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Wednesday, March 22, 2017

Southern European blues


Not sold on this; not unless we see direct evidence from ancient DNA:

Abstract: Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.

Pereira et al., Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe, Proceedings of the Royal Society B, Published 22 March 2017.DOI: 10.1098/rspb.2016.1976

151 comments:

xyyman said...

I told you so. "Near east" = African/North African. lol! More and more will come out to support. Lazaridis made it clear it was a North South cline. All DNA evidence supports this.

This is not rocket science. Europeans are depigmented Africans.

Romulus said...

Makes sense given that new Mesolithic Sardinian mtDNA.

Gioiello said...

More and more closer to the truth!

Rob said...

Very interesting
Could explain the pattern of R1b

xyyman said...

Typical games they play. They never consider the real migration path. From Sahara Africa to Europe and the Near East. Read the article.

----
Quote from the study
We ((performed founder analysis)) using in-house Founder Analysis software that applies an algorithm for choosing the best tree. We calculated the age estimate for the migration of each founder using the ρ statistic and obtained the effective number of samples associated with each founder as before [13-15] by multiplying the number of samples in each founder cluster by a ratio of the variance assuming a star-like network and the variance calculated with the method of Saillard et al. (Supplementary Data 2) [16]. We performed the founder analysis of mitogenome data in three ways: ***(1) from the Near East (including Anatolia) to Mediterranean Europe (including Iberia); (2) from the Near East and eastern/central Mediterranean Europe to Iberia; and (3) from the Near East and Mediterranean Europe to central/northern Europe (excluding the British Isles and Volga Tatars from Russia).*** Additionally, we performed the founder analysis considering Mediterranean Europe and the Near East as independent sources to Iberia as well as to central and northern Europe. We also performed a reciprocal founder analysis, reversing the migration direction of all the models described to confirm that all sources and sink regions were correctly assigned.


batman said...

From the paper:

"We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe.

This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe."

The only refugia known from the hot part of the Meds are bound to the North-African coast, where y-dna E obviously spent the Younger Dryas.

Just after YD the post-glacial carriers of y-dna E (re-)appear in the Levant, as well as Alger and Atlas.

Though, at the same time we find that NW Europe get populated by y-dna I, basically, while the Northern Meds are dominated by y-dna G. From France to Iran, where they seem to border a dyansty of y-dna J, east of Tigris while a y-dna H gets established in (southern) India.

We still do NOT know just where these GHIJK-men survived the Younger Dryas. But we do know that they all start to appear - across arctic and semi-arctic Eurasia - at about 11.500 years ago. Which is why we know that their (common) history, background and late, ice-time refugia must have been arctic. Otherwise we couldn't explain their re-occurance at places like Gibraltar and North Cape within the very same pioneeer-phase, as of 10.800 - 11.800 C-14-calibrated years ago.

As the Mesolithic y-dna found in NW Europe is hg I we may conclude that their "brother-lines" G, H, J and K share their paleolithic/arctic origin. Their common arctic traits, known as "caucasian", seem to underline just that.

capra internetensis said...

Though the Iberomaurusian mtDNA results were nigh-useless HVS-I only, a couple of the later ones from Afalou looked like legitimate J and 1 looked like T2b. If accurate then these are more Neolithic-like haplogroups present in the Western Mediterranean, in this case in the Epipalaeolithic.

I would dearly love to see genome-wide data from those samples.

xyyman said...


To those who don’t get it what I posted. They ran all the possible migration routes even the ones that make absolutely no sense and did not run the one that makes more geographic sense. Why? Because they know the answer. This “Near East” label is a game. (sometimes they using Africanized bedoiuns as a proxy)Because the genetics show the Near East and the Sahara are yes, similar but there are differences between them and similarities between the Sahara and Europe. Common sense would suggest the Sahara was the source for BOTH. I have to do a deep dive of the paper. Remember Natufians are now confirmed NOT to be ancestral to modern Europeans which was a common misconception going back 100years.
aDNA has proven that is NOT the case.

Roy King said...

Yes!! Finally some support for what I've been arguing for years that there was a Mesolithic migration from the Near East to Mediterranean Europe (Greece/Sardinia/Italy) that was post-LGM and pre-Neolithic. Didier Binder, the CEPH archaeologist, terms it fancifully, "From the Caspian to the Capsian". Impressed ware Neolithic followed along the same path and, likely, North Africa participated in the movement.

Chris Davies said...

"and, likely, North Africa participated in the movement."

I agree.

Gioiello said...

Ex Oriente non lux, sed nox. Rex.

Arch Hades said...

So they are basically saying that Anatolian-Aegean farmer [EEF minus the 10% WHG input] is very old in Southeastern Europe.

Gioiello said...

Not only it is what I am saying from so long, but it was clear also from aDNA from Anatolia: only Northern-Western regions, nothing to do with Middle East and Iran.

Roy King said...

@Gioiello
Et nox et lux, Jewel!

Rafs said...

"Could explain the pattern of R1b"

Um, derp, no it couldn't. R1b has never been found in European or Near Easterner farmers.

xyyman said...

The pattern of R1b(East-west )has a clear bifurcation pattern. Similarly for mtDNA U5b and U5a, yDNA R1b and R1a. Also for mtDNA H1/H3 and H2 etc. BB/CWC. The pattern is clear. There is clear demarcation with the African Sahara as the source. The real question is why the sudden dominance of R1b-M26 immediately AFTER the bronze age. To me is has to be cultural or sociological. Hence my comment about Maternal societies. Keep in mind Hunter Gatherers or Europe were Black. The incoming women into Europe carried the light pigmentation gene. The men carried G and later African E1b1b*. Germans as much as 10% E1b1b* while Greeks carry as much as 25% E1b1b. Italians? Don’t want to piss off Gioiello. So no comment on this. Why did R1b suddenly dominate?

MfA said...

Looks like J1b3 originated in or around Iranian plateau, having both basal and the daugther clades based on modern samples. J1b3a seems to be found in Armenia.

J1b3 tree

Age estimates: J1b3a has a very recent mrca data, from Armenia to Iberia. Slovakian samples belong to Romani people, and it's widespread across all European Romani groups according to previous papers.

Genbank submissions:

http://www.ianlogan.co.uk/sequences_by_group/j1b_genbank_sequences.htm

Salden said...

Not a single example of pre-historic human remains within West Eurasia is genetically similar to any Tropical African populations.

Samuel Andrews said...

@xxyman,
"Because the genetics show the Near East and the Sahara are yes, similar but there are differences between them and similarities between the Sahara and Europe."

Near Easterners have Saharan ancestry, Saharans have Near Eastern ancestry, but the two very different. Unique strains of relation between Africa and the Near East certainly exist but for the most part Middle Easterners and Africans are apart of hugely separated genetic lines.

Y DNA E1b1b is definitely an example of one of those unique strains of relation between the Middle East and Africa. There are probably many more but overall the two regions aren't very related. Europeans certainly share some of those unique strains but is even less connected to the Sahara than the Middle East.

There's nothing which indicates any special relationship between Europeans and anyone in Sahara Africa, besides shared Middle Eastern ancestry. The ancestors of Europeans who lived in the Middle East 10ky+ didn't have any closer of a relation to Saharans than modern people in the Middle East.

"This is not rocket science. Europeans are depigmented Africans."

Really different facial features, hair texture, even different body builds.

Samuel Andrews said...

@xxyman,
"Keep in mind Hunter Gatherers or Europe were Black."

They *probably* had dark skin. That doesn't mean they were Black Africans.



Samuel Andrews said...

@xxyman,

History doesn't have a narrative. History is random and sporadic. I think you wanna believe the narrative Europeans are depigmented Black Africans because you like that idea. But the fact is they aren't.

Matt said...

Sigh. And the ratio of nutcases:people who are not nutcases rises in the Eurogenes comments section once again...

Romulus: Makes sense given that new Mesolithic Sardinian mtDNA.

Arch Hades: So they are basically saying that Anatolian-Aegean farmer [EEF minus the 10% WHG input] is very old in Southeastern Europe.

Sensible comments. These are plausible. As Davidski says, ancient autosomal from Mesolithic regions of Italy-Balkans-Greece (after the Upper Paleolithic - Villabruna) will confirm or reject.

Alberto said...

We had before some clues from Mesolithic Greece, where 2 samples (IIR) had Anatolian mtDNA, and the early and late Neolithic samples from Greece didn't have any WHG admixture, so it's quite likely that the Mesolithic inhabitants of the southern Balkans where just like Anatolians. This might have extended all the way to Sardinia during the Mesolithic, but a different question would be if these Hunter-gatherers contributed significantly to modern populations. Genetically it would be difficult to measure, if they looked just like the farmers. But the only way they might have contributed more than WHGs to modern Europeans would be if for some reason (connection with language or culture to Anatolians, for example) it might have been easier for them to adopt agriculture than it was for WHGs.

The connection with North Africa seems quite plausible given the Early Neolithic samples from Iberia, and they're not even from the south. I think that EN samples from south Iberia and south Italy will show this connection more clearly.

https://www.researchgate.net/publication/235915451_The_Mesolithic-Neolithic_transition_in_southern_Iberia

capra internetensis said...

@Alberto

I was just thinking of that paper.

I wonder about the pre-Neolithic obisidan trade and spread of the pressure bladelet production technique. Could be connected to pioneer seafarers from the Eastern Mediterranean? But seems too late for the Sardinian Mesolithic samples, and much too late for Afalou.

Ryan said...

@xyyman - can you stop with this asinine nonsense. Yes, every derives most of their ancestry from Africa if you go far enough back. Stop being pedantic. We're not talking about 50-100 kya. By your logic we're all giant European lemurs since that's where primates evolved before migrating to Africa. Give it a rest.

Ryan said...

@Roy - I think Fu et al pretty much proved that there was ongoing admixture in Europe from the Near East FWIW.

batman said...

The "ratio of nutty cases" is usually paralell to the ratio of confusion surrounding the questions of "refugia(s)" and "bottleneck(s)".

In which case "the plausible" remains a question of reference, preference and/or bias.

Ignoring parts of the geological, climatical, biological or archaeological facts usually follows due.

Ignoring a known, well-documented refugia is obviously major part of the reason why this discussion has gone waco. Even among the pros of the gentic community.

The NW refugia were obviously existing - throughout both LGM, Older and Younger Dryast - as the only one proven to exist, so far.

Which, of course, had obvious ramafications for the re-population of northern Euraisa - as this refugia were responsible for the re-production of the arctic traits found in todays populations along the entire Eurasia, from Gibratltar to Vladivostok.

Which is why the Mesolithic distribution of y-dna F->GHIJK actually reflecti a pretty rational and effective spread of these mainlines - in dynastical formats - just after ice-time.

Thus it's a proven facts that we had (at least) ONE arctic refugia - between Brittain and the Baltics - that formed what today is known as the "caucasian aetnos".

Whatever references one may prefer, to find and explain the basic structures of the Euroepan Genome one have to start with the "re-shuffle" that came out of the YD refgugia - when a major bottle-neck changed the common genome (of paleolithic Eurasia) through an extreme decimation.

Given that there's still no signs of evidence that we had significant refugias during the same time north of the 40th paralell. Which so far leaves the proposed "canto-ibrerian", "carpatian", "caucasian" or "anatolian" refugees as 'mere suggestions'.

The identities sampled from NE Europe showing mesolithic traits could very well originate from the same pool of F->GHIJK, who had to be the ones re-populating the barren and depopulated lands of arctic Eurasia, as of 12.000 years BP. We know they reached the Oslofjord area 11.900 years ago. Moreover they had started to repopulate the west-coast of Norway, as of 11.700 years ago - reaching North Cape as of 11.200 BP.

Meanwhile their brotherlines and cousins started to repopulate the Atlantic Facae and the northern rim of the Mediterranean, reaching Gobekli Tepe 11.600 BP.

A northern branch develops around y-dna I2/11. A southern spreads as y-dna G. Both are boatbilders, deep-sea-fishers and mariners - par exelence in their time.

batman said...

Looking at the entire plaedra of historical facts the histoy of the Euroepan Genome - as well as the Human Genome at large - becomes a bit less confusing. As ancient DNA keeps confirming this NW refugia - and the consequences thereof - I think it's due time for any gentician to start consider the possibility of a NW refugia as the start of the repopulation of northern Eurasia.

Thus it's a notion that aDNA now does confirm that we had a North-African refugia during the LGM-YD-period as well, turning out to be the closest (male) relatives to the NW refugia, who all descended from a y-dna F.

The female marker U5b1a have been focused. It does occur among the y-dna I that populated Scania, where it's (still) apparent in todays population. From extant dna we know that it hiked north with y-dna I and south with y-dna G - to be found amongst Samis of the North Cape as well as the Basques of Iberia.

Moreover it has been found as far north-east as the Yakuts of Siberia and as far south as the Fulabis in Guinea-Bissau. The last distances proves U5b1a could marry into pioneer-farmers too, with R1a or b, as well as the woodlanders the Eurasian Boreal-zone - today dominated by y-dna N.

The recongnized distribution of U5b1a makes two pretty plain lines on the map. One follows the Atlantic facade, the other follows the waterways from the North Sea to the Caspian Sea. These lines still meets at the islands of the Western Baltics - just like the archaeological traces describing the major routes of travel and trade within Mesolithic AND Neolithic AND Eneolithic Europe.

Cunliffe and Renfrew are right about all of that. Adding the ditribution of lactase persistence to the equation it should be possible to identify the true origin of agriculture, as a logic consquence of a need to persist and survive climatical fluctations, as a major drop in annual temperatures. Which is exactly what happened to the populations that survived the entire Late Paleolithic north of the 45th parallel.

Rob said...

@ Albert and Roy

It's often been considered for a while actually about a pre-Neolithic migration to Europe, including the backed blade industry in the EpiGravettian (Kozłowski) as well as later Mesolithic (eg http://dlx.booksc.org/47600000/libgen.scimag47666000-47666999.zip/browse/10.1016/j.quaint.2015.07.059.pdf). The latter looking to North Africa

---/-
The 2nd issue is even if Southern European Mesolithics were like Anatolian farmers, did they actually contribute the bulk of farmer ancestry ?
Here again contextual archaeological analysis is required- as many sites for example in Greece even the famous cave at Franchthi shows a stratigraphic hiatus between the latest Mesolithic and the earliest neolithic layers, with a complete cultural shift. Similar phenomena in the Adriatic apart from key locales such as the Trieste basin.

Richard Holtman said...

I'm confused here, is Haplogroup I neolithic now? Or is G Mesolithic?

Annie Mouse said...

Yep supports what I have been saying but I think that this population has been Mediterranean for longer.

Rob said...

@ Richard Holt

No. nothing has changed as yet. This was a review article.

Richard Holtman said...

Ok thanks Rob!

PF said...

Not sure why the focus is on the Balkans for potential Anatolian-like HGs. Across many pre-Neolithic sites, ZERO G and tons of I -- across multiple Neolithic sites, tons of G and a bit of I.

