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Re: Family Finder tests entering the Y-DNA haplotree
Hello CB There has always been a significant difference in SNP tested men in the Public Haplotree compared with the Discover Haplotree Reports. That difference is now 11,281 more in Discover, but a few days earlier it peaked at 26,942 in the opposite direction. Clearly this reflects the FF Y-DNA results being added to Discover in their usual end of week update. In most weeks we see the difference reduced daily, before it reverts to a similar higher number when Discover is updated at the end of most weeks. At the end of June Discover had 9,621 more, and this has increased gradually ever since. I imagine these might be academic and other results, but uncertain. My guess is that FTDNA have added about 36,000 FF results now; in a process that they expected to take several months. Initially it included some men who already had a Big Y result, but they seem to be excluding them now. However there are several with other results; Deep Clade, Geno 2.0, SNP Packs, single SNP, etc. In some instances FF results are deeper; and I have seen one (with R-Z253) contradicting a Geno 2.0 result. Kind regards John |
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Re: Family Finder tests entering the Y-DNA haplotree
The public tree shows 4,474 for Z156 and the discover reports show 4,516. It seems like it is going to be a long slow process if there are 750,000 male FF testers.!!!!! Only 5 of my 629 M269? 25 marker YSTR matches have lost their M269 status in the past two weeks.
On Saturday, December 16, 2023 at 07:39:00 PM UTC, Ewenn <gwenng008@...> wrote:
Hi, ? To compare with that corresponding to November 18: ? The FTDNA autosomal database would include approx. 1.5M testers, around half of which may be men. Even if certain transfers from other companies will not be included in the data, there would still be several hundred thousand male autosomal kits to be added to the Y-DNA Haplotree, of which ~10% could belong to the R-U106 branch... ?
1) Barrie et al.. 2023:
? ? 2) Bonczarowska et al. 2022:
Ewenn |
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Re: TRYON surname group at FTDNA advice/coordination with U106
#BigY
Back in April of this year I posted this introduction to the group: ? "I'm new to this group (just got BigY results and I'm U106) and wondering about possible mutual benefits between the Tryon surname group and the U106 group (I could be naive - I'm learning). I'm co-administrator of the FTDNA Tryon surname group which is Y-DNA focused. We have 12 Tryon members who have done at least Y-37 testing and all have 3 or less mismatches with the modal values. 7 of us can document our origins back to three sons of William Tryon (1646-1711) who immigrated from England about 1665 and settled in Wethersfield, CT. 4 of us have brick walls in the mid to late 1700s but have significant circumstantial evidence leading us to believe we're also descendants of William of Wethersfield. The last member is a descendant of Benjamin Tryon who is believed to have been a separate immigration event in 1696 but of a close relative of William. His Y37 result is the same as the modal values for the group except DSY438, one of the slowest changing markers. I know of another non-member who has this same ancestor and the same mutation of DSY438. We have not been able to bridge the gap to records of the family in England. Another member of the group is a documented descendant of the only other known group of Tryons who themselves were immigrants to England in the 1500s from Flanders. He is not related to the rest of us within at least 25 generations. Research seems to indicate there were a group of Tryons in the Glocestershire area in the 16th century from whom essentially all American Tryons descended, with the vast majority of them being direct descendants of William of Wethersfield. At this? point, I am the only member who has done BigY. I doubt I can convince most of them to do BigY (I'm not sure we're all still living at this point) but I'm sure I can get a few, especially if I pay for it. My question is, is it worth it? With this small but well documented group, would this better refine timing of variants? Would this potentially help resolve the 4 brick walls? Would a study like this help with others in the U106 group?" ? Now, months later, I can answer my own question to some extent. Yes, it was worth it. Yes, it resolved the brick walls. Maybe it is of help or interest to this group. Here is what we did and what we found. ? Thirteen members participated in this study, ten who were prior members with Y-37 results, and three new recruits. These represent descendants of four of the six sons of William and nine grandchildren of William. The four sons and number of participants are David (3), Thomas (2), Abel (4), and Ziba (4). At least one participant from each group has documentary evidence linking them directly to the son of William. While some questions remain regarding each ancestor in the lineage, all can now be linked to William through specific sons. ? Each of us in the test group share 17 SNP mutations that we do not share with anyone else. We all are members of haplogroup R-FTD91363 whose most recent common ancestor (MRCA) was born about 1635, clearly William Tryon (1646-1711). Since William, each of us has accumulated another 2-7 mutations over the average 9 generations since William. Descendants of William's son David are all in haplogroup R-FTE27603 and represent descendants from two of David's sons. Descendants of son Thomas are in haplogroup R-FTE65276 and also represent descendants of two of Thomas's sons. Descendants of Abel are in haplogroup R-FTE32270 and are descendants of two of his sons. The last of the