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 about 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 people are large ethnic groups (over 10 million each) that are distributed throughout different West African countries, whereas 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 found in more than 10% of West Africans.  Altogether, including L3d, these subclades 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 considerably 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 among Khoisan-speaking people (in particular Khwe and Kung) at a considerably high frequency.  The spread of L3d to Southern and Southeastern Africa is likely to be associated with Bantu expansion (Salas 2002).

Outside of Africa, L3d is mainly found in African American with frequency of ~ 6% of African Americans (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).  

The following table outlines the Y-DNA STR markers available at Genebase and the corresponding motifs used for allele designation in Version 3.4.  Click here to view the conversion chart for Version 3.3 to Version 3.4.  Please note that Users from previous versions will be automatically converted to 3.4.

 *Variable regions in each motif are indicated in blue.

*Motifs used for allele designation in Version 3.4 are compared to NIST nomenclature, and marked as “same” or “different” accordingly. 

*Question mark (?) indicates that NIST data is currently unavailable.

What is “NIST nomenclature”?

NIST stands for “National Institute of Standards and Technology”.  NIST is a non-regulatory federal agency within the U.S. Department of Commerce with the mission to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology in ways that enhance economic security and improve our quality of life. 

NIST has compiled and maintained a Short Tandem Repeat DNA Internet Database called STRBase, a valuable STR information resource.  Click here to view the NIST standards for the most commonly tested Y-chromosome STR markers. 

To facilitate Y-DNA STR data comparisons between different laboratories and research groups, many laboratories choose to follow the standard NIST nomenclature to avoid differences in allele values due to different nomenclatures (motif and counting method) between different laboratories.  Most motifs in the NIST nomenclature follow the ISFG (International Society of Forensic Genetics) guidelines.  Click here to view the latest ISFG recommendations on the Y-STR nomenclature.

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.

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. 

DNA Lesson Series: The mtDNA and its role in Ancestry
mtDNA Part I - mtDNA 101
mtDNA Part II - Facts about mtDNA
mtDNA Part III - mtDNA Structure
mtDNA Part IV - Ancestral Markers
mtDNA Part V - Detecting Mutations in the mtDNA
mtDNA Part VI - mtDNA Ancestral Markers
mtDNA Part VII - The Cambridge Reference Sequence
mtDNA Part VIII - mtDNA Test Types
mtDNA Part IX - mtDNA Haplogroup Determination
mtDNA Part X - mtDNA Subclades
mtDNA Part XI - mtDNA Haplogroup H
mtDNA Part XII - Subclades of mtDNA Haplogroup H
mtDNA Part XIII - Distribution of Subclades of H
mtDNA Part XIV - Descendents of Maria-Theresa
mtDNA Part XV - Luke the Evangelist
mtDNA Part XVI - Empress Feodorovna
mtDNA Part XVII - James “Earthquake McGoon” McGovern  <<– you are here

In the last three blogs, we have been discussing the topic of how anthropologists have used mtDNA to solve historical questions.  In particular, we have been focusing on the analysis of historical figures who may have belonged to Haplogroup H, one of the largest European Haplogroups.  We will wrap up our Haplogroup H series with this case about a World War II fighter ace and CIA pilot who died in combat in Vietnam. 

Case #4:  James “Earthquake McGoon” McGovern

Who was he?

James McGovern was a World War II fighter ace who died in a plane crash in Laos on May 6, 1954 when the Civil Air Transport plane that he was flying to provide ammunition to French troops was hit by groundfire.  McGovern and Buford (an American co-pilot) and two French Corporal Chiefs were killed instantly, making McGovern and Buford the first two Americans to die in combat in Vietnam. 

The source of his nickname:

At six feet and 260 pounds, McGovern was considered large for a fighter pilot, prompting his nickname “Earthquake McGoon” after the fierce and primitively charismatic (hulking hillbilly) wrestler from the popular Li’l Abner comic strip.

What were the anthropologists trying to find out? ie why was his DNA tested?

Between 1997 and 2002, multiple investigations of the site of incident were done by different teams (including joint US-Lao teams); however, only small fragments of aircraft wreckage were found, but no human burial sites were located.  In 2002, while investigating an unrelated crash near the Ban Sot area, the JTF-FA team discovered an old C-119 (the type of plan that McGovern was flying) propeller.  A few months later, human remains of a single individual were discovered from an unmarked grave, leading to speculation that the grave may have belonged to James McGovern.

The main purpose of the project was to determine whether the remains belonged to James McGovern.

Who’s Who in researching this project:

• Irwin et al from Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Rockville, USA.
• Holland et al from Joint POW/MIA Accounting Command - Central Identification Laboratory, Hawaii, USA

Top peer reviewed research publications for genetic identification of James McGovern: