Pennington DNA Study Phase III

PENNINGTON DNA STUDY BEGINS TO SHOW

HOW PRA FAMILY GROUPS ARE RELATED

Third Project Report, April 2003 - Revised January 2004, December 2004 and April 2005

by Nick Penington
(Additional help from Alan Pennington, Family Group 6)

There are about 14,000 households in the US with the surname Pennington (or a spelling variant) and 2,500 in the UK. We currently have 69 Pennington results in our study, most chosen from different lineages that apparently did not converge by paper genealogy. Of course there might be some statistical sampling error because of the relatively small number of participants that could lead us to incorrect conclusions. This should be rectified in the future with greater numbers of participants in the study.  It is interesting to note the breakdown of the volunteers by country since it shows that we need more Pen(n)ingtons from countries other than the US.  Currently we have 61 US, 5 UK, 1 AUS, 1 NZ and 1 Canadian Pennington volunteers.

What are we trying to do with this PRA Study?

We are building a database of the DNA sequences of male Penningtons who have documented lineage within specific PRA Family Groups or established lineages. We see now that some PRA Family Groups share a DNA sequence with other Family Groups, and hence we know their family trees have a common ancestor at some point in the past. Already we are often able to tell people who have no paper trail at all that they belong to a specific documented lineage because of their DNA analysis. Any male with the surname is welcome to get tested and find out where they fit in. A female relative of such a candidate can also sponsor a male with the Pennington surname to get tested if they would like to determine where their maternal line Penningtons fits in.

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Possible Breakthrough:

Group 20 was recently shown to match with the largest group of related Pennington families. If Group 20 is successful in proving that they are indeed Group 1 (the descendants of Ephraim of CT b~1620) this development may yield a significant breakthrough in Pennington genealogy. Much of this progress will come from new leads in the indispensable tracking of paper trails and its correlation with our DNA results. It is now very possible that we will identify the DNA sequence of Ephraim Pennington of the New Haven colony. If that happens, we will be able to tell, using our DNA test, if an individual is a descendent of Ephraim of CT.

There are however other distinct Pennington lineages and clusters that share a different common ancestor. Two other Groups, 6 and 23 appear to share a common ancestor and Groups 29, 26, 19 and 9 appear to share a different common ancestor. Group 33 now can be counted as a defined lineage since two members of this group with a common ancestor born in 1857 matched closely.  Individuals from Group 10 (represented by 4 almost identical sequences now) had DNA signatures that were distinct and this suggests that this Group is a separate lineage within the PRA.

At the top of the accompanying table you will see that one test of a British Pennington showed that he is quite close to the largest group, in fact, only 1 marker different from Groups 5 & 14!

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How to understand a Y chromosome analysis

Each participant elected to have 12 or 25 sites on their DNA strand analyzed. 25 is slightly more expensive but gives much more information and we can be more confident of the relationship with this test.

Each site in our table below can be thought to be a bucket with a given number of BBs. If the buckets are numbered B1 to B12 then we look in each bucket to see how many BBs are in the bucket. Then we compare the number in each bucket to the corresponding bucket (DNA site) in another individual to see how many pairs of buckets have the same number of BBs.

If the first 12 sites don’t match closely then testing 25 won’t tell us much more. But, if the first 12 sites match, the two participants most likely have a common ancestor in 14 generations or less. Matching all 25 means a common ancestor within 7 generations. Even a match of 11 out of 12, 23 of 25, or 24 of 25 still indicate 2 people are from the same line, they just may not be quite as closely related. To summarize:

*A match of 11 out of 12 doesn’t necessarily mean that two members are less closely related than a 25 to 25 match, just that the common ancestor may be further back than 7 generations. In other words, my brother could have 15 BBs in bucket 4 and I could have 14 BBs in bucket 4. If we didn’t know we were related, a match of 11 of 12 would tell us that we most likely have a common ancestor within 35 generations. A study of even more DNA sites would narrow down the number of possible past generations even more. A match of 24 of 25 would narrow down the results so we could say we most likely have a common ancestor within 17 generations, but we already know that the common ancestor we have is our fatherundefined1 generation.

Look at it another way. If 1000 men matched 25/25 markers and they all traced their ancestry for 7 generations, 500 of them would encounter their common ancestor at some point before 7 generations. The other 500 would have to keep going until they got lucky (probably not too much further back in time).