sons of William, Ziba, did not produce a SNP mutation and the four testers who represent descendants of three of Ziba's sons, do not share a unique SNP and do not form their own haplogroup. They do however share a unique STR mutation (DYS557=17) which no other Tryons have. They also have unique SNP mutations dividing them into lineages from three of Ziba's sons. ? Mostly, the results confirmed documentary evidence, both direct and circumstantial. In one case we had the right family but the wrong brother as ancestor. Two testers with long-standing brick walls in the mid 1700s were clearly linked to David and their lineage has now been worked out. One of our biggest Tryon mysteries has been Benjamin Tryon of Coxsackie (b. abt. 1720). Family lore says the Tryons of Coxsackie were descendants of an English sailor who came to America about 1697, resigned on Long Island, and then moved up the Hudson to settle in Coxsackie. Benjamin's descendant shares the same haplogroup with another tester, a descendant of William's son Thomas. This was a big surprise but with that knowledge, the lineage was worked out. ? This has all been very satisfying and clearly worth the time, effort, and money. All of the major uncertainties of the family of Tryons in America are now settled. Can we contribute to the broader U-106 group? Here are some observations: ? If you want to run this sort of study, be prepared to pay for it. It took very little to convince people of the value and interest of this work but very few were willing to pay. I covered about 2/3 of the cost with participants and/or their relatives covering the rest. ? Luck is important. We were testing descendants of four sons of William. Three of them had their own unique SNP mutation. ? Of the 10 original members with archived samples at FTDNA, 4 failed and required new samples. One of those failed two more times before a result passed QC. This was a man in his 90s and that is an age problem that has been reported on this forum before. ? Final SNP results were reported by FTDNA in 4-6 weeks on all but one sample from batching to online results. There was no difference in timing between Y-37 upgrades and new tests. Y-111 results were consistently reported in 3 weeks. ? The occurrence of new SNP variants is quite variable. While overall we averaged 2.3 generations per new SNP (76 years), it varied from a low of 2 in 9 generations to a high of 7 in 9 generations. At a finer scale, we had one with 4 in 4 generations and one with 6 in 7. We likely had one or more instances of 2 new SNPs in a single generation. Time estimates based on the number of mutations are clearly only valid over long time frames. ? It is important to go through the results in detail and, if possible, download the VCF and develop ways to dig deeper into the files. The myth of the manual review is real. This is mostly all done by machine and there are software issues that FTDNA are aware of that are significant (see my earlier posts). Two main problems are 1) their software can't deal with multiple mutations at a single location, i.e., C>T and C>A at the same location; and 2) their software can't deal with INDELS well, i.e., a C>CC mutation. At a minimum, check every identified variant for one individual against the rest of them. The difference between a positive result and a no-call is just one read. Don't take this as a complaint against FTDNA. They're doing a good job for their customers. But if you want to make a research project out of this, it's on you. ? When you have questions about results, it is important to be patient, polite, and persistent with the FTDNA reps. You will eventually move up the ranks and get informative answers. ? Lastly, strange stuff happens that seems like it has to do with actual manual, not mythical, review. For example, the individual who had multiple failed tests showed up on the "time tree" months before his results were released. He was clearly among the R-FTE27603 haplogroup there but did not appear on the "block tree" and remained as R-M269 everywhere else. When I asked about this I was told "Occasionally, our Phylogeneticist will get a head start on reviewing SNP data from Big Y testing prior to the results posting to the accounts." ? I hope this was of some help to the community. I will try to post a pdf of an anonymized version of the Tryon block tree, though I've had mixed success with posting graphics here. ? Cheers Mike Tryon |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
I did the Genographic 2.0 test in 2016, and imported the results into FTDNA in the same year. Genographic reported my haplogroup as Z160, now dated 2170 BCE (95% confidence interval: 2816-1610 BCE). FTDNA immediately advanced this to CTS3777, now considered part of the S3251 block, dated 1055 BCE (1577-608 BCE). I can still see my Genographic SNP results along with my Big Y results. I would think that Genographic results have already been advanced as far as they can be. |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
In general one needn¡¯t worry about FTDNA/MH transfers as FTDNA processed all of them and the SNP overlap is very high. Some people like their MH ethnic origins %, but many people would place them at the very bottom. ? These estimates are several years old and very outdated. |
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Re: Family Finder tests entering the Y-DNA haplotree
Hi, ? To compare with that corresponding to November 18: ? The FTDNA autosomal database would include approx. 1.5M testers, around half of which may be men. Even if certain transfers from other companies will not be included in the data, there would still be several hundred thousand male autosomal kits to be added to the Y-DNA Haplotree, of which ~10% could belong to the R-U106 branch... ?
