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 Introduction to the Y Chromosome

Humans have 23 pairs of chromosomes. Sex is determined by two sex chromosomes referred to as X and Y. A female has two X-chromosomes (XX); while a male has one X and one Y-chromosome (XY). Because Y doesn't recombine with other chromosomes, it's unusually good for tracing how men have traveled and settled around the world. A recent example in American history is how the Y-chromosome settled a long-standing debate about President Thomas Jefferson and his direct line male descendants.

Assuming you have now ordered a Y-DNA kit, how do your genetic results relate to the genealogy?  As genealogist, we have been primarily tracing our ancestors by following the family surname "paper trails." [Our documented paternal lines.] In order to do the same genetically, we must follow the Y-chromosome trail of two living males to an ancestor they have in common. Living males with the same surnames can be genetically tested and their respective Y-chromosomes compared to determine if they share a common ancestor who lived after the usage of surnames became common in Europe in the 13th and 14th centuries (sometimes referred to as genealogical time).

Y-DNA passed from Father to son is relatively unchanged from generation to generation. If, for example, their Y-DNA was compared, the probability will be  very high they are a perfect Y-Chromosome match. If this son passes his Y-DNA to his son — this grandson's comparison to his grandfather will result in a  perfect genetic match. In an ideal world, this would continue through generation after generation. However, we do not live in an ideal world. 

What is an SNP

All people have a past that traces back to Africa. Over thousands of years, different groups have traveled and settled around the world. Each group has its own path and history recorded in DNA. Part of that record is found on the Y chromosome. Population geneticists study it using changes in the genetic code called Single Nucleotide Polymorphisms (SNPs). Once discovered, SNPs are placed on the Y chromosome Consortium’s (YCC) phylogenetic tree. This tree can then be used to explore our own shared past and place our — or a representative relative’s  — Y chromosome in the context of historic migrations.

The Y chromosome contains two types of ancestral markers. Short Tandem Repeats (STRs) trace recent ancestry (mostly within genealogical time). The second type of ancestral marker, SNPs, document ancient ancestry. SNPs are small "mistakes" that occur in DNA and are passed on to future generations. SNP mutations are rare. They happen at a rate of approximately one mutation every few hundred generations. [Source: Quoted from FTDNA. For a more in-depth discussion, go to their web page entitled Haplogroups & SNPs.]

What is a Haplogroup? (Following from 2008 Y-Chromosome Plylogenetic Tree Chart)

Haplogroups are major branches on the Y-chromosome tree. ["Haplo" comes from the Greek word for "single". ] All Haplogroups ultimately descend from a single Y-chromosome that was carried by a male that lived in the distant past. As this Y-chromosome was passed from father to son, mutations accumulated along different lineages giving rise to a tree-like branching pattern. Geneticists can reconstruct this Y-chromosome tree by discovering and typing mutations in different male human populations. Haplogroups are assigned letters of the alphabet, and refinements consist of additional number and letter combinations. For example, a common haplogroup among Stark Project Members is R1b1. "R" is the Haplogroup and "1b1" are additional number and letter combinations within the major Haplogroup "R" that are called Subclades. If you are interested in learning more, I suggest visiting the Wikipedia web page entitled "Haplogroup."

All males living today descend from a single man who lived in Africa approximately 100 thousand years ago; and his male descendants living today have been assigned the letter "A" along with additional number and letter combinations (16 total have been identified). As populations migrated to different parts of the world over time, mutations occurred leading to new Haplogroups. These later Haplogroups have been assigned the letters "B" through  "T" and also will have refinements consisting of additional number and letter combinations as illustrated above in the R1b1 haplogroup.

When we compare two individuals with the same surname belonging to different Haplogroups, say for example R1b1 and I1, the probability they share a common ancestor who lived after surnames were established will be "Zero." Why would this be the result? By the calendar year 1500, surnames were well established. This would be approximately 20 generations earlier than the present generation. Using the 2008 Y-Chromosome Plylogenetic Tree Chart, one will find the common ancestor in this genetic comparison would be the progenitor of the "F" haplogroup who lived about 45 thousand years ago. The "I" progenitor evolved from "J" while "J" evolved from "F." The "R" haplogroup evolved; from "P"; while "P" evolved "K"; and "K" evolved from "F." In this example, it is obvious the men compared in this example could not have shared a common ancestor who lived about 500 years ago. Therefore, you can expect you will not be recently related to members in the project who test in a different haplogroup — especially those Haplogroups that do not start with the same capital letter from the alphabet.

