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Author Topic: New ht35 SNP-tested clade! >>> L150-  (Read 2661 times)
argiedude
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« on: October 29, 2009, 08:55:34 PM »

http://isogg.org/tree/ISOGG_HapgrpR09.html

http://ytree.ftdna.com/index.php?name=Draft&parent=root

You can't see L150 yet in the first link, isogg.org, but Thomas Krahn has decided it's good enough to include it in his version (2nd link), so if he thinks it's good enough, it probably is.

L23- samples are L150-. All L23* samples are L150+, except one. Thus, all L23* samples except that single one should be relabeled as L150*, while the single L23+ L150- should be the only one to retain the title of truly L23*.

Immediately upstream of L150 is L23 (its parent lineage). L23* is the typical ht35 clade, whose modal is 393=12, and its mostly found in Anatolia and the Caucasus, with gradually lower rates in southeast Europe, Italy, Middle East, Iraq, and Iran.

Immediately downstream of L150 is L51. This is an extremely rare lineage, always found at rates of just a fraction of 1 percent. It's been found all over Europe, Turkey, and recently was detected in a Yemenite. It has 393=13, like ht15. It's other curious feature is 426=13.

So L150 lies between these 2 haplogroups. It's known from one person, who is a member of my North Italy Project!  [sample N37658] >>

http://www.familytreedna.com/public/northitaly/default.aspx?section=yresults

And I understand that every L23* in the ht35 Project is being tested right now for L150, is that right?
« Last Edit: October 29, 2009, 09:05:18 PM by argiedude » Logged

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Maliclavelli
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« Reply #1 on: October 30, 2009, 02:20:42 AM »

I thank you for having started this thread.
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Maliclavelli


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« Reply #2 on: October 30, 2009, 02:26:11 AM »

Argiedude, we know that also the son of Angelo Romitti, Zeno Romitti, has been tested by 23andME (I have all the family in my sharing data). Perhaps it would be interesting to invite Romitti to post also his son's data to Adriano Squecco. Then the RL23+/L150- tested so far should be two.
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Maliclavelli


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argiedude
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« Reply #3 on: October 30, 2009, 06:37:36 PM »

Or to ask him simply to disclose his value for the mutation in question, so we can be certain there's no issue of a false call with his father's test.
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argiedude
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« Reply #4 on: January 19, 2010, 10:37:27 PM »

About the Romitti sample. He and his son only tested with 23andme, which is not a very reliable company. The marker found only in Romitti is problematic, it can be misinterpreted. I would treat their results as dubious until confirmed by a reliable company, namely FTDNA. You've already talked to them, maybe you could tell them this and ask them if they'd like to confirm their result by testing with FTDNA. The fact that father and son got the same result may seem like confirmation, but it could be that the father had a "situation" in that section of his y-dna that particularly complicated 23andme's testing, which isn't good to begin with, and his son would naturally inherit the same y-dna and produce the same misinterpretation by the 23andme lab. If his sample were confirmed by FTDNA, the matter would be settled.

vineviz's argument that this mutation should be considered a private SNP until a second sample confirms it isn't serious, but what is serious is that the marker is very troublesome and 23andme is unreliable, so because of that special situation, it really needs to be confirmed by FTDNA before we can start talking about a new R1b haplogroup.
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argiedude
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« Reply #5 on: January 22, 2010, 07:06:20 PM »

vineviz wrote today that the L150- sample has just been confirmed by FTDNA!

Remember, there was an issue with the validity of his result because 23andme isn't very reliable, but now that FTDNA has confirmed it, the matter is settled.
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vineviz
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« Reply #6 on: January 22, 2010, 11:03:53 PM »

Remember, there was an issue with the validity of his result because 23andme isn't very reliable, but now that FTDNA has confirmed it, the matter is settled.

Not quite "settled".  The mutation remains private to the Romitti family, and as long as that's the case we can't know whether this is a rare clade or simply a back mutation in that family.

VV
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argiedude
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« Reply #7 on: January 23, 2010, 12:32:23 PM »

I meant the matter of wether 23andme's call was a mistake or not. But this notion of the lineage being private seems like something out of the blue. There must be a dozen other clades that have been split up thanks to the discovery of a single sample that had an ancestral value in what were previously phylogenetically equivalent SNPs for its haplogroup. You're taking the definition of private to a different realm than its original intent: this isn't the end node of a clade.

In Squecco's file there are 150 M269- samples, none of which is derived for L150, and 120 L51+ samples, none of which has suffered a back mutation in L150. So if L150 is prone to quirky behaviors, it's a very rare occurence. The L150 mutation occured between M269 and L51, and that's where Romitti's sample is located; everything fits. And anyhow, how common is it for an SNP to back-mutate? The case of P25 is so unique a study was written up about its odd behavior.

