Devils-Gate-Neolithic close modern populations

**Zoro** · 07-02-2020, 04:58 PM

......

**Zoro** · 07-02-2020, 05:04 PM

..........

**Zoro** · 07-02-2020, 05:06 PM

Originally Posted by vbnetkhio

but in plink you can't use outgroups, right?
i'm interested in comparing BA and IA samples to moderns, and qpAdm is perfect for this.
because i can include that ancient stuff like WHG, EEF etc. as outgroups, and then the algorithm actually comapres the BA onwards drift

Yes but you can do good work in plink if you do this:

1- Prune your dataset for QC so that no sample has any missing genotype: /plink --bfile Reich_set --keep a.txt --geno 0.005 --make-bed --out Test

2- Check to make sure no sample as missing genotype: /plink --bfile Test --missing. You'll get a report of how many SNPs each sample is missing

3- To remove common alleles common to Africans and Eurasians : /plink --bfile Test --max-maf 0.25 --make-bed --out Test1. This will get rid of allleles with MAF>25%

4- /plink --bfile Test1 --genome. You'll get a text file with distances, IBD Z2, Z1, Z0, Pi-Hat, PPC which is really good.

**Zoro** · 07-02-2020, 05:59 PM

Originally Posted by Zoro

Out of curiosity I went to Vahuado site to see if the G25 results also make sense for Devils-Gate-N. Unfortunately the G25 results were NONSENSICAL as you can see below.

You don't have to take my word for it. Just go to Vahuado and copy Devils-Gate from G25 SCALED AVG Ancient spreadsheet and paste it in TARGET in G25 SCALED AVG Moderns calculator.

Hopefully this will convince those who are still on the fence to not take the G25 outputs seriously.

Here are some G25 nonsensical results compared to my PLINK IBS results above. You maybe able to spot even more illogical results.

LIST OF G25 NONSENSICAL RESULTS
NO	NONSENSICAL RESULT	IBS- PLINK	DAVIDSKI – G25
1	Devils-Gate closer to many S.& W Asians & Europeans than to E. Eurasians	NO	YES
2	Devils-Gate closer to Libyans, Algerians, Egyptians, Berber than to Lithuanians & Armenians	NO	YES
3	Devils-Gate closer to S. Iranians than to Kurds	NO	YES

G25 Modern Averages scaled, official datasheet
POPULATION	Distance to RUS_Devils_Gate_Cave_N
Mongola	0.09648
Korean	0.12362
Japanese	0.12374
Tibetan_Gangcha	0.12467
Kalmyk	0.13047
Mongolian	0.13589
Buryat	0.13749
Han_Jiangsu	0.15949
Han_Shanghai	0.16224
Han_Zhejiang	0.16848
Han_Hubei	0.17012
Han_Sichuan	0.17243
Koryak	0.18688
Yakut	0.19216
Dai	0.24433
Kazakh	0.24489
Brahmin_Manipuri	0.28047
Karakalpak	0.28056
Uygur	0.31489
Uzbek	0.36435
Bashkir	0.37197
Turkmen	0.42475
Gond	0.42698
Paniya	0.45062
Irula	0.45444
Pulliyar	0.45849
Burusho	0.46823
North_Kannadi	0.46981
Hakkipikki	0.47077
Uttar_Pradesh	0.47749
Mala	0.47761
Yadava	0.47845
Maratha	0.47910
Dusadh	0.47939
Kol	0.48416
Tatar_Kazan	0.48508
Piramalai	0.48621
Kanjar	0.48656
Punjabi_Lahore	0.48694
Mixtec	0.48810
Zapotec	0.48925
Pima	0.48936
Velamas	0.49030
Brahmin_Tamil_Nadu	0.49132
Tajik	0.49203
Gujarati	0.49562
Kashmiri_Pandit	0.49853
Mayan	0.49890
Mixe	0.49892
Quechua	0.50299
Brahmin_Gujarat	0.50491
Brahmin_Uttar_Pradesh	0.50595
Tatar_Mishar	0.51283
Pashtun	0.51377
Tajik_Ishkashim	0.51603
Gujar_Pakistan	0.51798
Sindhi	0.51821
Punjabi_Jatt	0.51933
Pashtun-Yusufzai	0.52017
Pashtun-Uthmankhel	0.52148
Tajik_Shugnan	0.52207
Bolivian_LaPaz	0.52214
Pashtun-Tarkalani	0.52294
Tajik_Rushan	0.52785
Kalash	0.52873
Brahui	0.54727
Balochi	0.54963
Parsi_India	0.55047
Parsi_Pakistan	0.55150
Makrani	0.55650
Circassian	0.55678
Iranian_Bandari	0.55968
North_Ossetian	0.56144
Finnish_East	0.56274
Karitiana	0.56404
Iranian_Fars	0.57057
Surui	0.57266
Finnish	0.57687
Adygei	0.57706
Australian	0.57981
Iranian_Lor	0.58065
Tabasaran	0.58172
Iranian_Zoroastrian	0.58288
Kurdish	0.58813
Syrian	0.59025
Abkhasian	0.59109
Jordanian	0.59519
Russian_Kursk	0.59637
Moldovan	0.59668
Libyan	0.59770
BedouinA	0.59798
Russian_Orel	0.59873
Egyptian	0.59881
Algerian	0.60187
Estonian	0.60205
Berber_Tunisia_Sen	0.60223
Hungarian	0.60227
Belarusian	0.60644
Albanian	0.60646
Armenian	0.60886
Spanish_Asturias	0.61105
Spanish_Andalucia	0.61165
Lithuanian_RA	0.61167
Spanish_Galicia	0.61185
Spanish_Soria	0.61193
English	0.61247
Lithuanian_SZ	0.61545
Sardinian	0.63860
Somali	0.65247
Masai	0.71578
Papuan	0.75843
Ethiopian_Gumuz	0.75873
Ethiopian_Mursi	0.76359
Ethiopian_Anuak	0.79354
Luhya_Kenya	0.80931
Yoruba	0.83579
Mbuti	1.00219

If anyone is interested in reading the paper on Devils-Gate-N it's here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287702/. It also shows Devil-Gates closer to Japanese than Mongols like my Plink IBS run and unlike the G25