Following is a presentation I gave on genetic genealogy as it relates to John Cooley (c1740-c1811) of Stokes county, North Carolina. Additional information can be found in the following articles and pages:

Stephen Oppenheimer's findings, which I discuss briefly below, are controversial in some circles. His own interpretations of the genetic data, as well as those by other population geneticists, are certain to be revised as more data enters the public domain. Our Cooley genetic heritage is bound "to suffer the slings and arrows" of changing academic analysis.

Note that there are a number of graphics, including a Google map. It could take a few moments to download the entire page. Also note that the appellation of "George" is entirely my invention. I've used it merely because it is easier to say and write, and is for more comprehensible, than "R1a1-2b". Perhaps "Olaf" would have been a slightly better choice. After all, among the several proposed etymologies for Cooley is MacOlaf (later MacAuley).



Reunion of the Officer-Cooley Family Association

Cooley's Gardens, Silverton, Oregon, June 12, 2010


Genetic Genealogy

©2010-2014 Michael Cooley

Genetic genealogy is a large and complex subject. But I doubt that any of you are geneticists (I'm not), and many of you are probably not even genealogists. This is, after all, a family reunion, not a scientific seminar or genealogical convention. Although there's much I'd like to tell you, I've spent several hours trying to trim off the fat. I hope I've whittled it down to just enough information to make it comprehensible and still useful. If we have time, I'll be happy to answer questions after the presentation.

I'm here today to present the genetic proof that Joseph and James Cooley, whose children and grandchildren traveled the Oregon Trail in 1845, were brothers, that my Edward Cooley (whose descendants did not make that trip) was another brother, and that they were sons of John Cooley of Stokes county, North Carolina. I'm going to try to prove to you, through genetics, that our tribe of Cooleys were of ancient Scottish origin, that they were related to the MacDonalds and to the great Scottish chieftain Somerled. I'm going to try to prove to you that the so-called "Dutch Theory", of which some of you are familiar, is bogus. I'm going to prove to you that our John Cooley did not marry a woman named Elizabeth Firmin and that he probably never lived in Maryland. There is no evidence that he was born in Goshen, New York. That distinction belongs to another man.

Before we start, let's take a brief look at some relationships. Mike Cooley, your former president, is a patrilineal descendant of Joseph's. Your current president, Rick Ernst, is descended from James Cooley through his mother. I'm a fifth cousin twice removed to Mike and a sixth cousin once removed to Rick.

John Cooley (bef 1740-c1811)
Edward Cooley (1763-1822) James Cooley (1772-1821) Joseph Cooley (1767-1826)
John Cooley (1789-1866) Cornelius Cooley (1814-1843) Jackson L Cooley (1816-1883)
David Cooley (1815-1865) Mathias Cooley (1837-1915) John Pearce Cooley (1852-1934)
Greenbury Cooley (1844-1899) Cornelius John Cooley (1870-c1951) Albert Sidney Cooley (1879-1950)
Joseph William Cooley (1867-1947) Rholin Melba Cooley (1899-1971) Homer Alvin Cooley (1913-1962)
McCabe Cooley (1899-1958) Miriam Cooley Mike Cooley
Allison Claude Cooley (1925-) Rick Ernst
Michael Cooley (1950-)

Everything that I'm going to tell you hinges on the simple fact that some of you are women and some of you are men. In the end, it really is that simple. Here's the reason: the Y chromosome.

http://www.medgadget.com/archives/img/xy.jpg

On that chromosome is the male sex gene. If you have the chromosome, you have the gene and you are male. A woman doesn't possess a Y and, therefore, cannot be a contributor to her son's Y. If you are male, your Y chromosome came from your father. It stands to reason that he got his Y from his father—not from his mother or his mother's father.


Patrilineal Descent

I'm going to demonstrate this with my own five-generation genealogy.

