Nepalese DNA

**Zoro** · 10-30-2021, 03:08 PM

Originally Posted by Komintasavalta

Yeah maybe the reason why in my IBS run the French were closer to Finns than to Romanians was that all of the Romanian samples had under 580,000 SNPs out of a maximum of 597,573. When I made another dataset with just Finnish, Romanian, and French samples, and I used `--geno 0` to remove every SNP that was missing from any sample, then the French were closer to Romanians than to Finns.

If you use `--geno 0` so there is no SNP with missing data, then does it matter if you combine samples from different sources? Even though I used `--geno 0`, I was now able to make a dataset with 387,406 SNPs and 568 samples, because I only used samples with at least 588,000 SNPs, and I only selected up to 4 samples from each population based on which samples had the highest SNP count. But even now it's weird how Forest Yukaghirs are so close to the French, and the French are still closer to Finns than to Bulgarians:

It still matters. Try doing one just based on 1000G and one based on Simmons only. I wouldn’t worry about French-Bulgarian because IBS is total shared drift and not just recent drift. It’s probably correct but see what you get when you run one dataset at a time

**~~Komintasavalta~~** · 10-30-2021, 04:03 PM

Originally Posted by Zoro

It still matters. Try doing one just based on 1000G and one based on Simmons only. I wouldn’t worry about French-Bulgarian because IBS is total shared drift and not just recent drift. It’s probably correct but see what you get when you run one dataset at a time

The run below included only samples from 1000 Genomes, only samples with at least 1.14e6 SNPs, only up to 4 samples with the highest SNP count from each population, and only SNPs with no missing data (`--geno 0`). But still Great_Britain is closer to Finland than to Iberia_Spain:

In an f2 run of the same samples, Finns are much further from Great_Britain:

**Zoro** · 10-30-2021, 04:15 PM

Originally Posted by Komintasavalta

The run below included only samples from 1000 Genomes, only samples with at least 1.14e6 SNPs, only up to 4 samples with the highest SNP count from each population, and only SNPs with no missing data (`--geno 0`). But still Great_Britain is closer to Finland than to Iberia_Spain:

In an f2 run of the same samples, Finns are much further from Great_Britain:

The IBS makes more sense to me

**Kaazi** · 11-03-2021, 08:01 AM

@Godardt

Nepalese royal family is an interesting royal family of South Asia. I'm simulating a profile of some modern Shah Kings of Nepal taking Prithivi Narayan Shah as the endogamous Thakuri ancestor. https://en.wikipedia.org/wiki/Shah_dynasty

King Pratap Singh (https://en.wikipedia.org/wiki/Pratap_Singh_Shah) 1/2 Thakuri, 1/2 UP Rajput (Benares).

Code:

S-Indian:           	38.57%
Baloch:             	29.82%
Caucasian:          	3.81%
NE-Euro:            	7.30%
SE-Asian:           	1.07%
Siberian:           	2.58%
NE-Asian:           	13.01%
Papuan:             	0.66%
American:           	1.00%
Beringian:          	0.29%
Mediterranean:      	1.68%
SW-Asian:           	0.13%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.08%
W-African:          	0.00%

King Rana Bahadur (https://en.wikipedia.org/wiki/Rana_Bahadur_Shah) 3/4 Thakuri, 1/4 UP Rajput (Benares).

Code:

looks like a generic Rajput from Uttarakhand. 
S-Indian:           	35.22%
Baloch:             	26.29%
Caucasian:          	3.96%
NE-Euro:            	6.83%
SE-Asian:           	1.27%
Siberian:           	3.28%
NE-Asian:           	19.26%
Papuan:             	0.79%
American:           	1.14%
Beringian:          	0.30%
Mediterranean:      	1.37%
SW-Asian:           	0.19%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.11%
W-African:          	0.00%

King Girvan Yuddha (https://en.wikipedia.org/wiki/Girvan_Yuddha_Bikram_Shah) 3/8 Thakuri, 1/8 UP Rajput (Benares), 4/8 Maithil Brahmin (Janakpur).