The accompanying chart shows the “raw” results. That is, how many BBs are in each bucket for each individual. For example, participant 1 has 13 BBs in the first bucket, 23 in the second, 14 in the third, and so forth.  As you can see, the first 34 participants (from Groups 4, 5, 7, 11, 12. 14, 16, 20,28, 30, 31 and 32) show very close results (many buckets with the same number of BBs). 

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The Meaning of the Table

• In the table if there is a “?” in the Group column it means the individual was not sure which Group they belonged to. The different groupings shown with different background colors show the genetic families. The numbers highlighted in shocking pink show mutations within genetic families. For 25 markers, up to two of these mutations are expected within a group of closely related individuals within the time period covered by written pedigrees (about 500 years). However recently this criterion has been relaxed a little if the markers are considered to be amongst those with a more labile character. There is a sense that some of these markers mutate faster than others in the order: 464, 449, 439, 385, 458 from fastest to slowest. That means the mutations we see, within clear groupings, are not unexpected.  We can see that there is a good indication that there are at least 6 different families in the U.S. or U.K., genetically speaking, and this number will grow somewhat as we get more participants that match the individuals currently represented by only a single sequence.
• The 3 Group 6 members that participated are related (phew!) two of them with 2 mutations (23/25). What’s more, an individual from Group 23tested just one mutation away from one of our Group 6 individuals 24/25 and another Group 23 person was two mutations away from this Group 6 individual 23/25. This is very interesting as there were Isaacs in both Groups 6 and 23 back in about 1770. Some PRA researchers had suspected a relationship between Groups 23 and 6 all along but could not prove it!
• Our database appears to be large enough already to assign Penningtons who know little about their ancestry to PRA Groups. One member that was uncertain of his ancestry was placed clearly in Group 28. Another member that was uncertain of his ancestry was placed clearly in Group 10.  Eight participants were placed in the super cluster (4, 5, 7, 11, 12. 14, 16, 20, 28, 30, 31 and 32). The presence of mutations in the sequence of the “super group” allows one to distinguish between branches of this family subdivided as cluster 30, 31 and 32 on the one hand and cluster 5 and 14 on the other. Interestingly one Group 7 individual is identical to the 30/31 branch and another nominally Group 7 person was one jump away from both groups of the clusters 5/14 and the 30/31 branches of the same family but identical to Group 32 (see diagram below).
• Some Group 28 members felt that the DNA result for Group 28 meant this Group was close enough to be included in the largest group of U.S. Penningtons and up till now I have been a bit rigid in my interpretation of Group 28s result by excluding them from the main grouping.  I was only following the early advice of FTDNA and the experts on the DNA-Genealogy list at Rootsweb. A couple of months ago I started to have a crisis of confidence about the 3 step mutation which Group 28 has in  the marker 385a and the one step difference in 385b. I corresponded with a statistician who has an interest in DNA and genealogy and the general consensus was that group 28 was indeed very distant from our Groups4, 5, 7, 11, 12. 14, 16, 20, 30, 31 and 32. Just recently a number of prominent experts have stated that they do not trust 385a and 385b! They think that they are not well behaved and may show mutations in an unpredictable way! One theory is that some regions of our DNA are bound to proteins that protect that sequence. Other regions are not protein bound and so are more susceptible to mutations. Anyway they suggest now all of a sudden that (where these markers show differences) we should ignore them. This now brings Group 28 into the fold with the other U.S. Pennington Groups! This means that the latest articles published on our DNA in the Pedigrees and on the web up to now are incorrect when they discuss Group 28 and we will publish an errata in both media.  An additional technical detail. With the marker 385a and 385b one cannot tell which value is the value for “a” and which is the value for “b”. This is the case for all of the multicopy markers. As a result we are allowed to line up the results so that we get the best match with them. If one of the results is a 14 then we will call it 385b!
• One caveat. I still think that Group 28 is the most distant of the groups of cousins and the common ancestor is unlikely to be found after Penningtons came to the colonies. There is still a real possibility that the common ancestor is before the surname Pennington was adopted! 

Knowing that these two Penningtons (one Group 28 and the other a representative of the super grouping) could not have had a common ancestor in the last 10 generations, FTDNA calculates, and their 25 marker comparison shows, that the probability that they shared a common ancestor within the last... 

