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Friday, October 17, 2014

Analysis of Hinxton3 - ERS389797


Hinxton3, or ERS389797, is one of five ancient English genomes stored at the Sequence Read Archive under accession number ERP003900. However, this analysis is based on the genotype file of Hinxton3 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

Despite the exaggerated North Sea score in the Eurogenes K15, Hinxton3 could easily pass for a present-day Briton from the eastern coast of England or Scotland, albeit with a stronger than usual pull towards Scandinavia. Indeed, the f3-statistics show that it shares most genetic drift with the British and Icelanders from Eurogenes and Human Origins, respectively.



Shared drift stats of the form f3(Mbuti;Hinxton3,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton3,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton4 - ERS389798

Analysis of Hinxton5 - ERS389799

Hinxton ancient genomes roundup

68 comments:

barakobama said...

You called it Hinxton-2 in one of the sentences.

Davidski said...

Fixed now.

barakobama said...

Did you get a call for any of the Hinxtons in SNP rs1805008, or any other red hair associated SNP. It would make sense something around 30% or more of early Germans and Belgea-Britons were carriers of red hair.

Davidski said...

Which SNPs do you want to check? Maybe make a list and I'll post the genotypes here.

barakobama said...

Thanks alot.

Red hair associated.

rs1805007
rs1805008*
rs1805009
rs11547464
rs1110400
rs34474212

Eye color

rs12913832
rs4778241
rs1129038
rs12593929

Selected Hirisplex SNPs
rs16891982*
rs12821256*
rs4959270
rs1800407
rs2378249
rs12896399
rs1393350
rs2228479

Lactose tolerance
rs4988235

"Warrior gene"
rs4680

Others
rs7632287
rs180095

Chad Rohlfsen said...

Is Hinxton 4's shared drift and plot almost done? I am still wondering if 3 is in fact a Celt, with number 5, being an Anglo-Saxon.

Chad Rohlfsen said...

David,
Which plot up top is the Eurogenes one? Top or bottom?

Davidski said...

Bazza, here...

https://drive.google.com/file/d/0B9o3EYTdM8lQU2FjNk9kRzdva2M/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQVU96TG1EcEpLX0U/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQb1N1WElFSm94T0E/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQeUQ5bGNXekhJX1U/view?usp=sharing

Keep in mind that the Hinxton4 files are still incomplete.

Chad,

The first plot is the Eurogenes one. The PDF is labeled Eurogenes.

I probably won't have Hinxton4 done until Monday morning, and Hinxton5 not until the mid week. But I doubt Hinxton3 is a Celt, considering its crazy North Sea score.

There's a slim chance that Hinxton1 might be a Celt, but I'm expecting 4 and 5 to be the Iron Age Celts, with North Sea scores well under 40% and West Med just over 10%.

Grey said...

""Warrior gene"
rs4680"

Interesting thought.

If there are warrior/psycho genes then it seems likely (to me anyway) that "barbarians" from those times would have a higher proportion.

(barbarian specifically as everyone is expected to fight whereas i think settled populations specialize over time towards professional soldiers)

barakobama said...

"If there are warrior/psycho genes then it seems likely (to me anyway) that "barbarians" from those times would have a higher proportion.

(barbarian specifically as everyone is expected to fight whereas i think settled populations specialize over time towards professional soldiers)"

I wasn't so much interested in the Hinxtons results, as in stone age ones. You never know there may have been character traits of ancient ANE, WHG, and EEF, that have been diluted overtime. I don't trust the warrior gene, so I threw out a few other behavior-associated SNPs.

I think the warrior gene is a bit exaggerated and gets attention for obvious reasons, including ethnocentrism.

I bet people were a little tougher in that era simply because of their life-style, culture, and circumstances. It's not like they were naturally more aggressive than their descendants though. 2/3 of the Anglo-Saxon samples were old women so......

Chad Rohlfsen said...

