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West Eurasia, North Africa and South Central Asia (MDS map, dimensions 1&2)
http://img98.imageshack.us/img98/2087/eumescao.gif
with labels
http://img221.imageshack.us/img221/3...scalabeled.jpg
http://eurogenes.blogspot.com/2010/1...and-south.html
* as always I'm NO2.
Not sure what the new data proves...
Norwegians
NO1:
South Indian: 2.3%
Amerindian: 0.8%
Mediterranean: 20.7%
Middle Eastern: 0.7%
North Eurasian: 0%
West African: 0%
East Asian: 0.5%
East African: 0%
West Eurasian: 4.2%
North/Central/EastEuropean: 70.6%
NO2(me):
South Indian: 0.8%
Amerindian: 0%
Mediterranean: 17.3%
Middle Eastern: 0%
North Eurasian: 1.6%
West African: 0%
East Asian: 1.5%
East African: 0%
West Eurasian: 4.6%
North/Central/EastEuropean: 74%
NO3:
South Indian: 1.1%
Amerindian: 0.1%
Mediterranean: 16%
Middle Eastern: 1.6%
North Eurasian: 1.6%
West African: 0%
East Asian: 0.1%
East African: 0%
West Eurasian: 7.5%
North/Central/EastEuropean: 71.6%
NO5:
South Indian: 0%
Amerindian: 0.02%
Mediterranean: 16.7%
Middle Eastern: 0%
North Eurasian: 0.7%
West African: 0%
East Asian: 2.5%
East African: 0.03%
West Eurasian: 7.2%
North/Central/EastEuropean: 72.6%
Swedes
SE1:
South Indian: 0.9%
Amerindian: 1.4%
Mediterranean: 14.3%
Middle Eastern: 4.4%
North Eurasian: 0%
West African: 0%
East Asian: 0.2%
East African: 0.06%
West Eurasian: 6.2%
North/Central/EastEuropean: 72.1%
SE2:
South Indian: 1.9%
Amerindian: 0%
Mediterranean: 15.1%
Middle Eastern: 7%
North Eurasian: 1.2%
West African: 0%
East Asian: 1.5%
East African: 0%
West Eurasian: 2.6%
North/Central/EastEuropean: 70.3%
SE3:
South Indian: 2.8%
Amerindian: 0%
Mediterranean: 19.6%
Middle Eastern: 1.2%
North Eurasian: 4.1%
West African: 0%
East Asian: 0%
East African: 0%
West Eurasian: 4.2%
North/Central/EastEuropean: 67.7%
SE4:
South Indian: 0%
Amerindian: 1%
Mediterranean: 12.6%
Middle Eastern: 2.3%
North Eurasian: 2.5%
West African: 0%
East Asian: 0.09%
East African: 0.1%
West Eurasian: 3.1%
North/Central/EastEuropean: 78%
Quote:
Originally Posted by Lemminkäinen
New K-12 run
.........................NO1,NO2, NO3, NO5.
North European: 68.5%,71.2%, 68.9%, 69.5%
South Indian: 0%, 0.05%, 0.04%, 0%
North Eurasian: 0%, 0.06%, 2% ,1.2%
Central American:1%, 1%, 0%, 0.9%
South American: 0%, 0%, 0.06%, 0%
East African: 0%, 0%, 0%, 0.03%
West African: 0%, 0%, 0%, 0%
North African: 0.08%, 0% 0%, 0%
Oceanian: 1%, 0%, 0.02%, 0.04%
Mediterranean: 11%, 8.4%, 10.3%, 10.5%
West Eurasian: 16.3%, 17.2%, 16.5%, 16.3%
East Asian: 1.1%, 0.9%, 0.6%, 0.5%
I'm not sure what to make of this, my North Eurasian went from 1.6%(K-10) to 0.06% in this one, while some Portuguese fellow is 2% North Eurasian... also NO1's South Indian score went from 2.3% to 0%, it might be a glitch.:confused:
Can you make a pie of the average of all Spaniards ?Quote:
Originally Posted by Soten
I can say so far that most of the clustlering sounds pretty fine.
Well I looking at such examples as North Russian with Lithuanian and Finnish or the French, The British Isles with Norwegian and even Belarus well not much suprises here.
The french also cluster with the spaniard.Quote:
Originally Posted by asterox
Spaniards average : 52 % Northern European / 31 % Med / 12 % West Eurasian
http://oi52.tinypic.com/335gmd4.jpg
NO1 who is west Norwegian is closer to the British and Central Europeans out of all the Norwegians, while the east Norwegians(NO2, NO3 and NO5) are dragging towards Lithuania and Finland
* edit: I only assume that NO3 and NO5 are from eastern Norway, since they are closer to me(NO2), NO1 is evon from FroumBiodiversity.
