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  <<– you are here
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

In this blog, we will discuss the technology used to detect mutations in your mtDNA.  A basic understanding of DNA testing techniques will help you to understand the science behind DNA ancestry testing.  

DNA Testing 101

The two most common methods used to detect mutations in mtDNA are 1) DNA Sequencing, and 2) SNP Testing.  Let’s talk about each one and how they work.

1.  DNA sequencing. 

DNA sequencing is a special process which is used to read the chain of nucleotides in a specific segment of your DNA, much like reading a book. 

This technology allows the lab read the entire genetic code of a whole section of your mtDNA.  The following report is an example of the results of a sequencing test in the HVR1 region of an individual’s mtDNA. 

As you can see, all of the nucleotides in HVR1 region (locations 16001 to 16520) have been decoded.  All mutations detected in the sequence are indicated in pink.  

The benefit of DNA Sequencing technology is that it can accurately read entire lengths of your DNA.  The limitation of DNA Sequencing technology is that only approximately 400 to 500 nucleotides can be read at a time (in one test). 

This technology is used for testing the HVR1 and testing the HVR2 (D-Loop) region of your mtDNA.  The HVR1 region is approximately 500 nucleotides in length (spans location 16000 to 16569).  The HVR2 region is approximately 400 nucleotides in length (spans locations 1 to 400). 

DNA Sequencing technology is the best test method to detect mutations in the HVR1 and HVR2 regions (D-Loop):

1. A single sequencing test can detect all of the markers in the HVR1 region (called the HVR1 test), and another sequencing test can detect all of the markers in the HVR2 region (called the HVR2 test). 
2. Most of the mutations found in the mtDNA are located in HVR1 and HVR2 (high concentration of mutations compared to the coding region)
3. The HVR1 region is the most widely studied region of the mtDNA for ancestral studies and provides the most ancestral information. 

However, DNA Sequencing is not the best method for examining mutations in the Coding Region of your mtDNA because the Coding Region is extremely long, over 15,000 nucleotides in length. 

Since each sequencing reaction can only test approximately 500 nucleotides at a time, a lot of reactions would be required in order to sequence the entire coding region, making it impractical and costly.  Also, as discussed in previous blogs, there are very few mutations in the coding region, making it unnecesary to sequencing every single nucleotide in the coding region.  Thus, DNA Sequencing is not the best way to look for mutations in the coding region.

2.  SNP Test Panels

The second method to detect mutations in the mtDNA is called “SNP” testing.  Unlike DNA Sequencing, this technique does not read the entire length of DNA.  Instead, it targets specific nucleotides.  Only the nucleotides that provide useful information are tested, and all other nucleotides are ignored.  This is the best method for efficiently testing large regions of DNA. 

For example, if the presence of a mutation at location 16223 is an important indicator that someone does not belong to Haplogroup H, then the laboratory will pinpoint and specifically test location 16223 to see if a mutation exists in this location. 

This is like “sharp shooting”.  Instead of testing an entire region of the DNA, we are specifically targeting exact locations and nucleotides that are important for answering a specific question. 

SNP Test Panels are special handpicked panels of SNP markers which will answer a specific set of questions.  For example, a mtDNA Haplogroup Backbone SNP Test Panel will examine all markers which will tell us which mtDNA Haplogroup an individual belongs to.  We will talk more about specific SNP Test Panels in the further blogs. 

In Part VI, we will discuss how mutations in our mtDNA allow us to trace our maternal ancestry.

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  <<– you are here
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

In this blog, we will talk about ancestral markers, what they are and where they are found in the mtDNA.

What is an ancestral marker? 

mtDNA is a circular chain consisting of 16,569 pairs of nucleotides.  Let’s unwind the DNA double helix and take a closer look at its genetic code. 

DNA consists of two chains of nucleotides, designated A, C, T, and G.  “A” is always linked to “T”, and “C” is always linked to “G” on the opposite chain.  In this diagram, we will take a closer look at a short segment of mtDNA, namely locations 1 to 45.  The unique combination of nucleotides in the chain is called a “genetic code” and holds genetic information. 

Ancestral markers are “mutations”, little changes or “hiccups” that occur in the genetic code of the mtDNA.  There are many types of mutations, but the type of mutation most commonly found in mtDNA is called “SNP” (single nucleotide polymorphism).  A SNP mutation occurs when a single nucleotide is replaced with a different nucleotide.  For example, in this diagram, the “T” at location 40 is replaced by a “G”. 