1) Barrie et al.. 2023:
? ? 2) Bonczarowska et al. 2022:
Ewenn |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
That is very interesting. If the rate of false positives "child-only matches" is so high then I also wonder how it affects the ethnic origin estimated in MH, although for my mother the estimate matches reasonably well the family history, although it still shows anomalies like a quite significant Anglo-Saxon ancestry. I did not manage to test my father so I estimate his ancestry by comparing my mother's and mine, basically doing a primitive phasing.
The comparison of different chips gives a very concerning information, frankly. I tested myself and my mother at FTDNA and later transferred to MH. Thank you again Debbie. |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
¿ªÔÆÌåÓýMyHeritage have a database of 7.7 million whereas FTDNA¡¯s Family Finder database is only about 1.5 million so you would expect many more matches at MyHeritage though I¡¯m sure you¡¯re right that MyHeritage have many more customers from Poland. ? When MyHeritage wrote that blog post about their matching algorithms the companies were all using the Illumina OmniExpress. The move to the Illumina Global Screening Array made everything much more complicated and has resulted in many more false matches. There are only about 150,000 SNPs out of about 700,000 in common across the two different chips. See the ISOGG SNP Comparison Chart: ? ? I suspect that if MyHeritage were to repeat that trio analysis today the ratio of child-only matches would be much higher. ? I have two kits at MyHeritage. One is an AncestryDNA transfer done on the OmniExpress and the other is a new test on the Global Screening Array. Here is a comparison I did at the beginning of November this year. ? Illumina OmniExpress transfer ? 10,288 matches for Debbie ? 3,274 DNA matches shared with Debbie¡¯s dad ? 2,954 DNA Matches shared with Debbie¡¯s mum ? 4,060 matches not shared with either parent (39%) ? New test on Global Screening Array ? 8,856 matches for Debbie ? 2,303 DNA matches shared with Debbie¡¯s dad ? 2,004 DNA Matches shared with Debbie¡¯s mum ? 4,549 matches not shared with either parent (51%) ? 1,432 matches not replicated on GSA (14%) ? Best wishes ? Debbie ? ? From: [email protected] <[email protected]> On Behalf Of Centropol
Sent: Thursday, December 14, 2023 3:55 PM To: [email protected] Subject: Re: [R1b-U106] FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests ? Thank you very much Debbie. That really clarifies a lot and explains why I have 2x more matches in MH compared to FTDNA, although MH is a bit more popular in Poland, I think, also because of the multiple languages it can be used in. |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
Thank you very much Debbie. That really clarifies a lot and explains why I have 2x more matches in MH compared to FTDNA, although MH is a bit more popular in Poland, I think, also because of the multiple languages it can be used in.
