If there are studies with data that hasnt been converted to G25 provide them here

[Capsian20]

Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus

https://www.nature.com/articles/s41598-021-95996-3

I also did this one and sent to Davidski. It was too low coverage

Oh well anyway thank you
do you have any info about K36 or K12b this sample ?
Thanks again

[Mokordo]

Thank you i see there only sample belong to mtDNA V back a Early Middle Ages , maybe its V22 or V25 ?

I haven't been able to find anything else apart from what I posted about those "V", sorry.

[Mokordo]

@ilabv , I haven't seen any answer about the Aldaieta medieval samples. I suppose that G25 coordinates cannot be made with the type of genetic data collected by the study.

(Temporal Mitochondrial DNA Variation in the Basque Country: Influence of Post-Neolithic Events)

[Арсен]

@ilabv
https://www.biorxiv.org/content/10.1101/...y-material
how about this job? maybe I missed it and there was a post here

[ilabv]

@ilabv
https://www.biorxiv.org/content/10.1101/...y-material
how about this job? maybe I missed it and there was a post here

I don't see any evidence of the data being available.

[ilabv]

@ilabv , I haven't seen any answer about the Aldaieta medieval samples. I suppose that G25 coordinates cannot be made with the type of genetic data collected by the study.

(Temporal Mitochondrial DNA Variation in the Basque Country: Influence of Post-Neolithic Events)

This is a paper from 2005 right? Autosomal DNA will be garbage at best from this. And I'm looking to do ancients.

[Mokordo]

@ilabv , I haven't seen any answer about the Aldaieta medieval samples. I suppose that G25 coordinates cannot be made with the type of genetic data collected by the study.

(Temporal Mitochondrial DNA Variation in the Basque Country: Influence of Post-Neolithic Events)

This is a paper from 2005 right? Autosomal DNA will be garbage at best from this. And I'm looking to do ancients.

Well, they are from Middle Age so they are "ancient", but ok, thanks.

[Арсен]

@ilabv
https://www.biorxiv.org/content/10.1101/...y-material
how about this job? maybe I missed it and there was a post here

I don't see any evidence of the data being available.

I apologize, but how can I find evidence of the presence of data in the work?

[AimSmall]

@ilabv
https://www.biorxiv.org/content/10.1101/...y-material
how about this job? maybe I missed it and there was a post here

I don't see any evidence of the data being available.

I apologize, but how can I find evidence of the presence of data in the work?

Usually by searching for the phrase "Data Availability"

Here's an example:

Data availability
The aligned sequences of all individuals with new genomic data
reported in this study are available at the European Nucleotide Archive
(ENA) under study accession number PRJEB51862. The compiled genotype
file used for analyses, including re-genotyped published genomes,
has been uploaded at the Edmond Data Repository of the Max Planck
Society (https://edmond.mpdl.mpg.de/dataset.xhtml?persistentId=
doi:10.17617/3.Y1KJMF).

From here you go to https://www.ebi.ac.uk/ena/browser/ and enter the accession number to see the raw data available.
https://www.ebi.ac.uk/ena/browser/view/PRJEB51862

One example at least

[AimSmall]

Do we have these in G25?  

Published: April 27, 2023

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK
https://journals.plos.org/plosgenetics/a...360#sec011

https://www.ncbi.nlm.nih.gov/bioproject/PRJEB58104

https://www.ebi.ac.uk/ena/browser/view/PRJEB58104

There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. AD 300-900), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century AD resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

Ajeje has these in his collection.  Not sure if from this study.

Scotland_Pict_EMA:BAL003.merged__AD_478__Cov_unknown,0.12862,0.133034,0.062979,0.049742,0.040623,0.020638,0.00047,0.000231,0.004909,0.010752,-0.008444,0.003897,-0.021407,-0.014175,0.020629,0.005171,-0.005737,-0.003674,0.002137,0.003377,0.008735,0.004204,-0.003697,0.002651,0.003832
Scotland_Pict_EMA:LUN004.merged__AD_518__Cov_unknown,0.134311,0.12491,0.064111,0.044897,0.040315,0.008088,0.003525,0.002077,0.007772,0.007472,-0.012991,0.010341,-0.01888,-0.015414,0.020494,-0.005304,-0.022556,0.002787,0.004399,-0.00963,0.00574,-0.001113,-0.00949,0.003976,-0.003712

UPDATE:  Yes, those are from the study.
Ancient Samples from York
UK
Human sample from Homo sapiens
BAL003
LUN004
Ancient genomes from Iceland reveal the making of a human population
tooth
Capture and/or shotgun data from aDNA libraries
137 ancient human genomes from across the Eurasian steppes

[ilabv]

Do we have these in G25?  

