Q. What is a SNP and how can I use them to figure out how I'm related to my matches?

A. SNP is short for single nucleotide polymorphism. They are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. When this occurs it is a mutation (or change in your genetic code) that we can then use to determine how people are related to each other. Since these mutations occur in individuals, that means that people who share the same SNP ultimately inherited them from the same individual—a common ancestor.

A SNP occurs approximately every 120-140 years.   So if you have a terminal SNP assignment like I2-M223 (most common in this group) that occurred around 12,200 years ago, it is likely that you are ALSO positive for 85-90 additional SNPs that occurred AFTER that time.  Next Generation testing has revealed much more recent SNPs.  Unfortunately, no one in this group has yet done Big Y.  So most of you only know the name of a mutation/SNP that occurred around 5000 years ago.  (This SNP will not be the same as your SNP assignment unless you have paid to do additional testing).   Once our group has multiple Big Y results, we will be  discover SNPs that you share with your matches within the genealogical time frame.   Then as time goes on these new SNPS will be available for others to test quite inexpensively.  

Q. Why does Family Tree DNA show that my Y-DNA Haplogroup is something different than what you are showing on the phylo tree? Did my Y-DNA Hapolgroup change?

A. Haplogroups are named after SNPs, and in many cases Family Tree DNA makes a prediction about your haplogroup based on your Y-chromosome STR/match results. Since SNPs are mutations that occur in individuals, and thus indicate common descent, haplogroups are not mutually exclusive. (Take a look at the trees provided on the results page).   

Most of you are members of the Haplogroup I2-M223. As you can see, that haplogroup is a sub-haplogroup of I2-P215, which is a subset of many other earlier SNPs.  Thus you are also all members of every preceeding SNP haplogroup.  

So your haplogroup will never change, it is just being gradually revealed as more recent SNP mutations become known. Your precise haplogroup will only be discovered if you do a test like Big Y or full genome testing. If you are in the M223 haplogroup, you will notice that some of your matches show their terminal SNP as M223 and others have been assigned Y7244 or P53_3.  

The difference in how these SNPs have been assigned may be because one person tested 10 years ago when a particular SNP was not known, or it may be because one person has paid to test for a specific SNP. Unfortunately, Family Tree DNA does not update predictions as new SNPs are discovered, so a father's prediction will be different from his sons if they were tested years apart. Still you are all the same! 

Also, keep in mind that just because someone does Big Y doesn't mean that their SNPs are available for purchase at FTDNA, or even recognized by the genetic community. A SNP has to be found in a certain number of individuals before it becomes "officially" recognized.   

Q. What is Big Y and how can it benefit me?

A. Big Y is a direct paternal lineage test that looks at 12 million locations on the Y Chromosome. Big Y is able to detect new branch markers that are unique to your paternal lineage, surname, or even you. Because a SNP will mutate approximately every 144 years (one of the nucleotides A,C,G or T will change), the age of a SNP can be calculated.  The more men who do Big Y, the more accurate this date becomes.

When two or more men share a SNP, that SNP becomes a common SNP and its position on the SNP tree can be determined and a date can be predicted. But as you can see that leaves scores of SNPs that have been found in some of your matches. If you also do Big Y you will be able to pull out even more of these SNPs, get them dated and contribute even more of your own novel SNPs.  

Q. I just got my Big Y Results.  What is the next step?  

A. The next step is to get your results analyzed by haplogroup administrators and even outside sources like  YFull for both analysis and inclusion in their experimental Y Tree.   In order to do this, you  will need to send them your BAM file.  However, this file needs to be requested from Family Tree DNA.    You can request it by clicking on the  "contact us" link at the bottom of the page.  On the next page select "Open Request".    The fourth item down is "Big Y BAM Request".  Select this and just say that you want your BAM file.   

In about 4 working days you should be able to access this BAM file.  You can find it on your Big Y result page in the top right hand corner.  Select "Download Raw Data".  Next select "share BAM file".  After that you will need to copy the link in order to share it.   The administrators in your haplogroup project is also likely to  want your BAM file.  Every haplogroup is different, so contact them for more information.   YFull will not charge your for adding your results to their experimental tree, but it will cost $49 if you want access to your results.  You do not get charged until your results are ready.

Update:  In mid January FTDNA reported that BAM links would not be available for 6 weeks.  They still have not reinstated the BAM links.  So stay tuned on this issue.

Q. Should I upgrade to 111 markers, or buy a SNP Pack?

A.  Frankly, if you are at 67 markers, please save your money and do not upgrade.  WE NEED BIG Y!!  Not a single cluster in our group has discovered a SNP that occurred within the genealogical time frame.  So even the best SNP Pack is going to only give you the name of a SNP that occurred around 5000 years ago. 

Additionally, Big Y is reveling that STR/marker results are highly unreliable.  We are discovering that BACK MUTATIONS occurred much more often than previously thought.  (What this means is that a "19" might change to a "20" and then later mutate back to a "19").   Consequently, your best matches may not really be your best match and matches who do not appear to be very close could be your best.  The future of genetic genealogy is SNP testing, and I feel very confident that in the future we will have a SNP/Phylogenic tree that merges with the paper trail.  When this occurs groups will be split into much smaller groups and we will know with great accuracy when one group split away from another.  

Before ordering an upgrade PLEASE check with an administrator.  

Q. How can I attach my branch to the Phylogenic/DNA tree if I can’t afford Big Y?

A.  A SNP Pack is the only way at the present time that you can do this.  However, as the SNPS in this SNP pack are not recent, they will only place you on a very distant branch.  Then once we do have some Big Y results in your cluster, you will need to test additional SNPS.  So some may benefit from a SNP panel if they have no clue where they fit, but in most cases please hold off.  Once we have Big Y results it is possible for you to test some of these newly discovered SNPs at an independent company called YSeq for $17.50/SNP. Depending on interest in this group, we could look into putting together our own SNP panel.  By testing positive for one of these SNPs, you will add yourself to the SNP tree. Of course, this is more of a "guess and check" approach, but as we learn more about each of these SNPs and are able to place and date them there will be much less trial and error involved in figuring out what to order.

Q. I've already taken a Y-Chromosome test through Family Tree DNA. Why should I take more tests?

A.  Most of you have taken one of the basic Y-DNA tests which only test Short Tandem Repeats (STR). STRs are a little different than SNPs in that they represent a certain section of DNA that tends to repeat itself often. These tests are very useful to determine relatively close relationships, but they aren't good for establishing the tree shown above because they tend to mutate back and forth, and are therefore less precise.

In many cases, an STR test is the best test to take. Not only does it allow you to find close genetic matches, it can also be used to predict your SNP by comparing your STR results to others who have also taken SNP tests. If it wasn't for your STR test, you would not have been identified as a member of one of the Speer-Spear-Spier haplogroups.   However, STR tests can only go so far,  and for the type of research we are hoping to do in this project, SNP tests are also necessary.