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Author Topic: Why using the letters "R1b" make sense in terminal SNP hg labels?  (Read 3949 times)
Mike Walsh
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« on: October 05, 2012, 11:38:44 AM »

Just like the name of this forum is "R1b and Subclades", it makes sense to continue using the "R1b" label.

I recommend that when we talk using short label/terminal Y SNP names within the R haplogroup that we don't use the single letter "R", but rather use R1a, R1b or R2 as is appropriate, since these haplogroups are only distantly related and both R1a and R1b are quite large.

Some may ask, why three letters instead of four, etc. ?

I think the answer is that R1a and R1b are de facto standards both across the academic and hobbyist community.  Most people know what they are.

As a case in point. This new paper was just published yesterday!
 
"A calibrated human Y-chromosomal phylogeny based on resequencing" by Wei, et al.
http://genome.cshlp.org/content/early/2012/10/04/gr.143198.112

If you open the free PDF text file and scroll down to the last page you will see very clearly that R1a, R1b and R2 are clearly broken and levels below that are just referred to as son, father, etc. No standard is shown below the R1a and R1b depictions.

R1a, R1b, R2 are commonly accepted terms that have meaning.  R1a and R1b are too big to clump together.
« Last Edit: October 05, 2012, 12:10:06 PM by Mikewww » Logged

R1b-L21>L513(DF1)>L705.2
rms2
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« Reply #1 on: October 05, 2012, 02:37:15 PM »

I understand your thought on this, but the intent of the shorthand is to be as brief as possible while conveying all the necessary information to allow one to locate the terminal SNP on the appropriate tree. For that purpose, the single-letter major branch prefix is all that is needed. It directs one to the right tree, then all he has to do is scroll down until he finds the terminal SNP, a process that doesn't take more than a couple of minutes of scanning.

The addition of a couple of extra characters isn't all that helpful, except perhaps in the case of R2, since it is usually placed at the bottom of the R tree. R1a is so high on the tree that an "R1a" prefix is useless, and that's how I feel about an "R1b" prefix, as well: it only gets you to M343, which isn't a lot of help. One is still going to have to scroll down and scan to find the right SNP.

The thinking behind the shorthand also included the likelihood that names like "R1a" and R1b" will change, whereas the single-letter major branch designator, while not totally immune to change, is less likely to be changed.

I think it best to get used to using the accepted shorthand, in which, by the way, there is no "R1b", only R-M343. ;-)

I have no problem with individuals using whatever system they prefer, but I do think standardization is desirable, and that, whatever system one uses, if it departs from the standard, he should keep that in mind and realize he is using his own pidgin version and not the real thing.

Of course, if ISOGG and/or the YCC go to placing R1a, R1b, and R2 on different and separate tree pages, then those three-character prefixes would actually be useful and necessary.
« Last Edit: October 05, 2012, 02:39:06 PM by rms2 » Logged

df.reynolds
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« Reply #2 on: October 05, 2012, 03:04:50 PM »

I understand your thought on this, but the intent of the shorthand is to be as brief as possible while conveying all the necessary information to allow one to locate the terminal SNP on the appropriate tree. For that purpose, the single-letter major branch prefix is all that is needed. It directs one to the right tree, then all he has to do is scroll down until he finds the terminal SNP, a process that doesn't take more than a couple of minutes of scanning.

The addition of a couple of extra characters isn't all that helpful, except perhaps in the case of R2, since it is usually placed at the bottom of the R tree. R1a is so high on the tree that an "R1a" prefix is useless, and that's how I feel about an "R1b" prefix, as well: it only gets you to M343, which isn't a lot of help. One is still going to have to scroll down and scan to find the right SNP.

The thinking behind the shorthand also included the likelihood that names like "R1a" and R1b" will change, whereas the single-letter major branch designator, while not totally immune to change, is less likely to be changed.

I think it best to get used to using the accepted shorthand, in which, by the way, there is no "R1b", only R-M343. ;-)

I have no problem with individuals using whatever system they prefer, but I do think standardization is desirable, and that, whatever system one uses, if it departs from the standard, he should keep that in mind and realize he is using his own pidgin version and not the real thing.

Of course, if ISOGG and/or the YCC go to placing R1a, R1b, and R2 on different and separate tree pages, then those three-character prefixes would actually be useful and necessary.

I always have browser windows open for both the Hg R page and the SNP Index page. I think folks are going to have to get used to the fact that the haplotree is too complicated for most of us to have memorized anymore.

When M526 was found, it should have became Hg K (rather than KxLT), and M9 should have been renamed from K to KT. I talked to Thomas about it at the time (and he was in communication with the Hammer Lab), and he indicated that it created too much confusion to change a major branch designator, and besides, with the shift to mutation based naming, what did it matter anyway. My take from this is that the major branch designators are cast in concrete at this point.

I lobbied to have the Hg R page split up, both while I was Hg R content co-ordinator and afterwards. First go round, it was to split off R1a, R1b, and R2. Second go round, it was to split off R1a, R-U106, R-P312, and R2. My rationale being that the Hg R page was just way too big, too many indent levels, with radically diverse clades. Couldn't talk Alice into it. I would expect the current Hg R behemoth page to continue as-is for the foreseeable future.

Regards,
david
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Mike Walsh
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« Reply #3 on: October 05, 2012, 03:11:53 PM »

I understand your thought on this, but the intent of the shorthand is to be as brief as possible while conveying all the necessary information to allow one to locate the terminal SNP on the appropriate tree. For that purpose, the single-letter major branch prefix is all that is needed. ...
If brevity is all that is desired, we can eliminate two characters for everybody, the single letter, i.e. "R", and the dash "-" that follows it.

Properly notated SNPs are all the information you need. L176.1 is in R1a. L176.2 is under Z196 under R1b.

ISOGG does not need to separate their haplogroup trees by letter (A thru T.) That structure is a force fit for those who like the old haplogroup letters. There is serious work going on back at the very early branches of the tree. I'm not sure A0, B and all this stuff fits properly. If it does now, it won't soon.

ISOGG has a handy little (well, big) all in one screen that is an index to all of the Y tree SNPs. http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html
All you need to do is go to that link, do a "find" (ctrl-F) from your browser and , you are at the right point in the index.  Click on the label beside it and you jump into the correct branching on the tree.

FTDNA doesn't use ISOGG anyway and they fit all of their haplotree into a single dynamic screen.

Someone on another forum compared keeping an R1b and/or R1a designation as just tree-hugging. Perhaps, yes, but is it bad to lend continuity in the conversation over the years. If that is not deemed beneficial, what's the point of the letter R? A terminal SNP stands alone anyway.

It's a moot point in the broad community anyway.  A hobbyist like me doesn't control anything and I don't think any one academic nor commercial institution does either. The R1b and R1a terminology have been used for years and will not go away, as evidenced by yesterday's paper by Wei et al.  If you want to write something that people will understand easily, why fight R1b and R1a as labels?

R1a is so high on the tree that an "R1a" prefix is useless, and that's how I feel about an "R1b" prefix, as well: it only gets you to M343, which isn't a lot of help. One is still going to have to scroll down and scan to find the right SNP.
If your only concern is to find the right location on the Y tree, you are right M343 is useless, but again we don't even need the letter "R." M343* people are pretty rare, as are a number of other paragroup stragglers on early branches. A reference to R1b in Europe pretty much tells you what the conversation is about. In conversations and papers the references R1b versus R1a and R2 are very useful.

umm... just thought of something. The confusion about phylogenetically equivalent or truly identical SNPs will only get worse with additional focus on the terminal SNP as the reference point.  Right now, there are some people who have tested P310+, but not for L11, others P311+ but not for P310 or L11.   R-L11, R-P310, R-P311 are equivalent.... and that's not including other testing organizations. R-S127 is equivalent also.

This also gives novices a problematic perspective. The SNP is just a marker on the branch. The essence or substance of the branch can be confused, but I guess we've always had that problem.
« Last Edit: October 05, 2012, 03:31:06 PM by Mikewww » Logged

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df.reynolds
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« Reply #4 on: October 05, 2012, 03:48:18 PM »

...

ISOGG does not need to separate their haplogroup trees by letter (A thru T.) That structure is a force fit for those who like the old haplogroup letters. There is serious work going on back at the very early branches of the tree. I'm not sure A0, B and all this stuff fits properly. If it does now, it won't soon
...
umm... just thought of something. The confusion about phylogenetically equivalent or truly identical SNPs will only get worse with additional focus on the terminal SNP as the reference point.  Right now, there are some people who have tested P310+, but not for L11, others P311+ but not for P310 or L11.   R-L11, R-P310, R-P311 are equivalent.... and that's not including other testing organizations. R-S127 is equivalent also.
...

Hg A is a giant mess, and is just going to get worse. Hg BT is actually a subclade of Hg A1b these days (at least on the ISOGG tree).

I have expressed my concern within ISOGG about how phylogenetically equivalent SNPs, as well as SNPs which are synonymous, would be handled if ISOGG moves away from clade based names. It is a serious issue, in my opinion. Discussion is ongoing within ISOGG, and final plans are still in the air.

BTW, if you talk a look at the YCC 2002 definition of mutation based names, you will see that it specifically states that the mutation actually tested should be used. Following that, you might have one person who is R-L11 and another who is R-P310.

--david
« Last Edit: October 05, 2012, 03:51:26 PM by df.reynolds » Logged
Mike Walsh
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« Reply #5 on: October 05, 2012, 04:20:29 PM »

...

ISOGG does not need to separate their haplogroup trees by letter (A thru T.) That structure is a force fit for those who like the old haplogroup letters. There is serious work going on back at the very early branches of the tree. I'm not sure A0, B and all this stuff fits properly. If it does now, it won't soon ...

Hg A is a giant mess, and is just going to get worse. Hg BT is actually a subclade of Hg A1b these days (at least on the ISOGG tree)....

It is apparent that the old single letters are obsolete. No using worrying about making sense of a structure using 26 alphabetic characters. Why would we think that 26 has something to do with the nature of branching in the human family tree anyway?

umm... just thought of something. The confusion about phylogenetically equivalent or truly identical SNPs will only get worse with additional focus on the terminal SNP as the reference point.  Right now, there are some people who have tested P310+, but not for L11, others P311+ but not for P310 or L11.   R-L11, R-P310, R-P311 are equivalent.... and that's not including other testing organizations. R-S127 is equivalent also. ...

BTW, if you talk a look at the YCC 2002 definition of mutation based names, you will see that it specifically states that the mutation actually tested should be used. Following that, you might have one person who is R-L11 and another who is R-P310.
Ouch! I now actually feel like something is wrong. I am forming the opinion that the phylogenetic labels really should not go way, even if their usage or structure is different. This doesn't mean we need to use them in everyday conversation or that the terminal SNP shouldn't be display on the Y classic report screen.

Phylogenetic equivalence is what it is. With all of these z SNPs and WTY on-going, there could be many, many SNPs that are equivalent. What a mess? It's not right to make everyone in a group test for all of them, particularly if their STRs align.  Pots are not people and SNPs are not subclades. Should I bring this up on the ISOGG Yahoo group or somewhere else?

We need to not dumb down the Y tree and created a convoluted mess of redundancies.
« Last Edit: October 05, 2012, 04:22:39 PM by Mikewww » Logged

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df.reynolds
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« Reply #6 on: October 05, 2012, 05:00:37 PM »

...

ISOGG does not need to separate their haplogroup trees by letter (A thru T.) That structure is a force fit for those who like the old haplogroup letters. There is serious work going on back at the very early branches of the tree. I'm not sure A0, B and all this stuff fits properly. If it does now, it won't soon ...

Hg A is a giant mess, and is just going to get worse. Hg BT is actually a subclade of Hg A1b these days (at least on the ISOGG tree)....

It is apparent that the old single letters are obsolete. No using worrying about making sense of a structure using 26 alphabetic characters. Why would we think that 26 has something to do with the nature of branching in the human family tree anyway?

umm... just thought of something. The confusion about phylogenetically equivalent or truly identical SNPs will only get worse with additional focus on the terminal SNP as the reference point.  Right now, there are some people who have tested P310+, but not for L11, others P311+ but not for P310 or L11.   R-L11, R-P310, R-P311 are equivalent.... and that's not including other testing organizations. R-S127 is equivalent also. ...

BTW, if you talk a look at the YCC 2002 definition of mutation based names, you will see that it specifically states that the mutation actually tested should be used. Following that, you might have one person who is R-L11 and another who is R-P310.
Ouch! I now actually feel like something is wrong. I am forming the opinion that the phylogenetic labels really should not go way, even if their usage or structure is different. This doesn't mean we need to use them in everyday conversation or that the terminal SNP shouldn't be display on the Y classic report screen.

Phylogenetic equivalence is what it is. With all of these z SNPs and WTY on-going, there could be many, many SNPs that are equivalent. What a mess? It's not right to make everyone in a group test for all of them, particularly if their STRs align.  Pots are not people and SNPs are not subclades. Should I bring this up on the ISOGG Yahoo group or somewhere else?

We need to not dumb down the Y tree and created a convoluted mess of redundancies.

Learn something new everyday; I didn't know this software could do marquee scrolling. :)

I too am coming to the somewhat reluctant conclusion that the clade based names should be retained in some context for the ISOGG tree. I just don't see how to equitably handle the multiple names that may be associated with a node on the tree, otherwise.

At this at this point the different positions are well understand, I think, and there are multiple ISOGG folks who have voiced their support for retaining clade based names, and will continue to do so. Dr Tim in particular put together a well-reasoned argument for retaining them. I suspect what will push the ISOGG discussion to a decision is when FTDNA rolls their "shorthand" tree out--my expectation is that we will look at it, say that's fine for a proprietary company who can arbitrarily pick-and-choose which SNPs to show, but not an appropriate role model for an organization that is attempting to provide high-quality information in a vendor/lab neutral fashion.

