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. 

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.

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  <<– you are here
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

In the last blog, we introduced “Subclades”, which are the finer branches of the Haplogroup tree.  One of the most well studied is mtDNA Haplogroup H.  In the next few blogs, we will discuss the latest research findings for mtDNA Haplogroup H and its subclades.

Who’s who in the field of Haplogroup H Research

Studies have shown that Europeans fall into one of several main mtDNA haplogroups:  H, I, J, K, N1, T, U2e, U3, Ur, X, W, U5, and V.  Haplogroup H is one of the most dominant family groups in Europe, representing approximately 40% of the mtDNA gene pool in populations in various parts of Europe and extending as far as western Asia.  Recent publications by the following researchers have provided significant advances in our understanding of Haplogroup H and its subclades:

• Roostalu et al. from the University of Tartu and Estonian Biocentre, Estonia
• Brandstatter et al. from the Innsbruck Medical University, Austria
• Pereira et al. from Universidade to Porto, Portugal
• Grignani et al. from Universita di Pavia, Italy
• Loogvali et al. from University of Tartu, Estonia
• Achilli et al. from Universita di Pavia, Italy

Table 1: Top peer reviewed research publications for mtDNA Haplogroup H 

This table lists the most significant papers for Haplogroup H in peer reviewed journals, with links to access the original publications.  These papers have provided significant advances in the current understanding of Haplogroup H and form the basis for the Haplogroup H subclade test panel. 

Let’s summarize the peer reviewed findings to date for Haplogroup H:

Several of the recent papers aim to provide resolution for the distribution of Haplogroup H and its subclades and begin to answer the fundamental questions of the origins of Haplogroup H:  where did it come from and where is it most concentrated in Eurasia?

To follow is a summary of what is currently known about Haplogroup H.  As more details are confirmed, this list will be updated: 

Despite the broad geographic distribution pattern of Haplogroup H, further investigation of each Subclade of Haplogroup H provides further resolution and reveals a much more specific and distinctive distribution pattern for each Subclade of Haplogroup H.

Haplogroup H is the most prominent European Haplogroup, and the papers were able to successfully sub-classify members in Haplogroup H into subclades H1 to H16 based on characteristic SNPs in the mtDNA, many of which are located in the coding region.  Next, let’s talk about the Subclades of Haplogroup H.

Subclades of Haplogroup H

The sub-clades of Haplogroup H surprisingly show more restricted and disctinctive regional geographic distributions. 

Based on the recent papers for defining the subclades of Haplogroup H, a subclade test panel is now available to test for sub-clades H1 to H16.  Individuals who are confirmed to belong to the Haplogroup H family can now take the H Subclade SNP Test to find out which sub-clade of Haplogroup H they belong to. 

Subclades H1 to H16 account for over 70% of individuals who belong to Haplogroup H.  The remaining 30% of individuals who belong to Haplogroup H belong to yet unidentified subclades of Haplogroup H.  As the studies progress, more subclades of H will be identified and will provide further classification.

The subclades of Haplogroup H can be defined by the following panel of coding region SNPs:

The mtDNA Haplogroup H Subclade Tree:

The 16 subclades of Haplogroup H can be summarized in the following phylogenetic tree.  Click here to view a more detailed version of the mtDNA Haplogroup H Subclade Tree.

In the next blog, we will discuss the features and distribution pattern of each subclade of mtDNA 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  <<– you are here
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

In mtDNA Part IX, we discussed how to use your mutations to determine your Haplogroup.  In this section, we will show you how you can trace your ancestry further by using your mutations to determine your “Subclade”. 

What are Subclades?

All people living today can trace their maternal ancestry back to one of 26 core mtDNA Haplogroups.  Haplogroups are the main “trunks” of the mtDNA phylogenetic tree and represent extremely ancient family groups which arose tens of thousands of years ago.  Over time, the descendents of each Haplogroup formed further subgroups, called “Subclades”.  Once you discover which Haplogroup you belong to, you can further fine tune your results by tracing which sub-branch of your Haplogroup you belong to through “Subclade” analysis. 

Subclades are named using numbers and letters.  For example, Subclades of Haplogroup H include H1, H2, H3, H4,…. and so on.  The Subclade H2 can be further classified as H2a, H2b, etc.  Similarly, the Subclade H5 can be further classified as H5a, H5b, etc.

Which mtDNA Subclade tests are available? 

Subclade testing will be launched over the next few months.  Refer to the following chart for the launch dates of upcoming mtDNA Subclade test panels.  Once the subclade test is available, it will appear automatically as an upgrade option from your control panel.

