Michael Cooley's Genetic Genealogy Blog
9 August 2022

Y-SNP Mutation Rates: The Pilgrims Pettit Y-DNA Project

New Big Y results for the Pettit-Mellows Y-DNA Project have arrived for kit #157822, a descendant of Andrew Pettit (1716-1748). Andrew was a grandson of Nathaniel I (c1645-c1718) and great grandson of Thomas (1609-1688). He has five novel markers not found to date in anyone else. (Such SNPs are called private variants or novel SNPs.) For those who simply want to know the bottom line, that's it. No new surprises and no new genealogy has been discovered. But the five SNPs are somewhat anomalous and raise a number of questions across the project. Those of you who want to learn more about that, please read on.

Pettit-Mellowes Y-DNA Project

Janet Wood and I have been working diligently on two Pettit groups. It had long been suspected, perhaps for a century) that John Pettit (c1608) and Thomas Pettit (c1609) were brothers. It makes sense. They arrived to Massachusetts about the same time and, according to some secondary sources, they were both indentured to Abraham Mellowes. Otherwise, no records have ever been found that describes the relationship between them — until the Y chromosome. (I'll explore this further in a future article.) Let's start with the new test results.


Andrew Pettit

Understanding and determining what to do with a wealth of Y-DNA SNPs (Y-SNPs) is the crux of this article. How do we place them on the tree? How does the placement inform the genealogy? The first step toward that understanding is to recognize that a Y-SNP mutation occurs at the creation of the sperm cell that makes the man. The SNP, then, can be seen as being somewhat analogous in name to the man. (Pause on that a bit.) The chromosome, with the new marker, slightly alters the SNP stream from that point on. It's cloned into every son and then forward to future generations. Genetic genealogists try to place these SNPs with the precise generation in which they emerged. Once done, we've acquired a unique genetic name for the man, whether or not we know his "social" name. But here's the catch. SNP mutations occur, on average, only every four generations. (And keep in mind that we're talking about one single-point mutation among 57 million "points.") Our new tester defies the odds but, as we'll see, not terribly.

 

The five new novel SNPs discovered for the Andrew lineage would theoretically take us back to the period between 1400 and 1500 CE and, perhaps, as many as twenty generations! Unless the genealogy is wrong (not likely), we'd not expect the arrival of five SNPs into the Y chromosomal stream over eight generations. However, SNP mutations are random. I've seen testers with next to no novel SNPs over considerable periods of time. And I've seen new SNPs emerge in both father and son. I've even seen two new SNPs emerge at the birth of a single male. Why not three new SNPs? Why not a combination of the two possibilities?

A mathematical model has been devised to deal with this problem: Average out the SNP counts across the project to arrive to a fairly reasonable estimate of the overall mutation rate. It's certainly possible these five SNPs can be accounted for in the same way a roll of dice might win you a fortune. On the other hand, anomalies such as this might point to an error in the lineage. In this case, I'd say a single anomalous tester is insufficient evidence to suspect a genealogy problem.

We can make far better sense of the five unmatched SNPs in Andrew's lineage by first understanding that none of Andrew's brothers had them. (See the project's Hybrid Tree.) They had to have emerged with Andrew and/or any number of his descendants — five SNPs over eight generations. We can place them on the tree by testing descendants of the brothers of two or more generations in the tester's lineage. I would suggest we start somewhere in the middle with any known brother of John Pettitt (1799-1879), if he exists. Any of the five SNPs that match the new tester will have emerged before or with John and be placed just above him. We continue up or down the lineage depending on the results. One caveat, though. Such an exercise beyond finding an anchor SNP for Andrew would be largely academic, especially if the genealogy for his descendants is sound.


Increase Pettit

But we have a bit more severe case of too-many-SNPs for Increase Pettit (1726-1795), a probable descendant of Thomas Pettit II. Two testers have eleven novel variants between them, an average of 5.5 SNPs per lineage or roughly 22 generations. Having two extremely SNP productive, collateral lineages would be a pretty decent confirmation that the mutual ancestor lived between about 1400 to 1488! That's certainly not when Increase lived. Between the two, they have a real-world average of seven generations. That's a lot of doubling up of new SNPs per generation. And with so many PVs (personal variants), I'd expect some matching between the lineages, especially some that were pre-Increase. That would make a bit more sense. To be sure, though, what we see isn't impossible, but I deem it rather unlikely. To resolve this, a bottom-up approach is needed by testing more MLDs (I just made that up for Male Lineage Descendants). Furthermore, a detailed and strict study of the genealogy is probably in order.