Regards,
david
« Last Edit: October 05, 2012, 05:15:10 PM by df.reynolds » Logged
Mike Walsh
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« Reply #7 on: October 05, 2012, 05:35:12 PM »

Charles is the U106 project admin. Here is what he posted today.
Quote from: Charles Moore
Consider using the > key.  My major Haplogroup is R1b-U106, and my subclade Z7 is 6 steps below that.  I don't want to > my way down all 6 steps, so I can just report myself as R1b-Z7*, and that's good enough when discussing things with other R1b-U106ers who know where Z7 is.

But when that's not the case, I can say R1b-U106 > Z7*, and then anyone can see that I belong to the large Haplogroup R1b-U106 via its Z7 subclade, even though Z7 isn't immediately below R1b-U106.

On my project subgroup labels, I carry the > concept through step by step > after > after >.  But that is simply so that the relationships of the subgroups to one another is clear in a project ordering Subgrouping system.

So just a thought.  I think the > key and also the = key can be very helpful sometimes for various purposes to simplify relationships of various sorts.

I've been flip-flopping about this on myself too.  I figure a lot of people didn't know about L513 (which is also DF1, S215) so I changed my signature to  R1b-L21/L513(DF1) but my real terminal SNP is L705.2, which I'm pretty sure most people don't know about. If I follow Charles' suggestion I'd go with R1b-L21>L705.2 and could expand it to R1b-L21>DF13>L513>L706.2>L705.2 if I was really trying to be articulate.

The truly private and private/maybe public SNPs add a little spice to the equivalent and identical SNPs convolution. A private SNP guy like Templeton (Scots modal) could do R1b-L21*>L743.

I have a little fun with searching complexities when I look for L513, DF1, L705 and L705.2 on. I just hope someone doesn't order test L705.1 that should be in my group.  I guess I need to change my searches to include L705.1 too.

EDIT: ooops, forgot DF13.
« Last Edit: October 06, 2012, 03:48:52 PM by Mikewww » Logged

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« Reply #8 on: October 05, 2012, 07:52:59 PM »

...

ISOGG does not need to separate their haplogroup trees by letter (A thru T.) That structure is a force fit for those who like the old haplogroup letters. There is serious work going on back at the very early branches of the tree. I'm not sure A0, B and all this stuff fits properly. If it does now, it won't soon ...

Hg A is a giant mess, and is just going to get worse. Hg BT is actually a subclade of Hg A1b these days (at least on the ISOGG tree)....

It is apparent that the old single letters are obsolete. No using worrying about making sense of a structure using 26 alphabetic characters. Why would we think that 26 has something to do with the nature of branching in the human family tree anyway?

umm... just thought of something. The confusion about phylogenetically equivalent or truly identical SNPs will only get worse with additional focus on the terminal SNP as the reference point.  Right now, there are some people who have tested P310+, but not for L11, others P311+ but not for P310 or L11.   R-L11, R-P310, R-P311 are equivalent.... and that's not including other testing organizations. R-S127 is equivalent also. ...

BTW, if you talk a look at the YCC 2002 definition of mutation based names, you will see that it specifically states that the mutation actually tested should be used. Following that, you might have one person who is R-L11 and another who is R-P310.
Ouch! I now actually feel like something is wrong. I am forming the opinion that the phylogenetic labels really should not go way, even if their usage or structure is different. This doesn't mean we need to use them in everyday conversation or that the terminal SNP shouldn't be display on the Y classic report screen.

Phylogenetic equivalence is what it is. With all of these z SNPs and WTY on-going, there could be many, many SNPs that are equivalent. What a mess? It's not right to make everyone in a group test for all of them, particularly if their STRs align.  Pots are not people and SNPs are not subclades. Should I bring this up on the ISOGG Yahoo group or somewhere else?

We need to not dumb down the Y tree and created a convoluted mess of redundancies.

Learn something new everyday; I didn't know this software could do marquee scrolling. :)

I too am coming to the somewhat reluctant conclusion that the clade based names should be retained in some context for the ISOGG tree. I just don't see how to equitably handle the multiple names that may be associated with a node on the tree, otherwise.

At this at this point the different positions are well understand, I think, and there are multiple ISOGG folks who have voiced their support for retaining clade based names, and will continue to do so. Dr Tim in particular put together a well-reasoned argument for retaining them. I suspect what will push the ISOGG discussion to a decision is when FTDNA rolls their "shorthand" tree out--my expectation is that we will look at it, say that's fine for a proprietary company who can arbitrarily pick-and-choose which SNPs to show, but not an appropriate role model for an organization that is attempting to provide high-quality information in a vendor/lab neutral fashion.