Please remember the following rules for subclade testing:

1. You can only take a subclade test if your Haplogroup is known (either confirmed, or strong prediction)
2. You can only take a subclade test for your own Haplogroup.  For example, if you belong to Haplogroup T, you will not qualify for Haplogroup H subclade testing. 
3. If a Subclade test is not yet available for your subclade, check back occasionally as the control panel is updated as the science progresses.  Once more information is known about your Haplogroup and its Subclades, it will automatically be announced here.

Coming up next, H Subclades!

Since the next Subclade test to become available is the mtDNA Haplogroup H Subclade SNP Test, in the next blog, we will discuss Haplogroup H, and provide an overview of current scientific research and discoveries for Haplogroup H. 

In preparation for the next blog, we recommend downloading and printing the Haplogroup H Subclade Map.  You will need this map when we talk about Haplogroup H subclades in the next blog. 

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  <<– you are here
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

In mtDNA Part VI, we discussed two ways that mtDNA testing can be used to trace ancestry: 

1. Direct Comparisons - search for matches, confirm or refute findings from ancestral studies
2. Ancestral Tracking - tracing your deep ancestry through “haplogroup” determination

 In today’s blog, we will focus on #2 “Ancestral Tracking”, and show you the science behind how the mutations in your mtDNA are used to determine your haplogroup “deep ancestry”.  We will always automatically predict your haplogroup for you after you take the mtDNA test.  However, the more you understand the science behind the technology, the more you will get out of your genetic genealogy experience.  New studies and data become available all the time in this fast moving and exciting field, so it is a good idea to know the basics behind how the technology works.

Let’s begin with a basic step-by-step guide on how to use your mutations in your mtDNA to determine your mtDNA haplogroup:

Step #1:  Download and print the Haplogroup Reference Guide	Click here to download and print the mtDNA Haplogroup Reference Guide.  This guide is a valuable reference tool for you.
Step #2:  Gather your mutations	Determine which mtDNA tests you have taken and which ones you did not take yet. The HVR1 Test will show you all mutations between 16000 to 16400 (shown in blue). The HVR2 Test will show you all mutations between 1 to 400 (shown in red). The SNP Haplogroup Backbone Test will show you all relevant mutations in the Coding Region (shown in black).
Step #3:  Identify your mutations on the Reference Map	Your mtDNA results report will always include a mutation table.  Examine your mutations table and circle your mutations on the Reference Map. Starting from the CRS, circle the mutations that you have.  Follow the path of your mutations away from the CRS.  Ignore the markers that you did not test. The final destination of the path mutations is the haplogroup that you belong to.

Let’s take a look at an example for a sample individual, Scott Mckenzie:

Let’s assume that Scott has only taken the HVR1 Test.  Scott has not yet taken the HVR2 or SNP Haplogroup Backbone Tests.  This is an example of an actual mutation table for Scott’s HVR1 Test:

Let’s see if we can tell which haplogroup Scott belongs to by examining the mutations in his HVR1 region.

1.  Find the CRS on the Reference Guide.  The first marker you encounter when moving away from CRS is “263″.  263 is located in the HVR2 region (HVR2 includes locations 1 to 400), so it is included in the HVR2 Test.

• Tip #1:  If you took the HVR2 Test, then look at your HVR2 mutation results and see if you have a mutation at location 263.  If you have a mutation at 263, then you can trace your ancestry away from CRS towards “Haplogroup H”.  If you do not have a mutation at 263, then you stay within CRS, and your haplogroup is likely the same as CRS.
• Tip #2:  If you did NOT take the HVR2 Test, then ignore 263 and move on to the next marker.

Scott did not take the HVR2 Test, so we can skip this marker for now because we do not know whether Scott has a mutation at 263.

2.  The next marker is “7028″.  7028 is located in the Coding Region, so it is included in the SNP Haplogroup Backbone Test.

• Tip #1:  If you took the SNP Haplogroup Backbone Test, look at your results and see if you have a mutation at location 7028.  If you have a mutation at 7028, then you can trace your ancestry away from Haplogroup H towards “Haplogroup HV”.  If you do not have a mutation at 7028, but you do carry a mutation at 263, then you belong to Haplogroup H. 
• Tip #2:  If you didn’t take the SNP Haplogroup Backbone Test, then ignore 7028 and move on to the next marker.

Scott did not take the SNP Haplogroup Backbone Test yet, so we can skip this marker for now because we do not know if Scott has a mutation at 7028.

3.  Next are markers 14766, 16067, 16298 and 72:

14766 leads to Haplogroup Pre-HV.  14766 is located in the Coding region and included in the SNP Haplogroup Backbone Test.

