Fennoscandia Biographic Project(Scandinavian genetics)

[Pallantides]

This is a project started by Anders Pålsen from DNAforums and it currently have 20 participantes(7 Swedes, 5 Norwegians, 5 Finns and 3 Saami)


BGA Local

D1-2
http://img215.imageshack.us/img215/9683/bgalocalthirdroundd12.jpg

D1-3
http://img138.imageshack.us/img138/7232/bgalocalthirdroundd13.jpg

D1-4
http://img52.imageshack.us/img52/595/bgalocalthirdroundd14.jpg


BGA regional

D1-2
http://img801.imageshack.us/img801/4887/bgaregionalthirdroundd1.jpg

D1-3
http://img63.imageshack.us/img63/4887/bgaregionalthirdroundd1.jpg

D1-4
http://img36.imageshack.us/img36/4887/bgaregionalthirdroundd1.jpg

SA - Saami
SWE - Swedes
NO - Norwegians
FI - Finns


In all the local (Fennoscandia) plots the norwegian/swedes, finnish and saami all clusters seperate in all 4 dimensions. In the regional view including three reference populations all the local groups cluster seperate from each other but the swedish/norwegian and the finns in several dimensions have some overlap or are very close to the reference populations.




*
I'm NO4

[Pallantides]

The labeling of the Swedes in the last two plots are wrong, here are the correct ones:
http://img651.imageshack.us/img651/6151/bgapcaregionalthirdroun.jpg
http://img246.imageshack.us/img246/6151/bgapcaregionalthirdroun.jpg

[Pallantides]

http://img256.imageshack.us/img256/1581/bgaadmixtureregionalthi.jpg


* I think SWE7 must be a Finn or have very recent Finnish ancestry.

[Pallantides]

Better and update admixture plots(I'm NO4)
http://img818.imageshack.us/img818/9255/bgaadmixturer4k4update.jpg
http://img593.imageshack.us/img593/5950/bgaadmixtureaveragesr4k.jpg

clusters according to the project leader

Serie4 - Finnish and Saami
Serie3 - Central Europe and France
Serie2 - Lithuanian and Belorussian
Serie1 - Orcadian

[Pallantides]

Admixture sheets:
http://img530.imageshack.us/img530/7302/bgaadmixtureregionalk2k.jpg
http://img19.imageshack.us/img19/3800/bgadistregionalr5.jpg



ADMIXTURE:

- At K2 or assuming two populations Europe is split into a southern (RED) and northern (BLUE) part with the Sardinians, Cypriots and the Caucasus populations cleary at the southern extreme while the Finns, Saami and the Chuvashes at the northern extreme. North in this context appears to point north-east geographically.

- At K3 or assuming three populations Europe is splitt into 1) south-east Europe populations (BLUE) the the Georgians at the extreme 2) south-west Europe populations (GREEN) with the Sardinians at the extreme 3) north/north-east Europe populations (RED) with the Saami at the extreme.

- At K4 or assuming four populations Europe is splitt into 1) Lithuanians at the extreme (BLUE) 2) Chuvasshes at the extreme (PINK) 3) Sardinians at the extreme (RED) 4) Georgians at the extreme (GREEN).

- At K5 or assuming four populations Europe splitt into 1) Basque at the extreme (RED) 2) Chuvashes at the extreme (PINK) 3) Lithuanians at the extreme (CYAN) 4) Sardinians at the extreme (BLUE) 5) Georgians at the extreme (GREEN).

COMMENT: At the highest K=5 the ADMIXTURE result *alone* seem to suggest that Norwegians, Swedes, Finna and Saami main ancestry is "Lithuanian" but that Finns and especially the Saami have a considerable "Chuvash" influences.


