Fennoscandia Biographic Project(Scandinavian genetics)

Quote:

---

Originally Posted by Jackson

It'd be interesting to see them do more IBD runs. Personally admixture is my favourite because you get the numbers to deal with, PCA's always seem a bit vague to me, even though they are better at picking up certain admixtures apparently.

---

Unfortunately the Chromopainter and Finestructure pipeline dont give you the percentages, but Chromopainter do have chromosone painting functionality where it is possible to design an ancestry painting by segments of the chromosome that will give percentages or more exactly probabilities both on segments and in total. I have done several experimental trials with the X-chromosome.

Quote:

---

Originally Posted by Jackson

So what is the current Focus of the Fennoscandia project? I saw that he had identified a number of clusters, in the most recent entry, but i didn't read the whole of the blog. Am reading through it now though.

---

The genetic clustering and origin of the Fennoscandian populations.

Quote:

---

Originally Posted by AndersP

It could be phasing error. I have increased the phasing accuracy in this run and for some individuals their affiliation have changed for example for FI2 who now (but not before) appears to have a Saami affiliation as some Finns with more recent Saami ancestry.

---

I will look at the various samples in reverse later today when i have time...if they match lots of Europeans its clearly a mixed sample or something is off?

Quote:

---

Originally Posted by AndersP

Romania3 and Romania7 samples clusters with the Pakistan-India samples. I suspect they are Rom-people.

---

My grandmother has Norwegian Romani ancestry, and she has many Roma cousins via 23andme and several Romani cousins FTDNA, we all have Indian cousins also, see my blog entry for more details:
http://scandinaviangeneticshq.blogspot.no/

Quote:

---

Originally Posted by evon

My grandmother has Norwegian Romani ancestry, and she has many Roma cousins via 23andme and several Romani cousins FTDNA, we all have Indian cousins also, see my blog entry for more details:
http://scandinaviangeneticshq.blogspot.no/

---

I cant see anything in the Chromopainter/Finestructure based analysis data.

Quote:

---

Originally Posted by AndersP

I cant see anything in the Chromopainter/Finestructure based analysis data.

---

You might see small traces of it in my uncle NO16, but i dont think you will see it in me NO5...I have not sent you my Grandmothers file..

By the way, looking at the new spreadsheet, i see the same signals as before......

Quote:

---

Originally Posted by AndersP

Your Scandinavian ;)

---

Thanks, I wasn't aware:D

Quote:

---

Originally Posted by Pallantides

The result looks a bit faulty...

---

LAMP 2.5 is not easy to use. You need to guesstimate some parameters.

Quote:

---

Originally Posted by evon

By the way, looking at the new spreadsheet, i see the same signals as before......

---

See it now to the Melanasian. It seems like Saami and some Finns have a similar elevated sharing.

Quote:

---

Originally Posted by AndersP

See it now to the Melanasian. It seems like Saami and some Finns have a similar elevated sharing.

---

Yeah, it makes sense then, must be something Eurasian, very old, like the common link between Scandinavians and Native Americans ect that often manifest itself in DNA..

Do anyone know if the La Brana 1 and 2 hunter gatherers had any south European (farmer) ancestry?

Quote:

---

Originally Posted by AndersP

Do anyone know if the La Brana 1 and 2 hunter gatherers had any south European (farmer) ancestry?

---

Iknow they are Iberian samples, but from what i can remember they are Mesolithic..

Quote:

---

Originally Posted by evon

Iknow they are Iberian samples, but from what i can remember they are Mesolithic..

---

Just did test run using about 10k SNP on Chr1 for La Brana 1. His position on the PCA was on the horizontal as most of the Saamis and some Finns but on the vertical more like the position of the Tuscans.

Quote:

---

Originally Posted by AndersP

Just did test run using about 10k SNP on Chr1 for La Brana 1. His position on the PCA was on the horizontal as most of the Saamis and some Finns but on the vertical more like the position of the Tuscans.

---

What do you think that might suggest?

Should really keep an eye on this thread, looks interesting. Good work. :)

Quote:

---

Originally Posted by Jackson

What do you think that might suggest?

---

This is only chromoosme 1, it may change when accumulating more chromosomes.

Anders, could you check if the "Roma" match my granny if i send you her raw file? also, do you do chromosome paintings at all?

Quote:

---

Originally Posted by evon

Anders, could you check if the "Roma" match my granny if i send you her raw file? also, do you do chromosome paintings at all?

---

I am not sure yet of what "threshold" the Chromopainter-Finestructure pipeline use but as far as I can see its not visible neither on the heatmaps or PCA plots. I plan to increase the number of SNP from the current 289k it may be able to see more subtle differences in ancestry.

Quote:

---

Originally Posted by Jackson

What do you think that might suggest?

---

I see La Brana 1 is in about the same position as in the research paper supplement. So it seems I have it right.

Quote:

---

Originally Posted by Jackson

What do you think that might suggest?

---

Only with 1 chromosome and 10k there is not really any good resolution of the variation at the European level but at global level you can see variation. My first interpretation of this is that the La Brana 1 pull away from the main European cluster because of part Siberian or East-Asian like ancestry and pull toward the Africans for the same reason.

It got the genotypes from both La Brana individuals and a total of 183k SNPs that match the 1000K project. I have also done a test run vs the 1000k project European panel (Brits, Iberians, Finns, Tuscans) + Chinese + Yoruba in Chromopainter-Finestructure, and some genetic distance runs through other analysis software. It looks good, see similarity vs the findings in the original research paper and I already see interesting things vs modern populations NOT seen in this paper. I will later today begin the process to analyze this vs the project participants and European reference panels. This new run will not be ready tonight.

