PDA

View Full Version : Cheddar Man, Mesolithic Britain, GEDmatch results



Tomenable
23-02-19, 09:36
I have uploaded him to GEDmatch Genesis:

Cheddar Man England 7150 BC, GEDmatch Genesis kit number - NW6414429

Eurogenes K36:

137669 SNPs used in this evaluation

Population
Amerindian -
Arabian -
Armenian -
Basque 8.81 Pct
Central_African -
Central_Euro -
East_African -
East_Asian -
East_Balkan -
East_Central_Asian -
East_Central_Euro 17.68 Pct
East_Med -
Eastern_Euro 9.69 Pct
Fennoscandian 36.88 Pct
French -
Iberian -
Indo-Chinese -
Italian -
Malayan -
Near_Eastern -
North_African -
North_Atlantic 7.78 Pct
North_Caucasian -
North_Sea 19.15 Pct
Northeast_African -
Oceanian -
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian -
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med -

Similarity Map:

https://i.imgur.com/21TlwPH.png

Edit:

DNA Land Ancestry Report for Cheddar Man:

https://i.imgur.com/dqG1qND.png

halfalp
23-02-19, 10:15
Was Cheddar Man part of the Villabruna Cluster?

Ygorcs
23-02-19, 10:25
Fascinating. Some people rich in WHG like Basques and Sardinians do not look similar at all to Cheddar Man in the map. Does it suggest that "WHG" is maybe a generic cluster, and there was actually a lot of regional genetic structure? Or is it just because compared to Northern Europeans, who also have a lot more EHG, the sum of Mesolithic European Hunter-Gatherer (WHG+EHG) is lower in the other regions?

bicicleur
23-02-19, 13:02
Was Cheddar Man part of the Villabruna Cluster?

9.1 ka in Britton, he is bound to be

Tomenable
23-02-19, 13:24
I uploaded him to DNA Land, let's see what was his coffee consumption etc. :) Here are his pigmentation SNPs:

https://www.eupedia.com/forum/threads/35388-First-modern-Britons-had-dark-to-black-skin-Cheddar-Man-DNA-analysis-reveals/page7?p=567964#post567964

I don't think he was "black" in a Sub-Saharan African way, rather something between "Pakistani" and "Dark Finn".

Dark Finn:


https://www.youtube.com/watch?v=v65-ErfUyVM

davef
23-02-19, 14:36
Fascinating. Some people rich in WHG like Basques and Sardinians do not look similar at all to Cheddar Man in the map. Does it suggest that "WHG" is maybe a generic cluster, and there was actually a lot of regional genetic structure? Or is it just because compared to Northern Europeans, who also have a lot more EHG, the sum of Mesolithic European Hunter-Gatherer (WHG+EHG) is lower in the other regions?
Actually it's strange that in the map, Sardinians score only one point higher than Cypriots (2 vs 1) when in reality they have much more WHG ancestry. It makes 0 sense for their WHG to be close to Cypriot levels

markod
23-02-19, 15:13
Fascinating. Some people rich in WHG like Basques and Sardinians do not look similar at all to Cheddar Man in the map. Does it suggest that "WHG" is maybe a generic cluster, and there was actually a lot of regional genetic structure? Or is it just because compared to Northern Europeans, who also have a lot more EHG, the sum of Mesolithic European Hunter-Gatherer (WHG+EHG) is lower in the other regions?

If Chad Rohlfsen (https://populationgenomics.blog) is right WHG might be a relatively complex admixture of Magdalenian on the one Hand and Anatolian + Gravettian + ANE + ENA on the other. This could explain the similarity to Finno-Ugrian groups who have additional Gravettian and ENA admixture from Siberia.

It would be interesting to investigate whether the HG admixture in Basques is more similar to Magdalenians.

Joey37
23-02-19, 15:29
Hmm, pigmentation. Maybe he was like an Arab, since the WHG were I haplogroup and Arabs are J, so they descend from the same ancestral stock on the male line. With his clustering with Northern Norway and Estonia, maybe we need to come up with a new group, Northern Hunter-Gatherers.

markod
23-02-19, 15:54
Hmm, pigmentation. Maybe he was like an Arab, since the WHG were I haplogroup and Arabs are J, so they descend from the same ancestral stock on the male line. With his clustering with Northern Norway and Estonia, maybe we need to come up with a new group, Northern Hunter-Gatherers.

AFAIK the scientists in question looked at more SNPs than just those in the Hirisplex system. Is there any good reason to doubt the skin color of the reconstruction?