I was really surprised to see that 16-20 percent of child-only matches are considered a good result. "The last step of DNA Matching is filtering out false positives and estimating the specific relationship between two individuals with shared DNA segments. Because many of us are descendants of the same very ancient ancestors, we often have tiny shared DNA segments with individuals we wouldn¡¯t really consider family. We sought a method to filter out such matches that only frustrate genealogists. To this end, we measure false positives internally by looking at?trios?¡ª these are sets of child, mother, and father who were all tested with MyHeritage DNA kits, and received results that validated that the relationships between the parents and child is correct. Any match that a child has with another individual, who does not match neither the father nor the mother is suspected to be a false positive and is called a?child-only match. We measure the percentage of child-only matches among all matches that are returned for children in all known trios on MyHeritage, and this figure is called the percentage of suspected false positives indicated by child-only matches. We managed to bring this figure down to 16¨C20 percent, which is a good result that as far as we know is equivalent to or better than all other DNA services.?Our improved classifier algorithms have succeeded in bringing our false positive rate to an all-time low." |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
¿ªÔÆÌåÓýHello Centropol ? MyHeritage use a complicated process using imputation and stitching to compensate for the low overlap of markers on the different chips. The process is described in this blog post: ? ? I suspect that some of these long blocks of 40 cM are not really a single segment but lots of small segments that have been incorrectly stitched together. ? Another problem is that a lot of the seemingly high matches are in fact made up of lots of small false segments. I have an example I used recently in a presentation of a match I had at MyHeritage which shared 49.5 cM with me with one test and 35.7 on my other test. This person did not match my dad but only matched my mum on 8.9 cM. When I looked in the chromosome browser I could see that this seemingly large match was made up of lots of tiny segments, only one of which appears to be valid. See the attached screenshot of my slide. ? If you can find a genealogical connection with any of your matches at MyHeritage then all well and good but I just don¡¯t think we can use those small matches as evidence because of the uncertainty. ? One good feature at MyHeritage is the filter which allows you to sort your matches by country of residence. I tend to focus on matches living in the UK which is where I live and where my ancestry is from and I don¡¯t generally look at the lower matches below about 30 cM unless something of interest really jumps out at me. Like you I get hundreds of matches at MyHeritage living all over the world in countries where I have no recent genealogical connections (France, Germany, the Netherlands, Sweden, Norway, Denmark, etc). These are either false matches or very distant matches reflecting the fact that all Europeans share common ancestry within the last thousand years. ? Debbie ? ? From: [email protected] <[email protected]> On Behalf Of Centropol
Sent: Thursday, December 14, 2023 12:16 PM To: [email protected] Subject: Re: [R1b-U106] FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests ? Hello Debbie, ? Could you please elaborate more on the below? I do not have any close matches on MH, except my direct family which I asked to test, but plenty of remote ones and I was wondering how I can have some unknown relatives in Scandinavia having a single common with me block of ~40cM. On the other hand I could verify via the traditional genealogy the link with other people having even a smaller common DNA. So I have strated wondering maybe they are false positives, what I understood was not likely with commom DNA patch of >6cM, hence the action FTDNA took a while ago to increase the matching threshold. ? "In practical terms the difference in matches is not an issue as it¡¯s the low matches are affected. MyHeritage has a major problem with false matches and inflated cM totals so I don¡¯t trust matches there much under 30 cM anyway and have even had problems with matches up to 50 cM." ? Thank you, Centropol |
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
Hello Debbie,
?
Could you please elaborate more on the below?
I do not have any close matches on MH, except my direct family which I asked to test, but plenty of remote ones and I was wondering how I can have some unknown relatives in Scandinavia having a single common with me block of ~40cM. On the other hand I could verify via the traditional genealogy the link with other people having even a smaller common DNA. So I have strated wondering maybe they are false positives, what I understood was not likely with commom DNA patch of >6cM, hence the action FTDNA took a while ago to increase the matching threshold.
?
"In practical terms the difference in matches is not an issue as it¡¯s the low matches are affected. MyHeritage has a major problem with false matches and inflated cM totals so I don¡¯t trust matches there much under 30 cM anyway and have even had problems with matches up to 50 cM."
?
