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An Introduction to Y-chromosome DNA Analysis for Genealogical Purposes.

This page was begun 27 September 2003.

Rather than try to reinvent the wheel, the following discussion began with the presentation in the Dowie Family DNA website.  I deleted and added in an effort to be clearer and more up-do-date.  I could have failed.  To see the original go to:  Dick Kraus, 9 September 2003.


Genetic Genealogy Utilizing the Y-chromosome

The following attempts to explain how modern developments in DNA profiling can help us unravel more information about our distant past and to discover or prove relationships of which we were unaware or uncertain.  It will help any living and participating male Kraus to establish the probability of a common ancestor with other participants.


Deoxyribonucleic acid - DNA - is present in every living cell & contains the blue print for life. Twenty-three chromosomes carry the genetic instructions that define who we as humans are and why we have the characteristics we do.

Our species, homo sapiens, has twenty three pairs of chromosomes each pair of which wrap around each other to resemble an incredibly long twisted ladder.  Both sides of this "ladder"  are made from sugar & phosphate molecules.  The rungs are made from nitrogen-containing chemicals called Bases.  Each of the two ends of a rung consists of one base, a sugar molecule and a phosphate molecule. There are four bases (A = adenine, T = thymine, C = cystosine, and G = guanine) which pair together in the middle of a rung.  For instance, AT & CG would be two Base Pairs.  The order that they create along the phosphate "backbone", or side of the ladder,  is referred to as the DNA Sequence or pattern.  It is the patterns that these base pairs form that is the basis of Y chromosome testing.

Chromosomes are paired packages of long segments of DNA.  In humans there are 23 chromosomes.  In twenty-two, the DNA segment pairs essentially reflect each other.  In the 23rd females again have a pair that are alike – both sides of the pair are called "X" chromosomes -- but in this 23rd pair, males have two very dissimilar chromosomes one called "X" and the other called "Y".  When a child is conceived it gets one chromosome in this 23rd pair from its mother - always an X, and one from the father - which may be either X or Y.

If the Y Chromosome is present the baby is a male.  Y is only transmitted from father to son, and is inherited mostly without alteration through the generations.  It is the only chromosome 90% (always the same 90%) of which escapes the continual reshuffling (recombining) of parental genes.  This makes it very useful to genealogists.  It is sometimes called the “non-recombinant Y” gene.

The Y chromosome “lives” in the nucleus of each cell in a male.  The good news is that it is a “small” chromosome.  The bad news is that this means it only has about 60 million specific, identifiable parts! – They are the bases mentioned above.  Fortunately there is one gene within the chromosome that does its real work – which is to determine that its host baby will be a boy.  That gene is known as the SRY gene.  It turns out that much of the material within that gene is duplicated material – copies of copies – a redundancy which provides super guarantees that its bearer will be a boy.


Y Chromosome Testing

The SRY gene is ideal for learning whether or not two or more males are descended from a common ancestor because, as part of the Y chromosome, it is passed on from father to son through all generations with only tiny changes (mutations) that do not occur very often. 

The SRY gene has definable segments of DNA with known genetic characteristics.  These segments are known as Markers.  A marker occurs at an identifiable physical location on a chromosome known as a Locus.  Many loci are designated by a number (known as its DYS#), according to international accepted usage.  The Marker is what is tested and the Locus is the address of the Marker on the chromosome.  There are two types of markers used in Y-Chromosome tests, STR and UEP.  

STR Testing sets one's Y-Chromosome Haplotype.

For testing for the most recent common male ancestors, Short Tandem Repeat (STR) markers are used.  STRs are short sequences of DNA, (usually 2, 3, 4, or 5 base pairs long), that are repeated numerous times in a head-tail manner.  Simply put, those markers are places on the Y-chromosome where the DNA "stutters".  The sequence at that point repeats a certain pattern over and over.   For example, at a particular Locus, a stretch of the DNA molecule might look like: GATA GATA GATA (remember G, A and T are three of the four Bases).  In this example, the same pattern is repeated three times.  It is the variation in the number of such repeats that enables discrimination between individuals as to their paternal ancestors.

DNA labs have found that they can use as few as 12 loci from within the SRY to test whether two or more males are descended from a common male ancestor, although in rare instances it is necessary to expend that to 25 bases to clarify ambiguous situations.  Just for future reference, I have had all 25 checked and recorded.  The number of mutations that vary between two males of common descent can be used to estimate how long ago their common male ancestor lived.

