Stolarek et al: Genetic history of East-Central Europe...

[alexfritz]

So Kowalewko 38 and Czarnowko 547 appear not to be contaminated?

I suspect that all R-YP6048 samples from Stolarek et al. are contaminated (including Kowalewko 38) by someone who was in contact with the genetic material.

Out of 17 officially contaminated samples, 4 (!) belong to R-YP6048:
PCA0332 (BTW, labelled incorrectly as Ostrow Lednicki 322 by FTDNA)
PCA0333
PCA0403
PCA0496

PCA0038 (Kowalewko 38) has no Y-DNA calls in the .bam file - https://www.ebi.ac.uk/ena/browser/view/S...show=reads

not sure about the .bam file but in Table S3 there is a slot called 'Derived SNPs (Haplogroups:Marker: Position:Mutation)' to retrace the 'Terminal SNP' assignment and Kowalewko 38 is assigned R1a1a1b1a1a M458+

now whether YP6048 is a correct assignment or not remains to be seen, but Kow38 is nonetheless M458+ and not listed as contaminated in Table S1
rolling with that

[tylerkiz]

SLAZ - Upper Silesians
GORA- Gorals (Highlanders)
KASZ- Kashebians
LEMK - Lemkos
BAMB - Bambrzy (Bambers) polonized descendants of Bamberg (Frankonian) German colonists, living near Poznan in Wielkopolska.
It is interesting that Bambers are quite similar to Podkarpackie voivodship but also to Lemkos. If common thing for last two is medieval German admixture from WaldDeutsches (Głuchoniemcy), presumably also central/south German, which makes them artificially similar to Bambers?

There might be something about it, because I noticed shared segments between these areas (Posen and Carpathian region of Poland) and Western Germans. A lot of those Posener matches were protestant settlers though, and not Bamberger, but I didn't always check for the religion.
The same applies to some haplogroups which seem to be shared, which I can confirm especially for E-V13. A bit surprising is the low frequency of R1b in the Bambergers, but this might be due to the very small sample size and could change with more data. The rather low E-V13 in Gorals and Silesians is a bit surprising. Probably it was higher in German Silesians.

Either the data on Gorals is somehow flawed or they have waaay less Vlach input than the Rusyns like Lemkos.

Maybe they have some people who aren't fully gorals. For example like a one parent who is goral and one who isn't. But  hey that is a theory, a game theory

Or they could be from specific families/villages where R1a is predominant or the data is corect and Gorals are diferent from other Carpathian Slavic groups like the Rusyns or Slovkas and Moravian Vlachs and realy do have Medieval Northern/Polish origins. You can notice its not only E-V13 and G2a that is lower they also have lower Slavic I2a which again suports a Northern/Polish origin for them. It would be interesting to see what specific R1a branches they belong to ie M458vsZ280.

I joined the forum just to share here on this topic, I have been looking for more true and accurate "goral" samples for some time. The only readily available Southern Polish G25 coordinate looks very Ukrainian. 

I am mixed so my G25 admixtures are often confusing but I am about 40% modern day Polish, 40% French and 20% british/irish give or take. My father's side (polish) come from Rzyki near Andrychów, a village that was settled under Wallachian law in around 1550. The Vlachs, who reached the area of today's Rzyki around the mid-16th century, were a Ruthenian-Romanian-Slovak-Hungarian ethnic conglomerate. My surname (Kizner/Kiznar) has been found in the region as early as 1530 and is suggested as possibly Romanian or Hungarian in origin.

My Y-DNA Haplogroup is (R1a) R-CTS3402, most commonly found in Southern Poland and Croatia.

I am not sure how accurate it is, but IllustrativeDNA's ancient mixed mode which plots in various periods identifies this Polish side as Baltic and a small bit of some type of Greek or Italian in Iron Age, by Roman Age it is almost entirely what they identify as Byzantine Slav (Tragurium) or Pannonian Slav (Avar Period) and in the Middle Ages it is Medieval South Slav (Bitola), Post-Medieval Syrmia, Rus' (Sunghir) or Medieval Pole (Polan), However Medieval south slav shows as most prominent.

All of this to me indicates migration out of the Baltic area, into the Balkans and then finally a remigration back into Poland through the Carpathian (as it is known the Vlachs did). This storyline follows the supposed migration of the White Croats (except for the coming back part). 

Below is how I plot with modern day Slavic samples. It is closer to Slovenian or Croatian but I think my French side pull me in this direction. In any case, I have run my coordinates through many calculators and PCA charts and it is never very similar to modern Romanian, which is what would be expected for "Vlach". 

I am probably too mixed to serve as the best example but wanted to share in any case.