Regards,
david


David,

I agree with many of your comments.

"The study also poses challenges for the field, among which are
(1) integrating sequence data generated by different technologies with different error modes on different samples;
(2) the question of whether an inferred ancestral reference sequence would be more useful than the current hybrid of modern sequences;
(3) the need to develop a compact and useful nomenclature system that can accommodate extensive sequence information, for example based on major haplogroups and significant sub-clusters that provide a memorable but not complete indication of the location in the phylogeny;
and
(4) the difficulty of understanding the archaeological events associated with the male expansions detected, and the standards of evidence that should be required in order to accept links.

If we continue using the clade based names we will quickly reach a stage of using up to 38 characters to name a sub clade. Of course this is unsustainable. In the Internet world we don't generally use IP addresses because they are too difficult to remember. We use Domain Name Servers DNS to translate a common sense name to an IP address. Could a similar approach be used here.
Alternatively we have a standard called GEDCOM which is used in genealogy and which is designed for handling ancestry trees. Phylogenic trees are Ancestry trees. could we extend the GEDCOM standard to support the Phylogenic trees in a way that is acceptable to all stakeholders.
The advantage is that it is widely used and comes with an abundance of existing free and commercial software.
My personal opinion is that we will end up with a hybrid of ISOGG and the rs........ naming convention.
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R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
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Mike Walsh
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« Reply #9 on: October 05, 2012, 08:01:35 PM »

If we continue using the clade based names we will quickly reach a stage of using up to 38 characters to name a sub clade. Of course this is unsustainable. In the Internet world we don't generally use IP addresses because they are too difficult to remember. We use Domain Name Servers DNS to translate a common sense name to an IP address. Could a similar approach be used here. ...

Right, but the internet IP addresses are still there. It's just we don't use them in our conversations. Under the cover, they are more than just critical, they are the essence of the system.

We still need a phylogenetically intelligent labeling system. That does not mean we should use it in the conversations. Of course, that would be more than laborious. However, for things like research, analysis and defining the structure for the tree, every branch must be labeled in some manner and every branch tag must have a parent and a place for multiple children.

There has to a map and the map has to have coordinates like any graphing scheme. The average person may not read the lattitude and longitude but there has to be some relative referencing system.
« Last Edit: October 05, 2012, 08:03:21 PM by Mikewww » Logged

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« Reply #10 on: October 05, 2012, 09:54:29 PM »

I, of course, strongly agree with your original ost on this thread.

As I've said before, I''m Miles Kehoe R1b DF23
« Last Edit: October 05, 2012, 09:54:54 PM by eochaidh » Logged

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« Reply #11 on: October 06, 2012, 03:57:59 AM »

I also agree with all you folks. I am R1b> Z156>?>?>?>?>?>?>?>private SNP. Hopefully the Geno 2.0 will find some or all of these.
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rms2
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« Reply #12 on: October 06, 2012, 07:43:08 AM »


If brevity is all that is desired, we can eliminate two characters for everybody, the single letter, i.e. "R", and the dash "-" that follows it . . .

That would be fine with me, except that without the single letter prefix, one does not know which y tree to check. The single letter prefix directs one to the correct tree, so it is necessary. It does the required job of directing one to the right tree without the aid of any other characters, so it is all that is needed.

I do think breaking the tree up into major branches, while somewhat arbitrary, is desirable because it chunks information into relatively digestible bites, and that is an aid to understanding.

David's idea (a couple of posts back) of dividing the R tree up into separate R1a, R-U106, R-P312, and R2 pages sounds good, although I must admit I am rather attached to the R designator and the old single R page..

« Last Edit: October 06, 2012, 08:14:39 AM by rms2 » Logged

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« Reply #13 on: October 06, 2012, 07:53:33 AM »

I, of course, strongly agree with your original ost on this thread.

As I've said before, I''m Miles Kehoe R1b DF23

In the shorthand system FTDNA has rolled out (and, really, we've been using since 2008), that would be redundant, since "R1b" is R-M343. "R1b DF23" would translate to R-M343 DF23, something more cumbersome than the simple R-DF23, which, after a brief explanation, even a child could find on the ISOGG R tree.

But, like I said, if someone wants to use "R1b" as a prefix, fine. It might be more desirable to use an even longer prefix, if getting one closer to the terminal SNP in the prefix is the goal. But why stop there? Why not just roll out the whole enchilada: R1b1a2a1a1b3a1a?
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« Reply #14 on: October 06, 2012, 07:58:31 AM »

Someone mentioned the current shorthand system as a "private proprietary" thing.

