The following table outlines the Y-DNA STR markers available at Genebase and the corresponding motifs used for allele designation in Version 3.5. 

Click here to view the conversion chart for Version 3.3 to Version 3.4. 

Click here to view the conversion chart for Version 3.4 to Version 3.5. 

Please note that Users from previous versions will be automatically converted to 3.5.

 *Variable regions in each motif are indicated in blue.

*Motifs used for allele designation in Version 3.5 are compared to NIST nomenclature, and marked as “same” or “different” accordingly. 

*Question mark (?) indicates that NIST data is currently unavailable.

What is “NIST nomenclature”?

NIST stands for “National Institute of Standards and Technology”.  NIST is a non-regulatory federal agency within the U.S. Department of Commerce with the mission to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology in ways that enhance economic security and improve our quality of life. 

NIST has compiled and maintained a Short Tandem Repeat DNA Internet Database called STRBase, a valuable STR information resource.  Click here to view the NIST standards for the most commonly tested Y-chromosome STR markers. 

To facilitate Y-DNA STR data comparisons between different laboratories and research groups, many laboratories choose to follow the standard NIST nomenclature to avoid differences in allele values due to different nomenclatures (motif and counting method) between different laboratories.  Most motifs in the NIST nomenclature follow the ISFG (International Society of Forensic Genetics) guidelines.  Click here to view the latest ISFG recommendations on the Y-STR nomenclature.

Genetic distance is defined as the total difference in allele values of different genetic markers between two individuals. The smaller the value of the genetic distance, the closer two individuals are related, and the more recently they shared a common ancestor (TMRCA). The method used to determine genetic distance for four different Y-DNA STR marker types is explained below.

A. Calculation of genetic distance for single-copy markers

For single-copy markers, the calculation is straightforward. The genetic distance for each single copy marker between two individuals is the absolute value of the difference between the value of the markers:

The total genetic distance between two individuals is the sum of the genetic distances of all markers compared.

B. Calculation of genetic distance for multi-copy markers Markers DYS385, DYS459, DYS464 and YCAII are multi-copy Y-STR markers.

For most multi-copy markers, genetic distance can be calculated by adding the differences in allele values for each of the two copies.

C. Calculation of genetic distance for multi-copy marker DYS464 - using Infinite allele model

Assuming mutations at different copies of the same marker took place in a single generation, the Infinite allele method counts the total difference between all copies of the same marker as 1, despite the fact that more than one mutation exists.

The genetic distance for DYS464 is calculated using this method.

D. Calculation of genetic distance for DYS389i/ii

DYS389i is embedded in DYS389ii; therefore, the DYS389i values are included in DYS389ii values. Genetic distance can be determined by adding up two differences: differences in DYS389i values and differences in the second part of DYS389ii values, which are obtained by subtracting the DYS389ii values by DYS389i values.

The Y-DNA Test examines several different STR Marker Types:

A. Single-Copy Markers

Single-copy markers are DNA markers that occur only once in the human genome, resulting in one allele value for the marker.

B. Multi-Copy Markers

Markers DYS385, DYS459, DYS464 and YCAII are multi-copy Y-DNA STR markers that typically have two copies.

Marker DYS464 can occur in 4 to 7 copies in the human genome and the method for calculating genetic distance for DYS464 differs from the method used for other multi-copy markers.

Multi-copy markers are genetic/DNA markers that occur more than once (ie more than one copy) in the human genome, resulting in different allele values for each copy. For example, the markers DYS385, DYS459 and YCAII are typically present at two different locations on the Y-chromosome; therefore, they are also termed “duplicated markers”. For each multi-copy marker, the same primer pair binds to different locations on the Y-chromosome, thereby amplifying more than one region simultaneously, resulting in more than one allele value for that marker. The allele values for each copy are not reported in any specific order, as the exact order of copies cannot be determined, but typically, the smaller allele value is reported first, followed by the larger allele value.