When the correlation between Y-DNA and ancestry is SO strong it's senseless to ignore... indeed this is a case when looking really closely at the Y may be wise. At quick glance it seems the G2a clades found so far in Anatolia do look more related to central European G2a, and less to the (maritime?) G2a in some Italians, Jews, Greeks, Turks, etc. For example haven't seen anything ancestral to M406.

It does make sense that very closely related yet less WHG-shifted Anatolians existed and account disproportionately for the farmer ancestry in the middle east and southern europe. (I think between the northern Levant and western Turkey is a simple Anatolian_Neolithic cline modulated by small but significant variation in WHG.)

And yeah, I'm open to the idea that Anatolian-like HG populations existed way before the Neolithic, but guessing they would have been living around eastern Turkey and not the Balkans. This corresponds with G2a phylogeny and of course is the exact region where we see the earliest agricultural developments, so why not look there first?

Rob said...

@ PF
We don't have any Y DNA Mesolithic samples from Balkans or Italy yet

John Smith said...

@ Ryan ''Yes, every derives most of their ancestry from Africa if you go far enough back.'' No direct evidence exists for this. Before ancient dna R1b came from Spain/Near East disproven. Before ancient dna no one would have guessed that C1 y-dna or pre NO was found in ancient Europe or M. The evidence of an African origin of humans is week with no ancient dna proof all evidence is based on modern distributions combined with speculation and political heresy type science. Africa mostly has diversity because of A and B and L0, L1 ect. However this has problems. First if we exclude these lines they have less diversity than Eurasians and many groups in Africa at least on the male side have little diversity (eg almost all R1b-v88, all E1b1b,all E1b1a). If we factor the Neanderthals in and the Denisovans Eurasia has (possibly) more diversity. More diversity does not = homeland or else R1b came from Near East which it probably did not. Plus Toba could have killed most humans except Africans which could be the reason for the survival of A and B lines in Africa and not Eurasia. Plus before about 40kya haplogroups seem to have no correlation with modern haplogroups (K2a-pre NO in Europe,C1, and M mtdna in ancient Europe, as well as U6 which scientists used to think come from Africa but clearly comes from Europe and maybe the near east but probably Europe) Even E1b1b was found in the Levant 14kya and may have originated there or nearby. I hate to say this but the African origin of modern humans is just a weak hypothesis with a lot of political connections maybe it is true but maybe it isn't it most definitely is not a fact. Of course scientist will keep treating it like fact until it is disproven which is fine if it is true but a tragedy if it is not. Some very strong evidence exists against it and I think that humans probably did not originate in Africa from the evidence given. If Ancient dna proves this correct/incorrect than I will be happy to know the truth.

Colin Welling said...

@xyyman

You dont understand. Europeans and Asians do not come from modern day africans, which is ultimately your insinuation. They mostly come from a people who happened to live in africa 100k years ago. If you want to say those people are somehow more similar to modern africans just because the ancestors of modern africans didnt as far, then you are just saying that africans have evolved less.

Anyways, the fact the most of humanity originated in africa results in modern africans being the least related group to the rest of humanity. Modern africans represent the first outbranching of ancient humans. Theres also neandertal like dna in modern non africans.

John Smith said...

The fact they are least related proves nothing.
Image if somehow now a disaster occurred (Toba) and all humans died except a large group in America with all haplogroups and a small group in Central Asia with only y-dna R1a and mtdna C (or chose any). Image if the large American group populated all the Americas 40kya latter while the Central Asian group populated the Rest of the world with some overlap on both Continents. It would appear all humans come from ancient America when they do not.

John Smith said...

There is several problems with Colins 'fact"
first ancient dna showed people moved (i.e M and C1 and K2a* in Europe ) and that 40kya ancient people all over the world were very different than modern times therefore using a modern population for ancient origins is useless: Second bottlenecks occurred and migrations which caused complete region extinctions and easy introgression of Neanderthal Admixture (i.e K2a in Europe) which means that OOA is a theory or hypothesis but it is not a fact and it could be wrong. Basically you cant use modern populations to say where people come from to far ago without ancient dna because A) They go extinct and have bottlenecks and B) They clearly move long distances esp before 40kya.

Richard Holtman said...

I agree we need more ancient DNA to come to these conclusions but it really looks like G is a neolithic marker.

Rob said...

@ Richard

"I agree we need more ancient DNA to come to these conclusions but it really looks like G is a neolithic marker."

What is Neolithic in Europe is Epipalaeolitihc in Anatolia. :)

SetMind InMotion said...

"Keep in mind Hunter Gatherers or Europe were Black."

xyyman, if look at the prevalence of hunter gatherer genes (I1 and I2) amongst Europeans it simply doesn't make sense that hunter gatherers were black or dark because I haplotypes are most prevalent amongst the whitest Europeans i.e. North, North Western and Slavic populations!

I've seen this erroneous point made elsewhere on this blog too and no one else seems to refute the argument. My knowledge of genetics is nothing like the other commenters here but common sense helps me deduce that European hunter gatherers can NOT have been dark!

I believe the only reason you get dark Meditterenean Europeans is only because of later movements from the Roman period onwards, invading pirates, Moors and Ottomans etc.

The Near East Farmers cannot have been dark either because they contribute a lot to the European gene pool, and if they were dark then it would be evident within the genes and it's not. They were probably a bit tanned but this is not the same as 'black' like xyyman seems to argue.

xyyman said...

@Blogger Salden said... “Not a single example of pre-historic human remains within West Eurasia is genetically similar to any Tropical African populations.”
Lie!! Haven’t you ever seen admixture chart. Europeans are more African than Non-African @K2. Villabruna has balck pigmentation and tropical body proportion. Closest to Africans. Listen man. Iam not making this up. Read the papers and prove me wrong. This is NOT Ostrich time! Lol!

Have YOU read up on KOS14. You know he was classified as “negroid”? Not my words. Becaseu I don’t believe there are races. This from the author. But you wouldn’t know that because you don’t read scientific papers. You read comic-books.. Place you in that fantasy world. Lol!

--
@ Blogger Samuel Andrews said...” Really different facial features, hair texture, even different body builds. , Saharans have Near Eastern ancestry, but the two very different etc”
No my man. Saharans and Near easterner have “shared” ancestry. The question is who got it from whom. E1b1b* and it’s sub-clades is clearly African. E-V13 found in Europe is African. @K2 Euroepans are almost purely African. Show me an unsupervised admixture chart @K2. All show Europeans can be as much as 80% African. I am not making this up. READ!!!! Forget about the visuals on hair, skin and eyes. You do know YRI carry more variation for the SLC24A5 locus than Europeans, don’t you. You understand the implication? Don’t you! Yes, this is not rocket science! They were black like YRI(based upon pigmentation genes and were from Africa. Ok, I will say it a different way to make you feel good about yourself. They were black like Dravidians but from Africa. Feel better? Lol! SMH. Why aren’t they FACTS again? Because you said so? Lol!

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@ Matt – ignore nonsensical ramble response

--
@Alberto – “The connection with North Africa seems quite plausible given the Early Neolithic samples from Iberia, and they're not even from the south. I think that EN samples from south Iberia and south Italy will show this connection more clearly.”
Logical thinker. Thumbs up!
https://www.researchgate.net/publication/235915451_The_Mesolithic-Neolithic_transition_in_southern_Iberia

--
@ Blogger Ryan said _ Ignore, he hasn’t read Lazardis 2014. Or doesn’t belive what Lazaridis co-authored with over 100 genetic researchers. Yes, over 100 Ryan!!! Read it.


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@ batman ramble – ignore. No scientific proof to his nonsense. He does not know the Refugia Theory by Achilli is debunked because R1b did not originate amongst the Basque also mtDNA H. He does read updated papers.he also does not know that ALL yes ALL version of LCT exist IN Africa. Indicative or the origin to Arabia and Europe. Africans carry their own version not found OUSIDE Africa. Dream on batwoman! Lol!
“Both are boatbilders, deep-sea-fishers and mariners - par exelence in their time. As I said. Great story tellers- You are the man!! Will give Ricky competition for made up short stories. Lol!

---


Ryan said...

@xxyman - Did you even read what I wrote?

xyyman said...

--
@ Blogger Ryan said _ Ignore, he hasn’t read Lazardis 2014. Or doesn’t belive what Lazaridis co-authored with over 100 genetic researchers. Yes, over 100 Ryan!!! Read it.


----


@ batman ramble – ignore. No scientific proof to his nonsense. He does not know the Refugia Theory by Achilli is debunked because R1b did not originate amongst the Basque also mtDNA H. He does read updated papers.he also does not know that ALL yes ALL version of LCT exist IN Africa. Indicative or the origin to Arabia and Europe. Africans carry their own version not found OUSIDE Africa. Dream on batwoman! Lol!
“Both are boatbilders, deep-sea-fishers and mariners - par exelence in their time. As I said. Great story tellers- You are the man!! Will give Ricky competition for made up short stories. Lol!

---


@ Blogger John Smith said...Ignoring his belief that OOA did not occur! Lol! Let us anaylze what he just said.

1. Toba killed off all human in Asia leaving only Africans,. Siiighhh! At a lost for words. No comment on hypotheticals
2. Agreed A and B account for most of the diversity of modern Africans.
3. He forgot Africans carry the ancestral form of U5 and carry their own UNIQUE version of U6. The U from in 35kyo Romania was basal. There is no aDNA found in Africa comparable because Africa is untested mostly.
4. Even E1b1b was found in the Levant 14kya and may have originated there. Fool! E1b1* is as African as they come. E1b1b is over 18,000year old! Unlike the sibling which may be ONLY 7,000yo. You will not find E1b1a in aDNA in Europe except classical Greeks. Maybe?!
--

@ Colin Welling . Another one who hasn’t read much or don’t read at all. Hasn’t read Lazaridis. Doesn’t know that All humans carry Neanderthal ancestry including SSA. And It is not really Neanderthal ancestry. It is called “Sub-structure”. he does not know E1b1a is only 7000year old. There one of the youngest humans. Need I respond to the rest of his ramble?

--

@ Blogger SetMind InMotion said
I think you are getting confused bro. Lineage has nothing to do with skin color. Let Davidski explain that to you. Nothing more to add for you. You are a novice. I don’t really debate novices. Someone else will explain ii to you. BTW have you read Shriver et al etc. Someone will explain to you that the Neolithics brought in light skin about 5000BC. “I debate my equals all others I teach” John Henrik Clark

--



xyyman said...

Ryan said..."@xxyman - Did you even read what I wrote?"


Ryan. Listen. You don’t know what you are talking about. “ Have you read Lazaridis et al”? do you understand it/ Europeans are made up of 3 ancestral populations. Everyone knows that. Now. If you don’t. Coon and Sergi showed Neolithics came from Africa. Neolithics entered Europe ONLY about 6-7K years ago. WTF are talking about? Man. These are the FACTS. Let someone explain to you what is “basal Eurasian” and where it originated. I don’t debate novices. I “teach” novices when they ask a question.

I post on other sites. Search for me. I have all my references . Any questions you have I can answer but don’t argue with me on stuff you know nothing about. Just sit back and take notes. Thanks SMH He! He! He!


xyyman said...


To all of you! I am only the messenger. I am trying to talk you off the ledge. Sorry to burst your bubble. This reality, I am waking you up from your dream of Eurasian Steppes man ONLY migration smashing their way into Western Europe. …comedy. I don’t want ot make thing worst. But I have to tell you this.
Davidski, Capra and Rick…you there? Do you know the pigmentation of the Steppes nomads you speak of. Tic! Tic! Toc! Remove any razors in the room before you find out?! Lol! I am the bearer of god news. No bad news! Lol!


Breton Cambro-Norman said...

@xxyman

The reason Blacks are prognated is due to inbreeding. OOA theory will be debunked, Negroes are inbred.

The tamer the people = Diversity = mutations.

Black people don't have diversity within their societies like the rest of the world, hence a small sample set of features is rewarded. The more civilized a people becomes, the more diverse they are. Black people aren't diverse, Eurasians are Diverse, hence Eurasians come in every color and size.



xyyman said...

@Breton. I have no idea what you just said there and what your politics has to do with what I am post. Do you have anything to add or debunk my postings? Or you just want to rant about modern politics. Davidski? Do you allow modern politic discussion here or is that for another forum? he! He! . Guess I am hitting some raw nerves with the truth. Want me to leave Breton? You don;t want to hear the truth, I guess You want like minds around, right. Spouting lies to one another?

xyyman said...

I guess Breton wanted to get that off his chest. He needed to say it. Now that you have said it. Any counter argument to what I posted?

Breton Cambro-Norman said...

@xyyman

You can't even master the English language, and you want to lecture a geneticist on his discipline? You're trash.

have no idea what you just said there
Exactly, you don't understand the fundamentals genomics. I'm not a part of this community and either are you, you're a moron.

Davidski? Do you allow modern politic discussion here or is that for another forum?
I see you're suddenly running now, huh? I thought this was your new corner of the world? begging the moderator to step in already.

And what is political about Inbreeding?

xyyman said...

Breton.
You are a genecist? big FAT lie!!

"Moron", "trash", "begging". You do have an extensive vocabulary. Ok! you are geneticist(sic). lol!


In case you missed it I was being cynical to Davidski, but you knew that already being a geneticist and all. wink!


Breton Cambro-Norman said...

@xxyman
You are a genecist? big FAT lie!!
I clearly said I was not part of this community. But there are people who view this blog, interact with it, who also who are disciplined in genomics, you on the other hand are a Afrocentrist rapist.


So what is political about Inbreeding?


xyyman said...


@Breton.Sorry I can tell now.


I am still waiting on a geneticist NOT like you to debunk what I am posting? Read the paper and tell me what is the pigmentation of The Steppes Nomads? Don’t look around to your friends for help, now. As a last resort ask Davidski, he is your “life line”. Want to be a millionaire. Did I spell Millionaire correctly? Where is my thesaurus?

So ,what were their pigmentation? Anyone?


xyyman said...

Wooops! another word, " Afrocentric rapist". You on a roll. Man! you are in therapy today. any thing else to vent off. I am your sounding board. I am here to help get over your inhibitions. ...and fear.

Breton Cambro-Norman said...

@xxyman

Thought so, you're a bitch, I asked you a simple question, and you've ran for the hills. You don't understand mutations at all. Mutations come from Social Change, or Diversity within populations = Mutations.

The more diverse a people is = the more diverse they become genetically. The more civilized a people = fairer features, less primitive.

Dogs are a perfect example of this, humans rewarded the tamer animals, killed the aggressive ones. This caused unexpected consequences for the humans, the tamer animals mutated genetically which is why we have dogs of every color and size.

Go see the longitudinal study on the Silver Fox breeding (Tame vs Wild).

xyyman said...

^
Off in La La land hypotheticals. If I am a betting man I would say you did NOT finish high school?!

Wow! In two days here. I have been called “Jew Nigger”, “afrocentric rapist”, "Moron", "trash", "begging/beggar", “bitch”. Not to mention the many innuendos, Wow! You are a friendly group here. Guess I am not welcomed? Did realize this was a Storm front-like hate site. My bad. Lol!


Breton Cambro-Norman said...


@xyyman

Off in La La land hypotheticals. If I am a betting man I would say you did NOT finish high school?!
I was just informing you of the basics of mutations, which you don't seem to have a inkling of.

