Michael Cooley's Genetic Genealogy Blog
26 February 2019

Why Every Genealogist Must Understand the Y Chromosome

Autosomal DNA test results are great for finding second and third cousins, no matter which side of the family they sit. Careful analysis can uncover proofs for ancestors going back several generations. For example, a close study of several tests has indicated that Missourian Joseph Pettet, born in Pennsylvania in or about 1816, might not have been illegitimate after all.

Mitochondrial DNA (MT-DNA), which follows the tester's very specific maternal lineage, has provided evidence that shatters a long-held family myth — that Prudence Eldridge (died 1778), a.k.a. Princess Snowflower, was Native American. She might have had native blood, but she was undoubtedly of a European haplogroup. (Besides, Princess Snowflower, her native American name being Toudl-Hkilig, and her brother, Algonquian tribal chief King Nummy, probably lived a hundred years earlier than did Prudence.)

Like MT-DNA, the Y chromosome similarly follows a very specific inherited pathway. In this case, the fatherline. Because my Y is my dad's Y, which was his dad's Y, I know there once was a man (who lived in Britain...), straight up the paternal line, born perhaps five hundred years ago with a Y-DNA mutation we now know as YP4491. No, ifs, ands, or buts about it (other than the exact year the mutation emerged). In celebration of this remarkable fact, I've written a limerick.

There once was a man in Great Britain
Of whom a young lass was then smitten.
      In each their sons' genes
      (Even now it is gleaned)
Did their daddy's Y-markers get written.1
– Michael Cooley, 2019

Thanks to the popularity of Ancestry.com, autosomal DNA has become the go-to test for almost anyone interested in DNA for genealogy. However, perhaps for that very reason, a large percentage of the public remains unfamiliar with the power of MT- and Y-DNA. This has caused endless confusion and an incomplete understanding about the nature of genetic genealogy. The fact is that the Y chromosome just might be the most powerful tool in any genealogist's arsenal — better even than death certificates, wills, and census records. Simply put, biological truths can neither be ignored nor successfully disputed.

It's perhaps understandable that this has happened. Only men have a Y chromosome, which means that Y testing can be marketed directly to only half the population. Everyone, on the other hand, has autosomes (chromosomes 1 through 22). No matter who we are, an autosomal test will be just as relevant to the understanding of our genetic makeup as the analysis of the air we breath can be to our health. But personal experience has taught me that it's often difficult to explain that a woman's DNA had no influence over the sexes of her children. Yes, her father contributed to the genome of each child, but sex determination is solely the result of the genetic composition of the gamete (sperm cell) the father delivered to the egg.

We have two versions, two distinct copies, of each of our 23 chromosomes, each one coming from the other parent, and each one being a unique representation of half of the parent's own parental copies (see Figure 2). That is to say that every gamete (the mother's egg and the father's sperm) are individually-crafted halves of the parent's chromosomes. It's this reshuffling of the genetic pieces during meiosis — the process by which any one germ cell becomes four unique daughter cells — that makes us individuals (see Figure 1). But the arbitrarily-named X/Y, the 23rd pair, evolved differently from one another, certainly because the male sex gene (the SRY gene) lives only on the Y. Despite all our genetic similarities, the French are correct in celebrating la difference, which is simply due to the remarkably different characteristics of the 23rd pair.2

We know this from our childhood biology classes (see Figure 3). Women have two X chromosomes and men have an X and a Y. When procreation occurs, the woman contributes either her mother's X or her father's X. Men contribute either his father's Y (the presence of which made him a male) or that X he inherited from his mother. In fact, both men and women owe their very gender to Dad's little gamete (sperm) that could. (Yes, half of a male's output of sperm can be considered "female.") Because of this direct father-to-son inheritance, the Y chromosome follows a single and very slender thread up through the genealogical tree.

As noted, my Y chromosome says something about my father's Y and, in turn, about his father's Y. In fact, for all practical consideration, the Y is a clone from one generation to the next. Not only can I label each of the blue boxes, above, "Cooley," I can just as easily (and more accurately) label them "R1a-YP4491," the terminal haplogroup to which my brand of Cooleys belong. And herein lies the Y's first power: the biological truth of SRY inheritance neatly follows the social convention of the passing of surnames — that is, at least, in the European tradition.

