Re: Transformations in early medieval England: the perspective from population genetics
Further studies of aDNA in the U.K.
is exciting, and hopefully will continue to move the needle in
understanding the composition of migration waves over vast swaths of
time.
Thanks, Tom.
pk
On Sunday, October 16, 2022 at 06:47:54 AM CDT, T J Little via groups.io <t.little72@...> wrote:
You may enjoy this article that was posted in the U106 group, regarding ancient DNA and the change in the population of Britain.
-Tom Little
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Transformations in early medieval England: the perspective from population genetics
You may enjoy this article that was posted in the U106 group, regarding ancient DNA and the change in the population of Britain.
-Tom Little
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Re: FTDNA's New Time Tree
That's true, Daryl, "daughtering out" does have a profound effect on a lineage. Something I've noticed, while searching for genealogy threads, is that many rich land owners would also include their illegitimate children in their wills, which I initially found to be a bit awkward. I wondered if by acknowledging these children, there was a better chance that their lineage would continue, even through a bastard son. Royalty obviously did it, but I would say lesser land owners could do it as well, and for the same reasons. I have a particular affinity for wills because of the wealth of information they can provide. Unfortunately, these can be a rare find, especially the further back in time you go.
pk
On Saturday, September 10, 2022 at 04:42:47 PM CDT, Class1 Driver <class1driver@...> wrote:
I haven't done an indepth study of the above TMRCA methods, and this is the first of heard of a 'strict clock' which I doubt is possible. I have checked Ian's TMRCAs, and didn't find strictness, if I'm understanding it's meaning. I have a few questions for him, like "if you're using 160 yrs/SNP then why do I sometimes only find ~60 years in between SNPs that are accepted as only having one SNP between the father SNP 'block' and son SNP (no equivalents)"?
Concerning brother SNPs and force fitting, I don't think it works well in some haplogroups like M222 which can sometimes have extremely more equivalents than their brother subclades. Yfull may be on the right track here where they just average all the brothers, and keep doing so as far back in time as possible. L513 may be lucky in that Yfull's # of SNPs 'average' for all son SNPs of DF13 seemed to contain the exact average number of SNPs within it.?
Here's something I've been pondering lately: the 'daughtering out' of male lineages, which I think, but not sure, is 9/10 male lineages eventually disappear due to no males being born, which is called daughtering out. I wonder if the gifted mathematicians have included "daughtering out" in their algorithms.? In the current time period I suspect some of our male lineages, like mine, may have a skinny appearance to them, especially going back in time for the last 700 years or so. Skinny would mean not enough son's having son issue. My own g grandfather was the single male, + one sister, born to my gg grandfather who died before his 21st birthday.
When I see "bushy" lineages, like some in M222 with many more SNPs than their brother SNPs, I think 'rich' vs 'not so rich' and/or 'poor'. If everything is passed down to the oldest son this makes it more difficult for the other sons to thrive. While not true in all cases, the richest can afford to have more issue, and if there are big titles attached to their names they will want plenty of sons in order to increase their riches and influence for hundreds of years to come. It's likely not as simple as just riches, but gamblers looking for an 'edge' will tell you that any edge above 50% is very exciting for them to exploit. So if the prince is handed a kingdom his chances of successfully exploiting it to his lineage's advantage is greater than his younger brothers. What's the algorithm for that? ;-)
Daryl?
Interesting short summary on the announcement but it is sparse on the underlying details of the algorithms themselves... The 'relaxed' method simply sounds like a means to 'force-fit' apparently confusing SNP stacks of one family lineage against another brother line under the same genetic cluster (branch node).? The whole discussion appears to contradict Iain McDonald's contention that a "strict" clock applies to all.
leake
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Re: FTDNA's New Time Tree
Thanks for posting these, Tom.