So, here's a question. Is that true? Is this shorthand merely FTDNA's in-house decision, or does it represent a wider consensus among at least part of the scientific community, like the YCC?

Since Dr. Hammer has endorsed this "new" shorthand system, and he is one of the key YCC people, I would guess it is more than merely a private FTDNA proprietary system. In fact, it seems to me this shorthand went from the University of Arizona and the YCC to FTDNA and not the other way around.
« Last Edit: October 06, 2012, 08:05:10 AM by rms2 » Logged

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« Reply #15 on: October 06, 2012, 08:13:04 AM »

Someone mentioned the current shorthand system as a "private proprietary" thing.

So, here's a question. Is that true? Is this shorthand merely FTDNA's in-house decision, or does it represent a wider consensus among at least part of the scientific community, like the YCC?

Since Dr. Hammer has endorsed this "new" shorthand system, and he is one of the key YCC people, I would guess it is more than merely a private FTDNA proprietary system. In fact, it seems to me this shorthand went from the University of Arizona and the YCC to FTDNA and not the other way around.

The YCC 2002 article introduced the current form of the haplotree we know and mostly love. The article describes two forms of names, clade based (what I call Rutabaga names) and mutation based (what FTDNA calls short-hand name). So "shorthand" names are not proprietary and and a standard for them has existed for over ten years.

Genome Res. 2002 February; 12(2): 339–348.
doi:  10.1101/gr.217602
PMCID: PMC155271
A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
The Y Chromosome Consortium
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155271/

Regards,
david
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« Reply #16 on: October 06, 2012, 08:20:33 AM »

Someone mentioned the current shorthand system as a "private proprietary" thing.

So, here's a question. Is that true? Is this shorthand merely FTDNA's in-house decision, or does it represent a wider consensus among at least part of the scientific community, like the YCC?

Since Dr. Hammer has endorsed this "new" shorthand system, and he is one of the key YCC people, I would guess it is more than merely a private FTDNA proprietary system. In fact, it seems to me this shorthand went from the University of Arizona and the YCC to FTDNA and not the other way around.

The YCC 2002 article introduced the current form of the haplotree we know and mostly love. The article describes two forms of names, clade based (what I call Rutabaga names) and mutation based (what FTDNA calls short-hand name). So "shorthand" names are not proprietary and and a standard for them has existed for over ten years.

Genome Res. 2002 February; 12(2): 339–348.
doi:  10.1101/gr.217602
PMCID: PMC155271
A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
The Y Chromosome Consortium
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155271/

Regards,
david


Thanks, David.

That seems to me to amount to a strong argument for the use of the shorthand the way the YCC uses it rather than altering it according to taste.
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« Reply #17 on: October 06, 2012, 08:34:47 AM »

Charles is the U106 project admin. Here is what he posted today.
Quote from: Charles Moore
Consider using the > key . . .

Some of you may have noticed that I stole that idea from Charles for the R-L21 Plus Project a couple of months ago when I revamped the Y-DNA Results page categories according to terminal SNP.

I know the use of ">" can be confused with "greater than" in mathematics, but even that makes sense when you think of it in terms of population or of time, age or precedence.
« Last Edit: October 06, 2012, 08:46:25 AM by rms2 » Logged

eochaidh
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« Reply #18 on: October 06, 2012, 01:00:26 PM »

I, of course, strongly agree with your original ost on this thread.

As I've said before, I''m Miles Kehoe R1b DF23

In the shorthand system FTDNA has rolled out (and, really, we've been using since 2008), that would be redundant, since "R1b" is R-M343. "R1b DF23" would translate to R-M343 DF23, something more cumbersome than the simple R-DF23, which, after a brief explanation, even a child could find on the ISOGG R tree.

But, like I said, if someone wants to use "R1b" as a prefix, fine. It might be more desirable to use an even longer prefix, if getting one closer to the terminal SNP in the prefix is the goal. But why stop there? Why not just roll out the whole enchilada: R1b1a2a1a1b3a1a?

I cannot understand why the name of this forum hasn't been changed from R1b and Subclades to R-M343 and Subclades.

EDIT: Okay, I now realize how stupid I've been and what a waste of space it is to refer to myself as R1b DF23, so I'll start using R-DF23 (L21>DF13>DF49>DF23) to save space and get rid of that ridiculous "1b".
« Last Edit: October 06, 2012, 02:26:06 PM by eochaidh » Logged

Y-DNA: R1b DF23
mtDNA: T2g
Mike Walsh
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« Reply #19 on: October 06, 2012, 03:16:48 PM »

g140684 date=1349488469].... But, like I said, if someone wants to use "R1b" as a prefix, fine. It might be more desirable to use an even longer prefix, if getting one closer to the terminal SNP in the prefix is the goal. But why stop there? Why not just roll out the whole enchilada: R1b1a2a1a1b3a1a?