Intra-Eurasian MDS 1&2
http://img823.imageshack.us/img823/9830/eurasia.png
my position:
http://img301.imageshack.us/img301/3528/45092669.png
How have these categories been created?Quote:
Originally Posted by Iberia
1. With real DNA of peopleQuote:
Originally Posted by Curtis24
2. Running SNP's with a special software for dna and admixture analysis
Pallantides latest examples here on this thread look fine so far.
Are Pole usually cluster closer with Russian ?
*double post*
I think I'm the Norwegian with the most "Fenno-Scandic" in this one.Quote:
Originally Posted by Iberia
http://eurogenes.blogspot.com/2010/1...eurasians.html
Genetic structure of North Eurasians (aka. Baltic Finns in a North Eurasian context)Quote:
Unravelling the genetic story of North Eurasia, a largely ignored part of the world by population geneticists, is the main reason I started my BGA project. That's because understanding the genetic substructures within this zone is pivotal to understanding the makeup of my own "Balto-Slavic" genome. I'm now happy to report that in the last few months I've collected enough samples, from Northwestern Europe to the Bering Strait, to be able to run at least some meaningful analyses on the subject, so here goes...
The comparison below is, as far as I know, the first time ever that a decent number of Baltic Finns, from all over Finland, have been publicly analyzed alongside samples from across North Eurasia using high-density genome-wide markers. What you're seeing is the output from a model-based algorithm called ADMIXTURE, with eight ancestral populations assumed (K=8), based on 320,000 SNPs (spreadsheet available here). And yes, I'm as surprised as anyone that it took this long to do it, and that it's me doing it.
http://img209.imageshack.us/img209/8954/neura8j.png
Now, before you get all worked up about the results, it's vital to understand that ADMIXTURE doesn't actually show admixture. It doesn't even show any ancestral components. All it does is tell us the chances of each of the samples in the comparison being mixed up for the others. It does this by working out the maximum likelihood of the samples sharing membership in clusters, with the number of clusters picked by the user (me, in this case). From this information it's possible to infer admixture. So yeah, it can be a bit fickle, arbitrary and "noisy", but it's still fairly useful, especially when the results are cross checked with those from other types of analyses, like MDS and IBD.
The most striking part about the plot above, for us Eruos anyway, is probably the so called Fenno-Scandic (cream colored) cluster. I tagged it "Fenno-Scandic" because it peaks in the Baltic Finnish samples, but the name isn't important. Interestingly, it shows up in hefty amounts all the way from the British Isles to the Volga-Ural region (note its presence in the Chuvash samples). But it drops like a rock as one moves towards Central Europe. So does this mean there was a Baltic Finnish invasion of Ireland on one hand, the Volga-Ural on the other? Nope, it doesn't.
That cluster is there because I clearly oversampled the Baltic Finns, letting the algorithm easily deduce their relatively unique characteristics, and in large part making them set the tone of the analysis for the other European samples. It's actually made up of several quite different ancestral components carried by Baltic Finns; Northwestern European, Northeastern European and Uralic. So if we go back to what ADMIXTURE really shows (ie. the probability of the samples being mixed up for one another) everything makes sense. Indeed, a recent analysis done by the Institute for Molecular Medicine Finland (FIMM) basically showed the same thing:
Genetically, Finns have more in common with, for example, the Dutch or Russians living in the area of Murom, to the east of Moscow, than with our linguistic relations, the Hungarians; genetic closeness clearly follows geographic distance more closely than linguistic distance.
Also, note how on my plot above some of the Finns come out very differently from their kinfolk, ie. less Finnish and more North/Central European. This too was picked up by the FIMM.
Owing to our settlement history, the genetic differences among Finns are great on both the east/west and north/south axes; the greater the geographic distance is, the greater the genetic differences are. In comparing the Finnish dialect areas, the greatest genetic differences are found between Finns of Southwest Finland and inhabitants of Kuusamo in Northeast Finland.
The linguistic link between Swedish-speaking Finns living in coastal areas and Swedes is also reflected in the greater genetic closeness of these two groups in comparison with Finnish speakers.
Like I say above, the large number of Baltic Finns makes it easy for the algorithm to come up with a Baltic Finnish specific cluster, so only some of them end up scoring clear North, Central and/or East Asian admixtures. The rest of their Eastern ancestry is contained within the Fenno-Scandic component. This shows in the Fst (genetic) distances between the eight clusters:
http://img507.imageshack.us/img507/6529/neurafst.png
The Fenno-Scandic cluster is the European cluster closest to the Asian clusters. Also, check out the presence of what I call the "North Eurasian" cluster, which is about the same distance from Europe as it is from East Asia. This so called component peaks in the Selkup and Ket samples, and is marked blue on the above ADMIXTURE plot. It also shows up all over Northern Europe. So this might well be a sign of ancient genetic continuity across North Eurasia, at least to some degree anyway.
