Can you show examples of SNPs in a genealogical time frame?

+12 votes
691 views

Are there examples in WikiTree where Big Y or YFull or FGC testers have SNPs in a genealogical time frame?  That is - from the SNP tests of distant direct paternal line cousins and you know in which (or approximately which) generation a particular SNP occured? (And this information is pointed out in WikiTree).

Thanks and sincerely, Peter

in The Tree House by Peter Roberts G2G6 Pilot (523k points)
edited by Peter Roberts

Its easier to answer if you tell us why you are asking... are you just interested to see how things are documented in WIkitree or if profiles exists that have Y-DNA proof?

In Sweden we have a "famous" family Buhre and a lot of Y-DNA testing has been done by Peter Sjölund he has documented that in Swedish on http://buredna.sjolunds.se/

They assume there is a Common Ancestor start 1500

I think some of the Bure people are on Wikitree but I have not spent time on documenting this and check how well sourced they are

I'm asking because people have spent hundreds of thousands of dollars on Big Y type tests yet none I know of are willing to demonstrate in WikiTree how it has confirmed a direct paternal line.

Thanks and sincerely,

Ok I think Bure is a good example but that was done in big scale many people involved but outside Wikitree. Also was on a meeting in the local genealogy society in Stockholm and Jakob Norstedt-Moberg had a good lecture. He is not on Wikitree but has a web

http://hoijen.se/category/dnaresultat/

He has also done some work with my branch I am YF02234 in I1-SwF cluster / I1-JN38 subclade – status 2015-10-08

2 Answers

+6 votes
 
Best answer

I have taken the Y Elite test from NGS and do have some SNPs known to have occurred in a genealogical time-frame.  In particular, I am positive for FGC3199 and a third cousin 1R of mine is negative for this SNP.  So I know that my great great great grandfather James Williamson-4958 is negative for this SNP and that the mutation I carry happened in one of several earlier generations.  My haplogroup is R-FGC3199, while that of my ggggrandfather is R-FGC3198.

I do have this information in WikiTree, but that information is poorly included.  Granted, none of my profiles are particularly well filled out.  :(  I have my FGC results included as "Other yDNA".  There is no existing option for BigY or FGC tests.  Interestingly, text in the DNA section wrongly states that tests such as Geno 2.0 or those at BritainsDNA can't even be used for genealogy.  Given the current lack of support within WikiTree for NGS/Y-SNP DNA results, it doesn't surprise me we don't see much use of it.

In the other answers provided to this question, I notice that they reference trees external to WikiTree.  Referencing data outside of WikiTree makes sense, having to reference trees does not.  Currently, WikiTree simply lacks the infrastructure necessary to support this sort of data.  I would be much happier if it were possible to show or provide a link to a WikiTree branch instead, with names and mutations on it.

by Alex Williamson G2G3 (3.5k points)
selected by C S

Which Geno 2.0 or BritainsDNA SNPs are within the last 2,000 years?

Here's a list of Chromo2 SNPs I pulled from the YFull website for a few branches of R1b-L21:

S968, S951, S966, S964, S967, S957, S960, S3862, S954, S959, S956, S962, S953, S190, S3033, S425, S302, S422, S421, S303, S3068, S420, S781, S679, S676, S682, S660, S659, S658, S661, S6151, S588, S603, S668, S675

One could probably go through the site and identify many more.

The Geno 2.0 Next Generation test came out after the Chromo2 and I believe includes some SNPs also discovered from the first BigY results.  It should have even more SNPs from within the past 2000 years, but I've never checked.

Neither BritainsDNA tests nor Geno 2.0 would be the first tests I would recommend for genealogy.  That said, they are not void of any value.  I don't think the presence of very recent SNPs on the Chromo2 or Geno 2.0 tests is what makes them useful for genealogy.  They can't identify new branches like the NGS tests can, but they can help people rule out connections in much the same way mtDNA results can.

Hello Alex, you noted "Currently, WikiTree simply lacks the infrastructure necessary to support this sort of data.  I would be much happier if it were possible to show or provide a link to a WikiTree branch instead, with names and mutations on it."

Can you create an example of  how a WikiTree branch would look with names and mutations on it?

