The following table outlines the Y-DNA STR markers available at Genebase and the corresponding motifs used for allele designation in Version 3.5. 

Click here to view the conversion chart for Version 3.3 to Version 3.4. 

Click here to view the conversion chart for Version 3.4 to Version 3.5. 

Please note that Users from previous versions will be automatically converted to 3.5.

 *Variable regions in each motif are indicated in blue.

*Motifs used for allele designation in Version 3.5 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. 

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).  

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:

This table lists the most significant papers for the James McGovern case and the DNA tests that were performed to identify his remains in peer reviewed journals.  Links are provided to access the original articles.

These papers provide the extent of what is known today about the DNA of James McGovern and provides answers to the question of whether the remains discovered in the grave belong to the James McGovern.

As further information becomes available, this table will be updated.

Solving the case: Collecting DNA samples

The first step in solving the case involved collecting DNA samples from the remains and locating living relatives of James McGovern for DNA testing. 

1. The remains:  DNA was extracted from the left femur obtained in the excavation (putative McGovern).
2. The relatives:  DNA samples were collected from living relatives of James McGovern including: 1 maternal cousin (McGovern’s mother’s sister’s son), 1 sister-in-law, 4 nieces (daugthers of sister-in-law), 1 nephew (sone of sister-in-law)

The relationship of each individual tested in relation to James McGovern are shown in the pedigree below:

The DNA testing process:

Mulitple DNA testing types were performed on the remains and the relatives.  To follow are the DNA test types used in this study:

1. mtDNA HVR1 and mtDNA HVR2 sequencing - to confirm maternal lineage
2. mtDNA SNP testing - to supplement the HVR1 and HVR2 results by improving the discrimination power of the test
3. Autosomal STR testing - to confirm relationships
4. Y-DNA STR testing - to confirm paternal lineage

The goal of the various test types is to firmly establish the identity of the remains by looking for proof of relationship along the maternal and paternal lines to known descendents of McGovern’s family.

Results of the DNA tests:

Summary of Results:

The results of the DNA tests were able to confirm the following:

1. The mtDNA profile of the Remains was identical to the mtDNA profile of McGovern’s Maternal Cousin.
2. The Y-DNA STR haplotype of the Remains was identical to the Y-DNA STR haplotype of McGvoern’s Paternal Nephew.

Based on statistical analysis of data available, the likelihood ratio that the Remains belong to a male individual who is related to McGovern’s living family members is 96,900, thus successfully establishing that the remains are indeed those of McGovern who died in 1954.

According to Dr. Thomas Holland (director of JPAC’s Central Identification Laboratory), McGovern was the second person ever identified by their laboratory through forensic analysis of Y-DNA.  Most cases involving old and highly degraded samples tend to rely on mtDNA analysis since mtDNA is far more stable than Y-DNA when examining extremely old or degraded samples. 

The Aftermath:

A military funeral was held in New Jersey on October 28, 2005 to honor this well-known US military pilot. 

Haplogroup Analysis:

Although the original researchers did not intend to determine the haplogroup of James McGovern, amateur genetic genealogists have stated that McGovern belonged to Haplogroup H.  Let’s take a look at how they have arrived at this conclusion:

Step 1:  To begin, click here to download the mtDNA Haplogroup Map.  You will need to use this map to follow along in this discussion.

Step 2:  Identify the presence and absence of McGovern’s mtDNA markers on the map.  Starting from the CRS, move outwards and cross off all markers that McGovern does not have, circle all of the markers that he does have and put a question mark next to the markers that have not been tested:

Based on the coding region results, McGovern is negative for the marker 7028, thus excluding him from all haplogroups except Haplogroup H.  The absence of markers in his HVR1 (except for 16519), and the absence of coding region marker 4580 further suggests that McGovern belongs to Haplogroup H. 

Can we determine his subclade?

If McGovern is truly a member of Haplogroup H, let’s see if we can find out which Subclade of H he belongs to.  To proceed, click here to download and print the H Subclade map, as you will need it to follow along with this discussion.

Again, circle the markers that McGovern does have and cross out the markers that McGovern definitely does not have.  In this case, we will leave all unknown markers untouched.

McGovern is positive for the coding region marker 3010, which is a defining marker for Subclade H1.  However, he is negative for 477, indicating that he is not from sublineage H1c, and he is negative for 12858, indicating that he is not likely H1c2.  Other coding results indicate that McGovern is negative for 5004, indicating that he is not likely H4; he is negative for 4793, indicating that he is not likley H7; and he is negative for 14470, indicating that he is not likely H10. 