An MDS analysis of the same samples, using the same 320,000 markers, produces very similar results. The Baltic Finns stream towards North Eurasia from the North/Northwest European cluster, overlapping with the Russians and some of the North Russians (from Vologda Oblast, just east of Finland). At the same time, the Selkups and Ket position themselves roughly between the far Northeast Eurasians and Europeans. Indeed, you can see a hint of a stream flowing across the north, with the Europeans seemingly more attracted towards the lower left of the plot than to the upper left, where Turko-Mongols and East Asians proper reside.
http://img255.imageshack.us/img255/6818/neura12.png
I've also run some preliminary intra-North Eurasian Identity by Descent (IBD) comparisons. I won't post any details because my methodology is still a bit unorthodox (ie. I'm using PLINK, which tends to overestimate IBD sharing when non-homogeneous sample sets are being compared). However, it's definitely worth a mention because it shows that, even at very low thresholds, Baltic Finns don't share IBD segments with Asians, while Selkups don't share any with Europeans (except one Selkup, who also shows European, possibly Russian, influence on the above ADMIXTURE plot). So it certainly seems, as far as I can tell, that the aforementioned Selkup "North Eurasian" cluster, phylogenetically about halfway between Northeast Asia and Europe, is pretty damn old. Similarly, the North/East Eurasian affinity of the Baltic Finns is also looking like an ancient phenomenon. On the other hand, I am seeing some hits between Anatolian Turks, Uzbeks, Uygurs, Hazara and Pathans. We'll see how that goes as I try different types of software and thresholds.
http://img255.imageshack.us/img255/1281/selkupman.jpg
Above is a Selkup man, courtesy of Wikipedia. He reminds me a bit of Charles Bronson, who was a Lithuanian Tatar by descent. But anyway, by posting his photo, I'm not suggesting that those who show around 1-2% membership in the Selkup "North Eurasian" cluster in the spreadsheet above, including many Northern Europeans, had an ancestor like this at some point in time. Perhaps, but there's no way to tell at the moment, because all we're looking at via the stats above is allele sharing and various probabilities stemming from it. It's all too easy to get the same results because of very different reasons, and in the end, it usually comes down to a best fit scenario based on the available resources (for example, reference samples).
Locating and visualizing minority non-European admixtures across our genomes
I only have a faint red one on chr 5.
http://img140.imageshack.us/img140/7...hmapperno2.png
From what I have seen most North Europeans get 3 to 7 red hits.
Based on maps Lithuanians or Sardinians seem to be most European populations depending on how you look at it.
The purest are the Basques, they are 99.9 Euro (n.euro+s.euro)Quote:
Originally Posted by Breedingvariety
Labelled by Warwick over at ABF
Europe 1&2
http://img12.imageshack.us/img12/509...pedec82010.png
Europe 1-2-3 (side view)
http://img413.imageshack.us/img413/8...wlabeledde.png
West and Central Eurasia 1&2(labelled by Warwick at ABF)
http://img697.imageshack.us/img697/2...rasialabel.png
Intra-West Eurasian ADMIXTURE analysis for 23andMe users
http://bga101.blogspot.com/2010/12/i...-analysis.html
Spreadsheet
http://cid-5223cc821fdfeb45.office.l...20Eurasia.xlsx
Me(NO2)
Basque 0,055473
West-Northwest-Central European 0,66598
North African 0,00001
Northeast European 0,176283
Middle Eastern 0,00001
Mediterranean 0,102234
Anatolian 0,00001
* I wonder if there is an error here, that 3 Finns score 3-4 % North African seem rather strange.
Could you make one for me also please.:D
Quote:
Originally Posted by Pallantides
Thank you:thumb001:Quote:
Originally Posted by Soten
http://img704.imageshack.us/img704/7...uro1282010.pngQuote:
Originally Posted by warwick
http://img829.imageshack.us/img829/4...raleuroped.pngQuote:
Originally Posted by warwick
error error
^evon made a mistake with the graphs, SE1 is not 4.1% in the Mideastern cluster and according to Davide he did a lot of other calculating mistakes... but I'm to lazy to look at the spreadsheet right now, so I just remove the graphs.
West and Central Eurasia 3D view
http://img64.imageshack.us/img64/209...eurasia123.png
To my eye, these charts seem to show something of a ring. The main connection between populations is the Europe - Middle East - South Asia - Far East one, with a more tenuous one linking the extremes of the circumpolar peoples.
