Saturday, November 3, 2012

Understanding Y-DNA Genealogical Testing


Good Day Everyone,

   How is everyone doing? In this document, the Y-DNA genealogical test will be explained. Some people are confused as to exactly what a Y-DNA test is. This document will serve to remove the confusion that surrounds a Y-DNA test. Currently, Family Tree DNA is the premier DNA testing company that performs a Y-DNA genealogical test. This is mainly due to FTDNA's large STR marker system. (I will explain STR's shortly). The company known as 23andME currently doesn't perform a Y-DNA genealogical test. 23andME provides only a Y-DNA haplogroup assignment which is an add on. Let's begin.

Basic Principals
     The first principal is that when two or people share or match regions of DNA, they share a common ancestor in their past. It is from that common ancestor that the shared DNA segments or regions are inherited. In this case, the common ancestor was a male.

     The second principal is that the more DNA you share with someone, the more closer you are to that person. This means your shared common ancestor lived in a more recent time. For example, a brother and sister's last common ancestor is their mother. On the other hand, two first cousin's last common ancestor would be their grandmother. As we are going to see, this principal is extremely important when considering Y-chromosome given its moderate rate of change.

Y-DNA Basics
     So first off - ladies please don't be upset LOL. But a Y-DNA test is strictly for men. Here is why!! Humans have 46 chromosomes. In men, the last chromosome, (46th chromosome) is known as the Y-chromosome. The Y-chromosome is sometimes called the Y-DNA. The Y-DNA has a gene on it called the SRY gene. This master swtich gene (which switches on a bunch of genes) converts a human embryo into a male. Therefore, by definition, only a male has a Y-chromosome (Y-DNA). The Y-DNA has an area of DNA that a Y-DNA genealogical test looks at. This Y-DNA area contains a type of DNA called STRs. STR stands for short tandem repeat. A STR is a repeat of a DNA sequence. I will explain.

     DNA has four bases called A,T,C,G. For example, a DNA sequence would be -> "GCATCATG". The DNA sequence,"CAT", is a STR marker. As you can see, the STR is repeated 2 times (CATCAT). Researchers have a STR naming convention called the DYS system. DYS stands for DNA Y Segment. For example, a common studied DYS marker is DYS393. DYS393 has the STR sequence known as "AGAT". If you see a statement that says "DYS393 = 3", then it means that the DNA sequence, "AGAT", is repeated 3 times like this -> AGATAGATAGAT.

   A Y-DNA genealogical test looks at the DYS markers that currently all modern human men have along their Y-chromosome. Let's take a look. 

Y-DNA Genealogical Test
     A Y-DNA test looks at the DYS markers along the Y-chromosome between any two men. All modern human males have the same set of DYS markers which are situated in the same order along their Y-chromosome. For example, along the Y-chromosome you will see DYS393-DYS390-DYS19 in this order from left to right. The reason for this is that all human men have a common distant paternal ancestor who is known as Y-Chromosome Adam

    A Y-DNA test will look at a set of studied DYS markers and values between any two men. If there are enough matching DYS marker values, then a common paternal ancestor has been revealed between two or more men. This common male ancestor may have lived within a genealogical time frame (last 100 to 200 years). STR markers can change between generations. For example, Male A may have DYS393=10. Male B may have DYS393=12. The difference is 12-10 which is 2. This difference is known genetic distance. Genetic distance is a property of a Y-DNA genealogical test. It's used to get a degree of the relatedness between two or more men.  

     The Y-DNA has a strict inheritance pattern. The pattern is son -> father -> father's father -> father's father's father -> etc. Like the Y-DNA which is passed from father to son, your surname (last name) is typically inherited in a similar fashion. Therefore, a Y-DNA is typically used to see if a group of men who have the same last name, are related. For example, the last name of Williams is fairly common. If you want to know if a group of say, male Williams are related, then a Y-DNA genealogical test would be used. This is commonly used today for adoption, name change, etc. Currently, FTDNA has a panel of 111 DYS markers which makes their Y-DNA test a very popular option.

     Companies such as Family Tree DNA (FTDNA) typically market, package, and sell their Y-DNA tests based on a set number of studied DYS markers. For example - a 12 marker Y-DNA test means a set consisting of 12 popular DYS markers will be analyzed by the DNA testing company. Your specific set of DYS markers and values is known as a Y-DNA haplotype. For example shown below is a picture my personal 12 marker Y-DNA haplotype:

If you click this picture shown toward the left, it will show my set of 12 DYS markers and their values. For example - my DYS393 marker has a value of 15. This means I have a DNA base sequence or STR of "AGAT" that is repeated 15 times along the length of my Y-DNA. 

