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Parasayan et al 2024, Late Neolithic collective burial reveals admixture_France
#1
Take a look at this one and comment. 

Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome
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Let us now praise famous men, and our fathers that begat us.

- Wisdom of Sirach 44:1
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#2
"We reconstructed the genome of an unsampled individual through its relatives’ genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. "

This seems a little dubious on the face of it.
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#3
BRE445FK (2567-2339 cal BCE). In table S1 he is R1b1a1b1a1a which is R-L151 so I got the same result they did. I also found that he is ancestral for S1194/AM01876, A8053, U106, L21, U152 and no-calls for P312 and Z195. However it turns out BRE445HI is his son and he is ancestral for P312. I don't have any of the FTA1 SNPs in my database so I didn't check those.

SMGB54 (2410-2129 cal BCE) is derived for P312, has a no-call for U152, he is ancestral for L21, 6 out of 8 reads shows he is derived for DF27, ancestral for Z195 and ZZ12_1. I don't know about the other 3 subclades of DF27. It will be interesting to see what FTDNA finds.

RISE563 (U152) 2572-2512 calBCE is still the oldest R-P312 specimen.

GBVPK (Z195) 2461-2299 cal BCE is still the oldest proven R-DF27 specimen.

Since EHU002 (P312) 2562–2306 cal BCE does not have a read for R-DF27 it is still unknown if he is actually DF27+ or not.

There is still no R-L23 in western Europe prior to Auvernier A297/MX304 (P311) 2866-2601 calBC

Parasayan et al. 2024 reaffirms that R-L23 subclades and Steppe autosomal showed up in western Europe simultaneously. One does not exist without the other in western Europe and neither existed at all in western Europe prior to 2500 BCE.

sidenote: FTDNA still hasn't fixed the dating of CLL007, which was never directly C14 dated, at https://discover.familytreedna.com/y-dna/R-P312/ancient
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#4
(06-22-2024, 12:21 AM)AimSmall Wrote: "We reconstructed the genome of an unsampled individual through its relatives’ genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. "

This seems a little dubious on the face of it.

Why do you say that? The autosomal DNA of BRE445FK (2567-2339 cal BCE) shows that he had a father with about 70% steppe ancestry based on his 35% steppe ancestry. His mother was in the same burial and is devoid of steppe ancestry. The earliest specimens with steppe ancestry in France is CBV95 (2574-2452 BCE). The earliest steppe ancestry in western Europe is in Switzerland between 2860-2460 BCE. Auvernier A297/MX304 (R-P311) is one of those specimens. One of the earliest specimens in Spain with steppe ancestry is EHU002 (2564-2299 BCE),(R-P312)

So here is a family that descends from a person with steppe DNA and R-L151 Y-DNA that was in France during the early stage of the arrival of steppe ancestry in France. It is just one family but they are showing that sometimes migrants with Steppe DNA mixed with the autochtonous people with Neolithic ancestry.

edit: They also say the following -

The presence of admixture pulses between individuals with steppe ancestry and Neo-ancestry suggests that most steppe ancestry individuals preferentially interbred with individuals of similar ancestries and only rarely mated with Neo-ancestry carriers except during the pulse periods, thus preserving high levels of steppe ancestry for many generations. In contrast, when an individual with steppe ancestry integrated into a Neo-ancestry farmers’ group, his/her steppe ancestry would have been diluted in a few generations. Such an event can be detected clearly only in the first generations, as observed here in the collective burial of Bréviandes.

edit2:

the bimodal pattern of ancestry on the X-chromosome appears to result from a mating bias: Men of steppe ancestry occasionally mated with women of Neo-ancestry, whereas women of steppe ancestry mated less frequently with men of Neo-ancestry. Such a pattern of admixture is also supported by the vast excess of steppe ancestry Y haplotypes detected during the Late Neolithic to Bronze Age transition in western Europe (11, 15) as well as in the dataset analyzed herein where 22 of 24 male individuals carry a R1b1a1 Y haplotype. Although admixture of steppe ancestry men with Neo-ancestry women occurred at various points in time, the bimodal pattern detected in the admixture timing indicates that these admixture events were more frequent during the two phases of westward expansion of individuals with steppe ancestry.
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#5
(06-21-2024, 11:05 PM)rmstevens2 Wrote: Take a look at this one and comment. 

Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome
 a good paper 
Nothing too surprising in it but very nicely written paper which confirmed most of what I thought
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#6
(06-22-2024, 08:46 AM)ArmandoR1b Wrote: BRE445FK (2567-2339 cal BCE). In table S1 he is R1b1a1b1a1a which is R-L151 so I got the same result they did. I also found that he is ancestral for S1194/AM01876, A8053, U106, L21, U152 and no-calls for P312 and Z195. However it turns out BRE445HI is his son and he is ancestral for P312. I don't have any of the FTA1 SNPs in my database so I didn't check those.

SMGB54 (2410-2129 cal BCE) is derived for P312, has a no-call for U152, he is ancestral for L21, 6 out of 8 reads shows he is derived for DF27, ancestral for Z195 and ZZ12_1. I don't know about the other 3 subclades of DF27. It will be interesting to see what FTDNA finds.

RISE563 (U152) 2572-2512 calBCE is still the oldest R-P312 specimen.

GBVPK (Z195) 2461-2299 cal BCE is still the oldest proven R-DF27 specimen.

Since EHU002 (P312) 2562–2306 cal BCE does not have a read for R-DF27 it is still unknown if he is actually DF27+ or not.

There is still no R-L23 in western Europe prior to Auvernier A297/MX304 (P311) 2866-2601 calBC

Parasayan et al. 2024 reaffirms that R-L23 subclades and Steppe autosomal showed up in western Europe simultaneously. One does not exist without the other in western Europe and neither existed at all in western Europe prior to 2500 BCE.

sidenote: FTDNA still hasn't fixed the dating of CLL007, which was never directly C14 dated, at https://discover.familytreedna.com/y-dna/R-P312/ancient

The United Nations considers Switzerland as part of Western Europe, so technically Auvernier would fit the bill around 2700 BC. Also, there is AF007 from Antheit, Belgium dated to 2828-2626 calBC. Using dated SNP capture, he was only tested to M269, but it is logical that he was derived for L23. Your point still stands however, both L23 and steppe ancestry showed up simultaneously everywhere it was found, including Western Europe.
Paternal: R1b-U152+ L2+ ZZ48+ FGC10543+ PR5365+, Crispino Rocca, b.~1584, Agira, Sicily, Italy
Maternal: Haplogroup H4a1-T152C!, Maria Coto, b.~1864, Galicia, Spain
Mother's Paternal: Haplogroup J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b.1879, Caposele, Avellino, Campania, Italy
Father's Maternal: Haplogroup T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
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#7
It was an organized invasion on the largest scale.

Quote: These European- wide third millennium BCE cultural transformations were seemingly accompanied by population transformations. Paleogenomic analyses revealed large genomic shifts over short time periods, hinting at migrations to northwest Europe of people from the Samara steppe in present- day Russia, whose genomes can be modeled as a mixture of Steppe Eneolithic, i.e., Zagros-Caucasus and Eastern Hunter Gatherers (60), and Caucasus Eneolithic/Maykop ancestry comprising early Neolithic Anatolian farmer ancestry (61).

The same continued in the American Continent.

The starting point of the movement/admixture process begun in the Southern Caucasus and I hope they can find the first generations of the admixture there as well with more sampling.
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#8
(06-23-2024, 02:18 PM)R.Rocca Wrote:
(06-22-2024, 08:46 AM)ArmandoR1b Wrote: BRE445FK (2567-2339 cal BCE). In table S1 he is R1b1a1b1a1a which is R-L151 so I got the same result they did. I also found that he is ancestral for S1194/AM01876, A8053, U106, L21, U152 and no-calls for P312 and Z195. However it turns out BRE445HI is his son and he is ancestral for P312. I don't have any of the FTA1 SNPs in my database so I didn't check those.

SMGB54 (2410-2129 cal BCE) is derived for P312, has a no-call for U152, he is ancestral for L21, 6 out of 8 reads shows he is derived for DF27, ancestral for Z195 and ZZ12_1. I don't know about the other 3 subclades of DF27. It will be interesting to see what FTDNA finds.

RISE563 (U152) 2572-2512 calBCE is still the oldest R-P312 specimen.

GBVPK (Z195) 2461-2299 cal BCE is still the oldest proven R-DF27 specimen.

Since EHU002 (P312) 2562–2306 cal BCE does not have a read for R-DF27 it is still unknown if he is actually DF27+ or not.