Based on the known DNA markers results for McGovern obtained to date, it is safe to conclude that he is very likely a member of Haplogroup H.  If he is indeed a member of Haplogroup H, his most likely a descendent of Subclade is H1.  However, in order to confirm his Subclade, a Subclade test would be required to examine markers 1638, 6776, 13101, 4310, 8448, 3936, 14872, 11377, 6352, 1039, 3915, 13708, 14869 and 8494 to exclude the possibility of other H Subclades, including H2, H3, H8, H9, H11, H12, H13, H14, H15, H16, H17, H18, H19, and H21.  Other markers that would be useful to examine are 6365, 8271, 3796, 9066 and 9150 to determine which further sublineage of H1 he belongs to. 

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. 

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. 

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  <<– you are here
mtDNA Part XVII - James “Earthquake McGoon” McGovern

In the last few blogs, we have been discussing the topic of how anthropologists have used mtDNA to solve historical questions.  In this blog, we will continue our analysis of historical figures who may have belonged to haplogroup H.

Case #3:  Empress Alexandra Feodorovna of Russia

Who was she?

Empress Alexandra Feodorovna of Russia, the granddaughter of Queen Victoria was born on June 6, 1872 as Princess Alix of Hess and by Rhine in Darmstadt (Germany).  She was the sixth child of Grand Duke Louis IV of Hesse and by Rhine and Princess Alice of the United Kingdom.  She was the princess consort of Nicholas II, and the last Tsaritsa of Russia. 

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

At the end of the February Revolution of 1917, Tsar Nicholas II was forced to abdicate.  The Romanov family were imprisoned in Ipatiev House at Ekaterinburg in the Urals of Central Russia in 1918 with three servants and the family doctor.  On the night of July 16, 1918, the entire Romanov family was shot and killed by the Bolshevik firing squad. 

According to legend, two bodies were burnt and the others were buried in a roadside pit.  To hinder identification, sulphuric acid was said to have been thrown into the open grave and a truck was driven back and forth over the grave. 

The case remained a mystery until July 1991, when nine human skeletons were discovered in a shallow pit around 20 miles from Ekaterinburg, Russia.  Historians speculated that the remains belonged to the Romanov family.  To help solve the mystery, DNA testing was performed to identify the remains.

Who’s who in researching the history of the Romanov family:

• Gill et al. from the Central Research and Support Establishment, Forensic Science Service, Aldermaston, Reading, Berkshire, UK
• Ivanov et al. from Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
• Hagelberg et al. from Department of Biological Anthropology, University of Cambridge, Cambridge, UK
• Wadhams et al. from Armed Forces DNA Identification Laboratory, Office of the Armed Forces medical Examiner, Armed Forces Institute of Pathology, Rockville, Maryland, USA
• Hofreiter et al. from Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
• Loreille et al. from Armed Forces DNA Identification Laboratory, Office of the Armed Forces medical Examiner, Armed Forces Institute of Pathology, Rockville, Maryland, USA
• Knight et al. from Department of Anthropological Sciences, Stanford University, Stanford, USA
• Zhivotovsky et al. from Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
• Kass et al. from Department of Biology, Eastern Michigan University, Ypsilanti, USA
• White et al. from Bioscience Division, Los Alsmos national Laboratory, Los Alamos, USA
• Mountain et al. from Department of Genetics, Standford University, Stanford, USA

Top peer reviewed research publications for Tsarina Alexandra and the Romanov family:

This table lists the most significant papers for the Romanov family and the DNA tests that were performed to identify their remains in peer reviewed journals.  Links are provided to access the original articles.

These papers provide the extent of what is known today about the DNA type of Tsarina Alexandra and provides answers to the question of whether the bodies discovered in the grave belong to the Romanov Family.

As more articles become available, they will be listed here.

Solving the case:  Collecting DNA samples from the Ekaterinburg remains

The first step in solving this case is to test the DNA of the Ekateringburg remains.  After the DNA type of the remains is known, it can be compared to the DNA type of known relatives in the royal family.  Since Tsarina Alexandra is the maternal granddaughter of Queen Victoria (Queen Victoria is her mother’s mother), Tsarina Alexandra must have inherited her mtDNA from Queen Victoria.  A living descendent of Queen Victoria who carries Queen Victoria’s mtDNA type is Prince Philip.  The following diagram shows in purple how the mtDNA is passed down from Queen Victoria to her descendents and which one of her descendents carry her mtDNA:

Individuals who inherited the mtDNA type of Queen Victoria are highlighted in purple.