Did realize this was a Storm front-like hate site.
Projection, Projection, Projection. Again I'm not a part of this community, which I've stated from the outset. I don't know what "Storm front-like" is, so I cannot respond to that.

Guess I am not welcomed?
I'm not a part of this community, so you cannot really make such a statement in regards to the regular contributors.

Gioiello said...

@ xyyman
"Wow! In two days here. I have been called “Jew Nigger”, “afrocentric rapist”, "Moron", "trash", "begging/beggar", “bitch”. Not to mention the many innuendos, Wow! You are a friendly group here. Guess I am not welcomed? Did realize this was a Storm front-like hate site. My bad. Lol!"

As always the devil (i.e. the truth) is in the details.
I named only one person "Jew Nigger", the only one who has a Jewish father and an Afro-American mother. Ask Gordon Whittaker who Gioiello Tognoni is. I am a literate, a literary critics, I wrote about the "varianti" (critica delle varianti), I practised psychoanalysis... Non solum nox ex Oriente, sed etiam noxa.


Colin Welling said...

xyyman.

The main point is that Europeans and Asians did not come from modern africans. Modern Africans are simply the first group to branch off from the rest of humanity. Them not moving far and staying in close proximity to these common ancestors means nothing in itself.

Where in lazaridis' paper was it said that all people have neandertal dna as opposed to just non africans. I was under the impression that there was substructure in africa (basically, modern africans and modern non africans split even before leaving africa) and neandertal dna is only in non africans. I also remember reading that modern africans may have their own type of local archaich heritage.

All of these variable just change the time of divergence between modern africans and modern non africans. In all cases, however, modern africans are the first to branch off from the rest of humanity. It means they are the least related to all other human populations. So to suggest that non africans come from modern africans is silly. It would be similar to saying that humans come from chimpanzees because humans and chimpanzees share a common ancestor and chimpanzees have stayed in the same habitat. Its just not true. Chimpanzees and humans descend from a common ancestor but that common ancestor is not owned by chimpanzees.

Now, it may be true that Europeans and Asians have changed more due to experiencing more bottle necks but that doesnt justify saying that Europeans and Asians come from modern africans as you suggested when you say african without qualifier.

xyyman said...

@ Blogger Colin Welling said...
No response needed with this juvenile logic. I am not even sure what point you are making. I guess you have never seen a K2 admixture map? Showing Europeans and Africans. If you haven’t you should not be in the conversation. Secondly, if you haven’t read enough papers where OTHER geneticist have debunked Paabo nonsense about Neanderthal admixture again this conversation is above your pay grade. Capra, Ricky, Davis can you explain it to him. Explain Basal Eurasian, EFF, WHG etc.



But I understand your confusion. Why Europeans look so different to Africans but are so much the same under the skin. I will tell you why if you say "pretty please'.

xyyman said...

@ Colin BTw – Humans did NOT descend from Chimps. You may be a bible nut and uneducated So I am stetting you straight. Nope! Humans did not descend from Monkeys. Next you will be asking me why monkeys don’t become humans? You need to attend high school to get that answer. I don’t teach that stuff here.

Salden said...

AYO HOL UP!

Salden said...

KANGZ

xyyman said...

Yep! Anther one who doesn't know how to refute me so he post BS above like that would get under my skin. Yep young and dumb high school drop outs hanging out on Euroblog.

What's next? Monkey sounds to debunk what I am saying. My advice. Read a book.


Because NO ONE on this site can refute what I post. Nein!. Like that nazi part? He! HE! HE!

"ya'll here me. WAZ up!". respond to dat! He! hE! he!

Ryukendo K said...

No populations from outside Africa descend from modern Africans. After modern Africans split in a bifurcation from the ancestors of Eurasians 70-100 kya bp, Africans are Africans and Eurasians are Eurasians. Villabruna is ~10x more related to East Asians and Australian Aborigines, if you compare sites straight out using shared drift measures--they are from one branch, and Africans from the other. Africans are just the half of humanity that stayed put.

Saying populations that have outward shared characteristics with Africans are African is like saying a furry Tibetan Mastiff is actually a lion, or a talking parrot is actually a human, or a flying bat is actually a bird, or an albino African is actually a European--no sense whatsoever. East Asians are also ancestral at the site that gave Villabruna dark skin--are they also African? Complete idiocy. Not to mention that after the split most gene flow has been from Eurasians to Africans, not the other way round.

xyyman said...

What is it with you people. Davidski what kind of ship are you running here? This crew is very out of touch. Can you explain to them K2 and what is Basal Eurasian, the age and the source. I thought the guys at Egyptsearch were behind the times but this crew is ....totally clueless

Davidski said...

Well, they know that Basal Eurasian is not Sub-Saharan African, and that's why it's called Basal Eurasian.

Moreover, Villabruna only has minor Basal Eurasian admixture and no African admixture, and that's why he's a typical European Hunter-Gatherer and genetically closest to Northeast Europeans.

Really not sure why you're still not getting any of this?

Ryukendo K said...

You're not understanding the stuff you're reading... Natufians, who are the most Basal Eurasian population there is at this point, is no closer to Africans than other Eurasians are... Basal Eurasian is the first member of among the Eurasians to split off, and has nothing to do with Africans.

John Smith said...

I used to think E and E1b1b had origins in Africa however since the Natufians of 14kya were no closer to Africans than other Eurasians and completely dominated by E1b1b this line seems to come from Levant area or Nearby. And maybe even other E lines and the macrogroup as a whole come from Asia or West Asia. I was certain E came from Africa until I saw the Natufians result.

John Smith said...

Did the Natufians have Neanderthal at all?

xyyman said...

Since many of you don’t seem to ACTUALLY read and UNDERSTAND these research papers when they are published I will pull out a few excerpts for those interested. Remove all sharp instruments from the room. Lol! Anyone who still “believes” YDNA E is NOT African should not be even in the discussion. (Wink at John Smith). Davidski If you are not going to tell these guys the truth I will. You are the captain of the ship. I expect more and better representation from you.
Only someone who did NOT read or understand the latest paper on Natufians will comment that they did not originate from Africa when the authors clearly state that they DID most likely originated from Africa. All indications are they did. But Should I continue to educate you guys?


André de Vasconcelos said...

Even if they were indeed originally from Africa, they were not SSA folk. Neither was Villabruna or any other WHG, regardless of what their skin pigmentation was like.

jeanlohizun said...

@xyyman

I will engage you once, and only once, because my time is rather limited. You appear to claim that European Hunter Gatherers were "black". If you mean they had darker skin than modern day Europeans, the answer is some did, others did not. Let's take a quick look at the mutations that play out in the skin color:

"Variations in the KITL gene have been positively associated with about 20% of melanin concentration differences between African and non-African populations. One of the alleles of the gene has an 80% occurrence rate in Eurasian populations.[52][53] The ASIP gene has a 75–80% variation rate among Eurasian populations compared to 20–25% in African populations.[54] Variations in the SLC24A5 gene account for 20–25% of the variation between dark and light skinned populations of Africa,[55] and appear to have arisen as recently as within the last 10,000 years.[56] The Ala111Thr or rs1426654 polymorphism in the coding region of the SLC24A5 gene reaches fixation in Europe, but is found across the globe, particularly among populations in Northern Africa, the Horn of Africa, West Asia, Central Asia and South Asia.[57][58][59]"

You seem to be making your claims in the notions that WHG collectively lacked the derived mutations for SLC24A5, and SLC45A2. Which is indeed true, however they did not have any significant genetic connection to Sub-Saharan Africans, therefore they were most likely not of recent African descent. In addition, they did have derived mutations that play a role in skin color. Many(if not all) WHG were derived in the IRF4 gene, and the KITL gene. Therefore, their skin color was not that of Sub-Saharan Africans, it might have been closer to Southern Indians, though their derived status in IRF4 brings about the point that they might have been lighter skinned that modern day South Asians.

See here: https://genetiker.wordpress.com/2016/05/05/phenotype-snps-from-ice-age-europe/

You can see that Villabruna carried all the derived mutations for ASIP, rs2424984, ASIP, rs6058017, and IRF4, rs12203592. A quick search will reveal that Loschbour and La Braña also carried those mutations at least in the heterozygous state. In case you are wondering about the IRF4 mutation effects here you go:

https://www.snpedia.com/index.php/Rs12203592

"plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent"

Morphologically the WHG were also very different from Sub-Saharan Africans. Their facial features were more aligned with their descendants modern day Europeans. In case you are wondering what does a dark skinned individual with European morphology looks like, here is a picture to help you out:

https://upload.wikimedia.org/wikipedia/commons/4/45/CroMagnon.jpg

Finally, there are plenty of Hunter Gatherers namely SHG, EHG had the genotypes commonly associated with modern day European pigmentation. Therefore, they were likely no different than modern day Europeans in terms of pigmentation. Also, SLC45A2 mutation rs16891982 as not derived in most farmers from the Middle East. Only a very small percentage of Anatolian farmers had the derived mutation, and none of the Levant farmers nor the Iranian or Caucasus Hunter Gatherers had it. On the other hand, the mutation has been found in European Hunter Gatherers, so its origin is likely European. Sri-Lankans have SLC24A5, yet they uniformly lack SLC45A2, they are not exactly "light-skinned", so to think that farmers were the ones that brought light skin to Europe, is erroneous in the face of evidence we have right now.

xyyman said...



Says - André de Vasconcelos said...
"Even if they were indeed originally from Africa, they were not SSA folk. Neither was Villabruna or any other WHG, regardless of what their skin pigmentation was like."

An analytical mind breaks things down in compartments. They work on it. So......we got the ORIGIN out the way. So Modern Europeans are .....Africans. You prefer NOT to use SSA. You also agree that Villabruna was black skinned like Nigerians. But you prefer black Onge since Onge are NOT Africans. Whatever float your boat. But You do know Onge are 4000miles away from Iberia while Africa is only 7 miles away. But whatever makes you sleep good at night. Keep in mind even the dogs came from Nigeria. Lol! But whatever, let's move on. Anyways can we stop the nonsense now about Villabruna being any else but black.....North African. Happy?


Open Genomes said...

Did I miss the party? 3:)

There are a series of Y clades that could very well show that some rare Y lineages arrived in Europe Post-LGM (notice, POST-LGM, not any European "Refugium") from the Near East AND NORTH AFRICA.

There's also a big "surprise!" about R1b1a-L389* in Italy. NO, it's not the ancestor of any other R1b1a-L389s - except perhaps one Puerto Rican family ... and one other from Italy.

It's very difficult to detail all the evidence here on this group, so I invite everyone (@Nick Patterson!) to join the Facebook YFull group where it's easier to post images of YFull tMRCAs and the like. I might be able to repost those here, afterward.

"ET LVDOS INCIPERE"! :D

Gioiello said...

@ Ted Kandell

You aren't so stupid as xyyman, thus: out the data. We may begin the play...

Open Genomes said...

@David and all:
For those that want a link, here is the YFull group on Facebook, because it's "all about the tMRCAs":

YFull.com: Y-Chr Sequence Interpretation Service

FYI, YFull got the "Yamnaya" R1b-KMS75 (aka R-Y20993) 100% right, based on three actual apparent "Yamnaya" descendants:

YFull R-Y20993 (aka R1b-KMS75) v5.02 Tree showing the tMRCA of 4700 ybp / 2700 BCE
Y haplogroup assignment of 20 aDNA R1b samples sequenced by Haak et al. 2015, Allentoft et al. 2015, and Mathieson et al. 2015 by Sergey Malyshev, showing I0440 Poltavka, Lopatino II, 2885-2665 calBCE

YFull v5.02 tMRCA calculations for R1b-KMS75/R-Y20993 age: 4739 ybp

As we can see, YFull's tMRCA for R1b-KMS75 at 4739 ybp is exactly at the median of the radiocarbon date of I1440 from Poltavka at 2885-2665 calBCE.

The importance of this is that we have hard evidence that we can rely on YFull's tMRCAs for the various candidate Mesolithic POST-LGM (not "European Refugium"!) Y clades that could have also arrived in Europe along with Villabruna in R1b1a-L389*. Like Villabruna, these are generally quite rare in Europe as befits pre-Neolithic hunter-gather Y-clades.

After presenting images there, we can come back here and discuss the evidence ...

Gioiello said...

@ Ted Kandell

I have written a lot about that: KMS75 is linked with Yamnaya, but not my Z2110 and other subclades close to it as you can see in the smal's tree, more detailed than the YFull one because has more samples tested. Neither comes from Yamnaya the intermediate subclades till CTS9219. Read what I wrote before risking to have a meager figure.
Also R-M73 is very likely older in Western Europe, having Eastern Europe and Asia only M478 subclades.

John Smith said...

Modern DNA suggests that E comes from Africa however the Natufians remains suggest otherwise. I can't wait for more a DNA to find the truth.

Gioiello said...

This is my last post on my FB page about that, but I wrote tons of letters:

OLDEST R-L23-Z2105
It seems that there are other data to add to what I said before about the oldest haplotypes also of R-L23-Z2105 in Western Europe than in Eastern Europe also amongst the descendants of Samara.
Also the R-L23-Z2015* have some haplotypes older in Western Europe, as YF07907 from Parma (Italy), to be added to these htps above all from Western Europe
526066 Daniel Frank/(Francis?) Jordan, b ca 1909 Unknown Origin R-L23
12 24 13 10 12-14 12 12 13 13 13 29 16 9-10 11 11 25 16 19 28 14-15-16-18 10 10 19-23 15 16 14 17 36-39 11 12 11 9 15-16 8 10 10 8 10 11 12 23-23 17 11 12 12 15 9 12 22 20 12 12 11 13 10 11 12 12
557529 John Carter, 1752-1841 United Kingdom R-Z2103
12 24 14 10 11-15 12 12 13 12 13 28 16 9-9 11 11 25 15 18 28 15-15-16-17 11 12 20-23 17 16 17 18 37-37 12 12 11 9 16-16 8 10 10 8 10 10 12 23-23 16 10 12 12 15 9 12 22 20 13 12 11 13 11 11 12 11 34 13 9 16 12 26 26 19 12 11 13 12 10 9 12 12 10 11 11 31 12 13 24 13 10 10 19 15 17 12 24 20 12 15 24 12 24 18 10 14 17 9 12 11
310308 Najd سبيع Saudi Arabia R-L23
12 24 15 11 11-14 12 12 13 13 13 29 17 9-10 11 11 25 15 19 30 15-16-16-18 10 12 19-23 16 15 18 17 37-37 12 12 11 9 15-16 8 10 10 8 10 11 13 23-24 16 10 12 12 14 9 12 24 20 14 12 11 13 11 11 12 12 33 15 9 16 12 26 26 19 13 11 13 12 10 9 12 12 10 11 11 30 12 13 24 13 10 10 22 15 18 12 22 18 12 15 24 12 24 18 10 14 17 9 11 11
and also at the base of R-L23-Z2106-Z8131*. These are the mutations from YFull at this level (STRs):
DYR152 10 → 10.a
DYS607 15 → 16
DYS456 16 → 15
DYS447 25 → 24
DYR75 13 → 14
But
62899 Rev. William Holmes, b. 1739 and d. 1823 Ireland R-Z8131
12 24 14 11 11-15 12 12 11 14 13 32 15 9-10 11 11 25 14 19 27 15-16-16-16 12 12 19-23 16 17 20 17 34-36 11 12 11 9 15-16 8 11 10 8 10 11 12 23-23 15 10 12 12 15 8 13 23 21 12 12 11 13 11 11 12 11
maintains DYS456=16, DYS447=25. Of course these markers may mutate forward and backward, in fact they changed also from R-Z2106 to R-Z2108/Z2109 and to my R-Z2110, but very likely Holmes doesn't derive from the eastern European or Asian haplotypes, demonstrating once more that linked hpts were not only at Samara but remained in Western Europe (from where I think they came).