There is still no R-L23 in western Europe prior to Auvernier A297/MX304 (P311) 2866-2601 calBC

Parasayan et al. 2024 reaffirms that R-L23 subclades and Steppe autosomal showed up in western Europe simultaneously. One does not exist without the other in western Europe and neither existed at all in western Europe prior to 2500 BCE.

sidenote: FTDNA still hasn't fixed the dating of CLL007, which was never directly C14 dated, at https://discover.familytreedna.com/y-dna/R-P312/ancient

The United Nations considers Switzerland as part of Western Europe, so technically Auvernier would fit the bill around 2700 BC. Also, there is AF007 from Antheit, Belgium dated to 2828-2626 calBC. Using dated SNP capture, he was only tested to M269, but it is logical that he was derived for L23. Your point still stands however, both L23 and steppe ancestry showed up simultaneously everywhere it was found, including Western Europe.

Yes, I messed up prior to 2500 BCE. I already knew Swtizerland is part of western Europe my mistake was due to something else So yes, it should state prior to 2900 BCE using the rounded upper date of the range.

I am only going to go by derived reads since there is too much contention when there is no proof of subclades of R-M269. I can't find the BAM or fastq files for AF007 so I assume that they have not been uploaded anywhere. The Fichera thesis has it as R1b1a1a2a1a2c1a5b1a1a which is obviously going to be due to a false positive or recurrent SNP or similar. Do you have a copy of the BAM or fastq file?

At least part of the main point is understood. Also since the TMRCA of R-L23 is 4300 BCE and between that year and 2900 BCE there is no R-L23 in western Europe is an important fact, not just that L23 and steppe ancestry showed up simultaneously. Both are important.
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#9
Bréviandes 445-HI and Bréviandes 445-FK are now in the FTDNA Discover tree at https://discover.familytreedna.com/y-dna/R-L151/classic

I still can't find Saint-Martin-la-Garenne, Yvelines, Île-de-France (SMGB54) in the Discover site.

Grotte Basse de la Vigne Perdue K (GBVPK) is also there. I don't know how long it has been there. I assume that the ancestral read for R-DF27, which isn't reliable, is causing them to leave it as R-L151.
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#10
(06-23-2024, 03:30 PM)ArmandoR1b Wrote:
(06-23-2024, 02:18 PM)R.Rocca Wrote:
(06-22-2024, 08:46 AM)ArmandoR1b Wrote: BRE445FK (2567-2339 cal BCE). In table S1 he is R1b1a1b1a1a which is R-L151 so I got the same result they did. I also found that he is ancestral for S1194/AM01876, A8053, U106, L21, U152 and no-calls for P312 and Z195. However it turns out BRE445HI is his son and he is ancestral for P312. I don't have any of the FTA1 SNPs in my database so I didn't check those.

SMGB54 (2410-2129 cal BCE) is derived for P312, has a no-call for U152, he is ancestral for L21, 6 out of 8 reads shows he is derived for DF27, ancestral for Z195 and ZZ12_1. I don't know about the other 3 subclades of DF27. It will be interesting to see what FTDNA finds.

RISE563 (U152) 2572-2512 calBCE is still the oldest R-P312 specimen.

GBVPK (Z195) 2461-2299 cal BCE is still the oldest proven R-DF27 specimen.

Since EHU002 (P312) 2562–2306 cal BCE does not have a read for R-DF27 it is still unknown if he is actually DF27+ or not.

There is still no R-L23 in western Europe prior to Auvernier A297/MX304 (P311) 2866-2601 calBC

Parasayan et al. 2024 reaffirms that R-L23 subclades and Steppe autosomal showed up in western Europe simultaneously. One does not exist without the other in western Europe and neither existed at all in western Europe prior to 2500 BCE.

sidenote: FTDNA still hasn't fixed the dating of CLL007, which was never directly C14 dated, at https://discover.familytreedna.com/y-dna/R-P312/ancient

The United Nations considers Switzerland as part of Western Europe, so technically Auvernier would fit the bill around 2700 BC. Also, there is AF007 from Antheit, Belgium dated to 2828-2626 calBC. Using dated SNP capture, he was only tested to M269, but it is logical that he was derived for L23. Your point still stands however, both L23 and steppe ancestry showed up simultaneously everywhere it was found, including Western Europe.

Yes, I messed up prior to 2500 BCE. I already knew Swtizerland is part of western Europe my mistake was due to something else So yes, it should state prior to 2900 BCE using the rounded upper date of the range.

I am only going to go by derived reads since there is too much contention when there is no proof of subclades of R-M269. I can't find the BAM or fastq files for AF007 so I assume that they have not been uploaded anywhere. The Fichera thesis has it as R1b1a1a2a1a2c1a5b1a1a which is obviously going to be due to a false positive or recurrent SNP or similar. Do you have a copy of the BAM or fastq file?

At least part of the main point is understood. Also since the TMRCA of R-L23 is 4300 BCE and between that year and 2900 BCE there is no R-L23 in western Europe is an important fact, not just that L23 and steppe ancestry showed up simultaneously. Both are important.