Elaishousse
23-02-19, 16:07
Cheddar Man Genetic analysis showed that it was Y DNA I2a2b-S10750 Or I-L38*
Cheddar Man is a "partial" I-L38*, a line ancestral to all I-L38s today as follows:
Y11324/FGC29600+
Y11319/FGC29553+
S2524/SK1263/V2774+
S2519+
Y13463/FGC29582+
S2592+
S8646 (2/3 reads derived)
The other SNPs are ancestral
https://yfull.com/tree/I-L38/ (https://yfull.com/tree/I-L38/?fbclid=IwAR10W1mgl0e5zT04OWbRdHKoPSEiM5HZz-t_MDlWvRUWlmGZ_WcOVeF4w38)

Tomenable
23-02-19, 16:25
AFAIK the scientists in question looked at more SNPs than just those in the Hirisplex system. Is there any good reason to doubt the skin color of the reconstruction?

I have seen several skin color reconstructions ranging from:

This: http://www.early-man.com/cheddar-man.html

... to this:

https://www.euronews.com/2018/02/07/cheddar-man-shows-white-skin-could-be-a-recent-phenomenon

https://ichef.bbci.co.uk/news/660/cpsprodpb/7DFC/production/_99925223_8f56221a-56fe-4f6a-bd46-27eddd3d1255.jpg

These are quite different, 2nd looks MENA, 1st looks Black.

=====

Here is a good article:

https://www.gnxp.com/WordPress/2018/02/06/the-genome-of-cheddar-man-is-about-to-be-published/

Salento
23-02-19, 17:13
I have uploaded him to GEDmatch Genesis:

Cheddar Man England 7150 BC, GEDmatch Genesis kit number - NW6414429

Eurogenes K36:

137669 SNPs used in this evaluation

Population
Amerindian -
Arabian -
Armenian -
Basque 8.81 Pct
Central_African -
Central_Euro -
East_African -
East_Asian -
East_Balkan -
East_Central_Asian -
East_Central_Euro 17.68 Pct
East_Med -
Eastern_Euro 9.69 Pct
Fennoscandian 36.88 Pct
French -
Iberian -
Indo-Chinese -
Italian -
Malayan -
Near_Eastern -
North_African -
North_Atlantic 7.78 Pct
North_Caucasian -
North_Sea 19.15 Pct
Northeast_African -
Oceanian -
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian -
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med -

Similarity Map:

https://i.imgur.com/21TlwPH.png


From a K36 Oracle

http://i.imgur.com/CA6qnTW.jpg

http://i.imgur.com/aYc3Die.jpg

Salento
23-02-19, 18:38
Actually it's strange that in the map, Sardinians score only one point higher than Cypriots (2 vs 1) when in reality they have much more WHG ancestry. It makes 0 sense for their WHG to be close to Cypriot levels

Cheddy:
Eurogenes Hunter_Gatherer vs. Farmer Admixture Proportions

Population

Anatolian Farmer -
Baltic Hunter Gatherer 94.00 Pct
Middle Eastern Herder -
East Asian Farmer 0.09
Pct South American Hunter Gatherer -
South Asian Hunter Gatherer -
North Eurasian Hunter Gatherer -
East African Pastoralist -
Oceanian Hunter Gatherer 0.35 Pct
Mediterranean Farmer 5.56 Pct
Pygmy Hunter Gatherer -
Bantu Farmer -

MOESAN
23-02-19, 18:47
I have seen several skin color reconstructions ranging from:

This: http://www.early-man.com/cheddar-man.html

... to this:

https://www.euronews.com/2018/02/07/cheddar-man-shows-white-skin-could-be-a-recent-phenomenon

https://ichef.bbci.co.uk/news/660/cpsprodpb/7DFC/production/_99925223_8f56221a-56fe-4f6a-bd46-27eddd3d1255.jpg

These are quite different, 2nd looks MENA, 1st looks Black.

=====

Here is a good article:

https://www.gnxp.com/WordPress/2018/02/06/the-genome-of-cheddar-man-is-about-to-be-published/

I 'll came back later but I just say here the discrepencies between the two reconstructions show us how unreliable these things can be; the first one seems to me the less reliable, not specially about skin colour but about features: nose flesh, lips... a provocative one for sure...
I think the 'cromalike' heritage was for thin lips, the 'brünlike' one was for thicker lips, so some choice in Mesolithic, but even like that, these curious lips???

markod
23-02-19, 19:59
I have seen several skin color reconstructions ranging from:

This: http://www.early-man.com/cheddar-man.html

... to this:

https://www.euronews.com/2018/02/07/cheddar-man-shows-white-skin-could-be-a-recent-phenomenon

https://ichef.bbci.co.uk/news/660/cpsprodpb/7DFC/production/_99925223_8f56221a-56fe-4f6a-bd46-27eddd3d1255.jpg

These are quite different, 2nd looks MENA, 1st looks Black.

