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Monday, July 13, 2020

Don't believe everything you read in peer reviewed papers


Case in point, here's a quote from a recent paper at the Journal of Human Genetics (emphasis is mine):

The Mordovian and Csango samples have a moderate to slight orientation toward the Central-Asian and Siberian Turkic groups. This could suggest the more significant East Eurasian or Turkic ancestry of these populations, which should be further investigated. German samples are inhomogeneous, and some of the German samples also show this tendency, which can be the result of the recent 20th century Turkish immigration into Germany [42].

Nope, these German samples don't show anything even remotely resembling recent Turkish ancestry. The authors of the paper, Ádám, V., Bánfai, Z., Maász, A. et al., should've been able to figure this out, even with the standard analyses that they ran. Failing that, the peer reviewers at the Journal of Human Genetics should've noticed that the authors were confused.

Moreover, if the authors and peer reviewers actually bothered to take a closer look at metadata for these samples, which were sourced from the Estonian Biocentre, they'd see that they're not even from Germany. In fact, they represent self-reported ethnic Germans from Russia.

My own quick and dirty analysis of these individuals suggests that many of them harbor East Slavic and/or Volga Finnic ancestries. Indeed, only some of them can pass genetically for run of the mill Germans from Germany. The Principal Component Analysis (PCA) below is self-explanatory. It was plotted with the Vahaduo Custom PCA tools freely available here. The relevant PCA datasheet can be gotten here.


That's not to say, of course, that some Germans don't have recent Turkish ancestry, because an increasing number of Germans nowadays do, nor that people with German heritage in Russia shouldn't identify as Germans, because that's entirely their choice.

This blog post isn't about what it takes to be German, and this is not something that I ever want to discuss for obvious reasons. The point I'm making here is that the authors and peer reviewers of the said paper at the Journal of Human Genetics were sloppy and half-arsed in their approach. And, sadly, this isn't an isolated case in peer reviewed scientific literature dealing with human population genetics.

I feel that the Estonian Biocentre is also partly to blame for this cock up, due to its somewhat peculiar sampling and labelling strategies. For instance, its scientists rely solely on self-reported identity to establish the ethnic origins of their samples, and they apparently never remove genetic outliers from their datasets or even try to identify them.

Unfortunately, I fear that this relaxed approach will eventually lead to basic errors and even unusual conclusions in a number of so called peer reviewed papers.

I first raised this issue with the Estonian Biocentre about five years ago, when I noticed that some of the supposedly Polish individuals in its dataset were genetically more similar to various groups from northern Russia than to Poles from Poland. These individuals also showed significant Siberian ancestry, which was very unusual indeed. Where the hell did the Estonian Biocentre find Poles who resembled people from near the Arctic Circle, you might ask? Apparently in Estonia.

OK, I can imagine that sampling ethnic Poles from Estonia may have been easier for the Estonian Biocentre than sampling Poles from Poland. And Estonian Poles certainly make for interesting and useful data points. However, as you can see in the PCA below, some of these individuals (labeled Polish_Estonia by me) aren't representative of the native Polish population, and yet the Estonian Biocentre not only lumps them with their Poles from Poland, but even labels them with the word "Poland". The relevant PCA datasheet can be gotten here.


However, based on my communications with some of the scientists at the Estonian Biocentre, including head honcho Mait Mestpalu, it seems that nothing will ever change there in regards to this issue. Who knows, perhaps some day we'll see a paper based on Estonian Biocentre data in the Journal of Human Genetics claiming that Poles originated near the Arctic Circle? I wouldn't be shocked if that actually happened.

Citation...

Ádám, V., Bánfai, Z., Maász, A. et al. Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania. J Hum Genet (2020). https://doi.org/10.1038/s10038-020-0799-6

See also...

Like three peas in a pod

42 comments:

Onur Dincer said...

A very good and constructive criticism. I should add that in the Hungarian paper you linked to at the beginning they use in their genetic analyses solely East Eurasian-rich Turkic populations to calculate amounts of Turkic ancestry in the Hungarians and other populations without using any East Eurasian-rich Uralic population to distinguish Turkic ancestry from Uralic ancestry. They use enough East Eurasian-rich Turkic populations in their analyses, but do not use any East Eurasian-rich Uralic population. The non-inclusion of the Khanty and Mansi populations in the analyses is especially appalling, considering they are the closest modern linguistic relatives of the Hungarians. In order to discern Turkic ancestry, they should also include the East Eurasian-rich Uralic groups in their analyses.