MDS-PLOTS:

- D1-2: The Norwegian and Swedish common clusters together with Belorussians and Lithuanians appear to bridge the space between Orcadians/French and Finns and Volgoda-Russians. The Saami appears to go further past the latter cluster outside towards the Chuvash. The Hungarians appear to neighbour the swedish/norwegian cluster to the upper-right.
- D1-3: The same story as above, but here the Chuvash share the far lower part of the plot with the Sardinians even the distances are large. Also here the Saami appear to pull from the Russians/Finns toward the Chuvashes. In the earlier plot the Chuvashes shared the higher part of the plot with Cacausus populations even the distances where large. The Lithuanians and Belorussians appear to seperate further lower away from the Finns and the Russians.
- D1-4: The same as above.
- D1-5: The Finns appears to have seperatet from the Russian and appears to pull toward the Saami who are alone at the extreme lower-left of the plot. Else much the same as above.
- D1-6: The Finns cluster with the Chuvashes with the Norwegian/Swedish cluster to the right. Russians and Lithuanians below. Saami alone at the upper-left extreme.
- D1-7: The Finns and the Saami appears to cluster alone to the lower-left. Norwegian-Swedish cluster partly with Belorussians/Orcadians.
- D1-8: Mostly the same as above.
- D1-9: Mostly the same as above.

COMMENT: The plots appears to show a more complex picture of the ancestry and relationship than the ADMIXTURE plots. In the lower dimensions the Saami appears to pull toward the Chuvashes but seem to seperate clearly often togheter alone with Finns in higher dimensions. Norwegians and Swedes appears mostly as expected to bridge between the more western populations with the more eastern.

DIST GRAPH:

The graph shows the average distance between populations seen from the four nationalities Norwegians, Swedish, Finns and Saami.

- Norwegians are more similar too Swedes, Belorussians, Orcadians and Lithuanians than themself (!). (Yes I have checked for errors).
- Swedes closest relatives are the Norwegians, Lithuanians and Belorussians. The most distant the Chuvashes, Cypriots and the Georgians.
- Finns closest relatives are the Lithuanians, Swedes and the Belorussians. The most distant are the Cypriots, Adigey and the Chuvashes.
- The Saamis clostest relatives are the Finns, Swedes and the Belorussians. The least distant the Cypriots, Armenians and the Georgians.
- There is very high correlation in the DIST plots between Norwegians and Swedes at 0.9842, then the Finns-Swedes at 0.9387, then Finns-Swedes at 0.9099, then Saami-Finns at 0.725, then Saami-Swedes at 0.511 and finally Saami-Norwegians at 0.4531.
- Saami appears to have consistently much lower genetic affinity with all other populations than the other three. The exception is to the Chuvashes where all appear to have somewhat similar genetic distance.
- Saami affiliation with continental and especially southern European populations are much smaller than the others.

MDS-PLOTS:
http://img80.imageshack.us/img80/7992/bgamdsregionald12.jpg
http://img26.imageshack.us/img26/1686/bgamdsregionald13.jpg
http://img98.imageshack.us/img98/8074/bgamdsregionald14.jpg
http://img339.imageshack.us/img339/8016/bgamdsregionald15.jpg
http://img208.imageshack.us/img208/1298/bgamdsregionald16.jpg
http://img508.imageshack.us/img508/1127/bgamdsregionald17.jpg
http://img339.imageshack.us/img339/1558/bgamdsregionald18.jpg
http://img593.imageshack.us/img593/5820/bgamdsregionald19.jpg

I'm NO4 and seem fairly vanilla Scandinavian, but it seems NO6 and NO7 are clear outliners and cluster close to the SA(Saami)

[Pallantides]

http://img196.imageshack.us/img196/4971/r6localanalysisd12.jpg
http://img851.imageshack.us/img851/5518/r6localanalysisd13.jpg
http://img29.imageshack.us/img29/4845/r6localanalysisd14.jpg


Whats new?

- 7 new persons, where 1 is an Estonian.

Results?

- Much the same as earlier. Finns and Saami cluster clearly seperatly from Swedes and Norwegians who mostly overlap each other.
- The Estonian ES1 appears to cluster close to a Finland-Swede and not with other Finns.
- New participant SWE11 appears to deviate away from the Swedish/Norwegian clusters towards mostly Finns and maybe a little towards the Saami cluster.