On Saturday, September 10, 2022 at 09:28:54 AM CDT, Leake Little <leakelittle@...> wrote:
Interesting short summary on the announcement but it is sparse on the underlying details of the algorithms themselves... The 'relaxed' method simply sounds like a means to 'force-fit' apparently confusing SNP stacks of one family lineage against another brother line under the same genetic cluster (branch node).? The whole discussion appears to contradict Iain McDonald's contention that a "strict" clock applies to all.
leake
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Re: FTDNA's New Time Tree
Daryl,
You need to git outta my noggin '!
Well stated sir?
Brad?
I haven't done an indepth study of the above TMRCA methods, and this is the first of heard of a 'strict clock' which I doubt is possible. I have checked Ian's TMRCAs, and didn't find strictness, if I'm understanding it's meaning. I have a few questions for him, like "if you're using 160 yrs/SNP then why do I sometimes only find ~60 years in between SNPs that are accepted as only having one SNP between the father SNP 'block' and son SNP (no equivalents)"?
Concerning brother SNPs and force fitting, I don't think it works well in some haplogroups like M222 which can sometimes have extremely more equivalents than their brother subclades. Yfull may be on the right track here where they just average all the brothers, and keep doing so as far back in time as possible. L513 may be lucky in that Yfull's # of SNPs 'average' for all son SNPs of DF13 seemed to contain the exact average number of SNPs within it.?
Here's something I've been pondering lately: the 'daughtering out' of male lineages, which I think, but not sure, is 9/10 male lineages eventually disappear due to no males being born, which is called daughtering out. I wonder if the gifted mathematicians have included "daughtering out" in their algorithms.? In the current time period I suspect some of our male lineages, like mine, may have a skinny appearance to them, especially going back in time for the last 700 years or so. Skinny would mean not enough son's having son issue. My own g grandfather was the single male, + one sister, born to my gg grandfather who died before his 21st birthday.
When I see "bushy" lineages, like some in M222 with many more SNPs than their brother SNPs, I think 'rich' vs 'not so rich' and/or 'poor'. If everything is passed down to the oldest son this makes it more difficult for the other sons to thrive. While not true in all cases, the richest can afford to have more issue, and if there are big titles attached to their names they will want plenty of sons in order to increase their riches and influence for hundreds of years to come. It's likely not as simple as just riches, but gamblers looking for an 'edge' will tell you that any edge above 50% is very exciting for them to exploit. So if the prince is handed a kingdom his chances of successfully exploiting it to his lineage's advantage is greater than his younger brothers. What's the algorithm for that? ;-)
Daryl? Interesting short summary on the announcement but it is sparse on the underlying details of the algorithms themselves... The 'relaxed' method simply sounds like a means to 'force-fit' apparently confusing SNP stacks of one family lineage against another brother line under the same genetic cluster (branch node).? The whole discussion appears to contradict Iain McDonald's contention that a "strict" clock applies to all.
leake
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Re: FTDNA's New Time Tree
The default way to do TMRCA estimates is use predetermined mutation rate. You can all this a strict clock or whatever? you want, but as far as we know (the scientific studies to date), the Y chromosome mutates basically at the same rate across geographies, ethnicities, subclades.
We know from reality, that some subclades are different from other. That doesn't change the expected rate of mutation, though.?? You can flip a coin five times and get five heads in a row, but the expected rate of heads/tales for the next flip is still 50/50. Still five heads in a row can come up.
Therefore, if you have a subclade with a known difference, there are mathematical models that allow you introduce a constraint. You can call this a force fit if you want, but it basically says a certain SNP was around at a certain regardless of what the expected rate of mutations are. What FTDNA is calling a relaxed clock is just this. It is the introducing of reality points into a statisical model.
When I first learned computer software development, I had to write linear programming software and computer simulations. There are various math models that all of these things are based on. FTDNA is just using them, with the guidance of Dr. Iain McDonald. To me, it is obvious logical thing for FTDNA to do.
Unfortunately, YFull does not have an advanced math model so rather than use linear programming techniques they essentially just fudge their TMRCAs when the expected rates don't produce results that account for reality (like ancient DNA finds).