This mutation is documented as follows:

• Location:  40
• Nucleotide Change:  T>G

When you test your mtDNA, your results report will document the mutations that you carry in your mtDNA.  Let’s take a look at a sample report:

In this report, “Location” refers to the locations on the mtDNA where a mutation has been detected.  “Mutation Type = Substitution” means that a nucleotide has been substituted by a different nucleotide.  “Nucleotide Change” indicates what was substituted.  Let’s take a look at the first mutation in the list.  Location “16126″ means that a mutation has been detected at location “16126″.  T>c means that a “T” has been replaced by a “c” at this location.

A second way to look at your results is to take a look at the actual sequence.  In this example, the sequence shows the results for the HVR1 region, from locations 16001 to 16520.  Remember, only one of the two chains in the pair is shown when reporting the sequence!

Fifty nucleotides are listed per line from left to right.  In this example, the first line shows the results for locations 16001 to 16050, the second line shows the results for 16051 to 16100, and so on.  Mutations in the sequence are highlighted in pink.  In this sequence, the nucleotide at location 16126 is highlighted in pink, indicating that a mutation is detected here, and the nucleotide has been replaced by a “c”. 

The unique set of mutations that you carry in your mtDNA holds information about your maternal ancestry.  In Part V, we will talk about the technology used to detect mutations in your mtDNA. 

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  <<– you are here
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

In this blog, we will talk about the structure of the mtDNA.  Understanding the structure of the mtDNA will help you to understand the types of ancestral markers found in it.   

mtDNA is a circular loop of DNA.  DNA is the chemical that carries genetic information.  DNA looks like a long ladder twisted into a “double helix”.  The sides of the ladder are the ”backbone”, and the rungs of the ladder consist of “nucleotide bases”.  There are 4 types of bases:  A, C, T, and G.  “A” is always connected to “T”, and “C” is always connected to “G”. 

Let’s take a closer look at the mtDNA loop.  The mtDNA has 4 main regions:  1) D-Loop, 2) rRNA, 3) tRNA and 4) genes that code for protein.  The regions that code for rRNA, tRNA and protein are called the “coding region”.   

The mtDNA loop is 16,569 base pairs in length.  The location of each base pair in the mtDNA can be specified with an accession number according to its position in the mtDNA.  When numbering the base pairs, we start at the “origin”.  The origin is arbitrarily located in the D-Loop region. 

The position of any base pair in the mtDNA is relative to the origin.  The position of any base pair in the mtDNA is designated by counting from “1″ clockwise around the mtDNA.  Thus, the positions are named 1 to 16,569 (remember this because it is important when we start talking about ancestral markers).

Let’s take a closer look at the D-Loop Region (aka Hypervariable Region) of the mtDNA since it is the region most frequently tested for ancestral studies. 

The D-Loop contains two regions, the HVR1 region which spans locations 16,000 to 16569, and HVR2 region which spans locations 1 to 400.  Unlike all of the other regions of the mtDNA, the D-Loop does not have any functional genes. 

Most of the ancestral markers are found in the D-Loop.  The D-Loop is considered a non-vital part of the mtDNA because it does not have a useful biological function.  Thus, whenever a mutation occurs in this region (we will discuss ancestral markers and mutations in the next blog), the individual does not die and survives to pass the mutation along to future generations.  However, the coding region of the mtDNA is considered essential for the survival of the individual, so usually, whenever a mutation occurs in this region, it is often lethal and the organism dies.  Thus, mutations which occur in the coding region are usually not passed down to future generations.  For this reason, over a period of thousands of years, many mutations accumulate in the D-Loop, but very little are found in the coding region.  Mutations are found at a much lower frequency in the coding region because only the mutations which do not end up being lethal are passed down.  When tracing ancestry, scientists usually begin by testing the D-Loop because of its abundance of mutations or “ancestral markers”.

In Part IV, we will continue this topic by discussing the types of ancestral markers which are found in the HVR1, HVR2 and coding regions of the mtDNA.

DNA Lesson Series: The mtDNA and its role in Ancestry
mtDNA Part I - mtDNA 101
mtDNA Part II - Facts about mtDNA  <<– you are here
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

This blog is a continuation of mtDNA Part I.  Click here to view Part I.

In this blog, we will continue to give a little more background information about mtDNA.  A good understanding of the background of mtDNA will help you to better understand mtDNA ancestry discussions in further blogs in this series.

