Haplogroup D-CTS3946

This article is about the human Y-DNA haplogroup. For the human mtDNA haplogroup, see Haplogroup D (mtDNA).

Haplogroup D-CTS3946
Possible time of origin	80,700-64,700 years ago (ca. 72,700 years ago)[1]
Possible place of origin	Africa[1]
Ancestor	DE
Descendants	D-M174 (also known as D1) D-A5580.2 (also known as D2 and D0)
Defining mutations	CTS3946, CTS4030/Z1605

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

Proposed migration of haplogroup D according to Haber et al. (2019)

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^[2] and others an Asian origin.^[3] 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.^[1] 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.^[4]

Distribution

Frequency of Y Haplogroup D

Three other samples of D2 were also found (also in 2019) by FTDNA: two in Al Wajh on the west coast of Saudi Arabia^[5][6] and another one in a Syrian (he is D2b-FT51782).^[7][5] A D2b-FT51782 sample was also found in al-Qirbi from Bayda^[8] in Yemen that turned out to be several thousands of years related to that of the Syrian.^[7] There is another person (surname unknown) in the neighbouring Shabwah Governorate with TMRCA 1700 y. ago with the first one.^[9] It was announced in 2020 by Michael Sager of FTDNA that another sample had been found in an African American^[10] and one in another African American.^[10][11] The samples found in the Syrian descendent and in one of the African Americans are to date the most basal samples of D2.^{[10][5][6][11]} The other African American sample shares a branch with the three Nigerians.^[10] 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).^[5]

Subclades

D1

Main article: Haplogroup D1

Haplogroup D1 is a subclade of haplogroup D-CTS3946.

D2

Main article: Haplogroup 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.^[5][6]

Phylogenetic trees

ISOGG (version: 14.151).^[12]

• 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, Tibet^[13]
                  • 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,^[12] Central Asia,^[13] and Altai Republic
        • D1a2(Z3660)
          • D1a2a (M64.1/Page44.1, M55) Japan^[13]
            • D1a2a1 (M116.1)
            • D1a2a2 (CTS131)
              • D1a2a2a (CTS220)
              • D1a2a2b (CTS68) Japan(Rebun Island)
          • D1a2b (Y34637)　Andaman Islands^[14]
      • D1b (L1378) Philippines^[15]
    • D2 (A5580.2) Nigeria, Saudi Arabia, Syria, United States, Yemen

References

1. Haber M, Jones AL, Connell BA, Arciero E, Yang H, Thomas MG, et al. (August 2019). "A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa". Genetics. 212 (4): 1421–1428. doi:10.1534/genetics.119.302368. PMC 6707464. PMID 31196864.
2. Underhill PA, Kivisild T (2007). "Use of y chromosome and mitochondrial DNA population structure in tracing human migrations". Annual Review of Genetics. 41: 539–64. doi:10.1146/annurev.genet.41.110306.130407. PMID 18076332.
3. Cabrera VM (2017). "Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago". bioRxiv 10.1101/233502.
4. Hallast P, Agdzhoyan A, Balanovsky O, Xue Y, Tyler-Smith C (February 2021). "A Southeast Asian origin for present-day non-African human Y chromosomes". Human Genetics. 140 (2): 299–307. doi:10.1007/s00439-020-02204-9. PMC 7864842. PMID 32666166. Taking into account a rare African D0 lineage and the timeframe summarized above, we have argued (Haber et al. 2019) that the initial splits within CT are likely to have occurred in Africa before the exit, and that three lineages, C, D, and FT, were carried out by the ancestors of present-day non-Africans. Each of these three lineages subsequently expanded: C and D moderately, and FT massively." Also (from earlier in the study): "The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000–70,000 years ago, followed by a mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. This article incorporates text from this source, which is available under the CC BY 4.0 license.
5. Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained – Genetic Genealogy. Retrieved 2019-07-06.
6. "Image".
7. "FamilyTreeDNA – Y-DNA D Haplogroup Project".
8. "D YTree".
9. "D-Y330435 YTree". Archived from the original on 2023-05-01.
10. Sager, Michael (February 2020). The Tree of Mankind fromFTDNA (Mike Sager).
11. Estes, Roberta (2020-12-10). "New Discoveries Shed Light on Out of Africa Theory, and Beyond". DNAeXplained – Genetic Genealogy.
12. Y-DNA Haplogroup D and its Subclades – 2019
13. Hammer MF, Karafet TM, Park H et al. (2006). "Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes". J. Hum. Genet. 51 (1): 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082.
14. "D YTree". www.yfull.com. Retrieved 2019-09-03.
15. Y-DNA Haplogroup D and its Subclades – 2014