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Haplogroup D (mtDNA)

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In human mitochondrial genetics, Haplogroup D is a human mitochondrial DNA (mtDNA) haplogroup.

Haplogroup D is believed to have arisen in Asia some 48,000 years before present. It is a descendant haplogroup of haplogroup M.

Possible Time of Origin: 40,000 - 60,000 YBP

Possible Place of Origin: East Asia

Ancestor: M

Defining Mutations: 4883 5178A 16362

Distribution: It is found in Northeast Asia (including Siberia). Its subclade D1 (along with D2 and D4) is one of five haplogroups found in the indigenous peoples of the Americas, the others being A, B, C, and X.

Haplogroup D is also found quite frequently in Central Asia, where it makes up the second most common mtDNA clade (after H). Haplogroup D also appears at a low frequency in northeastern Europe and southwestern Asia.

D4 is also frequent to Koreans according to latest study.

Subclades: There are two principal branches:

Tree: This phylogenetic tree of haplogroup D subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation and subsequent published research.

Popular Culture: In his popular book The Seven Daughters of Eve, Bryan Sykes named the originator of this mtDNA haplogroup Djigonasee.

 

* The Human Genetic History of East Asia: Review Weaving a Complex Tapestry by Mark Stoneking, et al.

Map Depicting the Distribution of Major mtDNA Haplogroups in East Asia

 

Tai: Taiwanese Aborigines

 

 

* East Asian mtDNA Haplogroup Determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis by Lee HY, et al.

Abstract: The present study analyzed 21 coding region SNP markers and one deletion motif for the determination of East Asian mitochondrial DNA (mtDNA) haplogroups by designing three multiplex systems which apply single base extension methods. Using two multiplex systems, all 593 Korean mtDNAs were allocated into 15 haplogroups: M, D, D4, D5, G, M7, M8, M9, M10, M11, R, R9, B, A, and N9. As the D4 haplotypes occurred most frequently in Koreans, the third multiplex system was used to further define D4 subhaplogroups: D4a, D4b, D4e, D4g, D4h, and D4j. This method allowed the complementation of coding region information with control region mutation motifs and the resultant findings also suggest reliable control region mutation motifs for the assignment of East Asian mtDNA haplogroups. These three multiplex systems produce good results in degraded samples as they contain small PCR products (101-154 bp) for single base extension reactions. SNP scoring was performed in 101 old skeletal remains using these three systems to prove their utility in degraded samples. The sequence analysis of mtDNA control region with high incidence of haplogroup-specific mutations and the selective scoring of highly informative coding region SNPs using the three multiplex systems are useful tools for most applications involving East Asian mtDNA haplogroup determination and haplogroup-directed stringent quality control.

 

* Admixture, Migrations, and Dispersals in Central Asia: Evidence from maternal DNA lineages by David Comas, et al.

Abstract: Mitochondrial DNA (mtDNA) lineages of 232 individuals from 12 Central Asian populations were sequenced for both control region hypervariable segments, and additional informative sites in the coding region were also determined. Most of the mtDNA lineages belong to branches of the haplogroups with an eastern Eurasian (A, B, C, D, F, G, Y, and M haplogroups) or a western Eurasian (HV, JT, UK, I, W, and N haplogroups) origin, with a small fraction of Indian M lineages. This suggests that the extant genetic variation found in Central Asia is the result of admixture of already differentiated populations from eastern and western Eurasia. Nonetheless, two groups of lineages, D4c and G2a, seem to have expanded from Central Asia and might have their Y-chromosome counterpart in lineages belonging to haplotype P(xR1a). The present results suggest that the mtDNA found out of Africa might be the result of a maturation phase, presumably in the Middle East or eastern Africa, that led to haplogroups M and N, and subsequently expanded into Eurasia, yielding a geographically structured group of external branches of these two haplogroups in western and eastern Eurasia, Central Asia being a contact zone between two differentiated groups of peoples.

 

* Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia by Miroslava Derenko, et al.

Abstract: More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia – the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.

 

 

Major mtDNA Haplogroups

(Haplogroups found among Taiwanese and East Asian peoples in green)

 

L (Mitochondrial Eve)
• L0
• L1-6
  • L1
  • L2-6
    • L5
    • L2'3'4'6
      • L2
      • L3'4'6
        • L6
        • L3'4
          • L4
          • L3
            • M
              • M8: CZ
                • C
                • Z
              • M9: E
              • M12'G: G
              • M29'Q: Q
              • D
            • N
              • N1: I
              • N2: W
              • N9: Y
              • A
              • S
              • X
              • R
                • RO (FMKA pre-HV)
                  • HV
                    • H
                    • V
                • pre-JT or R2'JT
                  • JT
                    • J
                    • T
                • R9: F
                • R11'B: B
                • P
                • U (formerly UK)
                  • U8: K