G25 coordinates for ethnic minorities from China

[norseking]

Yao/Miao from Guizhou and populations from Gansu

 

Hey, can you re-share the coordinates from the Sudanese study and the following; the original links have expired!

https://anthrogenica.com/showthread....-Human-Origins

[altvred]

https://drive.google.com/file/d/1tZf...ew?usp=sharing

 

The samples with abbreviated pop names are from here:

https://zenodo.org/record/6816509
https://www.frontiersin.org/articles...22.995783/full

We collected saliva samples from 239 individuals from the Tai-Kadai-speaking populations in Guizhou, southwest China. There were 50 individuals of Congjiang Zhuang in southeastern Guizhou (Zhuang_Congjiang), 51 individuals of Guanling Bouyei (Bouyei_Guanling), 22 individuals of Majiang Mulao in southeastern Guizhou (Mulao_Majiang, 木佬), 48 individuals of Liping Dong in southeastern Guizhou (Dong_Liping), 20 individuals of Dong in Dong_Tongren, and 48 individuals of Wuchuan Gelao in Zunyi (Gelao_Wuchuan). The geographical locations of the above six populations are shown in Supplementary Figure 1. Participants whose parents and grandparents are indigenous people reside in Guizhou for at least three generations and should have no consanguineous marriage with other groups. The Medical Ethics Committee of Guizhou Medical University approved the study (2019 Ethics Approval Document No. 74). We followed the recommendations provided by the revised Helsinki Declaration of 2000. All the participants signed written informed consent before participating in the study.

There were no supplementry files that I could locate that included precise sample or population labels. So I decided to keep it brief instead of guessing bassing on ID or number of samples.

[altvred]

Hey, can you re-share the coordinates from the Sudanese study and the following; the original links have expired!

https://anthrogenica.com/showthread....-Human-Origins

https://drive.google.com/file/d/1Kpl...ew?usp=sharing
https://drive.google.com/file/d/1tj1...ew?usp=sharing

[Michalis Moriopoulos]

This is a significant update for East Asia. Great work as always, Altvred! Keep 'em coming!

I wish we could find some publicly available Ainu genomes.

[Michalis Moriopoulos]

There were no supplementry files that I could locate that included precise sample or population labels. So I decided to keep it brief instead of guessing bassing on ID or number of samples.

Not sure I understand this part. Are those abbreviations you give to samples in the Google drive sheet also used in the genotype files themselves for those specific samples? Because if they give those abbreviations then it should be pretty clear what's what, right?

[altvred]

Not sure I understand this part. Are those abbreviations you give to samples in the Google drive sheet also used in the genotype files themselves for those specific samples? Because if they give those abbreviations then it should be pretty clear what's what, right?

The pop labels I assigned were based on sample IDs.

The original FAM file lacked FIDs (the first column, which is usually used for population labels).


https://zenodo.org/record/6816509

We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China.

There are actually 251 individuals in that dataset, not 239.

We collected saliva samples from 239 individuals from the Tai-Kadai-speaking populations in Guizhou, southwest China. There were 50 individuals of Congjiang Zhuang in southeastern Guizhou (Zhuang_Congjiang), 51 individuals of Guanling Bouyei (Bouyei_Guanling), 22 individuals of Majiang Mulao in southeastern Guizhou (Mulao_Majiang, 木佬), 48 individuals of Liping Dong in southeastern Guizhou (Dong_Liping), 20 individuals of Dong in Dong_Tongren, and 48 individuals of Wuchuan Gelao in Zunyi (Gelao_Wuchuan).

Here is the number of samples for each abbreviated pop label.

     51 CZ
     48 GBY
     46 LD
     39 MM
     20 TD
     47 WGL

Now,
TD=Dong_Tongren (only pop with 20 samples)

WGL=Gelao_Wuchuan

According to the way they cluster, I am fairly confident that is the case.

The Gelao_Wuchuan and
Dong_Tongren clustered with southern Han Chinese with
amounts of Sino-Tibetan-related components.

 

The rest probably are:
LD=Dong_Liping
MM=Mulao_Majiang
CZ=Zhuang_Congjiang
GBY=Bouyei_Guanling

https://pastebin.com/pbsYVmXV

There are some outliers that need to be removed. The GBY ones are fairly obvious.

 

[altvred]

This is a significant update for East Asia. Great work as always, Altvred! Keep 'em coming!

I wish we could find some publicly available Ainu genomes.

Cheers.

Btw

I just sent David the dataset from Fortes-Lima et al 2022.

SNP coverage isn't an issue with the Illumina Omni2.5-v8 chip. There were 327 samples from the Sahel, 109 of them from Chad. G25 definitely has a blind spot there.

Here is where they plot on a PCA alongside the Sudanese samples from Hollfelder 2017. (If you're wondering, this isn't G25, but rather my own smartpca run.)

 

[PLogan]

Can you educate me... never seen these before.



What are these data files they provide?

XXX_R01C01_Grn.idat
XXX_R01C01_Red.idat

32MB each

Each strand of SNPs read?

UPDATE: Found the plink format files...

[altvred]

Can you educate me... never seen these before.



What are these data files they provide?

XXX_R01C01_Grn.idat
XXX_R01C01_Red.idat

32MB each

Each strand of SNPs read?

Idat are the Illumina DNA microarray intensity raw data files, the way it works is that you use Illumina software to call genotype from the raw data and then convert to whatever you want.

I recommend using the gtc2vcf bcftools plug in.

https://github.com/freeseek/gtc2vcf#...-and-cel-files

Anyway the data is available in plink format for that particular dataset.
https://www.ebi.ac.uk/biostudies/fil...l_MBE_2022.bed
https://www.ebi.ac.uk/biostudies/fil...l_MBE_2022.bim
https://www.ebi.ac.uk/biostudies/fil...l_MBE_2022.fam

[PLogan]

Those Savannah samples are seriously high quality.... 2.2 million SNPs.

Average of 99.05% complete within that 2.2 million.


Missing SNPs

Mean	0.00946244
Standard Error	0.002189761
Median	0.004009
Mode	0.003748
Standard Deviation	0.039597762
Sample Variance	0.001567983
Kurtosis	135.6833522
Skewness	11.17522859
Range	0.540847
Minimum	0.002953
Maximum	0.5438
Sum	3.094218
Count	327

Population	Samples
Chad_ArabBaggara	25
Chad_Dangaleat	25
Chad_Daza	22
Chad_Maba	25
Chad_Zaghawa	12
Guinea_Fulani	25
Senegal_Bedik	25
Senegal_Halpularen	25
Sudan_ArabBaggara	23
Sudan_ArabKababish	25
Sudan_ArabRashaayda	20
Sudan_Daju	25
Sudan_NubaKoalib	25
Sudan_Zaghawa	25
Grand Total	327