Published: April 27, 2023

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK
https://journals.plos.org/plosgenetics/a...360#sec011

https://www.ncbi.nlm.nih.gov/bioproject/PRJEB58104

https://www.ebi.ac.uk/ena/browser/view/PRJEB58104

There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. AD 300-900), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century AD resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

Ajeje has these in his collection.  Not sure if from this study.

Scotland_Pict_EMA:BAL003.merged__AD_478__Cov_unknown,0.12862,0.133034,0.062979,0.049742,0.040623,0.020638,0.00047,0.000231,0.004909,0.010752,-0.008444,0.003897,-0.021407,-0.014175,0.020629,0.005171,-0.005737,-0.003674,0.002137,0.003377,0.008735,0.004204,-0.003697,0.002651,0.003832
Scotland_Pict_EMA:LUN004.merged__AD_518__Cov_unknown,0.134311,0.12491,0.064111,0.044897,0.040315,0.008088,0.003525,0.002077,0.007772,0.007472,-0.012991,0.010341,-0.01888,-0.015414,0.020494,-0.005304,-0.022556,0.002787,0.004399,-0.00963,0.00574,-0.001113,-0.00949,0.003976,-0.003712

UPDATE:  Yes, those are from the study.
Ancient Samples from York
UK
Human sample from Homo sapiens
BAL003
LUN004
Ancient genomes from Iceland reveal the making of a human population
tooth
Capture and/or shotgun data from aDNA libraries
137 ancient human genomes from across the Eurasian steppes

Are those studies listed at the bottom there ones without G25?

[ilabv]

There have been many papers without G25 coordinates (recently and perhaps older ones too).

If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward

https://www.sciencedirect.com/science/ar...4223022927

https://www.sciencedirect.com/science/ar...4223011112

Bioarchaeological analyses reveal long-lasting continuity at the periphery of the Late Antique Roman Empire: https://www.sciencedirect.com/science/ar...4223011112

Code:

Scaled

switzerland:Grave_1,0.121791,0.149283,0.071653,0.053618,0.052625,0.034025,-0.007285,0.006231,-0.0045,0.002551,-0.00747,0.00045,-0.015758,-0.022432,0.028773,0.025722,0.01343,-0.005701,0.001885,0.008004,-0.001248,0.01051,0.010969,0.01458,0.01449
switzerland:Grave_9,0.127482,0.13405,0.067127,0.051357,0.050471,0.022869,0.00611,0.01223,-0.009817,-0.003827,-0.003735,0.009442,-0.00446,-0.015001,0.019815,0.027579,0.014473,0.007221,0.010433,0.008754,0.007861,0.000742,0.002218,0.014701,-0.00455

Raw

switzerland:Grave_1,0.0107,0.0147,0.019,0.0166,0.0171,0.0122,-0.0031,0.0027,-0.0022,0.0014,-0.0046,0.0003,-0.0106,-0.0163,0.0212,0.0194,0.0103,-0.0045,0.0015,0.0064,-0.001,0.0085,0.0089,0.0121,0.0121
switzerland:Grave_9,0.0112,0.0132,0.0178,0.0159,0.0164,0.0082,0.0026,0.0053,-0.0048,-0.0021,-0.0023,0.0063,-0.003,-0.0109,0.0146,0.0208,0.0111,0.0057,0.0083,0.007,0.0063,0.0006,0.0018,0.0122,-0.0038

[ilabv]

There have been many papers without G25 coordinates (recently and perhaps older ones too).