I can't discuss this fully on multiple forums but you can talk to Dr. McDonald on the U106 groups.io.? I'm tracking updates and sharing what I find on Anthrogenica under FTDNA.
I've said this for a number of years as I use to maintain STR based TMRCA spreadsheets.
----?? TMRCAs are no panacea. If a method produces a result that fits your hypothesis or meets what you are otherwise are accustomed to,? you are likely to think that TMRCA method is the greatest things since sliced bread. If it doesn't fit, then you will think it is worthless.? ----
One thing we all can do is update our Family Trees on our kit dashboards on FTDNA and link our kits and known cousin kits to people on the family tree. Make sure to include birth dates. FTDNA is using this data for BIg Y testers as validation for their TMRCA methodology.? This is still all in beta, so more changes will be made.? FTDNA will eventually expand their FTBED regional defintions, which math-wise, should provide more accuracy.
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Re: FTDNA's New Time Tree
I haven't done an indepth study of the above TMRCA methods, and this is the first of heard of a 'strict clock' which I doubt is possible. I have checked Ian's TMRCAs, and didn't find strictness, if I'm understanding it's meaning. I have a few questions for him, like "if you're using 160 yrs/SNP then why do I sometimes only find ~60 years in between SNPs that are accepted as only having one SNP between the father SNP 'block' and son SNP (no equivalents)"?
Concerning brother SNPs and force fitting, I don't think it works well in some haplogroups like M222 which can sometimes have extremely more equivalents than their brother subclades. Yfull may be on the right track here where they just average all the brothers, and keep doing so as far back in time as possible. L513 may be lucky in that Yfull's # of SNPs 'average' for all son SNPs of DF13 seemed to contain the exact average number of SNPs within it.?
Here's something I've been pondering lately: the 'daughtering out' of male lineages, which I think, but not sure, is 9/10 male lineages eventually disappear due to no males being born, which is called daughtering out. I wonder if the gifted mathematicians have included "daughtering out" in their algorithms.? In the current time period I suspect some of our male lineages, like mine, may have a skinny appearance to them, especially going back in time for the last 700 years or so. Skinny would mean not enough son's having son issue. My own g grandfather was the single male, + one sister, born to my gg grandfather who died before his 21st birthday.
When I see "bushy" lineages, like some in M222 with many more SNPs than their brother SNPs, I think 'rich' vs 'not so rich' and/or 'poor'. If everything is passed down to the oldest son this makes it more difficult for the other sons to thrive. While not true in all cases, the richest can afford to have more issue, and if there are big titles attached to their names they will want plenty of sons in order to increase their riches and influence for hundreds of years to come. It's likely not as simple as just riches, but gamblers looking for an 'edge' will tell you that any edge above 50% is very exciting for them to exploit. So if the prince is handed a kingdom his chances of successfully exploiting it to his lineage's advantage is greater than his younger brothers. What's the algorithm for that? ;-)
Daryl?
Interesting short summary on the announcement but it is sparse on the underlying details of the algorithms themselves... The 'relaxed' method simply sounds like a means to 'force-fit' apparently confusing SNP stacks of one family lineage against another brother line under the same genetic cluster (branch node).? The whole discussion appears to contradict Iain McDonald's contention that a "strict" clock applies to all.
leake
|
Re: FTDNA's New Time Tree
Interesting short summary on the announcement but it is sparse on the underlying details of the algorithms themselves... The 'relaxed' method simply sounds like a means to 'force-fit' apparently confusing SNP stacks of one family lineage against another brother line under the same genetic cluster (branch node).? The whole discussion appears to contradict Iain McDonald's contention that a "strict" clock applies to all.
leake
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Re: FTDNA's New Time Tree
I was remiss by not adding the FTDNA's new paper on aging:
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FTDNA has added a "Time Tree" feature to it's Discover More tool.? It reminds me of the Scientific View in YFull, You may enjoy checking it out.
