YFull results for Pashtun

[Coldmountains]

Two likely Pashtun samples from KPK. It is interesting that one of them has a close mtDNA match (TMRCA 700 YBP) with a South Pashtun L1c and Ghazni R1a-Z2123 sample. It is unlikely that they all belong to the same tribes so if they are not recently mixed this seemingly shows historic intertribal mixing (especially on the female side which makes sense for tribal people). About H-Y155269 not much can be said (ultimately of IVC/ASI origin) except that so far it looks like a basal clade with not many relatives which will probably change with more DNA from the region.

H-M82>H-M2914>H-Z4361>H-SK1225>H-Z5875>H-PH4549>H-Y155269
https://www.yfull.com/tree/H-Y155256/

https://www.yfull.com/mtree/R30b1a1a2/

[Coldmountains]

L-Y12419>L-Y17950>L-FGC40778>L-Y61970>L-Y63043>L-BY184086

A very important Pashtun line is L1c-BY184086 (formed 1650 ybp, TMRCA 1250 ybp). This and parallel clade seem to be typical for Durrani and especially Sadozai Pashtuns. It is also the likely lineage of the Barakzai dynasty and Afghan kings of the last 200 years. But so far it seems to be absent in non-Durrani Pashtuns and seemingly it split from Balochs/Brahui just around 0 B.C. so we can not be 100% sure it was a Proto-Pashtun lineage actually. But we also lack samples from Pashtuns around the Proto-Pashtun homeland (Zhob/North Balochistan) which maybe will show more of it even when they are of non-Durrani origin.

https://www.yfull.com/tree/L-Y63043/

[Coldmountains]

L-L1307>L-M2398>L-Y12415>L-Z20267>L-Z5920>L-Y12419>L-Y17950>L-FGC40778>L-Y61970>L-Y63043>L-BY184086

A very important Pashtun line is L1c-BY184086 (formed 1650 ybp, TMRCA 1250 ybp). This and parallel clade seem to be typical for Durrani and especially Sadozai Pashtuns. It is also the likely lineage of the Barakzai dynasty and Afghan kings of the last 200 years. But so far it seems to be absent in non-Durrani Pashtuns and seemingly it split from Balochs/Brahui just around 0 B.C. so we can not be 100% sure it was a Proto-Pashtun lineage actually. But we also lack samples from Pashtuns around the Proto-Pashtun homeland (Zhob/North Balochistan) which maybe will show more of it even when they are of non-Durrani origin.

https://www.yfull.com/tree/L-Y63043/

My R1a>Y920>FT70760 line shows a similar pattern in terms of affinity to Balochs (TMRCA with a sample of likely South Pashtun/Baloch/Brahui/Sindhi origin based on his mtDNA around 0 B.C). It also seems to be absent in non-Pashtun groups more in the north and low if not absent in KPK Pashtuns (the group of Pashtuns which is best and most reliably sampled). So my suspicion is that my R1a lineage and this Baloch/Durrani L1c originate from a related Pre-Iranic population in North Balochistan/Arachosia.

[dkhanux]

A new Pashtun sample (Pakistan NW-Frontier) at Yfull under a likely Swat_IA J2 clade. There is Pakistani Syed sample at theYtree with the same clade so likely Sayed from Swat

J2>J-Z8344>J-FT125450>J-Y180494>J-MF51332

https://www.yfull.com/tree/J-Z8344/

I think I know the guy, he was on the J2 Facebook group. He's from Swat and is a Professor in Quetta now. He mentioned being Syed and is also on the J2 FTDNA groups now as well.

[Coldmountains]

The sample turned out to be of Afghan (likely East Pashtun via father's side) origin.

Looking closer at Pashtun and Baloch YP413 it is interesting that they are quite distant related despite both living so close to each other (split before 2000 B.C!). This is very different from the L1c of South Pashtuns (very high frequency in Durrani Pashtuns probably much higher than R1a) which just split around 0 B.C from Balochs/Brahui https://www.yfull.com/tree/L-Y61970/

This is either showing some old diversity of YP413 in the region or maybe it arrived via different migrations. But ironically Pashtun YP413 seems to be closer related to Kurds and West Iranians than Baloch YP413 which looks more basal. Pashtun-related R-YP1127 (TMRCA around 1000 B.C) is found in Dungan and some Chinese but this looks like some Khotanese/Kaschgar or Muslim era admix from South Central Asia. Very unlikely related to older or more northern populations in Xinjiang considering the lack of any YP413 in Iron Age samples from Xinjiang, Siberia and the Eurasian Steppe.