Whats next?

- Regional MDS plots and ADMIXTURE graphs.
- Genetic distances
- Shared segments

[Pallantides]

I'm begining to become a bit sceptical about this project.

In LAMP 2.5 I have a very small Finnish segment, rest is Norwegian
http://4.bp.blogspot.com/-952RqqemXPM/Ta1qLWuWnTI/AAAAAAAAABA/-x6aqUo6CD4/s1600/LAMP25.jpg
Purple - Finnish
Red - Swedish
Blue - Norwegian
Green - Saami

Admixture, I'm 100% Norwegian
http://2.bp.blogspot.com/-jJujW_8XwHg/Ta1qIoHjgtI/AAAAAAAAAA8/N1KKqT_-9dk/s1600/ADMIXTURE.jpg
Red - Finnish
Blue - Norwegian
Purple - Swedish
Green - Saami

The result looks a bit faulty...

[Olavsson]

Is it still room for more participants?

[Pallantides]

http://i.imgur.com/Xc662.gif

My position is a bit hard to spot, but I'm NO4 above SWE15

[Pallantides]

According to the Feenoscandia blog - SWE7, SWE11 and NO7 are of South Saami background.

About the South Saami samples: SWE7 is confirmed at least partly of Saami background but not of North Saami background. SWE11 have also some geneological confirmed minor Saami background and have most of the origin from current and earlier known non-North-Saami areas. No information is known about NO7.

As comparisment NO6 who have geogaphical origin in the North-Saami area seperate very clearly from NO7, SWE7 and SWE11 by pulling straight at the North-Saami cluster (SA1-SA4) and appearing immediate between the Scandinavain and North-Saami cluster demonstrating that the Saami origin is different for NO7, SWE7 and SWE11.

So apparantly SWE7, SWE11 and NO7 have South-Saami background

It was a bit confusing that they were not labelled as SA like the North Saami participants.

[Pallantides]

Fennoscandia and Europe
http://i.imgur.com/0zZ6l.jpg

[Jerry]

I took part as well, I'm FI15 marked with blue arrow. Halfway between Finns and Swedes it seems (100% Finn, western)

http://img51.imageshack.us/img51/9236/231sl.jpg (http://imageshack.us/photo/my-images/51/231sl.jpg/)

[Pallantides]

I have beeing looking at the raw data without Finestructure to find eastern connections. I compared the data between Finns, Saami and umixed Nganassans (and other Siberians). I compared both averages, standard deviations and minimum and maxium lengths and their averages.

Saami - Nganassans: Avg lenght: 1.64, Stddev: 0.91, Max avg 2.58 Min avg 0.87. Max: 3.99 Min: 0.33
Finns - Nganassans: Avg lenght: 2.1, Stddev: 0.54, Max avg 3.27 Min 1.45. Max 4.15 Min 1.26

I also made a control calculation using Scandinavian clustering Norwegians:

Norwegians - Nganassans: Avg lenght: 1.83 Stddev: 0.30, Max avg: 2.45 Min avg: 1.48, Max: 2.86 Min: 1.33



This is the result from the mutational matrix. It appears Finns is at average but the max's indicate that some Finns have more related haplotypes. Saami and Norwegians appears to have closely related numbers vs the Nganassans.

Id Sam Fin Nor
Max 1,4 5,4 1,2
Min 0,1 0,1 0,1
Avg 0,4 0,4 0,3
MaxAvg 0,7 2,0 0,8
MinAvg 0,2 0,1 0,1
StdDev 0,3 0,7 0,2

---------- Post added 2012-02-29 at 14:17 ----------

This is the result for the number of number shared segments (chunkcounts). Here the numbers for Finns look similar to Norwegians vs the Nganassans.