250 - 350 years is 34.47%

450 years is 60.47%

550 years is 77.50%

650 years is 87.74%

750 years is 93.53%

850 years is 96.68%

Still I have changed the background color on our table of results to gold to signify that Group 28 is part of the larger family, but I have marked 385a and 385b in red as a warning.  More Group 28 individuals are being tested all the time and three of them have only the 4 step jump at 385a.

• From the DNA Study so far one general thing that we can say is that 80% of all Penningtons yet tested seem to be members of one of 6 distinct families!
• Another result that just came back is very interesting.  Groups 29, 26, 19 and 9 are all just one or two jumps away from each other with a predicted root sequence that is only one jump away from all three (this is Group 26). This strongly suggests that these groups have a common ancestor who lived maybe within 27 generations of the present. Mutation rate studies suggest it might be more recent than that.  Recently a Pennington from Group 26 was tested and he had the sequence that connects these three groups (9, 19 and 29 see figure below).
• Group 8 now seems to be showing signs of benefiting from this study. Group 8 has been informally split into Groups 8 A, B & C for the purpose of this test. Now we find that two group 8B individuals (Lawrence Co. TN) have tested identically (25/25). This suggests a common ancestor within 7 generations and appears to have identified the sequence of Jacob Pennington an early member of Group 8.
• The recent development is that an Australian Pennington whose earliest ancestor born around 1750 in Lancashire and who spelt his name Pinnington has tested just one mutation away from Group 5 and 14! This seems to confirm some of Dr. Bailey’s recent ideas about the British origin of this family (first edition of Pennington Pedigrees of 2003).

Recently PRA Group 16 tested just two mutations away from Groups 30 and 31 on 25 markers. This suggests that this group is also descended from Ephraim of NC (b 1745).

I realized recently that we need to draw diagrams using all 25 markers for each cluster of related families which shows in a much clearer way how each cluster of Family Groups are related. Below we show the first three that benefit from this approach. The main "super group" is one diagram, and Groups 6 and 23 are shown in the another.

The red numbers indicate where mutations occurred.  Rad 1 has the surname Radcliff(e) (see below).  A diagram showing how groups Groups 29,26, 19 and 9 are related has been added most recently.

In these diagrams the sequences are shown by circles whose size is proportional to the number of people with that sequence. One normally considers those groups to be related if they are only two steps away from another group (using 25 markers). Of course, if  group "X" is connected to group "Y" by two mutations and group "Y" is two mutations away from group "Z" then we may have a network of groups X,Y & Z that are two steps away from a central sequence "Y". Since this diagram is based on 25 markers we must use a criterion for relatedness of only a two step difference.  We could add Group 28 to this diagram if we ignore the markers 385a and b.

These diagrams include all the 25 marker tests to date that can be compared to each other. Some individuals appear to be from different European populations.  One in Group 8 is Haplogroup “J” the origin of this group is thought to be the people who brought farming to Europe from the Middle East about 8000 years ago.  Four Penningtons  are from a Haplogroup predicted to be I1a (of Germanic or Norse origin).  If more individuals from these groups turn up (as I am sure they will) they will have their own diagram. The fact that so many Penningtons seem to be close but not really related in recent time stems from the hypothesis that all these families came from the same population pool or geographic locality. In addition it is thought that one male is the ancestor of all Haplogroup1 (now known as R1b individuals and representing the majority of Penningtons yet tested) Penningtons who lived in Western Europe 40,000 years ago.  Those who are interested in what these results can tell us about deep ancestry, thousands of years ago, should visit: http://freepages.genealogy.rootsweb.com/~dgarvey/DNA/markers.htm

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Placing all this in the context of what the PRA thought it knew about migrations of Penningtons in the US

Consider the article by Robert Sloan in which he summarizes:

"To summarize, it would appear that the cluster of Groups 1, 4, 7, 11, 12, 13, 15, 16 and possibly 6 are probably descended from a single immigrant ancestor, Ephraim, who came to New Haven, CT in 1643. They were closely associated, follow similar migration patterns from 1750 to at least 1800, and share certain name frequencies and unusual names. Groups 3, 5, and 14 form another cluster, all probably derived from the earliest Quaker convert among Penningtons, Paul of Sunbreak (near Pennington), Lancashire, England, whose son William migrated to the Philadelphia area in 1717 with his sons Daniel, Paul, and Thomas. Still another cluster is formed from Groups 2, 8, and 9, all apparently derived from the Cecil County, MD Henry who bought land in 1671, one of the two Henrys who immigrated to MD in 1665 and 1667. It would appear that Groups 10, 17, and 18 (new number for Sir Isaac’s real descendants) are descended from immigrant ancestors different from each other and from any of the other groups".