The descendent tree for Queen Victoria indicates that Tsarina Alexandra should have the same mtDNA profile as Prince Philip as well as other living and deceased descendents from the same line.  By collecting the DNA sample from known family members, scientists can find out the expected mtDNA type for Tsarina Alexandra and her children and use it to identify the remains.

Who was tested to solve this case?

1. A blood sample was collected from Prince Philip, a living descendant of Queen Victoria (maternal grandmother of Tsarina Alexandra).
2. Bone fragments from each of the nine skeletal remains found in Ekaterinburg.

Three Types of DNA tests were performed to confirm the identity of the Ekateringburg remains:

1. Gender determination:  To identify the gender of each of the nine skeletal remains.
2. Autosomal STR testing:  To determine whether the nine skeletons are related to each other, ie in the same family.
3. Mitochondrial HVR1 and HVR2 sequencing:  To examine whether the skeletal remains are members of the Romanov family by comparing the mtDNA profile of the remains to the mtDNA of known royal family members.

Step 1:  Autosomal STR Testing:  To determine whether the 9 skeletons are related to each other

Autosomal STR testing (the same technology used for paternity testing) was used to determine whether the nine skeletons are from the same family. 

The results of the autosomal test confirmed the following:

1. Skeletons 3, 4, 5, 6, and 7 belonged to the same family.
2. Skeletons 3, 4, 5, 6 and 7 are likely a family group consisting of three children and both of their parents. 
3. Skeletons 1, 2, 8, 9 are not related to skeletons 3, 4, 5, 6, and 7.

This information is consistent with the skeletons belonging to members of the Romanov family. 

Step 2:  Determining the gender of the skeletons

The next set of tests sets out to determine the gender of the skeletons.

The results of the gender determination tests showed that four of the skeletons are male and one was female.  The combined results of the autosomal test and gender test leads to the speculation that skeleton #4 is the father, skeleton #7 is the mother, and skeletons 3, 5, and 6 are their daughters.

Step 3:  What if the skeletons belonged to the Romanov family?

If the remains truly belong to the Romanov family, then:

• Skeleton 4 “father” should belong to Tsar Nicholas II
• Skeleton 7 “mother” should belong to Tsarina Alexandra
• Skeletons 3, 5, and 6 are three of their 4 daughters

The next step is to confirm the speculated identities by comparing each skeleton to living royal family members. 

Step 4:  Solving the mystery.  Confirming the identity of Skeleton #7, Tsarina Alexandra and her daughters, Skeletons 3, 5, and 6

Now that the preliminary studies indicate the possible identities of each of the skeletons, the next step is to confirm the identity by comparing to the DNA of living royal family members.  Tsarina Alexandra is the grandaughter of Queen Victoria, and her mtDNA should be identical to the mtDNA of Prince Philip, a living descendent of Queen Victoria. 

The next step is to test the mtDNA of Prince Philip and compare it to the mtDNA of the skeletons.

Prince Philip’s mtDNA:

Prince Philip is a direct descendent of Queen Victoria and he carries the mtDNA type of Queen Victoria. 

The mtDNA of the Skeletons:

 Conclusion:  The results of the mtDNA test confirm the following:

1. The putative Tsarina Alexandra’s mtDNA (skeleton 7) is a perfect match to the mtDNA profile of Prince Philip, indicating that it is the actual skeleton of Tsarina Alexandra.
2. Tsarina Alexandra’s mtDNA is a perfect match to the mtDNA profile of Skeletons 3, 5, and 6, her putative daughters.
3. Skeletons 3, 5, and 6 are also identical to Prince Philip’s mtDNA, indicating that they are the actual skeletons of Tsarina Alexandra’s daughters.
4. The putative Tsar Nicholas II’s mtDNA (skeleton 4) does not match the mtDNA of Prince Philip.  This is expected since Tsar Nicholas II is not a direct descendent of Queen Victoria.  We will discuss the set of analysis that was conducted to confirm the identity of Tsar Nicholas II in a separate blog.

In summary, the DNA studies confirm that five out of the nine skeletons discovered truly belonged to the Romanov family, namely Tsar Nicholas II, Tsarina Alexandra, and 3 of their 4 daughters.  The skeleton of one of their daughters and their only son, Alexei, remain missing.

The Aftermath:  Doubts and Controversies

Since the findings, the skeletons were reburied with honors in the imperial-era capital of St. Peterburg.  The two remaining children remain missing.

The scientific findings and results have since been challenged by Knight et al, suggesting irregularities and sample handling deficiencies.

Recent Findings from the summer of 2007

In the summer of 2007, using metal detectors and metal rods as probes, two burned partial skeletons were discovered at a bonfire site near Ekaterinburg, 900 miles east of Moscow.  15 intact bone fragments and more than 40 pieces of charred bone were discovered.