Code:

profile looks like the Aswal Rajput from Uttarakhand.
S-Indian:           	39.13%
Baloch:             	31.17%
Caucasian:          	4.20%
NE-Euro:            	9.03%
SE-Asian:           	0.93%
Siberian:           	1.91%
NE-Asian:           	9.77%
Papuan:             	0.64%
American:           	1.02%
Beringian:          	0.44%
Mediterranean:      	1.58%
SW-Asian:           	0.12%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.06%
W-African:          	0.00%

King Rajendra (https://en.wikipedia.org/wiki/Rajendra_Bikram_Shah) assuming his mother to be a Thakuri princess. 11/16 Thakuri, 1/16 UP Rajput (Benares), 4/16 Maithil Brahmin.

Code:

Again Pahadi Rajput like profile. 
S-Indian:           	35.50%
Baloch:             	26.97%
Caucasian:          	4.16%
NE-Euro:            	7.69%
SE-Asian:           	1.20%
Siberian:           	2.94%
NE-Asian:           	17.64%
Papuan:             	0.78%
American:           	1.15%
Beringian:          	0.37%
Mediterranean:      	1.32%
SW-Asian:           	0.18%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.10%
W-African:          	0.00%

King Surendra (https://en.wikipedia.org/wiki/Surendra_Bikram_Shah) His mother was a UP Rajput from Gorakhpur. 11/32 Thakuri, 17/32 UP Rajput, 4/32 Maithil Brahmin.

Code:

Again Aswal Rajput (uttarakhand) like profile.
S-Indian:           	40.39%
Baloch:             	31.93%
Caucasian:          	3.83%
NE-Euro:            	7.97%
SE-Asian:           	0.94%
Siberian:           	2.06%
NE-Asian:           	9.08%
Papuan:             	0.59%
American:           	0.93%
Beringian:          	0.33%
Mediterranean:      	1.82%
SW-Asian:           	0.09%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.06%
W-African:          	0.00%

Crown Prince Trailokya (https://en.wikipedia.org/wiki/Trailo...rince_of_Nepal) His mother was a Thakuri.

Code:

S-Indian:           	36.13%
Baloch:             	27.35%
Caucasian:          	3.97%
NE-Euro:            	7.16%
SE-Asian:           	1.20%
Siberian:           	3.02%
NE-Asian:           	17.29%
Papuan:             	0.75%
American:           	1.11%
Beringian:          	0.31%
Mediterranean:      	1.44%
SW-Asian:           	0.17%
San:                	0.00%
E-African:          	0.00%
Pygmy:              	0.10%
W-African:          	0.00%

King Prithvi Bir Bikram (https://en.wikipedia.org/wiki/Prithvi_Bir_Bikram_Shah) His mother was a Rana princess (half Kunwar (Khadka) Chhetri + half Thakuri).

Code:

S-Indian:           	34.21%
Baloch:             	25.89%
Caucasian:          	4.29%
NE-Euro:            	7.10%
SE-Asian:           	1.35%
Siberian:           	3.42%
NE-Asian:           	19.93%
Papuan:             	0.77%
American:           	1.14%
Beringian:          	0.41%
Mediterranean:      	1.14%
SW-Asian:           	0.25%
San:                	0.01%
E-African:          	0.00%
Pygmy:              	0.09%
W-African:          	0.01%

King Tribhuvan (https://en.wikipedia.org/wiki/Tribhuvan_of_Nepal) Taken Minhas Dogra sample for his Kangra royal (Katoch?) mother.

Code:

S-Indian:           	35.28%
Baloch:             	32.14%
Caucasian:          	6.25%
NE-Euro:            	8.20%
SE-Asian:           	1.41%
Siberian:           	2.54%
NE-Asian:           	11.17%
Papuan:             	0.39%
American:           	0.57%
Beringian:          	0.21%
Mediterranean:      	0.57%
SW-Asian:           	0.97%
San:                	0.13%
E-African:          	0.00%
Pygmy:              	0.17%
W-African:          	0.00%

King Mahendra (https://en.wikipedia.org/wiki/Mahendra_of_Nepal) Mother was a UP Rajput from Oudh.