What does mtDNA look like?

1.  Its round!  Unlike all of the other DNA in our body which are linear, mtDNA happens to be a round circle, called a “plasmid”.

2.  It’s small!  While nuclear DNA (DNA found in the nucleus of the cell) is a staggering 49,530,000 to 247,200,000 bases in length, mtDNA is only 16,571 bases in length (don’t worry if you don’t know what a “base” is.  We will be talking about bases in detail in the next blog). 

Why is mtDNA so different from all of the other DNA in our body?

The strange appearance of the mtDNA in comparison to the other DNA in our body has something to do with its origins.  Mitochondria has many of the same features as single cell organisms called “prokaryotes”.  Bacterial cells are prokaryotes.  The mtDNA that is found inside the mitochondria is a circular plasmid, just like the DNA in bacteria, which is also circular.  The “endosymbiotic hypothesis” suggests that the reason for this close resemblence is that 1.7 to 2 billion years ago, mitochondria were originally bacteria that were “engulfed” by a cell and became permanently incorporated in the cytoplasm of the cell.  This is called a “symbiotic” relationship because the cell and the bacteria provided a survival advantage to each other (mitochondria produces energy “ATP” for the cell, and the cell provides protection).  This explains why the mtDNA is circular and found in the cytoplasm instead of the nucleus of the cell.

What does mtDNA do?  What’s its function?

The mtDNA contains the genetic code for 37 very important genes (13 of the genes are responsible for producing proteins, 22 of the genes hold the genetic code to produce transfer RNA (aka tRNA), and 2 genes hold the genetic code to produce ribosomal RNA (rRNA), all are necessary for our survival).  Thus, the mtDNA is very important, and when something goes wrong with the mtDNA, it can lead to mtDNA diseases such as exercise intolerance, Kearns-Syre syndrome and even death. 

The 1) size, 2) structure and 3) importance of mtDNA for survival, all play a role in where ancestral markers are located in the mtDNA and will allow you to understand the testing methods used to detect ancestral markers in the mtDNA. 

In Part III, we will discuss the different regions of the mtDNA. 

DNA Lesson Series: The mtDNA and its role in Ancestry
mtDNA Part I - mtDNA 101  <<– you are here
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

Ok, the topic of this blog is going to get quite technical.  We’ll start off with the easy stuff like “what is mtDNA”, but we feel that in order to fully understand the power of mtDNA testing and its applications in ancestry, it would be good to understand the science behind the technology.  That’s why over the next few blogs we will dissect the mtDNA, learn the nitty gritty details of mtDNA markers and hopefully give you a full technical understanding of how mtDNA ancestral tests work. 

You don’t need to understand how mtDNA testing works to understand your results, but the more you know about “how”, “why” and “what’s next” when it comes to mtDNA testing, the more you will get out of your experience at Genebase.

mtDNA 101:

mtDNA stands for “mitochondrial” DNA.  All of us, both males and females, carry mtDNA.  mtDNA is found in most of the cells in our body.

mtDNA is unique because while most of the DNA in our body is found in the nucleus of our cells, the mtDNA is found in small stuctures or organelles called “mitochondria”.  Mitochondria is found in the cytoplasm of our cells, NOT in the nucleus (remember this, because it’s important when we discuss how mtDNA is inherited). 

Mitochondria is important for producing energy “ATP” for our cells.

Many copies of mtDNA are found in every mitochondria and many mitochondria are present in each cell.  That means that we have a lot of mtDNA in our cells compared to most other types of DNA which are present in only one set per cell.  The huge abundance of mtDNA as well as its small size makes it an excellent candidate for forensic studies of old or degraded samples.  Many archaeological studies of ancient DNA samples which are hundreds of years old focus on mtDNA testing.

Where do we get our mtDNA?  Our mtDNA comes from our mother, and our mother got her mtDNA from her mother, and so on.  The reason for the maternal inheritance pattern of mtDNA is due to its localization in the cytoplasm.  When an egg is fertilized, the cells of the resulting embryo contain the cytoplasm of the egg, not the sperm.  As the embryo continues to develop into a full grown human, all of the cells in the resulting human contain the cytoplasm and mtDNA of the mother. 