I think that DNA virtually proves that Groups 30 and 31 are descendants of one of the Ephraims of NC (Group 4) [PPs 34 #2, page 25]. Their progenitors might be the Aaron and Abel who were thought to be sons of Ephraim (b. about 1745) but DNA cannot actually prove this lineage in terms of the individuals concerned. What we know is they are from the same male line and they share the same Y chromosome. I predict that one day these two groups will be merged with Group 4. Incidentally, the only Ephraim found in the UK section of the IGI in this time period, with a source attached, is one born in 1605 in Bolton-le-Moors Lancashire. This parish is simply part of Bolton now.

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More About Why You Want to be in the PRA DNA Study

• Compared to almost any other type of genealogical research the $169 plus $2 postage and packing spent on a thorough Y-line determination is money well spent. In fact it's positively an investment if it ends a fruitless line of investigation or identifies your PRA group.
• Only the DNA study coordinator and you need to know your result. When we publish anything, we will use general labels such as: "so many people in Group X had this sequence".
• The part of the Y-chromosome measured  for these studies are not really of interest to anyone but genealogists. VERY RARELY about 1 in 4000 men there may be a large deletion of part of the Y-chromosome DNA. This is probably a copying error. These men would probably be sterile but this is just one of many causes of this condition. Our test would pick this up.  So far in testing 69 Penningtons none have encountered this delicate issue but confidentiality between the person taking the test and the study coordinator will be maintained by our study if such a occasion arises.
• If there is a strong presumption that you should match someone else from a certain group, and if you don't match them … well, wouldn’t you want to know?

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APPENDIX; Some Penningtons appear to be related to Radcliffes New Data from 37 Markers

If you recall my article about the association between Radcliffes and Penningtons in the 12th century (Pennington Pedigrees V32,#2 p32,) a Margery de Pininton married a Hugh de Radcliffe in 1220, they adopted the surname that became Pennington and they had sons who had sons etc. I thought the Y-chromosome DNA of some Radcliffes should match some Penningtons if they descend from this line.

A Penington living in the UK called UK1 (yes one "n" but not related at all closely by DNA to the author) is related to the main super Cluster of Penningtons! This result is very interesting as it is only 1 mutation away from representatives of our Groups 5 and 14, meaning a 50% chance of finding a common ancestor within 17 generations! This also suggests a little more distant relationship to our Groups 4, 7, 11, 12, 16, 20, 28, 30, 31 and 32. Even more startling is this individual has some genealogical clues that point to an origin in Leigh Lancashire in about 1690!

Just recently we upgraded members of Groups 5 and 14 and UK1 to 37 markers since the two Radcliffes had already done this. The new mutation calculator at FTDNA shows that with a genetic distance of 4, there is a greater than 95% chance that Groups 5 and 14 are related to UK1 within the last 650 years. The results were also interesting in that UK1 now showed three mutations away from the closest Radcliffe on “fast” moving markers and 2 on “slow” moving markers. It is suggested that we use an average mutation rate for all 37 markers in any calculation (best guess as of 12/02/04 is 0.0054 per marker).  This gives a result that suggests that, if two individuals shared a surname, they have a 50% chance of being related within 15 generations and a 95% chance within 27 generations. However the two individuals do not share a surname and theoretically should not be related before the 12th century. Interestingly Groups 5 and 14 had 5 mutations away from the nearest Radcliffe but they were all on markers thought to mutate at the highest rates. The bottom line is the DNA result is consistent with the possibility that these Radcliffes are related in the male line with these Pen(n)ingtons but it is not firm proof.

The next few months should yield exciting further insight into the structure of the Pennington family.

Parts of this article were written and/or edited by Alan Pennington (Group 6) and with editorial contributions from Paul L. Pennington (Group 28) and John Pennington (Group 4) thank you for helping to make it more intelligible. Last but not least, thanks to the DNA committee for advice and support.

The DNA Study Group wishes to thank the following sponsors for their generous donations to the DNA Study: Richard Bailey (Family Group 14); Henry B. Hearn III (Family Group 29); Thomas R. Williams (Family Group 8); Joan Flint (Family Group 28); W. Harry Schaffer (Family Group 9?); Christine Borrus (Family Group 28) and Linda Ballard (Family group 9).

Copyright 2005 Nick Penington