Slumbery said...

@Onur Dincer

I do not know whether involving Mansi would have resulted something interesting, maybe not, however there is a possibility of confirmation bias. Under the previous post I mentioned that the minister of human resources is listed as an author under the article about the Y-Hg of the Árpád dynasty. (This might be a breach of ethics as the ministry financed the study, but that is another story.) The minister is a big fan of the idea of Hun origin and not shy to spend some taxpayer money on his hobby. (Well, maybe even something interesting comes out from it, there are people in the current cabinet with much more expensive and more stupid hobbies.) This study is also financed by his ministry. That does not mean that the scientist did not do a honest work, but one thing is clear: as far as the minister is concerned, the very purpose of these studies is to prove the Hungarians are the descendants/heirs of the Huns. That means that the researchers are not paid to look for alternative explanations when their first one is compatible with that hypothesis.

Their mistake with the Russian-German samples is awkward and unfortunate.

Sofia Aurora said...

The thing David is not to accept or not accept everything you read!

That's common sense!
The thing is WHY "PRESTIGIOUS" PUBLISHING HOUSES AND JOURNALS ACCEPT AND PUBLISH SUCH THINGS!!!

And to become more specific, why always when there is an anti-White, anti-European "out of the jungle" crap it becomes adopted and promoted, while when there are UNDENIABLE ANTI-AFROCENTRIC, ANTI-MULTIRACIAL and ANTI-GLOBALIZATION findings, these findings almost NEVER SEEN PUBLISHED in the various "prominent and highly esteemed" journals, blogs, conferences, etc.

Right now there are more than 14 papers in Biorxiv suggesting IMPORTANT archaic hominin introgression in Africans!

Some even prove that homo sapiens as a species is moriband because it is the result of amlgamation of different archaic hominins not to mention that after the emergence of "homo sapiens" again it mixed severely with other species.

Have you seen any of these papers being published? No!
Why?
Because it will destroy the unique and only african origin of the "political correct" Homo sapiens dogma?

Is this practice different to e.g. what kurganists were experiencing till 2014?

a said...

Hi, My family is "German-Russian", German speakers that entered Russia / Ukraine from 1820 - 1850. My DNA is pretty much all North Sea / Doggerland. My half-brothers has MtDNA from Yemen and can trace family into Turkey.

So, some self-reporting Germans with Odessa / Russia / Ukraine roots may consider themselves German, but it was a large area without a lot of people and there was some marriage outside the village!

Samuel Andrews said...

Population genetics papers seem to often make beginner mistakes like this. I would say Reich's Harvard lab makes the best papers.

There were papers which used Polish Jews to represent Poland. Was that also EstoniaBiocentre?

Someone needs to teach them what a disparso population is, the fact disparso populations are almost always mixed and not representative of any population.

G2a-M406 Anatolian Farmer said...

David do you have any idea what is next?

Davidski said...

Next in regards to?

Samuel Andrews said...

@Rob,

David Reich is a geneticists with no background in history, archaeology. I know you know archaeology best so I think this is why you don't like him. His interpretation of genetic data has always been very good. When he connects it to archaeology, sure he doesn't always do a good job.

His lab has been behind most of the breakthroughs for understand European population history. Most of it was not easy to understand. For example, no lab could have done as well in analysis as his lab did in 2013 when they published three high coverage Neolithic/Mesolithic genomes. The basic claim they made in 2013 is still correct.

His overall claims about European population history have been shown to be correct. He has made clear mistakes, like claiming WHG was from Middle East. But overall he does a good job. He's much better than other ancient DNA labs.

Samuel Andrews said...

@Davidski,

Would you not agree, Harvard lab does better than other ancient DNA labs? It seems every other ancient DNA paper makes beginner mistakes in their qpADM analysis. They certainly wouldn't use disparso population, like Russian Germans, to represent host population.

Rob said...