David,
On your k13 spreadsheet, you've replaced Hinxton 1's data with Hinxton 4. Just an FYI.

Davidski said...

No, that's the updated K13 for Hinxton1 based on the new file. It's similar to that of Hinxton4, but with some important subtle differences IMO.

Hinxton1 K13

North_Atlantic 51.9
Baltic 25.21
West_Med 11.63
West_Asian 7.24
East_Med 0.03
Red_Sea 2.28
South_Asian 0
East_Asian 0
Siberian 0
Amerindian 0.34
Oceanian 0.21
Northeast_African 1.07
Sub-Saharan 0.08


Hinxton4 K13

North_Atlantic 51.42
Baltic 25.07
West_Med 15.8
West_Asian 4.23
East_Med 0.02
Red_Sea 0
South_Asian 2.58
East_Asian 0
Siberian 0
Amerindian 0
Oceanian 0
Northeast_African 0
Sub-Saharan 0.87

Chad Rohlfsen said...

Hinxton-1 45.69%EEF 38.47%WHG 15.83%ANE
Hinxton-2 41.37%EEF 41.89%WHG 16.74%ANE
Hinxton-3 45.00%EEF 38.79%WHG 16.21%ANE
Hinxton-4 44.80%EEF 39.60%WHG 15.60%ANE

Chad Rohlfsen said...

It looks as if Hinxton 4, may fall just 'West' of Hinxton 1.

Davidski said...

Hinxton4 clusters with Cornish and some northern French samples on the Eurogenes and Human Oirgins West Eurasian PCA based on the SNPs from the four runs available, but I guess we'll see if that's the case with the full file from the 10 runs.

Chad Rohlfsen said...

With his EEF 10% lower than northern French? That's different.

Davidski said...

I don't think I've seen any EEF estimates for northern France. But they'd probably be lower than for the unsorted French bunch from Eurogenes/HGDP.

Tesmos said...

Davidski,

Do you know why alot NW europeans have significant higher Baltic than Eastern Euro and vice versa?

Davidski said...

I don't yet know, but I suspect it's related to WHG/ANE ratios and the Indo-European expansions.

It seems that Baltic is associated more with WHG, while Eastern Euro is linked to ANE and the Indo-Europeans.

apostateimpressions said...

"You never know there may have been character traits of ancient ANE, WHG, and EEF, that have been diluted overtime.

Yes or emphasised over time. I posted this comment at the bottom of the old thread:

Another factor to bear in mind for genetic changes (and the increase in EEF) - the massive expansion of the peasantry into the urban lower classes during and since the IR. If the Norman upper classes were predominantly Nordic (WHG+ANE), and the peasant life-style gradually favoured EEF amongst that caste during the Middle Ages, then the change in survival patterns with the IR may have led to a further expansion of EEF with the lower classes. Peasants/ farmers/ EEF. (Aristocrat/ conqueror/ ruler/ Nordic)

Chad Rohlfsen said...

Apparently, Hinxton-1 is testing positive for markers down around DF25.

Chad Rohlfsen said...

Laz, had the French at 55/31/14, or there about. English are 50/35/15.

Matt said...

Comparing 1 and 4 mostly trading off West Asian plus Red Sea for West Med by the looks of it? Also some trading off of Northeast African for South Asian, may just be noise.

4 does from this seem to look basically like the Southwest English sample average, replacing a minority 2.5% East Med (in SW English) with Baltic (in Hinxton 4), assuming the South Asian is just noise. Or alternatively 4 is like the Orcadian average if its 2.5% East Med was switched to West Med.

barakobama said...

Everyone would agree that the main source of the extra-southern affinity of modern NW Europeans compared to Anglo-Saxons and Iron age Britons one way or another had to of come from France, Iberia, and or central Europe, right? There's no way everyone in NW Europe at this time was that northern, unless Gaul was swarmed by Iberians. There obviously isn't a high amount of Italian, Balkan, and west Asian ancestry, that would have probably come through the Roman empire. The change came from other regions of west Europe.