Open Genomes said...

For those who like so "fun" with African origins, here's some previously posted evidence about a partial (about 25%) Mesolithic African origin for the Natufians:

Eurogenes Lazaridis (2016) 3-D PCA closeup showing Natufian origins in Africa

Eurogenes Lazaridis (2016) 3-D PCA overview showing Natufian origins in Africa

For those that care about such things based on certain "accusations", using the Y-DNA as examples:

• I'm a "Levantinist" when it comes to Neolithic G-M201 and H2-M282 origins in the Fertile western and northern Fertile Crescent
• I'm a "Caucasianist" when it comes to J1 origins among the Mesolithic Caucasus Hunter-Gatherers (CHGs)
• I'm a "Eurasianist" when it comes to R1b, R1a, and R origins in general in Central / South / Eastern Eurasia and the later Steppe origins of R1b1a1-P297*
• I'm an "Afrocentrist" when it comes to the African origin of R1b1b-V88 (or maybe the main part, R-Y8451, the African origins of E1b1b1-M35.1
• I'm a "scientist" (like Charles Darwin) when it comes to the African origin of Anatomically Modern Humans (AMH) 240,000 years ago in West Africa (Southwest Cameroon) when the earliest known AMH fossils are Omo II from Ethiopia from 195,000 years ago

• I'm a "Multiregionalist" when it comes to the specific early Out of Africa Eurasian origins of the Neanderthal-Denisovan clade, which because of back-migration, carried alleles into many parts of Africa

People, genetically (that is to say, "scientifically"), there are "Three Races of Mankind":
• Neanderthal
• Denisovan
• African Anatomically Modern Human (AMH)

"That's All Folks!"

Most of us are mixed with the first two, even many Africans.
If Tibetans have a high-altitude EPAS1 adaptation allele of clear Denisovan origin, then why can't that "French" have low levels of specifically Denisovan ancestry, something that Reich saw in his D-statistics but discounted as "impossible"?

Nature: Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

"Archaic" (i.e. true "Multi-Racial") ancestry is much more widespread than anyone believes, and ask yourselves if the SNPs used PC plots also include chr6 HLA immune system alleles:

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

Open Genomes said...

There may even be a specific human HLA allele, HLA-B*73, which is within a chimpanzee clade, the clear result of "incomplete lineage sorting" combined with "balancing selection":

Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression?

HLA-B*73 frequencies in worldwide populations, highest to lowest

Funny, Italy ties for the 2nd highest frequency in this "chimpanzee" HLA-B clade, at 2%. Any Europeans and specifically Italians here like to check their own HLA-B alleles?

rs2071288=T isn't the tag SNP for HLA-B*73:01, but it does include it:
SNPedia: Rs2071288

So according to "Racialists", what does that make people who carry it?
Go check!

This isn't "Leftist", "Alt-Rightist", or "Religious Fundamentalist".

It's just Science.

jeanlohizun said...

It seems the level of ignorance being spewed here is rampant. Thereby, we need to go back to basic concepts and then expand from there. Phenotype arises from functional SNPs, that is SNPs that cause functional changes to genes, thereby resulting in a phenotypical expression. Mutations that characterize pigmentation, while diverse are only a small subset of the total human variation, which is in the order of some ~10-11 Million SNPs. While South Asian Onge, and Melanesian share a similar skin tone to Sub-Saharan Africans, they are by no means "Black Africans", this is easily testable through Principal Component Analyses(PCA), and MDS plots. As such, we can effectively see that the European Hunter Gatherers do not cluster anywhere near modern day Sub-Saharan Africans. Therefore, calling them Africans, is plain wrong. Their distant origin may be in Africa, but that does not make them Africans.

In addition, there is clear evidence that even amongst the darkest pigmented European Hunter Gatherers, that is the WHG, their skin color was no where near the color of Sub-Saharan Africans. This can be easily deduced by looking at a series of mutations.

Let start with the following functional SNP:

ASIP, rs2424984

It's modern frequency can be found here:

http://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=20:34262069-34263069;v=rs2424984;vdb=variation;vf=1784800

It obviously shows an Eurasian preponderance being only found in its Homozygous derived state (i.e TT) in 3.5% of YRI, 10% of LWK, 16.8% of MKK, and 4.1% ASW. Yet, in ancient samples we find:

Kostenki Russia 38,684-36,262 Unassigned TC (1/1)
Villabruna Italy 14,180–13,780 Epigravettian TT (1/1)
La Braña Spain 6000 ybp Mesolithic TT (7/7)

ASIP, rs6058017

It's modern frequency can be found here:

http://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=20:34268692-34269692;v=rs6058017;vdb=variation;vf=3331807

No breakdown by haplotypes, but allele count shows AFR only 29% A.

Goyet Q-2 Belgium 15,230–14,780 Magdalenian AA 1/1
La Braña Spain 6000 ybp Mesolithic AA (2/2)

IRF4, rs12203592

It's modern frequency can be found here:

http://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=6:395821-396821;v=rs12203592;vdb=variation;vf=7190893

This is fixed in the ancestral allele C/C in all African populations, with the exception of African Caribbeans in Barbados ACB, and African Americans Southwest ASW, only 1 ASW has T/T.

Villabruna Italy 14,180–13,780 Epigravettian TT (10/10)
Loschbour Luxembourg 6220–5990 BC Mesolithic TT
La Braña Spain 6000 ybp Mesolithic TC (26/63)

Here are the effects of IRF4:

https://www.snpedia.com/index.php/Rs12203592

So anyone claiming that Villabruna had the same pigmentation as modern day Nigerians, is either being dishonest, or deeply ignorant of the data.

jeanlohizun said...

European Hunter Gatherers showed some variation in skin color, for example:

ASIP, rs2424984
Motala HG I0012 2/2
Motala HG I0014 3/3
Motala HG I0017 3/3
ASIP, rs6058017
Motala HG I0012 1/1
Motala HG I0014 1/1
Motala HG I0017 4/4
EDAR, rs3827760
Motala HG I0012 2/5
Motala HG I0014 0/12
Motala HG I0017 6/11
IRF4, rs12203592
Motala HG I0012 3/3
Motala HG I0014 4/4
Motala HG I0017 9/9
KITLG, rs642742
Motala HG I0017 2/2
OCA2/HERC2, rs12913832
Motala HG I0012 6/6
Motala HG I0014 9/9
Motala HG I0017 15/15
SLC24A5, rs1426654
Motala HG I0012 3/3
Motala HG I0014 3/3
Motala HG I0017 8/8
SLC45A2, rs16891982
Motala HG I0012 5/5
Motala HG I0014 10/20
Motala HG I0017 4/13


We can see that Motala HG I0014 had the pigmentation of any modern day Scandinavian. Motala I0012 had ligther skin pigmentation than Motala HG I0014 and Motala I0017 in light of SLC45A2 being GG vs GC for the other two, but they had the heterozygous EDAR mutation, however I have seen people with the heterozygous form of the EDAR mutation and all other pigmentation SNPs as Motala HG I0012, and they look European. Again, in the Scandinavian Hunter Gatherers, Baltic Hunter Gatherers, and Eastern European Hunter Gatherers, we find the pigmentation alleles found in modern day Europeans. So not only are European Hunter Gatherers not of recent African origin as evidence by genome-wide PCA, but their pigmentation SNPs are also not similar to modern day Sub-Saharan Africans.

Case closed...

xyyman said...

@Open Genome. Nice spiel. But don’t let Gioiello get you all worked up. He likes hearing himself speak. Like many Italians he is too emotional. But that is not the point. Yes, Natufians are Africans. Regardless of what people “believe’ here. Belief is one thing FACTS is another. Some believe the earth is flat. Ask Shaq. Lol! Anyways. E1b* and its downstream clades are as African is they come. Within modern Italy there are isolated populations that still carry E1b* the upstream clades and of Course E-V13. Anyone who hasn’t seen a haploTree of E will talk nonsense. Italy/Sardinia and Iberia has always been the entry point when Africans migrated to “Europe”. But that is a given. The real question as I keep asking intelligent people is Why the sudden emergence of R1b-M269 in Western Europe? Less than 2000years. Now some of you may ask , what do I mean ONLY 2000years. Why? Most high Ranking skeletons from Europe tested so far are NOT of R1b-M269. Example , Richard III North African Lineage in BOTH the mother and father haplogroups. Some may ask, WTF is he talking about. Also. The Vikings that were actually tested were about 50% non-European lineage..again WTF is he talking about? If you are asking these questions you should not be in the discussion and just read on. The Vikings were NOT white and it looks like many of the European Royal families up about 1000AD did NOT carry typical modern European lineage. Eg Richard III carried mtDNA J2? Found mostly in North Africa , West Africa and Near East. So was a black….eh..tan or bronze woman his mother. What was his male line again? I can go on and on but I am getting ahead of myself. Tic! Tic! Toc! One step at a time. Hit me up.


capra internetensis said...

@jeanL

no use trying to cure ignorance when it's willful

Does EDAR even affect pigmentation?

@Gioiello

Western Europeans + a Saudi = sample bias

Finding the Samara Z2103 subclade in Bashkortostan and Daghestan, it is not a wild leap to suppose we might find more southern and western modern Z2103 subclades in more southern and western locations areas of the Yamnaya horizon. They did migrate into southeastern Europe, and their immediate descendants probably into the Transcaucasus via Daghestan.

Well, only ancient DNA will solve the question, of course. But I hope you will not be too distraught if your Copper Age great-grandpa shows up buried under a kurgan in Ukraine.

xyyman said...

Jeanlohizon

I don’t get your point. In fact you just made my point.

Villabruna, La Brana, Loschbour , Nigerians carried ANCESTRAL states of the two KEY genes for pigmentation. SLC45A2 and SLC24A5. You are being a conman when you posted SELECTIVE SNPs. LOL! Once we get MAJOR ones out the way. Let’s us go on to the other minor genes.

eg
ASIP*84 TT also found in Nigerians.
ASIP*17 AA also found in Nigerians.

The genetic profile of Villabruna, La Brana and Loscuhbour are virtually the same as Nigerians.

So again I repeat Villabruna was black. You cannot “make up” a color like “bronze” and “tan” and “red” when the gene-profiles are the same. If the genotype is the same then common sense dictate the phenotype is the same. This is simple logic.


xyyman said...

@ Capra. That was your boy who mentioned EDAR as a pigmentation gene. But I believe he was just listing data that he pulled. Sides EDAR*760 derived is Asian(high frequency) although found in West Africans. Yes! it is found in West Africans. But more importantly it is not found in Europeans. Which most likely means it is NOT Neolithic/EEF or is from ANE portion of Ancient Europeans. Did that go over your head Capra?


Capra did you understand what Jean just posted and my response to him.

BTW - any of you have access to the BAM files for these ancient Europeans? I am trying to get their LCT breakdown.

xyyman said...

In case you missed the key point JeanL. ALL the derived minor genes for pigmentation is found in Africa. The "Turn Key" is SLC45A2 and SLC24A5 which is NOT found in Villabruna, La Brana etc. That is why the TWO genes were listed in the Villabruna paper. Villabruna was ancestral for BOTH SLC45A2 and SLC24A5. He was black.

jeanlohizun said...

People need to up their reading comprehension skills:

"Variations in the KITL gene have been positively associated with about 20% of melanin concentration differences between African and non-African populations. One of the alleles of the gene has an 80% occurrence rate in Eurasian populations.[52][53] The ASIP gene has a 75–80% variation rate among Eurasian populations compared to 20–25% in African populations.[54] Variations in the SLC24A5 gene account for 20–25% of the variation between dark and light skinned populations of Africa,[55] and appear to have arisen as recently as within the last 10,000 years.[56] The Ala111Thr or rs1426654 polymorphism in the coding region of the SLC24A5 gene reaches fixation in Europe, but is found across the globe, particularly among populations in Northern Africa, the Horn of Africa, West Asia, Central Asia and South Asia.[57][58][59]"

SLC24A5 accounts for 20-25% of the variation between dark and light skinned populations of Africa. So neither SLC24A5, nor SLC45A2 account for 100% of the variation. Ergo, having the ancestral variant in both of them, does not make one's skin color automatically similar to Nigerians.

Villabruna was derived for IRF4, rs12203592 and OCA2/HERC2, rs12913832, so are Loschbour, Motala, La Brana, and other HGs. Are Nigerians or any other SSA derived for those SNPs? The answer is NO!

Once again, genomewide association aside, which clearly shows that WHG cluster nowhere near Africa, their pigmentation genotype is nowhere near modern day SSA. In addition, no words from the ignorant masses on the FACT that Motala HGs were derived for SLC24A5 and SLC45A2, in addition to IRF4 and OCA2/HERC2. Last I checked they lived in Europe during the Mesolithic.

Therefore neither the darkest European Hunter Gatherers, WHG, nor the lightest ones (SHG, EHG, BHG) have the same pigmentation as modern day Sub-Saharan Africans. Anybody, suggesting they do, is an idiot who clearly is either ignorant or the data, or wants to misinterpret it. Either case, no point in wasting more of my precious time in educating Morons. The masses, can clearly see that the arguments are laid out. For once, be f... proud of your culture, instead of trying to steal others people's culture.

Open Genomes said...

Apologies, in the "fray" I forgot to add:

• I'm a "Europeanist" when it comes to I-M170 and C1a2-V20 origins in Upper Paleolithic Europe.

• Now what would we say about Oase1, who was the first AMH European and 1/8th Neanderthal, who is in K2a1-M2335 (pre-NO1) like Ust'-Ishim from the Irtysh river in Central Siberia, when that's found today only among Tamils from Sri Lanka. On the PC plots, both cluster with the possibly Indo-Pacific remnant Kusunda from Nepal. What is that, a "Dravidianist", "South Asianist", or an "Oceanist"?

• Scandinavian Q-L804 clusters with Native American "Kennewick Man" Q-M3 in Q-L930, and Q-L930 is a sister clade to "Anzick-1 Clovis" Q-Z780. Given that the YFull tMRCA of Q-L930 is 15,500 ybp, it seems almost certain that Q-L930 originates in Beringia, which before the Antarctic Meltwater Pulse 1 (MP-1)at 14,700 BP, included Alaska. YFull Q-M1107 tree This might explain the similarity of the Solutrean culture of Mesolithic Europe to the Clovis culture of North America. Does this make me "Germanized" or a "Dzeibelist"? 3:) (Guess not, 'cuz they weren't what he would call "White".)

