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Friday, October 24, 2014

Analysis of Hinxton5 - ERS389799

Hinxton5, or ERS389799, 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 Hinxton5 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

Despite its relatively low North Sea score in the Eurogenes K15, and pronounced western shift on the Principal Component Analysis (PCA) plots, this genome appears mostly Germanic. In my opinion, the shared drift stats and also oracle results are quite convincing in this regard. If this were a modern sample it could probably pass for 3/4 north Dutch and 1/4 Irish. By the way, the Sub-Saharan admixture just looks like noise; this is, after all, a low coverage genome.

Shared drift stats of the form f3(Mbuti;Hinxton5,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton5,Test) - Human Origins dataset

Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton3 - ERS389797

Analysis of Hinxton4 - ERS389798

Hinxton ancient genomes roundup


PersonaMan said...

What do you make of 5's relationship to 2 and 3 and the impact it had on the conclusions (and perhaps the changes from the abstract) during the presentation? To me AS5 seems more what would be expected for ~700AD, a bit east and north of the modern population. Do you think there is a rational explanation for why these Anglo-Saxons seem to be part of two very distinct populations - one that doesn't seem to exist in whole anymore - and another that lies pretty much exactly where you might expect if you had to go just on modern populations. 1 & 4 look perfectly reasonable for Iron Age Britons to me as well.

Because at the moment it seems not so clear cut as it was when the abstract was presented, or during the presentation. Two individuals could use the same data to come to opposite conclusions if they discounted either 5 as unusual, or 2 and 3 as unusual. Or they may decide that no clear conclusion can be reached.

Davidski said...

Hinxton4 actually looks west Irish to me, while 3 could easily pass for someone from the eastern coast of England. Also, Hinxton1 appears more Irish than English, although Scottish is probably overall a better fit, while 5 seems like a continental/British mix, but could still easily pass for English.

Only Hinxton2 looks like it could be someone fresh off the boat from the Jutland peninsula.

So I'd say different conclusions can be reached from this data depending on whether the samples are treated as individuals or groups based the context they were buried in.

Lumping 2, 3 and 5 together as Anglo-Saxons might indeed produce an overall effect that is just outside the range of modern UK variation (ie. more continental Germanic). But if we treat 2 as an outlier, then 3 and 5 really just look English, and in fact much more so than 4, or even 1 and 4 together.

My opinion is that 4 doesn't represent the present-day English very well, and is in fact a smoking gun for a significant genetic shift in England to the east. Looking at 1, it's probably useful to keep an open mind when this eastern gene flow arrived in England, because this sample suggests that it started coming during the Iron Age, and can't be exclusively associated with the Angles, Saxons, Jutes and Danes.

But the argument put forward at the ASHG presentation that 1 and 4 look like modern Brits, and therefore the Anglo-Saxons had little impact on the present-day British gene pool, doesn't make much sense to me. I'd say the English of the Iron Age looked rather Irish and Scottish until the Romans, Anglo-Saxons, Danes and Normans arrived, and then became more like the present-day English after all of these groups mixed, albeit in different proportions. Not only is that logical, but it does also fit the data from the five ancient genomes.

In any case, I suspect Hinxton4 will turn out to be a very valuable sample, because it's a high coverage genome that appears to be an excellent example of an Iron Age Celt. There are a lot of interesting things that can be done with this genome.

PersonaMan said...

Thanks for the reply (I'm 'Unknown'). That does make sense, it seems like there's not going to be an easy answer to an age-old question about the subject.

Yeah i agree about Hinxton4 - it's also great to hear about that new method that the people who did the article on Hungarian Plain have come up with - i guess there will be lots more high-quality ancient DNA in the years to come.

Grey said...

"it seems like there's not going to be an easy answer to an age-old question about the subject."

I think there will be actually but it will be buried under the politics.

For a long time the dominant view was English = macho Germanic conquerors, rar! rar! and then there was a 180 degree reaction to that and the dominant view became A-S invasion = non event.

The truth is probably somewhere in the middle.

Ryukendo K said...

One observation.
The Hinxton genomes can be divided into two categories. 1) When North sea exceeds Atlantic by a wide margin, East Euro is higher than Baltic by a wide margin. This is the pattern of 1, 2, and 3.

2) When North Sea is only somewhat higher than Atlantic, Baltic is higher than East Euro by a wide margin. This is the pattern of 5 and 4.

Not sure what this means, but the categories they are lumped in according to burial might just be discordant with their autosomal origin.

PersonaMan said...


I agree wholeheartedly. And i think the wonders of modern genetics & especially palaeogenetics may help bridge a gap that has been created between peoples and their material culture by the shift in archaeological approaches during the last ~50 years. Instead of resolutely sticking to either one or other idea that material culture = distinct people, or the reduction in importance of associating ethnicity with material culture, people will be able to investigate on a case-by-case basis the relationship between these two things, and see how their interaction really plays out.

Unknown said...

I have matches to Hinxton 2,3,4 and 5 according to Archaic matches on GEDmatch, is this right? Am I reading it correctly?

Davidski said...

I don't know. I didn't design that test, and I'm not sure how it works.

Unknown said...

Okay, thank you. I see you designed the Eurogenes tests at GEDmatch, great work! I find it all fascinating and it has shown similarity across tests and I now know recent and ancient ancestry that I wasn't aware of. Though not sure how to analyse the data on the oracles especially the 'distance' part and the mixed mode population sharing.