So going off trends would these general admixtures explain west Europeans.

Gaul+Balt+Anglo Saxon=Germans and Danes.

Balt+Anglo Saxon=Swedish-Norwegians.

Iberian-Gaul+Briton=Gealics.

Iberian-Gaul+Hinxton+Italian=Welsh and Cornish

Iberian+Italian+NW African=Spainish and Portuguese.

Iberian-Gaul+Briton+Anglo Saxon+Italian+Balt=English

I know there may have been other distinct populations in ancient west Europe, but these represent general trends of ancestry in my opinion.

Grey said...

"Do you know why alot NW europeans have significant higher Baltic than Eastern Euro and vice versa?"

Just a guess but i think it will turn out that the big division between WHG and ANE is coastal/riverine vs deep interior.

Tesmos said...

barakobama what do you think about the general admixtures in the Dutch?

Davidski and Grey, thank you for the information.

Chad Rohlfsen said...

Here's my k36, which is going to be about average for SE English

16.76 North Sea
15.61 Iberian
12.45 North Atlantic
11.26 Fenno Scandia
10.54 Italian
9.13 French
6.18 East Euro
5.61 Central Euro
5.21 East Central Euro
4.14 Basque

The rest is small amounts of East Med and Balkans

Chad Rohlfsen said...

Hinxton 3

k36

31.86 North Sea
21.30 North Atlantic
11.64 Fennoscandia
8.13 Central Euro
6.39 French
5.25 Iberian
4.66 Basque
3.28 West Caucasian
2.76 Italian
2.23 North Caucasian
1.09 South Central Asian

The rest is trace amounts



Chad Rohlfsen said...

BTW, Hinxton-1, is now DF25/S253+

Chad Rohlfsen said...

Hinxton-2

27.73 North Sea
24.90 North Atlantic
10.55 Italian
10.40 Fennoscandia
7.25 Central Euro
5.80 Eastern Euro
5.70 French
2.77 Basque
2.24 East Central Euro
1.87 Volga Ural
0.79 South Central Asian

That's all she gets.

Fanty said...

Some playing around with the 3 German groups came up with stuff like (limited to a single German group at a time):

Northgerman:
2pops: North-Dutch + Danish
4 pops: 50% Irish + 25% Danish + 25% Hungarian

Westgerman:
2 pops: French + Swedish
4 pops: 75% South Dutch + 25% Greek

Eastgerman:
2pops: 50% South-Dutch + 50% South-Polish
4pops: 50% Southpolish + 25% Southwest English + 25% Soutwest French

Average Joe said...

barakobama:

Who are the "Gealics"?

Average Joe said...

Davidski:

There's a slim chance that Hinxton1 might be a Celt

If Hinxton1 is not a Celt, what do you think it will be?

barakobama said...

"Who are the "Gealics"?"

Celtic speaking people who lived in Ireland at least as far back as Roman times, and conquered northern Britain and Isle of man. Basically what I mean is Irish and northern Scottish, Celtic people who were never under the Roman empire.

barakobama said...

Chad, I'm not attacking you but do you remember when you said R1b-L11 slowly rose in percentage independently across western Europe, and only got as high as it is today after the middle ages? 1 Anglo Saxon and 1 Iron age Briton, both have L11. There's plenty of Y DNA from early medieval Spain to add on.

Chad Rohlfsen said...

I said it may not have been over 50% until the Early Middle Ages (500CE). England is at 67% Spain 69%, Portugal 56%, Wales 83%, France 59%. Still possible, for almost all of those places.

Chad Rohlfsen said...

If it weren't for the Basque and Catalonia, R1b would be about the same in France and Spain.

Denis Anderthal said...

The DF25 marker of Hinxton-1 looks to be overwhelmingly a Scottish/Irish/Welsh marker.

Chad Rohlfsen said...