Id Sam Fin Nor
Max 17,92 12,54 12,82
Min 6,25 5,41 5,46
Avg 9,55 8,32 8,21
MaxAvg 13,07 10,33 10,79
MinAvg 7,34 6,46 6,33
StdDev 2,68 1,70 1,63

So it appears Saamis have more shared segments in number than Finns but these are so small in total length that they still is smaller than for the total for Finns.

[Pallantides]

http://i1116.photobucket.com/albums/k573/maurimy/BALTIC-SCANS-CROSSSECTION-NRU-FR2-1.gif


I'm NO4 here - the one with the highest blue bar(French)

[Jerry]

My three-dimensional distances (FI15) from other project participants, top 20. Pretty interesting what a mix of Swedes,Estonians.Finns and Norwegians this is for me whereas many Finns score a list of only Finns in top 10-15 and then some others.

Swede in the top of my list even

FI15 FI15 0,0000
FI15 SWE20 0,0456
FI15 FI4 0,0487
FI15 SWE18 0,0568
FI15 FI5 0,0666
FI15 FI9 0,0694
FI15 FI11 0,0865
FI15 FI1 0,0893
FI15 SWE31 0,0978
FI15 NO7 0,0991
FI15 SWE7 0,1011
FI15 FI12 0,1052
FI15 ES1 0,1142
FI15 SWE11 0,1152
FI15 FI2 0,1183
FI15 SWE21 0,1187
FI15 NO6 0,1189
FI15 FI13 0,1206
FI15 SWE12 0,1216
FI15 ES2 0,1231
FI15 FI3 0,1299

[Pallantides]

Marked my position red(NO4)
http://i.imgur.com/Bzq5m.jpg

[Olavsson]

I'm now participating in Fennoscandia as NO15. :thumb001:
You can of course find me on that genetic plot posted by Svåse above... :cool:

[Pallantides]

NO4

American 0,0%
Oceanian 0,6%
East Asian 0,9%
Siberian 2,8%
Mediterranean 9,8%
European 77,6%
Central Asian 7,3%
African 0,8%

For comparison

NO5(evon) - West Norwegian

American 0,9%
Oceanian 1,3%
East Asian 2,0%
Siberian 0,0%
Mediterranean 11,7%
European 75,1%
Central Asian 9,0%
African 0,0%

NO15(Olavsson) - East Norwegian

American 2,9%
Oceanian 1,4%
East Asian 0,0%
Siberian 2,5%
Mediterranean 10,6%
European 77,1%
Central Asian 5,4%
African 0,0%

[Pallantides]

ID CL

SWE25 83,42
FI12 77,98
belorus8 77,33
SWE8 76,24
lithuania10 75,85
SA3 75,80
NO9 74,90
SWE22 74,67
LI1 74,55
SWE18 74,52
NO6 74,52
SWE24 74,03
NO13 73,70
NO15 73,49
NO1 72,92
SA1 72,67
SWE28 72,38
LI4 72,35
belorus6 71,59
SWE4 71,27
NO11 71,26
NO12 69,93
NO3 69,14
FI4 69,09
FI8 69,04
SWE34 68,95
ES1 68,94
SA2 68,51
NO2 68,15
lithuania7 67,88
FI2 67,79
SWE12 67,75
lithuania3 67,70
SWE23 67,55
SWE14 67,33
FI7 67,27
SWE20 67,20
SWE3 67,17
FI18 67,06
NO4 66,79
FI9 66,78
FI20 66,44
FI11 66,44
belorus3 66,19
belorus10 66,06
SWE2 66,05
belorus4 66,04
SWE10 65,98
SWE9 65,93
FI3 65,77
SWE6 65,71
SWE11 65,55
SWE21 65,42
NO10 65,34
belorus5 65,00
FI6 64,99
SWE7 64,83
FI5 64,80
SWE13 64,39
NO14 64,10
SWE27 63,63
SWE19 63,53
SWE5 63,41
lithuania8 63,23
lithuania6 63,22
SWE15 63,05
belorus1 62,97
SWE26 62,91
NO8 62,80
SA4 62,49
lithuania1 62,38
ES2 62,33
belorus7 62,04
SWE29 61,72
lithuania2 61,66
lithuania5 61,47
FI10 61,41
LI3 61,32
SWE30 61,08
FI1 60,72
SWE16 59,96
SWE17 59,77
FI14 59,52
FI13 59,47
lithuania4 59,26
FI15 59,20
SWE1 59,14
FI17 58,95
FI19 58,93
NO7 56,57
belorus2 56,18
LI2 53,51
FI16 52,34
NO5 52,21

These are the averages of x and y axis of the CL matrix vs the composite ancient gotlander.