@ Sam

You’re too easily impressed by Harvard stating “steppe migrations”. That’s nothing new (although downplayed in recent literature)
But in details; Reich hasn’t got much right.
It’s not that he just doesn’t get it. He is actively dishonest. Massive conflict-of-interest in collaboration with David Anthony. He obviously has no ethical constraints.

G2a-M406 Anatolian Farmer said...

@ David


Papers etc.Any upcoming study?

G2a-M406 Anatolian Farmer said...

@ Sofia


This 'Political Correct' exists only in western societies.And as we know these Labs have 'Western' Rulers-Βosses.You will not find 'Political correctness' in Russia,Turkey,Poland,Iran,China etc.I would like to see upcoming papers or studies from non-western scientists.It would be great to have a different opinion..Btw i agree with everything you write above and keep in mind i am not European.I have mention in previous thread about the debate with the IE homeland.All the purpose behind,it has to do with the immigration issue in Europe...and i am not joking here.They will try to prove that IE's come from somewhere near caucasus-Iran or even Mesopotamia to prove that modern Europeans travelled from somewhere else as refugees-Immigrants.

Samuel Andrews said...

@Rob,

Two early Harvard/Reich lab papers which prove their expertise in population genetics.

India paper 2013.
https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/2013_AJHG_Priya_India_Date_0.pdf

Europe paper 2013.
https://www.researchgate.net/publication/259441354_Ancient_human_genomes_suggest_three_ancestral_populations_for_present-day_Europeans#:~:text=We%20analyzed%20these%20and%20other,%3B%20Ancient%20North%20Eurasians%20(ANE)

Since 2015 they haven't made new insights. But, overall they know how to interpret data better than most.

Btw, Reich's lab made a theory about an ANE population who contributed to Ameridians and Europeans before Mal'ta boy's DNA was sequenced. This was thinking outside the box in a way few would do back then.

Davidski said...

@Ιωαννης θεοδωρος Γαβρας

There are lots of papers coming, but I don't know when we'll see them.

These things take time, partly because there are usually different opinions about how to frame the data and so the discussions go on and on.

Unfortunately, some papers might take many months to appear, even though the samples have been ready for a while.

Onur Dincer said...

@Slumbery

I do not know whether involving Mansi would have resulted something interesting, maybe not

Of course it would. There is a clear separation between the Turkic and Uralic genetic clines:

https://drive.google.com/file/d/1BF_4ssthNhsGlrfDSsQs64BahlHPjO1c/view?usp=sharing

The Tubalars are between both clines as they have well-known significant Samoyed and Ket ancestry. The Yakuts and especially the Dolgans have significant ancestry from various Northern Tungusic and Samoyedic groups.

however there is a possibility of confirmation bias. Under the previous post I mentioned that the minister of human resources is listed as an author under the article about the Y-Hg of the Árpád dynasty. (This might be a breach of ethics as the ministry financed the study, but that is another story.) The minister is a big fan of the idea of Hun origin and not shy to spend some taxpayer money on his hobby. (Well, maybe even something interesting comes out from it, there are people in the current cabinet with much more expensive and more stupid hobbies.) This study is also financed by his ministry. That does not mean that the scientist did not do a honest work, but one thing is clear: as far as the minister is concerned, the very purpose of these studies is to prove the Hungarians are the descendants/heirs of the Huns. That means that the researchers are not paid to look for alternative explanations when their first one is compatible with that hypothesis.

Then the minister should change his hobby and leave science to scientists. Otherwise the quality of the human population genetics papers coming out of Hungary will not pass beyond a certain level, especially when they are concerned with Hungarian origins. Even the Chinese make much higher quality papers with their oppressive dictatorial regime.

Onur Dincer said...

Forgot to mention, the Chuvash and the Volga Tatars, especially the former, have more Uralic ancestry (through the Uralic natives of the Volga region) than Turkic ancestry as can also be seen in this ADMIXTURE plot:

https://drive.google.com/file/d/0B9n4j3PQ81RcNGpTODFXQVhNWFk/view?usp=sharing

The same plot shows that the Hungarians have more Turkic ancestry than Uralic ancestry, albeit in a very tiny amount today (you should zoom in to see it clearly), which is partly understandable given the relatively high percentage of words of Turkic origin in the Hungarian language (was apparently even higher during the times of the Hungarian conquest of the Carpathian Basin) and the apparent Turkic origin of some of the leaders and tribes involved in the conquest (including even the Arpad dynasty, it seems). So apparently the Hungarian paper did not have to play a trick in their analyses and could serve their purposes better by including the East Eurasian-rich Uralic populations in them.