Maternal inheritance pattern of mtDNA:

mtDNA has a very unique inheritance pattern which differs from all the other types of DNA in our body.  It is passed down along the maternal line from a mother to all of her children.  Males will carry the mtDNA of their mother, but when they have children, their children will carry the mtDNA of their own mother, not their father.  Thus, only daughters will pass the mtDNA on to future generations.   

Why does it hold ancestral information?

The maternal inheritance pattern of the mtDNA has important significance for ancestral studies.  While most of the other types of DNA in our body are mixed as they are passed down from generation to generation, the mtDNA remains unmixed because it has a strict line of descent from mother to child.  This means that our mtDNA is the same as our mother’s and our mother’s mother’s mtDNA from hundreds, even thousands of generations ago.  By testing our own mtDNA, we are in fact able to indirectly read the mtDNA genetic code of our own maternal ancestors from thousands of generations ago.

This is a brief overview of mtDNA.  In Part II, we will take a closer look at the mtDNA. 

This blog is a continuation of Haplogroups Part I.  Click here to view Part I. 

In Part II, we will go over how to use the Haplogroup feature at Genebase.  For the purpose of this demonstration, we will trace the Y-DNA Haplogroup of a hypothetical individual who belongs to Haplogroup R1b:

 1.  After logging in to the Genebase Control Panel, click “DNA Ancestry”:

2.  Next, click “Haplogroups” to go to the haplogroup tool:

3.  Select the Y-DNA haplogroup (paternal), or the mtDNA haplogroup (maternal), then click “Begin Analysis” to proceed:

4.  A list of all people in your family who have been tested will appear.  Find the line in your family that you would like to trace from the list and click “Proceed”:

5.  The Haplogroup Predictor tool will predict the haplogroup and generate a migration map.  The migration map shows the path of migration for ancestors in this haplogroup as they journeyed out of Africa and indicates where they travelled.  All people living today can be traced to one of 18 main Y-DNA haplogroups and one of 26 main mtDNA haplogroups:

In this hypothetical example, the predictor indicates that the individual specifically belongs to Haplogroup R1b.  R1b happens to be one of the largest family groups in Europe.  Many individuals of European descent are descendents of this ancient family group.  More specifically, the predictor is stating that this individual belongs to haplogroup “R”, subclade “R1″, and further subclade “R1b”. 

The prediction can be confirmed through haplogroup backbone testing.  To proceed with backbone testing, click “Confirm this haplogroup prediction”.  The backbone test will confirm whether the individual is indeed a member of the R Haplogroup. 

The R Haplogroup and even the R1b sub-clade have many further sub-branches.  The R1b family group can be further classified into over 18 known subclades.  14 of the R1b sub-clades can be confirmed through sub-clade testing. 

The 14 subclades of R1b which can be determined through sub-clade testing are as follows:

• R1b1a
• R1b1b
• R1b1c
• R1b1c1
• R1b1c2
• R1b1c3
• R1b1c4
• R1b1c5
• R1b1c6
• R1b1c7
• R1b1c9
• R1b1c9a
• R1b1c9b
• R1b1d

Users who are confirmed members of the R, R1a, or R1b haplogroups may consider R sub-clade testing to further investigate the R branch, in particular, the R1b branch of the haplogroup family tree.  The R sub-clade test panel will be launched in the control panel in the upcoming month.  An update will be posted here once the launch date for the R sub-clade test panel is confirmed. 

Let’s take a peek at what’s in development in our research facilities.  A lot of the upcoming developments in the lab are sub-clade refinement panels.  Users can expect to see sub-clade panels for the following haplogroups in the next few months:

Y-DNA sub-clade tests will become available for the following haplogroups:

• R
• Q
• I
• O
• J
• L
• E
• G

mtDNA sub-clade tests will become available for the following haplogroups:

• R
• M
• H

Watch for release dates of each sub-clade test in upcoming blogs. 

6.  To view the human phylogenetic tree and see how you fit into it, click “Haplogroup Tree of R1b”. 

The phylogenetic tree feature shows how haplogroup R1b is connected to all other haplogroups.  Click on the individual haplogroups in the phylogenetic tree to navigate the tree and view other branches.  The phylogenetic tree will illustrate how you are linked to all of the people living in the world today and shows how we have all descended from a common ancestor. 

7.  To read more about haplogroup R1b, click “About R1b”.  From here, you can read the latest information about R1b.

You can also trace the haplogroup of other lines in your family tree by selecting a family member from the list on the left column.  All family members who have been tested will be listed here so you can work together with other family members to trace the deep ancestry of multiple lines in your family tree.