Two new Pashtun samples under YP1123 were added and the new sample from the UK is likely of Pashtun origin too. Most interestingly is that one of them is a Karlani<Khattak (most Karlani and Khttak are G2c so far) unlike most of the other published YP1123 samples which fall under the Kharshbun group of tribes. One Ghilzai (Amarkhel) was also under YP1123 so we have here a Y-DNA link between different tribal confederations and so far it is the only known common and recent Y-DNA link between different Pashtun tribal confederations.

Yfull has YP1123 with a TMRCA of 2200 ybp. Considering the usual underestimation we can expect the corrected TMRCA to be around 500 B.C. Upstream R-YP1127 (found in Dungan/Chinese but not in IA Steppe/modern steppe Turkics so likely of Khotan/Kashgar/Pamiri_IA or Muslim era origin) has already a TMRCA of 3000 ybp + likely underestimation so we probably have with YP1123 an Iron Age Iranic line that himself or his recent ancestor around 500-1200 b.c migrated from the Pamir/Badaskshan region into the south.

https://www.yfull.com/tree/R-YP1123/

[MiranZai]

Any ideas about this linkage ancestor haplogroup’s?

*





* Image from “Pashto” website : http://www.khyber.org

[Coldmountains]

Any ideas about this linkage ancestor haplogroup’s?

*





* Image from “Pashto” website : http://www.khyber.org

I have not seen deeper Bangash Y-DNA results yet. I think they very loosely fall today under the Karlani tribal confederation because of an old alliance with Khattak but their ultimate origin is unclear and likely both Pre-Pashtun + Pre-Karlani. So probably not G2c like most other Karlani. Karlani themselves based on Y-DNA and historical legends look like a Pre-Pashtun tribal group assimilated/mixing into the Pashtun tribal confederation hence their very specific and unique Y-DNA. We really have a poor idea about the Y-DNA of many Pashtun tribes and it looks more and more like Pashtun Y-DNA can be very different from tribe to tribe and that lot of modern Pashtun tribes/clans were original of non-Pashtun origin but joined the Pashtun tribal confederation in the last 1500 years (political alliance or being surrounded by Pashtuns).

Your line is Miranzai/Bangash?

[Coldmountains]

I really hope we can get deeper Y-DNA results for these Pashtun and non-Pashtun Afghan samples. They are enough coverage for deeper Y-DNA analysis?

https://journals.plos.org/plosone/ar...l.pone.0242168

Blood group typing from whole-genome sequencing data

Abstract

Many questions can be explored thanks to whole-genome data. The aim of this study was to overcome their main limits, software availability and database accuracy, and estimate the feasibility of red blood cell (RBC) antigen typing from whole-genome sequencing (WGS) data. We analyzed whole-genome data from 79 individuals for HLA-DRB1 and 9 RBC antigens. Whole-genome sequencing data was analyzed with software allowing phasing of variable positions to define alleles or haplotypes and validated for HLA typing from next-generation sequencing data. A dedicated database was set up with 1648 variable positions analyzed in KEL (KEL), ACKR1 (FY), SLC14A1 (JK), ACHE (YT), ART4 (DO), AQP1 (CO), CD44 (IN), SLC4A1 (DI) and ICAM4 (LW). Whole-genome sequencing typing was compared to that previously obtained by amplicon-based monoallelic sequencing and by SNaPshot analysis. Whole-genome sequencing data were also explored for other alleles. Our results showed 93% of concordance for blood group polymorphisms and 91% for HLA-DRB1. Incorrect typing and unresolved results confirm that WGS should be considered reliable with read depths strictly above 15x. Our results supported that RBC antigen typing from WGS is feasible but requires improvements in read depth for SNV polymorphisms typing accuracy. We also showed the potential for WGS in screening donors with rare blood antigens, such as weak JK alleles. The development of WGS analysis in immunogenetics laboratories would offer personalized care in the management of RBC disorder


DNA samples

Seventy-nine samples were used in this study formerly analyzed for anthropogenic markers and described in [12]. All samples were obtained from unrelated male Afghan volunteers after obtaining written informed consent. The study protocol was registered by the Ministere de l’Enseignement Superieur et de la Recherche in France (committee 208C06, decision AC-2008-232). Institutional review board Ministere de l’Enseignement Superieur et de la Recherche in France committee 208C06, (decision AC-2008-232) specifically approved this study.