As described above, every new SNP emerges at the birth of a man. Because 100% of the Y chromosome passes from father to all his sons, we have a living record of each Y-SNP arrival. Matching these SNPs between two men finds their paternal MRCA (Most Recent Common Ancestor), whether or not we know his name. Every now and then a beautiful moment arrives when we can attach a man's social name to his genetic name. We did this with Samuel Pettit, Jr. by virtue of the fact that two MLDs have F7174 but the MLD of Sam's brother, Isaac, didn't have it. All of Sam's MLDs will have it. I call these anchor SNPs. F7174 is anchored to a specific person (Sam Jr) with a specific birth date and place. Unfortunately, however, we don't know with which of Thomas Pettit's sons to place Samuel.

Similarly, all MLDs in the Thomas I lineage have all those SNPs named at the top of the tree, proving that each one are related through a common patriarch. And all fingers point to Thomas I as the "culprit." And that's even true for my Pettit 4th cousins establishing a fact that I had resisted for decades. It boils down to this: Where two men have matching SNPs, they have a common ancestor. Ancient matching will not, of course, tell genealogists much as there were no published genealogies. (Such matching does greatly aid population geneticists, one of the pursuits being the tracking of ancient tribes across the globe.) But for matches within the genealogical timeframe, we have a fighting chance to ID SNPs to men that just might reside on someone's tree. We've done that with Samuel Jr and with George Pettit (1719-1775). We can keep doing it. After all, where's there's a SNP there's a man.


Thomas Pettit II

Indeed, SNPs are the thing. We're close to accomplishing the perfect top-down with Thomas II just as long the surmised genealogies are correct. We've got excellent SNP coverage for those lineages with Y42738 ruling at the top. But for lack of proper documentation, we need to turn, at least for now, to the traditional descent in order to make some sense of it, yet only in a way that doesn't conflict with the all important genetic facts, the new overlord of surname studies.

Although it makes sense that Increase and Joshua II were brothers, the topic has been a debated due to the lack of documentation. To be sure, the genetic data doesn't dispute the matter, but neither does it settle it. Still, for the sake of argument, let's make it so.

It's entirely possible that those of subclade FT95921 (far right of the SNP tree) are also descended from Increase, but there's not even a known theoretical lineage describing any possibilities — except that we know that they did have the Y42738. Both Increase and Joshua II (Increase's presumed but not proven brother) were born with Y42738 as shown through the testing of their MLDs. But is it anchored to Increase as F7174 is to Samuel Jr? We have no idea at present. Recall first that we need to test one of Increase's brothers. According to some online genealogies his father, Joshua I, had sons John (1746-1820), Joshua (1751-1818), William (1754-1818), and James (1757-1775). There appears to be several well-established genealogies among them. Finding descendants is a real possibility.

In brief, if any descendant of Increase's brothers has Y42738, then we can move the SNP up to Joshua I and examine his brothers for it. If any single brother does not have it, then it's anchored to Increase making him the progenitor of all Y42738 testers. But if Joshua did it, we check his brothers' descendants to see whether Thomas III had it. We have an apparent wealth of genealogical targets. For example, here's the will for the 3rd generation Thomas.

In the name of God, Amen, July 24, 1715. I, Thomas Pettit, of New Rochelle, in the County of West Chester, yeoman, being sick. I leave to my wife Catherine, all estate during her life. I leave to my eldest son Thomas, 10 shillings, and what I have already given him by deed of gift. I leave all the rest of my houses, lands, and tenements to my sons Benjamin, Joshua, Samuel, Bartholomew, and Nathan, and my son-in-law, Daniel Baruch. I leave to my daughter Christian, wife of Daniel Baruch, £24. I make my wife executor. Witnesses, John Moreau, Stephen Garison, Edward Fitzgerald. Proved, September 13, 1715.

It's a simple, binary proposition. Either a tester has a target SNP or he doesn't. This can potentially be done (as long as the right people are living) for virtually every SNP on our tree. Of course, there are caveats. We lack the paper trail for some of the key actors in this little drama. And then there's the too-many-SNPs conundrum for the Increase testers.


The Nathaniel Pettits

It's clear that no new SNPs emerged at the births of either Nathaniel I or Nathaniel II and perhaps for several more generations in some cases. Where Tom is SNP rich, Nat is SNP poor. We can't go top-down on those lineages. We need to go bottom-up in the way I proposed for Increase's descendants. More testing will find new novel SNPs and more opportunity for matching, creating more haplogroups and genetic MRCAs. With well-matched SNPs, structure will begin to form suggesting genealogical connections not previously known. Just as we've gotten this far, we can likely get that far for the Nats. But trying to cross a SNP desert of two, three and more generations, will be a tough trek. We just need to make the best of what we have. For example, haplogroup FTC17094 was formed by the matching of two of my distant Pettit cousins. Thomas Pettet (c1765-1830+) is the main man in this clan. I suspect his father, Elias Pettet (proved by will), was a grandson of Elias Pettit (1673-) who first married Jane Furman and secondly a Miss Havens. The senior Elias was a son of Nat I. However, the Nats had no SNPs by which to prove the descent, and the genealogy is less than flimsy. Other than the haplogroup match, we have a clue in that Thomas had Pettit neighbors in Morgan County, Ohio with origins in the Pettit-Bailey region of New Jersey. It's not much but something might be learned by walking FTC17094 up the SNP tree. Did Thomas's son Elijah have it? Did any of the sons of the elder Elias have it? The SNPs know. We just need to excavate and query them. Similarly, we have two SNPs in the Jonathan Pettit and Mary Shourds lineage.