What is a Haplotype?

A haplotype is defined as a collection of two or more DYS markers (DNA Y-chromosome Segment number). The markers chosen by FTDNA are a mix of Y-DNA markers that mutate at higher and lower rates --- ideal for genetic comparisons that can identify men related to each other through a recent common ancestor. For the purpose of analysis, our DYS Markers have been organized into three separate haplotypes identified as numbered "Panels." For example, DYS Markers 1 through 12 would be Panel 1; DYS Markers 13 through 25 would be Panel 2; and DYS Markers 26 through 37 would be Panel 3. Panel 1 in our analysis will be labeled as the H12 Haplotype. When Panel 1 and Panel 2 are combined into 25 markers, they will be labeled as the H25 Haplotype. When all three panels are combined into 37 markers for analysis, they will be labeled as the H37 Haplotype. When available for analysis, the H67 Haplotype will consist of 67 markers.

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The Presentation of Your Y-DNA Results

A comparison of the Y-DNA of two males with the same surname can determine if they have an ancestor in common who lived after the usage of surnames became common in Europe in the 13th and 14th centuries. Comparisons of your Y-DNA to other members of the Project with the same surname establishes your genetic distance from that individual. The number of observed genetic differences (observed genetic distance) produces a "mathematical probability" you could have shared a common ancestor with that person within "X" number of generations. The greater the genetic distance, the less likely you share a common ancestor who lived after surnames were introduced. The smaller the genetic distance, the greater the probability you share a common ancestor who lived after surnames were introduced. Let's now discuss the significance of your Haplogroup designation.

Table 1 is an illustration of how your test results will appear on the Project Results Web Page.

Table 1: Example Presentation of Your Y-DNA Results

When you order a test kit from from a Genetic Testing Lab similar to FTDNA, you will be assigned a "Kit Number." The Project uses this number to uniquely present and identify your test results on one row of the Project Test Results web page. In this example, your assigned kit number will appear in the first column in the cell with this background color. The cell above "Your Kit #" is the label for this column. The entries in the columns to the right of "Your Kit #" present the test results reported by the laboratory that tested your DNA sample. Only your Kit # will be presented, not your name, which appears on the Member Web Pages. [Group 1 Members; Group 2 Members; Other Members.]

On Your Kit # Row in the next column is your Haplogroup reported by FTDNA; in this example, R1b1b2;  Above this entry is a shorthand label for this column; "Haplo." The next 37 columns report "number values" related to test results at specific "Markers" tested by the genetics lab.

Examine the first column after your haplogroup result. The number value is 13; and the label above this is 393. The number value in this column is reporting the test results from a DNA sequence at a particular region on your Y-Chromosome. Geneticists refer to these DNA sequences as Short Tandem Repeats (STR); each sequence assigned a unique DYS number (DNA Y-chromosome Segment number.) STR, DYS#, and Marker definitions are as follows:

In our example, the number value 13 would be the number of Short Tandem Repeats occurring at the DYS-393 Marker Location on your Y-Chromosome. Above this DYS-393 label is the label number 1. In the column left of this number is the label Marker #; entered in the first column of this row. In our example Marker #1 is another label for DYS-393 assigned by the FTDNA and the Project. When we discuss Marker #1, we are referring to your test result value at DYS-393. There are 37 DYS Markers evaluated by the Project; the other 36 identified in the columns right of DYS-393. In the row above each DYS Marker label is the Marker # used by the Project. 

At each DYS marker, your test results will have an "ALLELE" value which is the number of STR repeats. The following is the definition of Allele: 

While I could go into a lengthy and complicated discussion of how the labs obtain the allele values you will observe in your test results, I suggest you click HERE for a more technical explanation and demonstration of how the allele values are obtained.

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Your Haplotype

The following is a definition of Haplotype:

Table 2 is an illustration of the presentation of Panels 1, 2, and 3 and the corresponding haplotypes.