Cooley group CF01

But this cloning effect occurs not only vertically, it spreads horizontally. The same Y is passed to every son and to each of their sons, down through the generations. The Y's second great power, then, is that men who are removed by several generations yet have the same paternal ancestor will all exhibit virtually the same Y chromosome. For example, at least fourteen male Cooleys (Cooley DNA Project group CF01) known to descend from John Cooley (c1738-1811) of Stokes County, North Carolina, have the same Y chromosomal markers. This is a powerful fact. Furthermore, there are seven additional testers who have the same Y configuration but appear not to have been descended from John. That means they were likely a closely-related collateral line. And to make it more interesting, the four testers that clearly belong to this Pennsylvania-born group (left-side of graphic) have a couple of STR markers that resemble distant non-Cooley lineages, including Cochran. For this reason, I've dubbed them Old CF01 and the Cooley-Whitfield group, from which I descend, New CF01. We don't yet what the generational gap is between the two subgroups. It can be anywhere from two to, say, six generations. We probably need the genealogy to figure that out, but it needs to be backed up by testing.

Cooley group CF02

Staying with the Cooleys for awhile, we've found an even better delineation of subgroups among the CF02 Cooleys. We know for fact that three of the four lineages shown in this graphic emerged from Tring, Hertfordshire, England. The founders of these lineages were born there during the early 1600s, but the number of differences in their markers suggest that they could not have been brothers. The Most Recent Common Ancestor (MRCA) likely lived a hundred years or so earlier. Further, test results have shown that the two Cooley families who lived in Goshen, New York actually shared an ancestor. We've yet to determine, however, whether the Goshen lineages immigrated together or separately. Still, it's noteworthy that a long-told family story tells us that Abraham Cooley (c1740-1820), a Goshen inhabitant, first immigrated from England to New York to be near relatives. In this case, the DNA lends credence to that story.

And this highlights the third strength of Y chromosomal testing. Despite its cloning characteristics, the Y mutates slightly every few generations, and those mutations are passed down to the sons. The rate of mutation is not, of course, clockwork — like the once-in-seven-years Vulcan-mating ritual that has long amused Star Trek fans. But a statistical analysis tells us that there is an overall average of about one SNP mutation every 144 years.3 In contrast, MT-DNA, which is inherited through the motherline (and has fewer than 17,000 bases) mutates much slower, sometimes just once every thousand years or more. That, plus the fact that most Europeans do not use matronyms, makes finding meaningful matrilineal matches difficult. It's this degree of granularity, the unique male-to-male inheritance, and surname conventions that makes the Y so powerful, as witnessed with the Tring Cooleys. It also makes for a great myth-busting tool because, as I said above, nothing can beat biological evidence.

While researching for a seminar I called "The Honest Genealogist," I ran into this one-hundred-year-plus old passage. It presents a dilemma long known to serious genealogists: myth has its way of creeping into family histories. Many of us are aware of the Three Brothers Who Immigrated... and the My Great-Grandmother was Cherokee myths. I've encountered both on numerous occasions. Certainly, in many genealogies these are facts. But by sheer preponderance of their appearance, we know they are most often not true.4 The author (unattributed but probably The Monthy Review's editor, Henry Newbolt) could never imagine that, a century later, his fellow practitioners would be given an exacting tool with which to combat the problem.

“Family history, on the contrary, has been not only forgotten but forged, its evidence weighed in the false balances of personal pride, and its true origins concealed under masses of ignorant or even fraudulent legend. It follows that the first duty of the honest genealogist must always be to provide himself with a destructive apparatus criticus, and to use it, if without pedantry, yet with an unshrinking hand. And since he will often be taking from us the picturesqueness of tradition, he is bound to give in return as much as possible of the pleasure which belongs to criticism and the humour which especially attends the downfall of the pretentious” (1904).5

But lest I'm charged with being too Cooley-centric, let's look at a couple of interesting cases among other surnames, the presentations of which would surely allow me to win any number of bar bets. (Believe it or not, I once looked on as a saloon fight nearly broke out between a couple of bikers over DNA results — pool cues brandished.) The following graphics illustrate mutations known as STRs, repetitions of specific strings of genetic letters, X number of times. A difference of just one among these first markers indicates there was likely no common patriarch.

Despite the fact that nothing about it makes sense, the claim that Richard Wright (c1730-c1784) of Rowan County, North Carolina was a son of Daniel Wright (1674-1764) of Connecticut, a scion of what has become known as the Kelvedon Hatch Wrights, persisted for decades, even generations — and is still around. But Y-DNA results, including multiple samples from each line, tells us a very different, and very much more reasonable, story. This graphic from The Wright Stuff shows that Richard, now known to have been the son of Philbert, was not remotely related to the Connecticut Wrights.

Similarly, the openness of the Duncan DNA Project has allowed researchers to learn something about three or more families of Fauquier County, Virginia that are often confused with one another. Although we don't know the parents with any certainty, descendants of Charles Duncan and his twin brother William match the descendants of John Duncan Jr and his wife Dinah Bradford. A relationship to Duncan/Holtzclaw, often cited as the brothers' parents, is out of the question. Landon Duncan was a Duncan only though his mother, Chloe, a Duncan/Bradford daughter. This comes from Three Y-DNA Duncan Haplotypes.