Code:

Looks so close to a UP Kshatriya. 
S-Indian:           	40.27%
Baloch:             	34.51%
Caucasian:          	4.87%
NE-Euro:            	8.22%
SE-Asian:           	1.04%
Siberian:           	1.86%
NE-Asian:           	5.85%
Papuan:             	0.39%
American:           	0.64%
Beringian:          	0.24%
Mediterranean:      	1.44%
SW-Asian:           	0.48%
San:                	0.07%
E-African:          	0.00%
Pygmy:              	0.10%
W-African:          	0.00%

King Birendra/Gyanendra

Code:

S-Indian:           	36.40%
Baloch:             	29.82%
Caucasian:          	4.81%
NE-Euro:            	7.56%
SE-Asian:           	1.26%
Siberian:           	2.76%
NE-Asian:           	13.88%
Papuan:             	0.58%
American:           	0.87%
Beringian:          	0.28%
Mediterranean:      	1.16%
SW-Asian:           	0.47%
San:                	0.05%
E-African:          	0.00%
Pygmy:              	0.12%
W-African:          	0.00%

King Dipendra/Prince Paras- Finally ended up as the generic Pahadi Rajput average lol.

1355/2048 Thakuri, 273/2048 UP Rajput, 256/2048 Kangra Rajput, 4/2048 Maithil Brahmin, 160/2048 Chhetri. Their mothers were sisters.

Code:

S-Indian:           	34.30%
Baloch:             	26.88%
Caucasian:          	4.62%
NE-Euro:            	7.09%
SE-Asian:           	1.36%
Siberian:           	3.29%
NE-Asian:           	18.79%
Papuan:             	0.71%
American:           	1.03%
Beringian:          	0.29%
Mediterranean:      	1.06%
SW-Asian:           	0.41%
San:                	0.03%
E-African:          	0.00%
Pygmy:              	0.13%
W-African:          	0.00%

King Mahendra was genetically the least Nepalese (21%) and was the most South Asian shifted Shah king and was estimated close to 90% UP Rajput like profile.

Interestingly, they've very low Chhetri blood (<10%) and are primarily mixes of various Nepali Thakuris + UP Rajputs + West Himalayan (Kangra) Rajputs.

@Godardt, Finally the Shah line (Paras) seems to have ended up genetically like a native Pahadi Kshatriya lol to the irony of these Thakuris excessively boasting Rajputana high caste-ness pride over others but at most, they look like the Pahadi commoners.

**Godardt** · 11-03-2021, 08:19 AM

Dear Bhai. How did u manage to estimate their genomes by their facial profiles or by their ancestry.

Sent from my Mi 10 using Tapatalk

**Kaazi** · 11-03-2021, 09:14 AM

Originally Posted by Godardt

Dear Bhai. How did u manage to estimate their genomes by their facial profiles or by their ancestry.

Sent from my Mi 10 using Tapatalk

Facial profiles would be pseudo scientific.

Look at Wikipedia and Royal Ark for their ancestry. How can you estimate someone's UP or Kangra Rajput ancestry in the face lol.

Btw, RIP Dipendra and Paras were genetically similar born (their fathers are bros and mothers are sisters) but their pheno was drastically different. Another very good example of not to take phenotypes for genetic assumption.

Dipendra

Spoiler!

Paras

Spoiler!

**Godardt** · 11-03-2021, 10:43 AM

Absolutely correct.

Sent from my Mi 10 using Tapatalk

**Kaazi** · 11-04-2021, 12:16 PM

Nepali Khas Brahmin (Adhikari) 52402 SNPs used in this evaluation Quite high Med.
Admix Results (sorted):

# Population Percent
1 S-Indian 33.43
2 Baloch 32.98
3 NE-Euro 12.46
4 Caucasian 6.82
5 NE-Asian 4.15
6 Mediterranean 3.76
7 Beringian 1.9
8 American 1.71
9 SE-Asian 1.7
10 Pygmy 0.38
11 Siberian 0.37
12 San 0.18
13 Papuan 0.16

Single Population Sharing:

# Population (source) Distance
1 nepalese-a (xing) 5.82
2 up-muslim (harappa) 6.65
3 up-brahmin (harappa) 8.32
4 singapore-indian-c (sgvp) 8.81
5 punjabi-brahmin (harappa) 8.88
6 punjabi (harappa) 8.94
7 bengali-brahmin (harappa) 8.97
8 kashmiri-pandit (reich) 9.41
9 punjabi-ramgarhia (harappa) 9.71
10 brahmin-uttar-pradesh (metspalu) 9.72
11 kashmiri (harappa) 9.73
12 punjabi-jatt-muslim (harappa) 9.85
13 punjabi-jatt-sikh (harappa) 9.87
14 kashmiri-pahari (harappa) 9.88
15 haryana-jatt (harappa) 9.93
16 bihari-muslim (harappa) 10.87
17 gujarati-muslim (harappa) 10.9
18 punjabi-khatri (harappa) 11.08
19 vaish (reich) 11.64
20 punjabi-arain (xing) 12.75