Barak,
For Western Europe, as a whole, it's still possible.

barakobama said...

"Barak,
For Western Europe, as a whole, it's still possible."

Sure, I mean it's all speculation. We can both agree L11 becoming the dominate paternal lineage everywhere west of Poland wasn't by luck there was a common reason. I tend to think it's been dominate like today since at least the Iron age.

I wouldn't separate west Europe in a way as Spain, France, Portugal, England, etc, especially for Romance speaking nations(not exactly an Iron age ethnic bound like in Ireland). We should break down the best we can.

Davidski said...

Maciamo at Eupedia reckons that some of these Hinxton samples are similar to eastern Germans from Mecklenburg or thereabouts.

He based his analysis on the calculator results provided by our schizophrenic friend Genetiker.

Comedians, both of them. :)

Chad Rohlfsen said...

Barak,
It had to be gradual. R1b didn't sweep in and instantly replace 60% of the ydna. It's in pockets today too. One part of Ireland is 94%, the next is 70%. One part of France is 80%, another 30%. It goes back and forth.

Davidski said...

Tweets from the ASHG are at this link...

https://twitter.com/hashtag/ASHG14?src=hash

The talks on ancient DNA aren't until Monday morning San Diego time, starting at 10:30am.

But I have no idea if anyone will be tweeting or blogging from the Corded Ware and Hinxton talks.

Grey said...

If you had R1b northern herders (more WHG/ANE) over-running central farmers (more WHG/EEF) with a lot of surviving farmer dna (especially mtdna) (but perhaps low status i.e. peasantry) with a bounce back in the percentage of autosomal farmer dna either over time or through some particular event e.g. the IR, then it seems to me that would fit the data quite well.

I think some specifically north Wales mountain dna (relatively unmixed) would clinch it.

The variation across Europe would then mostly revolve around the original proportions of herder to surviving farmer dna i.e. more in north Germany than west Germany and more in West Germany than in France etc.

Graham Little said...

Hinxton-2 on that K36. Has no iberian at all, which I haven't seen in any modern Brit-Irish population. But scores very high on North Sea.

Davidski said...

Sorry, I haven't been paying attention to the type of R1b carried by Hinxton1.

So it's DF25 is it? That would match the admixture and f3 shared drift results very nicely.

But isn't this sample the one with little or no Gedrosia? OMG, is it possible for someone with very little Gedrosia to belong to R1b? Gee, I dunno, maybe we should consult Genetiker about this? Is there a Genetiker hotline that we can call?

barakobama said...

"Is there a Genetiker hotline that we can call?"

1-800-dumb-ass.

Nirjhar007 said...

@David and Obama
So! today is the day! though it is not sure how we will get the data...
But let be very specific here David,
On Samara before the turn around ~4000 B.C. What do you expect from aDNA? Do you expect them to be Totally ANE+R1a1a or You expect other Components+Hgs also! which is more practical?

barakobama said...

Felix uploaded the Iron age Brit; Hinxton-4, to GEDmatch(kit # F999925). His results in K13 are very similar to Irish, Orcadian, and west Scottish(about as similar as they are to each other). It's obvious now the most-Anglo Saxon-like samples are Hinxton 2 and 3, and that Anglo-Saxon Hinxton-1 had a significant amount of Breton ancestry.

In K15 Hinxton-4's closest to Irish, West Scottish, and southeast English(Cornish). He scores several percentages lower in North Sea, higher in Baltic, and lower in east Euro than Irish-west Scottish.

Cornish score around the same North Sea, but the differences Hinxton-4 had with Irish-west Scottish is even greater, including having less west Med and east med than Cornish and more Atlantic.

Felix confirmed that Hinxton-4 belongs to Df25, which people on Anthrogencia say is a popular branch of L21 all over Britain and Ireland today.

My guess is that he had mostly Breton ancestry not Belgea, because he's so similar to Irish-west Scottish, and belonged to Y DNA R1b-Df25. Of course though no one knows for sure what the Belgea were genetically, and what paternal lineages they belonged to.