Then how come the Hungarian language we know is a Uralic language with Uralic morphology, grammar and basic vocabulary and Uralic is the biggest contributor to its overall vocabulary among all the known language families? This mystery will likely be solved through more vigorous ancient DNA testing.

Bob Floy said...

OT, has anyone looked at wikipedia's page about Yamnaya recently?
It says "Eleven individuals were determined to belong to haplogroup R1b1a2 (R-V88) or various subclades of it, while one individual was determined to belong to haplogroup I2a2a1b1b." Makes no mention of Z2103. What the hell is going on?

Onur Dincer said...

@Bob Floy

OT, has anyone looked at wikipedia's page about Yamnaya recently?
It says "Eleven individuals were determined to belong to haplogroup R1b1a2 (R-V88) or various subclades of it, while one individual was determined to belong to haplogroup I2a2a1b1b." Makes no mention of Z2103. What the hell is going on?


They should, of course, have written "M269" in the parentheses. An inexcusable mistake.

ambron said...

Dawid, why is it impossible to distinguish Poles from Germans and Swedes on this new PCA?

Davidski said...

Not in this PCA, but in other PCA it is, after removing the Uralic speaking groups and adding more Slavs and also Balts.

Huck Finn said...

@ Onur and re: "Then how come the Hungarian language we know is a Uralic language with Uralic morphology, grammar and basic vocabulary and Uralic is the biggest contributor to its overall vocabulary among all the known language families?" The ethnogenesis of Hungarians is apparently based on a complex interaction between Oghur Turkic (i.e. Hunnic?) and Uralic speakers. Chuvash as we know is the only remaining Oghur Turkic speaking population, formerly apparently known as Volga Bulgars. Volga Tatars then possibly are in many cases later language shifters into Common Turkic, in the Russian so called Mongol Era. At some point the relative role of Uralic speakers vs. the relevant Oghur speaking population apparently was strong enough to motivate the adoptation of Uralic vs. Oghur. It may for instance have been related to male recources, because some 40 % of the Conqueror samples have so far been tested as N-Z1936?

https://link.springer.com/article/10.1007/s12520-019-00996-0/figures/6

Shaikorth said...

@Ambron
It's not too difficult to separate those populations even on a broad European PCA. See here.

http://2.bp.blogspot.com/-QQ-MokKfQ4A/VOsYSAyicVI/AAAAAAAAAhc/9p3Kmro4-OQ/s1600/plot13.gif

Separating the Belarusian-Polish-Ukrainian cluster or various Celtic and Germanic NW Europeans OTOH is better done with a PCA focusing on a specific part of Europe.

Shaikorth said...

Adding that the Germans on the previous PCA are EBC's "Volga Germans" which means many are outside the NW European cluster. Some are still like Germans from Germany though, as in Davidski's PCA.

Further picking apart NW Europe on a PCA can also be tricky, putting enough drifted samples gets you something like this:

https://upload.wikimedia.org/wikipedia/commons/d/d3/Joint_PCA_plots_of_877_Icelandic%2C_250_Norwegian_and_445_Scottish_samples.png

...where Icelandic populations don't cluster like anything you'd expect from their parent populations' proxies. Keep just a handful of Icelandic and Orcadian to get a more realistic picture.

ambron said...

David, note that the common genetic structure of Poles, Germans and Swedes, which seems deep, precludes the recent, significant exchange of Polish population.

Davidski said...

@Shaikorth & ambron

It's not really possible to cleanly split eastern Germans from western Poles, because they have very similar ancient and modern ancestries.

Otherwise, it's pretty easy to create all sorts of European clusters that correlate with geography and linguistics, including a northern Slavic cluster.

But yeah, you need to include specific populations in the PCA, and also to leave out relatively highly differentiated groups.

Matt said...

OT but relevant to some folks interests : https://phys.org/news/2020-07-ancient-evidence-horsemanship-bronze-age.html

Shaikorth said...

@Matt
A nice follow-up would be getting DNA from those horse burials. Within the next few years I'm hoping to see whether there were multiple independent instances of horsemanship forming and if modern breeds descend from a specific centre.

