mtDNA Test Types

In this section, we will provide a broad overview of the different types of mtDNA tests available and 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 ancestral 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 mtDNA haplogroup or family line.  Also, due to the large number of highly informative markers found in the HVR1 region, your mtDNA 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 later).

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:  mtDNA SNP Haplogroup Backbone Test

Overview:  While the markers in the HVR1 and HVR2 Regions can be easily detected by sequencing technology, the Coding Region is extremely large, making sequencing impractical.  The mtDNA 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 the SNPs that are examined in the mtDNA SNP Haplogroup Backbone Test:

Prerequisite:  The HVR1 and HVR2 tests are prerequisites for the mtDNA SNP Haplogroup Backbone Test.  The mtDNA 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 mtDNA 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.  Next, we will go over a case study to allow you to understand how these test types work together to uncover your ancestry. 

mtDNA Haplogroup Determination

We have just 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

Next, 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.  Next, we will dig deeper into the use of mtDNA mutations for deep ancestral analysis. 

mtDNA Subclades

Next, 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 test panels and upgrade panels are launched as they become available.  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.

Read the H Subclades tutorial!

The tutorial entitled "Learn about mtDNA Haplogroup H" provides an in depth overview of mtDNA Haplogroup H.  One of the most popular mtDNA Subclade tests is the mtDNA Haplogroup H Subclade SNP Test.  Next, we will discuss Haplogroup H, and provide an overview of current scientific research and discoveries for Haplogroup H.