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Haplogroup D or D-CTS3946 is a Y-chromosome haplogroup. Both D-CTS3946 and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP+ unique-event polymorphism, which is unique to Haplogroup DE. Subclades of haplogroup D-CTS3946 are found primarily in East Asia, though they are also found regularly with low frequency in Central Asia and Southeast Asia, and have also been found sporadically in Western Africa and Western Asia.

Overview
Haplogroup D was formerly the name of the D lineage D-M174. And the possible place of origin of Haplogroup D, and in some works even of DE and E, was presumed to be Asia.

However, a study (Haber et al. 2019) identified a haplogroup, termed "D0", in three Nigerian samples. The "D0" haplogroup is outside M174, but shares 7 SNPs with it that E lacks. The authors consider several possibilities, specifically an African origin or an Asian origin, but in part because of the likely 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, while noting the possibility of an Asian origin, for D0 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., D0 is a branch of the DE lineage near the DE 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 outside Africa eventually diverging into D-M174 (i.e. with the M174 mutation later arising from the D-CTS3946 that had spread to Asia). "D0" has also been named "D2", and former D (D-M174) has now also been termed "D1" due to this discovery.

Three other samples of D2 were also found in West Asia (also in 2019): two in Al Wajh on the west coast of Saudi Arabia and another one in a Russian who traced his paternal lineage to Syria. It was announced in 2020 by Michael Sager of FTDNA that another sample was found in an African American  The samples found in the Russian Syrian and in the African American are to date the most basal samples of D2. 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).

However previous studies, such as Cabrera et al. 2018 which analyzed maternal and paternal markers, their current distribution, and inferences from the ancient DNA of the Altai Neanderthals. Their results supports an Asian origin of paternal Haplogroup DE, its sub-clades D and E, as well as maternal haplogroup L3. The study suggests a back migration into Africa and a following admixture of the native Africans with immigrating peoples from Asia. It is suggested that DE originated about 70,000 years ago somewhere near Tibet and Central Asia. Additionally, the authors argue that the presence of DE* in Tibet, and that Tibet shows the greatest diversity concerning haplogroup D, supports the origin of DE* in this region.

A genetic study by Hallast et al. 2020 about 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 samplified by Haber et al. 2019), found that haplogroup D has its greatest diversity in Eastern Eurasia (East/Southeast Asia). They found, taking the "rare deep-rooted D0" into account, that C, D and FT were among the ancestral Eurasian groups which left Africa, and which gave rise to the modern people of Asia and later expanded westwards, replacing other local lineages. They concluded that haplogroup D underwent rapid expansions within Eastern-Eurasian populations and consists of 5 different branches which formed about 45,000 years ago. Tibeto-Burmese populations of East and Southeast Asia were found to have the highest amount of diversity and basal lineages.

Phylogeny of the subclades
ISOGG (version: 14.151).


 * DE (YAP)
 * D (CTS3946)
 * D1 (M174/Page30, IMS-JST021355)
 * D1a (CTS11577)
 * D1a1 (F6251/Z27276)
 * D1a1a (M15)
 * D1a1a1 (F849)
 * D1a1a1a (N1)
 * D1a1a1a1 (Z27269) Japan, China, Tibet
 * D1a1a1a1a (PH4979)
 * D1a1a1a1a1 (BY15119/Z29428)
 * D1a1a1a2 (Z31591) Nepal(Tamang), Kazakhstan, China(Yi)
 * D1a1a2 (F1070) China
 * D1a1b (P99)　Tibet, Mongol, Central Asia
 * 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, African Americans, Al Wajh in Saudi Arabia, Syria