=====

Here is a good article:

https://www.gnxp.com/WordPress/2018/02/06/the-genome-of-cheddar-man-is-about-to-be-published/

Not a good article IMHO. Same old "I feel he should be lighter".

ToBeOrNotToBe
23-02-19, 20:21
Not a good article IMHO. Same old "I feel he should be lighter".

It would be surprising though if people like him contribute a significant amount of N Euro ancestry (and N Euros are light skinned). They also chose the darkest possible estimate from a range of possible pigmentations, which says it all really

Something like Yemenis is a pigmentation I could “accept” as plausible

Megalophias
23-02-19, 20:27
Iain Mathieson said a few days ago on Twitter:


I would say that basically it is impossible to predict skin pigmentation of these populations [SHG and WHG] with any degree of confidence, partly because they likely had variants that are not common today, and partly because there is too much epistasis.... I mean if you had some of the light pigmentation alleles you would probably guess lighter than if not, but I would still be extremely skeptical of any kind of quantitative prediction. There are hundreds of GW-significant pigmentation variants in UK Biobank alone, and these sort of predictions involve a small fraction of those
It seems we have underestimated the complexity of pigmentation genetics until recently. People favouring relatively light skin (racists and conspiracy theorists aside) are figuring that selection would have worked on them as it has on modern high-latitude people. At this point we just don't really know.

markod
23-02-19, 20:38
It would be surprising though if people like him contribute a significant amount of N Euro ancestry (and N Euros are light skinned). They also chose the darkest possible estimate from a range of possible pigmentations, which says it all really

Something like Yemenis is a pigmentation I could “accept” as plausible

I think he's lighter than many Eurasians like Papuans, Australians and especially Onge to whom he might have some additional affinities. If he had lighter skin it would have been caused by allelles that got lost anyway.

G2ian
23-02-19, 22:02
Jesus some people are soo concerned about white skin color it's embarrassing. Almost like they're embarrassed to be related to someone with a dark skin... Face it guys, you are recent descendants of dark people. Caucasians are the true white people. xD

Carlos
24-02-19, 00:36
https://3.bp.blogspot.com/-jGQRSZ8-h4M/XHHGhbd4CGI/AAAAAAAAADc/9uelcjvJ7Kc--cIjYO4FBm72ACnbR0QEwCLcBGAs/s1600/chedarchedar2.jpg

I have made this recreation. I think they have done a good reconstruction, I have seen it working on it. The only thing that I think had given it a somewhat cannibalistic look and yet to my recreation I have seen more human aspects similar to modern man. His hair was graying gray and he could have had blue eyes or his children do not know, but he certainly did not have blue ones, it was rather that chestnut that looks red that would vary according to the light, there in the photo I was giving the light very fully it is understandable that they came out so red, poor man.

Tomenable
24-02-19, 00:57
^^^ "Red Skin" Amerindian? :)


he certainly did not have blue ones

What is this statement based on?

Tomenable
24-02-19, 01:06
Onge to whom he might have some additional affinities.

???

There are Onge and Jarawa on GEDmatch, they score like ancient Hoabinhians (also on GEDmatch):

https://en.wikipedia.org/wiki/Hoabinhian

They all score mainly South Asian, Malayan and Oceanian. Onge, Jarawa, Malaysia & Laos foragers.

Carlos
24-02-19, 02:38
^^^ "Red Skin" Amerindian? :)

What is this statement based on?

It's inexplicable.

Salento
24-02-19, 03:33
https://3.bp.blogspot.com/-jGQRSZ8-h4M/XHHGhbd4CGI/AAAAAAAAADc/9uelcjvJ7Kc--cIjYO4FBm72ACnbR0QEwCLcBGAs/s1600/chedarchedar2.jpg

I have made this recreation. I think they have done a good reconstruction, I have seen it working on it. The only thing that I think had given it a somewhat cannibalistic look and yet to my recreation I have seen more human aspects similar to modern man. His hair was graying gray and he could have had blue eyes or his children do not know, but he certainly did not have blue ones, it was rather that chestnut that looks red that would vary according to the light, there in the photo I was giving the light very fully it is understandable that they came out so red, poor man.

