Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps

[ChrisR]

It seems the data is not public yet: https://www.ebi.ac.uk/ena/browser/view/PRJEB60362
Davidski@Eurogenes as I have seen sometimes seems to have early access. In the latest G25 files those samples seem to be not included (yet): https://bga101.blogspot.com/2019/07/gett...bal25.html - at least I found nothing under Tyrol or Italy(_North)

[rafc]

Data is available now: https://www.ebi.ac.uk/ena/browser/view/PRJEB60362

[Capsian20]

Data is available now: https://www.ebi.ac.uk/ena/browser/view/PRJEB60362

Do you have any info about subclades this samples ?

[rafc]

For some reason I don't seem to retrieve Y-DNA from those BAMs. Maybe someone else has more luck ...

[R.Rocca]

For some reason I don't seem to retrieve Y-DNA from those BAMs. Maybe someone else has more luck ...

I only see FASTA files, no BAMS.

[rafc]

For some reason I don't seem to retrieve Y-DNA from those BAMs. Maybe someone else has more luck ...

I only see FASTA files, no BAMS.

Strange, I see Fastq and Bam, did you scroll all the way to the right?

[vlrs]

Seems that the individual 2069 - (7th century South Tyrol) was assigned by theYtree as E-PF4428 which is my own haplogroup, although this individual is from another branch:

https://www.theytree.com/tree/E-FGC62310

Ruderico, you will find this interesting, in case this is not some mistake

[R.Rocca]

For some reason I don't seem to retrieve Y-DNA from those BAMs. Maybe someone else has more luck ...

I only see FASTA files, no BAMS.

Strange, I see Fastq and Bam, did you scroll all the way to the right?

I had to turn on the column " bam_ftp" to see the BAMs. Thanks!

[lukpl]

There are bams in ENA, I tried two but no autosomal at all. I used the same method as usual for convertion.

[Sailgios]

Seems that the individual 2069 - (7th century South Tyrol) was assigned by theYtree as E-PF4428 which is my own haplogroup, although this individual is from another branch:

https://www.theytree.com/tree/E-FGC62310

Ruderico, you will find this interesting, in case this is not some mistake

From the paper:

However, five samples (2069, 2422, 2429, 2430 and 2324) shift in the plot more toward the genomic diversity of modern individuals from western and northern Europe (France and Great Britain, respectively) (Figure 2A).

The only other individual (2069) with more southern ancestry was buried in Area 8 which,
however, shows approx. 7% of relative ancestry from north Europe, which could explain its
intermediate position in the PCA plot of Figure 2A.

Additionally, our results show that the BSS samples (2324, 2069, 2422, 2429 and 2430),
which shift in the plot more toward the genetic diversity of central and northern ancient Europeans,
consistently retain higher percentages of the steppe-related component (from approx. 44% to 60%)

I2069 does have Northern European ancestry, he apparently plots amongst the north-shifted individuals, so somewhere in between modern-day French, North Italian and South Germanics - so typically modern Alpine. FGC62310 is interesting because it appears very specifically Arabian and only distantly related to our branch which is essentially European. How it got to the Alps is beyond me, maybe with Roman Limitanei hailing from the eastern provinces.

[rafc]

There are bams in ENA, I tried two but no autosomal at all. I used the same method as usual for convertion.

Since for me the Y-DNA failed, I guess it's safe to assume the Bam's are somehow corrupted.

[vlrs]

Seems that the individual 2069 - (7th century South Tyrol) was assigned by theYtree as E-PF4428 which is my own haplogroup, although this individual is from another branch:

https://www.theytree.com/tree/E-FGC62310

Ruderico, you will find this interesting, in case this is not some mistake

I2069 does have Northern European ancestry, he apparently plots amongst the north-shifted individuals, so somewhere in between modern-day French, North Italian and German - so typically modern Alpine. FGC62310 is interesting because it appears very specifically Arabian and only distantly related to our branch which is essentially European. How it got to the Alps is beyond be, maybe with Roman Limitanei hailing from the eastern provinces.

A very likely scenario of a remnant of the Imperial era - if this calculation made by theYtree is correct (which so far usually skews the TMRCA compared to Yfull/Ftdna), the date given for this sample's TMRCA is 1950 YBP which is a perfect candidate for an Imperial migrant from the Middle East. Since he isn't related to the EU branch, I guess that's the plausible explanation. If the sample is dated to the 7th century AD, then his autosomal admixture for 600 years has become pretty much similar to the other locals.

[ChrisR]

I was not able to extract/calculate anything on the raw data yet so I used the individual 2069 K12b data from theytree and with the Linear regression matrix at allelocator created a G25 Sim. 