Hi Peter.  Yes, I can do that.  I'll post back here when I have something drawn up.  I warn you now, you'll have to forgive my artistic skills.
Thanks Alex! I would like to see greater integration between WikiTree and the results we've discovered through DNA testing, but I'm not sure that I want to be responsible for tagging and updating records as I go along. Your project at ytree.com is excellent and I could envision a parallel view of WikiTree records against an index of DNA results better than I can another host of fields on a WikiTree profile page.

 

 

WikiTree yDNA Proposal

I've tried to draw out a rough idea of what I've been thinking about.  All of the black boxes in the image correspond to WikiTree profiles.  This is true for both the men/women that are known from genealogical records, as well as those whose existence is only known based on DNA.  The solid black arrows correspond to the usual father/son relationship connections that are currently available in WikiTree.  Haplogroup could be dropped.  It could be automatically generated to any depth desired.

In this diagram, all of the men, the relationships and the testing is real.  "Williamson-?/FGC3198" is the common ancestor of the Williamson men I have on the tree.  "Unknown-????/FGC3197" is the common ancestor of the McCorkle, Munro and Williamson lines.  "Unknown-????/S190" and up are most recent common ancestors who lived further and further into the past.

What I would like WikiTree to introduce are the dashed arrows in the diagram, as well as a proper place for SNP/INDEL mutations in the profiles.

The dashed arrows correspond to a father line relationship, but the number of generations isn't specific.  So it could be father/son, but it could also be grandfather/grandson or great grandfather/great grandson.  Family Finder/23andMe/Ancestry like tests are good for estimating the number of generations back in time but, unless you can use triangulation, there is no sense of direction.  On the other hand, Y-DNA/mtDNA is 100% accurate in terms of direction, but has poor resolution back in time.

For the SNPs and INDELs we wish to include in the profiles, it would be great if they had their own field.  They could be citations to mutations defined in another resource like YBrowse or, better yet, WikiTree could house its own database of mutations.  From an amount of data perspective, it would actually be pretty small compared to everything else in WikiTree.  This would make it far easier for WikiTree to identify conflicting mutations/relationships, etc.

Currently, my own tree ends at Williamson-4959.  He was born about 1770 or so.  From STR and SNP testing, I know of other Williamson men that I am related to, but this relationship is older than what I can reach via paper genealogy.  Having these dashed arrows would also give me a way to include what I know of these yDNA known relationships into WikiTree.  When properly SNP test, I could say they were all descendants of "Williamson-?/FGC3198" (I could give him a real profile).  Rather than confirmed by DNA, it might be more appropriate to say inferred from DNA for these situations.

For the older haplogroup/branch like profiles, additional information could be included.  For the more recent ones, a last name may be known.  By counting SNPs or STR analysis, estimated dates of when these men lived could also be introduced.  YFull supplies many dates that could be cited.  Based on where the children were from one could also guess at where these men may have lived.  I think WikiTree would be a convenient place for this sort of analysis/speculation.

The same situation I described above would also hold for mtDNA.

 

Hello Alex,

Regarding the dashed lines, have you seen

http://www.wikitree.com/wiki/Category:H1a3a1_mtDNA_Group_1   ?

Sincerely, Peter
Hi Peter - the DNA category approach is interesting but very outdated for NGS test results. I'm not sure I even agree with the philosophy much less the accuracy of "confirming" father-son relationships with over-the-counter consumer STR or atDNA tests on WikiTree. SNP data and mtDNA are much better data for lineal descriptors, such as dates, names, etc. Linking the DNA descriptors, versus categorizing them, is an essential difference.
Hello Leake,

The DNA category appoach is pointing out a connection where the ancestry is missing.  Similar to missing ancestry in direct paternal lines which have matching terminal SNPs in a geneagical timeframe.

If direct paternal line 5th cousins both named Sasser are a 35/37 match then you do not agree that it would be accurate to confirm the father-son relationships on each of their direct paternal lines back to their MRCA?  If so, why?

Sincerely, Peter
Peter,

No, I hadn't seen that before.  It looks like the right idea.  It's certainly one way to group of a number of men or when who descend from a common ancestor.  It could be used for my Williamson men for instance that I know descend from some unknown common Williamson ancestor.

