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Tuesday, November 5, 2019

Modeling your ancestry has never been easier


An exceedingly simple, yet feature-packed, online tool ideal for modeling ancestry with Global25 coordinates is freely available HERE. It works offline too, after downloading the web page onto your computer. Just copy paste the coordinates of your choice under the "source" and "target" tabs, and then mess around with the buttons to see what happens. The screen cap below shows me doing just that.


Another free, easy to use online tool that works with Global25 coordinates is the Principal Component Analysis (PCA) runner HERE. Below is a screen cap of me checking out one of the eight PCA that it offers.


See also...

Getting the most out of the Global25

48 comments:

Davidski said...

Also please note that there are now two sets of Global25 datasheets, featuring ancient and modern samples respectively. See HERE.

claravallensis said...

Vahaduo doesn't allow to choose the number of cycles to perform and always does twice the amount of sources in the input. While this doesn't seem to create much problems for "properly mixed" samples so to say, I noticed that you can get weird results if you have the same population in the sources and in the target.
For instance if you put in the sources Barcin_N, Wezmeh_N, Natufians and CHG and try to model Barcin_N itself with these, you won't get ~100% Barcin_N but always something around 90% Barcin_N plus something from the rest. Something similar happens regardless of the choice of target, if it's included in the sources. I think the problem is simple, in that starting from a random distribution of slots and a random point built from the sources, the number of cycles simply isn't enough for the algorithm to update the best point until it closely matches the same source. The problem disappears increasing the cycles even to just, say, 50, and the speed of the algorithm isn't terribly affected. I assume this could cause problems also if you don't have exactly the same source and target but very closely related ones. I tried this by rewriting the same algorithm in R.

Samuel Andrews said...

Wow, these are great tools which save a lot of time. Is it possible to add your own samples to those PCAs? Or put entirelly new PCAs on there?

EastPole said...

Great tool, very easy to use, very fast.

My results:

https://i.postimg.cc/KjSyMYFz/screenshot-32.png

https://i.postimg.cc/TPFzzPK9/screenshot-33.png

It looks like I have to study KAZ_Golden_Horde_Euro. Where can I get some info about him?


On PCA I am not far from Sintashta, which explains why I like Rigveda so much.

https://i.postimg.cc/h4YX2kb1/screenshot-35.png

Davidski said...

@EastPole

It looks like I have to study KAZ_Golden_Horde_Euro. Where can I get some info about him?

That's a European, very Baltic-like-individual from the Medieval Kazakh steppe from one of the recent Damgaard et al. papers.

https://www.nature.com/articles/s41586-018-0094-2

Each sample has a unique individual ID that can often be searched online in Google and various databases, such as the "anno" files here.

https://reich.hms.harvard.edu/downloadable-genotypes-worlds-published-ancient-dna-data

Gabriel said...

@Davidski

How did that guy end up in the Kazakh steppe?

Davidski said...

@Gabriel

How did that guy end up in the Kazakh steppe?

He was probably a captive from somewhere in western Russia raided by the Mongols.

rozenfag said...

@EastPole , @Gabriel : Here is an article in English about this sample from Kazakhstan: https://www.academia.edu/36877181/E.R._Usmanova_I.I._Dremov_I.P._Panyushkina_and_A.V._Kolbina._Mongol_Warriors_of_the_Jochi_Ulus_at_the_Karasuyr_Cemetery_Ulytau_Central_Kazakhstan

Our guy is from kurgan 5.

Davidski said...

@claravallensis

That's a fair point.

But it doesn't have a significant impact on well designed models that don't include very similar (highly correlated) source populations.

The source populations in models should always be relatively highly differentiated, otherwise the algorithm is likely to produce unrealistic results just to get the lowest (best) statistical fits.

So the right way to analyze fine structure ancestry (gene flow from very similar sources) is to try similar populations one by one to see how the statistical fits change. You probably know this already, but I just mentioned it for the benefit of others.

And, of course, for more advanced analyses, it's best to use nMonte in R.

Mikkel said...

These tools are great and really easy to use.
I was playing around with PCA in PAST3, but it seemed a bit difficult to adjust labeling of graphics etc to see who were exactly who (without having it all blued out by row labels). Grouping also took a lot of time to do.
This is much faster and the mouse hover info on individual samples and the zoom and pan functions make it much easier to study the PCA.
A Mediterranean/South European PCA preset would also be nice, though. :)

Just got the Vahaduo thing working as well. This will be a great future tool for studying lesser described samples in further detail which have been neglected in some of the big studies.

