Michael Cooley's Genetic Genealogy Blog GEN • GEN
2 March 2017

New Cooley CF02 Big Y Results

Firstly, some technical background. SNPs (Single Nucleotide Polymorphisms) are single-point mutations. A "G", for example, might have been miscopied during germ cell division to a "T." In the case of SNPs found in the Y chromosome — which carries the male sex gene — these mutations first appear with the birth of a man and are subsequently passed on to all his sons, their sons, and so on, virtually forever.

Secondly, some genealogical background. Thanks to Mortimer Cooley's fabulous book, The Cooley Genealogy (Rutland, Vt.: Tuttle, 1941) and his founding of the Cooley Family Association of America, Benjamin Cooley (1615-1684) of Springfield, Massachusetts is the most noted of all Cooley immigrants to America. He was born in Tring, Hertfordshire, England. Even a cursory search of the records reveal a large family of Cooleys present in Tring at his birth. To this day, there are representatives of the family living in the area.

Thirdly, some project background. The CF02 Cooley group at the Cooley DNA Project has altered considerably as new test results have come in. It's presently divided into three subgroups. Members of CF02/A have had no advanced SNP testing but are assumed to belong to haplogroup R1b-A12020. Members of CF02/B, which is comprised largely of known descendants of Benjamin Cooley, are positive for the SNPs A12022 and/or A12024.1 And members of CF02/C are negative for those same two SNPs.

We now have three Big Y test results for the CF02 Cooleys, those families associated (in some way, at least) with the immigrant Benjamin Cooley. The first two Big Y results (kits 128108 and 316005) — proved descendants of Benjamin's — established the R1b-A12020 haplogroup, a long series of SNP mutations that stretch back 3,000 and more years. We've also had two individual SNP testers (kits B3646 and 323365). That is to say, rather than doing the Big Y (which studies ten million positions on the Y chromosome), select SNPs were observed so as to determine whether the bearer is positive or negative (has the mutated value or the ancestral) for the tested values. Of these testers, one is descended from Samuell Coley (1614-1684) of Connecticut, the other from James Cooley, born in 1830 in Indiana. These test results carved out a small notch into the A12020 cloud in that neither tester has SNP mutations A12022 and A12024, which were formerly part of the broader A12020 haplogroup. Those SNPs, then, belong to the Benjamin descendants and, therefore, constitute its own subclade, haplogroup R1b-A12022.

The recently-arrived third Big Y (kit 559256) backs up these later SNP tests. A descendant of Nehemiah Cooley (c1685-1759), another Tring-born Cooley, also lacks the Benjamin SNPs. Furthermore, three additional SNPs (A14974, A14975, and A14976) are found in his results.2 So far, these are unique to the tester's lineage, if not to Nehemiah himself.

The R1b-A12020 cloud is so deep and vast that we will never see it fully resolved. In time, niches will be filled by other families having different surnames anciently associated with Cooley. Eventually, the top part of the cloud will be determined to be so old as to belong to an upstream haplogroup that emerged long before the time of surnames.

The Venn diagram, below, is another way to represent the relationships. Three things need to be pointed out:

The upshot is that we now have the ability to categorize all CF02 testers according to the presence of these SNPs. What is the value in doing so? If a tester lacks SNPs A12020 and A12024, the researcher is barking up the wrong tree if looking for descent from Benjamin. If the tester has, say, A14976, then he would do best to explore how he might be related to Nehemiah.

Short Tandem Repeats

These diagrams have the potential for becoming very much more complex. Still, it's likely that no more than three or four SNP mutations emerged in any one line from the Cooley MRCA (living, say, in the mid-1500s) through to the present day. SNPs may provide us with no more than "the big chunks" of the family tree — those SNPs that prove to be "Benjamin-like," "Samuell-like," "Nehemiah-like," etc. — but the Big Y also tests for nearly 500 STRs, those values found on the results page of the Cooley DNA Project.

STRs are Short Tandem Repeats, each being a unique series of genetic letters that are repeated X number of times. For example, DYS385a and DYS385b each has two repeating motifs, TCTG and TCTA. In the case of the CF02 Cooleys, DYS385a has 10 repeats of the two motifs and DYS385b has 15. This can be expressed at DYS385 = 10-15. But they mutate quite differently than do SNPs. SNPs — an A mutated to a C for example — are stable, and are known even to have passed from one generation to the next for 300,000 years. Repeats, on the other hand, often lose or add copies of the repeating motif, and that can happen multiple times — more than one addition (or deletion) in a single generation.

Because of the volatile nature of repeats, genetic genealogists look at the trend in a group by counting and comparing the "genetic distance" (GD) — the number of differences shown between any two samples. Indeed, the members of CF02 haven't been grouped together because they share the values of any particular STRs, but because the GD (the number of differences) does not exceed a certain number. Too many differences and the common ancestor is considered to be so ancient as be genealogically irrelevant. In other words, trend-wise, the greater the GD, the greater the supposed degree of cousinship.

These differences become more evident with a larger sampling of STRs. For example, if two testers have a GD of 1 over 12 markers, they could have a GD of 7 over 67 markers. That doesn't necessarily change the assumed degree of relatedness; it simply gives us more resolution. In my own group, CF01, I am a GD of 2 over 67 markers from my fellow Big Y tester. But the nearly 500 STRs pulled from our Big Y's show a GD of 14 over 414 STRs. That's an average of nearly one marker difference per each generation down each line. The two Benjamin testers have a GD of 22 over 382 STRs — again, close to one marker difference per generation.

FTDNA does not report the STRs picked up through a Big Y. Instead, the company provides a raw data file, known as a BAM file, to the tester. The BAM can be uploaded to YFull.com for further analysis. Although YFull reports SNPs within a few weeks, it takes several months before STR results are returned. It is my hope that the reported GD between the Nehemiah tester and the Benjamin testers will provide a clue as to the degree of relationship between the two men of Tring.

Is CDY = 37-38 Special?

There's another point to be made about STRs in relationship to this study. Despite the general rule of thumb not to trust the values of any one marker (as opposed to the trend of the many), some markers do prove themselves to be relatively stable, at least within the confines of a specific group. Occasionally, some variation within a group can be trusted. There are two such tell-tale markers in the CF01 group. Given that, it's worth noting that the three CF02/C non-Benjamin testers, including the third Big Y, share the CDY values of 37-38. Is this indicative of being negative for the Benjamin SNPs? We don't know yet. Indeed, CDY is a fast-moving marker. Although these values are in the minority in the group, they are shared by five other testers. If these testers are not descended from Benjamin, they will be negative for the Benjamin SNPs. There's nothing in concrete here, but it is worth looking into.

Further Testing

Those in CF02 who wish to pursue further genetic testing in an effort to determine a genealogy research plan can choose between three sets of tests:

This isn't exactly doing genealogy by genetics, but CF02 is closer to that than the other Cooley groups. And the group has a large number of Y-STR testers. With greater involvement, combined with an exhaustive study of the Tring Hertfordshire Cooleys, we stand to make significant headway.

1 I've just added kit 266911, a descendant of Reuben Ransom Cooley, to CF02/B for being positive for A12022 but so far unknown for A12024. If he turns out to be negative for that, there will be a fourth group.
2 It remains to be seen whether the others in the CF02/C subgroup have any of these SNPs.