Haplogroups relate to our deep ancestry.  Deep ancestry is not traditional genealogy:  it is not for tracing family or confirming family linkages.  Deep ancestry is a look at our ancient ancestral roots from tens of thousands of generations ago and shows how all people living today are connected to an ancient ancestor who lived in Africa over 100,000 years ago. 

Haplogroup studies have been around for many years in the scientific community.  Many will remember seeing the traditional biology 101 textbook diagram (phylogenetic tree) which shows how all living organisms are connected:

A phylogenetic tree shows the evolutionary relationship of biological species believed to have common ancestor.  In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendents. 

Humans represent one branch of the phylogenetic tree of all living organisms.  The human branch of the phylogenetic tree was built based on DNA, in particular, SNP markers found in human DNA. 

Our Y-DNA, which is passed down from father to son shows that the Y-DNA of every male living today can be traced back to a common male ancestor who lived in Africa over 100,000 years ago.  He is often termed the “Y-Chromosomal Adam”.

Likewise, our mtDNA, which is passed down from a mother to her children shows that all people living today shared a common female ancestor who lived in Africa over 100,000 years ago.  She is often termed the “Mitochondrial Eve”.

The type of genetic markers used to build the human phylogenetic tree are called SNP (single nucleotide polymorphism) markers.  SNP markers are found in both the mtDNA and the Y-DNA.

The main branches of the human phylogenetic tree are called “Y-DNA haplogroups”.  The Y-DNA tree has approximately 18 main branches “Y-DNA haplogroups”, classified by the letters A to R.  Each Y-DNA haplogroup has many further sub-branches (subclades), classified by numbers and letters i.e. R1A, R1b1, R1b2, etc. 

The mtDNA tree has approximately 26 main branches “mtDNA haplogroups” classified by the letters ”A to Z”.  Each mtDNA haplogroup has many further sub-branches (subclades), classified by numbers and letter, i.e. L1A1, L1A2, L1B, etc.  All people living today have descended from of the main branches of the human mtDNA phylogenetic tree.

By testing the SNP markers in your Y-DNA and mtDNA, you will be able to tell which branch of the haplogroup tree you belong to.

Of course, each main branch has further sub-branches or “subclades”.  Once you know which haplogroup you belong to, you can then focus on your sub-clade through “subclade testing”.

In Part II of this blog, we will go into detail about how to use the haplogroup feature at Genebase.

Facts and Common Misconceptions:

• No, haplogroups are not the same as haplotypes.
• Yes, all people living today fall into one of 18 main Y-DNA haplogroups on their paternal line, and one of 26 main mtDNA haplogroups on their maternal line.
• No, haplogroups will not show if you are related to someone (unless you count distant relationships from thousands of years ago).
• Yes, once you know your haplogroup, you will be able to view how your haplogroup migrated out of Africa and retrace their migration routes.
• No, haplogroups will not add people to your family tree or allow you to trace your surname (that’s the job of STR haplotypes).
• No, haplogroups will not tell you precise migration routes, it will show a broad migration route and population distribution.
• No, if you and someone else belong to the same haplogroup, it does not mean that you are closely related.
• Yes, once you know your haplogroup, you can often fine tune your branch of the haplogroup tree through subclade testing.
• No, you cannot confirm your haplogroup through STR testing or HVR1 testing.  A Y-DNA STR test and HVR1 test will often allow you to predict your haplogroup, but only a SNP backbone test will confirm the prediction.
• No, SNP backbone testing will not give you information about sub-clades.  It will confirm your haplogroup.  Once your haplogroup has been confirmed, a subclade panel test for your particular haplogroup will trace your subclade. 
• Yes, STR testing can give predictions for haplogroups and even some sub-clades, but the backbone test can only confirm the haplogroup, not the sub-clade.
• Yes, subclades are determined through SNP subclade testing (once your haplogroup has been confirmed)
• No, your haplogroup will not tell you if you are Welsh or Irish.  It will not tell you your ethnicity.  Although there are associations between ethnic groups and haplogroups, you must remember that haplogroups represent deep ancestry, tracing events from tens of thousands of years ago.  It does not tell you what your ancestors have been up to over the last few hundred years (that’s the job of Y-DNA STR markers, and applications such as Surname Projects, which will be the topic of another blog). 
• Yes, all people living in the world today are connected in the human phylogenetic tree.  Just like how all people belong to a certain blood group i.e. A, B, AB, O which can be determined through testing, all people also belong to a certain haplogroup which is unique to their ancestry, and their haplogroup type can be determined through genetic genealogy testing.