The site appeared to match the site described in Yurovsky’s (the Bolshevfik officer in charge of the Romanovs’ captivity) memoirs.  According to his memoirs, the bodies of nine victims were doused with sulphuric acid and buried along a road.  Alexei’s body and one of his sister’s bodies was burned and left in a pit nearby

Preliminary analysis of the bones showed that the remains were from a boy roughly between the ages of 10 to 13 years old at the time of death, the putative Alexei and a young woman roughly between the ages of 18 to 23 years old at the time of death, attributed to one of the Romanov daughters, likely Maria or  Anastasia.

Genetic investigations were performed in the Sverdlovsk Regional Forensic Medicine Bureau, a lab in Moscow, and a US laboratory, the University of Massachusettes Medical School. 

On April 30, 2008, the groups claimed that DNA testing (mainly mitochondrial DNA analysis) proved that the remains belonged to Tsarevich Alexei and one of his sisters (likely Maria) were released in several major newspapers and news sources (including New York Times, BBC, and MSNBC).

What is the haplogroup of Queen Victoria’s descendents?

Now that the mtDNA type of Queen Victoria’s line is known, amateur genealogists from around the world have used the data to compare to their own families to see if they may have links to royalty.

Although the original researchers never attempted to use the data from the study to determine the haplogroup of this royal family line, amateur genealogists have tried t use the data from the study to determine the mtDNA haplogroup of Queen Victoria’s line, concluding that Queen Victoria and her descendent Tsarina Alexandra belonged to Haplogroup H.  Let’s take a look at the raw data and see how accurate they are.

Step 1:  Click here to download and print the mtDNA Haplogroup map so that you can follow along with the discussion.

Step 2:  Identify the presence and absence of HVR1 markers on the map.

Tsarina Alexandra only had two HVR1 markers, namely 16111 and 16357.  On the map, all HVR1 markers are in blue.  Starting from the CRS, move outwards and cross off all of the HVR1 markers that Tsarina Alexandra does not have, circle the ones that she does have and put a question mark next to the ones that are unknown:

The results of the HVR1 test helps to eliminate the haplogroups that Tsarina Alexandra definitely does not belong to, and shows that Tsarina Alexandra must belong to either Haplogroup R, Pre-HV, HV, H, or the CRS branch of H.

Step 3:  Identify the presence or absence of HVR2 markers on the map:

Tsarina Alexandra has 2 markers in her HVR2 region, namely 263 and 315.1.  On the map, all HVR2 markers are red.  Starting from the CRS, move outwards and cross off all of the HVR2 markers that Tsarina Alexandra does not have and circle all of the HVR2 markers that she does have:

The results of the HVR2 test helps to eliminate Haplogroup R and shows that Tsarina Alexandra must belong to either Haplogroup Pre-HV, HV, or H.  Tsarina Alexandra has marker 263 which brings her away from CRS, indicating that she is unlikely to belong to CRS, but the presence of 263 cannot eliminate her from CRS as such a conclusion woudl require more data from the coding region.

In conclusion, the results of the scientific studies show that Tsarina Alexandra can belong to any one of the following Haplogroups:

• H
• HV
• Pre-HV

These results are similar to those of Marie Antoinette, even though the exact mtDNA mutations that they carry are slightly different.  To confirm whether Tsarina Alexandra is really a member of Haplogroup H, one would need to test the coding region of her mtDNA to confirm that she does not have markers 7028 and 14766.  However, no coding region data was ever available for Tsarina Alexandra or for any of her living or deceased relatives, so there is no way to confirm that she is a member of Haplogroup H.  Since the original researchers were aiming to identify her remains rather than to determine her haplogroup, the coding region was never examined and in this particular case, coding region SNP test is required to confirm her haplogroup.

In conclusion, it is pre-mature to conclude that Tsarina Alexandra is a member of Haplogroup H, but the data from the studies to date do serve to narrow down her possible haplogroups to H, HV, and Pre-HV.  Further studies woud need to focus on markers 7028 and 14766 in the coding region which would provide a determination of which Haplogroup Tsarina Alexandra actually belongs to, and if she does in fact belong to Haplogroup H, further H subclade testing using the H subclade test panel should confirm which branch of H she falls into.

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  <<– you are here
mtDNA Part XVI - Empress Feodorovna
mtDNA Part XVII - James “Earthquake McGoon” McGovern

In the last blog, we began discussing how anthropologists have used mtDNA to solve historial questions.  In this blog, we will continue our analysis of historical figures who may have belonged to haplogroup H.