41th from the list.

[evon]

New update, i have not yet looked at the results, but will do so later:)

http://fennoscandia.blogspot.no/2012/11/extending-reference-populations-looking.html

[evon]

Great, he forgot to add me (NO5), or i am blind :(

[evon]

Updated post:

http://fennoscandia.blogspot.no/2013/01/updated-chromopainterfinestructure.html

[Jackson]

Interesting. Although i never really understood those heat-maps, do you know how they work?

[evon]

Interesting. Although i never really understood those heat-maps, do you know how they work?

Yes, but i wish he could have released the numbers instead as they are far easier to read then looking for colour, basically the stronger the colour the closer the genetic match between two individuals..i will ask if he can post the spreadsheet also..

[Jackson]

Yes, but i wish he could have released the numbers instead as they are far easier to read then looking for colour, basically the stronger the colour the closer the genetic match between two individuals..i will ask if he can post the spreadsheet also..

Ahh i see, cool. Cheers. Yeah numbers are a much better format imo.

[evon]

Ahh i see, cool. Cheers. Yeah numbers are a much better format imo.

I got the sheet, now i am just waiting for a confirmation that i can post it here without breaking any codes of conduct he might follow..

[Jackson]

I got the sheet, now i am just waiting for a confirmation that i can post it here without breaking any codes of conduct he might follow..

Nice one! Will be good to see. If you can't post it then no worries, at least that means you can examine it in your own time. It pertains more to you and your people anyhow, especially as you are also a project member.

[evon]

Nice one! Will be good to see. If you can't post it then no worries, at least that means you can examine it in your own time. It pertains more to you and your people anyhow, especially as you are also a project member.

I checked my aunt and uncles results nothing special to report, just subtle differences...but at least the projects are still going, its been so boring since Eurogenes and Dodecad took a "vacation".. :(

[Jackson]

I checked my aunt and uncles results nothing special to report, just subtle differences...but at least the projects are still going, its been so boring since Eurogenes and Dodecad took a "vacation".. :(

Yes that is true. I started off mostly with Dodecad, i didn't trust Eurogenes at first. But he puts a lot of time and effort into it.

I should probably follow the MDLP, Harappa, and Fennoscandia projects - I only see them occasionally. Still i guess you are right - And even if they are just subtle variations, it's all more information that might be useful.

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.

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.

[evon]

I am a member of all the projects :P i will ask Harappan to look into my Roma ancestry, thank you for remind me of the project:)

[Jackson]

I am a member of all the projects :P i will ask Harappan to look into my Roma ancestry, thank you for remind me of the project:)

Ahh cool. Yeah i never thought about joining other projects after Dodecad and Eurogenes, although should have. Don't know if Harappa or Fennoscandia want British Isles samples though. Although i could give them 6, as long as them being related doesn't matter.

You're welcome. :thumb001:

[Mazik]

New update yesterday:

http://fennoscandia.blogspot.no/2013/02/updated-europe-analysis.html

I've replaced myself (SWE35) with my grandfather who is SWE40.

[Pallantides]

Marked my position
http://i.imgur.com/ZiPp1DF.png

[evon]

updates:
http://fennoscandia.blogspot.fi/

[evon]

Anders, now that you are a member here i can ask you if you are planning to release the segment matching data in a text form so that we can look at the numbers rather then colors?