Generation 1 Generation 2 Generation 3 Generation 4 Generation 5
http://ancestraldata.com/ahnentafel/bin/5gen.pl?1

I have a Y chromosome. It came from my dad. If Dad had had another son, he would have received a copy of the very same chromosome. We might not have been twins but our Y's would have been. Dad got it from his father, McCabe, which came from his father, etc. When we look five generations back, only Greenbury Cooley was a contributor to my Y chromosome. But, in fact, I have a genetic inheritance from all the people listed in the fifth column—statistically, anyway—but my Y came only from Greenbury and, of course, his father. When it comes to the Y chromosome, none of the others were contributors. It came down to me only through this specific line of Cooleys.

Look at it this way. Greenbury had a baton. He passed it on to Joseph. Joseph gave it to McCabe. It went to my dad and now I have a baton—my Y chromosome. The mutual ancestor of Mike, Rick and myself, John Cooley, had a baton. Actually he had three. He gave one to Edward and one to Joseph and one to James. Mike has the one that came down to him from Joseph. I have the one that came down from Edward. But Rick's baton wasn't passed down the Cooley line to him. It came from his father. Rick has the Ernst Y—and that has a unique story of its own.

In point of fact, John also gave batons to sons John Jr, Daniel, Perrin and Reuben—and probably to at least two others. Most of those other batons are still out there and they have characteristics identical to those that Mike and I received.

The coincidence with Y inheritance is that our surnames passed down the same way. That naming convention is, of course, a human invention—and not practiced in the same way in all societies. What's fabulous about genetic inheritance is that it is biology—not human convention, which varies among cultures. Just as surely as we're all genetically human, we can rely on Y inheritance.

To be clear, and to help drive home the point, the other men on this chart had batons too. They were also in the race; this unrelenting march forward into time. The difference is that none of those batons found their way to me. Their passing to me was broken. Just as the Cooley Y could not pass to Rick Ernst, these other Y's went to guys named McDowell, Hogue and Hart. My "baton", like my name, was passed down through this one thread. None other. And it's this specific thread we're going to talk about. It goes back well beyond Greenbury, of course. Back to and beyond our mutual ancestor, John Cooley of Stokes county. We can trace it back to the beginning of mankind.


DNA Testing

We know for fact that at least nine people have this same Y. How do we know that? All nine of us tested. Here's a simplified breakdown of the results from the testing of eight male Cooleys. I've removed all the data and all other identifying information except for the colors. White boxes represent matched markers. Grey boxes are unmatched markers. The others weren't tested. Family Tree DNA participant #98452, a descendant of James Cooley (Joseph's brother), is represented by the first column. My results are in the second column. Mike is the fourth.

These tests look at specific locations on the Y chromosomes, specific "markers." Even a glance quickly tells us that we closely match. Through a chemical analysis at a lab Mike and I have learned that we match on 61 of the 67 markers tested. I match with the first tester 65 of 67 markers (a "genetic distance" of two) That there are only two to four mismatched markers in seven to nine generations is remarkable. You don't see that in a random sampling of the population. But consider that we also have the same surname and all of our Cooley ancestors came from the same area. It strongly suggests that all of us are related—with or without the supporting genealogical information.

Stokes County Cooleys

http://ancestraldata.com/ahnentafel/256/ydna.html

In contrast, here are the test results from several other Cooleys. In most of these, mismatches outnumber matches. The "genetic distance" (number of mismatches) is so great that we'd need to go back 10,000 years or so to find the common patrilineal ancestor. For all practical purposes, these Cooleys are not even remotely related to us.

Represented here are descendants of the well-known Ensign Benjamin Cooley who immigrated to Massachusetts in, I believe, the 1640s. A descendant of Daniell Cooley of Maryland, also immigrated in the 17th century, is found here. The last column are the test results from two men who matched to one another perfectly—37 out of 37 markers. Their results are going to figure prominently into our discussion in a few minutes.

Other Cooleys

http://ancestraldata.com/ahnentafel/256/ydna.html

Genealogy

We know, of course, how Mike and I are related. We know through the understanding of genetics that we're related partilineally—through our male lines. But how do we know our common ancestor was John Cooley? Our case is the perfect illustration as to how genetics can inform scant genealogical data (public records such as land deeds).