-Tom LIttle
Little Project
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Re: General L513/ L193 Discussions
Thanks for that explaination Mike. I guess it was the inconsistent SNPs that I wasn't factoring in which made the term "phylogenetically consistent" difficult to grasp. A "SNP that shows up on and off across multiple unrelated lineages" is something I didn't know, or had forgotten. Probably the latter. I guess until now I had just presumed it was a machine misread, and didn't realize the many different characteristics of an "unstable" SNP. Perhaps "what constitutes an unstable SNP?" should have been my question to ask. I had assumed unstable SNPs would be easily spotted and excluded, but that assumption made the need for the creation of a terminology -- "phylogenetically consistent", which was an already understood concept -- confusing. ;-)
Switching topic back to the McIntosh, 281409, that showed as BigY700, about 13 days ago, on my personal account, and with a terminal SNP of L193: He's now in our L513 Project as BY138237 (thanks to Mike's invite). This is one of many times that FTDNA has fooled me. I wish they wouldn't label men as BigY until they've determined his terminal SNP.? It looks like he's breaking up Alex W's block of several equivalent SNPs under FGC32127 -- the one which includes the 2 Walker's terminal SNP of BY66304.
Mike: It's good to hear about FTDNA's plans. I like that STRs are being looked at also. Years ago they seemed to have big plans for STRs. I have always believed more STRs would help us pin down closer relatives.
Mike, I know you suggested I invite the 1067* McLean, B99182, in the McLean Project,?to our L513 Project, but I was thinking he might be more receptive to an invite from you -- as our Project Administrator. What do you think. ;-)
Thank you Leake for the post that included Ian McDonald quotes. I'd like to follow/read those conversations you mentioned if you can provide a link to them.
Best,
Daryl?
On Wed, Aug 31, 2022, 7:54 AM Tiger Mike < mwwdna@...> wrote:
Daryl requested, "I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it".
Here is a description of phylogenetic comparison methods.
For Y DNA, "consistency" is just a matter of following the reality that every son has a father, only one father, and that he is from whom each son gets his Y chromosome.
There is no mixing of Y chromosomes
like there is of autosomal DNA.
Consistency with Y DNA would mean things like:
- My brother and I have the same SNPs our father does although my brother or I each might have an additional SNP.
- My male line cousins would have the same SNPs that our paternal grandfather has.
An inconsistency would be an SNP that shows up on and off across multiple unrelated lineages. Something is going on that we don't understand and that particular SNP perhaps is unstable or the test is having a hard time reading that location.
_._,_._,_
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Re: General L513/ L193 Discussions
Please, please do not repost this - MNPs are excluded.?
We need to be patient and wait for the white paper.
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Re: General L513/ L193 Discussions
Daryl requested, "I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it".
Here is a description of phylogenetic comparison methods.
For Y DNA, "consistency" is just a matter of following the reality that every son has a father, only one father, and that he is from whom each son gets his Y chromosome.
There is no mixing of Y chromosomes
like there is of autosomal DNA.
Consistency with Y DNA would mean things like:
- My brother and I have the same SNPs our father does although my brother or I each might have an additional SNP.
- My male line cousins would have the same SNPs that our paternal grandfather has.
An inconsistency would be an SNP that shows up on and off across multiple unrelated lineages. Something is going on that we don't understand and that particular SNP perhaps is unstable or the test is having a hard time reading that location.
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Re: General L513/ L193 Discussions
Something we need to consider about TMRCA statistically based methods is they have (and should have) error ranges. Oftentimes the 95% confidence interval is long range of time. We should try to focus on the range of dates and not the specific mean or median date.? That is not very satisfying but consider that R-L513 has 765 subclade. Therefore, there are probably around 40 subclades that have TMRCA estimates outside the 95% range. Yikes!? This is true of all the TMRCA math based methods I know of.
We do not know FTDNA's method as they have not published it. .
I have been told by FTDNA:
1) Their methodology uses both SNPs and STRs.
2) Their methodology uses regional definitions they will call FTBED regions.? (McDonald uses something he calls McDonaldBED regions. YFull uses something called ComBED regions as defined by Adamov.)