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 63.6% haryana-jatt (harappa) + 36.4% bengali (harappa) @ 3.05
2 77.4% bengali-brahmin (harappa) + 22.6% tajik (yunusbayev) @ 3.62
3 87% nepalese-a (xing) + 13% romanian-b (behar) @ 3.77
4 94.2% nepalese-a (xing) + 5.8% sardinian (hgdp) @ 3.97
5 84.8% up-brahmin (harappa) + 15.2% uyghur (hgdp) @ 4
6 92.7% nepalese-a (xing) + 7.3% puerto-rican (1000genomes) @ 4.1
7 92.8% nepalese-a (xing) + 7.2% tuscan (hapmap) @ 4.14
8 66.9% haryana-jatt (harappa) + 33.1% sri-lankan (harappa) @ 4.14
9 92.8% nepalese-a (xing) + 7.2% tuscan (1000genomes) @ 4.14
10 93.1% nepalese-a (xing) + 6.9% colombian (1000genomes) @ 4.17
11 93.1% nepalese-a (xing) + 6.9% italian (hgdp) @ 4.17
12 92.8% nepalese-a (xing) + 7.2% ashkenazi (harappa) @ 4.25
13 93.1% nepalese-a (xing) + 6.9% morocco-jew (behar) @ 4.28
14 92.9% nepalese-a (xing) + 7.1% ashkenazy-jew (behar) @ 4.29
15 53.2% bengali-brahmin (harappa) + 46.8% haryana-jatt (harappa) @ 4.29
16 72.2% vaish (reich) + 27.8% tajik (yunusbayev) @ 4.3
17 77.1% haryana-jatt (harappa) + 22.9% chenchu (metspalu) @ 4.3
18 93.2% nepalese-a (xing) + 6.8% sephardic-jew (behar) @ 4.32
19 84.1% up-brahmin (harappa) + 15.9% uzbek (behar) @ 4.33
20 93.7% nepalese-a (xing) + 6.3% spaniard (1000genomes) @ 4.34

Spoiler!

First time I saw a "Pushtikar Brahmin" as a top match for a Bahun.

Nepali Khas Brahmin (Dhungel) 163946 SNPs used in this evaluation
Admix Results (sorted):

# Population Percent
1 S-Indian 33.57
2 Baloch 33.33
3 NE-Euro 12.43
4 Caucasian 11.67
5 Siberian 3.74
6 SE-Asian 2.24
7 Mediterranean 1.23
8 NE-Asian 1.19

Finished reading population data. 377 populations found.
16 components mode.

--------------------------------

Least-squares method.

Using 1 population approximation:
1 pushtikar-brahmin_harappa @ 5.091119
2 nepali_harappa @ 5.828478
3 up-muslim_harappa @ 6.205473
4 rajasthani-brahmin_harappa @ 7.307971
5 kashmiri-pandit_reich @ 7.729126
6 kashmiri_harappa @ 8.054354
7 punjabi_harappa @ 8.164864
8 nepalese-a_xing @ 8.316539
9 punjabi-brahmin_harappa @ 8.394017
10 punjabi-jatt-muslim_harappa @ 8.663432
11 singapore-indian-c_sgvp @ 9.060476
12 punjabi-khatri_harappa @ 9.267936
13 punjabi-jatt-sikh_harappa @ 9.738752
14 up-brahmin_harappa @ 9.943675
15 punjabi-ramgarhia_harappa @ 10.102674
16 gujarati-muslim_harappa @ 10.140615
17 kashmiri-pahari_harappa @ 10.388577
18 haryana-jatt_harappa @ 10.910979
19 bihari-brahmin_harappa @ 11.153680
20 bengali-brahmin_harappa @ 11.599608

Using 2 populations approximation:
1 50% nepali_harappa +50% pushtikar-brahmin_harappa @ 4.318383

Using 3 populations approximation:
1 50% nepalese-a_xing +25% stalskoe_xing +25% vysya_reich @ 3.261522