If another male has the exact set of DYS marker values that I have, then we would be considered a match. This means that me and the other male gentlemen share a paternal common ancestor.  The more DYS markers you share with someone, the more likely you are closely related to that person. I placed the word "likely" in bold, because a Y-DNA test is not always a clear cut test in terms of measuring the relatedness of two or more men. Here is what is meant.

The current thinking is that a male should match to another male on at least 37 DYS markers and above to be considered related within a genealogical time frame (last 100 to 200 years). This is logical and reasonable thinking. However DYS markers can change between generations. 

For example - ideally a father and son, whom are closely related, should match on all known DYS markers. This is true since a son inherits a copy of his father's Y-DNA. However, it's possible even a father and son may differ in DYS marker values. 

To make things more interesting - sometimes the opposite is true. Two or more men can be an exact match on all of their shared DYS marker values and yet be distantly related. There are known cases where two or more men have been an exact match at 111 DYS marker values and yet turned out to be very distantly related (10th cousins). Cases such as this can happen in Y-DNA testing so one should be aware of this.   

While a Y-DNA test is typically used for recent ancestry, a Y-DNA test can be used to reveal deep distant ancestry. This is where haplogroups come into the picture.

Y-DNA Haplogroups
     A Haplogroup is a population of people who are all descendants of a single man or woman who lived in the distant past. In this case - we are talking about Y-DNA haplogroups. Each Y-DNA haplogroup has a unique set of markers that define that haplogroup. Every member of a single haplogroup bears the same unique set of Y-DNA markers which sets them apart from being a member in a different haplogroup. These unique markers arose in a single individual, the haplogroup ancestor, a long time ago. Letters of the alphabet are given to the different Y-DNA haplogroups. A popular Y-DNA haplogroup is E1B1A. Every person, male or female, has a Y-DNA Haplogroup. In essence, a Y-DNA haplogroup, such as E1B1A, represents a single male that lived in the very very distant past!!!  

     The DNA markers used for haplogroup assignment are known as SNPs (pronounced "snip"). A SNP is a DNA base that has changed. For example, suppose a DNA sequence changes from CATG -> CATA. In this case, "G" changed to "A". The base "A" would be considered a SNP. SNP's change very slowly which is why they are used for haplogroup assignment.

    There are approximately 29 known Y-DNA haplogroups. By definition, all modern human men fit into the African Y-DNA Haplogroup known as A. Haplogroup A is then split into the two major Haplogroups, B and CT respectively. From the Y-DNA Haplogroup known as CT, the remaining African and Non-African Y-DNA haplogroups (DE, F, etc) are descended.

    Because of people's different religious, marital, and social practices/histories, certain people tend to be strongly associated with certain haplogroups. For example, the Y-DNA haplogroup known as E1B1A is very strongly associated with African-American males. The Y-DNA known as Q1a3a1 is strongly associated with Native American males.

    It's important to know that your last common paternal ancestor and a haplogroup paternal common ancestor are two different men. Your Y-DNA haplogroup ancestor lived thousands of years ago, whereas your last common paternal ancestor (father or grandfather, etc) lived recently within a genealogical time frame.  All men are related distantly but not all men are related recently.

  Well that's it!!!! As always, it has a pleasure. If anyone has any questions, please feel free to ask.

Thanks
Steve

17 comments:

  1. Thank you very much, this article was very helpful.

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  2. Hi Steve
    I have read the above and still have trouble, I have had a mtDNA done and they have advised that I have a maxtch with someone with the 1-M223 Y-DNA Haplogroup, Im not sure what this meanx, are you able to help?

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    1. Mt DNA is mitokondrier = from your maternal side and has nothing to do with y DNA. A gentleman with that haplogroup share your maternal linage as it would seem

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  3. Hi Steve - I am at a loss here as I have never known who my father was and I carry my mothers surname of PHILLIPS but i am not a Phillips obviously and as we do not speak I will never find out the truth. However, I took YDNA test through FTDNA and it has come back with lots of YDNA12 0 Exact Match and 2 Step Exact match and one with a 1 step exact match. What does all of this mean. Also looking at the picture you have put on here with your first row of markers, we share 3 matches along the very same line - what does this mean ?
    Here is my first row just like yours : DYS 393 : 13 DYS 390 : 23 DYS19 : 14 DYS 391 : 10 DYS381 : 14-15 DYS 426 : 11 DYS 388 : 14 DYS 439 : 11 DYS 389-I : 12 DYS 392 : 11 DYS389-II : 28
    I am sorry to sound so lost here but all of this is complete gibberish to me at the moment and I would really like to understand it.
    Great article by the way !
    Thanks
    Anthony

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    Replies
    1. Hi Anthony how are you? The Y-DNA uses a series of repeated DNA markers known as STR or standard terminal repeat

      For example the DNA sequence CATCAT is an STR. Since the sequence (CAT) is repeated twice we give it a number of 2. Studied known STRs on the Y-DNA are called DYS markers. For example DYS393 is a known STR on the y-DNA. It's known DNA sequence is AGAT.