[AndersP]

Anders, now that you are a member here i can ask you if you are planning to release the segment matching data in a text form so that we can look at the numbers rather then colors?

Yes sure. It has taken some more time than expected to get all the Finestructure analysis done. I am working on the last piece now and I hope to sendt it out during the day.

[evon]

Noticed some subtle trends for my NO16 (uncle), and NO17 (aunt) compared to the Other Norwegians, though i wish there were more samples from these regions so i could clarify the data, as its likely just noise...

https://imageshack.us/scaled/large/94/49912571.jpg


To clarify, the first row is total number of chunk counts shared (CC) and the second row is a total chunk length shared (CL).

[AndersP]

Noticed some subtle trends for my NO16 (uncle), and NO17 (aunt) compared to the Other Norwegians, though i wish there were more samples from these regions so i could clarify the data, as its likely just noise...

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.

[AndersP]

Your Scandinavian ;)


Marked my position
http://i.imgur.com/ZiPp1DF.png

[AndersP]

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


I am a member of all the projects :P i will ask Harappan to look into my Roma ancestry, thank you for remind me of the project:)

[AndersP]

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.

[AndersP]

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.

[evon]

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?


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/

[AndersP]

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.

[evon]

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......

[Pallantides]

Your Scandinavian ;)

Thanks, I wasn't aware:D

[AndersP]

The result looks a bit faulty...

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

[AndersP]

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.

[evon]

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..

[AndersP]

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

[evon]

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..

[AndersP]

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.

[Jackson]

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?

[Graham]

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

[AndersP]

What do you think that might suggest?

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

[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?

[AndersP]

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.

[AndersP]

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.

[AndersP]

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.

[AndersP]

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.

[AndersP]

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.

[AndersP]

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

[AndersP]

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

http://fennoscandia.blogspot.no/2013/05/la-brana-individuals-and-1000g-european.html

[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%.

[evon]

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 :)

[Jackson]

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?

[AndersP]

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.

[AndersP]

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/fennobga/CCPCA1-2INDEuro183kREF2V2.png

[AndersP]

Blog update: http://fennoscandia.blogspot.no/2013/05/la-brana-and-saamis.html

[AndersP]

Blog update: http://fennoscandia.blogspot.no/2013/05/la-brana-and-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.

[AndersP]

https://sites.google.com/site/fennobga/CCPCA1-2INDEuro183kREF2V2.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.

[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.

[evon]

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...

[AndersP]

New blogpost: http://fennoscandia.blogspot.no/2013/05/la-brana-and-modern-european-variation.html

https://sites.google.com/site/fennobga/AncientIberianEuriopeD1-D2.png

I dont think any more comments are needed :)

[AndersP]

I have been able to narrow it further :)

https://sites.google.com/site/fennobga/CCEuropeUNLINKED55KV2.png

[Aila]

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

Latest update:
http://fennoscandia.blogspot.com.au/2013/09/saami-ancestry-and-mdlp-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%

[Sippola]

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

[Aila]

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/ff455/Ailapics/Pre-Saami.jpg (http://s1236.photobucket.com/user/Ailapics/media/Pre-Saami.jpg.html)

[Norrbottning]

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

[Aila]

^ 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% ?

[AndersP]

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

Thanks :) I have been working to improve the analysis even more.

[AndersP]

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

It managed to capture that your of majority Saami ancestry. I think it is the best it can do. The rest I would call noise more or less.

[AndersP]

Would be curious to know what other Fennoscandos get here.

Would be interesting to know if its something general among Finns or if it is only seen in individuals with more recent Saami ancestry.

[Jusarius]

I (FI32) got this kind of results from MDLP K=5:

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

Admix Results:

# Population Percent
1 East_Eurasian 13.49
2 West_Eurasian 65.41
3 Caucasian 3.11
4 South_Asian 0.98
5 Paleo_mediterranean 17.00


Pct. Calc. Option 1

1 KRL 88.21%
2 SRD 6.28%
3 HKS 3.00%
4 TTR 1.65%
5 BLG 0.58%
6 KSV 0.24%
7 MNT 0.03%
8 MCD 0.01%
9 UZ 0.00%
10 RMN 0.00%

My ancestry is from Eastern Finland from both sides.