C. Special Multi-Copy Marker DYS389

DYS389 is a special marker. Unlike other multi-copy markers, only one location is amplified. The forward primer for DYS389 binds at a specific location on the Y-chromosome, whereas the reverse primer binds at two different locations. Such amplification yields two PCR products:  the shorter DYS389I fragment and the longer DYS389II fragment.

Once your buccal swabs arrive in the testing laboratory, the following steps are involved to obtain your Y-DNA haplotype:

1. When the laboratory receives the cheek swab samples, the cells are removed from the swab into an eppendorf tube.

2. The cells are then lysed (broken apart) to release the DNA.

3. The DNA is purified and quantitated.

4. The STR markers on the DNA are amplified using a process known as polymerase chain reaction (PCR). During PCR, the specific regions of the DNA to be analyzed are amplified so that they can be analyzed. A primer pair is used to amplify each marker.

5. The DNA strand is heated to separate the strands and the primers anneal onto the DNA template. TAQ polymerase amplifies the region between the primers. The primers are designed to surround the STR marker. Using a series of heating and cooling steps, the DNA is repeatedly amplified using this technique. In a matter of an hour, millions of copies of the Y-STR markers are produced from a single original DNA strand. Each specific primer pair is labelled with a colored dye. Thus, all of the PCR products have a color coded label attached.

6. The DNA fragments produced by the PCR reaction are examined using a laser (capillary laser sequencing). During sequencing, an electrical current is used to force the DNA fragments to pass through a gel matrix within a fine capillary tube into a laser beam. As the DNA passes across the laser beam, the laser beam records the type of dye associated with the fragment, and the size of the fragment is recorded (smaller fragments pass more quickly through the gel and larger fragments pass through more slowly).

7. The results of the analyses appear as peaks on a computer output and these peaks each correspond to a Y-Chromosome marker. Based on the position of the peaks, the laboratory will be able to determine the exact number of repeats in the DNA marker and thus obtain the exact haplotype of that individual’s DNA.

Your Y-DNA haplotype is the specific set of results obtained after testing a set of STR markers on your Y-DNA. For example, if you take the 44 marker Y-Chromosome test, the combined result of all 44 markers is your unique haplotype and represents the unique genetic code for your paternal ancestral line.

Using your Y-DNA haplotype to search for or verify family linkages:  Your haplotype is the same or very close to that of all males who have descended from the same forefather as yourself.  That means that your father, grandfather and great-grandfathers along your paternal lineage all carry the same Y-DNA haplotype as you.  Also, all males living anywhere in the world today who descended from the same forefather as you will have the same or very similar Y-DNA haplotype as you.  Once you have tested your Y-DNA STR markers, you can use your haplotype to search for people who are linked to you on your paternal line.  You can also use it to verify whether any two individuals are descendents from the same paternal line.  Another common application is Surname Projects, which uses the Y-DNA haplogroup to determine how males with the same surname (last name) are connected to each other.

What is the difference between Y-DNA haplotype and Y-DNA haplogroup?

Y-DNA Haplotypes should not be confused with Y-DNA Haplogroups.  An individual’s Y-DNA Haplogroup represents his “deep ancestry”.  All males living today are descendents of a single individual who lived in Africa approximately 150,000 years ago.  Over time, our ancestors migrated out of Africa in waves and populated the world.  All males can be traced to one of less than two dozen main haplogroups (haplogroups are designated by letters, such as Haplogroup J).

Haplogroups are determined by testing a type of marker on the Y-DNA known as SNP (single nucleotide polymorphism) markers.  STR marker testing will not tell you your haplogroup, but in some instances, it can be used to predict your haplogroup as there are some correlations between certain haplotypes and haplogroups.  However, confirmation of haplogroups must be made through SNP testing. 

Haplogroups are useful for scientists who are studying human migration patterns and has archeological value.