• Two of the most basal samples in R1b-Z2106, the ancestor of "Yamnaya" R1b-Z2109 (R1b-KMS67) and Mediterranean and "Italian" R1b-CTS7822/Z2110, are found in a Han Chinese from Beijing and a Bhutanese. I guess that makes me a "Maoist", but there's that "small matter" Tocharians, so I guess that makes me an "Indo-Europeanist".

What about this just being "Science"?!

Open Genomes said...

@David

Remember many years ago when you asked why a certain region on chromosome 6 looked like it had low recombination and I pointed out that this was the immune system HLA region?

Would you like to do something original?

How about a PCA using ancient samples of just the HLA-B region with SNPs from chr6:31,237,743-31,324,989 ?

Of course you realize that some HLA region alleles mimic the Yersinia adhesin sequence ... how about Y. pestis, Steppe ancestry, and HLA-B*27 (which I myself carry).

Tag SNPs:
rs13202464
rs4349859
rs3819299
rs116488202

Molecular mimickry between HLA B27 and Yersinia, Salmonella, Shigella and Klebsiella within the same region of HLA alpha 1-helix.

I think you will find some rather striking differences between Mesolithic, Neolithic, and Steppe ancestry, not to mention the various other regions.

Interested? :)

Open Genomes said...

What's this about Richard III?

Richard III tested as G2-P287, but I can say that it's very likely based on some unique features of his STR haplotype that he and the Plantagenets are G2a2b1b1b1-Z6029. G-Z6029 under G2a2b1-M406 is found among about 8% of Druze, and so far, South Italians and Sardinians, as well as scattered other Europeans. The <a href="https://yfull.com/tree/G-PF3316/>tMRCA as of right now is 6200 ybp</a>, which is a bit too recent to be early Neolithic, but it fits a later Neolithic migration from the Near East. As has been pointed out here, G2a2b1-M406 is entirely absent so far from the Early Neolithic in Europe - and everywhere else.

Open Genomes said...

The upshot is that G2 (or G in general, see SG21 from Godin Tepe) is Neolithic from the Near East. Every ancient G sample so far has been found in a farmer, not a single one is a hunter-gatherer. This includes Bon004 in G2a2b2b-F705 (equivalent to PF3359) from Boncuklu, 6 km north of Çatalhöyük, from as far back as > 10,300 BP (8,300 BCE), which was earlier than Kotias in J2a1b from Georgia and contemporary with the earliest PPNB samples from 'Ain Ghazal.

A second sample from Boncuklu from 8212-7952 calBCE was G2a2b2b1a-PF3422.

Two samples from the Starcevo culture of Early Neolithic Hungary, I1880 and I1877 (5704-5556 calBCE), were also in G2a2b2b-PF3359, and so was one, I2739 from the Transdanubian LBK (LBKT) (5309-5074 calBCE).

What's fascinating is that I1314 from the Iberian Chalcolithic from 2880-2630 BCE in El Mirador Cave, Atapuerca, Leon, Spain, was G2a2b2b1a1-PF3378.

Yet, today the earliest branch of G2a2b2b-PF3359, G2a2b2b2-CTS293, is found among a high percentage of HGDP Palestinians, a single 1000 Genomes CEU, and aparently among comple of Armenians (including one from the Lake Van region) and a set of closely matching haplotypes of Southern Iraqi origin. Given that the earliest Neolithic farmers arrived in Central Anatolia somewhat before 8,300 BCE from further east, I think we can say that this extremely branch of G2a, which is only really "common" in Sardinia and among 1% of Dutch in Karmin (2015), originated in the Mesolithic in the Levant or the northern Fertile Crescent, and expanded with the PPNA. (The YFull tMRCA is 13,100 ybp.)

It certainly wouldn't surprise me at all if some G2a2 was also found in the Neolithic in the Nile Valley and North Africa. That just means that it's "Neolithic". That doesn't make it in modern terms not "European", "African", "South Asian", "Central Asian" or even "North Chinese". (There is a single Han Chinese from Ningxia Zhong (2010) who is G2a2b2b1a2a1b-F807, which is so far otherwise found among Dutch.) There are in fact G2a people in West Africa without an sign of recent European admixture. As I've pointed out in other places, goats are clearly a Near Eastern Neolitic domesticated animal, and they are found from North China (think of the Year of the Goat in the traditional Chinese calendar) to West Africa, where goats are a staple of agriculture. There are G2a-P15 people in parts of West Africa that otherwise have R1b1b-V88 as the only other Y-DNA haplogroup of ultimate Eurasian origin. We know a bit about these African (Nile Valley, North African, Sahelian, and Sierra Leonian) G clades, but we don't know specifically about some of these found in the interior of say, Cameroon.

Open Genomes said...

The same G2a branch, G2a2b2a1a1c-CTS342, was found in Barcin in NW Anatolia 6500-6200 BCE, the Late Neolthic Lengyel and Baden cultures of Europe, and also today in a 1000 Genomes Han Chinese from Beijing, Brahui from the Indus Valley, Arabians, Sardinians and other Europeans, and a Mende from Sierra Leone. It's just "Neolithic" and eventually ended up in various places. (No Steppe or Chinese aDNA Ys have turned out to be G however.) Saying something that spread so long ago is "African", "European", "South Asian" or even "East Asian" is relative, and in some sense meaningless.

I think it's very possible that at least one very rare specific G2a clade may have come to Southern Italy via Egypt, and there may be others, although we can't prove it yet. Would such a G clade be both "African" and "Early Neolithic from the Fertile Crescent"? Yes. The route is important, but one can't say that it's exclusively African. On the other hand, what if a G clade has been in Africa since the Early Neolithic? We could legitimately claim it to be "African" as well. (That would predate the Bantu-speaking expansion.)

The point is, that these kinds of divisions are somewhat meaningless, because the ancestral components we know about don't divide up along so-called "Racial" lines. European Neolithic vs. EHG/Steppe were quite different from each other (until they admixed) but is one more "_______" (fill in the blank with your favorite Racial term, "White", "Caucasian", or something else) than the other? That doesn't mean anything.

The arguments here are about "categorization". "Race" isn't "sortal" because it's not one dimensional like a spectrum. Ancestral components are multidimensional, and while there's distinct human variation, "Races" among AMH don't exist, because human ancestry cannot be divided up that way. Skin color is one of the lousiest ways of categorizing someone's ancestry, because those alleles were under strong selective pressure.

Here's one you probably didn't know about:
rs4988235=T in the MCM6 gene is the most common allele for lactase persistence. The derived allele is virtually fixed among Dutch.

However, this same allele is found among 21%-39% of Fulani. Arabs on the other hand, for example, carry it at a rate of around 2.5%.

Hakka carry it at 2.4%, and even unadmixed Native Americans like the Surui carry it at 1.1%.

ALFRED Allele Frequency For Polymorphic Site: MCM6 intron 13 C/T (-13910 ) SNP

Does that make the Fulani "White" or the Dutch "Black"?

This lactase persistence allele is thought to be "quintessentially European".

And if I don't carry it - unlike most people of European descent, but like Samaritans, Yemenite and Ethiopiean Jews, Mbuti, Han Chinese, and Onge - does that make me "neither"?

We've got to start thinking past these "traditional Racial classifications" and think of the complexities of human ancestry. Then we won't be fighting as much over nonsense, SNPs that are adaptations ...

Samuel Andrews said...

@Open Genomes,

We've discussed whether race exists before and I'll go at it again.

The racial classifications we have weren't created by racist! This is a misconception I think you and many modern people have. Our racial classifications were created by people who accurately described the diversity they saw around them.

And if you look at DNA there actually is an East Asian cluster, a West Eurasian cluster, and an African cluster. Those really are the biggest genetic families/clusters in the world and as a result they correlate with phenotype. There's nothing wrong with calling them races. Yes they don't derive from single streams of ancestry, yes the origin of those clusters are complex, but they are infact distinct genetic groups which can explain a lot of modern human diversity.

""Race" isn't "sortal" because it's not one dimensional like a spectrum"

If you compare East Asians, West Eurasians, and Africans it is kind of one dimensional. For example there's a collection of mtDNA haplogroups found in every part of West Eurasia that you'll basically never find in Africa or East Asia. There's a collection of African-exclusive mHGs and a collection of East Asian-exclusive mHGs.

Of course there are many exceptions to the rule; Western Siberians are as much West Eurasian as they are East Asian, North Africans have a huge amount of African admixture, etc., but there really is a decent amount of one dimensionality in human genetics.

"We've got to start thinking past these "traditional Racial classifications" and think of the complexities of human ancestry."

I agree. We have to let the data teach us and not fit the data into what we belief are already facts. At the same time not deny the validity of traditional racial classifications and not condemn the use of the term race.

batman said...

@ Sammy

Well said.

@ OG

The 'evolutionalry principle' is well documented as the causeway of the various plants and animals populating the Globe. Furthermore we can say that we (still) divide plants and animals into various species - eventhough we have to admit that the basic genomes involved crosses these divides. Keeping the focus on the variety and the multitude of 'life-forms' we better divide nature according to structural and other characteristics into 'kinds'/'species' and 'forms'/subspecies. Aka 'families', 'breeds','stocks' or 'races'.

Which is why denying the existance of sub-species becomes a contradicition of terms - and an alienation of common sense as a premise of science. Dismissing terms like plant-families, livestock breeds and races of cats, dogs and humans can't errase the reality of any of them - historically and commonly known. Redefining these scientific terms is mere politics - and nothing else.

Regarding clasifications based on current archaeology one may be somewhat precausious not to adopt terms like Mesolithic and Neolithic without a closer definition of what they actually represent and not. A dogmatic view of terms explaining "agriculturalists" and "hunter-gatherers" as widely differeent periodes and/or cultures have a sparse udnerstanding of both. All the more so as present archaeology have discovered agricultural traits, plants and animals to be domesticated already during ice-time, within a number of paleolithic sites.

Finally, OG - to make valid claims about any refugia you need some KNOWN archaeological sites to refer to. Besides dates from Billeroed/Alleroed you also need it to cover the last and deepest cold-phase - 12.000 to 13.000 years ago.

To gain some further clearification from the genetic diversity developing during the Late Paleolithic it would be useful to determine what lines (dynasties) of y-dna and what circles of mt-dna that had their roots in the arctic part of paleolithic Eurasia, rather than the tropical climate-zones of the late Paleolithic.

AFAIK the makro-dad F was arctic already. Which means he had developed the traits neccesary to SURVIVE north of the 45th paralell - such as pale skin and light hair. Please note - several phenotypic traits - such as narrow nostrils and ligth pigmentation was adaptions NESSECARY to survive up north - for mopre than one generation...

1. Isn't it clear that A makro-dad (F) of Cro-Magnon/Caucasian origin - were responsible for the ALL the descendant male-lines that spread across Mesolithic Eurasia - counting GHIJK/NOQRST?

2. How is the old I-E term "aet" and "aetnos" - meaning family/breed/et-ni-ci-ty - related to the "aets" (family-lines) represented by dynasties like G2, H2, J2, R1a and R1b? Doesn't they all represent various "races" - whatever skin-color they may have had...?

3. What mt-dna-groups are following the same division - rooted in pale-arctic vs. pale-tropic?

Gioiello said...

@ batman

"1. Isn't it clear that A makro-dad (F) of Cro-Magnon/Caucasian origin - were responsible for the ALL the descendant male-lines that spread across Mesolithic Eurasia - counting GHIJK/NOQRST?"

Read Shi Huang and his Chinese colleagues.

Open Genomes said...

@Samuel Andrews

You said: "And if you look at DNA there actually is an East Asian cluster, a West Eurasian cluster, and an African cluster."

No, what you actually see is this:

Eurogenes Lazaridis (2016) Ancient Near East Interactive 3-D PCA Plot

(Note that this plot leaves out the Mbuti and San.)


There are 3 African and 4 Eurasian poles of diversity.
There is even on minor one in the Americas.
Almost everyone today falls on a continuum between these:

Africa:
• Ju'hoan San (Namibia) to Yoruba
• Yoruba to Mota (who is similar to the "Gummuz" [Ethiopian Sudanese Nilotic-speakers] and Hadza)
• Yoruba to Mozabites, and other North African Berber groups

Eurasia:
• Neolithic Europeans (today, somewhat close to Sardinians) to Taiwanese Aboriginals
• Neolithic Europeans / Sardinians to Anzick-1 (Clovis) and Kennewick, (today closest to North American Amerinds)
• Taiwanese Aboriginals to North American Amerinds
• Kusuda and South Asian Austroasiatic-speakers to Australian Aboriginals

Americas:
• North American Amerinds to the Surui

There are two Eurasian "streams":
• Neolithic Europeans to Taiwanese Aboriginals via Iranians, South Asians, Onge, and Austroasiatic speakers
• Neolithic Europeans to Taiwanese Aboriginals via Central Asians, Han Chinese, and Daic-speaking groups

Open Genomes said...

@Samuel Andrews

First, about your "East Asian", "West Eurasian" and "African" clusters:
What we see on the autosomal PC plots are "poles of diversity", and "dimensions", not "macro-clusters" or "Races of Mankind", such as you enumerated above.

I think the roots of your "clusters" are in fact political.
To give some examples, why don't you list an "Australian" or a "Sardinian" cluster?
What about "Bushmen", "Berbers", and "Surui"? (I know about the terms "Australoid" and "Paleoafrican" but they weren't mentioned in the above list.) The thing is that these groups are not politically important. "African" vs. "European" (or "Black" vs. "White") ancestry is a political issue in the US and Europe (think "BLM") and "East Asians" (namely, Han Chinese and Japanese) are politically and culturally important in a way that say Taiwanese or Australian Aboriginals are not.

And where would "ASI" South Asians - including the Onge - fit in this model?
(If you're from South India and you live in the UK, you're "Asian" but if you live in the US, you're "White". ;) )

Just because a group is very small today (the Surui, the Australian Aboriginals, or the Bushmen), or completely extinct in their original form (the Early Neolithic Europeans) doesn't mean that they aren't important in terms of human diversity.
Notice btw, that the "epitome" of "West Eurasians" are extinct in their unadmixed form, and the ones responsible for that were the ... Proto-Indo-Europeans, at times known as the "Aryans".

Your incredibly "simplifed" "East Asian", "West Eurasian" and "African" clusters was first formulated in a [pseudo-] "scientific" way by the French Aristocrat Arthur de Gobineau (1816-1882). He called these clusters "yellow", "white", and "black", terms still used today. (The term "Black" has had a big revival lately, and so have the terms "White" and "People of Color" [as opposed to "White"?].) Gobineau was certainly a "Scientific Racist" in the strict sense that he believed in a hierarchy of "Races", and the "separation of the Races".

Open Genomes said...

Some other points:

We know the Surui were identified as having some kind "2% Papuan-like" ancestry (Denisovan admixture?) that was absent among most other Native Americans except the Karitiana. Apparently, it is this unique component that accounts for the "extra dimension" among Native Americans, that is almost at a "right angle" to the main "Neolithic European to North American Amerind" axis (aka an "ANE" dimension).