We know from two deeds recorded in Stokes county, North Carolina that John gave land to his son James. The genealogical and historical record tells us that the tester in the first column in the "matching" table is a descendant of James. The deeds, then, prove that he is descended from John Cooley. Since we know that he has the same Y chromosome that Mike and I have, we have proven that Edward, Joseph and James, all born in the 1760s and 70s, were closely related. We're confident they were brothers because of the existence of a number of other documents. For instance, John also deeded land to Edward. Although the relationship is not stated, genealogical proof of my descent from Edward does exists. Because column one and I have the same Y and he is proved descent from John, we can likewise say that Edward and I also descend from John. It's pretty clear. We also know that Joseph, James and Perrin emigrated together from Kentucky to Missouri in 1811, appearing together on the earliest records of Fort Hempstead. The relationship between the three men is not described anywhere in the public record. But when we compare the extant documents with the genetics—that the descendants of these three Cooleys had an identical Y—we have overwhelming evidence of the relationship. In short, the same Y chromosome, plus the same surname, plus the same location and the same time period almost certainly equals a close family connection. That does not mean to say, however, that our genealogical quest is finished. We should continue to look for documents that specifically state the relationships. It's good genealogy. Genetically, however, the case is virtually closed.


Haplogroups

To better understand what we're looking at, to understand what it can tell us about John's history, how he was or was not related to other Cooleys, we need a very basic understanding of the term haplogroup.

A haplogroup is a branch, in this case a branch of Y chromosomes that have common attributes, much like the markers that Mike and I have in common. This hierarchical ordering is used in linguistics. We all know about language branches. English, for example, is a Germanic language of the Indo-European branch of languages. Zoology uses a similar type of hierarchical structure. Genetic groups can be classified in much the same way.

This is a good time to be clear that this has nothing to do with the classification of race and has nothing in common with eugenics and the horrific practices that resulted. Although haplogroups are sometimes associated with ethnicity, it is so only in the most general sense—and that in respect to frequency only. For instance, there are men in India, as I'll show in a moment, who are of my haplogroup—whose yDNA look very much like Mike's and mine. Therefore, it is far more accurate to suggest that haplogroups are relevant in terms of frequency in geographic regions rather than in racial groups. Just as we might associate redheads with northern Europe, redheads can be found in varying degrees everywhere. In fact, when it comes to the Y, there is nothing about it that will determine what we look like. Its principal reason for being is to determine an individual's sex. Apart from that, it's largely useless. And therein resides one of its principal values. Because the Y does not express itself in physical attributes and capabilities it is not a factor in natural selection. It is a silent, neutral witness to the evolution and co-minglings of mankind and not an influence on evolution.

With that said, most Europeans are of Haplogroup R. We can be more specific. Most Europeans are of haplogroup R1. (Remember, I'm talking only about that single thread of patrilineal descent.) In fact, most Western Europeans are haplogroup R1b. The ancient cave dwellers of Southern France, the Cro-Magnons, who made those fabulous cave paintings of bison and horses, were R1b. But I'm of Y chromosomal haplogroup R1a. Mike's patrilineal ancestor was not Cro-Magnon. R1a is believed to have been those people to have first spoken the earliest Indo-European language.

Here's a map showing Y chromosomal descent.


http://en.wikipedia.org/wiki/File:Yhaplotree.JPG

Here's another chart, far more attractive.


http://www.familytreedna.com/img/snp_tree/backbone_SNP_chart.png

We're near the bottom. Haplogroup R1a1. We can see our descent up through the chart, through the mutation of markers going back to who some call Scientific Adam.

But who was Scientific Adam? It took me awhile to sort this out for myself. This is not Biblical Adam, a single man fashioned out of the earth. There were other men living alongside yDNA Adam. This Adam had cousins and uncles, tribe mates and neighbors. But he is the one man from whom everyone descends partilineally. That's the key word through this whole discussion. Patrilineal. Everyone's father's father's father, going back through to about 60,000 years, traces back to this man. Somewhere along the line, as we moved toward the present, those other men's patrilineal descent, their Y chromosomes, became extinct.

This extinction of the Y is still taking place. Here's a good and very pertinent example. My grandfather, McCabe Cooley, had two sons. Between them, my grandfather was blessed with four fabulous grandsons. Two of us had no children and the other two had two daughters each. In others, McCabe's Y chromosome was not carried into the fourth generation. At our death, it will become extinct.