3) The FTBED regions are fairly restrictive but more expansive that ComBED. (This seems to contradict Iain's statement somewhat.)
4) The SNP counting does not count SNPs that have less than six reads in the supporting Big Y700 results.
5) The SNP counting excludes not pure SNPs.
6) They plan to add another statistical technique soon (like maybe next week) that may help address some concerns in older haplogroups
I don't know if the "not pure" SNPs means they are excluding the MNPs. I agree they should exclude those or count them differently.? We do need to wait for their white paper.
I personally think they are more focused on genealogical time estimates and want those to be the best possible. They position themselves as a genetic genealogy company, not a haplogroup research institution. That requires some precision since each branch has less data for a shorter time period than the huge ancient branches.
?
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Re: General L513/ L193 Discussions
Hi Daryl - to be fair to Iain I thought I would provide some of his contemporary comments on similar subject (time estimates and aging)... There are all sorts of nomenclature used in these discussions - I would hardly claim to understand the precise meaning of every term. Loved the way Bucky Fuller would make up words (geodesic dome, dymaxion car) as he went along! "phylogenetically" may be one of those terms but I hear a taxonomist's concern for some criteria consistency - whether that's by number or morphology I assume. Even 'homologous markers' are not what I would have expected by the term alone... position on the chromosome appears to have some heft in the equation. And here's Iain: "Calls of SNPs will vary between analyses of the same BAM file, whether it's done by FTDNA, YFull, FGC or anyone else. This is because different choices are made regarding what constitutes a high-quality SNP call: how many reads it needs, what base quality those reads need to be, what mapping quality those reads have, the repetitiveness and other features of the surrounding genome, etc. Each test contains many shades of grey between having no reads at a position and SNPs of unquestionable quality."
"For TMRCA estimates, there are two things that matter. Maximising data is important to improve precision: more tests, better tests, better reference comparisons to provide better coverage, and so on. However, precision is nothing without accuracy, and self-consistency is the key here. If you count SNPs based on one interpretation of a BAM file, you should also count the test coverage according to the number of base pairs with good-quality reads in that BAM-file interpretation. That should also overlap with the base pairs that you are using to define your mutation rate."
"The key to a good TMRCA calculation is to maximise precision without sacrificing accuracy, while maintaining a computation that can be done with reasonable effort in reasonable time. All TMRCA calculators work on similar principles, but make different balances between these three factors. YFull sacrifice precision to ensure accuracy, by restricting the portion of the test they use to a specific subset of base pairs. FTDNA's methods aren't announced yet, but the numbers they provide for the upper haplogroups in R-U106 suggest they trade accuracy to obtain the most precise numbers. The exact methodology I personally use these days tries to keep both precision and accuracy to obtain the best TMRCAs, but requires very in-depth analysis that could not easily be rolled out to an entire haplotree. What balance anyone else wants to take is up to them!"
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Re: General L513/ L193 Discussions
Mike, and all:
A mere quest for knowledge below.?
I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it, if you know of one. I can't seem to grasp exactly what he is referring?to.
I know choosing a 'good' SNP can be subjective, and Mike has explained some of the reasons for that already, but when does "consistency" come into play, especially to include the phylogenetic part?
Also, per a Sinkler BigY2 test below, I'm wondering if it's okay to label mutations as "good" SNPs when they are found very close together. Ian McDonald, below, doesn't seem to think so, but I could be misinterpreting him.?
Ian McDonald's website link here:
The first paragraph at top of Ian's page: "Time to most-recent common ancestor (TMRCA) estimates for targetted pairs" Then >>> "How to use this chart:
- Look vertically for the number of SNPs the differ between two tests. >>>>> MNPs (e.g. SNPs at sequential positions, or positions very close to each other) should be ignored."