Do we think that if we had complete samples for all ethnic groups, we'd 'fill in the gaps'? I played around on paint with one graph, trying to work out from geography and ethnohistory WHO would be in the gaps;
http://img837.imageshack.us/img837/9...acolshrink.png
The big red circle with a Ч in it is the Turkic speaking Chuvash on the middle Volga. Seems to me that we ought to stick the following in to tie them in better with the wider scheme; more Komi, Ob Ugrians (Mansi and Khanty), Nenets Samoyeds (to link the arctic continuum).
Gagauz, Crimean Tatars, Mordva, Kazan Tatars, Siberian Tatars (to link the central Europeans with the Turkics).
Nogai, Turkmen and Tajiks to get the southern Eurasian link.
And a big fat load of Tibetans to plug the gap in the south east. :p
Do we expect that there'll still be gaps?
Fascinating to see single ethnoses break down into cluster to demonstrate the plural origins that history often suspected... :thumbs
I'm wondering, though; why do the peoples roughly in the middle - Uygurs and Hazara - look so 'stretched'? Is this just a result of how the graph was made, or does it really reflect a greater diversity within their populations?
My result(NO2)Quote:
Originally Posted by Lemminkäinen
SE 6,71
NO 5,67
UK 5
HU 4,95
US 4,74
FR 4,39
North_Russia 4,36
PL 4,33
BY 4,11
ES 3,5
RU 3,43
PT 3,25
RO 3,07
DE 3
FI 3
IE 3
LT 2,9
Chuvash 2,82
GR 2,6
IT 2,56
Adygei 2,53
AJ 2,43
Selkup 1,89
Pathan 1,59
ASY 1,56
IR 1,53
TR 1,5
UZ 1,4
Uygur 1,2
Burusho 1,04
IN 1
Hazara 0,86
Altai 0,83
Yakagir 0,75
Nganassan 0,69
AA 0,69
ET 0,63
East Greenland 0,5
Tuva 0,5
Athabaks 0,47
Yakut 0,43
Buryat 0,42
Evenk 0,4
Orogen 0,33
West Greenland 0,33
Mongol 0,28
Daur 0,22
Dolgan 0,2
TU 0,2
Yoruba 0,19
CO 0,14
Pima 0,14
Xibo 0,14
Maya 0,11
She 0,1
Tujia 0,1
Han 0,09
Koryak 0,07
Bantu 0,06
JP 0,03
[YOUTUBE]4aMD4uy-QGc[/YOUTUBE]Quote:
Originally Posted by Pallantides
Something interesting...
NO1 - FI 6
NO2 - FI 3
NO3 - FI 5,75
NO5 - FI 5
I'm from East Norway and supposedly have some Forest Finn ancestry from the 17th century, while NO1 is a West Norwegian.
Can someone help me out with the new admixture analysis?
I'm going to guess none of that is enough to indicate admixture? :confused:
Soten, that's the overall picture. Here are your details:
Code:rs1029145 AFR
rs10492520 EAS
rs10514241 EAS
rs10779907 EAS
rs10825468 AFR
rs1105391 EAS
rs11060233 EAS
rs12089636 AFR
rs12217685 EAS
rs12220022 EAS
rs13232076 EAS
rs1334572 AFR
rs1364017 EAS
rs1463427 EAS
rs16839883 EAS
rs16883494 EAS
rs16903010 EAS
rs16903648 AFR
rs16920051 EAS
rs16934416 EAS
rs16957551 AFR
rs16957597 AFR
rs16957664 AFR
rs16988825 AFR
rs17011662 EAS
rs17013664 EAS
rs17013810 EAS
rs17014788 EAS
rs17015638 AFR
rs17044715 EAS
rs17067539 EAS
rs17078801 EAS
rs17087075 AFR
rs17087095 AFR
rs17251648 EAS
rs17599262 EAS
rs17748939 EAS
rs1858022 AFR
rs1892868 AFR
rs2069683 EAS
rs2073358 EAS
rs213135 EAS
rs2638298 AFR
rs264701 AFR
rs307274 EAS
rs3756514 EAS
rs3777456 EAS
rs3780660 EAS
rs3811842 EAS
rs3845461 EAS
rs3862609 EAS
rs401522 EAS
rs4939591 EAS
rs4987774 EAS
rs6499781 EAS
rs6812580 AFR
rs6928877 EAS
rs7190322 EAS
rs7201539 AFR
rs7271632 AFR
rs7275620 EAS
rs7290364 EAS
rs763880 EAS
rs7784129 EAS
rs877180 EAS
rs879017 EAS
rs9453955 AFR
rs951954 AFR
rs9556725 EAS
rs9812589 AFR
rs9912490 EAS