Case #2:  Luke the Evangelist

Who was he?

Luke the Evangelist is the patron saint of physicians and surgeons and his feast day is October 18.  He is said to be the author of the third Gospel and the Acts of the Apostles.  Luke was born in the city of Antioch (an ancient city in the Roman province of Syria, present day Antakya, Turkey).  He died around A.D. 150 at the age of 84 years in Thebes, the capital of Boeotia, Greece. 

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

Although the body of Saint Luke was initially buried in Thebes, it was later transfered from Greece to Constantinople (capital of the Byzantine Empire, present day Istanbul, Turkey) during the second year of reign of emperor Constantius around A.D. 338.  The body was transferred a second time around A.D. 1177, this time from Constantinople to its current resting place in Pauda, Italy. 

Figure 1:  The transfer of the body of Saint Luke

Historians have long questioned the identity of the body attributed to Saint Luke that now lies in Padua, Italy.  In particular, they wonder whether the body may have been replaced in Greece or Turkey and are curious about whether the body was of Syrian origin (the location of St. Luke’s birthplace) or of Turkish or Greek origin (the locations where the body may have been replaced).  Using modern DNA technology, anthropologists set out to answer this question by obtaining DNA samples from the body attributed to Saint Luke and comparing it to the mtDNA type of population samples from Syria, Turkey and Greece to see if they can determine the most likely geographic origin of the body.

Who’s who in researching the history of Saint Luke:

The main research groups studying this area are:

• Vernesi et al from the Department of Biology, University of Ferrara, Ferrara, Italy
• Caramelli et al from Institute of Anthropology, University of Florence, Florence, Italy
• Simoni et al from Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Geneva, Switzerland
• Malaspina et al from Department of Biology, University of Rome, Rome, Italy
• Novellotto et al, Department of Biology, University of Calabria, Arcavacata di Rende, Italy
• Marin et al, Institute of Pathological Anatomy, Univerity of Padua, Padua, Italy

Table 1:  Top peer reviewed research publications for Saint Luke

This table lists the most significant papers for Luke the Evangelist’s DNA profile in peer reviewed journals, with links to access the original publications. 

These papers provide the extent of what is known today about the DNA type of Luke the Evangelist and provides answers to the question of whether the body attributed to Luke the Evangelist belongs to a Greek or a Syrian.

As new papers become available, they will be added to this list.

Investigating the case:  Collecting a DNA sample from the body attributed to Saint Luke and collecting DNA samples from individuals from Greek and Syria:

The first step in solving the mystery is to decode the mtDNA of the body attributed to Saint Luke.  Once the mtDNA code is known, it can be compared to the mtDNA code from individuals from different parts of Europe to gain clues into the ancestral origin of the body. 

First step:  Collecting DNA from the body attributed to Saint Luke in Italy:

What was collected?  A whole canine tooth, a tooth root and some bone fragments were collected from a sarcophaagus containing the body traditionally attributed to St. Luke.  Only the whole canine tooth contained sufficient DNA to perform the DNA test and subsequent studies focussed on DNA obtained from the tooth.

What were the results? 

The researchers sequenced the HVR1 region of the mtDNA extracted from the tooth.  No analysis was performed on the HVR2 region.  The researchers also tested a single SNP marker, namely marker 7028 from the coding region of the mtDNA.

The next step:  Gathering mtDNA from individuals from Syria, Greece, and Turkey

Next, the researchers obtained the mtDNA HVR1 sequence for individuals from Syria, Greece and Turkey for comparison with the results of the mtDNA from the body attributed to Saint Luke.

What was concluded from the results?

Upon comparing the HVR1 region of the mtDNA obtained from the body attributed to Saint Luke against the HVR1 region of the mtDNA from individuals currently living in Syria, Greece and Turkey, the researchers found the closest match to individuals from Syria.  The researchers claimed that statistical interpretations of the data suggest that the match to individuals from Syria was three time greater than the match to individuals from Greece, and the also detected a slightly closer matching frequency to people from Syria versus people from Turkey.  The results of this study indicate that the body is most likely of Syrian origin, the original birthplace of Saint Luke, thus helping to dispel theories that the body was replaced which it was transfered to Greece or Turkey.

Further studies comparing more regions of the mtDNA, including the HVR2 region and coding region as well as studies comparing the DNA from the body to a larger group of people from Syria, Greece, and Turkey would increase the power of this study.

The aftermath:  What has happended since this study was completed?

With the mtDNA HVR1 region of Luke the Evangelist known, amateur genealogists from around the world have used the data to compare to their own familites to see if they have any ties to Luke’s maternal family line.