I don't know that such an idea would be extendable to an entire tree.  Would you want to organize men in thousands of nested categories?  That seems more like a workaround than a real solution.  Is there a way to visualize such nested categories in WikiTree?
That's an extremely generous example Peter - not what we typically see in surname projects at 37 markers and 5th cousins. STRs are not reliable over such time periods. There are also issues with regard to which STRs mark the family line, and we have seen limits to acceptable likelihoods at 111 markers. Some family lines may see limits at 400 STRs - we just don't know yet. I don't think we can confirm anything in the 4th or 5th cousin range without NGS and an accurate paper trail. The line of SNPs is better for imputing relationships by order of descent - that is why Alex's suggestion is so strong.
Note this discussion has potential overlap with a very preliminary technical discussion of how SNP testing results might best be integrated into Wikitree profiles. At the minimum, a way to indicate chrY sequencing has been done should be standardized, ideally as a new type of test beyond Y-STR and Y-SNP. At a maximum, all lineage defining SNPs (regardless of whether they were tested by single SNP, microarray biochip, or NGS) could be integrated into the profile system. https://www.wikitree.com/g2g/341255/can-dna-has-been-tested-section-be-extended-for-big-y-test?show=343802#c343802
Hello Eric,

I may not understand "...a way to indicate chrY sequencing has been done should be standardized, ideally as a new type of test beyond Y-STR and Y-SNP."   My understanding has been that next generation Y chromosome testing is an advanced form of Y-SNP testing in that it reveals lots of Y-SNPs.

There are some features that WikiTree already uses which I hope could be adapted to make use of Y-SNPs in a genealogical time frame. For example lets pretend you know (through Y-SNP testing of you and your direct paternal line cousins) that your 5th great-grandfather (Noah Mercer) was the first to have the Z12345 Y-SNP.  There could be a radio button for Noah's relationship with his father called something like "New SNP". Selecting that button would stop the association of Z12345 with your earlier Mercer ancestors on your direct paternal line.  That would be similar to what the radio button for non-biological relationship already does.

I believe the information a Next Gen Y tester includes about their test needs  to have a field for Terminal SNP and a hierarchal path field (e.g. L21>M4321>Z12345  ) among other fields.

Sincerely, Peter
Hi Peter... SNPs are the focus of the reports generated from chrY sequencing data, because that's what is most useful for genetic genealogy at this time. But the data itself is the DNA sequence, and so in addition to single base substitutions (SNPs) it also shows any simple indels, STRs or other duplications, and inversions. Those are just as valid as DNA markers, and can be critical if you are interested in genetic diseases.

We focus on SNPs (and only biallelic ones at that) in genetic genealogy because of the various DNA changes they're cheapest to test and arise at a frequency that makes them useful tools. But just because we aren't using the other info available doesn't mean it isn't there -- so NGS is more than just an "advanced form of Y-SNP testing." When sequencing becomes cheap and routine, we'll probably become more interested in using more than just SNPs, because all DNA markers are potentially useful.

I've added a new question, under WikiTree Tech, that gets at a more fundamental issue of what direction additional technology should take to expand the smart tools. This discussion has wandered away from the specific original posted question into something much larger. And very interesting.

Can DNA test data entry be changed from testing product-based to DNA marker-based?

+4 votes
I think none of the big projects (like the R1b) has documented anything on WikiTree. Most centers around the projects on FTDNA, that's how they became a household name in Y-DNA in the first place.

While they aren't ideal in documenting specific "inofficial" phylotrees (as most people revert to their own websites and use different software to visualize their findings) they provide one single platform where all contributors and the project organizers can communicate.

WikiTree has nothing even close in comparison. Surely there must be people that have done the Big-Y or FGC and are also on WikiTree but I haven't come across it. Remember, we're still a nice in the big world of genealogy (we have only 11 million profiles so far).
by Andreas West G2G6 Mach 5 (53.9k points)
I have had BigY tests done for my father and maternal uncle, but have not posted the findings on Wikitree. The results so far are placed to about 2000 yrs ago. I will have to wait until more test results modify the Y-tree. Would gladly post what I do have if there was a format provided.

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