Matt said...

@shaikorth, yeah, and as they have a hypothesis of relationship between horses being buried with riders, would be interesting to see if any genetic relationship between horses that mapped with that (e.g. some burials associated with lines of horses and such). As well as obvious overall genetic structure.

Early military horse poses some interesting questions - why are chariots still so important in post 1600bce cultures and probable dispersals? I get the impression there's a notional model where chariots and superceded by military horse riding once it develops, fairly quickly, but may not have been like that. And why does military horse riding not seem to disperse so early (or have we misinterpreted and it does?)

Ric Hern said...

@ Matt

Maybe it is because bigger horses needs more care especially when used for riding and heavy draught work. Ponies and smaller horses needs much less. So maybe it had to do with the economy.

George said...

Slightly off recent discussion:

https://phys.org/news/2020-07-ancient-evidence-horsemanship-bronze-age.html

Early evidence for horse utilization in the Eurasian steppes and the case of the Novoil’inovskiy 2 Cemetery in Kazakhstan
AuthorS: Igor V.Chechushkova, Emma R.Usmanovab, Pavel A.Kosintsevc
https://www.sciencedirect.com/science/article/pii/S2352409X2030211X

Behind paywall - From the Abstract:
- The horse crania demonstrate pathologies that could be due to the bridling.
- The cheekpieces demonstrate use-wear due to the utilization in bridles with soft bits.
- The bone pathologies and the cheekpieces’ use-wear are most consistent with utilization the horses for riding or chariotry.

We conclude that the key horsemanship practices were already fully established during the Bronze Age, as horse remains demonstrate evidence for bridling, which can be linked to the utilization of bridles with cheekpieces and soft bits. If these horses were used for riding, the radiocarbon age of the complex (cal. 1890–1774 BCE) pushes the gradual shift from chariot to horseback riding towards the beginning of the 2nd millennium BCE.

Archi said...

@George
"- The bone pathologies and the cheekpieces’ use-wear are most consistent with utilization the horses for riding or chariotry.
We conclude that the key horsemanship practices were already fully established during the Bronze Age, as horse remains demonstrate evidence for bridling, which can be linked to the utilization of bridles with cheekpieces and soft bits. If these horses were used for riding, the radiocarbon age of the complex (cal. 1890–1774 BCE) pushes the gradual shift from chariot to horseback riding towards the beginning of the 2nd millennium BCE."

For this time and context, rather a pair of horses harnessed to a chariot.

" The lumbar vertebra of sheep/goat found underthe horse's head was probably also placed there intentionally. Finally,after the installation with the horses had been covered with soil, abovine’s head with a horn cut-offand some bones were placed on top."

This is a well-known ritual among the Indo-Aryans.

RVI.162
"What time they bear before the Courser, covered with trappings and with wealth, the grasped oblation, The dappled goat goeth straightforward, bleating, to the place dear to Indra and to Pusan.

Dear. to all Gods, this goat, the share of Pusan, is first led forward with the vigorous Courser, While Tvastar sends him forward with the Charger, acceptable for sacrifice, to glory.

When thrice the men lead round the Steed, in order, who goeth to the Gods as meet oblation, The goat precedeth him, the share of Pusan, and to the Gods the sacrifice announceth."

163
"The strong Steed hath come forward to the slaughter, pondering with a mind directed God-ward.
The goat who is his kin is led before him the sages and the singers follow after."

Goats carry Pusan.

VI.57
"
1 Indra and Pusan will we call for friend ship and prosperity And for the winning of the spoil.
3 Goats are the draft-animals for the one; two fallow bay horses, fully
equipped, are for the other;
along with those two (horses) he keeps smashing obstacles."

Goat-borne, the guard of cattle, he whose home is strength, inspirer of the hymn, set over all the world; Brandishing here and there his lightly. moving goad, beholding every creature, Pusan, God, goes forth.

May Pusan, drawn by goats, be our protector, and on all his paths Bestow on us our share of maids.

O Pusan, may those goats of thine turn hitherward thy chariot-pole. Friend of all suppliants; art thou, born in old time, and arm and sure.

Archi said...

Pusan went in chariots drawn by goats. And with the goats were buried the horses that participated in the ritual chariot races, this was a sign that this team brought rewards.

