Michael Cooley's Genetic Genealogy Blog GEN • GEN
2 September 2016

Y-STRs & Y-SNPs & the CF01 Cooleys

I wrote earlier about the difference between SNPs and STRs. But how do these mutations compare to one another as genealogical tools? All Y chromosome mutations occur at the birth of a man and pass to his sons who, in turn, pass them on to their sons. But STR mutations are rather flaky in that they can mutate regularly through the generations. Still, they remain effective in placing testers into general groups according to the number of shared mismatches. You can see this at the Cooley DNA Project. The fewer the mismatches, the closer the likely relationship. The greater the number of mismatches, the older the connection. It's called genetic distance and can be used to broadly estimate when the most recent common ancestor (MRCA) might have lived. SNP mutations, however, can nail it; they pass through hundreds of generations without change, allowing the population geneticist, as well as the genetic genealogist, to obtain a more accurate fix on the MRCA. But let's first start by looking closer to home. Not only to the descendants of John Cooley (c1738-1811) but to the present time. We'll reach down deep into the bottom of the barrel — me — and work our way into the past.

I'm a mutant. The STRs (Short Tandem Repeats) at the Cooley DNA Project show that all CF01 testers, save me, have 33 repeats of TTTC at DYS449. I have 34 repeats. Testing my father's sample for the marker, I found that he also had 33 repeats at that location. In other words, the sperm cell that created me — and it would have been very much alone among its mates — had an additional repeat of TTTC. And I have a second STR that varies from the CF01 modal (the average results of all participants). Testing for that one, too, it turns out that my father also had the mutation. This repeat was either born with Dad in 1925 or passed down to him from his father. I refer to it here as DYS609=15. W know little of its origin. John Cooley of c1738 did not have it, but neither did his son Edward. We know that because a collateral line from Edward doesn't possess it. Therefore, the additional repeat came into the lineage between 1789, the birth of John's grandson John, and 1925.

Before discussing STRs in respect to the group as a whole, let's dwaddle a time on my SNPs (Single Nucleotide Polymorphisms), single point mutations that occurs when one of four molecules flips to another. I have four "private" SNPs, that is four that have not yet been found in any other sample. These mutations have the names A7497, A7498, A12123, and Z11827. Due to a sort of triangulation, discussed in article #20 and below, we know what SNPs John Cooley had in his genetic code at his birth. This knowledge comes to us from the Big Y results for myself and another tester descended from another son of John's. (Remember that the Big Y looks at ten million positions on the Y chromosome.) The SNPs he and I both have could only have come from John. Because John didn't have my private SNPs, they came into the lineage sometime between the birth of his son Edward in 1763 to my own birth in 1950, a period of about 187 years. Let's look at the lineage below, taking note of the three SNPs John was born with, my four private SNPs, and the STR that my father had:



The horizontal line represents not only the genealogical lineage moving from left to right but also the genetic continuum, which passes from one generation to the next and is virtually immortal. We know these mutations came about during the passing of eight generations, or 187 years, but can we be more precise than that? With the right testers, yes, we can. It merely takes one tester in each of the collateral lines. For example, I've been in contact with three men descended from Edward who descend from sons other than my John (1789-1866). If testing were to indicate that one of these mutations originated with Edward, all his patrilineal descendants would have it. The advantage in such testing is largely academic, but if a marker is found to have been present it could be used to prove descent from Edward.

With five mutations, including DYS609, the number of possible lines of descent is quite large (58 = 390625). This graphic illustrates a small handful of possibilities. A descendant of David Cooley through his son Thompson, an older brother of my Greenberry, already has such a test (all five markers) in the hopper at yseq.net. We'll soon know which mutations came prior to Greenberry. What's left came into being since David.



When we consider the tens of thousands of SNPs now on record, it's estimated they appear, on average in a given lineage, about once every 144 years (a number that changes as new samples are added to the database). My four private SNPs came at a fairly fast clip over just eight generations (from Edward to myself), an average of one every 47 years, far greater the average rate. Of course, the pattern for any one line can be considerably different than the average (mutations, after all, are random), just as tossing a coin six times will likely not result in 50/50.