PS: Can you give us a breakdown of the origin of the L23+ L51- samples that have tested so far for L150? I'd like to know how many Italians, southeast Euros, other Euros, Jews, and/or Anatolians.
« Last Edit: January 23, 2010, 12:34:57 PM by argiedude » Logged

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vineviz
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« Reply #8 on: January 23, 2010, 01:22:19 PM »

You're taking the definition of private to a different realm than its original intent: this isn't the end node of a clade.

A SNP is private until it shows up in two or more unrelated people.  That's always been the general definition, and still is.  For example, L51 didn't get on the tree as a node until we had a second, confirming, sample.

And anyhow, how common is it for an SNP to back-mutate?

About 1.5% of the 23andMe SNPs changed states two or more times that we know about within the customers in Adriano's file.  That could be either back or parallel mutations.
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argiedude
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« Reply #9 on: January 23, 2010, 02:04:05 PM »

A SNP is private until it shows up in two or more unrelated people.  That's always been the general definition, and still is.  For example, L51 didn't get on the tree as a node until we had a second, confirming, sample.

A newly discovered SNP is private until confirmed in several people. We can't know if they occured in that single person, his father, a few relatives, or if it exists in an entire population, until we find it in other unrelated people.

But what we have in L150 is an SNP whose transition from X to Y was until now phylogenetically equivalent to L50, but Romitti's result changed that. There's nothing private here in the traditional sense. It has nothing to do with the notion of a private SNP.

About 1.5% of the 23andMe SNPs changed states two or more times that we know about within the customers in Adriano's file.  That could be either back or parallel mutations.

Really? If true, this would mean that P25's back-mutating status is the norm! I've just looked at several well known SNPs in Squecco's file, and I didn't find any case of an SNP back-mutating. By your 1.5% figure, I should've found half a dozen.
« Last Edit: January 23, 2010, 02:04:39 PM by argiedude » Logged

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vineviz
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« Reply #10 on: January 23, 2010, 04:50:38 PM »

But what we have in L150 is an SNP whose transition from X to Y was until now phylogenetically equivalent to L50, but Romitti's result changed that. There's nothing private here in the traditional sense. It has nothing to do with the notion of a private SNP.

There is one guy in the whole world with this status (L23+ L150-).  That is private, by any definition.  I don't see why that should be hard to grasp.

If true, this would mean that P25's back-mutating status is the norm! I've just looked at several well known SNPs in Squecco's file, and I didn't find any case of an SNP back-mutating. By your 1.5% figure, I should've found half a dozen.
If you tested every single human alive for every possible SNP, you'd find them all flipping states multiple times.  So, yes, parallel and back mutations are the norm.  With dense enough sampling, that becomes readily apparent.

But some SNPs are more stable than others.  And geneticists (now, at least) try to avoid using the least stable ones as haplogroup markers, so the most well-known will tend to be more stable than the unknown ones.

Check out L21, L22, L127, M228, P164, and L88 among others.
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argiedude
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« Reply #11 on: September 01, 2010, 06:48:53 PM »

There are now 200+ y-dna samples in Squecco's file which belong to obviously L150+ clades (P312+ and U106), and not one of them has suffered the back-mutation event that supposedly affected Romitti's sample. Romitti's sample isn't in an obviously L150+ position on the y-dna tree, it's located precisely where we would expect the transition from L150- to L150+ to occur.

Vineviz looked at the raw data of the test of Romitti's sample and found that the segment being amplified in Romitti's sample was different from the other samples. The primer is picking up some other segment of the dna. I don't remember if the other tested samples were all R1b1b2 or not, possibly they were because after the position of the SNP was established within R1b1b2, it wouldn't make sense to test people that belong to E1b1b or J for this mutation. If so (they were all R1b1b2), then could it be possible that L150-, wether in Romitti or in a J or R1a or G2a sample, will always return this erroneous mismatch that vineviz observed in Romitti's sample?
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Wayne Kauffman
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« Reply #12 on: September 01, 2010, 09:27:39 PM »

One could look in the http://finch2.ftdna.com/Finch/ADB/alleleList results for L150.  Since the end of March there are 14 C- and 3 T+ results listed. There should be data there to evaluate what segment the primers are picking off. 

Time to get ready for an extended holiday.
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« Reply #13 on: September 02, 2010, 12:14:26 PM »

There are now 200+ y-dna samples in Squecco's file which belong to obviously L150+ clades (P312+ and U106), and not one of them has suffered the back-mutation event that supposedly affected Romitti's sample. Romitti's sample isn't in an obviously L150+ position on the y-dna tree, it's located precisely where we would expect the transition from L150- to L150+ to occur.