• Tip:  If you carry the 14766 marker, but not 16067, 16298 or 72, then you can trace your ancestry away from Haplogroup HV towards Haplogroup Pre-HV.

Scott did not take the SNP Haplogroup Backbone Test yet, so we do not know if he has a mutation at 14766.

16067 leads to Haplogroup HV1.  16067 is located in the the HVR1 region (HVR1 includes locations 16000 to 16400), so it is included in the HVR1 Test.

• Tip:  If you carry the 16067 marker, but not 14766, 16298 or 72, then you can trace your ancestry away from Haplogroup HV towards Haplogroup HV1.

Scott’s mtDNA HVR1 results indicate that he does not have a mutation at location 16067, so he is unlikely to belong to Haplogroup HV1.

16298 and 72 lead to Haplogroup Pre-V.  16298 is located in the HVR1 region so it is included in the HVR1 Test.  72 is located in the HVR2 region so it is included in the HVR2 Test. 

• Tip:  If you carry a mutation at 16298 and 72, but not 14766 or 16067, then you can trace your ancestry away from Haplogroup HV towards Haplogroup Pre-V.

Scott’s mtDNA HVR1 results indicate that he does not have a mutation at 16298, so he is unlikely to belong to Haplogroup Pre-V.

Scott did not take the HVR2 test, so we do not know if he has a mutation at 72, but based on the HVR1 results, we can predict that he is unlikely to belong to Haplogroup Pre-V.

In summary, based on a process of elimination (HV1 and Pre-V are eliminated), Scott’s ancestry can be traced through to Haplogroup Pre-HV.

4.  Next are markers 11719, 73, 16126, and 16362:

11719 and 73 lead towards Haplogroup “R”.  Both 11719 and 73 are located in the coding region.  Scott did not take the SNP Haplogroup Backbone Test, so we do not know if he has mutations at 11719 and 73.

16126 and 16362 lead to Haplogroup “Pre-HV1″ and they are included in the HVR1 Test.  Scott’s mtDNA HVR1 results indicate that he has a mutation at 16126, but does not have the 16362 mutation.  It is remotely possible that Scott might belong to Haplogroup “Pre-HV1″, and had a “back-mutation” at location 16362 (we will explain back-mutations in another blog).  Back mutations are rare, but it would explain why Scott has 16126 but not 16362.  We should hold onto Pre-HV1 and continue tracing to see if there is a better match for Scott.

5.  Next are markers 11251, 16126, 16278, 16311, 16071, 151, 12308, 16189, 10310, 16304, 249:

11251 and 16126 lead to Haplogroup JT.  11251 is located in the coding region, and 16126 is located in the HVR1 region.

Scott did not take the SNP Haplogroup Backbone Test, so we do not know if he carries the 11251 mutation.  Scott’s HVR1 results indicate that he carries the 16126 mutation so we can move through to Haplogroup JT.

16278 and 16311 lead to Haplogroup R1.  Scott does not have either of these mutations, so he is unlikely to belong to Haplogroup R1.

16071 and 152 lead to Haplogroup R2.  Scott does not have a mutation at 16071 so he is unlikely to belong to Haplogroup R2.  Scott did not take the HVR2 test, so we do not know if he has a mutation at 152. 

12308 leads to Haplogroup U.  Scott did not take the Haplogroup Backbone test, so we do not know if he belongs to haplogroup U, but we can look beyond Haplogroup U to the U Subclades to see if he falls into any of the Subclades of Haplogroup U:

• 16249 and 285 lead to Subclade U1.  Scott does not have a mutation at 16249 so he is unlikely to belong to U1.
• 16051 and 16219 lead to U2.  Scott does not have a mutation at either locations, so he is unlikely to belong to U2.
• 16343 and 150 lead to U3.  Scott does not have a mutation at 16343 so he is unlikely to belong to U3. 
• 16356 and 195 lead to U4.  Scott does not have a mutation at 16356 so he is unlikely to beong to U4.
• 16270 leads to U5.  Scott does not have a mutation at 16270 so he is unlikely to belong to U5.
• 16172 and 16219 lead to U6.  Scott does not have either mutations so he is unlikely to belong to U6. 
• 16318 leads to U7.  Scott does not have a mutation at 16318, so he is unlikely to belong to U7.
• 16224 and 16311 lead to K.  Scott does not have a mutation at either 16224 or 16311 so he is unlikely to belong to K.