The "North African / Berber" pole of African ancestral variation seems to be the African component in Natufian ancestry. Some people may argue that this is just the result of "Eurasian" and "Sub-Saharan African" admixture. However, there are two facts we know know from ancient DNA:
• Mota from Ethiopia had zero "Eurasian" ancestry, and he was E1b1a2-M329.
• mtDNA U6 was found in Muierii2, a Gravettian from Romania 33,760-32,840 calBP.

Y-DNA E cannot have originated in Eurasia, unless you say that almost all "African" ancestry was also of "Eurasian" origin. He's also autosomally extremely similar to Nilotic people from Sudan who are primarily Y-DNA A1b1b2b-M13, so the difference is not between "A and B" and "C-T" as Anatole Klyosov would have it. The vast majority of Berbers are E1b1b1b-Z827 of some kind (mostly E-M81) and many are mtDNA U6. However, it's clear this "North African" component had formed at least at the time of the LGM, when "Natufian" E1b1b1b2a1-M123 split from its exclusively African parent clade. If mtDNA U6 had a "back-migration" from Europe to North Africa during the Upper Paleolithic (and we also see Neanderthal ancestry in North Africa as well), then that could be at least 1/2 the time back to the most recent "Out of Africa" event. (The split of Y-DNA E and D datable to 65,200 ybp according to YFull.) So we can't quite call this "North African" component "admixture", because it clearly falls on one end of the "axis of variation" that includes the Yoruba and Mota. Maybe Africa wasn't quite as "separate" as many people think during the Upper Paleolithic?
And if anything that's the result of "Upper Paleolithic admixture" has to be discounted, then why not throw out anything that might involved Neanderthal and Denisovan admixture as well, which is what seems to be producing some of these Eurasian "dimensions", aside from isolation and drift?

Open Genomes said...

Notice that this specific North African pole of variation is not regarded as
"Black" by Afrocentrists, or really "White" by others, but it is in fact ancient and distinctively African as much as anything else in Africa. Those same two main light skin color alleles, SLC24A5 rs1426654 and SLC45A2 rs16891982 are also found in Africa, but based on what we see in European aDNA, they seem to have been propagated as a result of the dietary changes caused by the Near Eastern Early Pre-Pottery Neolithic. It's a good bet that the Mesolithic North Africans, like the Mesolithic Europeans, were also ancestral for these alleles (but like the Mesolithic Europeans, they may have carried other "minor" lighter-skin variations.) If people knew that they were first "Black" (apparently meaning to some people ancestral for SLC24A5 and SLC45A2), then "White" (derived for both SLC24A5 and SLC45A2), would that make a difference to some people's attitude about how "African" this Mesolithic North African component is? If it does, that just makes no sense, that's just the "modern politics of skin color" at work, superimposed on the ancient past.

So "East Asian" "West Eurasian", and "African" are just the traditional "Yellow" ("Mongoloid"), "White" ("Caucasoid") and "Black" ("Negroid") "Great Races of Mankind", and reflect present day social and political circumstances, rather than "poles of variation" in a multi-dimensional PCA.

Seinundzeit said...

Sam,

Technically speaking, OG is correct.

Mainly because, the amount of genetic divergence that exists between the most extreme poles of contemporary human genetic variation is still much smaller compared to what we see with actual Chimpanzee subspecies (in scientific work, "race" = subspecies).

Though, actual human "races" have existed.

For example, you can construe Neanderthals as another human subspecies. So, I guess Eurasians are "multiracial", because of Neanderthal and Denisovan ancestry. Although, Sub-Saharan Africans are probably also admixed with different human subspecies.

Regardless, in genetic terms, the classical "races" envisioned by physical anthropologists don't qualify. Everyone alive today is Homo sapiens sapiens.

And, even if we ignore the amount of genetic divergence in question, the fact remains that one of the classic races of physical anthropology is exceedingly muddled/ambiguous in terms of deep genetic ancestry.

Of course, I'm referring to the "Caucasoid" race, which is actually a mix of WHG/UP European-related, Northern Eurasian-related, ENA-related, and Basal Eurasian ancestries.

The WHG/UP European-related and Northern Eurasian-related ancestries are connected, but in very deep history.

ENA is a totally different branch from them, but it seems all West Eurasians have it. The Lipson and Reich model is actually very solid, and based on it even Europeans that are usually at 0% ENA with ADMIXTURE/PCA are actually 25% or more ENA.

And Basal Eurasian ancestry is very divergent from the other branches, yet all living West Eurasians have it.

Not to mention Sub-Saharan African ancestry in North Africa (with trace amounts in some Southern Europeans), or ASI in South Central Asia + northwestern South Asia, and these populations have always been regarded as "Caucasoid".

Basically, the classic "Caucasoid" race is the product of mixture between deeply diverged genetic components, unified by clinal gene-flow, and distinct historical processes which have played out across millennia (like the Neolithic expansions, events during the Bronze Age, etc).

In addition, no physical anthropologist has ever seen a connection between East Asians and Australians/Papuans. In fact, Australians/Papuans have always been a source of debate. Some had them as their own thing (Australoids), some claimed they were "Archaic Caucasoids", others lumped them with Africans.

Finally, we now know that Sub-Saharan Africans like Yoruba are much more closely related to Eurasians than they are to populations like Biaka or Mbuti! I mean, would anyone expect this, if they went by physical anthropology? I highly doubt it.

At the end of the day, typology is a waste of time.

John Smith said...

Open Genomes it is correct that current DNA evidence suggests E originated in Africa and E being a macro haplogroup we can not use E1b1b to infer the origins of the others. However E1b1b dominanted Natufians only a few thousand years after it was born and Natufians had no sub Saharan Admixture this suggests contrary to modern distributions which are useless for finding origins E1b1b is probably from the Levant or nearby of course there is a few thousand year gap so hopefully we have more ancient DNA soon to prove this correct or incorrect. This is the way I understand it please tell me if I'm wrong.I don't really care about the origin of E as much as R however I do find the Natufians fascinating and do they have Neanderthal Admixture?

John Smith said...

You can not just assume based on modern DNA that Natufians E1b1b has an African origin. People move aka K2a1 in Europe 40kya. We do know U6 comes from Europe based on ancient DNA tho that is fascinating. The population with K2a1 also had U6 no one would have guessed that using modern DNA no one.

capra internetensis said...

@John Smith

The Natufians are about 13 000 years old. According to Y-Full the TMRCA of E1b1b-M215 is about 35 000 years ago. If you meant M35, then 24 000 years ago. The split of M215 from V38 (the Y haplogroup of Mota and YRI) was around 43 000 years ago.

E1b1b1-M35 is typical of North and East Africans with recent West Eurasian ancestry. Our relatively 'pure' African reference samples have E branches that split ~30 000 years or more before the Natufians existed.

Lack of Natufian relatedness to Sub-Saharan references means that not only did they not mix into Natufians, but Natufians did not mix into them. We just don't have a good reference for what the original source population for E1b1b looked like.

Presumably the first people carrying E were descended from the ancestral Out-of-Africa population before it left Africa - or possibly early back-migrants. Since both male and female (L3) lineages of this type are frequent in Africa we can suppose that there is a widespread Para-Eurasian ancestry well-mixed into most Sub-Saharan Africans, which is quite difficult to separate both from Sub-Saharan and from Eurasian ancestry.

Open Genomes said...

@Samuel Andrews:

You said: "The racial classifications we have weren't created by racist!"

Not true. And it didn't even just involve so-called "Scientific Racism" either.
More about Arthur de Gobineau (1816-1882) and his Essay on the Inequality of the Human Races (1853-1855):

Quote:
Gobineau wrote that "The white race originally possessed the monopoly of beauty, intelligence and strength" and that whatever of the positive qualities the Asians and blacks possessed was due to subsequent miscegenation. Within the white race, there was a further subdivision between the Aryans who were the epitome of all that was great about the white race and non-Aryans.
Gobineau later came to use and reserve the term Aryan only for the "German race" and described the Aryans as 'la race germanique'. By doing so he presented a racist theory in which Aryans – that is Germans – were all that was positive.

Gobineau was a transitional figure between Traditional Christianity and a secular, "scientific" outlook. He believed in a literal Adam and Eve. The "Three Great Races of Mankind" correspond directly to one interpretation of the "Three Sons of Noah", or a rearrangement to include East Asians, as was often done with the Late Medieval and Renaissance paintings of the "Vistation of the [Three] Magi". Certainly, the Biblical "Curse of Ham" which was used by some Christians to justify African slavery was applied to "Blacks".

(Ironically, almost all the peoples listed as "descendants of Ham" in the Biblical "Table of Nations" are Afro-Asiatic speakers, including "Semites". Bronze and Iron Age tribal people could detect that certain languages were related, and that's why they grouped "Sidon" [Phoenicians] with Libyans, Kushites, and "Put" [Punt, Somalia] and South Arabians, rather than by skin color.)

If Gobineau was from another religious tradition - say Hinduism - would he have written about four "colors" (varnas) instead of three? Note that people that the Classical world were unaware of, like Bushmen, Native Americans and Australian Aboriginals, didn't even enter into his "model".

So these "clusters" are really based on a combination of the Biblical "Three Sons of Noah" with Classical awareness of the Han Dynasty. Interestingly, since the Ancient Greeks, who ruled part of Northwest India for centuries, apparently didn't regard the "Indians" as any different than any other (non-Greek) "barbarian", and because the "Brahmans", "Sarmanas" (sramanas, Buddhist monks), and "Gymnosophists" ("naked wise men", i.e. Jains) were held in high regard by the Greeks, Romans, and even authors like Josephus and the Christian Clement of Alexandria. Because the Greeks were in India, they didn't regard the South Asians as any more different from the Greeks than say the Germans. Because of this, and the fact that many South Asians speak Indo-European languages, Gobineau and many others "clustered" South Asians with Europeans, even though there could be many other ways of "clustering" Eurasians.

Open Genomes said...

@Samuel Andrews,

Gobineau was also responsible for the idea of the "Aryan Race" as a "subgroup" of "White". In the 19th and early 20th centuries, sometimes "Aryan" was synonymous with "White", but often it was restricted to certain European groups, rather than limiting it even to Indo-European speakers. Interestingly, by 20th century "Aryan" excluded Slavs, and Slavs, like the "Semitic Race", were not regarded as "White". (For Uralic people like Finns, it was "touch and go" and they were almost classified as "Asiatic" in the US for immigration purposes.) So these "Racial" classifications weren't even based on skin, hair, and eye color either.

The problem now, in the US, is that terms that refer to historic ethnicities such as "African-Americans" (African slave descendants, a historical social caste) are also used in their historical sense as "Races". An African person in the UK isn't "African-American", but a dark Aboriginal or South Asian in the US isn't "Black" in the sense of "African". Is "Black" referring specfically to African-Americans, the antonym of "White", so if "Black Lives Matter", what about "White Lives"? Is everyone who is not "White" a "Person of Color" (how is that different from "Colored Person"?) or is everyone who is not "Black", "White"? And "Yellow" is offensive, but "Black" and "White" aren't?

Again, here is the "classification" according to Gobineau, which just didn't fit the world then, and doesn't fit our society now, but is still a major part of our political discourse. (If you think it isn't, just say "Black Lives Matter" and then "White Lives Matter".)

And when was it decided that people from south of the Mediterranean, and east of the Bosphorus, and even many people from the Caucasus, are "People of Color", not "White"? Who arbitrarily decides these things? (Go check how a very fair-skinned Palestinian woman who was a leader of the recent "Women's March", was described as a "Woman of Color".)

When you say "West Eurasians" are a "cluster", would you include say North Africans, and South Asians in that, or Near Easterners? That "cluster" that you are naming - often called "Caucasian" or "White", is in the process right now of being arbitrarily (yet again) redefined. You will say "West Eurasian" and others will say "White", and name people that you yourself name as "West Eurasian" as "Persons of Color". People who espouse these classifications don't even have a fixed definition right now for these. Do you expect everyone to accept these "clusters" ("Races") as "universal" when people right here don't even agree about them? You can ask "xyyman" if he thinks North Africans are "Black", or ask others if they think that "Arabs" or even Armenians are "White".

Samuel Andrews said...

@Open Genomes,

In America the origins of the idea of "White" and "Negro" and "Indian" go back way before the 1800s to our earliest days. You can find documents using those terms back in the mid 1600s. The same is true for Latin America. Spanaird and Indian and African were and are seen as differnt races.

https://i0.wp.com/brewminate.com/wp-content/uploads/2016/12/SlaveTrade35.jpg

Sure scientists created all of the Aryan and White power stuff but that doesn't remove the fact that race is real and it was ordinary people who created the concept.

It's honestly hilarious that some people argue race doesn't exist. Look around you!! The proof is starring at you in the face. Arguing there's no such thing as race is like arguing there's no such thing as different languages or different colors.

OpenGenomes, you're afraid of the idea of race because of racism. All I believe is that there are large and relatively distinct genetic clusters with members who can be distinguished according to features. That's what race is to me. There's nothing scary or racist about what I believe.

People from your camp who aren't familiar with genetics at all argue there isn't a genetic difference between different races. But because you are familiar with genetics you know you can't argue that so what you do is exaggerate the complexity and fluidnesses of human genetics to argue there are just fluid trends not divisions in human diversity.

Samuel Andrews said...

@OpenGenomes,
"When you say "West Eurasians" are a "cluster", would you include say North Africans, and South Asians in that, or Near Easterners? "

Yes I would. But Europeans are another cluster which you could call the white race if you'd like. Europe's relationship to the Middle East is complex and even fluid but a genetic distinction can be made which can explain differences in looks.

Look I'm not arguing looks will always correlate perfectly with ancestry. The looks of some populations might become distinct quicker than in others. And other factors will affect how well looks correlate with ancestry. What I am arguing is that ancestry and looks do correlate with each other to some extent. Looks are inherited from our ancestors after all. This is simple stuff.

Open Genomes said...

"Race is sortal". Tell us if a Greek from Thrace is "European" (or is it "West Eurasian?), then us if a - say a Cappadocian or Ponitic Greek (you know, a "Pontikos" ;) ) is "European", then if an Armenian is a "European" ("Caucasian"?), then a Turk of Armenian or Pontic or Cappadocian Greek descent, a "Lesser Armenian", then an Alawite from Hatay Province whose granfather was an Arabic-speaking Syrian.
Now tell us if this particular Palestinian woman who led the Women's March is a "Woman of Color" - what if she was a Christian, instead of a Muslim woman wearing hijab?

Do you and everyone else notice something? These "clusters" supposedly aren't defined by the "Alt-Right" or the "Regressive Left" yet amazingly, they actually generally agree in their definition. They both seem to take these "clusters" very very seriously. But I thought that supposedly included all "West Eurasians" (except possibly the well over one billion Central and South Asians, who somehow are "unclassified" between the "incredibly obvious" "West Eurasian" and "East Asian" so we can just totally ignore them), but until ... two years ago? now? North Africans somehow showed up as "obviously" "West Eurasians" and not "Africans" even though on the PCA they are clearly on the African continuum, not on the "Eurasian plane".