Again, this is merely an academic exercise and is apropos only to Edward Cooley's descendants, but it illustrates the technique for finding shared markers through triangulation. Now let's take the longer view. The following tree is reconstructed from six Big Y tests and covers more than 2000 years. John Cooley's descendants have all five SNPs represented here, plus those listed below each slide. The Hackett tester has the upper four, Cochrane three. The Forsgren lineage branched off after the emergence of YP609 about 2500 years ago. From that point, Mr. Forsgren descends from a different line of SNPs, just as surely as he descends from a different lineage of men. The added benefit to mapping this out is that we can see the migration from Scandinavia to Scotland then England. John, of course, came to the American colonies where all his children, it's believed, were born.



Moving deeper into CF01 we find a group of Cooleys very closely related to John's descendants. Three men from this group have tested and one has tested positive for all three SNPs in the YP4491 block, which verifies their relatedness to John. Two descend from William Henry Cooley (1797-1877) born in Pennsylvania. Another is descended from James Cooley (1808-c1872) of the same state. Since both lines came out of Pennsylvania, we refer to them as the Pennsylvania Cooleys (not to be confused with CF04, the Pennsylvania Cluster). There's a case to be made that William and James were brothers, although we don't know that for sure. They lived near one another as young men in Ohio, just across the Pennsylvania border, and later went to different counties in Illinois. Coincidentally (or not), James took his family to Jack County, Texas where a branch of John Cooley's descendants were already living.


The fact that two of the STRs shared among the three are quite different from the values shared by John's descendants provides a significant clue to the degree of relationship to John Cooley. Furthermore, the values are yet different than those of the Hackett tester, and he shares those with the Starrys, Cochranes, and others, indicating they're the older values. Below we see that both Cooley groups share one or the other value with Hackett et al, which further affirms that the Hackett values are the ancestral values:



And now we arrive at the question du jour: Were the Pennsylvania Cooleys descended from or collateral to John Cooley? It's not impossible that William Henry Cooley and James Cooley were grandsons of John's, but the collateral descent is far more likely. For one thing, of all the sons that John had, we're unable to find any of them in Pennsylvania, the place of birth for William and James. The following two slides support further indicate a collateral lineages. In the collateral descent, the Pennsylvania line would have acquired the DYS376 mutation somewhere between the time of the formation of the YP4491 block of SNPs and John's birth ca. 1738. John's own DYS464b mutation would have occurred during the same interval.


Keep in mind that in order for William and James to have been descended from John, they almost certainly would have had the same father, a son of John's. For that to have worked, John needed to have been born with or inherited the DYS464b=13 marker. Then at the birth of his son, the same STR would have reverted back to the ancestral value of 15 and the son would have also acquired the added repeat for DYS376. This is not a likely scenario.

How can this question be resolved? The genealogy has certainly not been forthcoming. And there's no guarantee that further DNA testing would settle the matter. Still, among the tests now available, at least one Big Y would have a chance of succeeding. Because it looks at ten million locations, it's the only test that can discover previously unknown SNP mutations. Any mutations the potential tester has that I lack would become his private SNPs, those that only he is known to possess. They can be tested by the other descendants for $17.50 a piece at yseq.net. If none match, then we're back to where we started. But any matching SNPs would become highly significant and would further suggest a line collateral to John's. Additionally, the Big Y extracts nearly 500 STRs. FTDNA doesn't report them, but the data goes into a file that can be obtained and sent to YFull.com for reporting. There could be real nuggets hidden in them.

Why bother doing this? To date, William and James are at the end of the line for the three testers. No one knows the identity of their father(s). By the same token, no one knows who John Cooley's father was. Determining the degree of relationship between the two CF01 groups will take us a step in the right direction. And I've recently been contacted by a new tester who has a 100% 37-marker STR match to the North Carolina Cooleys. He's a descendant of William Whitfield born in 1751 somewhere in England. Judging from his STRs, he's likely closer related to John Cooley than are the Pennsylvania Cooleys. With advanced SNP testing within both camps, a point of convergence might be discovered. And there's also a matching Agerton tester. His father, however, was adopted, and an autosomal DNA match suggests he might have descended from John's son Perrin Cooley. In the way that more pixels on a TV screen provide better resolution so do more DNA data points. Of course, there's always a desire for more.

It's stuff like this that keeps me up at night.