[YP4648]

So Kowalewko 38 and Czarnowko 547 appear not to be contaminated?

I suspect that all R-YP6048 samples from Stolarek et al. are contaminated (including Kowalewko 38) by someone who was in contact with the genetic material.

Out of 17 officially contaminated samples, 4 (!) belong to R-YP6048:
PCA0332 (BTW, labelled incorrectly as Ostrow Lednicki 322 by FTDNA)
PCA0333
PCA0403
PCA0496

PCA0038 (Kowalewko 38) has no Y-DNA calls in the .bam file - https://www.ebi.ac.uk/ena/browser/view/S...show=reads

Do we know if ftDNA received their own samples to process? Or did they get data (like BAM files) from the Stolarek team?

[leonardo]

So Kowalewko 38 and Czarnowko 547 appear not to be contaminated?

I suspect that all R-YP6048 samples from Stolarek et al. are contaminated (including Kowalewko 38) by someone who was in contact with the genetic material.

Out of 17 officially contaminated samples, 4 (!) belong to R-YP6048:
PCA0332 (BTW, labelled incorrectly as Ostrow Lednicki 322 by FTDNA)
PCA0333
PCA0403
PCA0496

PCA0038 (Kowalewko 38) has no Y-DNA calls in the .bam file - https://www.ebi.ac.uk/ena/browser/view/S...show=reads

Do we know if ftDNA received their own samples to process? Or did they get data (like BAM files) from the Stolarek team?

It appears from the various studies. Foe example, Kowalewko 38: Reference: PCA0038 from Stolarek et al. 2018; Stolarek et al. 2023
For Prague 13780: Reference: I13780 from Patterson et al. 2021 and so on. FTDNA also gives this caveat: Phylogenetic Y-DNA analysis by FamilyTreeDNA. Ancient DNA samples are typically degraded and missing coverage, sometimes resulting in less specific haplogroup placements. Still, with that said, they obviously have faith in the sample to list it. As for some of these alleged contaminated samples., I thought another poster, maybe back on AG, mentioned that these samples were handled by women, to avoid possible contamination. I think it may have been @ambron?

[ambron]

Radko smells sensation where there is none.

Preliminary selection of samples due to contamination is a standard procedure in archaeogenomic research. If mtDNA and the X chromosome are contaminated, and the Y chromosome is clean, there are no obstacles to including it in some Y-DNA database, e.g. FTDNA. Even if the sample was not used in the study.

[leonardo]

Radko smells sensation where there is none.

Preliminary selection of samples due to contamination is a standard procedure in archaeogenomic research. If mtDNA and the X chromosome are contaminated, and the Y chromosome is clean, there are no obstacles to including it in some Y-DNA database, e.g. FTDNA. Even if the sample was not used in the study.

I don't want to speak for Radko, but I believe he is alleging the y-DNA is contaminated. Was that you who said the samples were handled by a woman?

[ambron]

Leonardo

No, it wasn't me who said that.

I once discussed procedures for detecting contaminants in archaeological samples with David on EG. Currently, they are so precise that no sample contaminated with modern DNA should slip into the further stages of the test.

Genetic testing of all team members who come into contact with bone and biological material is also usually standard.

[lukpl]

PCA0038 - https://www.ebi.ac.uk/ena/browser/view/S...show=reads
According to Pribislav without calls possible to determine such subclade R-YP6048 like FTDNA stated
I checked yesterday this bam. All Y calls, some are non-calls btw.

rs2534398 Y 2945498 TT
rs9782803 Y 4418534 AA
rs2580701 Y 6611498 TT
i703710 Y 6957380 AA
rs73614824 Y 8072664 CC
i703343 Y 8123518 TT
rs112215181 Y 8446082 TT
rs9786299 Y 8467732 TT
rs2538883 Y 9755694 CC
rs7474469 Y 9953367 GG
rs62611172 Y 9986197 AA
rs62608681 Y 10019975 GG
rs80033621 Y 10031963 AA
rs62608737 Y 10032021 CC
rs75364311 Y 13450642 CC
rs79967132 Y 13464597 TT
rs62611640 Y 13464775 CC
rs62611644 Y 13464951 --
rs796263837 Y 13485428 CC
rs796878764 Y 13485433 AA
rs368652465 Y 13485692 --
rs796308164 Y 13485741 AA
rs78127787 Y 13486243 CC
rs112466786 Y 13486257 CC
rs796696929 Y 13674284 AA
i708163 Y 13674331 TT
rs74652064 Y 13687378 AA
rs62602337 Y 13802265 AA
rs773988182 Y 13813181 GG
rs796253578 Y 13846503 TT
rs878899555 Y 13861950 --
rs796605204 Y 13869122 GG
rs200486163 Y 14024615 CC
rs747839864 Y 14418666 CC
i705677 Y 14899954 GG
rs35072519 Y 15309625 AA
i705348 Y 16042855 CC
rs112800323 Y 18018313 AA
rs72613046 Y 21815957 TT
rs372754770 Y 22179053 --
rs9785919 Y 28797422 TT
rs372439475 Y 58856082 CC
rs796728353 Y 58985047 TT
rs796569848 Y 58985631 TT
rs373137604 Y 58993935 AA
rs7067511 Y 59002734 CC
rs4047586 Y 59012354 --