The New John Pettit Project

And we get to a bit of the nitty-gritty stuff that some might find a bit unpleasant. The other night I published a report for the John Pettits, now officially known at FTDNA as the Pettit R1b-FT58002 Y-DNA Project. It comes down to this: Any MLD who tests positive for BY200368 is a descendant of Thomas Pettit 1609, and we now know that anyone who tests positive for FT58002 is a descendant of John Pettit I 1608. Two MLDs of Joseph Pettit II (1689-1765) have the John Pettit SNP as do at least three more testers believed to have been descended from Joseph I, a long-presumed son of Thomas I. Considering the available data, we have little choice but to prune Joseph I off the Thomas tree and graft him onto the John I tree while fully recognizing the two men were patrilineally related only via an ancestor thousands of years old and, therefore, were not brothers. Further, as far as I can tell, there are no primary records to support the notion that Joseph belonged to Thomas. Now remember, primary records are wills, deeds, birth records, etc — those records that were contemporaneous to the events and generally registered with governmental entities. Secondary records are largely two things: later interpretations of primary records in the form of books, articles, and letters, and interpretations that are often based on other secondary records and speculation. By definition, speculation ties in only loosely-defined evidence and a lot of guessing. Secondary records seriously need to be examined for the quality of their citations and reasoning before using. Frankly, We're at the point in this research that we can no longer futz around with poorly-cited sources. We need to look solely at primary records and, believe it or not, genetic records are primary records. They're markers written directly into every cell of each male member of the lineage at his birth, whether by a designing hand or nature selection. When it comes to genetics, science and belief systems speak in a single voice: read the genetic book.


Time to the Most Recent Common Ancestor

There's a new feature arriving on my groups pages, including for the Thomas Pettit page. Although I haven't written the description yet, it shows the SNP lineage for each tester in clear columnar format. (Remember, each SNP can potentially be replaced by a name.) From this, we're able to make a prediction for the time to the most recent common ancestor (TMRCA) who, of course, was Thomas Pettit 1609. Scroll down at the home page to "Timeline Report for Haplogroup BY200368." Here's a description.

SNPs occur about every four generations. I use an average SNP rate of once every hundred years in my calculations. Others, however, use once every 84 years. I'm using both for the chart.

Understand first that the scientific "the present" is defined at 1950. For our purposes, that works perfectly as I'd argue that the average birth year for Y-DNA testers is about 1950. In fact, it's my birth year. Indeed, calculating from 2022, 2023, 2024 or anything else makes no sense.

For starters, we count the total number of SNPs in the box in the TMRCA box, divide by the number of testers for the average number of SNPs across the board, in this case 3.25. Here are the calculations:

1950 - (65 / 20 * 100) = 1625 CE
1950 - (65 / 20 * 84 years) = 1677 CE

That's pretty right on. But better yet, we have a proposed birth year for Thomas I, if not set in stone — 1609. That's 341 years to the scientific present. We need only to change the multiplier to get an accurate SNP rate for this project. That's roughly 105 years.

1950 - (65 / 20 * 105) = 1608.75 CE

It's a little different for John Pettit I, however. If we assume he was born in 1608 (presumed only) under the FTA57533 haplogroup, the SNP rate would be once every 152 years. However, if he was of the FTA57533 haplogroup, we'd have to factor in the collateral Robert Pettit lineage. That would give us a mutation rate of only once every 49 years! Obviously, the average rate cannot be both 152 years and 49 years. Ah, but if we average them, we get 100.5 years. The randomness of biology just doesn't quite work with mathematical models — at least with small numbers of testers. On the other hand, it just might not be helpful when removed by only a few hundred years from our MRCA.

Here's my recommendation for moving the project forward. For those testers having novel SNPs, test the descendant of a second son of the EKA (Earliest Known Ancestor) in hopes of getting matches. We can identify those markers by scrolling along the bottom blue bar on the SNP tree. Where there are SNPs, there are possible matches. We see this with the above Samuel, with George 1719, with the Elijah/Joshua MRCA, with Fox/Pettit, and with my Thomas c1765. This can likely be done with all PVs — and in this case of Nat I, needs to be.


~~~

And this brings me to the clarion call of the day: "Give me your tired, your poor, your huddled Y-SNPs yearning to breathe free!" Janet and I will do our best to breath life into them.