You turned Cheddar Man into a stone-age Drag Queen. LOL

Carlos
24-02-19, 05:17
^^Already in the original photo that does not mean that it was so exactly looks something childish or even a little effeminate I mean in the aspect not in other connotations.

Tomenable
24-02-19, 19:56
DNA Land Ancestry Report for Cheddar Man:

https://i.imgur.com/dqG1qND.png

For comparison, Steigen (Northern Norway hunter gatherer):

https://www.eupedia.com/forum/threads/37957-North-Norwegian-Mesolithic-Hunter-GEDmatch?p=568120&viewfull=1#post568120

Tomenable
26-02-19, 01:01
North Slavs: taking British jobs since Upper Paleolithic: ;)

https://www.thecanary.co/wp-content/uploads/2018/02/Hopkins-Cheddar-Man-Main-Two.jpg

https://i.imgur.com/DVgdU4C.jpg

Ygorcs
26-02-19, 03:20
I uploaded him to DNA Land, let's see what was his coffee consumption etc. :) Here are his pigmentation SNPs:

https://www.eupedia.com/forum/threads/35388-First-modern-Britons-had-dark-to-black-skin-Cheddar-Man-DNA-analysis-reveals/page7?p=567964#post567964

I don't think he was "black" in a Sub-Saharan African way, rather something between "Pakistani" and "Dark Finn".

Dark Finn:


https://www.youtube.com/watch?v=v65-ErfUyVM

Dark Finn? His hair notwithstanding, that "dark" skin color is undoubtedly white and would be perceived as white virtually anywhere, I believe. He isn't darker than many Germans or French people out there. I mean, with that skin complexion he must definitely have all the main skin-lightening mutations that are fixed in Europeans, so he's certainly much lighter than Cheddar Man was. But as for "Pakistani" looks, I'll agree with you, that's also my personal hunch, but only if you're taking about average Pakistanis, not the lightest-skinned ones, who aren't much darker than Syrians or Armenians. In my opinion, Cheddar Man was dark-skinned, but not in the "tropical African" sense. I'd say something Yemeni-like or Pakistani-like.

Ygorcs
26-02-19, 03:28
If Chad Rohlfsen (https://populationgenomics.blog) is right WHG might be a relatively complex admixture of Magdalenian on the one Hand and Anatolian + Gravettian + ANE + ENA on the other. This could explain the similarity to Finno-Ugrian groups who have additional Gravettian and ENA admixture from Siberia.

It would be interesting to investigate whether the HG admixture in Basques is more similar to Magdalenians.

Interesting, that would make these results more understandable, but I still wonder why in the map Cheddar Man shows so more similarity with some populations much richer in WHG than in EHG than to populations like the Basques and Sardinians, with quite a lot of WHG for European standards (though not as much as the Baltic area). Is it possible that the fact that the non-WHG part is more ANF than anything else in Southern Europe, more distantly related than EHG, explains that? I'd be surprised if for instance the Basque WHG was more distant from Britain WHG than even EHG.

Ygorcs
26-02-19, 03:43
DNA Land Ancestry Report for Cheddar Man:

https://i.imgur.com/dqG1qND.png

For comparison, Steigen (Northern Norway hunter gatherer):

https://www.eupedia.com/forum/threads/37957-North-Norwegian-Mesolithic-Hunter-GEDmatch?p=568120&viewfull=1#post568120

Intriguing. I wonder how much do modern Baltic people, North Russian and Finnish people score in WHG (in a model that also accounts for EHG to try to differentiate the two sources of Hunter-gatherer ancestry)? Anything as much as 1/3?

PaleoRevenge
26-02-19, 15:35
The biggest surprise here is low IQ of the people in here who cannot grasp the whole Chedar man was black is clearly propaganda and has nothing to do with with facts or honest science. The GED match results show how black or paki this hunter gatherer survivor was, which is a big fat zero. His reconstruction is just ill intention fraud.

Ygorcs
26-02-19, 19:09
The biggest surprise here is low IQ of the people in here who cannot grasp the whole Chedar man was black is clearly propaganda and has nothing to do with with facts or honest science. The GED match results show how black or paki this hunter gatherer survivor was, which is a big fat zero. His reconstruction is just ill intention fraud.