ENA link: https://www.ebi.ac.uk/ena/browser/view/PRJNA662371

[MiranZai]

I have not seen deeper Bangash Y-DNA results yet. I think they very loosely fall today under the Karlani tribal confederation because of an old alliance with Khattak but their ultimate origin is unclear and likely both Pre-Pashtun + Pre-Karlani. So probably not G2c like most other Karlani. Karlani themselves based on Y-DNA and historical legends look like a Pre-Pashtun tribal group assimilated/mixing into the Pashtun tribal confederation hence their very specific and unique Y-DNA. We really have a poor idea about the Y-DNA of many Pashtun tribes and it looks more and more like Pashtun Y-DNA can be very different from tribe to tribe and that lot of modern Pashtun tribes/clans were original of non-Pashtun origin but joined the Pashtun tribal confederation in the last 1500 years (political alliance or being surrounded by Pashtuns).

Your line is Miranzai/Bangash?

I’m not sure about the “Bangash” side, so far I didn’t noticed any “Pashtun” linkage to my latest Y-DNA SNP root (Y218555) , it’s showing currently Brahui from HGDP sources;




“MiranZai” tribe seems to be also a common surname with some Brahui clans!




Unfortunately our family don’t have deep historical records & info about the paternal tree.

[Coldmountains]

I really hope we can get deeper Y-DNA results for these Pashtun and non-Pashtun Afghan samples. They are enough coverage for deeper Y-DNA analysis?

https://journals.plos.org/plosone/ar...l.pone.0242168

Blood group typing from whole-genome sequencing data

Abstract

Many questions can be explored thanks to whole-genome data. The aim of this study was to overcome their main limits, software availability and database accuracy, and estimate the feasibility of red blood cell (RBC) antigen typing from whole-genome sequencing (WGS) data. We analyzed whole-genome data from 79 individuals for HLA-DRB1 and 9 RBC antigens. Whole-genome sequencing data was analyzed with software allowing phasing of variable positions to define alleles or haplotypes and validated for HLA typing from next-generation sequencing data. A dedicated database was set up with 1648 variable positions analyzed in KEL (KEL), ACKR1 (FY), SLC14A1 (JK), ACHE (YT), ART4 (DO), AQP1 (CO), CD44 (IN), SLC4A1 (DI) and ICAM4 (LW). Whole-genome sequencing typing was compared to that previously obtained by amplicon-based monoallelic sequencing and by SNaPshot analysis. Whole-genome sequencing data were also explored for other alleles. Our results showed 93% of concordance for blood group polymorphisms and 91% for HLA-DRB1. Incorrect typing and unresolved results confirm that WGS should be considered reliable with read depths strictly above 15x. Our results supported that RBC antigen typing from WGS is feasible but requires improvements in read depth for SNV polymorphisms typing accuracy. We also showed the potential for WGS in screening donors with rare blood antigens, such as weak JK alleles. The development of WGS analysis in immunogenetics laboratories would offer personalized care in the management of RBC disorder


DNA samples

Seventy-nine samples were used in this study formerly analyzed for anthropogenic markers and described in [12]. All samples were obtained from unrelated male Afghan volunteers after obtaining written informed consent. The study protocol was registered by the Ministere de l’Enseignement Superieur et de la Recherche in France (committee 208C06, decision AC-2008-232). Institutional review board Ministere de l’Enseignement Superieur et de la Recherche in France committee 208C06, (decision AC-2008-232) specifically approved this study.

ENA link: https://www.ebi.ac.uk/ena/browser/view/PRJNA662371

First sample was already added at Yfull. A Pashtun sample from Baghlan (likely Ghilzai). I checked the other samples in the list and based on older str results they all seem to be R1a what is weird and bad for the research of non-R1a clades. I hope they are not all Z2125 too and there is also some of Z2125- (half of Tajik/Uzbek and 1/3 of Pashtun R1a was Z125-)



PT2_1 SRS7356013 R1a-Z2125 > R-YP413>R-M12280>R-M12298>R-YP1709>R-FGC22248>R-YP1127>R-YP1123>R-FT316309>R-BY94417

https://www.yfull.com/tree/R-BY94417/