17 April 2016

STRs & SNPs and the Cooley DNA Project

Y-DNA testers are very much aware of Y-STRs and those test results that generate a string of numbers, as illustrated in the Cooley DNA project. (The numbers represent the number of times a sequence of nucleotides repeats, say TTTA thirteen times.) By arranging closely-matched results, we end up with the groups. In the case of CF01, nearly all testers are known to have descended from John Cooley of North Carolina and the DNA evidence backs it up. On the other hand, it was presumed for a long time that most of those who have tested as CF02 likely descend from Benjamin Cooley of Springfield, MA. However, subsequent tests suggest that isn't the case. I've split the group, as best as I can, to better reflect the reality. But much more testing needs to be done.

Why?

But why test at all? The biggest reason for genealogists is that testing provides a record where there would otherwise be none. My John Cooley's family is not set out in any public record. If there was a will (I suspect there was), it burned along with the Casey County, KY courthouse in the nineteenth century. Earlier genealogists "reconstructed" a family using bits and pieces of information but it was DNA that cinched the likely into the probable. Nevertheless, DNA is better at disproving than at proving. The same DNA results, for example, have disproved the so-called Dutch Cooley lineage (hatched in the mind of Lura Coolley Hamil in the 1930s). In fact, there appears to be to merit at all to anyone of the name of Cooley having belonged to the Barent Cool family.

SNPs

But STRs can take us only so far. SNPs, or Single Nucleotide Polymorphisms, help provide a fuller picture. (A SNP occurs when a nucleotide, abbreviated to A, C, G, or T, mutates to another value.) For example, the CF01 Cooleys are a very close match, STR-wise, to a Hackett tester. The discovery of a new SNP, YP4248, suggests that the Hackett and Cooley lines split about 800 years ago, informing us that our Y-STR haplotype is far older than I, for one, would have expected. This also appears to be true with CF02. For example, the CF02/C is positive for U152 whereas CF02/A and CF02/B are negative for it. Rather than being separated by about the 375 years since Benjamin's immigration to Massachusetts, the common ancestor might have lived hundreds of years earlier.

Big Y

The best way to discover new SNPs is through a test called the Big Y, which looks at approximately ten million positions on the Y chromosome. David Cooley, former president of the Cooley Family Association of America and a Benjamin Cooley descendant, tested his Big Y about a year and a half ago. He matches to other testers down to a SNP called Y15926. Interestingly, tester 334918, in CF09, has it. But he also has the newly discovered downstream BY3233 SNP. Unfortunately, that position did not yield a good "read" in David's test. If he is shown not to have it, the two lines diverged about 2500 years ago. And that's the value in SNPs—it's possible to put lineage divergences into a realistic timeline.

David has twenty-five novel SNPs, those that have not yet been matched to subsequent testers. Once another Benjamin Cooley descendant tests, all new matches (and there will be some) would be attributed to their Most Recent Common Ancestor, whether that MRCA is Benjamin or a more recent generation, and David's novel SNPs will be reduced considerably. (I have only five remaining novel SNPs that came into my line since John Cooley. Everything else is matched to other testers.)

Other Tests

Other than the Big Y, there are two tests that are helpful. Only BY will yield new discoveries, but these can confirm someone's placement in a group. For example, anyone who thinks they belong to CF01 must have the YP4491 SNP, which may turn out to be a CF01-specific SNP. Individual SNP tests at FTDNA are only $39. But it's too expensive to test several SNPs so FTDNA has created SNP Packs. They start with a high level SNP and work down the tree to find the tester's *known* terminal SNP—the most recent SNP that can be identified among the currently-known data. The tests vary depending on how many SNPs are tested, but they work out to about $99-plus for 100-plus SNPs.

Recommendations

In a perfect world, each group should have two Big Y tests at $575 per test. (There are periodic specials amounting a $100 savings.) If the common ancestor is known, we learn what SNPs that person was born with. Those that are in variance with one another emerged later through individual lines.

David Cooley might want to test BY3233 ($39), but he'll learn the truth of it once another BY tester comes along, which much preferred.

Those who are not ready for the BY can do a SNP Pack. R1b testers (CF02, CF07, CF09, CF10, etc.) should do the M343 SNP Pack, which tests 138 SNPs for $99. CF04, which is of the R1a haplogroup, should do the Z284 SNP Pack, which tests 153 SNPs for $119. And E1b (CF06) should test the V68 panel, which tests 124 SNPs for $119.

But before testing, it's best to first contact me. I might have ideas that are more specific to your needs. Also keep in mind that, although these technologies have been around for awhile, genetic genealogy is still in its infancy. There's a lot of waiting involved for many of us. But new data, which is coming online at an ever-increasing rate, will propel the project forward. A year ago, my youngest known SNP was 2,000 years old. Through Big Y testing, I now know my SNPs down to my own birth. That doesn't tell me who John's father was, but one day SNP YP4491 probably will. And one day we'll be able to create a SNP tree like the one linked to above but having far greater detail and showing how the various Cooley groups and subgroups are related.

ANNOUNCEMENT: The CF07 Cooleys are of the Irish Clan Colla. Tester 140728 has recently received his Big Y results and a second tester in the group plans on taking it. Once done, they will know all common Y-SNPs down to their common ancestor.