Although no in depth haplogroup analysis was performed by the original scientists, amateur genealogists have tried to use the data from the study to determine the mtDNA haplogroup of Luke the Evangelist, stating that he belongs to haplogroup H.  Let’s take an in depth look at the raw data and see how accurate they are.

Step 1:  Click here to download and print the mtDNA Haplogroup map so that you can follow along with the discussion.

Step 2:  Identify the presence and absence of Saint Luke’s HVR1 markers on the map.

Saint Luke has two markers in his HVR1 region, namely 16235 and 16291.  On the map, all HVR1 markers are blue.  Starting from the CRS, move outwards and cross off all of the HVR1 markers that Saint Luke does not have, circle all of the markers that he does have, and put a question mark next to the markers that have not been tested:

The results of the HVR1 test helps to eliminate the haplogroups that Saint Luke definitely does not belong to, and shows that Saint Luke must belong to either haplogroup R, Pre-HV, HV, or H.  However, the results of the SNP test for coding region marker 7028 indicates that Saint Luke is positive for the 7028 marker, which brings him away from haplogroup H, towards haplogroups HV, Pre-HV, or R. 

Based on the results of Saint Luke’s mtDNA test, it is impossible, even possibly erroneous, to conclude that Saint Luke belongs to haplogroup H since there is not sufficient information from the HVR1 test results to reach that conclusion. 

The results of scientific studies to date show that Saint Luke can belong to any one of the following Haplogroups:

• HV
• Pre-HV
• R

The presence of marker 7028 brings Luke away from haplogroup H, but further studies would be required in order to exclude H.

In conclusion, it is premature or even erroneous to conclude that Saint Luke belongs to haplogroup H, and data so far suggests that Saint Luke more likely belongs to HV, Pre-HV, or R.  Further studies would need to focus on markers 11719 and 14766 in the coding region, and 73 and 263 in the HVR2 region, which would provide a conclusive determination of which haplogroup Saint Luke actually belongs to.

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  <<– you are here
mtDNA Part XV - Luke the Evangelist
mtDNA Part XVI - Empress Feodorovna
mtDNA Part XVII - James “Earthquake McGoon” McGovern

We have now had a chance to talk about mtDNA, what it is, what it tells us, and how mtDNA testing works.  Now, lets take a look at a fun topic and see how anthropologists have used mtDNA to help solve historical questions.  Since we have been focusing on mtDNA haplogroup H in the last few blogs, we will continue on that note and talk about some historical figures who may have belonged to haplogroup H.

Case #1:  The descendents of Maria-Theresa, Holy Roman Empress:  Using mtDNA to track the case of Louis XVII, son of Marie Antoinette

Marie-Antoinette (1755-1793), was executed in 1793 in Paris.  After her execution, her son and daughter remained imprisoned in the Temple of Paris.  According to official records, her son, Louis-Charles died of tuberculosis in the Temple on June 8, 1795.  Thoughout history, historians have wondered whether the boy who died in the Temple was truly Louis-Charles, or whether Louis-Charles had escaped and survived.  To add to this speculation, several individuals later claimed to be the son of Marie Antoinette.  The most notable was Wilhelm Naundorff, who died in 1845 and was buried under the name of Louis-Charles Duc de Normandie, ‘Louis XVII’, and his descendents were permitted to use the name ‘de Bourbon’, the name of the French royal family.

This case remained a mystery for historians for over a century, until modern DNA testing allowed historians to finally put this case to rest.  The studies conducted focused on testing the mtDNA of the remains of Wilhelm Naundorff and forensic samples from various members of Marie Antoinette’s family, descendents of Marie Antoinette’s mother, Maria-Theresa, Holy Roman Empress.

Who’s who in researching the history of Marie Antoinette’s family:

The main research groups studying this area are:

• Jehaes et al from Center for Human Genetics, University of Leuven, Belgium
• Peneau et al from Laboratoire de Genetique Moleculaire, CHRU, Nantes, France
• Petrie et al from Petrus Campussingel, Groningen, The Netherlands
• Boiry et al from Faculte Libre des Sciences de la Communication, Levallois-Perret, France

Table 1:  Top peer reviewed research publications for Marie Antoinette

This table lists the most significant papers for Marie Antoinette’s DNA profile in peer reviewed journals, with links to access the original publications.  These papers provide the extent of what is known today about the DNA type of  Maria-Theresa’s descendents and provides answers to the question of the true fate of Marie Antoinette’s son, Louis XVII.

