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Mitochondrial Full Sequence Analysis of Mother Line

A Work In Progress by Herbert Holeman, PhD.

Draft Workpaper Posted.

For discussion purposes, my DNA tests and findings are used as examples.

• Mitochondrial full sequence analysis identifies the earliest known ancestors genetically related to my mother-line.

• Four other mtDNA testers are exact matches in my mother-line ancestry with origins in the Philippines.

• My mother-line ancestors migrated to the Americas and reached Mexico.

• My concluding maternal ancestry is based on geographical coordinates of surveyed populations.


Mitochondrial full sequence analysis (MFSA) compares my mtDNA against a reference mtDNA sequence. Any differences between mine and the reference are identified and listed as a mutation. This list of my mutations reveals the ancient geographical origins of my mtDNA and the people in my Matrilineal line with whom we share an ancestor in common.

Figure 15

With reference to Figure 15 reported by the Farmily Tree company, the mtDNA – Ancestral Origins allows you to view your mtDNA matches' ancestral information.

The following information is displayed:

Country - This is the Matrilineal country of origin as reported by the individual customer. Your Matches – This is the number of matches for a specific country.

Match Total - This is the total number of matches who have reported their origin for a specific country.

Country Total - This is the total number of people with mitochondrial DNA (mtDNA) results from the country of origin in the Family Tree DNA database.

Percentage - This is the percentage from the country of origin compared to the total number from that country in the database, i.e., the Match Total column divided by the Country Total column.

It is known as the Reconstructed Sapiens Reference Sequence (RSRS). It shows the geographic origin and world migrations of my mother-line ancestors and other testers that match my specific mutation. This is the total number of testers with mitochondrial DNA (mtDNA) from the country of origin found in the Family Tree DNA database. Note the 4 ancestors from the Philippines are in the HVR 1 region, which means they match me exactly with no differences. Roberta Estes points out the match probabilities in Figure 16.

As for Figure 15, note under the CODING REGIONS matches is one tester from the Philippines who matches me at Genetic Distance 2 and two other testers from Mexico who match me at Genetic Distance 3. As for how long ago am I related to someone who has a genetic distance of 1 or 2, I'm mindful of Estes words that "there just isn't any good measure for mitochondrial DNA mutation timing. Mutations don't happen on any time schedule, unfortunately. I use genetic distance as a gauge for relative relatedness, no pun intended, and I keep in mind that I might actually be more closely related to someone with a slightly further genetic distance than an exact match."

Figure 16
Expected Time to a Common Ancestor with Exact Matches

My matrilineal migration mutations are shown in Figures 17 and 18 by regions. They have to do with mutation differences. These come about about when a descendant has a genetic trait that her ancestor (mother) did not have. This new trait, referred to as a mutation provides the definitive migration path of my matrilineal ancestors. These mutation differences are shown with mtDNA testing and divided into regions for genealogy purposes.

The Regions

HVR1 - Hypervariable Region 1 - locations 16021-16569 (548 total locations)

HVR2 - Hypervariable Region 2 - locations 1-437 (437 locations)

Coding Region - the balance of the mitochondria (15,445 locations)

The two HVR regions (in red) cover the fewest regions. The Coding Region shown in Figure 17 covers all the regions, including the HVR.

Figure 17
My mtDNA Regions

The specific mutation results in all the regions of my mitochondria are shown in Figure 18

Figure 18
My mtDNA mutations
from Family Tree DNA

As Figure 18 reports my results from full sequence analysis of my entire mitochondria, all 16,569 locations. This gives me a reliable match with other testers and provides a full haplogroup to look much farther back in time than autosomal and on one specific line.

There are two ways to view these results as shown by the two tabs at the top of the page for - rCRS and RSRS. They are abbreviations for "revised Cambridge Reference Sequence" and "Reconstructed Sapiens Reference Sequence." The RSRS is a more recent way and the best way to track the mutations backwards in time for comparisons to the Mitochondrial Eve, which simply means as far back as mtDNA could be traced and as human begining.

The alpha-numeric values are the locations in my mitochondrial DNA where a mutation has occurred. The first letter represents the letter that normally found to be present in the "Reference Sequence" and the last letter represents the letter found instead in my mitochondria. This represents a mutation, meaning the genetic trait the descendant's ancestor (mother) didn't have. An example of a mutation for me appears in the Region to the right for the value T9098C. It can be traced in the phylogenetic tree of global human mitochondrial DNA variation. While a study by Soares et al estimates the average mutation rate to be about 1 mutation in 3600 years, most of the 16,569 locations never change. Only the locations that have experienced a mutation are shown. Locations not listed have not experienced a mutation.

Matrilineal matches by person name, year, and location

The report in Figure 19 tells me very specifically about my mother's genetic match(es) and earliest identified ancestor(s). Ellen Hinkley emphasizes the header tab labed HVR1, HVR2 and coding regions tells me with a high level of certainty whether or not to accept sharing a recent Matrilineal ancestor with someone. It also determines Matrilineal haplogroup with certainty. Note the two names in Figure 19 are fictitious and are used for the purpose of illustration. Yet, the names reflect the heredity of the actual people matched.

Figure 19
My mtDNA Genetic Matches
from Family Tree DNA

The Genetic Distance shown in Figure 19 is a categorical measure. It refers to the number of mismatches in my 16,569 DNA mitochondrial locations compared to the name of the other person. Generally, the fewer the mismatches, the less the genetic distance and the more closely I am related to the other person named.

If there no mismatches between us, my genetic distance is zero, and it would bring my match into more recent times. In terms of closeness of relationship, it means that at the 50% CI, I have a 50% chance of sharing a common Matrilineal ancestor within the last 5 generations. That is about 125 years. At the 90% CI Confidence Level I would have 90% chance of sharing a common Matrilineal ancestor within the last 22 generations, which is about 550 years.

These markers can be viewed in the International Society of Genetic Genealogists (ISOGG), haplogroup O chart of May, 2018 and by the YFull timeline around the year 2,700 years ago as shown in Table 10. Thus, research reveals my Matrilineal clan can be traced back to the Asian mainland 43,000 years ago with mother-line ancestry in the Philippines before emenating to Mexico at a time yet to be determined.

Useful Links:

The Mitrochondrial Haplogroup Tree for haplogroup B.

Haplogroups B2 and B2c1 in the Americas.

Using the mtDNA tree.

A good video on the mtDNA Full Sequence panel from FTDNA by Elise Friedman.

Copyright © 2018 Herbert P. Holeman, Ph.D. All Rights Reserved.