Assuming Hinxton-4 is a good representative of Iron age Brits and Hinxton-2-3 are good representatives of Iron age Germans in Denmark, it can be concluded they largely came from the same bronze age stock. I hope tomorrow we'll learn the origin of their bronze age ancestors. The continental Celts probably just had more native-Neolithic descended west European ancestry than Germans and British-Irish Celts.

Chad Rohlfsen said...

Barak,
I agree for the most part. The big difference between the two is that Anglo-Saxons are probably more LBK and Funnelbeaker, while Britons are more Atlantic Megalith. Both come from Corded Beaker, so no surprise. Hinxton 2 and 3 could still be admixed. Let's wait for David's plot here. It could also be revealed that the English are more Briton, than Anglo-Saxon, when we consider that all of Northern Europe has become more Med and Baltic. That would move the Saxons more into the Sea/Danish samples, and Hinxton 4 into the core of England.

On your other point, yes it seems there was a massive divide between Northern and Southern Europe. More than today. I could imagine only a 50-60% EEF population in Northern Europe, prior to the Bronze Age. Then considering the Migration period of several Germanic tribes, one wonders how much EEF was lost in those movements. Probably minimal, but not totally insignificant.

Fanty,
Are you East Germanic? I am wondering how East Germanic people score on the k13, as far as a Baltic shift.

Chad Rohlfsen said...

When referring to the EEF loss, I am talking about the Alps region, plus France, Spain,... etc.. Gothic, Frank, and Alemannic migration.

Chad Rohlfsen said...

I'm off tomorrow. I'll follow the tweets.

barakobama said...

"I agree for the most part. The big difference between the two is that Anglo-Saxons are probably more LBK and Funnelbeaker, while Britons are more Atlantic Megalith. Both come from Corded Beaker,"

I never though of that. The whole Corded ware-Bell Beaker-Unetice phenomenon, plus Stuttgart-like decended Neolithic people must be why early Germans and Celts were so similar.

"On your other point, yes it seems there was a massive divide between Northern and Southern Europe. More than today"

Maybe geography has something to do with it. Northwest Europeans may have been at about the same EEF-WHG-ANE ratio as northeast Europeans back then. There's a big difference between Southwest Europeans and southeast Europeans though.

Southwest European's near eastern ancestry mostly comes from EEF, while southeast Europeans have a significant chunk of post-Neolithic near eastern ancestry. But still there's a big split between Greeks and Turks or Cypriots. Obviously because Greeks have a significant amount of European-specific WHG and near eastern ancestry.

Davidski said...

Nirjhar007,

I don't think today is the day. If we're lucky we'll hear which modern populations the different Neolithic/early Bronze Age Central European groups resembled most, and whether the Corded Ware, Bell Beaker and Unetice samples carried R1a and/or R1b. We might also hear if the Corded Ware and Unetice people were similar to the Samara Valley groups.

But that's if we're lucky. For more details we'll have to wait for the manuscripts at bioRxiv/arXiv, or even the full papers in journals. That could take months.

Nirjhar007 said...

@David
''I don't think today is the day. If we're lucky we'll hear which modern populations the different Neolithic/early Bronze Age Central European groups resembled most, and whether the Corded Ware, Bell Beaker and Unetice samples carried R1a and/or R1b. We might also hear if the Corded Ware and Unetice people were similar to the Samara Valley groups.

But that's if we're lucky. For more details we'll have to wait for the manuscripts at bioRxiv/arXiv, or even the full papers in journals. That could take months.''
No friends of your attending the conference who can give you the important data? BTW Is Y-DNA from Samara expected?...

Davidski said...

As far as I know, the chips used to test the Corded Ware and Samara genomes were the same. If so, SNPs from the Y-chromosome were tested for these samples.