Slumbery said...

@Onur Dincer

Of course it would. There is a clear separation between the Turkic and Uralic genetic clines:

I know. I meant that even when other possibilities tested, the East Asian genetic contribution _might_ still proven to be of Turkic origin.

ambron said...

Dawid, the case concerns not only eastern Germans and western Poles, but also Czechs, Slovaks and Hungarians. Generally speaking - Western Slavs, because East Germans was earlier Polabian Slavs, and Hungarians were earlier Pannonian Slavs. In this group, the exception are north-eastern Poles, some of whom are indistinguishable from Belarusians, and some from Lithuanians. The second exception is the Sorbs who have separated themselves from the Kashubians (Rębała paper). In the principal components analysis, Western Slavs differ quite substantially from the Eastern ones, so it is difficult to say that the genetics of the North Slavic group correlates with language and geography. Eastern Slavs are distinguished from the Western mainly by a high proportion of Balitic BA, which you call a Balto-Slavic drift. And this is because most of the Eastern Slavs (including north-eastern Poles) are Balts assimilated by the Western Slavs.

Above I presented what can be seen in the principal components analysis.

Onur Dincer said...

@Huck Finn

The ethnogenesis of Hungarians is apparently based on a complex interaction between Oghur Turkic (i.e. Hunnic?) and Uralic speakers. Chuvash as we know is the only remaining Oghur Turkic speaking population, formerly apparently known as Volga Bulgars. Volga Tatars then possibly are in many cases later language shifters into Common Turkic, in the Russian so called Mongol Era. At some point the relative role of Uralic speakers vs. the relevant Oghur speaking population apparently was strong enough to motivate the adoptation of Uralic vs. Oghur. It may for instance have been related to male recources, because some 40 % of the Conqueror samples have so far been tested as N-Z1936?

https://link.springer.com/article/10.1007/s12520-019-00996-0/figures/6


@Slumbery

I know. I meant that even when other possibilities tested, the East Asian genetic contribution _might_ still proven to be of Turkic origin.

See my reply to both of you:

https://eurogenes.blogspot.com/2020/07/first-taste-of-early-medieval-dna-from.html?showComment=1594764012159#c9074811230530194641

Rob said...

@ Sam

''But, overall they know how to interpret data better than most.''

Harvard are the worst.
You may disagree with other Lab's conclusions, or they may have a poor supplementary info
But the Reich Lab activily distorts and misinforms

Vladimir said...

@Rob "But the Reich Lab activily distorts and misinforms"

Because it does not support the " Balkan" hypothesis :)

Rob said...


@ Valdimir

You don't know what model I see, you illterate fool
Reich's factual distortions are very clear and pervasive; most of which have nothing to with the Balkans (eg BBC). They'd be clear to you too, if you had the cognisance to observe instead of running your constant verbal diarrhoea about topics you don't understand, including topics from your own Lands
So nice straw man; dipshit

Davidski said...

OK, moderation is going back on.

Simon_W said...

@ambron

"the exception are northeastern Poles"

I wouldn't be so sure about that. I already mentioned the case of my girlfriend: she's from Tarnow and surrounds, i.e. Podkarpackie, yet she's closest to Russians from Smolensk. And no, she isn't Ukrainian, she speaks Polish, she feels Polish, her maiden name is Polish and 23andme says she's Polish. According to Tomenable's fine scale sampling she's in fact closest to Poles from Lublin, even closer than to Smolensk. But this in turn means that Poles from Lublin are also rather eastern and Lublin isn't in the northeast. According to Tomenable Poles from Podkarpackie are more varied, some eastern, some more western. He thinks this might be because of German admixture.

weure said...

Meanwhile Davidski has given already a clue for the 'proto'-germanic speakers. Danish LNBA Rise71 is IMO a key sample. It's from the so called "Flint Dagger Period" and is basically a kind of BB/TRB mix. In the G25 North European PCA Rise71 clusters with a bunch of Dutch, Swedes and a Dane.

https://www.mupload.nl/img/otkaduwpyks.png

Prawder said...

Simon_W said...

"According to Tomenable's fine scale sampling"

What was that "fine" sampling? In what calculator? It was commercial?
And why he is an authority on that?