Table 2: Haplotype Illustration

The allele values having this background color are a collection of DYS Markers 1 through 12; labeled as the Panel 1 (1-12) Haplotype. Allele values with this background color are a collection of DYS Markers 13 through 25; labeled as the Panel 2 (13-25) Haplotype. Allele values with this background color are a collection of DYS Markers 26 through 37; labeled as the Panel 3 (26-37) Haplotype. While you can be tested over more DYS Markers than those above, these are the DYS Markers presently analyzed by the project. When you order a test from Family Tree DNA (FTDNA), you have the option to order a test over Panel 1 (Y-DNA12); test over Panels 1 and 2 (Y-DNA25); or a test over Panels 1, 2, and 3 (Y-DNA37). If you order test over Panel 1, upgrades are available to later add Panels 2 and 3 to your test results.

In our Project Analysis, we will be discussing your test results in comparisons to others using three specific haplotypes, each a combination of Panels 1, 2, and 3. These haplotypes will labeled as follows:

The following is an illustration of each of these haplotypes:

H12 Haplotype Illustration

H25 Haplotype Illustration

H37 Haplotype Illustration

If you have chosen to only be tested over the Panel 1 markers (Y-DNA12), your H12 haplotype can only be compared to those in the Project tested over DYS Markers 1 through 12. [Everyone in our Project has been tested over these Markers.] Because you will not have test results for Panels 2 and 3, your you will not have results that can compared to those in the Project who have the H25 and H37 Haplotypes. When comparing your test results to others in the Project, the number of Markers available in the above three Haplotype comparisons will have advantages and disadvantages and will be the subject of the next section entitled "Understanding Your Haplotype Comparisons and Genetic Distance."

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Haplotype Comparisons and Genetic Distance

Genetic Distance is a first test of relatedness between when the genetic results of two individuals are compared to each other. Table 3 illustrates some specific comparisons to explain the calculation of genetic distance. In this case, your example H12 haplotype will be Kit #A compared to kits numbers B through D. The cells with this background color are comparisons that do not match your allele value at that Marker.

Genetic Distance Comparisons.

Using Rules 1 and 2; your genetic distance in each of these comparisons would be as follows:

FTDNA provides general guidelines for interpreting genetic distance. In the above comparisons, FTDNA would interpret the following for the P12 Haplotype:

FTDNA has additional genetic distance interpretations for P25 Haplotype and P37 Haplotype comparisons.  

In my analysis, I will use FTDNATiP™ — a process that takes into consideration the mutation rates for each individual marker being compared. The Haplotype comparisons discussed will yield a "mathematical probability" the persons compared have a common ancestor who lived within the last "X" number of generations. The greater the genetic distance; the lower the probability they share a common ancestor who lived within a reasonable number of generations. In my analysis, I define a reasonable number of generations as 20. Why have I chosen this definition for "a reasonable number of generations?" By the calendar year 1500 (five hundred years earlier), surname usage was common throughout Europe and Great Britain. Before 1500, surnames were rarely assigned to male individuals.

A conservative probability of 80% or greater — for the purposes of this discussion — will be considered a confidence threshold of sufficient probability to declare that any two individuals compared most likely did have a common ancestor that lived within the number of generations specified. Probabilities below this threshold will be deemed insufficient. This threshold is intended as a guideline and should be the subject of further interpretation when the plots approach 80% from the direction of greater or lesser probabilities.

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Below is a Time to Most Recent Common Ancestor Chart. This is a comparison of two individuals who are a perfect match at all 37 Markers. The three plots are the resultant probabilities calculated using FTDNATiP™. Observe the H12 haplotype will have a probability of about 87% there is a common ancestor who lived within 20 generations earlier. Now observe the improved probabilities in the H25 haplotype having 13 additional markers to compare. There is now a 85% probability they share a common ancestor who lived within 8 generations earlier. There is a 89% probability they share a common ancestor who lived within 5 generations in the H37 haplotype comparison. 

This illustrates the advantages of testing over more than 12 markers. If there is a genetic distance of 1 over the H12 Haplotype, this will not be sufficient to prove you and the person compared have a recent common ancestor. You would then need to upgrade to 25 markers to have sufficient genetic evidence to make that determination. A perfect match over the H12 Haplotype has been found to be sufficient — so far — in our Project Member comparisons.

Now that you understand how your results will be presented, I suggest you go to the Y-DNA Results Web Page.