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Category: mtDNA » mtDNA SNP

The first member of mtDNA Subclade L3d arose approximately 30,250 years ago in Africa.  Today, descendents of L3d are found mainly in West Africa and African Americans (Salas 2002).  Individuals who belong to Subclade L3d are of African ancestry.  L3d is not native to any other continent. 

L3d is characterized by a mutation at location 8618 in the coding region of the mtDNA (the 8618 mutation is included in the mtDNA haplogroup backbone panel) and a mutation at location 16124 in the mtDNA HVR1 region.  

Today, within the continent of Africa, L3d is rarely found in Northern, Central and Eastern Africa.  The highest frequency of L3d is in West Africa (Allard 2005, Carvalho 2008, Rosa 2004, Salas 2002, Salas 2004, Silva 2006), ranging from 7% in Sernegalese to 12% in Niger/Nigeria, with an overall average of approximately 9% (Rosa 2004, Silva 2006). 

Within Western Africa, 10 to 11% of Temne, Mandinka and Fulbe people belong to L3d (Jackson 2005).  Mandinka and Fulbe are large ethnic groups (over 10 million people each) that are distributed throughout different West African countries, whereas the Temne people represent a smaller ethnic group consisting of ~ 2 million people that make up 30% of Sierra Leone’s total population.  Although L3d is very frequently found in West Africa, it is not the most common mtDNA haplogroup/subclade in West Africa.  Subclades L1b, L2a, L2c, L3b, and L3e, are also found in more than 10% of West Africans.  These subclades, together wtih L3d, represent approximately 70% of the Subclades of all West Africans.  

There are 3 known subgroups of L3d:  L3d1, L3d2 and L3d3.  L3d1 is found at a high frequency in a specific Fulbe lineage (Salas 2002).  Although L3d is occasionally found in Southern and Southeastern Africa at low frequencies, the subgroup L3d3 is present in the Khoisan-speaking people (in particular Khwe and Kung) at a considerably high frequency.  The spread of L3d to Southern and Southeastern Africa is likely associated with the Bantu expansion (Salas 2002).

Outside of Africa, L3d is mainly found in African Americans.  Approximately 6% of all African Americans are descendents of the L3d family line (Allard 2005).  When compared to other Haplogroup L subclades, including L2a, L1c, L1b, L3e2 and L3b, that are also present at high frequencies amongst African Americans (18.8%, 11%, 9.1%, 9.1%, and 8.1% respectively), members of L3d are not the largest contributors to the mtDNA lineages of African Americans (Allard 2005).

During the Atlantic Slave trade (15th to 19th century), ~ 8 million of people were forced to move from West Africa to the New World (~13 million including other regions of Africa), with Brazil being the major importer, receiving the largest number of African slaves.  This human movement is reflected by the similar pattern of haplogroup distribution/frequency in North/Central America and West Africa (Salas 2004).  

Name of Scientific Article Scientific Journal
Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set.  Allard et al.  Click here to view the abstract of the original publication. For. Sci. Int. 2005; 148(2-3):  169-179.
Mitochondrial DNA mapping of social-biological interactions in Brazilian Amazonian African-descendant populations.  Carvalho et al.  Click here to view and download a copy of the original publication. Genet. Mol. Biol. 2008; 31(1).
Mitochondrial DNA Genetic Diversity Among Four Ethnic Groups in Sierra Leone.  Jackson et al.  Click here to view the abstract of the original publication. Am. J. of Phy. Ant.  2005; 128:  156-163.
MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region.  Rosa 2004.  Click here to view the abstract of the original publication. Ann. of Hum. Gen. 2004; 68: 340-352.
The Making of the African mtDNA Landscape.  Salas et al.  Click here to view and download a copy of the original publication. Am. J. Hum. Genet. 2002; 71(5):1082–1111. 
The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade.  Salas et al.  Click here to view and download a copy of the original publication. Am. J. Hum. Genet. 2004; 74(3): 454–465.
mtDNA Haplogroup Analysis of Black Brazilian and Sub-Saharan Populations: Implications for the Atlantic Slave Trade.  Silva et al.  Click here to view the abstract of the original publication. Human Biology 2006; 78(1): 29-41.
Category: mtDNA » mtDNA SNP

The mtDNA SNP Haplogroup H Subclade Test Panel examines 17 unique SNP markers in the coding region of the mtDNA.  These 17 SNP markers define up to 16 different subclades of Haplogroup H (Subclades 1 to 16).  The chart below lists the 17 SNP markers that are included in this panel and the Subclades that they define.

SNP Location Mutations Subclades of H
1438 A > G Excludes H2
2259 C > T H13
3010 G > A H1
3915 G > A H6
3936 C > T H12
3992 C > T H4
4310 A > G H9
4336 T > C H5a
4769 A > G Excludes H2a
4793 A > G H7
6253 T > C H15
6776 T > C H3
8448 T > C H11
10394 C > T H16
11377 G > A H14
13101 A > C H8
14470 T > A H10

The diagram below is a phylogenetic tree illustrating the various subclades of H that are known.  The diagram also shows where each of the 17 SNP fall in the tree.  Click here to download a detailed copy of the Haplogroup H Subclade Map

mtDNA SNP H-Refinement

Category: mtDNA » mtDNA SNP


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Category: mtDNA » mtDNA SNP

The mtDNA SNP Backbone Test Panel examines 20 SNP markers in the coding region of the mtDNA.  These 20 SNP markers are the defining markers for determining an individual’s mtDNA haplogroup when used together with the HVR1 and HVR2 results.  The chart below lists the 20 markers that are included in this panel, and the haplogroups that they define. 

SNP Location Mutations Haplogroups
2352 T > C L1b, L3e, U6b1
3594 C > T L0, L1, L2, L5
3693 G > A L1b, L2d
4312 C > T L0
4580 G > A V
4833 A > G G
5178 C > A
C > T
D
7028 C > T H*
7055 A > C
A > G
L1
7598 G > A E
8618 T > C L3d
10086 A > G L3b
10310 G > A F
10400 C > T C, D, E, G, M, Q, Z
10873 T > C C, D, E, G, L, M, Q, Z
11251 A > G JT, J, T
11719 G > A Pre-HV, HV*
12308 A > G K, U
12705 C > T B, F, H, J, K, P, T, R, U, V*
14766 C > T HV*

The diagram below is a phylogenetic tree illustrating how all people living today share a common maternal ancestor, the “mitochondrial eve”.  The diagram also shows where each mtDNA SNP marker appears in the tree.  Click here to download a detailed copy of the mtDNA Haplogroup Map

mtDNA SNP Haplogroup

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