Code:

Rhaetia-Roman-Late:Burgeis-c500AD-BSS8-US113-2069-AU70996_Y-E_K12b-G25simAL,0.110830,0.165466,0.028774,-0.012953,0.040939,-0.009695,0.008374,0.012928,0.011073,0.027726,-0.001510,0.005859,-0.010645,-0.004469,0.001736,-0.002219,-0.000278,-0.000183,-0.000234,0.000658,0.002113,0.000971,-0.002772,-0.001500,-0.000003

His plot seems pretty spot on where one would expect him (near to Rhaeto-Roman/Ladin results):
   

However looking at Admixture proportions by using the same ancient clusters the Nordic...Germans (+12%), EtruscanLatins (+7%) and also Medit...CulturesUrban (+5%) components seem higher then in most modern Trentini while BB-Hallstatt...Gaul (-8%) is lower then Trentini average.
Particularly the "switched" Nordic...Germans and BB-Hallstatt...Gaul is intriguing as one would expect their proportions viceversa.
Having CordedWare-Unetice_LN-C-EBA, EarlyBaltoSlav_BA-IA and SteppeYamnaya_EBA all at 0 seems fitting and correct, unless the high Nordic...Germans is a false proxy for in reality CordedWare-Unetice.
   

Show Content

SpoilerTarget,Distance,NordicJastorfWielbarkGermans_IA-Antiq-EMedieval,MediterraneanCulturesUrban_BA-IA-Antiq,Etruscans-Latins_IA-Rep,EarlyEuroFarmer_N-C-BA_LBK-Remedello_Balkans2Iberia,BB-Hallstatt-LaTene-Noric-Gaul_C-BA-IA_Balkans2Iberia,WesternScythian_IA_Ukr,EarlyBaltoSlav_BA-IA,CordedWare-Unetice_LN-C-EBA,SteppeYamnaya_EBA
Rhaetia-Roman-Late:Burgeis-c500AD-BSS8-US113-2069-AU70996_Y-E_K12b-G25simAL,0.01429900,30.8,23.8,16.8,15.6,10.8,2.2,0.0,0.0,0.0
TRENTINO:Nogarè_Pergine_Valsugana:Italian_Trentino_Alto_Adige:Nei27,0.01534820,19.8,22.8,15.2,14.8,8.2,10.2,9.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP259,0.00467254,32.6,17.6,14.6,17.4,10.8,0.0,3.0,0.6,3.4
TRENTINO:Italian_Trentino_Alto_Adige:ALP200,0.00539271,25.4,30.6,14.0,12.6,2.8,6.0,4.4,0.2,4.0
Trentino:Val-di-Non:AGTT002-K36simScFE,0.00151829,14.0,17.0,12.0,24.0,14.2,2.4,6.0,7.2,3.2
Trentino:Alto-Garda_(Bolognano-Tenno):AGT001-K36simG25scGR,0.00016537,13.2,20.8,11.8,25.2,16.2,0.4,3.0,5.0,4.4
TRENTINO:Italian_Trentino_Alto_Adige:ALP114,0.00507651,0.0,23.4,10.8,7.6,34.8,14.4,0.0,3.6,5.4
Trentino:Non-50%-Fiemme-Tione:AGT004-K36simG25scMMG,0.00007335,23.0,19.8,10.4,16.8,16.8,0.4,1.8,8.2,2.8
Trentino:Valsugana-Bernstolar-1/4-Sopramonte:AGT006-K36simG25scDM,0.00008924,18.4,19.2,10.2,22.0,19.0,0.4,0.8,8.4,1.6
TRENTINO:Italian_Trentino_Alto_Adige:ALP071,0.00340859,7.4,7.0,9.6,25.8,26.0,8.8,10.6,0.0,4.8
TRENTINO:Italian_Trentino_Alto_Adige:ALP070,0.00524843,26.6,8.8,9.4,16.8,22.0,9.8,5.4,1.2,0.0
TRENTINO:Taio_Predaia_V-Non:Italian_Trentino_Alto_Adige:Nei18,0.01030720,23.2,18.6,3.8,12.0,34.2,3.2,0.0,3.4,1.6
TRENTINO:Italian_Trentino_Alto_Adige:ALP420,0.00497443,15.2,10.0,3.6,23.2,24.4,9.4,7.2,7.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP395,0.00802861,3.8,27.4,1.2,16.6,21.6,2.4,8.0,13.0,6.0
Average,0.00561446,18.1,19.1,10.2,17.9,18.7,5.0,4.2,4.1,2.7

EDIT: I added the standard Davidski Admixture Source Components for comparison. Here the elevated TUR_Tepecik_Ciftlik_N element (+17% to modern average) stands out. Will be interesting if official G25 values replicate this and what the slight admixture "anomaly" of this sample could be. Interesting one and I emphasis only one modern sample (ALP200) seems to have a similar "shift".
   