[AndersP]

My ancestry is from Eastern Finland from both sides.

Guess Karelians would be some kind of proxy for East-Finns in this calculator. Seems to catch it in your case.

[AndersP]

I dont think any more comments are needed :)

This particular analysis is now abit outdated. I have done new analysis separately of the La Braña 1 and 2. However as I learn more and got some feedback from the Chromopainter-Finestructure authors suggesting the most recent analysis I did may not be entirely correct either. So I will likely have to redo all the ancient genomes again following strictly the recommendations from the authors.

[Argang]

Anders has done a revised analysis (http://fennoscandia.blogspot.no/2014/03/la-brana-1-closest-to-basque-sardinians.html) on La Braña using the new sequence.

On the other hand the unlinked Finestructure analysis shows what we already know (La Braña is closest to Northeast Europeans in ancient ancestry, clusters with Finns in unlinked model), but a linked analysis also shows it has genealogical continuity with populations like Basques and Northwest Europeans with whom it clusters in that analysis.


As we can see the different models appear to give different results and its due to that in geneology the La Braña 1 closest to Basque, Sardinians and Western Europeans but in ancient ancestry closest to Finns and Saamis. The clustering in geneology with Basque, Sardinians and Western Europeans in the linked model make sense as the La Braña 1 individual was found in today northern Spain. This means that the La Braña 1 like haplotypes is still much present among Western Europeans of today suggesting continuity in the autosomes.

[karen1300]

I am new to this... Which is the best calculator? I get mixed results from different calcs on GEDmatch and Ancestry.

[Stanislav]

Karen, tray K-36 Eurogenes. It the best fore european.

[karen1300]

Karen, tray K-36 Eurogenes. It the best fore european.

Thank you, Stanislav.

Here is my K36:

Population
Amerindian 0.23%
Arabian -
Armenian -
Basque 2.65%
Central_African -
Central_Euro 6.75%
East_African -
East_Asian -
East_Balkan 0.43%
East_Central_Asian -
East_Central_Euro 4.28%
East_Med -
Eastern_Euro 6.20%
Fennoscandian 5.53%
French 7.58%
Iberian 10.67%
Indo-Chinese -
Italian 7.97%
Malayan -
Near_Eastern -
North_African -
North_Atlantic 21.43%
North_Caucasian 1.76%
North_Sea 18.39%
Northeast_African -
Oceanian 0.39%
Omotic -
Pygmy 0.70%
Siberian -
South_Asian -
South_Central_Asian 3.03%
South_Chinese -
Volga-Ural -
West_African 0.44%
West_Caucasian -
West_Med 1.57%

[Blanka]

So what happened to this project? Still active?

[Mazik]

So what happened to this project? Still active?

It's not active anymore :( is your mothers side from Norrbotten?

[Mazik]

So what happened to this project? Still active?

And where is your mtdna H11a2a traced? I know that it's most common in Västerbotten around Burträsk but only a few H11a2a are found outside Västerbotten.

[Blanka]

The Burträsk H11a2a is 2 steps from mine, so it's not an exact match. I have a 1 step in Scotland and the exact matches are in Norway (the oldest) and in central Sweden, Bergslagen and Västernorrland. I have an aunt who did some genealogy but when she moved house a few years back she accidentally threw it away, so the information she had on the female line has been lost, as in she doesn't remember. But it's not impossible that the female line is from Norrland. The one I that I do know the ancestry on is my grandmother's father and he's from the north. Not sure it's "just" Norrbotten, province or county. If there's anything I have learned about my family over time is that they've been moving around a lot. Staying put in one place is not our thing. I have heard that the database at Riksarkivet will open up after the New Year, so I'm planning on digging a bit then, see what I can come up with. When ever I have the time.
It's a pity the project is inactive. :(