Using 4 populations approximation:
++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++ +++
1 bengali_metspalu + nepalese-a_xing + oriya_harappa + stalskoe_xing @ 2.582158
2 bengali_metspalu + nepalese-a_xing + oriya_harappa + urkarah_xing @ 2.628903
3 nepalese-a_xing + oriya_harappa + srivastava_reich + stalskoe_xing @ 2.752786
4 nepalese-a_xing + oriya_harappa + south-african-indian_harappa + urkarah_xing @ 2.809407
5 brahmin-uttar-pradesh_metspalu + pushtikar-brahmin_harappa + srivastava_reich + tajik_yunusbayev @ 2.899612
6 nepalese-a_xing + oriya_harappa + sourastrian_harappa + stalskoe_xing @ 2.914411
7 dharkar_metspalu + nepalese-a_xing + oriya_harappa + stalskoe_xing @ 2.917006
8 kanjar_metspalu + nepalese-a_xing + oriya_harappa + stalskoe_xing @ 2.942174
9 nepalese-a_xing + oriya_harappa + stalskoe_xing + tharu_metspalu @ 3.003412
10 bengali-brahmin_harappa + pushtikar-brahmin_harappa + srivastava_reich + tajik_yunusbayev @ 3.017715
11 nepalese-a_xing + oriya_harappa + sourastrian_harappa + urkarah_xing @ 3.023630
12 brahmin-uttar-pradesh_metspalu + pushtikar-brahmin_harappa + sourastrian_harappa + tajik_yunusbayev @ 3.030467
13 bihari_harappa + nepalese-a_xing + oriya_harappa + stalskoe_xing @ 3.034277
14 dharkar_metspalu + nepalese-a_xing + oriya_harappa + urkarah_xing @ 3.035841
15 bengali_metspalu + nepalese-a_xing + stalskoe_xing + up-kshatriya_metspalu @ 3.040176
16 meghawal_metspalu + nepalese-a_xing + oriya_harappa + stalskoe_xing @ 3.054100
17 bihari-muslim_harappa + pushtikar-brahmin_harappa + srivastava_reich + tajik_yunusbayev @ 3.055295
18 bihari-muslim_harappa + oriya_harappa + oriya_harappa + urkarah_xing @ 3.088847
19 kanjar_metspalu + nepalese-a_xing + stalskoe_xing + up-kshatriya_metspalu @ 3.098613
20 nepalese-a_xing + oriya_harappa + singapore-indian-b_sgvp + stalskoe_xing @ 3.100043

Spoiler!

**Kaazi** · 07-19-2022, 04:05 PM

@Godardt, repost with new info; this guy's maternal grandmother is from your clan in Nuwakot. Both of these Gorkha region Chhetris are lowest East Asian types.

Khatri Chhetri father/Khadka Chhetri mother; Godar Thapa Chhetri maternal grandmother of Nuwakot district

Spoiler!

Shreepali Basnyat clan of Gorkha district -They're from the well known political-military aristocratic family of Gorkha- Abhiman Singh Basnyat's family. (https://en.wikipedia.org/wiki/Basnyat_family)

Spoiler!

He's C-M130 making all from the Abhiman Singh's lineage to be of the non-distinguished C lineage (could be C-P92 popular in whole South Asia or a rare C-M217 found in Himalayan upper castes-Jammu, Uttarakhand, Nepal).

Rest are at my spreadsheet
https://docs.google.com/spreadsheets...it?usp=sharing

**Godardt** · 08-08-2022, 01:44 AM

Originally Posted by Kaazi

@Godardt, repost with new info; this guy's maternal grandmother is from your clan in Nuwakot. Both of these Gorkha region Chhetris are lowest East Asian types.

Khatri Chhetri father/Khadka Chhetri mother; Godar Thapa Chhetri maternal grandmother of Nuwakot district

Spoiler!

Shreepali Basnyat clan of Gorkha district -They're from the well known political-military aristocratic family of Gorkha- Abhiman Singh Basnyat's family. (https://en.wikipedia.org/wiki/Basnyat_family)

Spoiler!

He's C-M130 making all from the Abhiman Singh's lineage to be of the non-distinguished C lineage (could be C-P92 popular in whole South Asia or a rare C-M217 found in Himalayan upper castes-Jammu, Uttarakhand, Nepal).

Rest are at my spreadsheet
https://docs.google.com/spreadsheets...it?usp=sharing

Thank you. Very interesting. I just saw it today. Have not been in touch off late.

Sent from my Mi 10 using Tapatalk