Unfortunately the thesis does not state that the data has been made available: https://eprints.hud.ac.uk/id/eprint/35254/
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Paternal: R1b-U152+ L2+ ZZ48+ FGC10543+ PR5365+, Crispino Rocca, b.~1584, Agira, Sicily, Italy
Maternal: Haplogroup H4a1-T152C!, Maria Coto, b.~1864, Galicia, Spain
Mother's Paternal: Haplogroup J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b.1879, Caposele, Avellino, Campania, Italy
Father's Maternal: Haplogroup T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
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#11
(06-22-2024, 08:46 AM)ArmandoR1b Wrote: BRE445FK (2567-2339 cal BCE). In table S1 he is R1b1a1b1a1a which is R-L151 so I got the same result they did. I also found that he is ancestral for S1194/AM01876, A8053, U106, L21, U152 and no-calls for P312 and Z195. However it turns out BRE445HI is his son and he is ancestral for P312. I don't have any of the FTA1 SNPs in my database so I didn't check those.

SMGB54 (2410-2129 cal BCE) is derived for P312, has a no-call for U152, he is ancestral for L21, 6 out of 8 reads shows he is derived for DF27, ancestral for Z195 and ZZ12_1. I don't know about the other 3 subclades of DF27. It will be interesting to see what FTDNA finds.

RISE563 (U152) 2572-2512 calBCE is still the oldest R-P312 specimen.

GBVPK (Z195) 2461-2299 cal BCE is still the oldest proven R-DF27 specimen.

Since EHU002 (P312) 2562–2306 cal BCE does not have a read for R-DF27 it is still unknown if he is actually DF27+ or not.

There is still no R-L23 in western Europe prior to Auvernier A297/MX304 (P311) 2866-2601 calBC

Parasayan et al. 2024 reaffirms that R-L23 subclades and Steppe autosomal showed up in western Europe simultaneously. One does not exist without the other in western Europe and neither existed at all in western Europe prior to 2500 BCE.

sidenote: FTDNA still hasn't fixed the dating of CLL007, which was never directly C14 dated, at https://discover.familytreedna.com/y-dna/R-P312/ancient

Also remember (since the older ranges overlap):
I5748 2579-2211 calBCE Oostwoud, Noord-Holland P312>DF19>Z302* Aceramic Single Grave/[pre?-]Beaker

^^He is ~66% steppe, and centuries older than both the two tumuli on the site, and also the layer of ceramic fragments that include beakers, so could be SGC.

This has been a broadcast of the DF19 network, we now return you to your regular programming.
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R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>FT354149

Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583; John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593; John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635
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#12
(06-23-2024, 06:10 PM)R.Rocca Wrote: Unfortunately the thesis does not state that the data has been made available: https://eprints.hud.ac.uk/id/eprint/35254/

I already had that thesis since 2022. That is where I got the erroneous haplogroup R1b1a1a2a1a2c1a5b1a1a for AF007 from - table 15. 

I was hoping that maybe the genomic files were finally shared.

I just realized that the 83,698 SNPs for AF007 might not be enough to know if it is actually derived for P312, U106, or even L11 or one of the equivalents of L11. I guess we'll find out if it ever published.

AF011 and AF029 look like they should have decent coverage but they aren't directly dated.
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#13
(06-23-2024, 09:14 PM)ArmandoR1b Wrote:
(06-23-2024, 06:10 PM)R.Rocca Wrote: Unfortunately the thesis does not state that the data has been made available: https://eprints.hud.ac.uk/id/eprint/35254/

I already had that thesis since 2022. That is where I got the erroneous haplogroup R1b1a1a2a1a2c1a5b1a1a for AF007 from - table 15. 

I was hoping that maybe the genomic files were finally shared.

I just realized that the 83,698 SNPs for AF007 might not be enough to know if it is actually derived for P312, U106, or even L11 or one of the equivalents of L11. I guess we'll find out if it ever published.

AF011 and AF029 look like they should have decent coverage but they aren't directly dated.

Correct, the reference to it being positive for M269 is in-line in the text of the thesis.
Paternal: R1b-U152+ L2+ ZZ48+ FGC10543+ PR5365+, Crispino Rocca, b.~1584, Agira, Sicily, Italy
Maternal: Haplogroup H4a1-T152C!, Maria Coto, b.~1864, Galicia, Spain
Mother's Paternal: Haplogroup J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b.1879, Caposele, Avellino, Campania, Italy
Father's Maternal: Haplogroup T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
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