Show Content

SpoilerTarget,Distance,TUR_Barcin_N,Yamnaya_RUS_Samara,WHG,TUR_Tepecik_Ciftlik_N,Levant_PPNB,Han,MAR_Taforalt,Gambian
Rhaetia-Roman-Late:Burgeis-c500AD-BSS8-US113-2069-AU70996_Y-E_K12bsimAL,0.03469224,41.0,27.0,9.4,21.4,0.0,0.0,0.6,0.6
Trentino:Val-di-Non:AGTT002-K36simScFE,0.02560165,57.2,35.4,7.4,0.0,0.0,0.0,0.0,0.0
Trentino:Valsugana-Bernstolar-1/4-Sopramonte:AGT006-K36simG25scDM,0.02450903,55.8,31.4,7.2,5.6,0.0,0.0,0.0,0.0
Trentino:Non-50%-Fiemme-Tione:AGT004-K36simG25scMMG,0.02743104,57.4,35.8,6.8,0.0,0.0,0.0,0.0,0.0
Trentino:Alto-Garda_(Bolognano-Tenno):AGT001-K36simG25scGR,0.02396134,62.6,30.2,7.0,0.0,0.0,0.0,0.2,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP070,0.04173202,50.8,35.6,9.8,3.8,0.0,0.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP071,0.02620823,53.0,36.6,10.4,0.0,0.0,0.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP114,0.01827417,58.0,30.6,7.0,2.2,1.6,0.6,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP200,0.02387550,43.6,33.6,6.4,16.4,0.0,0.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP259,0.03079004,58.4,32.6,9.0,0.0,0.0,0.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP395,0.02846082,57.6,34.4,8.0,0.0,0.0,0.0,0.0,0.0
TRENTINO:Italian_Trentino_Alto_Adige:ALP420,0.03749980,56.4,35.4,8.0,0.0,0.0,0.0,0.2,0.0
TRENTINO:Taio_Predaia_V-Non:Italian_Trentino_Alto_Adige:Nei18,0.03416764,58.2,33.2,8.6,0.0,0.0,0.0,0.0,0.0
TRENTINO:Nogarè_Pergine_Valsugana:Italian_Trentino_Alto_Adige:Nei27,0.03029173,58.6,32.4,8.6,0.0,0.0,0.4,0.0,0.0
Average,0.02910680,54.9,33.2,8.1,3.5,0.1,0.1,0.1,0.0

Looking forward to see official G25 with verification of others on the admixture and Y-DNA placement for all the samples.

[R.Rocca]

I was not able to extract/calculate anything on the raw data yet so I used the individual 2069 K12b data from theytree and with the Linear regression matrix at allelocator created a G25 Sim. 

Code:

Rhaetia-Roman-Late:Burgeis-c500AD-BSS8-US113-2069-AU70996_Y-E_K12b-G25simAL,0.110830,0.165466,0.028774,-0.012953,0.040939,-0.009695,0.008374,0.012928,0.011073,0.027726,-0.001510,0.005859,-0.010645,-0.004469,0.001736,-0.002219,-0.000278,-0.000183,-0.000234,0.000658,0.002113,0.000971,-0.002772,-0.001500,-0.000003

His plot seems pretty spot on where one would expect him: 

Looking forward to see official G25 and Y-DNA placement for all the samples.

So right about where modern samples sit. Perhaps the small switch can be attributable to more mixing with more traditional Alpine-type populations after this period?

[ChrisR]

Perhaps the small switch can be attributable to more mixing with more traditional Alpine-type populations after this period?

As I'm only using older ancient samples for comparison to this Burgeis-Vinschgau/Venost ca. 500AD sample I do not understand clearly to which period you are referring and how later admixture (Middle Ages?) would affect the results of this sample? Do you mean the descendants of this sample by staying in the area became more "Cisalpine Gaulish"? Seems odd nonetheless as the German component should also rise at least until Late Middle Ages.
Above I added the standard Davidski Admixture Source Components for comparison which also reveals one "unusual" component shift.
So the case part of his ancestry seems to be "unusual" seems to become more substantial. Hence possibly the calculator difficulty to arrange 10-15% of his admixture. Maybe some fitting ancient DNA is missing? So my confidence my current ancient DNA collection for Tyrol admixture is "good" is lowering. AU70996 and ALP200 maybe are samples which need further investigation with various LBA-IA-RomanEmpire Ancient models.

EDIT. Regarding uniparental markers I did a quick overview for myself: E-PF4428>Y30965,FGC62255 the over 6000 ybp Haplogroup seems seldom and expand from somewhere in or near Western Fertile Crescent: https://discover.familytreedna.com/y-dna...62255/tree , https://www.yfull.com/tree/E-Y30965/
Only by the ancestral Hg E-FT20896 (13400 BC) https://discover.familytreedna.com/y-dna/E-FT20896/tree ancient samples exist, interestingly from IA Swat Valley and IA Central Asia
His mtDNA I2 ~5600 BC seems broadly West Eurasian. https://www.yfull.com/mtree/I2/ Maybe a more recent Hg can be determined.
All pieces to possibly find his unusual ancestry