# Haplogroup D-CTS3946

Haplogroup D, also known as D-CTS3946, is a Y-chromosome haplogroup. Like its relative distant sibling, haplogroup E-M96, D-CTS3946 has the YAP+ unique-event polymorphism, which defines their parent, haplogroup DE. D-CTS3946 has two basal branches, D1 and D2. D1 and D2 are found primarily in East Asia, at low frequency in Central Asia and Southeast Asia, and at very low frequency in Western Africa and Western Asia.

## Origins

Haplogroup D was formerly the name of the D lineage D-M174. Varying proposals exist regarding the origin of haplogroup DE, the parent of D, with some suggesting an African and others an Asian origin. But D-M174 was, and generally is, assumed to be of Asian origin and is exclusively found in Asia.
Haber et al. (2019) identified a haplogroup, termed "D0", in three Nigerians. Defined by the SNP A5580.2, "D0" haplogroup is outside M174, but belongs to the D lineage, shares 7 SNPs with it D-M174 that E lacks, and was determined to have diverged early from the D branch (near the D/E split). Haber et al. (2019) considered several possibilities, including an African origin and Asian origin for the haplogroup, but in part because of the deep-rooting of haplogroup "D0", as well as recently calculated early divergence times for it and its parent haplogroup, DE, the authors conclude in favor of an African origin for D0 and DE, as well as for the common ancestor (now known as D-CTS3946 or "D") of D0 and D-M174. According to Haber et al. (2019), D0 is a branch of the DE lineage near the D/E split but on the D branch, diverging around 71,000 years ago. The authors find divergence times for DE*, E, and D0, all likely within a period of about 76,000-71,000 years ago, and a likely date for the exit of the ancestors of modern Eurasians out of Africa (and ensuing Neanderthal admixture) later, at around 50,300-59,400 years ago, which they argue, also supports an African origin for those haplogroups. Thus D-CTS3946 is proposed to have spread both within and outside of Africa: with one branch diverging into D0 in Africa, and another branch that left Africa eventually diverging into D-M174 (i.e. with the M174 mutation later arising from the D-CTS3946 that had spread to Asia).
Hallast et al. (2020), on ancient and modern haplogroups using a phylogenetic analysis of haplogroup C, D and FT sequences, including very rare deep-rooting lineages (such as D0/D2 sampled by Haber et al. 2019) argues, taking the "rare deep-rooted D0" into account, that the initial splits within haplogroup CT (ancestor of DE) occurred in Africa. They also argue that phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 55,000–50,000 years ago of all known surviving non-African male lineages (apart from recent migrants) soon after an initial 70–55,000 year ago migration from Africa of basal haplogroup D and other basal y-lineages. They argue that these lineages then rapidly expanded across Eurasia, later diversified in southeast Asia and then expanded westwards around 55–50,000 years ago, replacing other local lineages within Eurasia, and conclude that haplogroup D (as D-M174) then underwent rapid expansions within Eastern-Eurasian populations and consists of 5 different branches which formed about 45,000 years ago. They find that these haplogroups currently have their greatest diversity in Eastern Eurasia (east/southeast Asia). Tibeto-Burmese populations of East and Southeast Asia were found to have the highest amount of diversity.

## Distribution

Three other samples of D2 were also found (also in 2019) by FTDNA: two in Al Wajh on the west coast of Saudi Arabia and another one in a Syrian (he is D2b-FT51782). A D2b-FT51782 sample was also found in al-Qirbi from Bayda in Yemen that turned out to be several thousands of years related to that of the Syrian. There is another person (surname unknown) in the neighbouring Shabwah Governorate with TMRCA 1700 y. ago with the first one. It was announced in 2020 by Michael Sager of FTDNA that another sample had been found in an African American and one in another African American. The samples found in the Syrian descendent and in one of the African Americans are to date the most basal samples of D2. The other African American sample shares a branch with the three Nigerians. The recent evidence (as also proposed by Haber et al.) suggests that D2 is a highly divergent haplogroup close to the DE split but on the D branch and lacking the M174 mutation possessed by the other known D lineages (belonging to its sibling D-M174).

## Subclades
### D1

Haplogroup D1 is a subclade of haplogroup D-CTS3946.

### D2

Haplogroup D2 is an Upper Paleolithic subclade of haplogroup D-CTS3946. D0 has been renamed D2, and D-M174 has been renamed D1 due to this discovery.

## Phylogenetic trees

ISOGG (version: 14.151).
* DE (YAP) Caribbean, Guinea-Bissau, Tibet, Nigeria
** D (CTS3946)
*** D1 (M174/Page30, IMS-JST021355)
**** D1a (CTS11577)
***** D1a1 (F6251/Z27276)
****** D1a1a (M15) China (especially Miao, Yi, Tibetans, etc.), Southeast Asia, Mongolia, Central Asia
******* D1a1a1 (F849)
******** D1a1a1a (N1)
********* D1a1a1a1 (Z27269) Japan, China (particularly Tibet)
********** D1a1a1a1a (PH4979)
*********** D1a1a1a1a1 (BY15119/Z29428)
******** D1a1a1a2 (Z31591) Nepal(Tamang), Kazakhstan, China(Yi)
******* D1a1a2 (F1070) China, Thailand
****** D1a1b (P99) Found with high frequency in Tibet and occasionally in other parts of China, Mongolia, Central Asia, and Altai Republic
***** D1a2(Z3660)
****** D1a2a (M64.1/Page44.1, M55) Japan
******* D1a2a1 (M116.1)
******* D1a2a2 (CTS131)
******** D1a2a2a (CTS220)
******** D1a2a2b (CTS68) Japan(Rebun Island)
****** D1a2b (Y34637)　Andaman Islands
**** D1b (L1378) Philippines
*** D2 (A5580.2) Nigeria, Saudi Arabia, Syria, United States, Yemen
vtePhylogenetic tree of human Y-chromosome DNA haplogroups :
This article needs to be updated. Please help update this article to reflect recent events or newly available information. (February 2021) :
"Y-chromosomal Adam"
A00
A0-T
A0
A1
A1a
A1b
A1b1
BT
B
CT
DE
CF
D
E
C
F
F1
 F-Y27277
 F3
 GHIJK
G
HIJK
IJK
H
IJ
K
I  
J 
   LT
      K2
I1  
I2 
J1  
J2 
L  
  T 
K2e
K2d
K2c
K2b 
K2a
K2b1
  P
K-M2313
S
 M   
P1  
NO1
P1c
P1b
P1a
N
O
R
Q :
Y-DNA by population
Y-DNA haplogroups of historic people
Footnotes
↑ Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809. S2CID 23291764.
↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
↑ Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).
↑ Haplogroup A1 is also known as A1'2'3'4.
↑ F-Y27277, sometimes known as F2'4, is both the parent clade of F2 and F4 and a child of F-M89.
↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
↑ Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.
↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
↑ Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
↑ Haplogroup P (P295) is also klnown as K2b2.
↑ K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)
↑ Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)
↑ Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.) :