Saturday, February 9, 2019

"SNPS still hurt my head"

My cousin wrote "SNPS still hurt my head. Have not spent enough time with them." This is not my high school dropout cousin emailing. This is my PhD research chemist cousin who travels the globe to attend scientific conferences to share findings with fellow cancer researchers. If ySNPs still hurt your head too, you are in good company. 

What the heck are ySTRs?

This is a cousin who long since had tested his ySTRs to 111 markers. He and I match on 110 of 111 ySTR markers. My 5th great-grandfather, Peter Dowell, Sr. (1714-1802), is his 6th great-grandfather. Well maybe this is an opportunity to let him spend some more time wrapping his mind around ySNPs. Maybe, in so doing, I can begin to relieve some of his head pain. Maybe.

All of you who have used census records can relate to how data on ySTRs (short tandem repeats on the Y chromosome) are collected and compared. The locations visited for 12, 25, 37, 67 or 111 ySTR marker tests are not magical. They were picked originally because geneticists knew how to repeatedly and reliably locate them. Also they were thought to mutate just fast enough to be useful for genealogists. That means they are relatively stable for several generations so that men who share enough of them probably share a common patrilineal ancestor in genealogical times. At they same time they mutate frequently enough to differentiate between distinctly different lines of ancestors.

To use a simple example, let us assume that you know there is a village that has either 12, 25, 37, 67 or 111 distinct residences. You send a census taker to visit each residence and determine how many ySTRs reside at each location. In the lab this is what geneticists are doing when they collect data for ySTR comparisons. They sample the number of ySTRs "residing" on the Y chromosomes of men to give us an idea of whether or not those men are closely related. How many generations ago could a common patrilineal ancestor of those men have lived if the two men might be expected to have accumulated the number of variations that are observed in the current test results?

[from David R. Dowell, NextGen Genealogy: The DNA Connection, (2015), pp. 33-4.] 
Surname projects can apply these principles to reconstruct more complex descendant trees of family “founders.” In this case the “founder” was Philip Dowell, who appeared in the records of southern Maryland in the 1690s. By that time he was an established tobacco planter. His marriage in 1702 and death in 1733 are well documented, as are many other events in his adult life. However, no birth or christening records have yet been discovered. Although he is reported to have had four sons who passed his Y-chromosome DNA forward, living male Dowell descendants of only three of those sons have been identified and tested.
Five of those descendants have tested to 111 Y-STR markers. One was a descendant of Philip’s first son, one was a descendant of Philip’s second son, and three were descendants of Philip’s third son. The results of these tests were that all five agreed on 101 of the 111 markers. In addition, four of the five (including descendants of at least two of Philip’s sons) shared the same value on all 111 markers. In other words, none of the two mutations of the descendant of the eldest son, the six mutations of the second son, or the single mutations of two descendants of the third son occurred on the same marker. Philip can be assumed to have passed down the marker values that at least four of his five living descendants share because they were passed down through multiple lines that have no common ancestor more recent than him.

Triangulating 111 ySTR markers back to the founder of the Maryland Dowells                       

Since this chart was prepared another Dowell has tested who is a 111/111 match for the reconstructed yDNA signature for the Founder. However, we are still in the process of determining this man's exact line of descent.

What the heck are ySNPs?

While ySTR analysis has helped the Maryland Dowells understand much about their inter-relationships in North America, it has yet to connect them with specific ancestors across the pond. Could ySNP (Single Nucleotide Polymorphisms located along the y-chromosome) analysis help?

As noted above ySTR analysis is all about determining whether or not men share the same number of repeats at predetermined locations along their yDNA. In other words do they match. ySNP analysis can also be at that level as well. If a man is fortunate enough to have a supposed relative who has already been SNP tested, a test of individual ySNPs can be a cost effective method of way to validate a match and also a ySNP for that man. 

However, for the most part, ySNP analysis is a voyage of discovery along the approximately fifty-eight million locations of one's y-chromosome. We can now get reliable readings on almost one fourth of those locations. When testing for SNPs we do not target a certain number of predefined and well known locations. We travel down our chromosome and look for branching points. These are  points where closely related genomes permanently separate -- somewhat akin to taking an exit off the Interstate. Most of the group continue on unchanged on the main genetic highway but one branches off and passes this branching point "mutation" on to all his descendants. So far Family Tree DNA (FTDNA) has identified more than 408,000 such branching points (ySNPs) in the yDNA samples the company has tested. Additional SNPs are discovered with almost every BIG Y test conducted.  

These SNPs trace the paths our genomes have traveled through prehistory and down to the present. Now that more and more men have tested to this level it is beginning to be possible to see branching points in genealogical times when we had surnames and some paper records exist. Thanks to the work of Alex Williamson with his Big Tree of the major haplogroup found along the Atlantic Coast of Europe, we can begin compare SNP branching with the STR and paper trail documentation we have seen in previous decades. Comparing Alex's SNP tree with the one seen above, three branches emerge that help refine the genetic trails of Philip Dowell's three sons that had been put together from paper documents and STR data. 

For the purist this charting process reversed the chronological order of the sons. In this chart the descendant of eldest son is on the right and the descendants of the third son on the left. However, the main take away for today is that branching SNPs have been discovered that separate the lines of descent within the last three centuries. The eagle-eye readers will note that a fellow traveler of a different surname has joined the genetic migration. His family was associated by both location and business transactions in both Maryland and North Carolina. The SNP branching suggests the genomic link is with the second son although other evidence is more ambiguous. 

Is you head hurting even more now?


No comments:

Post a Comment