Thank you,
Centropol |
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Re: Family Finder tests entering the Y-DNA haplotree
Hi John, ? I think Iain has fully answered your questions. ? In addition, on your R-S15309 branch, downstream of R-Z18, only these two testers have appeared since the date given by Iain. If we go back 1 year, to November 29, 2022, 1 other new tester having carried out a bigY700 test, of American origin, appeared forming the haplogroup R-BY160407 with a tester of British origin (probably a bigY500). ? ? ? Hi Rob, ? Unfortunately, your fears currently appear to be well founded. However, the fact that your father is only identified as R-U106 could possibly only mean that his FF test only showed no calls for possible testable SNPs on your downstream branch of R-U106. On this small branch, only 6 testers of unknown origin have appeared since November 29, and these 6 for R-FGC57423. This haplogroup was discovered in 2016 by Full Genome Corp, and is composed of 8 equivalent SNPs with no other recurrence currently on the Y-DNA Haplotree. R-S19589 and R-S11493 were both discovered in 2014 (I don't know since when they were identified by FTDNA). It therefore seems strange that FTDNA selected a specific SNP from a haplogroup discovered in 2016 (and probably appeared a little later at FTDNA), which only had 3 individuals until 2021... ? R-S19589 is currently only ~2.4 per 10,000 bigY testers. Probably ~38,000 new FF testers have appeared. So we could expect ~9 new R-S19589 testers. We have 6, which doesn't seem that far away. We will probably have to wait a little longer to be fixed (I have identified several serious STR candidates for R-S11493, but they are still identified R-M269. If one of them also passed a FF test, we will have more material to conclude). ? I am quite surprised by the number of Y-SNPs that seem to be covered by the GSA chips used by FTDNA. I wonder if it is not possible for them to detect genotypes for SNPs very close (a few bp) to SNPs targeted by their chips. For example, SNP FGC57423 (Y position 16,277,160) is very close to Z15080 (16,277,158). Z15080 only appears in the E-L94 block, an ancient haplogroup whose TMRCA is estimated ~7400 BCE. Exactly 20 new testers appeared to be E-L94 this month (perhaps FTDNA selected several SNPs of the main haplogroups for their chips?)¡ This is only a hypothesis that might eventually have to be checked for other haplogroups covered in a rather improbable manner, like FGC57423, by the FF chips. |
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Re: Family Finder tests entering the Y-DNA haplotree
GAP admins can keep track of their updated FF Y matches by looking at the Received Lab Results which now reports ¡®Prediction¡¯ under Lab Procedure I believe you can only see them via the Family Finder (or Y or Adv) ?match list with no special designations or ?icons. ?You can use the YDNA sort and search to help a little? |
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Re: Family Finder tests entering the Y-DNA haplotree
Where can I see this new Y-dna results? It just appears on dashboard where FF DNA Results are shown? An icon appears or do we need to find it elsewhere? I got my final haplogropu on Yseq, so looking forward to see what ftdna will show.?
Cheers,? Damir |
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Re: Family Finder tests entering the Y-DNA haplotree
¿ªÔÆÌåÓýHi John, You can check the results whenever you like here: https://www.familytreedna.com/public/y-dna-haplotree/R;name=R-S9509 Click on the three dots on the right-hand side and choose one of the reports. The country report now shows four tests, two German tests (presumably yours) and two others without countries of origin. These two were not there on 29th November, so probably come from Family Finder tests. They are not yet in Discover - I think that update process occurs over the weekend normally. If these are Family Finder tests, then it is likely that they split your haplogroup. You may be able to use some combination of filtered Family Finder results or the Advanced Matches facility to identify them if they are an existing Family Finder match to you. Otherwise we don't yet know what facilities we will have here - this is uncharted territory still. Cheers, Iain. |
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Re: Family Finder tests entering the Y-DNA haplotree
Hi Ewenn, Can you check your data for R-S9509? There's been no change in that clade for at least 5 years as I manage both of the bigY kits.? (Unless the change is due to some FF result that I cannot see.) Thanks,? John Terwiske On Sun, Dec 10, 2023, 6:37 AM Ewenn <gwenng008@...> wrote:
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Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
¿ªÔÆÌåÓýHi Jason, What you're referring to is nothing to do with the test itself. There was a short period where Family Tree DNA predicted groups for Y-STR tests with better resolution than just R-M269. However, they very quickly stopped doing this. The reason behind this is that FTDNA treats this prediction as a guarantee: i.e., if you take an SNP test and prove you are not R-M269, then they will find out which haplogroup you do belong to for free. This is necessary because R-M269 is often the starting point for people to take SNP packs. It is sometimes possible to predict more refined haplogroups than R-M269, but it's not 100% successful. For example, if you are already M269+ and have DYS492=13, then you have a 97% chance of being part of R-U106. Some haplogroups have markers like this, some don't, and the probability of being correct varies. These days, this prediction and the guarantee it holds are fairly useless anyway. We don't hear much about single SNP tests or SNP packs these days, given the reduced cost and comaprative benefit of BigY and other sequencing tests, so the guarantee doesn't mean that much. FTDNA could, in most cases, accurately predict most people down to at least the level of the most recent SNP packs. However, a much better idea of a person's haplogroup can often be found simply by looking at the haplogroups listed in their STR matches - this isn't fool-proof, especially at the lower levels, but it is often instructive. Cheers, Iain. |