Huck Finn said...

Just by looking at West Eurasia PCA in PCA Runner (very good product BTW), it seems that the origin of Baltic Finnic is connected to Levänluhta_IA, Srubna_o and Sintashta_o type of samples and then there's a local cline connecting modern samples to Baltic_BA-type of samples. IA tarand grave sample OLS_10, (the fresh from a sledge guy), for instance seems to be a mixture of modern East Finn/Karelian (more or less the same thing in the past) and a Kivutkalns_BA related samples in the PCA. But, can Levänluhta_IA in reality get anyhow connected to Srubna_o and Sintashta_o outside a PCA, which may be misleading? In other words, to what extent PCA is biased in this case?

Huck Finn said...

P.S. just by looking at the same PCA it seems that there's a cline connecting the rather clearly visible cloud or continuum of different Uralic groups ultimately to neolithic West Siberia. The mainstream European continuum seems to meet this the Uralic cline in/at Baltic_BA, which of course makes a lot of sense.

Davidski said...

@Huck Finn

In regards to your question about PCA bias, I don't really know.

But I can tell you that Volosovo as the proto-Uralic culture looks like crap from where I'm sitting. There's no Y-hg N there at all.

Don't know about Garino-Bor yet.

Huck Finn said...

@ D: Garino Bor should be the place. If it's not, then I don't know. The map in page 7 is BTW pretty interesting:

http://www.kirj.ee/public/Archaeology/2012/issue_1/arch-2012-1-3-25.pdf

So, no N in Volosovo, interesting. Many thanks for the information.

weure said...

Thanks David, you have made clear now that the North Dutch/NW German Bell Beaker area is indeed the 'genetic hub' with linkages more NW-wards over Sea to England/Scotland, NE-wards to Poland and the Baltic and SE-wards into Germany/Austria and deeper! The linkages are very obvious now!

epoch said...

@Huck Finn

I think there is some sort of agreement that proto-Uralic and PIE must have grown up is adjacent area's. So, Garino Bor is pretty interesting as a PU Urheimat suggestion, as it is upstream from the Samara Bend where Khvalynsk resided.

Archi said...

No, there was no contact between the two languages at the time. This is proven. The Uralic languages did not come from Siberia until the middle of the second millennium BC, and it is proved that they came from Siberia, but not autochthonous in Europe.

Rob said...

It seems Seima-Turbino is also from Eastern Europe

Davidski said...

@epoch

Apparently there's a pretty strong consensus forming behind the scenes based on the latest linguistic and ancient DNA data that Proto-Uralic formed east of the Urals, and that only the Proto-Finno-Ugric homeland was in Europe.

Archi said...

The Ugric languages are also to the east of the Urals, so the proto-FinnO-Ugric languages are to the east of the Urals. But the Finno-Volga languages ones are already in Europe.

Seima-Turbino is connected with Altai.

epoch said...

@David

O, that is interesting. I have read in several papers the case for a European homeland and one of the consistently put forth arguments is that PIE must have been in the neighbourhood to explain for the list of old cognates.

Is this line of reasoning now obsolete?

Huck Finn said...

@D and re "Apparently there's a pretty strong consensus forming behind the scenes based on the latest linguistic and ancient DNA data that Proto-Uralic formed east of the Urals, and that only the Proto-Finno-Ugric homeland was in Europe."

I'm not aware of such a linguistic consensus but maybe there's one. In regards to Proto Uralic around 2000 BCE, Pre Proto Uralic is a different issue, it seems to me that many linguistics still support Volga Bend as the place of origin. According to Narasimhan et al 2019 West Siberian Neolithic type of features were BTW present there, which in my understanding supports your own qpAdm model based on Estonian Tarand grave sample OLS10, including WSHG type of features, if I'm right. On the other hand, the officially unpublished Baltic Finnic ancient DNA samples which I've seen, don't at least in PCA seem to be based on anything East Siberian. BOO and Levänluhta are a different story,as there's a clear Arctic substratum based vibe in those Saami related samples. So, I can't see too much support for the East Siberian origin of Proto Uralic. Some place in/or around Ural area makes much more sense.