But just as other non-Y genetic components of my grandfather's survive in the current generation, genetic traits of Scientific Adam's contemporaries are still with us, through a daughter's son, a son's daughter, and a daughter's daughter's son's daughter. But only Adam's Y chromosome comes to us directly through the patrilineal line.

How do we know all of this? We know it because geneticists have compared the DNA of people all over the world and have factored them into a huge "equation" derived from what we know from the historical record, from the archaeological record, from the geological record, and even from the genealogical record. Anthropology. Human Geography. Even things such as tree rings and star dust contribute to our understanding of our descent. And it all fits. The genetic record fits with what we already know. But it's also filling in cavernous gaps.

So coming back to Earth again. What does this tell us about John?

Remember the tables showing test results—the table listing those of us who have John's Y chromosome and the table of those Cooleys who do not match? Here's another table.


John Cooley was not Dutch

FAYETTE COUNTY PA COOLEYS
Subclade R1b1b2
STOKES COUNTY NC COOLEYS
Subclade R1a1-2b
John Cooley (1740-1823) m Annetje Decker William Cooley (-1810+) m Elizabeth Firmin John Cooley (by 1740-c1811)
John Andrew Cooley Sr (1767-1847) Frederick Cooley (1781-1845) Joseph Cooley (1767-1826)
Samuel Means Cooley (1800-1847) John Cooley (1822-1899) Jackson L Cooley (1816-1883)
Thomas Jefferson Cooley (1831-c1897) Arthur H Cooley (1849-1909) John Pearce Cooley (1852-1934)
William Franklin Cooley (1868-1897) Frank L Cooley (1875-1920) Albert Sidney Cooley (1879-1950)
Franklin Arthur Cooley (1893-1963) Frank H Cooley (1915-1975) Homer Alvin Cooley (1913-1962)
Franklin Arthur Cooley Frank Cooley Mike Cooley
Michael Arthur Cooley
See footnote #1 for a caution.

The last person named in each column had their DNA tested. The testers in the two left hand columns were in the non-matching table. The third column is our Mike Cooley's lineage. If we look at the earlier table, Mike and the Fayette county, Pennsylvania Cooleys match only 15 out of 37 markers. They are R1b (Cro-Magnon), we're R1a (Indo-European). The Fayette Cooleys are a subgroup, or subclade, of R1b called R1b1b2. We're in a subclade of R1a called R1a1-2b. These two groups do not have common patrilineal descent—at least going back several thousands of years.

This sets an old and inaccurate accounting straight. In the 1930s, Lura Coolley Hamil, an apparent newbie to genealogy, spent six months researching and compiling her notes. She died shortly afterward. Her work was published by her cousins twenty years later as A Story of Pioneering. Huge sections are wrong. Among other things, despite the source she cited, she misidentified Elizabeth Firmin's husband, saying she married John Cooley. In fact, Elizabeth married William Cooley, who turns out (if the genealogy is correct)1 to have been closely related to John. Hamil identified these people as being Dutch. That may be true, if unverified. But, as we can clearly see, that's neither here nor there when it comes to our Cooleys. Genetically, the third column does not match. Our John Cooley and the other John Cooley are not of the same subclade. To make matters worse, somehow—and I think it may have been because of a family group sheet put into circulation by Dale Walker in the 1970s—our John was guessed to be this John and, because of Hamil's error, Dale made our John's wife Elizabeth Firmin. DNA proves otherwise. John Cooley of Stokes county, North Carolina had a wife but she is not even close to being identified.

Apart from the DNA, the little historical evidence that's available supports this. The Biographical and Portrait Cyclopedia of Fayette County, Pennsylvania (1889) states that William was married to Elizabeth Firmin. (Hamil cites this book but mistakenly made John the husband.) William and his wife are found on the 1810 census records for Fayette county, Pennsylvania living near their sons, indicating the veracity of the 1889 statement. (Their grandson, another John Cooley, was still living at the publication of the book and was the likely source for the information in the biographical sketch.) Furthermore, William and Elizabeth had at least four descendants having the first name Firmin,confirming the notion that Firmin was the maiden name of William's wife, not John's wife.