In light of Ian's instructions I'm wondering why FTDNA has named these 4 snps below where they're all found within 44 bases of each other, and especially the bottom 2 which are within 2 bases of each other -- (11,072,631 to 633). Are they just potential SNPs or 'good' SNPs that are "phylogenetically consistent"? I'm just trying to understand what is a good acceptable SNP according to FTDNA. Note Alex's ** and box coloring in the right column. They're not the usual white background with a + sign that I would assume is a 'good' SNP.
"Sinkler BigY2: 127262
| 13228351-C-T | 11072675-C-T | | FT271494 | | | | | ** | | 13228320-C-T | 11072644-C-T | | FT441381 | | | | | ** | | 13228312-C-A | 11072636-C-A | | FT441380 | | | | | ** | | 13228309-A-G | 11072633-A-G | | FT441379 | | | | | ** | | 13228307-C-T | 11072631-C-T | | FT441378 " |
Also, will BigY3 700 results give me similar private SNP information for others, like Alex does above?
Best,
Daryl?
On Sun, Aug 28, 2022, 6:44 AM Tiger Mike < mwwdna@...> wrote: You had two inquiries. I'll answer below.
Daryl wrote:? ?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
[[MW: Every service has their own criteria for variant call analysis. They also have different depths and quantities of data. For instance, much of the Big Tree was built on VCF files. VCF files, particularly old ones, have less information than BAM files. FTDNA has and uses all of the BAM file data, and can and will even go back to the lab for more info.
Importantly, FTDNA also has the most NGS BAM file samples. This aids in phylogenetic analysis, which validates and/or invalidates variant call analysis in many situations.Read Alex's intro to the Big Tree. He says "The most important property of these mutations (SNPs) is that they are phylogenetically consistent." ]]
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Re: General L513/ L193 Discussions
YFull has moved their payment center to somewhere due to the war- France maybe. They now charge 45 Euros, and for us using $$, that goes up and down with the conversion rate. I've sent two kits recently and the PayPal amount was around $47 US.? ?Works fine. Just don't let the Euro's throw you.??
-Tom Little
Little Surname DNA Project
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Re: General L513/ L193 Discussions
You had two inquiries. I'll answer below.
Daryl wrote:? ?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
[[MW: Every service has their own criteria for variant call analysis. They also have different depths and quantities of data. For instance, much of the Big Tree was built on VCF files. VCF files, particularly old ones, have less information than BAM files. FTDNA has and uses all of the BAM file data, and can and will even go back to the lab for more info.
Importantly, FTDNA also has the most NGS BAM file samples. This aids in phylogenetic analysis, which validates and/or invalidates variant call analysis in many situations.Read Alex's intro to the Big Tree. He says "The most important property of these mutations (SNPs) is that they are phylogenetically consistent." ]]
On Sat, Aug 27, 2022, 8:43 PM Tiger Mike < mwwdna@...> wrote: I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers.
Daryl wrote:? Are pileups a true negative outcome? At least in a pileup we can see which Son SNP they belong to, in the case of L193 men. I suspect that some people just need to dip their toe in the water to get a sense of what it feels like. This may induce an interest to walk in further.?
? [[MW: What I'm calling a pile-up is caused by limited of SNP testing downstream of the haplogroup label for those in the pile-up. These folks end up being stuck, when their more youthful terminal haplogroup could be known with additional testing. As the tree grows with more and more Big Y testers, new downstream haplogroups are defined. These SNPs are missed by any prior targeted testing. They are not negative SNP results.
However, I think what you are saying is that the individuals stuck at a pile-up level is not bad to know. I agree it is fine to know but only leaves more and more questions that ultimately will only be resolved when there is a terminal haplogroup for every Earliest Known (genealogically) Ancestor. The targetted SNP testing is wasted until then. The efficient method time-wise and ultimately cost-wise, I think and there are many who agree, is to go straight to the real solution of Y SNP discovery testing, that is Big Y.? Ironically, it is a better investment to max out on Y STR testing to Y111 if you are looking for interim solutions. At least your expense is credited to you in a reduced upgrade price to Big Y.]]