Not only there are about 252 samples derived from R1b1b2a/L23+/150- which are all derived (TT), but there are also about 290 samples ancestral to R1b1b2a/L23+ which are ancestral (all CC). Also by a statistic point of view the thing seems to me "ultracerta" beyond any possible doubt. Say Vizachero to ask his friend Nordtvedt who enjoies with numbers.

Where are you going now, Wayne? We are going to have a plentiful fun.
« Last Edit: September 02, 2010, 08:53:50 PM by Maliclavelli » Logged

Maliclavelli


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vineviz
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« Reply #14 on: September 02, 2010, 07:01:00 PM »

One could look in the http://finch2.ftdna.com/Finch/ADB/alleleList results for L150.  Since the end of March there are 14 C- and 3 T+ results listed. There should be data there to evaluate what segment the primers are picking off. 
We couldn't conclusively evaluate where the errant segment was coming from the last time we looked, but maybe a fresh set of eyes would uncover something new.  Given how few people this will impact (it would be tiny subset of the L23+ L51- crowd), I can't imagine designing another set of primers for L150 would get very far up FTDNA's "to do" list.  It would take a lot of work to convincingly place an L150 reversion as a new node on the tree, and I doubt the appetite exists for it among either the labs or the customers.

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Maliclavelli
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« Reply #15 on: September 02, 2010, 08:39:47 PM »

We couldn't conclusively evaluate where the errant segment was coming from the last time we looked, but maybe a fresh set of eyes would uncover something new.  Given how few people this will impact (it would be tiny subset of the L23+ L51- crowd), I can't imagine designing another set of primers for L150 would get very far up FTDNA's "to do" list.  It would take a lot of work to convincingly place an L150 reversion as a new node on the tree, and I doubt the appetite exists for it among either the labs or the customers.

It's incredible! To ascertain this is important for me, because it is another point in favour of an Italian Refugium, and by what you say we all can retain that L150- of Romitti exists, not somewhere in the genome but exactly where others have a +, then the mutation.
With Argiedude I can say that "it's located precisely where we would expect the transition from L150- to L150+ to occur". And for me it is enough, and probably it is enough also for FTDNA (Thomas Krahn?), if maintains L150 in its tree between L23 and L51.
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Maliclavelli


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argiedude
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« Reply #16 on: September 02, 2010, 10:57:33 PM »

Maliclavelli, you could look at the data in the link Wayne posted, to see if there are pre-R1b1b2 samples and what their results are.
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vineviz
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« Reply #17 on: September 03, 2010, 12:34:09 AM »

With Argiedude I can say that "it's located precisely where we would expect the transition from L150- to L150+ to occur". And for me it is enough, and probably it is enough also for FTDNA (Thomas Krahn?), if maintains L150 in its tree between L23 and L51.
I can say that we also have one man who is L23- and L150+, which is also a problem result.  In our project, of the 42 results we have for L150 three are out of place (i.e. L23- L150+ or L23+ L150-).  It's a genuine problem marker.
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Maliclavelli
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« Reply #18 on: September 03, 2010, 01:10:20 AM »

Maliclavelli, you could look at the data in the link Wayne posted, to see if there are pre-R1b1b2 samples and what their results are.

Argiedude, I tried yesterday but I hadn't access not having been tested for Y by FTDNA (I have had with them only an FGS, but my code of it isn't valid for the Y).

The problem Vizachero speaks about is that of Sutherland (I spoke about in another thread): Wayne resolved it, if results will be confirmed, hypothesizing an L150.1 and an L150.2. But, as my statistics of my previous posting has demonstrated, the numbers is for an authentic L150- for Romitti, even more confirmed not only by 23andMe but also by FTDNA. Like I have said, the test on Romitti's son has failed and the father sent another
sample. And remember that Romitti-father was tested before his request by Vizachero, without asking an authorization, and also on this I spoke about (very angry) in the past.
Everything is at Vizachero's hands, and he has demonstrated which solution prefers.
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Maliclavelli


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vineviz
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« Reply #19 on: September 03, 2010, 08:57:01 AM »

But, as my statistics of my previous posting has demonstrated, the numbers is for an authentic L150- for Romitti, even more confirmed not only by 23andMe but also by FTDNA.
I have spent literally hours examining the sequences from the L150 tests done by FTDNA and agree with their conclusion:  the L23+ L150- results are due to amplification of a distinct piece of DNA.  It is likely that this results from an insertion onto the Y of a piece of DNA from elsewhere in the genome.  I've concluded this, Thomas Krahn of FTDNA has concluded it, and I published the sequences for anyone to examine so they can verify for themselves.  If you don't wish to accept it, that is your right.  But I can honestly say that if the case were different I would say so.  Future technological advances may reveal a proof you can accept, but for now all I can say is that everyone who has looked at it agrees.

