29 Apr 2016

Y-SNP Discovery, Part I

Go to Part II

First, a couple of announcements: A second tester from CF07 has ordered his Big Y. The Most Recent Common Ancestor (MRCA) is John A Cooley (1753-1794), married to Rachel Kinchen(?). Just as they share an ancestor in John, the testers' shared Y-DNA mutations would have come from him. Therefore, once the results come back and are analyzed, we will have a specific DNA profile for John, a profile that others can test for without the great cost.

And a second descendant of Benjamin Cooley of Springfield, MA has volunteered for the Big Y. In a few months, we'll have a specific profile for him, one that will fill in some of the obvious gaps in the Y-STRs in CF02 (see the Cooley DNA Project).

SNP Discovery

Things to know:

The Y holds about thirty-five million tiny molecules called bases. These bases are comprised of one of four chemicals, abbreviated to A, C, G or T. Now, remember that our cells regularly divide into cloned copies. This division continues through the reproduction cycle, from the making of sperm and eggs to the development of the zygote, the embryo and the child—one generation after another. It might be said that we're merely carriers for our immortal DNA, which has survived from the beginning of life and, hopefully, will survive long into the future.

But something happens to the Y every several generations—a tiny mutation occurs on one or more of the bases and its value (A, C, G, or T) flips to another. This is called a mutation, or SNP. Can you spot a mutation here?

From: A C C T G T T A
  To: A C C T A T T A

This mutation would have occurred with the production of a sperm cell belonging to a specific man—perhaps even thousands of years ago. If a son inherits it, he passes it on to all his sons, and so it goes. A new "line" of Y chromosomes has been created, one that is distinct from all others. Over the period of hundreds of thousands of years enough mutations occurred that we can build an elaborate as I've done with this simple tree for some of our Cooley families:

Many of us know enough about our recent ancestry that we can say things such as "I'm half German and quarter Italian" or even "I'm sixteenth Cherokee." We all understand that this person has a parent of German descent, a grandparent who is Italian and a great-great grandparent who was Cherokee. But if we slightly rephrase it as "my DNA is half German, quarter Italian, and sixteenth Cherokee" an obvious fact stands out: the more DNA you share with someone the closer you're related to them. We see this same relationship represented with "first cousins," "third cousins," etc. The degree of distance can likewise be determined by looking at a family tree. The closer on the tree two people are, the more DNA they share—simply because they share a larger number of ancestors.

Of course, because the Y chromosome is passed down only through the single father-line, which is just a tiny thread along our ancestry, there's only one "ethnicity" represented. But something similar occurs: just as sharing more ancestors means a closer relationship, the more shared mutations means likewise. This is because these mutations occurred at the births of specific individuals along the tree, whether we know their identities or not. We might as well call YP609, YP4248, and BY3233 Tom, Dick, and Harry. Just like determining relationship on a family tree, we can get an idea about how closely related Dick and Harry are by counting the number of mutations they share.

Now, ponder this SNP tree for Cooley group CF01 and related families:

Remember, each (or mutation) occurred in specific men at various times in the past. "Upstream" SNPs emerged in men who lived further into antiquity than did "downstream" SNPs. We know what SNPs these men possessed because they were passed down to the present generation: we have them. They can easily be sorted out into a tree by comparing test results of living men. For example, looking at the above tree, I have SNPs A7497, YP4491, YP4253, YP4248, and everything above that dating back more than 300,000 years. I share all but A7497 with the other Cooley tester, YP4491 being our "parent" SNP (John Cooley of Stokes County, NC). And we know that YP4253 is "his" parent SNP because the Cooleys share it with the Hacketts—they do not have YP4491.

As mentioned above, we could give SNPs more human names. In the meantime, we assign SNP names to forgotten souls much like we have with ancient skulls that sit in museums and archives, tagged with alphanumeric identities. We know the skulls but we don't know the men. We don't know the men in the SNP trees, but we do know something of their archived DNA. To a degree, we even know where these men (along with their SNPs) were born.