Despite what we've been told for several decades, our John Cooley was not the man born in New York in 1740, who lived in Maryland and had descendants living in Fayette county. That distinction belongs to the John who married Annetje Decker. For whatever reason—a typo or a misreading—our John was confused with "Dutch John". That confusion became nothing more than unfounded rumor, propagated literally thousands of times through several decades via the photocopying of an erroneous family group sheet.

If we cannot purloin the Fayette county Cooley heritage as our own, where does our Cooley heritage lay? What do we know about our John Cooley? There's good reason to believe ours was the John Cooley who served during the French and Indian War in 1755 from Caroline County, Virginia alongside his life-long friend and associate Richard Goode. Both men show up in the Townfork, North Carolina record by ca 1770. Before Virginia, we have nothing remotely tangible and can only guess. Although there is reasonable circumstantial evidence that suggests John was from England, I leave that discussion to the work published online at johncooley.net.

Although we find few clues in the historical record, the genetic record provides some hope. For that we need to back up a little bit—actually quite a bit—back to near the beginning.


John's Genetic Heritage

This beautiful map shows the migrations of major haplogroups out of the Fertile Crescent. The projection is a little skewed from what we're accustomed to seeing. For instance, we usually find the Mediterranean, shown in the left hand corner, running east to west. But we can clearly see the boot of Italy and, right up in the corner, Spain and the Iberian Peninsula. We see that haplogroup J moved into North Africa, F into the Arabian Peninsula, Q into China and M in the direction of Australia.


http://en.wikipedia.org/wiki/File:Haplogroup_F_(Y-DNA).jpg

Here's a modification of the same map, highlighting the movement of R1a. This group went into Eastern Europe—much of Russia is R1a—and southeast into northern India.


http://commons.wikimedia.org/wiki/File:Haplogroup_R1a_(Y-DNA).jpg

Next is a simplified map showing the movement of the major European haplogroups following the Ice Age of about 13,000 years ago. The Ice Curtain had kept us bottled up in the southern regions of Europe and central Asia. As it lifted, much of humanity migrated north. (You'll remember that R1b descended from Cro-Magnon and R1a descended from the early Indo-Europeans of the Caucasus Mountains.)


http://fettywww.com/europe_haplogroups.jpg

And here's an excellent map showing the current distribution of haplogroup R1a, our group, throughout Europe.


http://www.moonzstuff.com/images/dna_R1a_large_RG.jpg

According to world-renowned population geneticist, Stephen Oppenheimer, our R1a ancestors originated in the area between the Black Sea and the Caspian Sea, the Caucasus Mountains. Before the advent of farming, they traveled, along with their kith and kin, through Ukraine where we still see a cluster, into Poland—a very large cluster—and across to the Scandinavian peninsula, finally settling in or near present day Bergen, Norway. That's our clan—our single, slender thread of the ancient Indo-European peoples. Others, of course, made the trip. (It needs to be well understood that they were not all R1a1.)

Before we continue with John's story, here's a similar map showing R1b.


http://www.moonzstuff.com/dna/haplo.html

We see a large concentration of the descendants of Cro-Magnon still in southern France. We also see them—the descendants of their ancestors, at the other side of the map in the Caucasus region. That's where the Cro-Magnon and the Indo-Europeans had their common ancestry. We see that R1b is well-represented in most of western Europe and, especially, in the British Isles. Among those people we find the other Cooleys.

Here is a Google map locating Bergen, Norway. With this, we can start back at the Caucasus region and move up through Ukraine, Poland and into Norway.

Norway is the home of subclade R1a1-2b. For the sake of simplicity, let's call the genetic founder of this clan George. According to the work of Oppenheimer, this man was born about 5700 years ago. George is today what Oppenheimer calls the largest of the "Rostov clusters." (Rostov is the name of convenience, much like my George, Oppenheimer has given to R1a1.)