Several genealogical genetic testing labs are now selling kits that will allow one to take a cheek swab and return the sample for genetic testing. The tests return a "score” or value for the marker there, i.e. the number of times the pattern there is repeated at each locus tested. Those special "stuttering" locations or Loci are given names or addresses like DYS391 or DYS455.

Each of the numbers reported in a Y-chromosome test result refers to how many times a pattern is repeated at the indicated Locus.  The example above would return a value of "3" for the marker at that Loci.  The number of repeats found is referred to by geneticists as the alleles of a marker, and is the “value” or score of the Marker at those Loci.

An individual’s results, for all Loci reported, are his Haplotype, what I call a “DNA signature”.   Stronger the similarities between two haplotypes the more recent is their common male ancestor.  

Normally the Y-chromosome pattern is handed down unchanged from a father to a son.  But very occasionally small changes can happen in the copy of the Y-chromosome that the son inherits.  The changes that occur and are measured at STRs (for genealogical purposes) are that a son will have more or fewer repeats in the stuttering sequence at that location than did the father.  Usually the number of repeats, at the time of this change, will only differ by one. The son then passes the modified new version on to his own sons. 

These changes, i.e. mutations, happen to a STR marker only about once in 500 generations.  Twelve markers are ordinarily tested these days in genealogical testing.  So we can expect to see one mutation about every 40 generations (about 1000 years).  If 25 markers are tested, we might expect to see one mutation every 20 generations (about 500 years) or so.  That timing is very useful to genealogists.  With this mutation “clock” we can now begin to trace relationships in cases where records have been lost or back before the time when surnames came into use and accurate vital records began to be kept (in many cases that was only 300 years ago or less, except perhaps for noble families whose records might go back 700-1000 years.

We are witness to one recent such mutation in Uncle Joe Kraus’ line where the number of repeats at locus DYS#391 has within the last century decreased by 1 to 10, whereas the rest of us descended from David still have his 11 at DYS#391.

To see our status in terms of STR tests and Haplotypes, go to the Recent Story.

UEP Testing sets one's Y-Chromosome Haplogroup.

At present the human race is divided into 18 large groups (Haplogroups) of people who share a common male ancestor.  Each Haplogroup shows a different line of descent from the one male from whom we are all descended who lived some 140,000 years ago.   

Finding one's Unique Event Polymorphism (UEP) markers is the only way of identifying with certainty the haplogroup to which one belongs.  Haplogroups actually are defined by patterns of mutations found in these markers.   Often a UEP mutation involves a switch in a just one letter (i.e. a single base) in the DNA - known as an SNP (Single Nucleotide Polymorphism).  For example a "C" might have been changed to a "T".  UEP mutations have names like M170, M89, or SRY-2627.  

Once a UEP has occurred in one man’s chromosome, all the descendants of that man will also show that same mutation.  The real definition of a haplogroup is the group of all the male descendants of one man who first showed a given UEP mutation.  Each member of a haplogroup will have the same UEP mutation that first appeared in the haplogroup's founding father - along with the whole set of other UEPs that the founder himself had inherited from his forbearers.  Since these mutations are so rare, it is almost impossible that a second mutation would occur at the same spot to undo the UEP mutation back to its original state.  So UEPs are the ultimate "permanent record".  This is what allows population geneticists to identify the descendants of a group of people over periods of tens of thousands of years.

UEP mutations are very rare – only a few dozen have occurred in the last 150,000 years!  And they can happen to any one of the billions of letters (bases) that go into making up the whole DNA molecule!  That makes yours next to impossible to find -- unless the lab doing the testing has a hint.  In my case it did.  My Haplotype was "close" to several others who had already been identified as part of Haplogroup G.  So our lab was able, for an additional fee, to see if I had the UEP which identified Haplogroup G -- and I did!  Had I not, we, the Thuengen Krauses, would still be wondering to which Haplogroup we belong.

To check on our Haplogroup information, click on Ancient Story.

To get back to our DNA base page, click on it.  To get to the Kraus Project base page, click on it.  To get back to the Casebolt Project base page, click on it.  To return to the Casebolt Participant page, click on it.