[sirdan]

The PCA0038 from Stolarek et al 2023 is indeed fail, the bam is wrong format, and Y data is almost nonexistent


Bear in mind that FTDNA refers to: PCA0038 from Stolarek et al. 2018

There is second study here https://www.ebi.ac.uk/ena/browser/view/SRX2369808 2016 year
PCA0038 is there but it does not look same, however is bad sample too, looks like G haplogroup.

There is yet another previous saple source here http://gigadb.org/dataset/100310  2017 year
but here PCA numbers are not same numbers as KO_XX

I have dowloaded KO_038_MappingMPA_sorted_noPCR.bam and its wrong format too.
I have no time to look for PCA038 there.

[lukpl]

The PCA0038 from Stolarek et al 2023 is indeed fail, the bam is wrong format, and Y data is almost nonexistent


Bear in mind that FTDNA refers to: PCA0038 from Stolarek et al. 2018

There is second study here https://www.ebi.ac.uk/ena/browser/view/SRX2369808 2016 year
PCA0038 is there but it does not look same, however is bad sample too, looks like G haplogroup.

There is yet another previous saple source here http://gigadb.org/dataset/100310  2017 year
but here PCA numbers are not same numbers as KO_XX

I have dowloaded KO_038_MappingMPA_sorted_noPCR.bam and its wrong format too.
I have no time to look for PCA038 there.

Older bams were even worser, what are you talking about. And what would be a point to upload new but crappy bams. To make a bigger mess?

[sirdan]

It is written above clearly.
I was looking Stolarek et al. 2018 bam PCA 0038 that matches with that on FTDNA, but did not find it.

[ambron]

As for the Wielbark population, McColl's team is very enigmatic about it:

"The earliest individuals from Wielbark, Poland (~1900 BP) are primarily of Eastern Scandinavian ancestry, supporting a population migration from a region and population distinct from that of the West and North Germanic populations, a scenario potentially consistent with Gothic oral history."

This applies only to a few of the Wielbark samples included in the study - the earliest ones (approx. 100 AD) and those with the most Scandinavian genetics. Unfortunately, the authors nowhere present an analysis of the admixtures of the Wielbark Goths, although they do present the Iberian and Crimean Goths.

Fortunately, the authors place the Wielbark Goths on the IBD segment division maps. And here, on the first map in the first row from attachment 14, we can see that about 30 Wielbark individuals draw their ancestors from the Baltic BA source. The Wielbark population draws approximately the same amount of ancestry from the Baltic BA source as the Late Antique population of Öland, which is known (attachment 17) to have a relatively high share of the Baltic BA component. The Wielbark population from McColl's work therefore has a clear Eastern European admixture, the same as in Stolarek's work.

[leonardo]

As for the Wielbark population, McColl's team is very enigmatic about it:

"The earliest individuals from Wielbark, Poland (~1900 BP) are primarily of Eastern Scandinavian ancestry, supporting a population migration from a region and population distinct from that of the West and North Germanic populations, a scenario potentially consistent with Gothic oral history."

This applies only to a few of the Wielbark samples included in the study - the earliest ones (approx. 100 AD) and those with the most Scandinavian genetics. Unfortunately, the authors nowhere present an analysis of the admixtures of the Wielbark Goths, although they do present the Iberian and Crimean Goths.

Fortunately, the authors place the Wielbark Goths on the IBD segment division maps. And here, on the first map in the first row from attachment 14, we can see that about 30 Wielbark individuals draw their ancestors from the Baltic BA source. The Wielbark population draws approximately the same amount of ancestry from the Baltic BA source as the Late Antique population of Öland, which is known (attachment 17) to have a relatively high share of the Baltic BA component. The Wielbark population from McColl's work therefore has a clear Eastern European admixture, the same as in Stolarek's work.

Is this the work to which you are referring?
https://www.biorxiv.org/content/10.1101/...607v1.full

[ambron]

Leonardo

Yes!

[leonardo]

The idea of Eastern Scandinavian ancestry is interesting. We know linguistically, East Germanic differed noticeably from West Germanic.