In all due respect, your statement that I emboldened is a good example of...
Quote from: Wikipedia
An argument similar to reductio ad absurdum often seen in polemical debate is the straw man logical fallacy. A straw man argument attempts to refute a given proposition by showing that a slightly different or inaccurate form of the proposition (the "straw man") is absurd or ridiculous, relying on the audience not to notice that the argument does not actually apply to the original proposition.

There is a big difference between using "R1b" and "R1b gobbledy-gook..." in a conversation.

I'm going off on a tangent here, but I hope everyone is getting the point that we really do need both the abbreviated SNP-based labeling and the phylogenetically intelligent labels. The SNP-based acronyms for discussion and the long phylogenetic labels for analysis. A phylogenetic label is just another way of describing a tree. We still need graphically visual depictions, such as outline trees or descendancy trees, however, how the data for the tree is stored matters.

Internally, any system that sorts, derives or selects on subclade will have to have the phylogenetic intelligence. The long labels are just a way to define SNP positioning on the branches. FTDNA seems to be discontinuing this. I hope this does not mean they are either getting out of the haplotree graphic tree display business altogether. If they will continue to support the haplotree, I just requesting they expose (show in a report screen) that phylogenetic intelligence in a data format. That's exactly what a phylogenetic label is. If they won't, at least, hopefully ISOGG will provide that definition.

Hopefully, we all don't sit there and draw out phylogenetic trees in a drawing tool like powerpoint. Actually, I've done this but its crazy.  A good programmer/program can easily display trees in multiple formats if the data is formatted. The data design is not hard. I do this in spreadsheets in what I call the "Clades" table. You just need positioning data fields (columns) for tree depth(height of branch), upstream SNP (base limb), synonymous SNPs, downstream SNPs (off-shooting twigs) for each SNP.
  ....um, David do you know if the ISOGG tree screens are generated from a well designed SNP database?  I hope so. If not, it must be painful to update screens manually. One should be able to update the database positioning fields and press a button, and wala.. the graphic tree and affected long and short labels generated.

I think Heber was describing this an alternative in his post below.
....
Alternatively we have a standard called GEDCOM which is used in genealogy and which is designed for handling ancestry trees. Phylogenic trees are Ancestry trees. could we extend the GEDCOM standard to support the Phylogenic trees in a way that is acceptable to all stakeholders.
The advantage is that it is widely used and comes with an abundance of existing free and commercial software.
Maybe the GEDCOM standard is the answer.  It's a good idea!
« Last Edit: October 06, 2012, 04:02:31 PM by Mikewww » Logged

R1b-L21>L513(DF1)>L705.2
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« Reply #20 on: October 06, 2012, 03:55:04 PM »

Charles is the U106 project admin. Here is what he posted today.
Quote from: Charles Moore
Consider using the > key . . .

Some of you may have noticed that I stole that idea from Charles for the R-L21 Plus Project a couple of months ago when I revamped the Y-DNA Results page categories according to terminal SNP....

Yes, I like what you did. It gives people a clear idea of SNPs to consider.

I was thinking the R1b and Subclades project could be a great vehicle for all of the R1b1a2 predicted and unawashed. Perhaps that is where Geno 2.0 should be indicated. I'd like to somehow get FTDNA to give that project special authority so that when someone joins that project they automatically will be assigned to the proper subclade project, at least the first level, be it U106, P312, L21, U152 and ht35 when deep clade testing indicates this.
« Last Edit: October 06, 2012, 03:58:48 PM by Mikewww » Logged

R1b-L21>L513(DF1)>L705.2
gtc
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« Reply #21 on: October 07, 2012, 02:24:24 AM »

I'd like to somehow get FTDNA to give that project special authority so that when someone joins that [Geno 2.0] project they automatically will be assigned to the proper subclade project, at least the first level, be it U106, P312, L21, U152 and ht35 when deep clade testing indicates this.

What a great idea, as long as the kit owner has signed the agreement to go public.
« Last Edit: October 07, 2012, 02:24:49 AM by gtc » Logged

Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
mtDNA: I3b (FMS) Maternal lines Irish
df.reynolds
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« Reply #22 on: October 07, 2012, 03:16:43 AM »

 ....um, David do you know if the ISOGG tree screens are generated from a well designed SNP database?  I hope so. If not, it must be painful to update screens manually. One should be able to update the database positioning fields and press a button, and wala.. the graphic tree and affected long and short labels generated.

All of the ISOGG pages have been manually maintained to date.  Their has been a project in-progress for some time to to replace this manual system with an automated process which is db based. Alice is painfully aware that the current process does not work well when frequent or large updates are made.