Turbino, now that Seima Turbino was mentioned, is a place by Kama river, located in the same area as Garino Bor culture. Udmurts still live there. Seima, on the other hand, is located by Oka river, probably the birthplace of West Uralic (Mordva i.e. Erzya and Moksha speakers, Baltic Finns, Saami). Seima type of axes were for instance apparently first found in Finland and only after discovery of the famous Seima burial the axe type was renamed in Finland as Seima axe.

Matt said...

@epoch, on the question ("I have read in several papers the case for a European homeland and one of the consistently put forth arguments is that PIE must have been in the neighbourhood to explain for the list of old cognates. Is this line of reasoning now obsolete?"), with the caveat that the specifics of the loans may overrule this:

There is always the possibility that any early IE-U loans took place via a third (or more layers of) intermediary language group that was wiped out by later expansions. To enable apparent "sharing" over longer distances than usually thought.

Direct IE-U is probably just the most parsimonious solution from modern we can have without postulating extra languages, rather than one we can be clear about from modern data (which is extremely lossy).

On a similar tack, when it comes to loans from II-U, there are some elaborate schemes devised to try and prove the presence of different layers of II interacting with U, through II loans in U. But there is little evidence of the reverse loaning U->II.

This seems to have been put down to different technology and motivations for loanwords and so on. However I think it is more likely that it is simply the case that loans would be bidirectional, but that whichever specific variety of II language(s) was/were interacting with U languages (and would have likely received loans) is simply extinct today and not known. There are essentially a wide variety of II languages which are thought to have existed in the past, which have no attested form today to examine for vocabulary / loans.

Probably replaced by Turkic languages, if not the U languages themselves, or II languages which did not receive loans themselves, before the expansion of Turkic languages. (This would have nothing much to do with the question of where the II languages ultimately originated, and would be compatible with a variety of possibilities, including the most commonly held one).

claravallensis said...

Rome paper is out: https://science.sciencemag.org/content/366/6466/708

Ric Hern said...

Thanks claravallensis.

Rob said...

Mesolithic Italy dominated by I2a2; Neolithic R1b-P343, J2 and G2

Anthony Hanken said...

Tarands are are easily traced back to the LBA-IA upper-mid Volga (D'yakovo and Akozino-Akmylovo respectively). Both of these cultures are decended from the Netted-Ware culture of the upper Volga. I would assume N1c will be found in BA Netted Ware.

Netted-Ware was it self formed after Fatyanovo-Balanovo and Abashevo elites migrated into Volosovo territory. Netted Ware was also involved in the spread of Seima-Turbino materials.

The way I see it this really only leaves a few options, Garino-Bor and/or Seima-Turbino or Circum-Polar explorers like BOO making their way into Netted-Ware groups like Carlos believes.

Ric Hern said...

@ Rob

Isn't it R1b M343 ?

Rob said...

Yep; sorry

Romulus said...

I also bought the paper here is an interesting Figure: https://i.imgur.com/CXIghxD.png

Davidski are we ok to share?

Ric Hern said...

Wonder if they are relatives of the R1b V88 in Neolithic Spain....

Gaska said...

This gets interesting, there will be hundreds of Kurganists looking for SNPs to prove it's V88

Grotta Continenza 5.200 BC

claravallensis said...

Samples R437 and R851 seems like they may be derived for R-L2 too.

Romulus said...

There is only 1 Etruscan Y-DNA and it's J-M12

The iron age Latin y dna is:

R-M269
T-L208
R-P311
R-PF7589
R-P312
R-P312


Not so sure about Etruscans anymore

Romulus said...

They found Varna man's Y-DNA in the Latins

The other two Iron Age males, R474 and R850, belong to J-M12 (J2b) and T-L208 (T1a1a) haplogroups
respectively. As discussed above, the J haplogroup and its J2a subclade have already been present in early
farmers in Italy, the Balkans, and Anatolia (13, 14). In addition, a Bronze Age individual from Croatia
(1631-1521 calBCE) belonged to the J2b2a haplogroup (14) and carried exactly the M314 derived allele
that is also found in R474. Therefore,the observed J-M12 (J2b) could be a surviving lineage from local
Neolithic populations or due to recent migrations from the Balkans or the Near East. The T1a haplogroup,
although absent in our samples prior to Iron Age, has previously been found in early farmers in Bulgaria
(5,800-5,400 calBCE) (14) and Germany (5,500-4,850 BCE)(13), so it is possible that it was also present
in early farmers in central Italy.

