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.