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Re: General L513/ L193 Discussions
Mike:?
Thanks for posting that information.?
Yes, I think I have a chance of BigY matching with IN48416, but only genealogically before the 1700s and likely a few hundred years before that even. Of course I'm playing the fun game called guessing, because it really is fun to do so.? He has a possible 10 good SNPs on his Big Tree private page, most of them named by ftdna.?
?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
I should match at least one SNP with my Aussie Martin cousin, #44265, who only has two 'good' private snps, FGC40169 and FGC40170.?
See my comments (coloured) below in your post.? Yes, BigY is the first best choice, but some people are still leary of any DNA testing. Fears and doubts are big obstacles, and a major cause of SNP* paragroups without a near present day terminal SNP -- in my opinion.? Many people want to be 'sold' on a concept first, before dishing out the money.? I think it's slowly happening, but just not as fast as we'd like. ;-)
Daryl? ? On Sat, Aug 27, 2022, 8:43 PM Tiger Mike < mwwdna@...> wrote: I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers.
Are pileups a true negative outcome? At least in a pileup we can see which Son SNP they belong to, in the case of L193 men. I suspect that some people just need to dip their toe in the water to get a sense of what it feels like. This may induce an interest to walk in further.?
Unfortunately, some don’t test further so the tree has parts incomplete.
I've found that many people just need someone to help them further into the water.?
Targeted SNP testing can’t discover a new SNP. It can rule people out of a true terminal haplogroup, but negative results don’t help the tester, himself
Yes, negative results may not show any relatedness but the whole process may stir up an interest to know more and may even convert doubters into believers of more expensive tests like BigY.? For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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Re: General L513/ L193 Discussions
I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers. Unfortunately, some don’t test further so the tree has parts incomplete.
Targeted SNP testing can’t discover a new SNP. It can rule people out of a true terminal haplogroup, but negative results don’t help the tester, himself.
Thanks for that good information Mike. I haven't kept up on current events for a few years now (at least).
I like the idea of a BAM file, as one never knows when it might come in handy.? It's good to know that it can be ordered any time in the future. I'll probably order it at some point, even if it's to simply satisfy my natural curiosity, but even more so to preserve that data for as long as possible.
I'm hoping those private variants of others can be traced to specific people, like on the Big Tree, so that I can possibly recommend cheaper single variant testing methods like Thomas Krahn's Yseq company. It worked well in our A1067 Haplogroup.
Yes, definitely, more data is best, as variant selection can be very subjective.
Any new (easy) formulas/methods for SNP rates and the combination of old SNP tests and new that help people like me to make 'best guess' ages of SNP Births and TMRCA??
Thanks for all your efforts Mike, and for staying current for all of us.
Daryl
I might have to relearn how to do a Blat on my phone -- at some future time -- for those questionable variants where it's exact location can't be exactly pinpointed.? ;-) On Sat, Aug 27, 2022, 4:35 PM Tiger Mike < mwwdna@...> wrote: In terms of variant call analysis, the Big Y tool set includes Y chromosome browser and lists of private and non matching variants by location number. The chrome BAMsAway add-on can help.
The FTDNA VCF files are still free and YFull accepts them. If you want to use YFull I suggest sending them the VCF file and then waiting to see if there are close matches on the tree with you. At that point you may find variants you question and want a full BAM analysis from YFull.
I think the YFull charge is $49 and includes a free upgrade to BAM file analysis. The FTDNA charge for a BAM file is $99. When they started this with Big Y700 they lowered prices from $100 to $150 but then you add to pay for the BAM file if you wanted it. Few people actually order it.? People who already had Big Y500 always get their BAM files for free, regardless of whether they upgrade to Big Y700 or not.
Something to keep in mind is phylogenetic analysis. This impacts call variant analysis. The more samples analyzed the better. FTDNA (and I think YFull too) may change a call on a variant after comparing raw data from several different samples of the same subclade.
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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Scotland
T J Little
MagUidhir6
Leake Little