Thus, we can conclude that Scott does not belong to any of the Subclades of the Haplogroup U family.  If the Haplogroup Backbone Test was conducted, we could confirm that Scott does not carry 12308 and eliminate him Haplogroup U entirely. 

6.  Next are markers 16069 and 16294:

16069 leads to Haplogroup J.  16069 is included in the HVR1 Test.  Scott’s results show that he does not have a mutation at 16069, so he is unlikely to belong to Haplogroup J.

16294 leads to Haplogroup T.  16294 is included in the HVR1 Test.  Scott’s results show that he has a mutation at 16294, so we can move through to Haplogroup T.

7.  Next are markers 16163, 16186, 16189, 16304, and 16324:

16163, 16186 and 16189 lead to Subclade T1 (a branch of Haplogroup T).  All 3 markers are included in the HVR1 Test.  Scott’s results show that he has a mutation at all 3 locations, suggesting that he belongs to Haplogroup T1.

16304 leads to Subclade T2.  This marker is included in the HVR1 Test.  Scott’s results show that he does not have a mutation at 16304, so he is unlikely to belong to Subclade T2.

16324 leads to Subclade T4.  This marker is included in the HVR1 Test.  Scott’s results show that he does not have a mutation at 16324, so he is unlikely to belong to Subclade T4.

In summary, based on the results of the HVR1 Test, Scott most likely belongs to Haplogroup T1. 

The prediction strength is strong for the following reasons:

• There are multiple markers in the HVR1 region that lead from CRS to Haplogroup T1.  HVR1 Testing indicates that Scott carries all of the mutations leading from CRS to Haplogroup T1.
• By process of elimination, most of the other haplogroups have been eliminated, with the exception of Haplogroup B.  However, due to the large number of matching markers for Haplogroup T1, it is most likely that Scott belongs to Haplogroup T1.  This prediction can be further strengthened if Scott takes the SNP Haplogroup Backbone Test which includes marker 11251 which is specific for Haplogroup JT branch of the haplogroup tree.  If Scott is positive for a mutation at 11251, then it would further confirm that Scott belongs to Subclade T1.

The study also showed a single match at 16126 for Haplogroup Pre-HV1, but Scott does not have the 16362 marker which is usually found in Haplogroup Pre-HV1.  Due to the stronger match for Subclade T1, it is far more likely that Scott belongs to Haplogroup T1 rather than Haplogroup Pre-HV1.  To further confirm this, the SNP Backbone Haplogroup Test will confirm whether Scott carries the mutation at 11719.  The HVR2 test will confirm whether Scott carries the mutation at 73 which leads away from Pre-HV1 towards the direction of Haplogroup T. 

Haplogroup Confirmation:

If Scott indeed belongs to Subclade T1, as suggested thus far by the HVR1 test, then the HVR2 Test and the SNP Haplogroup Backbone Test will further confirm the following:

• The results of Scott’s SNP Haplogroup Backbone Test are expected to show positive mutations for the following markers:  7028, 14766, 11719 and 11251.
• The results of Scott’s HVR2 Test are expected show positive mutations for the following markers:  263, 73.

As you can see from this example, Scott’s haplogroup is predicted using his HVR1 results.  In his case, the prediction was quite strong because Haplogroup T1 contains a lot of mutations from HVR1.  The prediction can be confirmed with the HVR2 test and SNP Haplogroup Backbone Test.

We hope that this lesson will give you a good insight into how mutations are used to determine an individual’s haplogroup.  In the next blog, we will dig deeper into the use of mutations for deep ancestral analysis. 

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  <<– you are here
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

In this blog, we will provide a broad overview of the different types of mtDNA tests available, and in the next blog, we go over some case studies to help you understand when they are used, and what each one will tell you about your ancestry.

DNA Testing 101:  There are 4 main types of mtDNA tests:

1. HVR1 Test
2. HVR2 Test
3. SNP Haplogroup Backbone Test
4. SNP Subclade Test

Let’s take a look at the main differences between these test types:

Test Type #1:  HVR1 Test

Overview:  The HVR1 Test is the most informative mtDNA test, and it is always the first test that is performed when you start tracing your maternal ancestry (the Maternal mtDNA test). The HVR1 test uses “DNA sequencing” technology to read all of the nucleotides from locations 16,000 to 16,400 of your mtDNA.  This is the entire HVR1 region, located in the D-Loop of the mtDNA.