I bet we can start a big fight right here between xyyman and Samuel about whether the North Africans qualify as "Black" - but the question is - who will take which side?

One of two significant blonde hair allelles, rs3829241=A. This doesn't look very "West Eurasian", does it?
ALFRED Allele Frequency For Polymorphic Site: rs3829241
The other signficant blonde hair allele, rs35264875=T:
rs35264875 1000 Genomes Project Phase 3 allele frequencies


So it all apparently comes down to three alleles:
The derived SNPs for SLC24A5 rs1426654=A, SLC45A2 rs16891982=T, and EDAR rs3827760=C.

Surprise! The most "East Asian" clustering groups, the Taiwanese Aboriginals and the Ainu, have low frequencies of EDAR rs3827760=C, which is strongly associated with "East Asian" phenotypes:
ALFRED: Allele Frequency For Polymorphic Site: EDAR Val370Ala rs3827760
Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

Many people have in the past called the Ainu "Caucasoid" (or "White", or whatever) solely on the basis that they have thick facial hair and generally lack the derived EDAR Val370Ala allele. That's about as far from (truth of) the PC data as possible.

As was pointed out here, this allele is also present at low levels in some Sub-Saharan African populations.

As many of you know, several Swedish Hunter-Gatherers from Motala (I0011, I0012, I0016, I0017) were heterozygous for EDAR rs3827760, but guess what:
DevilsGate1 (love that name ;) ), a prototypical Neolithic East Asian from 7,700 BP, from the border between Russia and Korea, contemporary with the SHGs from Motala, was also heterozygous for EDAR rs3827760:
Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

What does that make the archetypal "Nordic" and "East Asian" people in terms of many peoples' definition of "Race"?

Open Genomes said...

However, these same "pole of human variation" Taiwanese Aboriginals carry the very same MC1R Val92Met rs2228479=A and haplotype that Neanderthals had, at high frequencies.
Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans

Go check in your typical "Forum Biodiversity" way photos of Taiwanese Aboriginals who have sandy brown hair, and no "typical Asian features". "Identify the Race of this person." Do they meet your criteria for "East Asian"? And if they do, would they be thought to be "East Asian" by the average "person on the street"? Yet, maybe it's this very same "slightly extra" archaic admixture (about 20% more), with a different set of alleles, which places them at one end of this "pole of Eurasian variation".

Shaikorth said...

On the topic of Austronesians and their extreme "East Asian" PCA position: Taiwanese Aborigines and Igorots, when measured with formal stats, aren't really more distant from South Asians or Europeans than other East Asians. Meanwhile various indigenous Southeast Asian populations like Onge actually might be more distant, but this doesn't show on PCA because the dimensions are dependant on sample sizes and East Asians usually outnumber Andamanese many times over.

"Principle Components Analysis (PCA) is closely related to the STRUCTURE model in the information that it uses, both in theory (Lawson et al., 2012) and in practice (Patterson et al., 2006) and has also been shown theoretically to be affected by sample size (McVean, 2009). Friedlaender et al. plot a neighbour-joining tree calculated based on Fst values between populations which instructively exaggerates the effect of drift (Figure 3G). Africa and the Middle East together make a small part of the diversity which is dominated by the isolated populations of Native Americans and PNG. If enough individuals are present in the sample, these populations are likely to be picked out as major axes of variation, either by STRUCTURE, ADMIXTURE or PCA."

https://www.researchgate.net/publication/305985032_A_tutorial_on_how_not_to_over-interpret_STRUCTUREADMIXTURE_bar_plots

Samuel Andrews said...

@OpenGenomes,

You're not giving any evidence against the idea of race. Plus you're fighting against a straw man. I never said the relationship between different races/large genetic clusters is a simple tree. Yet you're arguing against me as if I did.

North Africans btw really just support the idea of race/large genetic clusters because they're a mixture of "West Eurasians" and "Sub Saharan Africans.", two massive genetic clusters that encompass over a billion people each.

And while Middle Easterners and Europeans look pretty different, their shared ancestry does result in common phyiscal features.

jparada said...

I got a question. If African variation is basal, why are Africans usually shown close together on a corner on these PCAs, instead of widely spread? Is it due to undersampling of Africans, or are Eurasians so drifted that their variation takes over the main dimensions?

@capra

Presumably the first people carrying E were descended from the ancestral Out-of-Africa population before it left Africa - or possibly early back-migrants. Since both male and female (L3) lineages of this type are frequent in Africa we can suppose that there is a widespread Para-Eurasian ancestry well-mixed into most Sub-Saharan Africans, which is quite difficult to separate both from Sub-Saharan and from Eurasian ancestry.

What you describe here sounds a lot like that mysterious "Basal Eurasian" thing, indeed!

Open Genomes said...

Let me just say before I continue, in case any of you are wondering, why it is that I'm going on about this here:

First off, everyone I'm sure noticed that nearly every discussion of ancient DNA gets derailed in to a huge pissing match about "Race". Certainly, all that BS about the "Italian Refugium" is definitely part of it. (How did the accusation that a rather prominent academic posting here is a "nigger Jew" suddenly come up?

(That means it wasn't a "Refugium", by definition. We can toss that "crank theory" in the trash. And as I alluded, there appear to be way more Mesolithic Near East to Europe post-LGM migrations than just "Villabruna" with is near "dead-end" R1b1a-L389*, but that's another story entirely.)

For all you self-proclaimed "Genetic Genealogists", I traced that individual's genealogy on both sides in great detail, and I think I know more about his genealogy than any of your could possibly imagine, but I won't discuss that here, since it's totally irrelevant to whether there was a Mesolithic migration to Southern Europe post-LGM.

Unlike any of you, I've been specifically "deputized" by the US Government (the IRS, no less) and the Federal Republic of Germany (yep, Germany) - and the entire EU, Australia, and reciprocally Canada, Mexico, and Israel, to do "educate you" (and everyone else) about "unscientific myths that divide people". I bet 90% of you people live in these places. I also have my specific "legal" reasons to talk about this, when it concerns this person (and some other people) in particular. (That could be you too, if you'd like. If you want to use your own genomic data and ancestry as "public evidence" for your own theories - be our guest: Open Genomes Consent for the Donation of Data - just read it, and if you agree, download the consent, open it in Adobe Reader, select "Tools" and then "Sign" and place that "digital signature" on the right place on the last page, then email it to consent@open-genomes.org (or send it on Facebook to any one of us).

Yes, we'd like to use David's Eurogenes K10 analysis for your autosomal data too, and we can make the figures for those components public as well. Why not - it's good work, and very valuable.

Open Genomes said...

Second, and this is really much more important:

I know that both some of you posting here and many of you "lurkers", are going to run off to Stormfront and EgyptSearch and start quoting things you see here.
Then, others will start posting comments on HuffPost, Breitbart, and various Youtube channels.

How do I know that?

This is a discussion about "genetics", but it really isn't. There's a whole parallel "sociopolitical" subtext going on here, and people seem to be rather reluctant to admit it. (Others, unapologetically, aren't.)

I've seen comments on news articles that have nothing at all to do with genetics, where people unapologetically say things like "but, Yamnaya!" and talk about "Principal Components" Yes, you know who you are ...
Eurogenes and David Wesolowski's work is "ground zero" for supposed "scientific" discussions of "Race". You more sophisticated types who actually like to present "evidence" for your ideas look at this - and cite it "over there".

Hi (or is it "Hail" ;) Richard Spencer, Jared Taylor, Shaun King, Alicia Garza and co.! The "gang's all here".
And a special "shout out" to one of my heroes, Sam Harris. Let's here it for "rational skepticism" in a cesspool of insanity.

I read the comments on these news articles, and read the comments on various Youtube channels too - Young Turks, Cenk's nemesis AIU (got the boot), Sargon, Milo (he likes his shaft ancestral for SLC24A5 and SLC45A2 - except if it's wearing a white collar ;) - also got the collective "boot"), any channel about WWII history, you name it.

Some of you shout "Black Lives Matter!"
I hope you all know the story of Sopan Deb, the embedded reporter in the Trump campaign, who is a producer for the most respected American broadcast news outlet, CBS News, and how he got his ass thrown to the ground by a Chicago cop, a boot on his neck, and arrested for "assaulting an officer" just because he was filming a black man on the ground outside the cancelled Trump rally:
CBS journalist arrested outside Donald Trump's canceled Chicago rally
(both South and East Asians, apparently) in "Silicon Valley" because we have a "civil society". Some "code words" there huh, maybe "14" of them? Notice, he somehow "forgot" that the "main clusters" are only supposed to be "West Eurasians" and "East Asians", and somehow, for him, "South" became part of "East".

Open Genomes said...

Apropos the recent post about "Greek Confirmation Bias" and "The Slavs":
When someone says "14!" and you Slavs respond with "88!" just remember that Herr "HH" deemed Slavs to be sub-humans, and acted upon it. Millions died or were enslaved. (In case you forgot, or just listen to Herr Goebbels like some people here, "The Jews" were murdered in Katyn Forest and fought in the Red Army not the other way around.) On the other hand, he thought that certain Arabs and North Africans were "Aryans". When you say "88!", think about whose "Racial definition" of "Aryan" you're using, and what category you fall into. (Weren't Russians "Mongoloid" according to that definition? That would make Russians, and maybe Slavs in general "East Asians". "14/88", right?)

Yes, I know, "the Brahmins", MYEF2 rs2470102 and all that (BTW, WC1, GD13A, Tep002, Bon002 were all heterozygous, AH2 was ancestral, and Bar31 and Klei10 were derived) but ... but WC1, a very First Farmer from Wezmeh Cave, in the Central Zagros in Western Iran, from 7455-7082 calBCE (9465-9092 BP), Y-DNA "partial" G2b2a-Z8022 (you're welcome for that, let's hear it for the G2b's ;) ) and mtDNA J1d6, was ancestral for 3 out of 4 of these skin color alleles. (SLC24A5 rs1426654 heterozygous, but SLC45A2 rs16891982 ancestral.) "But he was Black!" - not.
You see, just like many of the European Early Neolithic Farmers, he carried HLA-B*51:01, an Archaic Neanderthal immune system allele associated with "Silk Road" (sorry, not) Bechet's Disease, along with the common "European" HLA "Super-B*08" immune system allele, where nearly the entire HLA region is in full LD. This includes the so-called HLA-DQ2.5 allele associated with Celiac Disease, which if you think about it, is an odd thing for breeders of Triticum aestivum (bread wheat) to carry. These are clearly adaptations to a new Neolithic farming and herding lifestyle. [CC BY-ND-NC International 4.0 Open Genomes]

For all you "cluster" Race-obsessed people, he was like a an "oreo", crisp chocolate Brown skin on the outside, and that creamy White immune system on the inside. 3:)

It's the HLA region parts that you can't see that count, go ask anyone with an autoimmune disorder, and now that includes MS and schizophrenia too.

The repeated outbreaks of the bubonic plague over the millennia, and first European smallpox outbreak of the Antonine Plague in 165 CE, devastated populations. Smallpox alone killed off 30% of children before vaccination, and a novel strain of Yersinia pestis could easily kill off 50% of the population in a few months.

The skin color alleles and EDAR were under strong selective pressure. We know about skin color alleles, diet, vitamin D and folic acid, and fertility, but we aren't sure about the adaptations for the derived EDAR allele, except that fixation in some East Asian populations is rather recent.

Open Genomes said...

Here's one about "Racial clusters" in principal components, phenotypes, and the uniparental markers that everyone here knows and loves:
Yuzhnyy Oleni ("Reindeer Island") in Karelia vs. Kennewick Man: Racist fantasy vs. actual principal components

Put a beard on the guy on the right and the look like fucking triplets. :D

Based on the Y, what "Races" would you call these guys? At least one of these is probably the actual ancestor of a lot of people here. Can you guess which one?
If you look at the actual PC plots, you might discover that they actually cluster rather "closely" together in one particular "Eurasian axis". We have no idea what AG2 looked like, but it's a pretty good bet it was something like this.
Eurogenes Lazaridis (2016) aDNA PCA (with Africans)


So what are you all obsessed about?
Yes, "Race" really is a "social construct". It's a real "social construct" that can have rather dire consequences in certain circumstances. But let's not pretend that it's biologically significant compared to say that "creamy immune system center" and those varying "sandy haired" and "type 2 diabetes" Archaic alleles that are driving the "poles of variation" on the PC plots. Every time you make some pseudo-intellectual statements about the "Biology of Race", the date is just going to pop up and smack you down. You won't be able to convince anybody, so ... just "give up". And BTW, go check your own immune system alleles, and you might find some really surprising things ...

Open Genomes said...

And now, it's time for a psychiatric experiment:

There's a brain, with just three neurons that respond to three stimuli.
Fire one, the others fire, and they trigger a "seizure".
Fire all three, and the seizure is guaranteed to take place. It's an involuntary reflex.

Let us begin:

The sole surivors of "not Black, but dark-skinned" Mesolithic "Villabruna" [#1] R1b1a-L389* in Italy, which was post-LGM and therefore not part of any "Italian Refugium", are [#2] "The Jews", specifically Ashkenazi Jews. These survived virtually in the same location for about 13,000 years, ending up about 50 km south of Villabruna, until 1509 and 1940. Then, something happened that had everything to do with "Race" which nearly killed off these sole survivors of post-LGM Mesolithic Villabruna R1b1a-L389*, except in some random places like Britain, the US, and Israel. There's both genetic and genealogical proof of this.

Oh, and [#3] "Leftists!"

Medical illustration of involuntary triggered epileptic / Tourette's seizure

That should keep this thread going for another 50 hours, or 5 days, or something. 3:)

Chris Davies said...

@ Open Genomes - "he carried HLA-B*51:01, an Archaic Neanderthal immune system allele.."

I am skeptical that it's Neanderthal as HLA B*51:01 is in linkage disequilibrium with C*16:01 in populations throughout sub-Saharan Africa.

'Super-B*08' allele is part of the long AMH1 haplotype in Europeans: A*01:01-B*08:01-C*07:01-DRB1*03:01-DQB1*02:01 (highest HLA frequency haplotype in NW Europe).
The same haplotype but with A*30:02 substituted for A*01:01 is found in Tunisia, Cameroon, Botswana, South Africa (the ones that we know about). Gambia probably has a similar haplotype also: https://www.ncbi.nlm.nih.gov/labs/articles/12859597/

Samuel Andrews said...

@Open Genomes,
"Unlike any of you, I've been specifically "deputized" by the US Government (the IRS, no less) and the Federal Republic of Germany (yep, Germany) - and the entire EU, Australia, and reciprocally Canada, Mexico, and Israel, to do "educate you" (and everyone else) about "unscientific myths that divide people"."

So you're telling me governments have told you to banter with posters at a random blog maybe 10,000 people at the most consistently read? I really really doubt that.

Rob said...

There is clear evidence for population discontinuity in Northern Africa between middle Stone Age and Upper Palaeolithic, and then at the early holocene; suggesting to me that it was more a "coridoor" than "population source".
Thus, E must be a back -migration to Africa from a Eurasian DE source

capra internetensis said...

@Rob

What's the discontinuity between the MSA and the Upper Palaeolithic?

Ric Hern said...

