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Longhand Versus Shorthand Y-haplogroup Nomenclature
#1
Question 
Apparently the old longhand Y-DNA haplogroup nomenclature is going the way of the Dodo. Unfortunately some scientific papers still report haplogroup assignments using the longhand, which forces one to resort to the ISOGG web site to decipher what is meant by it. I much prefer the shorthand, with its macro-haplogroup single-letter designator, followed by a dash and the name of whatever the terminal SNP of the sample is, or whatever terminal SNP is used to represent the block of SNPs at that position. 

Of course, that's not perfect either. Sometimes the terminal SNP that is detected is not the one we usually think of but is one of the others in that block, which forces us to look it up in order to figure out what is intended, i.e., what the more commonly known equivalent is. But even that, it seems to me, is preferable to the old longhand. 

All that kind of brings me to my point, which is the use of the single-letter macro-haplogroup designator in the shorthand versus a little bit longer version that preserves a bit of the old longhand. For example, R-M343 can also appear as R1b-M343, I-M253 as I1-M253, and so on. For those of us who cut our teeth on the old longhand, back before it became unmanageable, three or two character haplogroup designators preserve the image of old divisions that once seemed of essential importance, like the difference between old "I1a" versus old "I1b" and the difference between old "R1a" versus old "R1b".

I am beginning to wonder if any of the old longhand is worth preserving, since it has largely gone out of use and is almost totally unfamiliar to young people just entering the world of DNA testing. FTDNA doesn't use it anymore. 23andMe doesn't use it. One might still know the difference between the "1a" and "1b" divisions within his own Y-DNA haplogroup, but he is probably going to have to take the time and trouble to look them up when dealing with any other haplogroup. Is it even worth the trouble?

I also wonder if the old longhand could have obscured things that might have otherwise been easier to see without it. Calling one haplogroup "1a" and another one "1b" somewhat obscures their shared ancestry and common origin and perhaps makes them appear to be more separate and different than they really are. Perhaps the simple, single-letter designator is a better reminder of the common root. On the other hand, the old "1a" and "1b" designations can also make subclades that share them appear to be more closely related than they really are. Sometimes subclades that share a "1a" designator aren't closely related at all; the same is true of some subclades that share a "1b" designator. They might not have shared a common ancestor for 15,000 or more years, yet they are both "1a" or "1b". 

What do you all think? Which system do you prefer?
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#2
Shorthand
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#3
(02-14-2024, 06:37 PM)AimSmall Wrote: Shorthand

With the single letter designator or the two or three character designator?
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- Wisdom of Sirach 44:1
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#4
Of course, I only mentioned "1a" versus "1b". I didn't get into the 2's and 3's and so on.
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#5
Abbreviated.

R1b1a1a2a1a2b <-- Crap

R-U152 <-- Usable
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#6
(02-14-2024, 06:54 PM)AimSmall Wrote: Abbreviated.

R1b1a1a2a1a2b <-- Crap

R-U152 <-- Usable

I agree completely.

Of course, you can see that in the little profile under my username I used the three-character "R1b" designator in the shorthand version of my Y-DNA haplogroup and that of my maternal grandfather.

Maybe I'll change that.
Let us now praise famous men, and our fathers that begat us.

- Wisdom of Sirach 44:1
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#7
Shorthand is good for people, but for AI and all computer applications the longhand is better.
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#8
If the phylogenetic tree were known in advance, the longhand notation would be far superior because it encodes the phylogeny. This is very useful, for example, for ordering tables or parsing tabular data to load it into a graph.

Since this is not the case, I prefer shorthand notation. Updating the names every time a split appears is impractical.
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#9
Shorthand is more scientific because the tree can change, I used to be J1b for several years and then the next-sequence changed the J1 tree with new SNPs and branches in a new cascade of basal J1 branches.
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#10
(02-14-2024, 06:55 PM)rmstevens2 Wrote:
(02-14-2024, 06:54 PM)AimSmall Wrote: Abbreviated.

R1b1a1a2a1a2b <-- Crap

R-U152 <-- Usable

I agree completely.

Of course, you can see that in the little profile under my username I used the three-character "R1b" designator in the shorthand version of my Y-DNA haplogroup and that of my maternal grandfather.

Maybe I'll change that.

I updated my Y-DNA haplogroup nomenclature from the three-character "R1b" to the single-letter "R".
Let us now praise famous men, and our fathers that begat us.

- Wisdom of Sirach 44:1
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#11
I like the YFull version, which is shorthand with a few exceptions for some root haplogroups. Like I1, I2, J1, J2, R1b, R1a and perhaps a few others.
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#12
(02-15-2024, 07:59 AM)Hygelac Wrote: I like the YFull version, which is shorthand with a few exceptions for some root haplogroups. Like I1, I2, J1, J2, R1b, R1a and perhaps a few others.

I also like those, as outside of the specialists no one is able to remind the ramifications for example below R1b-L51, R1a, etc. but it is useful to diversify R1b from R1a, I1 from I2, J1 from J2, etc.
If used for automatic sorting in spreadsheets, projects, etc. as said the longhand has still a reason to be used, but for publications IMHO the terminal defining SNP should always be mentioned - be it shorthand, "main root Hg", or longhand Nomenclature
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#13
The paper on the Koksijde samples uses a different shorthand:
https://publicaties.vlaanderen.be/view-file/53623

If you look at the tree on page 33, they use R1b1 for U152, R1b5 for DF19, R1b8 for U106>Z19, and R1b6 for U106>S263.

On page 31, they combine it with a terminal SNP so SNPs read in the following manner:
R1b-P312, R1b6-S497, R1b5-S4268, R1b7-FGC17465, R1b6-L45, R1b1-Y1232, R1b8-L257, I1-M253
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R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>FT354149

Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583; John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593; John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635
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#14
My L (M20)>M22>M317>SK1412>SK1414 takes me in longhand to L1b2c. But longhand has been out for several years, and during that time, a lot more testers have come forward with common variants below that, so that my own line now continues SK1414>FGC51041>FGC51088>FGC51036. But I have absolutely no idea of how that would have been interpreted as longhand, because I find no reference below SK1414. L1b2c???. Therefore longhand has been made redundant. L-FGC51036 will do fine although it might require some explanation of route.
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The artist formerly known as A Norfolk L-M20
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