Bergen is, in many ways, the ancestral home of the ancient Cooleys—before, of course, they were Cooleys. Here's a photograph of modern Bergen.


http://en.wikipedia.org/wiki/File:Ulriken_view.jpg

About 5000 years ago our ancestor, obviously leaving other members of the George clan behind, crossed the North Sea. His descendants went into the Shetlands, the Orkneys and Scotland and traveled as far south as Norfolk, England. George's "grandson" didn't make this journey by himself, of course. There were other men with the Rostov (R1a1) Y chromosome who came with him—and men with different haplotypes. (I stress this fact because it is essential to avoid any kind of stereotyping or racial categorizing.) And there were numerous later migrations out of Norway. For instance, the patrilineal ancestor of the great Scottish Chieftain Somerled may have crossed 3,000 years later. Somerled was the founder of the MacDonalds who are also R1a1, Oppenheimer's Rostov. Through studies of the Y chromosomes by geneticist Bryan Sykes of the current MacDonald clan chieftains, the first 25 markers of Somerled's specific haplotype have been determined. My profile matches to 16 out of those markers. In contrast, I match to only 9 out of 25 markers with the Fayette county, Pennsylvania Cooleys. In other words, we're far more closely related to the MacDonalds than to the other Cooley clans.

This map shows our Cooley subclade, R1a1-2b (George), and its movements out of Norway.


And here is R1a1-3b, said by some to be the Somerled ancestral clan. Again, there may be only a nine-marker difference between "Somerled" and "George". Our ancestors may not have been MacDonalds but they probably lived among the clan.


http://www.ethnoancestry.com/index_files/index_data/R1a1_3b_Opp.gif

We've talked about John. We've followed him from the Caucasus Mountains, into Ukraine, Poland, Norway and finally into the British Isles about 5,000 years ago. That's his very specific thread. That's the story of his father and his father going back at least 13,000 years at the lifting of the Ice Curtain. We now have a low-resolution snapshot of that journey. But the real story is the mosaic, a broad tapestry of individual threads. Let's take just a moment to look at the bigger picture.

The greatest genetic diversity in the world is found in Africa. Why? Because that's where it started. As the human race, we developed there and became extremely diverse genetically. Then about 60,000 years ago, small groups of small numbers of African descendants—just tiny fragments, specific genetic subsets of the human race—moved out, crossed the Red Sea into Mesopotamia and the Fertile Crescent, leaving behind the vast majority of humanity and it huge genetic pool. The population of the rest of the world is, genetically, paper thin compared to what is still found in Africa.

R1a1 (Rostov) is not the entirety of our genetic heritage—most of the men in this room are probably not R1a1. We have inherited from our other ancestors non-Y genetic components of R1b ancestors. Although we may not be able to identify them by name, we can count among our ancestors men who were haplogroup N and haplogroup J. We're not of a single genetic tribe. And although we're proud American citizens our heritage encompasses a huge swath of the globe. We're citizens of the world. In the beginning, and in the end, we are all Africans.

Thanks to population genetics, we can now follow one thin thread out of Africa. A single man, perhaps with his sons and his father, certainly with other kin and tribe mates, crossed the Red Sea 60,000 years ago. We can follow this thread, this passing of the baton, across much of Eurasia into Norway and into Great Britain about 5,000 years ago. And then, perhaps fewer than 300 years ago, one of George's descendants found himself in a coastal British town, stepping onto a ship to embark on a journey to the New World. We don't know exactly where or when it happened. We can't be sure just who made the crossing but the baton was eventually passed to John. That five thousand year gap will never be filled by the historic record. R1a1-2b is rare in Britain. Few of John's patrilineal ancestors, if any, are likely to show up in the historic record. We need the genetic record. But once we find our boys in Britain, men living today who match John's DNA—and they are there—we may be able to fill in more of that picture.

Contrary to popular myth, John was not Dutch. We won't find what we're looking for in Holland. But we have found nine people to date, including Mike and myself, who carry John's haplotype, his Y chromosome, his "George". It has told us a great deal about this journey. More secrets are sure to be revealed.


1. The earliest generations for the Fayette Cooleys need to be firmed up genealogically. The table reflects longstanding beliefs. What's new here is that the two lines are so closely related. The relationship has been guessed at previously but the DNA has provided the proof. What is not known, however, is how they are related.