Some haploytpes can be seen more frequently in certain parts of the world. For example, people whose ancestors are from the western coast of Europe often share in common a small group of Y-Chromosome STR markers. The group of Y-Chromosome markers which are frequently found in western Europe is called the Atlantic Modal Haploytpe (AMH). The AMH is characterized by the following markers:

DYS19 = 14
DYS388 = 12
DYS390 = 24
DYS391 = 11
DYS392 = 13
DYS393 = 13

More information about AMH can be found in Wilson et. Al. Genetic Evidence for Different Male and Female Roles During Cultural Transition in the British Isles. PNAD April 24, 2001 vol. 98, no. 9 pgs. 5078-5083.  Click here to download and print a copy of the original article. 

The AMH is tied to the R1b haplogroup.

A number of STR markers can be tested on the Y-DNA. The more markers that are tested, the more discriminating the matches when comparing to other individuals.

For example, comparison of 12 markers alone is generally not powerful enough to distinguish family lines and can give inconclusive results. The more markers that are available for comparison, the more discriminating the comparison becomes.

There are two major advantages for comparing more markers:

1.  To prevent false positives
2.  To obtain conclusive results

Scenario:

Mr. Jones has been studying his family’s ancestry for several years and has started a “Jones” family study based in Arizona. He is interested in confirming that his family line is linked to a “Jones” line in New York. Although there are rumours that the two lines are related, Mr. Jones does not have the paperwork to prove this link. Mr. Jones is also interested in finding out whether his line is linked to any other Jones lines worldwide.

Mr. Jones had previously chosen to test just 12 markers. After testing, he uses the 12 markers to search the DNA database and finds out that he is a perfect match to the Jones line in New York. However, he also finds that he has a perfect match to over 200 individuals in the database, and over half of them do not even share his surname. How is this possible? Does it mean that he is related to everyone who matches him at the 12 markers? No, this simply means that data from only 12 markers is not powerful enough to distinguish Mr. Jones from other family lines.

To clarify this, Mr. Jones decides to increase his markers to 20. He enters the results of his 20 markers into the database and this time narrows down the number of matches.  In fact, now, only 18 people match him perfectly at his 20 markers, including the Jones line in New York. Surprisingly, many of the individuals who used to match perfectly at 12 locations only match at 14 or less out of the 20 locations tested, confirming that there is no familial link with most of the 200 individuals identified in the 12 marker test (more than 3 mismatches indicates that two family lines are not closely related).

To further clarify the findings, Mr. Jones decides to upgrade to a 44 marker test. This time, he finds out that he is a perfect match at all 44 markers to only two lines, a Jones line in England, and a Jones line in the United States. After contacting the two lines and comparing paperwork and stories, Mr. Jones was able to confirm that his line was indeed definitely linked to both lines and he is now able to add both new lines to his family tree.

Surprisingly, Mr. Jones was also able to find out that only 43 out of the 44 markers matched with the Jones line in New York. This confirms that although the Jones line in New York is related to his line, they are likely more distantly related.

Mr. Jones also discovered that he had a close match to 4 other Jones lines (43 out of the 44 matched) and he is now pursuing the possibility that the 4 other lines are also distantly related to him (MRCA analysis dictates that 1 mutation occurs every 500 generations, and thus we would detect a mutation every 12 generations with the 44 marker test).

Mr. Jones is now trying to recruit more Jones males from throughout Europe to try to reconstruct and relink his family line.

Conclusion:

12 markers were not discriminating enough for Mr. Jones to pinpoint his family lines. After increasing to 20 markers, Mr. Jones was able to obtain more useful information and was able to eliminate false matches generated by the 12 markers. However, after increasing to 44 markers, Mr. Jones was able to pinpoint the people that he was looking for and was furthermore able to accurately answer his questions about his relationship to the Jones line in New York. Mr. Jones can continue to carry on his research, and as more and more people globally are tested and are added to the database, Mr. Jones will be able to reconstruct his family line in great detail and re-unite with Jones worldwide who are descendents of his family line.