Quote:

---

Originally Posted by evon

Iknow they are Iberian samples, but from what i can remember they are Mesolithic..

---

The La Brana appears to show some affiliation to 1000k Iberian samples or at least some of them. It may suggest its partly continuity for the Iberians living today vs the ancient La Brana.

Do anyone know what affiliation the La Brana individuals had in previous analysis done by others except for the official research paper?

Not a project update but a pilot study confirming everything is alright with the La Braña individuals genotypes extracted.

http://fennoscandia.blogspot.no/2013...-european.html

I have now done a first initial test run with a few especially Northern European populations consisting of both reference panels and project participants. I cant find the connection Vadim Verenich claimed to have found between the La Brána and the Saami or at least not to that extend he seem to have found it. As I understand the found connection was as large as 80%.

Quote:

---

Originally Posted by AndersP

I have now done a first initial test run with a few especially Northern European populations consisting of both reference panels and project participants. I cant find the connection Vadim Verenich claimed to have found between the La Brána and the Saami or at least not to that extend he seem to have found it. As I understand the found connection was as large as 80%.

---

Looking forward to this :)

Quote:

---

Originally Posted by AndersP

I have now done a first initial test run with a few especially Northern European populations consisting of both reference panels and project participants. I cant find the connection Vadim Verenich claimed to have found between the La Brána and the Saami or at least not to that extend he seem to have found it. As I understand the found connection was as large as 80%.

---

What are you finding instead, just that the connection isn't as strong as Vadim had thought?

Quote:

---

Originally Posted by Jackson

What are you finding instead, just that the connection isn't as strong as Vadim had thought?

---

Difficult to say. I will not claim at Vadim's wrong. In the Chromopainter-Finestructure with a very small dataset of North-Europeans individuals the BRA composite individual appears to show the strongest affiliation first with the Lithuanians and secondary with some Finns. The affiliation to the Saami appears more distant. However the Lithuanians had affiliations with other populations the BRA individuals didn't have in that run. On the other han I just run a K2-K7 run with 63k in ADMIXTURE. At K7 the BRA clustered with what appear to be a North-East Europe component that peaks in Finns and Saamis and to less extent among Scandinavians and showed no affiliation with Lithuanians who peaked in a Eastern European cluster that goes all the way to the Chuvash.

I think Vadim is into something, look at this one :) This is a local Euro analysis. X-asis is dimension 1 and Y-axis dimension 2.

https://sites.google.com/site/fennob...183kREF2V2.png

Blog update: http://fennoscandia.blogspot.no/2013...nd-saamis.html

Quote:

---

Originally Posted by AndersP

Blog update: http://fennoscandia.blogspot.no/2013...nd-saamis.html

---

I need to add here that the La Braña and the Saamis also clustered in their own in dimension 4 in the "world" analysis.

Quote:

---

Originally Posted by AndersP

https://sites.google.com/site/fennob...183kREF2V2.png

---

This PCA arrangment is similar to what you would get if you had a larger samples of Europeans and added a couple of East-Asians or Siberians. The Europeans would line up more or less vertically.

I begun doing a new Chromopainter-Finestructure run for everybody vs the La Brãna yesterday. I tried to do it earlier but there was suddenly a Windows update that just had to reboot without being able to stop it.

Quote:

---

Originally Posted by AndersP

I begun doing a new Chromopainter-Finestructure run for everybody vs the La Brãna yesterday. I tried to do it earlier but there was suddenly a Windows update that just had to reboot without being able to stop it.

---

Windows = death machine...

New blogpost: http://fennoscandia.blogspot.no/2013...variation.html

https://sites.google.com/site/fennob...riopeD1-D2.png

I dont think any more comments are needed :)

I have been able to narrow it further :)

https://sites.google.com/site/fennob...INKED55KV2.png

First of all Anders, if you read this – thank you again for all your updates.

Latest update:
http://fennoscandia.blogspot.com.au/...-oracle-x.html

Would be curious to know what other Fennoscandos get here.

MDLP K=5 Oracle X "Pct. Calc. Option 1

FI8:

1 FIN 86.39%
2 SAM 12.77%
3 PRT 0.25%
4 MR 0.24%
5 UD 0.14%
6 ALT 0.13%
7 BLG 0.07%
8 MNT 0.01%
9 RMN 0.00%
10 TTR 0.00%

Aila

here are my results. Not sure exactly what it all means though. But I assume that KLR is Karelia; SAM is Saami; and BASQ is Basque.



Admix Results:

# Population Percent
1 East_Eurasian 11.56
2 West_Eurasian 68.82
3 Caucasian 1.10
4 South_Asian 0.73
5 Paleo_mediterranean 17.79


Pct. Calc. Option 1

1 KRL 89.32%
2 BASQ 7.86%
3 SAM 2.39%
4 GBRARG 0.37%
5 NRW 0.06%
6 SRD 0.00%
7 TTR 0.00%
8 CHU 0.00%
9 HKS 0.00%
10 GBRCORN 0.00%

Total RMSD: 0.581587

It had been my question whether the Ancestors from the Pre-Saami NW Ladogan "Lapp areas" were/are Saami related, and thus far I haven't been doing too badly.


http://i1236.photobucket.com/albums/.../Pre-Saami.jpg

^ that utility gave me almost 60% Saami. Much higher compared to the other ones, but still not enough.

Quote:

---

Originally Posted by Norrbottning

^ that utility gave me almost 60% Saami. Much higher compared to the other ones, but still not enough.

---

Still, 60% is pretty good - no?
How much Siberian (+Amerind) do you have _____ 15% ?