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Holmes yDNA

(Previous page: Nathan in Connecticut)

Beginning in 2008 yDNA testing was done by for two descendants of Hiram HOLMES and for a descendant of Peter HOLMES. The results were good news and apparent bad news for the ideas presented in these pages.

For privacy reasons I will refer in this page to seven living individuals as:

  • H1 and H2 – Hiram descendants
  • P1 – Peter descendant
  • Ja1 — Descendant of James HOLMES of Oxford, Maine
  • J1, J2, J3 – Descendants of Jabez HOLMES of Plymouth

The common ancestors and the divergences in these lines are:


John -+-> Nathaniel -+-> Elisha ... Nathan -+-> Hiram ... Jerome -+-> H1
      |              |                      |                     |
      |              |                      |                     +-> H2
      |              |                      |
      |              |                      +-> Peter --------------> P1
      |              |
      |              +-> Nathaniel ... James -----------------------> Ja1
      +-> John ... Jabez -+-> Palmer -------------------------------> J1
                          +-> Benjamin ... ? -+-> ? ----------------> J2
                                              +-> ? ----------------> J3

For H1, H2, and P1, out of the first 37 markers tested, 33 matched each other and those of four other Holmeses, J1, J2, J3, and Ja1, in the database. The tests for H1, H2, and J1 were later extended to 67 markers (plus an additional 3 markers for H1), and all three matched exactly on all the 30 additional markers. The haplotype is I-L160. This level of matching indicates a common ancestor for all seven individuals within the past few hundred years, and combined with the other information we have makes it nearly certain all seven are in fact descendants of John HOLMES. That’s the good news.

The apparent bad news is on four markers where mismatches occur: DYS 19, 460, 576, and 442. For H1 and H2 (who in fact are both descendants of Hiram’s grandson Jerome), the values for these markers are (16, 12, 21, 12) and (16, 11, 21, 13). For P1 they are (15, 12, 20, 13). (See table below.) Four mutations in the five generations since Nathan, and two in the three generations since Jerome, is surprising though not impossible. Moreover Ja1, J1, J2, and J3 have for these markers (16, 11, 21, 12), (17, 11, 21, 13), (16, 11, 20, 13), and (16, 11, 20, 13). Each of these differs only by one mutation from H2. None of this rules out the reconstructed lineage presented here, but it does give one pause.

DYS 19 DYS 460 DYS 576 DYS 442
H1 16 12 21 12
H2 16 11 21 13
P1 15 12 20 13
Ja1 16 11 21 12
J1 17 11 21 13
J2 16 11 20 13
J3 16 11 20 13

In particular, at DYS 576, three individuals have 20 and four have 21. If these indicate closeness of relationship then it means H1 and H2 are closer to Ja1 and J1 than they are to P1.

Is this possible?  To me it’s the nightmare scenario: it would mean Hiram was closer to Jabez than to Peter, implying he was not in fact a son of Nathan. But the evidence he was is very strong.

On the other hand, the values at DYS 460 suggest H2 is closer to Ja1, J1, J2, and J3 than to H1 and P1. But we know that’s wrong. We know H1 and H2 are closely related. The differences between H1 and H2 must have arisen since Jerome. In particular, Jerome either had 11 at DYS 460, and a mutation to 12 produced a coincidental match between H1 and P1, or he had a 12, and a mutation to 11 produced a coincidental match between H2 and Ja1, J1, J2, and J3. Either way, it is an established fact that the apparent grouping on DYS 460 into H1/P1 and H2/Ja1/J1/J2/J3 is illusory.

Similarly, at DYS 442, it looks as though H1/Ja1 is one grouping and H2/P1/J1/J2/J3 is another, and that’s also wrong. Altogether it looks as though there were at least three places where mutations to the same value occurred independently in different lines. I can’t prove this happened, but it seems to me less unlikely than a mistake in the lines back to Nathan. As a guess, maybe these markers for John were (16, 11, 21, 13); then DYS 19 mutations occurred on the P1 line at or after Peter and on the J1 line at or after Palmer; DYS 460 mutations on the H1 line at or after Clarence and the P1 line at or after Peter; DYS 576 mutations on the P1 line at or after Peter and the J2 and J3 lines at or after Benjamin (but before their split); and DYS 442 mutations on the H1 line at or after Clarence and the Ja1 line at or after Nathaniel Jr. Or something along those lines. More testing of John HOLMES descendants, especially of e.g. descendants of Jabez of Hamilton and of Henry, might clarify things, of course. (Since yDNA is inherited only on the male line, we cannot get information from yDNA testing of descendants of Eunice and Hannah, and I do not believe the younger Nathan has living descendants.)

By the way, these yDNA tests address an old uncertainty. In [Stratton’s] article “Descendants of Mr John Holmes, Messenger of the Plymouth Court” he writes:

“The evidence that Nathaniel2 Holmes was the son of John1 is not so conclusive, but must be inferred mainly from his being in Plymouth at the right time… he named children John and Sarah, the names of his supposed father, brother, and mother, and his brother John2 Holmes named one of his sons Nathaniel. That John2 and Nathaniel2 married sisters, Patience and Mercy Faunce, may be another indication that they were brothers… it must be understood that the relationship is not satisfactorily proven.”

To the best of my knowledge, the aforementioned seven men include the first male line descendants of Nathaniel2 and of John2 to do yDNA tests. Since the results indicate a common ancestor within the past few hundred years, it seems there now is genetic evidence that Nathaniel and John were close relatives — almost certainly brothers. So our DNA tests have helped settle an open question about the family of John HOLMES of Plymouth. (The question also appears to have been settled by the newly discovered evidence of John’s roots in England; see [Holmes].)

Finally, Alonzo HOLMES of Hamilton was noted as probably not a close relation of Nathan. A descendant of Alonzo’s brother Charles has tested as haplotype R-M269, entirely different from the haplotype of the John HOLMES descendants. Charles and Alonzo’s claimed ancestor, George HOLMES, came from Nazing in Essex, but this test result suggests he was not related in genealogical time to the Holmes family in Colchester, Essex. Of course confirmation of this with tests of other George HOLMES descendants would be needed to eliminate the possibility of genealogical errors or non paternal events.

(Next page: Summary: Nathan’s life and family)

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