His GED match results show nothing about the SNPs related to the polygenic trait of skin color pigmentation. Do you think people would stop to be autosomally European just because they had darker skin pigmentation? Would they change their autosomal makeup because of a few gene alleles that were not present in them? If you do, you know nothing about population genetics. I know you're perhaps too used to think that "dark skin = black = African or maybe some of those dark South Asians", but that's nothing but misconception about what race, ancestry and skin pigmentation are and how much they are related.

teepean
05-03-19, 22:37
Which one of the samples did you use to create the kit?

ewe2
17-04-19, 13:20
Cheddar man shares little DNA with modern English/Scots/Welsh. After him came Neolithic farmers of mediterranean appearance who wiped out the western hunter gatherers. After them came fairer, lighter skinned people from the steppes (who wiped out the earlier Neolithic farmers). Some of these later farmers had similar mtDNA to Cheddar man because they had mixed with relatives of the Western Hunter Gatherers on the Steppes

see Human Paleogenetics of Europe by Brandt G et al

and

Natural History museum 'ancient DNA shows migrants introduced farming to Britain from EU'

bicicleur
17-04-19, 14:34
Cheddar man shares little DNA with modern English/Scots/Welsh. After him came Neolithic farmers of mediterranean appearance who wiped out the western hunter gatherers. After them came fairer, lighter skinned people from the steppes (who wiped out the earlier Neolithic farmers). Some of these later farmers had similar mtDNA to Cheddar man because they had mixed with relatives of the Western Hunter Gatherers on the Steppes

see Human Paleogenetics of Europe by Brandt G et al

and

Natural History museum 'ancient DNA shows migrants introduced farming to Britain from EU'

cheddar man would be derived for 6 out of 73 SNP's for I2a2b-L38, an extinct clade

A tale of two Y sequences:
One a very famous ancient person, and another a single Big Y, and the YFull tree:
Cheddar Man, "the first Briton" who died 9150 years ago, and the Big Y id:YF07139 from France in I-Y10705. The I-L38 YFull tree. It looked like Cheddar man was ancestral for some I-Y10705 SNPs, and therefore he was a "partial" I-Y10705, even though he is derived for some SNPs of the I-Y10705 subclade I-L38.
It turns out that this ordering of SNPs is based solely on the single Big Y, id:YF07139. With the help of Antonios Kollias, we were able to determine that in fact the Big Y of id:YF07139 had no reads for all of these supposed I-Y10705 SNPs on the YFull tree that Cheddar Man was negative for.
These 9 SNPs are not really I-Y10705 SNPs at all, they are in fact I-L38 SNPs, and so Cheddar Man is positive for at least 6 I-L38 SNPs, and also positive for all actual I-Y10705 SNPs.People on Anthrogenica and most sites got it wrong, based on an "estimation" in the YFull tree which turned out to be wrong, based on this Big Y.

Cheddar Man is a "partial" I-L38, not just I-Y10705.
I-L38 has a few hundred people in it, and is found all over Europe, but mostly in the British Isles and Northwest Europe. This is the actual Y haplogroup of the fabled "lost land" of Doggerland, not R1b-M269.

The moral of the story is, if you want a good Y sequence and an accurate YFull tree based on it, it pays to be dead for over 9000 years and get a whole genome sequence instead of getting a Big Y!

https://docs.google.com/…/1aT79s3Hax7P1EdexDL6ups_piJ…/edit…

https://yfull.com/tree/I-Y10705/

Tomenable
23-04-19, 14:59
Polish Hunter-Gatherer (with similar pigmentation as Cheddar Man):

https://www.eupedia.com/forum/threads/38352-Mesolithic-Polish-Hunter-Gatherer

MOESAN
27-04-19, 12:53
Interesting, that would make these results more understandable, but I still wonder why in the map Cheddar Man shows so more similarity with some populations much richer in WHG than in EHG than to populations like the Basques and Sardinians, with quite a lot of WHG for European standards (though not as much as the Baltic area). Is it possible that the fact that the non-WHG part is more ANF than anything else in Southern Europe, more distantly related than EHG, explains that? I'd be surprised if for instance the Basque WHG was more distant from Britain WHG than even EHG.

I think that yes, the lower weight of ANF among today N-E European pops compared to S-W ones and the common DNA shared by WHG and EHG explain these apparent oddities, without having to depend too much on WHG substructures. What does not exclude some substrucutres among pops (Spain and Britain Mesolothics) which were separated then since some time. Maybe some closer light WHG elements were send to Britain (and to West Scandinavia) later along with more EEF, from Iberia, at the Megalithic/Long Barrows times, putting western modern people closer between them, but today britain farther from Cheddar? it explains too the closer proximity of Cheddar to N-E Europe more than to Britain.