And so it goes. Some myths are, of course, sometimes confirmed with DNA. Still, my McDowells are clearly genetically relegated to a remote corner of McDowell history. Yet DNA is clearly suggesting that my Fisks do connect with an ancient lineage going back to Lord Symond Fiske, a rather distinguished gentleman of the early fifteenth century. On the other hand, geneticists and historians are now learning that perhaps not all eighteen Plantagenet Kings of England were descended from the Angevin counts, one-time crusader kings of Jerusalem. Testing has made it easier to distinguish between at least six separate lines in the Akins DNA Project with a couple of meaningful Big Y's on their way. And upcoming Big Y results will soon give us a better idea as to how a family of Butlers were related to the Strother family (far right of the top graphic). But STR testing just starts us on the journey. Advanced SNP testing (again as seen with the Goshen Cooleys) can take us much deeper into the ancestral maze.

But my personal favorite myth-busted episode brings us back into Cooley territory and the so-called Dutch Cooleys, a story (and it is a story) concocted by Lura Coolley Hamil in the early 1930s. Judging from my research, there is no evidence that her correspondents took her seriously. Mortimer Cooley published none of her work in The Cooley Genealogy, and Mildred Tallant, a long-deceased Santa Barbara genealogist for whom I've gained a great deal of respect, dismissed it out of hand. (We now know Tallant belonged to Cooley group CF13 and Hamil to CF10.) Hamil's musings would have easily been lost to the genealogical dustbin, but her manuscript was discovered in a closet twenty years after her death and published in 1955 under the title The Story of Pioneering, a confused and ragamuffin volume of little genealogical value.6

Despite what is written in the "Hamil Catastrophe," Cooley groups CF01, CF02, CF04, CF10, and CF13 are not paternal descendants of Barent Jacobsen Cool. The descendants of Leendert Cool of New York, however, are. (That tester's results, below, are no longer publicly available, but the markers appear to match "M269 - Family Group 03" of the Cole DNA Project, to which no Cooley is known to match.) Thanks to DNA, even by means of the very inexpensive 12-marker STR test, we can say with absolute certainty that the descendants of the following groups, all referenced by Hamil, are not paternally related — at all — and are often separated by tens of thousands of years. (Yellow indicates mismatches to Leendert Cool.)

Unfortunately, Hamil's book was discovered by a distant cousin (who would be of CF01). He propagated the story through an abundance of correspondence and his newsletter, Cooley Cousins. But I don't blame him. He wasn't a bad genealogist. I do blame Hamil as she did nothing resembling the historic method nor employed good genealogical practices. Much of what she does cite, such as a will in Maryland, are now known to be have been utterly fabricated, and passages cited from specific books do not exist. (The books do. They just don't always contain the stated passages.) Yet continued fabrication followed her. A family historian, also now deceased but of a more recent passing, forged and circulated a copy of a 1930s-era biography, replacing "of English origin" with "of Dutch origin."

And thus, the Y chromosome has become of extraordinary utility to the honest genealogist, those among us who ordinarily make mistakes and even mixup or omit citations. Still, by being humanly-honest we stand to leave a legacy everyone should strive for. As it turns out, however, I'm not leaving behind any kind of genetic legacy: I had no children. But I have found one modest device with which I can pass one on:

So much for being anti-forgery!

1 I googled for "There once was a man in Great Britain" and was surprised to see no matches. This can easily be turned on its head, "There once was a gal in Great Britain / Of whom a young lad was then smitten. / In each their kids' genes / (Even now it is gleaned) / Did their momma's M-markers get written." In any case, with this I follow in the doggerel-writing footsteps of Selah Wright Cooley (1793-1870+) who, sometime in the mid-19th century, scribbled, "Some folks may think it very wrong / For Selah Cooley to make a song, / But let them think as they may / I've raised five sons to vote for Clay."

2 The male sex gene (there is no female sex gene) is also known as TDF, the Testis-Determining Factor.

3 SNPs are Single Nucleotide Polymorphisms, simple mutations from one genetic letter (A, C, T, or G) to another. This is not to say, however, that all lineages will mutate at the same rate. That's the average and says nothing about any one lineage.

4 It could be that I've planted the seeds for a brand new Three Brothers Myth via my research on the Goshen Cooleys, one of two families, now known to have been closely related, that resided in the small community by the late 18th century.

5 Henry Newbolt, ed. "On the Line." The Monthly Review 14, January-March 1904, 24.

6 Some very helpful letters, however, were published in the book.