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(02-28-2024, 09:20 PM)teepean Wrote: Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria
Summary
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
https://www.sciencedirect.com/science/ar...9X2400034X
Data and code availability
•
Raw and processed sequence reads are made available at the European Nucleotide Archive (ENA) accessions ENA: PRJEB31781 and ENA: PRJEB71330, respectively.
•
Pseudo-haploid genotypes for the newly reported ancient individuals and imputed variants are made available at Zenodo:
https://doi.org/10.5281/zenodo.10058388.
•
All code used for analysis has been previously published and is publicly available.
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Quote:14 14_70373430 0.647182 70373430 C T
14 14_70376038 0.647185 70376038 T G
14 14_70376069 0.647185 70376069 C T
14 14_70382737 0.6472 70382737 C A
14 14_70383295 0.6472 70383295 A G
14 14_70390305 0.647203 70390305 C T
14 14_70406715 0.647214 70406715 A G
14 14_70407046 0.647215 70407046 C T
14 14_70407978 0.647218 70407978 A G
14 14_70408192 0.647218 70408192 C T
14 14_70413656 0.647231 70413656 T G
However we have an issue here:
The SNP mapping was not done properly. Instead of using the rs_names here we see the positions numbers. So if you try to use this data with the regular processing software it will not find any snips.
We need someone to convert the map file to use the accepted snp names.
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Nice, finally some samples from Bahrain!
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Y-DNA (P): E-V257(×M81)
Y-DNA (M): V
mtDNA (P): L2b
who has G25 this samples ?
Target: CapsianWGS_scaled
Distance: 1.2510% / 0.01251049
37.2 Iberomaurusian
36.8 Early_European_Farmer
12.8 Early_Levantine_Farmer
8.0 Steppe_Pastoralist
4.8 SSA
0.4 Iran_Neolithic
FTDNA : 91% North Africa +<2% Bedouin + <2 Southern-Levantinfo + <1 Sephardic Jewish + 3% Malta + 3% Iberian Peninsula
23andME : 100% North Africa
WGS ( Y-DNA and mtDNA)
Y-DNA: E-A30032< A30480 ~1610 CE
mtDNA: V25b 800CE ? ( age mtDNA not accurate )
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03-01-2024, 09:19 PM
(This post was last modified: 03-01-2024, 09:24 PM by TanTin.)
(03-01-2024, 09:17 PM)Capsian20 Wrote: who has G25 this samples ?
They can not do G25 if bim file is not converted properly..
(I guess that's why Davidski said this data is garbage. "Garbage sequences.")
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Y-DNA (P): I2-BY79593
mtDNA (M): W1v T16311C!
MH1_LT; 432-561 AD; Madinat Hamad, Bahrain; Late Tylos-Sasanian period; J2a2-PF5008>L581>Z37823>PF5000>PF5033>PF4993>Y397526>Y24510>pre-FTA39465 (xFTA41741)
MH3_LT; 577-647 AD; Madinat Hamad, Bahrain; Late Tylos-Sasanian period; H2-P96>Z19008>FT1572>Z41295>Z41284>FT986>Z41289* (xZ41305)
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So they used a different format: GRCh38 /GRCh38.bim/
Reich datasets are using hg19 . (NCBI build 37 (UCSC hg19).)
To convert the data they use this terminology:
LiftOver - LiftOver is a necesary step to bring all genetical analysis to the same reference build.
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Something is wrong with these samples even after conversion to hg19 / build 37.
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(03-01-2024, 11:05 PM)Tomenable Wrote: Something is wrong with these samples even after conversion to hg19 / build 37.
Were you able to convert them ? Please share your data.
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Teepean converted them. I sent you in a PM.
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03-01-2024, 11:17 PM
(This post was last modified: 03-01-2024, 11:18 PM by TanTin.)
BTW, for those of you interested in genomic data from Bahrain, there is some old data here:
Quote:https://www.biologiaevolutiva.org/dcomas...submitted/
North African Affy 6.0 data (Henn et al., 2012)
Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Brenna M. Henn, Laura R. Botigué, Simon Gravel, Wei Wang, Abra Brisbin, Jake K. Byrnes, Karima
Fadhlaoui-Zid, Pierre A. Zalloua, Andres Moreno-Estrada, Jaume Bertranpetit, Carlos D.
Bustamante, David Comas (2012) PLoS Genetics 8(1)e1002397 Henn2012
The Affy 6.0 data can be downloaded here: NAfrica_Bas and NWAfrica_Qat_280K
The quality if this data is low, but it is not so bad, and there are hundreds of individuals included. Please take a look.
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(03-01-2024, 11:17 PM)TanTin Wrote: BTW, for those of you interested in genomic data from Bahrain, there is some old data here:
Quote:https://www.biologiaevolutiva.org/dcomas...submitted/
North African Affy 6.0 data (Henn et al., 2012)
Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Brenna M. Henn, Laura R. Botigué, Simon Gravel, Wei Wang, Abra Brisbin, Jake K. Byrnes, Karima
Fadhlaoui-Zid, Pierre A. Zalloua, Andres Moreno-Estrada, Jaume Bertranpetit, Carlos D.
Bustamante, David Comas (2012) PLoS Genetics 8(1)e1002397 Henn2012
The Affy 6.0 data can be downloaded here: NAfrica_Bas and NWAfrica_Qat_280K
The quality if this data is low, but it is not so bad, and there are hundreds of individuals included. Please take a look.
I think that paper has data from Qatar, but not from Bahrain?
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(03-01-2024, 11:37 PM)Tomenable Wrote: I think that paper has data from Qatar, but not from Bahrain?
Yes, mostly Qatar, but there are many others as well. There are more than 800 in total.
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(03-01-2024, 11:14 PM)Tomenable Wrote: Teepean converted them. I sent you in a PM.
The quality of this data is bad, really bad. I am not sure if the conversion was not successful or the data itself . For the moment it is not usable with my tools. Will wait for better data.
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(03-01-2024, 11:48 PM)TanTin Wrote: (03-01-2024, 11:37 PM)Tomenable Wrote: I think that paper has data from Qatar, but not from Bahrain?
Yes, mostly Qatar, but there are many others as well. There are more than 800 in total.
Which of these samples are from Bahrain?
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