Solving the case:  Collecting the DNA sample from royal family members:

The first step in solving this mystery is to find DNA clues for the royal family.  Since Louis-Charles is the biological son of Marie Antoinette, the true biological son of Marie Antoinette must have inherited his mtDNA from Marie Antoinette.  Marie Antoinette is a maternal descendent of Empress Maria-Theresa.  The following diagram shows in purple how the mtDNA is passed down from Maria-Theresa to her descendents and which one of her descendents carry her mtDNA:

The next step:

The descendent tree of Maria-Theresa indicates that the true Louis XVII should have the same mtDNA as Marie Antoinette as well as living descendents from the same line.  By collecting the DNA sample from living family members and collecting forensic samples from deceased members, scientists can find out the expected mtDNA type for the true Louis XVII.

Who was tested to solve this case?

A DNA sample was collected from the following descendents of Maria-Theresia:

1. A DNA sample was collected from a hair sample from Johanna-Gabriela (Marie Antoinette’s sister) - hair samples were removed from a rosary with medalions containing hair from Johanna-Gabriela.
2. A DNA sample was collected from a hair sample from Maria-Joseph (Marie Antoinette’s sister) - hair samples were removed from a rosary with medalions containing hair from Maria-Joseph.
3. A DNA sample from Marie Antoinette was collected from two sources.  The first source was medallions kept in a private collection in Cannes.  The second was hair that was taken from a document containing a lock of hair fixed with a silk thread belonging to Marie-Antoinette.
4. Queen Anne of Romania’s blood sample (a living descendent of Maria-Theresia). 
5. Andre de Bourbon Parme’s hair sample (a living descendent of Maria-Theresia).

A DNA sample was collected from the following specimens:

1. A piece of heart tissue from the boy who died in the Temple of Paris on June 8, 1795 - the heart was removed during autopsy in 1795 and preserved in a crystal urn at the Basilique Saint-Denis.
2. A bone sample obtained from the coffin of Carl Wilhelm Naundorff, who claimed to be Louis XVII, son of Marie Antoinette - hair samples and the right humerus, both removed from skeletal remains when Naundorff’s coffin was opened in 1950 for a different study.

Table 2:  The results of the mtDNA test:

In this study, the researchers tested the HVR1 region and HVR2 region of the mtDNA but did not test the Coding region.  Since many of the forensic samples were extremely old, the DNA was of extremely poor quality.  The quality of the DNA for each individual is listed in the table below together with the results.

The results for some of the ancient samples yielded partial and incomplete data.  As a result, the final mtDNA for Maria Theresa must also include the examination of living descendents for further confirmation. 

What was concluded from the results?

The ancient hair samples from Marie Antoinette and her two sisters were of extremely poor quality, and even though the samples were repeatedly tested several times by the researchers, only a partial profile could be obtained.  To supplement the findings from the ancient samples, a fresh blood sample and hair sample was obtained from living descendents of Maria Theresa, including a blood sample from Queen Anne of Romania and a hair sample from her brother, Andre de Bourbon Parme.  The final results of the study indicated the following mtDNA type for Maria Theresa and all of her true biological maternal line descendents:

The significance of this profile is that it is the key to all maternal line descendents of Maria Theresa.  All descendents of this line, including descendents living today, must carry this mtDNA profile.

Solving the mystery

Once the mtDNA type for descendents of Maria Theresa was obtained, the next task was to compare the mtDNA profile to Carl Wilhem Naundorff:

Conclusion:  The mtDNA type of Carl Wilhelm Naundorff was different from the mtDNA of true biological descendents of Maria Theresa’s maternal line, proving that Carl Wilhelm Naundorff was an imposter and not Louis XVII.

The next task was to compare the mtDNA type for the descendents of Maria Theresa to the mtDNA profile obtained from the heart of the boy who died in the Temple of Paris to see if the boy who died was truly Louis XVII.

Conclusion:  The mtDNA type of the heart from the boy who died in the Temple in 1795 was a perfect match to the mtDNA of tue biological descendents of Maria Theresa’s maternal line, indicating that the boy who died in 1795 was the true Louis XVII.

The aftermath:  What has happened since this study was completed?

Now that the mtDNA type of the descendents of Maria Theresa’s line is known, amateur genealogists from around the world have used the data to compare to their own families to see if they may have links to royalty. 

Although the original researchers, Jahaes et al, never attempted to use the data from the study to determine the haplogroup of this royal family line, amateur genealogists have tried to use the data from the study to determine the mtDNA haplogroup of Marie Antoinette, the most famous descendent of Maria Theresa, concluding that Marie Antoinette belongs to Haplogroup H.  Let’s take a look at the raw data and see how accurate they are.