      Let's say both you and I have the DYS393 marker which in fact we do as all human males do.

      Anthony DYS393 = 1 (AGAT)
      Steve DYS393 = 2 (AGATAGAT)

      Our genetic distance is difference between the number of repeats. Since I have one extra repeat - the difference is 1 or step count.

      Matching on the Y-DNA between two or more men means a single shared male common ancestor that lived in the past

      Hope that helps

      Steve (Sorry for the late response)

      Sent from my iPad

      On Aug 1, 2015, at 10:02 AM, "Anthony Phillips" wrote:

      Hi Steve - I am at a loss here as I have never known who my father was and I carry my mothers surname of PHILLIPS but I am not a Phillips obviously and as we do not speak I will never find out the truth. However, I took YDNA test through FTDNA and it has come back with lots of YDNA12 0 Exact Match and 2 Step Exact match and one with a 1 step exact match. What does all of this mean. Also looking at the picture you have put on here with your first row of markers, we share 3 matches along the very same line - what does this mean ?

      Here is my first row just like yours : DYS 393 : 13 DYS 390 : 23 DYS19 : 14 DYS 391 : 10 DYS381 : 14-15 DYS 426 : 11 DYS 388 : 14 DYS 439 : 11 DYS 389-I : 12 DYS 392 : 11 DYS389-II : 28

      I am sorry to sound so lost here but all of this is complete gibberish to me at the moment and I would really like to understand it.
      Great article by the way !

      Thanks

      Anthony

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  4. Head and shoulders the best simple explanation of Y-DNA testing terminology on the Internet. Thanks very much for taking the trouble to write it all up. I now know enough to start to ask intelligent questions of my own data.

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  5. I agree with the others. A very clearly written (therefore understandable) explanation for novices (like me). Question: For a given STR, say DYS393, is there a correlation with a corresponding rsid? If so, how does one find that? Thanks.

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  6. This comment has been removed by the author.

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  7. Hi I have my brother's test back can you help me understand

    PANEL 1 (1-12)
    Marker DYS393 DYS390 DYS19** DYS391 DYS385 DYS426 DYS388 DYS439 DYS389I DYS392 DYS389II***
    Value 13 26 14 10 14-15 11 12 11 12 11 28
    PANEL 2 (13-25)
    Marker DYS458 DYS459 DYS455 DYS454 DYS447 DYS437 DYS448 DYS449 DYS464
    Value 17 9-10 11 12 23 15 19 31 15-16-16-16
    PANEL 3 (26-37)
    Marker DYS460 Y-GATA-H4 YCAII DYS456 DYS607 DYS576 DYS570 CDY DYS442 DYS438
    Value 10 10 19-20 15 13 15 20 37-40 11 11

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    Replies
    1. The values at each marker unto themselves don't tell you a lot, but I suggest he join a similar surname group and compare these "mutations" to those persons. Then compare your family research with theirs. Your goal can then be to find a common ancestor by pooling your research.

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  8. Why is a 10th cousin so weird at 111 markers being matched, unless there are females along the direct line???? I have several 8th+ cousins who differ only slightly at 111. Our common ancestor was 12 generations ago in 1620+

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  9. I've learned more from this section than from many websites. Still, I haven't found yet what markers define each haplogroup. Thanks Steve.

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  10. I've learned more from this section than from many websites. Still, I haven't found yet what markers define each haplogroup. Thanks Steve.

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  11. Hi Steve, I have been researching a very common named ancestor, Williams, and had y-DNA of my brother compared to a man whose family I had researched through census and believed to be related to my great grandfather. Our family stories had him as an orphan, James Williams. I ordered 67 markers for both of the samples I sent and they match in all the markers except two. The Haplogroup for them is R-M269 for both. I'm confused if this does confirm the relationship because, according to my paper research, the common ancestor is connected at 4 generations (brother, father, great grandfather, gg grandfathers were brothers). The odd thing is that both of the kits I ordered from FTDNA never get the same matches. I'm confused to say the least. Becky

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  12. I should have added that the relationship on my testing says the two samples are connected farther out than 4 generations.

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