And remember that Romitti-father was tested before his request by Vizachero, without asking an authorization, and also on this I spoke about (very angry) in the past.
If you are suggesting that I tested Romitti for L150 without permission, that is a lie. All tests at FTDNA are either ordered by the customer  or are conducted with their explicit permission.
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Maliclavelli
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« Reply #20 on: September 03, 2010, 12:33:22 PM »

If you are suggesting that I tested Romitti for L150 without permission, that is a lie. All tests at FTDNA are either ordered by the customer  or are conducted with their explicit permission.
When Romitti-father and his son asked (for my invitation but transmitted them by Belgeri, who is in contact with them) for a test of L150, Romitti-father had immediately his result (L150-), whereas the son hasn't it yet. Ftdna failed a first run and asked for a new sample.
Perhaps you know who had already tested Romitti, why and for whom.
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Maliclavelli


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vineviz
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« Reply #21 on: September 03, 2010, 12:50:20 PM »

Perhaps you know who had already tested Romitti, why and for whom.
If you, or the customer, has a concern about this they should contact FTDNA directly.  All I know is that the order was entered and paid for by the father, and the result came after that.  That's the way it normally works, but then again I can't say "conspiracy theory" in twelve different languages.

The son is not a member of my project, so I have no information about any delay in his result.
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Maliclavelli
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« Reply #22 on: September 03, 2010, 12:57:54 PM »

21/01/2010

Sia il mio amico Nxxxxx che suo figlio Nxxxxx sono nello stesso Batch.. 344
previsto arrivo dei risultati all’08 marzo..
ma penso che arriveranno prima. .
 
ciao
Giuseppe.
 
Pending Lab Results
Below is a list of Pending Lab Results...
Pending Items
TESTS                        EXPECTED*               BATCH               NOTES
L150(L150)                     03/08      
         

22/01/2010

Sono già arrivati i risultati di L150 per il mio amico Angelo..
 
Haplogroup Info
Your Haplogroup
Your Haplogroup    Tests
R1b1b2a         L10- L150- L23+ L49+ L50- L51- L52- L7- L8- L9- M126- M153- M160- M173+ M18- M207+ M222- M269+ M343+ M37- M65- M73- P107- P25+ P310- P311- P312- P66- SRY2627- U106- U152- U198-   

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Maliclavelli


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argiedude
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« Reply #23 on: September 03, 2010, 07:15:05 PM »

I can say that we also have one man who is L23- and L150+, which is also a problem result.

But it's too much of a coincidence that the several problem results always occur in samples that are exactly at the point in the y-dna tree where the transition from L150- to L150+ is expected to occur. All the 200 M269- samples are uniformly L150-, all the 200 U106+/P312+ are uniformly L150+. I do agree that the sample with L23- L150+ is a problem result and doesn't make sense.

In our project, of the 42 results we have for L150 three are out of place (i.e. L23- L150+ or L23+ L150-).  It's a genuine problem marker.

One of the 2 is incorrect, but it doesn't follow that both should be incorrect. It's possible, if the 2 SNPs occured close together, that they are now synonomous, but that's precisely what has to be investigated.

the L23+ L150- results are due to amplification of a distinct piece of DNA.  It is likely that this results from an insertion onto the Y of a piece of DNA from elsewhere in the genome.

But this could be the reason why all L150- results occur. That's why I was wondering about looking at the results of L150 tests on samples from other haplogroups such as E1b or R1a: if we found that the reason they are L150- is due to the same strange phenomenon that affected Romitti's result, then Romitti's result wasn't a back-mutation, it was the ancestral state.


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vineviz
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« Reply #24 on: September 03, 2010, 07:44:03 PM »

But it's too much of a coincidence that the several problem results always occur in samples that are exactly at the point in the y-dna tree where the transition from L150- to L150+ is expected to occur.
This was precisely one of the reasons it took us so long to be convinced that something strange was going on.  I'm not saying it is entirely a coincidence, by the way.  The ultimate explanation of the recombination might, in fact, depend on this particular state of the Y chromosome.

One of the 2 is incorrect, but it doesn't follow that both should be incorrect.
I agree that it doesn't HAVE to be that both are incorrect, and in fact I'm not saying that either are technically incorrect.  But the Romitti result  is demonstrably NOT a case of L150 being the ancestral state:  it is a case of Y-recombination and FTDNA has convinced me of this.  I need to look at the Sutherland case more to understand it.


But this could be the reason why all L150- results occur.
I don't think so.  We've looked at the traces for other L150- results and they are not all due to the same recombination.  It is precisely because we've got sequences from two different L150- segments that are radically different at other positions besides L150 (more than 50 differences, I think) that we can see that Romitti's L150- result is from a recombination.

I acknowledge this is a confusing case, and can understand why it might seem fishy.  But Thomas and I have looked over all the sequences, and I don't think we're both wrong.

VV
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