Step 1:  Click here to download and print the mtDNA Haplogroup map so that you can follow along with the discussion.

Step 2:  Identify the presence and absence of HVR1 markers on the map

Marie Antoinette only has one HVR1 marker, namely 16519.  On the map, all HVR1 markers are in blue.  Starting from the CRS, move outwards and cross off all of the HVR1 markers that Marie Antoinette does not have:

The results of the HVR1 test helps to eliminate the haplogroups that Marie Antoinette definitely does not belong to, and shows that Marie Antoinette must belong to either Haplogroup, R, or Pre-HV, or HV, or H or the CRS branch of H. 

Step 3:  Identify the presence or absence of HVR2 markers on the map

Marie Antoinette had four markers in the HVR2 region, namely, 152, 194, 263, and 315.1.  On the map, all HVR2 markers are in red.  Starting from the CRS, move outwards and cross off all of the HVR2 markers that Marie Antoinette does not have and circle the HVR2 markers that she has:

The results of the HVR2 test helps to eliminates Haplogroup R, and shows that Marie Antoinette must belong to either Haplogroup, Pre-HV, or HV, or H or the CRS branch of H.  Marie Antoinette has marker 263 which brings her away from CRS.  However, the presence of 263 cannot eliminate her from CRS either (click here to view the H subclade map), as such a conclusion would require more data from the coding region. 

In conclusion, the results of the scientific studies show that Marie Antoinette can belong to any one of the following Haplogroups:

• H
• HV
• Pre-HV

To confirm whether Marie Antoinette is really a member of haplogroup H, one would need to test the coding region of her mtDNA to confirm that she does not have markers 7028 and 14766.  However, no coding region data was ever available for Marie Antoinette or for any of her living or decease relatives, so there is no way to confirm that she is a member of Haplogroup H.  The absence of coding region data is not unexpected since the scientists in the original study were never aiming to determine her haplogroup, so the coding region was never investigated. 

In conclusion, it is premature to conclude that Marie Antoinette is a member of haplogroup H, but the data from the studies to date do serve to narrow down her possible haplogroups to H, HV, and Pre-HV.  Further studies would need to focus on markers 7028 and 14766 in the coding region which would provide a determination of which haplogroup Marie Antoinette actually belongs to, and if she does in fact belong to haplogroup H, then Haplogroup H subclade testing should confirm which branch of H she falls into. 

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  <<– you are here
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

In the previous blog, we talked about the Subclades of mtDNA Haplogroup H and discussed what is currently known about the Subclades.  In this blog, we will discuss what is known about the geographical distribution pattern of the Subclades of H based on the latest peer reviewed research data and provide a summary reference table and map for the Subclades of H which you can download and print.

Geographical Distribution of the Subclades of H

The following reference table summarizes what is known today about the geographical distribution of the Subclades of Haplogroup H.  The studies were conducted by sampling the DNA of indigenous populations from around Europe, the Caucasus and Central Asia and determining which percentage belonged to Haplogroup H versus other Haplogroup types.  For individuals who were confirmed to belong to Haplogroup H, further analysis was performed in the coding region of the mtDNA to determine which Subclade of H they belonged to in order to derive an understanding of the geographical distribution pattern of the individual Subclades of H.

As more data on the Subclades of H become available, this table will be updated.

The following reference map illustrates how Haplogroup H is distributed throughout Europe and also summarizes the distribution pattern of the Subclades of H.

In the next blog, we will wrap up our mtDNA discussion by looking at some notable people in history who belonged to Haplogroup H.

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  <<– you are here
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

In the previous blog, we talked about mtDNA Haplogroup H and introduced the “Subclades of H”.  In this blog, we will discuss what is currently known about the subclades of H. 

Let’s take a closer look at the Subclades of H

Due to the large size of Haplogroup H and its wide distribution, there has been much research recently on the sub-clades of H, which surprisingly shows more restricted and regional geographic distributions. 

A study of the mtDNA of Haplogroup H individuals by examining the HVR1, HVR2 and control region of the mtDNA reveals a very large number of independent sub-branches, giving rise to subclades which have several further sub-branches themselves.  Studies to date reveal defined geographical patterns for Subclades H1 and H3.  All other subclades of H are found at a lower frequency and studies to reveal detectable geographic patterns are still ongoing. 

The following table summarizes what is known today about the subclades of Haplogroup H: (this table is based on a summary of current research published in peer reviewed journals and will be updated as more scientific data becomes available for the subclades of H)

In the next blog, we will begin to wrap up our discussion of mtDNA Haplogroup H by providing a detailed Haplogroup H distribution map.