--david
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Heber
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« Reply #23 on: October 07, 2012, 05:10:26 AM »

g140684 date=1349488469].... But, like I said, if someone wants to use "R1b" as a prefix, fine. It might be more desirable to use an even longer prefix, if getting one closer to the terminal SNP in the prefix is the goal. But why stop there? Why not just roll out the whole enchilada: R1b1a2a1a1b3a1a?

I think Heber was describing this an alternative in his post below.
....
Alternatively we have a standard called GEDCOM which is used in genealogy and which is designed for handling ancestry trees. Phylogenic trees are Ancestry trees. could we extend the GEDCOM standard to support the Phylogenic trees in a way that is acceptable to all stakeholders.
The advantage is that it is widely used and comes with an abundance of existing free and commercial software.
Maybe the GEDCOM standard is the answer.  It's a good idea!

I have converted the ISOGG R1b tree to GEDCOM and taken a screenshot using the very limited functionality of my IPad App. This is what it would look like using current GEDCOM App software.
It would take a small tweak of GEDCOM to represent only the male lines (Y) or the female lines (mtDNA). It may already exist on full functionality PC software. You can also show the full screen on one screen using multiple formats or produce detailed Phylogenic reports.
You could then attach your Clan Structure trees to your terminal SNP and further downstream attach your actual family tree to your Clan Tree.

http://pinterest.com/pin/32721534763945712/

« Last Edit: October 07, 2012, 05:19:03 AM by Heber » Logged

Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
Paternal L21* DF21


Maternal H1C1



rms2
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« Reply #24 on: October 07, 2012, 08:35:29 AM »

g140684 date=1349488469].... But, like I said, if someone wants to use "R1b" as a prefix, fine. It might be more desirable to use an even longer prefix, if getting one closer to the terminal SNP in the prefix is the goal. But why stop there? Why not just roll out the whole enchilada: R1b1a2a1a1b3a1a?

In all due respect, your statement that I emboldened is a good example of...
Quote from: Wikipedia
An argument similar to reductio ad absurdum often seen in polemical debate is the straw man logical fallacy. A straw man argument attempts to refute a given proposition by showing that a slightly different or inaccurate form of the proposition (the "straw man") is absurd or ridiculous, relying on the audience not to notice that the argument does not actually apply to the original proposition.

No, it's not.

Actually, Mike, reductio ad absurdum is absolutely not similar to the strawman fallacy. Your thinking my argument is a good example of the strawman fallacy is a good example of someone thinking that because reductio ad absurdum has absurdum in it, the method of argument itself is absurd. That is not the case.

Reductio ad absurdum is a legitimate form of logical argument that attempts to disprove a proposition by showing that it leads to absurd or unsupportable conclusions.

That is what I was doing rather than erecting a straw man. I was showing that arguing that "R1b" is so much more informative than "R" that it justifies creating a pidgin shorthand system is incorrect and that such reasoning could justify the use of ever longer prefixes in ever more cumbersome pidgin shorthand systems.

All that is needed is the single letter prefix "R" to get one to the right tree.

There is a big difference between using "R1b" and "R1b gobbledy-gook..." in a conversation.

There is, but the use of "R1b" instead of "R" does not accomplish enough to warrant altering the shorthand system in use by the YCC, Dr. Hammer, the University of Arizona, and FTDNA.

The argument for it, if I understand it correctly, is that it is so much more informative than the simple, single letter R, that it should be used as the shorthand prefix.

That's fine, if that is what one wants to do. I have no objection to it at all. But I disagree that it is necessary or even useful, unless and until the R1b part of the R tree starts appearing on a page separate from the rest of the R tree. Then the R1b prefix would be both necessary and useful. If the R tree is further subdivided, then the necessary prefixes might become even longer.

I'm going off on a tangent here, but I hope everyone is getting the point that we really do need both the abbreviated SNP-based labeling and the phylogenetically intelligent labels. The SNP-based acronyms for discussion and the long phylogenetic labels for analysis. A phylogenetic label is just another way of describing a tree. We still need graphically visual depictions, such as outline trees or descendancy trees, however, how the data for the tree is stored matters . . .

I wasn't arguing against "phylogenetically intelligent" labels (by which, I suppose, you mean the really long ones). I was arguing that altering the shorthand because R1b is more informative than R is unnecessary and doesn't accomplish enough to warrant it.

But everyone is free to devise the system he prefers and use it. I have noticed a lot of guys using R1b in the shorthand prefix. Cool. Whatever floats their collective boats.
« Last Edit: October 07, 2012, 08:45:21 AM by rms2 » Logged

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