Click here to read Part II of this blog.

This blog is a continuation of DNA Clans Part I.  Click Here to View Part I.

The Indigenous DNA database allows you to match your Y-DNA to a global panel of ethnic groups.  Since your Y-DNA is inherited along your paternal lineage, this database allows you to trace the ancestry of your paternal line (father’s, father’s, father’s…. line).

Let’s go over how to use the indigenous Y-DNA database.

Step 1:  After logging in to your control panel, click “DNA Clans”.

Step 2:  From the DNA Clans main page, click “Proceed”, then click “Begin Analysis”.

Step 3:  A list of all of the people in your family tree that have been tested will appear.  Next to the name of each individual, the ancestral line which will be uncovered is shown.  Select the line that you would like to trace and click “Proceed”. 

Step 4:  The total number of Y-DNA markers that you have tested will appear.  Select the number of markers that you want to use for comparison. 

For Keeners:  Why is this necessary?  The indigenous DNA database contains indigenous DNA marker data from many different research labs around the world.  The markers tested by different research labs are often not exactly the same markers i.e. the tested markers may not overlap.  Furthermore, the total number of markers which are tested by each research lab is often different:  some laboratories may test more markers, and others may test less.  The inconsistency in data collection between different research labs from around the world makes it difficult for you to compare your DNA to the results of multiple research groups at the same time.  While you may have tested 44 markers, the indigenous studies may have examined less markers or different markers from the ones that you have tested.  For example, research Laboratory A might only test 12 markers for the indigenous samples that they collect while research Laboratory B might test 14 markers, however, only 7 out of the 14 markers from Laboratory A are the same as the markers tested by laboratory A.  In this hypothetical situation, the overlapping markers to be compared between the two labs must be 7 or less.  This is the reason why even if you have tested 44 markers, you would select only a portion of them for comparison to the indigenous DNA database.  The benefit of testing more markers (i.e. 44 markers instead of 20) is that the system will have a larger pool of DNA markers to choose from when doing comparisons, and as a result, you will be able to compare to more ethnic groups. 

Regardless of the number of markers that you have tested, we recommend starting your search with 8 markers.  You can always increase or decrease the number of markers depending on the results that you obtain from 8.  Remember, the less markers that you use for comparison, the weaker your results, but the more ethnic groups you will be able compare to.  When you increase the number of markers that you use for searching, less ethnic groups will qualify for comparison, but the results will be much stronger and more precise. 

Step 5:  Based on the markers that you have tested and how many of them you want to use for comparison, a list of different groups of qualifying ethnic populations will be generated.  Select the group that you would like to use for comparison and click “Run Analysis”. 

For keeners:  Interested in knowing a little more about the algorithm used by the system to generate this list?  This list is automatically generated based on a number of factors:  the number of markers that you would like to use for comparison, the types of markers that you have tested, and the number and types of markers from each individual research group in the entire indigenous DNA database.  The system scans each of the DNA markers that you have tested, compares them to the DNA markers from each of the different research groups in the database to find “overlapping markers”, and then determines the best sets of markers which overlap the greatest number of populations in the indigenous DNA database (ie. from all the markers that you have tested, the system selects the sets of markers which allows you to compare to the greatest number of populations). 

Step 6: The result of your search is displayed as a graph which indicates the closest match to your ancestry.  The RMI (relative match index) shows how closely you match each ethnic group or region.  Additional information about interpretation of these results can be found in the FAQ section of DNA Clans.

Please remember that the matches are based upon the most current data in the indigenous database today.  Researchers from around the world continue to sample the DNA from new indigenous groups.  As new data and populations become available, they will automatically be included in the indigenous DNA database.  As the sciences continues, your journey will continue, allowing you to dig deeper into your ancestral origins and obtain more and more precise matches.  Use of the indigenous DNA database is free, so check back often and become part of this exciting and ever evolving journey of research and discovery. 

*For those who are interested in using indigenous DNA tracking technology to trace their maternal ancestry, Genebase will soon be announcing the world’s first public access indigenous populations mtDNA database.  Watch for it in upcoming announcements!

There are two distinct types of DNA databases that you can use to trace your ancestry:  The User Database, and The Indigenous Database.

