-equitorial Africa is particularly an unseen quality.

 

 

Edited March 25, 2018 by Vanamonde

[PB666]

For the amateur molecular anthropologist out there here are some resources mentioned today.
Here is European bioinformatics institute. (EBI) hooray Europeans!

https://www.ebi.ac.uk/ipd/imgt/hla/

https://www.ebi.ac.uk/ipd/imgt/hla/allele.html

http://allelefrequencies.net/default.asp

The Neanderthal genome browser, currently 5 (and growing) https://bioinf.eva.mpg.de/jbrowse/?loc=1%3A99696709..149546833&tracks=&highlight=

Run you fingers through some Neandertal DNA (pretty boring unless you know what you are looking for).

 

 

 

 

 

[Green Baron]

1 hour ago, PB666 said:

Zilhoa tends to think so, but he is in the Trinkhaus camp.

Camp ?

[snip]

Quote

Denisovans are a particularly early branch of Neanderthal, which you might compare with Arago or Early Sima de los heucos.

Huesos. Arago is Homo erectus (You mean Tautavel, right ?). Atapuerca the same, maybe early heidelbergensis. There is no genetic information from these.

Quote

http://www.cell.com/cell/abstract/S0092-8674(18)30175-2

Snipped pop science. The cell article has nothing to do with migration of Africa into Europe or Sardinia. It is about interbreeding, based on one (1) Denisovan individual and a pack of Neandertals. Relevance ?

Quote

https://www.ncbi.nlm.nih.gov/pubmed/24162011

Yeah. It states older mixture not supported in Africa, newer more probable. Actually a contradiction to your claim that several waves migrated directly out of Africa into Europe. Got the wrong paper ?

 

1 hour ago, PB666 said:

As I stated there is substantial evidence from Iberia from the second, gene flow that after the LGM spread into the rest of Europe.

What ? Neandertals after the last glacial maximum ? Together with Dinosaurs ? I'm sure there is genetic evidence

Edited March 25, 2018 by Green Baron

[Vanamonde]

A whole mess of personal remarks have been trimmed from this thread. If this keeps up, we'll have to just start closing threads about human evolution wherever they come up. 

[Green Baron]

Thanks, and sorry. Yeah, you're probably right ...

[PB666]

1 hour ago, Green Baron said:

Camp ?

[snip]

Huesos. Arago is Homo erectus (You mean Tautavel, right ?). Atapuerca the same, maybe early heidelbergensis. There is no genetic information from these.

Snipped pop science. The cell article has nothing to do with migration of Africa into Europe or Sardinia. It is about interbreeding, based on one (1) Denisovan individual and a pack of Neandertals. Relevance ?

Yeah. It states older mixture not supported in Africa, newer more probable. Actually a contradiction to your claim that several waves migrated directly out of Africa into Europe. Got the wrong paper ?

 

What ? Neandertals after the last glacial maximum ? Together with Dinosaurs ? I'm sure there is genetic evidence

Yes Arago, Arago and HdlH are sources of variation. Note that Denisovans have putatively erectine sequences in their DNA (ancient mtDNA and small amounts of primative sequence not in humans or other Neandertals.

When did we go back to discussing Sardinia, I was waiting to get a reference and clarify what you said earlier, still waiting.

Edited March 26, 2018 by PB666

[PB666]

2 hours ago, Green Baron said:

Yeah. It states older mixture not supported in Africa, newer more probable. Actually a contradiction to your claim that several waves migrated directly out of Africa into Europe. Got the wrong paper ?

Yes, that is correct and a point I made earlier. Normally I agree spot on with every thing Tishkoff says, but in this case, looking at the immune genes I cannot find a basis that either confirms or denies a north African versus middle Eastern admixture, in fact there is a bit of a slight bias for African, but this could be due entirely to recent backflow. From that perspective if the admixture did occur in N. Africa then there would be a stronger case for N contribution of common Eurasian immune genes (Namely 24:02 and a few others that concentrate in N.Africa and not other parts of SSA). From the Sahel to N.Africa the problem is there are more transflows than there are static elements. There are static elements but they are close to the S. edge and typically associated with groups with roots deeper in SSA. Tishkoff is mainly an expert on SSA and she is very familiar with some of the most long-term static populations in the world (of course I don't want to argue that I am an expert -or anyone else- on evolution of super equitorial Africa since humans left and spread). The manner in which Tishkoff paints the picture they admixed in SW Asia and then flow backwards in many directions into Africa and not specifically via N. Africa, In that model its easier to place these at the edge of L2/L3 expansion outward than to place them in the context of admixed  back flow specifically to N.Africa and avoiding S. Africa. In a two state model where some contribution originally comes from withing Africa at the time of admixing and other parts move into SW Asia, undergo drift and then move back into Africa again, its easier to see these. Technically her model is correct, Occam's razor requires a simplification of the hypothesis to the functional lower limit of complexity. 

Again taking the null hypothesis I have to allow for the possibility but in modeling assume it did not occur, and this again points to very low major antigen gene transfer from N to H relative to the contributions from D to H (which appears to be apriori of 4).

And there also has to be a qualification of some of the images. In terms of where this admixture occurred if in SW Asia, the models for human entry for M prefer the middle East and for N prefer S. Arabia, but N and M have very similar timings and likely entered at the same time or mixed at some later time, so there is no specification that humans went to the edge of where Neanderthals were commonly found and mixed with them, its simply uncertain. Over the broad range of uncertainty you have to also including NE Africa as a potential mixing place. The L3 and M combined (L3 is also found in India so it was also in the mix, M and N are derivatives) place a preference of initial entry on Horn of Africa (L3 modes in this region) and Arabia, but I don't think its plausible that Ns and Hs admixed in the Horn of Africa.

Anyway, as i have said take it or leave it. The papers I gave you are the state of the art, there is nothing that I can add today that improves upon these.

Edit: With regard to the https://www.ncbi.nlm.nih.gov/pubmed/24162011

I should point out that this is a foundation for comparing the more distilled SSA components from components of non-Africa origin. It more or less a template. later Tishkoff went on to write this paper indicating there were archaic derivative elements that mixed within Africa.

https://www.ncbi.nlm.nih.gov/pubmed/26888264

Therefore it is not completely outside the bounds of tolerance that some discussion of Neanderthal admixture in Africa occur in light of what she later wrote.

 

Edited March 26, 2018 by PB666

[PB666]

Since the PalAnth thread was blocked.

https://www.wolfcast.co.uk/all/2018/4/10/arabian-h-sapiens-fossil-key-information