The period between the Abbasia Pluvial and Mousterian Pluvial maybe ?

Davidski said...

@Gioiello

Quit posting full names of the people who post here.

How hard is that to understand?

Gioiello said...

@ Davidski

You deleted a post of mine in answering other previous post of Mr. Open Genomes. In that post I answered not only by a genetical point of view, but also from an historical one.
Of course the blog is yours and you may do all what you prefer, also permitting that someone names your researches "ground zero".Tell me if I am not permitted so far to post on your blog. Of course Open Genomes is "mad" as J. L. wrote to me, and also his compatriot Samuel Andrews perhaps is coming to get many doubts about that.
But he is wrong just from a genetic point of view, because the subclades R1b1-L389*, only one of them is owned from a Jewish line whereas Italy has the highest variance, have in common the following SNPs as to the S. M. tree we are waiting it is updated from last Summer: CTS10107/V3949, CTS3187, CTS6666, CTS995/V3884, V1274, V1636, V1956, V1977, V2146, V2238, V2313, V2365, V3217, and the Jewish cluster may not descend from Villabruna (given that that is demonstrated) and the other clades not.

"The sole surivors of "not Black, but dark-skinned" Mesolithic "Villabruna" [#1] R1b1a-L389* in Italy, which was post-LGM and therefore not part of any "Italian Refugium", are [#2] "The Jews", specifically Ashkenazi Jews. These survived virtually in the same location for about 13,000 years, ending up about 50 km south of Villabruna, until 1509 and 1940. Then, something happened that had everything to do with "Race" which nearly killed off these sole survivors of post-LGM Mesolithic Villabruna R1b1a-L389*, except in some random places like Britain, the US, and Israel. There's both genetic and genealogical proof of this".

After he entered Fiorio's in Turin and named his horse a senator...

Rob said...

@ Capra & Ric

after the end of the Nubian complex, MIS 5 until MIS 3, there is a marked drop in population due to dessication of the Sahara. In turn, the end of MIS 3 corresponds to the start of the LGM (c. 24 ky BP), and there is a sharp increase in settlement density, & diversification, in the Nile valley; which again ends, rather abruptly, c. 14 ky BP; before a final re-population in the mid Holocene.

http://www.sciencedirect.com/science/article/pii/S0277379115001328

Ric Hern said...

What is interesting is the Epi-Paleolithic site at 9000 years ago. Looks like this corridor was sparsely populated during this time.Could this be when domesticated cattle were introduced into North-Africa ? This was roundabout the same time as the start of the Neolithic Subpluvial. It kind of makes sense that herders could have moved easier with their herds through this sparsely populated area.

Ric Hern said...

Rob so basically what this says is that the dam formations within the Nile allowed people to stay longer than previous eras ?

Ric Hern said...

Or are you referring to the Pump Action the LGM may have had on the Near Eastern population with some migrating into Anatolia and others into Egypt ?

Samuel Andrews said...

@Gio,

Stop accusing me of stuff I know nothing of! There's no conspiracy going, this is just a blog for crying out loud.

Gioiello said...

@ Samuel Andrews

I apologize for having written "Of course Open Genomes is "mad" as J. L. wrote to me, and also his compatriot Samuel Andrews perhaps is coming to get many doubts about that".

Glad to know that you don't agree with my about the paranoia of OG.

ak2014b said...

@OpenGenomes,
and because the "Brahmans", "Sarmanas" (sramanas, Buddhist monks), and "Gymnosophists" ("naked wise men", i.e. Jains) were held in high regard by the Greeks, Romans

Current English translations of sources from classical antiquity since the era of Alexander still continue to refer to "Brahman Gymnosophists" too. "Gymnosophist" may therefore possibly be the Greek term for Indian "ascetic" in general. Jains were not the only naked Indian ascetics, furthermore.

In the Indian context of the era, "Sramanas" could refer to Buddhists and Jains and others, so perhaps the Greeks likewise referred to both Buddhists and Jains with the "Sarmanas" terminology back then.

Kurti said...

The theories and conclusions of this article make absolutely no sense. It almost sounds like we don't have any mesolithic South European sample at hand. But the truth is, we have! Villabruna from Italy and La Brana from Iberia both look genetically quite distinct and not EEF by genotype. In fac we also have Paleolithic samples from across Europe and those even look more distinct to WHG as well EEF as anything. The truth here is, we are dealing with a mesolithic migration wave, possibly from the region between Balkans and Levant, which brought WHG into mainland Europe and a Neolithic wave from Anatolia and northern Levant that brought EEF there.

batman said...

@ Sein

"Technically speaking, OG is correct."

No. He's just playing with semantics - converging confusion.

"Mainly because, the amount of genetic divergence that exists between the most extreme poles of contemporary human genetic variation is still much smaller compared to what we see with actual Chimpanzee subspecies (in scientific work, "race" = subspecies)."

The human sub-species - known as "races" or "etnicities" was never defined by "genetic divergence" - but by fenotypical characteristics. Pls check some etnological textbooks.

"Though, actual human "races" have existed.

For example, you can construe Neanderthals as another human subspecies. So, I guess Eurasians are "multiracial", because of Neanderthal and Denisovan ancestry. Although, Sub-Saharan Africans are probably also admixed with different human subspecies."

We used to consider Homo Neanderthalis and Heidelbergensis as different Species from H. Sapiens s. Today we know that was a mis-construction based on 'modern supremacy'. Since Svante & Co at Max Plank could show that the genetic traits of the Neanders, as well as the Denisovans, was found within the Human Genome - due to cross-breeding.

Moreover, as the team Pääbo found the FOX-2 in Neanders, later complemented by laryngeals from close-ups of Neander-skulls, it's clear that they had the very same biology, brains and capabilities as the Cro-Magnons.

This realization re-defined Neanders - as well as the Denisovans - to be "sub-species" rather than "species". Thus they have to be included in the classification "Homo Sapiens" - pointing towards a common ancestor (erectus) no younger than 1,8 mill. years BP.

As the ability to re-produce defines A Specie - we had to redefine the Cro-Magnons as a "sub-specie" (aka 'race') - side by side with the Neanderthalian and the Denisovanian subspecies - aka "races".

---

The various archaic populations that endured the last 30-50.000 years in the tropical areas of Africa, Asia and America would fall into the same category - as ancient 'sub-groups' of the same human family. Just as the Neanders, Denisovans and Cro-Magnons must be related to the 'archaic' Chineese (Pekingensis), SE Asians (Javensis and Florensis), Australians (Aborigines), S Asians (Onge), Africans (Omo) and Meso-Americans.

Based on these archaic sub-species - from various continents, developing throughout the Middle and Late Paleolithic - we find that a re-unification of the various sub-groups thrived as ice-time ended - and the paths and waterways across continents and oceans opened up - resulting in various "cross-breedings" and what many call "modern men".

---

In the genetic characteristics we find signs from these archaic groups - in both extinct, ancient and extant sub-species. Which is why we can deduct that the end of ice-time represents a new meeting of various sub-species - recombining the old, archaic haplogroups.

Today we find male descendants of the arctic Cro-Magnon subspecie that had left their ice-age refugia, carrying y-dna F->GHIJK, to reproduce with women from the archaic women from the tropical hemisphere - carrying mt-dna A, B, C, D, Z, etc. Just as we find tropical y-dna-lines, such as A, B, D and E, re-combining with women from the arctic Eurasia - such as U, V and T.

batman said...


To keep a valid definition of the old terms "race" and "sub-specie" we may follow the aetnos/etnicities of the various continents - as the agnatic dynasties bound to the y-line have been a defining factor in building the populations that developed the "high-cultures" and the consequent "civilizations" during mesolithic/neolithic time.

Duely, we may follow the dynasties comming from the arctic men of hg F-> G,H,I,J,K as they spread across northern Eurasia during the Mesolithic. Later to be complemented with y-dna O, Q, R and T, as stock-breeding spread throughout northern Eurasia - from the Atlantic to the Pacific.

The early dynasties of the y-dna-groups makes it possible and plausible to re-connect the terms of modern genetics with the nomenklatura of classical etnology - in plain definitions and simple connotations. Without the confused and confusing mumbo-jumbo from some political agenda.

batman said...

@ Kurti

No need to cross the river to find water.

The refugia you look for is already identified - surviving BOTH the LGM and the Younger Dryas between the Western Baltics and the Brittish isles.

Today we can even follow their tracks as they started to re-populate NW Europe and northern Eurasia - starting no later than 11.900 years BP, as soon as the Younger Dryas ended.

@ Gioello

Could you provide a link?

ak2014b said...

@batman
"Today we find male descendants of the arctic Cro-Magnon subspecie that had left their ice-age refugia, carrying y-dna F->GHIJK, to reproduce with women from the archaic women from the tropical hemisphere - carrying mt-dna A, B, C, D, Z, etc. Just as we find tropical y-dna-lines, such as A, B, D and E, re-combining with women from the arctic Eurasia - such as U, V and T."

Which paper refers to Cro-Magnons carrying y-dna F->GHIJK?

I've just now found the following on Cro-Magnon at Wikipedia, and there's only reference to I2a for the Y:

Genetics

A 2003 sequencing on the mitochondrial DNA of two Cro-Magnons (23,000-year-old Paglicci 52 and 24,720-year-old Paglicci 12) identified the mtDNA as Haplogroup N.[33]

A 2015 study sequenced the genome of a 13,000 year old Cro-Magnon from Switzerland. He belonged to Y DNA Haplogroup I2a and mtDNA haplogroup U5b1h.[61]


The dates for these remains aren't very early, and isn't more sampling through time required before it can be assumed that these haplogroups arose in Cro-Magnon? Without more intensive sampling, how can we be sure that one or more of these haplogroups in Cro-Magnons were not due to introgression? Alternatively, without better sampling, if I2a is a Cro-Magnon line, it could for instance still be due to introgression from upstream branches, which could then have introgressed back to other humans from Cro-Magnon afterwards. In that case, the rest of F->GHIJK need not have originated in Cro-Magnons.

MentalFloss mentions Cro-Magnon remains have also been found in the Middle_East,
Specimens have since been found outside Europe, including in the Middle East.
Maybe those Middle-Eastern Cro-Magnon remains could be genotyped as well.

Gioiello said...

@ batman

"@ Gio[i]ello
Could you provide a link?"

To what?

batman said...

@ ak2014b

The oldest y-dna we have from northern Eurasia shows that most - if not all - men were derivates of makrogroup F. Such as Ust-Isthim, Pestera cu Oase and Dolni Vestonice. All of them part of a rathger homogenous population of high-arctic populations.

I still don't get how the neighbouring examples of y-dna C1a and C1b relate to the early F and the further derivates (K2,I, J, R). Though, it seems clear that the F/GHIJK-line descends from a early C/F - since they appear continously within the higharctic parts of Eurasia between 45.000 and 13.000 years ago. To re-appear in renewed mutations some 9-11.000 years ago - in the same areas.

Thus we may conclude that y-dna C/F survived the LGM as well as the YD north of the Alps, from where a new lines as G and H, could appear together with new versions of hgs IJK, from which N, O, Q, R and T are supposed to derive.

Please note that we find only ONE human 'subspecie' north of the Mediterranean and the Middle East during ice-time - before 13.000 BP - apart from exceptional Neanders and Denisovans. The arctic population of Paleolithic Eurasia have traditionally been called "Cro-Magnons" - and regarded as the ancestors of modern Caucasians, due to their close, common traits - developed only in the arctic part of the world.

We may still discuss the origin of C1 and its relationship to makrogroup F.

But we can't isolate hg F from the male lines populating Eurasia during the early Holocene - when the Atlantic facade was populated by y-dna I2, while the northern coast of the Mediterranean (+ Balkan, Anatolia and the Middle East) was populated by G2, while J2 started off in Trans-Caucasus, Iran and India. Meantime a 'brother-line' from the same hg F, namely hg H, managed to find S India, while the first K's (M9) built the first, post-glacial timberhouses in the boreal forests between Carelia and Tocharia.

One may note that the site of Barcin - at the crossroad between east and west - had a old graveyard were both y-dna G2, H2, I2 and J2 was represented.

It's hard to find some realistic introgression on that map - except from the well-known fact that some of the women marrying these men came from the tropical parts of Asia. Which is why we have reason to believe that makrogtroup F is signatory of the arctic subspecie known as Cro-Magnon.

batman said...

@ Gio

Above you mention some chineese genetician, regarding F-GHIJK.

Gioiello said...

@ batman

I thought you were referring to that, but I wanted to be sure. We spoke about that so long with German Dziebel on January's thread East and West Eurasians separated at least 45,000 ... (.last posts)

capra internetensis said...

@Gioiello

Did you actually read that Chinese genetics paper? Pretty much anything can be put up on biorxiv: we are used to reading preprints there that end up being published in respectable journals. This is not one of those preprints.

These guys came up with their revolutionary new evolutionary theory years ago and have gained no converts. BTW, it is not specifically a theory of *human* evolution, but a general one, and their earlier work is about yeast, animals, etc.

capra internetensis said...

@Rob

Wsan't sure what you meant by MSA-UP transition. But is this not rather late for E and L3? They were diversifying in the earlier part of MIS 3, contemporary with the Emiran and Dabban and late manifestations of Mousterian and Aterian. Large-scale chert mining at Taramsa and Nazlet Khater but do we really have any idea what was going on in the Nile Valley (and Delta) itself?

Roy King said...

@Davidski
Please ban Gioiello--his comments are offensive, bullying and reprehensible.

@Gioiello
You are the pot calling the kettle black--an English idiom.

Davidski said...

@Gioiello

You're breaking the rules here by insulting African and Jewish people and talking about conspiracy theories.

I'll have to ban you if you keep breaking these rules.

Gioiello said...

@ Davidski

I apologize, but I would remember that I have been offended many times also from Open Genomes in any way, also by posting some stupid videos about Mussolini, not taking into account that I was born on 5 March 1948 and had nothing to do with that man and that vicissitudes, and I come from a family of socialists (my grandfather) and communists (my father). Of course if this were a blog owned from Others (we know who they are) I have been banned from so long. I am proud that a geneticist like Roy King, instead of disproving my theories, invokes his authority. I have discussed with everyone, even with people who offended and ridiculized me, never invoking banishments, becuse the truth, by a scientific point of view, may not be banned. If he is able, that disprove what I say, and also Chinese say, also about the "out of Africa".

Gioiello said...

@ Davidski

Of course you follow the rules of your blog, and the blog is yours, but permit me to say that I think it is wrong to delete the posts of xyyman. First of all because he is on the same plane of Open Genomes: "I am just educating the ignorant" he says, and don't you remember what OG wrote? Secondly because I may assure you that xyyman is a clever boy. If he were less knowledgeable he could be one of the Maghrebins who put bombs in our cities. It is well that he may speak. Beyond that there is the abyss not different from that of all the PhDs you take in great consideration. Look at this image, and everything will be clear:
http://freepages.genealogy.rootsweb.ancestry.com/~stewartroyal/r1broutes.png

Davidski said...

I'm going to delete most of the crazy posts from now on, so keep that in mind.

And since xyyman is a total crackpot, I'll probably be deleting most of his posts.