If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward

It'd be very helpful if we can get the coordinates of these 3 studies:

*16th century sub-Saharan African origin for all three individuals in Mexico City.

https://www.ebi.ac.uk/ena/browser/view/PRJEB37490


*Aridoamericans and Mesoamericans of pre-Hispanic civilizations thrived between 2,500 BCE.

https://www.ebi.ac.uk/ena/browser/view/PRJEB51440


*40 ancient northern Mexicans dating to 7400-200 years before present (BP).

https://www.ebi.ac.uk/ena/browser/view/PRJEB66319

Origin and Health Status of First-Generation Africans from Early Colonial Mexico: https://www.sciencedirect.com/science/ar...2220304826

Code:

Scaled

colonial_black_mexico:SJN001,-0.621474,0.062963,0.021496,0.014858,-0.004924,0.006414,-0.030316,0.025614,-0.038246,0.028064,0.011692,-0.007194,0.019772,-0.007294,0.0038,-0.010209,0.007693,0.011275,0.00993,-0.006128,-0.004492,0.000371,-0.002095,-0.008073,-0.001197
colonial_black_mexico:SJN002,-0.622612,0.053823,0.029038,0.017119,0.004308,0.014223,-0.013161,0.020768,-0.03661,0.012939,0.001137,-0.003447,-0.008176,-0.003165,-0.0038,0.005171,0.001565,0.00266,-0.003017,0.002626,0.006613,-0.003462,0.001972,0.003735,0.000239
colonial_black_mexico:SJN003,-0.626027,0.063978,0.021873,0.016796,-0.005847,0.01255,-0.019741,0.01523,-0.037837,0.020046,0.001137,-0.004346,-0.002973,0.00289,-0.008686,-0.001724,-0.004824,0.005321,-0.010936,0.001376,-0.001622,-0.003586,0.000246,-0.005784,-0.002395

Raw

colonial_black_mexico:SJN001,-0.0546,0.0062,0.0057,0.0046,-0.0016,0.0023,-0.0129,0.0111,-0.0187,0.0154,0.0072,-0.0048,0.0133,-0.0053,0.0028,-0.0077,0.0059,0.0089,0.0079,-0.0049,-0.0036,0.0003,-0.0017,-0.0067,-0.001
colonial_black_mexico:SJN002,-0.0547,0.0053,0.0077,0.0053,0.0014,0.0051,-0.0056,0.009,-0.0179,0.0071,0.0007,-0.0023,-0.0055,-0.0023,-0.0028,0.0039,0.0012,0.0021,-0.0024,0.0021,0.0053,-0.0028,0.0016,0.0031,0.0002
colonial_black_mexico:SJN003,-0.055,0.0063,0.0058,0.0052,-0.0019,0.0045,-0.0084,0.0066,-0.0185,0.011,0.0007,-0.0029,-0.002,0.0021,-0.0064,-0.0013,-0.0037,0.0042,-0.0087,0.0011,-0.0013,-0.0029,0.0002,-0.0048,-0.002

[ilabv]

Also, I sent two plague study samples from Europe to Davidski but they yielded <0.12x coverage so he didn't convert them: https://www.nature.com/articles/s41467-019-12154-0 https://www.nature.com/articles/s41467-023-38393-w


This concludes my backlog of ancient DNA studies to convert from (with exception of 1 sample from Calabria Neolithic)

PLEASE PROVIDE MORE PAPERS IF YOU KNOW OF ANY SAMPLES THAT DONT HAVE G25 COORDINATES

Thank you!

[VladMC]

It seems to me that these samples are missing

https://www.ebi.ac.uk/ena/browser/view/PRJEB44507

https://www.cell.com/current-biology/ful...all%3Dtrue

https://imgur.com/a/MP6TK9Q



Eurac ID Lab No MAMS
14C age [yr BP]
Cal 2-sigma range with 95.4% probability
Cal 2-sigma values with highest probability (%)
2604 46504 2525±27 791-545 cal BC 650-545 cal BC (50.4%)
2610 46505 2990±28 1376-1121 cal BC 1301-1121 cal BC (91.1%)
2611 46506 2508±25 776-544 cal BC 652-544 cal BC (65.2%)
2612 46507 154±23 1667-1950 cal AD 1720-1783 cal AD (30.4%)