Highlights of the HVR1 Test:  The HVR1 region is considered the most informative region of the mtDNA for ancestral studies for a number of reasons:

1. The HVR1 region contains an abundance of markers.  The HVR1 region is located in the D-Loop, so it contains an extremely high concentration of mutations (ancestral markers).  Thus, this region is highly informative.
2. The HVR1 region is easy to test.  The entire HVR1 region can be easily tested using sequencing technology.  All 400 nucleotides in the entire HVR1 region can be read from a single test.
3. The HVR1 region is well studied.  The HVR1 region is the most well studied region of the mtDNA due to its high concentration of mutations and ease of testing.  Most scientific studies to date, including indigenous data and other anthropological studies, have focused mainly on the HVR1 region.  Thus, there is more scientific data available for markers in the HVR1 region than any other region of the mtDNA, making the HVR1 region by far the most informative region of the mtDNA.

Prerequisite:  There is no prerequisite for taking the HVR1 test.  The HVR1 test is aways the first and most fundamental test that is performed when using mtDNA to trace ancestry.  The HVR1 test can be used “stand-alone” for User search and comparisons and haplogroup predictions.  All of the other test types serve to supplement the results of the HVR1 test.  There are usually enough markers and hypervariablity within the HVR1 region alone to differentiate between different individuals who are not part of the same haplogroup or family line.  Also, due to the large number of highly informative markers found in the HVR1 region, your haplogroup can often be predicted from examing just the markers in your HVR1 region. 

Test Type #2:  HVR2 Test

Overview:  Like HVR1 testing, the HVR2 test also uses “DNA sequencing” technology.  This test focuses on reading all of the nucleotides from locations 1 to 400 of the mtDNA.  This is the entire HVR2 region, the second most important region in the D-loop of the mtDNA. 

Highlights of the HVR2 Test:  Like HVR1, the HVR2 region is also located in the D-Loop of the mtDNA so it contains many ancestral markers.  The HVR2 region is always tested in conjunction with or subsequent to HVR1 Testing.  The HVR2 test will supplement the HVR1 results in the following ways:

1. Strengthen the results of User searches and comparisons.  The more regions of the mtDNA that are used for comparison, the more stringent and precise the results of the comparison.  For example, in cases where people are matching exactly at the HVR1 region, further comparison of the HVR2 region will provide greater resolution, and further confirm or refute the matches found in the HVR1 region. 
2. Assist in haplogroup prediction.  The HVR2 region contains quite a few markers which are important for haplogroup determination, and when used in conjunction with HVR1, will provide a stronger haplogroup prediction (we will examine a case study in the next blog).

Prerequisite:  The HVR1 test is a prerequisite for taking the HVR2 test.  The HVR2 region is rich in ancestral markers and HVR2 testing is an excellent way to supplement the results of the HVR1 Test.

Test Type #3:  SNP Haplogroup Backbone Test

Overview:  While the markers in the HVR1 and HVR2 Regions can be easily detected by sequencing, the Coding Region is extremely large, making sequencing impractical.  The SNP Haplogroup Backbone Test is a special panel of approximately 20 markers in the Coding Region which are specific for haplogroup determination.  By testing just the HVR1 or HVR2, you will only receive part of the “picture” of your mtDNA.  The SNP Haplogroup Backbone Test will allow you to view markers in the Coding Region of your mtDNA.

The following table illustrates all of the SNPs that are examined in the SNP Haplogroup Backbone Test:

Prerequisite:  The HVR1 and HVR2 tests are prerequisites for the SNP Haplogroup Backbone Test.  The SNP Haplogroup Backbone test examines markers in the Coding Region of the mtDNA and together with results of the HVR1 and HVR2 test, will allow you to confirm your haplogroup.   

Test Type #4:  SNP Subclade Test

Overview:  The SNP Subclade Test examines a special panel of markers in the Coding Region of the mtDNA which allows you to determine which “sub-clade” you belong to once your Haplogroup has been determined.

Prerequisite:  The HVR1, HVR2, and SNP Backbone Tests are prerequisites for the SNP Subclade Test.  Your Haplogroup must be confirmed before you can proceed with SNP Subclade testing.  At the moment, SNP Subclade Tests are available for the following mtDNA Haplogroups:

• R
• M
• H

If a subclade test is not available for your haplogroup, please check back often as new sub-clade tests are added occasionally.  Whenever a subclade test for your haplogroup becomes available, you will be able to access it from your control panel. 

The four types of mtDNA Tests are summarized in the following table:

The main goal of mtDNA testing is to gain a complete understanding of all of the important SNP mutations in your mtDNA.  The HVR1 test focuses on markers in the HVR1 region, the HVR2 test focuses on markers in the HVR2 region, and the SNP Test Panels focus on relevant markers in the Coding Region.  In the next blog, we will go over a case study to allow you to understand how these tests work together to uncover your ancestry.