1) The User Database - This public participation database allows you to compare your ancestral DNA markers to other Users from around the world to search for long lost relatives and make connections to people who share your ancestry.

2) The Indigenous DNA Database “DNA Clans” - This forensic quality database allows you to compare your ancestral DNA markers to indigenous DNA from over 148 populations from around the world to find out which ethnic groups and geographic regions match yours at the highest frequency. 

Let’s discuss the difference between the User database and the Indigenous DNA database.  The User database allows you to compare your DNA to other actual Users in the system and allows you to find matches to people from around the world.  The User database is really useful for people looking to expand their family tree and to find other people who share a common ancestry.  However, the User database is not a great way to find out about your ethnicity because the people in the database usually are not “indigenous” populations.  Indigenous people are peoples who are native to a certain part of the world and whose ancestors have lived in the same region many generations.  When a User joins Genebase, he/she is often from Canada or the US and not from their native country.  Even though Users are asked to indicate their native country of origin if known, the information provided by the User might not be reliable. 

For this reason, forensic laboratories rely soley on indigenous DNA when determining an individual’s ethnic origin.  Indigenous DNA is collected by research laboratories from around the world who focus on testing the world’s last remaining indigenous populations by sampling the DNA from native populations.  With advances in transportation, increasing global migrations and increased rates of immigration and emmigration, indigenous populations are rapidly disappearing in the 21st century.  Within the next few decades, it is likely that the last remaining indigenous populations will be gone forever. 

Because of this, research groups from around the world have been rushing to collect DNA samples from indigenous populations from around the world to document the DNA types which are characteristic of populations from different regions of the world.  Today, the DNA from tens of thousands of indigenous people have been sampled.  The indigenous DNA database at Genebase contains the DNA of tens of thousands of indigenous people from over 148 ethnic groups from around the world.  This forensic quality database allows people to compare their DNA to indigenous populations to find the closest matches and gain insight into the region of the world that most closely matches their genetic type. 

This is a brief introduction to ancestral DNA databases.  In Part II, we will go into detail about how the indigenous DNA database works and how to interpret the results.  Click here to view Part II.

The family tree tool has special features which allow you to work together with family members to trace the ancestry of multiple lines in your family tree using DNA. 

If you are male, you can test your own Y-DNA to trace your paternal line (that’s your father’s father’s father’s…. ancestral line), and you can test your own mtDNA to trace your maternal line (that’s your mother’s, mother’s, mother’s…. ancestral line). 

If you are female, you can test your own mtDNA to trace your maternal line, but females do not carry Y-DNA so if you want to trace your father’s line, you will need to test a male relative, such as a brother or male cousin on your father’s side of the family. 

The dilemma:  There are many lines in your family tree, but by testing yourself, you will only be able to uncover a maximum of 2 lines: your direct maternal and/or paternal lines.  What if you are interested in your father’s mother’s line, or your mother’s father’s mother’s line?  Even if you don’t carry the markers, other living members of your family might, and you can test them to uncover additional lines.  However, the genetics involved can get quite complex, so it’s often difficult to determine just who needs to be tested to trace a certain ancestor.

The solution:  The family tree tool has a built in calculator which helps you to determine how to trace multiple lines in your family tree.  As you build your family tree, the family tree tool automatically determines the genetic links between all individuals in the tree. 

How to use this tool:  Go to the family tree tool by clicking on the “family tree” link from the control panel.

Finding out which line you will uncover be testing yourself or another family member:  Identify the individual that you are considering testing (it can be yourself or any other family member). 

Click on the “ancestry” link.  A pop-up window will appear showing you who the most distant known ancestors are.  These are the ancestral lines that you will uncover by testing this individual. 

Tracing the ancestry of a particular ancestor:  To trace the ancestry of any ancestor in your family tree, find the ancestor of interest in your tree, then click “ancestry”. 

A pop-up window will appear.  If this line can be traced, you will see a green check box.  If this line cannot be traced, you will see a red “x”. 

To trace this line, click “investigate this line”.  All of the living people in your family tree who carry the genetic markers required to trace the ancestry of this line will be listed. 

Using this tool, you can find out what types of information you will retrieve by testing each member of your family.  This tool will allow you to work together with family members to uncover many ancestral lines in your family tree, and also helps you to save money by letting you known which individuals carry the same marker types, because in such situation, testing only one family member will be enough to provide the answer.