I don't know anyone personally who's attending the conference, but some people who I know online will be there, and maybe they'll share some info. Also, tweets from the talks are at this link...

https://twitter.com/hashtag/ashg14?f=realtime&src=hash

Chad Rohlfsen said...

Off topic, but interesting

.@1000genomes YH recent expansion in South Asian and East Asian populations more modern than African and European expansion from 3-5000ya

Nirjhar007 said...

@David
''As far as I know, the chips used to test the Corded Ware and Samara genomes were the same. If so, SNPs from the Y-chromosome were tested for these samples.

I don't know anyone personally who's attending the conference, but some people who I know online will be there, and maybe they'll share some info. Also, tweets from the talks are at this link...

https://twitter.com/hashtag/ashg14?f=realtime&src=hash''
I am keeping an eye on that link from before but whatever data you get please update us if possible with new posts, These aDNA data will be Monumental!...
Good Day Mate;)...

Chad Rohlfsen said...

David,
What do you think the chances are, of Goths leaving a signal that can be detected today? Check out the K15, North Sea, in Southern France and NW Iberia, with a trickle into NW Africa. Plus a strong possible signal of Germanic movement into Ukraine. Maybe it's bullshit, but very interesting correlation. Of course, some of it could be Celtic related, but still fun to play around with.

Chad Rohlfsen said...

Of course, some will probably be older than these recent tribes, but the upswings in percentages are in the right spots.

Chad Rohlfsen said...

David,
Do you think these components are older? Say North Sea is more Corded Beaker, and Baltic more Corded Ware, or is it likely not associated with any ancient groups, but modern constructs and drift?

Fanty said...
This comment has been removed by the author.
Davidski said...

Here's a West Eurasian PCA of Hinxton4 using the Human Origins dataset.

https://drive.google.com/file/d/0B9o3EYTdM8lQVW5rVVhnbHAyMEE/view?usp=sharing

Way out west baby.

Fanty said...

"Way out west baby."

http://berrymii.files.wordpress.com/2010/08/baby-shocked-face-03-copy1.jpg?w=400

Chad Rohlfsen said...

Bam! West of Hinxton 1. It doesn't look so impossible that the English are 30-40% continental, now.

Grey said...

"It doesn't look so impossible that the English are 30-40% continental, now."

30% E1b in parts of North Wales

http://www.bbc.com/news/uk-wales-north-east-wales-14173910

"So far, 500 people have taken part in the study which shows 30% of men carry an unusual type of Y chromosome, compared to 1% of men elsewhere the UK."

also

https://www.familytreedna.com/public/walesdna/default.aspx?section=yresults

https://www.sheffield.ac.uk/archaeology/research/copper-mines/index

If "North_Wales" was available as a reference population then might something like this:

Hinxton 3

k36

31.86 North Sea
21.30 North Atlantic
11.64 Fennoscandia
8.13 Central Euro
6.39 French
5.25 Iberian
4.66 Basque
3.28 West Caucasian
2.76 Italian
2.23 North Caucasian
1.09 South Central Asian

turn into something like:

31.86 North Sea
21.30 North Atlantic
11.64 Fennoscandia
35.20 North_Wales

?

Chad Rohlfsen said...

It's a haplogroup... doesn't mean a great deal, when it comes to autosomal comparisons. The Welsh are probably between the Cornish and Irish. There's Bashkir groups over 80% R1b. Does that mean that they are predominately Western European like? Of course not.

Grey said...

"It's a haplogroup... doesn't mean a great deal, when it comes to autosomal comparisons"

It's an odd (for the region) haplogroup in a possible refuge area.

This might mean a lot of things but one of the things it might mean is a distinct pre-Celtic population that survives in both y dna and mtdna in a small refuge region in North Wales but may have survived over a much wider area as mtdna - hence a possible autosomal effect without y dna.


http://i4.mirror.co.uk/incoming/article2235238.ece/alternates/s2197/catherine-zeta-jones-TOPIC.jpg

Italian or Welsh?