Samuel Andrews said...

"Steppe-related." Goddammit. Seriously? They are going to be that ambiguous and vague about it?

They should know exactly where comes from. It comes from Descendants Bell Beaker from North of the Alps who carried R1b U152>L2+ which most of the Iron age samples from Latium belong to. They had been living in Northern Europe since 2800 BC, so over 1,000 years, before they entered migrated into Latium in Central Italy.

It's common ancestor between ancient Romans, Gauls, Britons, and Iberians. Which is interesting and significant if you think about it.

Samuel Andrews said...

They say "Pointic-Caspien Steppe" not Eastern Europe, not Northern Europe. Which are the "Steppe-related" people who migrated into Italy came from.

They spoke of "Iran Neolithic", when they really should be speaking about Anatolia or NEar East. Because, there was no gene flow directly from Iran into Italy. Or directly from the "Pontic-Caspien Steppe" into Italy.

These bad descriptions give a inaccurate impression about who was moving into Italy at different times.

These researchers need to get a better understanding of Europe's population history as told by ancient DNA before they publish anything.

Rob said...

Sam
What they say is

“ qpAdm, we modeled the genetic shift by an introduction of ~30 to 40% ancestry from Bronze and Iron Age noma- dic populations from the Pontic-Caspian Steppe (table S15), similar to many Bronze Age popu- lations in Europe (10, 13, 14, 19, 22). The pre- sence of Steppe-related ancestry in Iron Age Italy could have happened through genetic ex- change with intermediary populations (5, 23). Additionally, multiple source populations could have contributed, simultaneously or subsequently, to the ancestry transition before Iron age”

Seems reasonable

claravallensis said...

Isn't it also quite interesting how that iron age sample from Croatia, I3313 I think, which seemed to resemble Bergamo so much, is consistent with forming a clade with these iron age Romans?
Frome the supplementary:
"The only well-fit one-way model is with an Iron Age individual from Croatia dated to 805-761 calBCE,
suggesting that this individual form a clade with Iron Age central Italians, with respect to all the
populations in the “right” set (ANC17). This result, together with those for Neolithic and Copper Age
individuals, points to tight connections between Italy and the Balkans from Neolithic to Iron Ages."

AWood said...

@Rob

Well there are only 4 Neolithic samples, one of which could be V88, 2 are J2 and 1 is G2. The V88 and G2 would be consistent with ancient Sardinians. Whatever happened to the alleged R1b and I1 "Etruscans"? I guess that wasn't true.

Romulus said...

Imperial Rome
E 1/24
G 5/24
J 13/24
R1a-Z93 2/24
R1 1/24
R1b-m269 1/24
T 1/24

Samuel Andrews said...

@claravallensis,
Iron age Italy has no ancestry from the Balkans. It's very clear cut. Most iron age Italians carry R1b L51 which comes from Bell Beaker. 99% of Bell Beaker in Germany, France, Czech carry R1b U152>L2 which is very common in Northern & Central Italy today. And apparently was the most common haplogroup in the Latin Tribes & Republican Romans.

Samuel Andrews said...

Generally speaking, some pops in Iron age Western Balkans were similar to Iron age Italy. This was not because of a direct relationship. But, because each was a similar mix between Anatolian farmers, European Hunter gatherers, and Eastern European Pastorlists.

Rob said...

@ Sam

“Generally speaking, some pops in Iron age Western Balkans were similar to Iron age Italy. This was not because of a direct relationship. “

There were clear and direct movements between west Balkans and Italy during BA - IA

claravallensis said...

@AWood
Weren't those from the other study that should be coming? That with the leaked PCA.
Or maybe they sharing these samples, not sure.

Richard Rocca said...

@Gaska said..."This gets interesting, there will be hundreds of Kurganists looking for SNPs to prove it's V88"

And if history is any indicator, they will succeed. On the flip side, there will be hundreds of Iberians looking for SNPs to prove it's M269 and they will fail miserably.

Ric Hern said...

Did R1b V88 migrate via Italy into North Africa during the Neolithic ?

Huck Finn said...

@ Anthony and re: "The way I see it this really only leaves a few options, Garino-Bor and/or Seima-Turbino or Circum-Polar explorers like BOO making their way into Netted-Ware groups like Carlos believes."

This indeed seems to be the case.