Archiver > GENEALOGY-DNA > 2009-05 > 1242972092

From: "Diana Gale Matthiesen" <>
Subject: Re: [DNA] Haplogroup naming conventions (was NPE)
Date: Fri, 22 May 2009 02:01:32 -0400
References: <><47C9E3601A204606AB17BF56D6CAD43F@DadPC><410B3974F11940B7978CC7552E0A95A0@HP><F3260C67038447D691C57DA40235C9BD@DadPC><BAY103-DS542C278CBC8454402E3FDC8590@phx.gbl><E029C7EB508D4240ABBC82FF79EF2880@DadPC><BAY103-DS7F050475FC12528C11C14C8560@phx.gbl>
In-Reply-To: <BAY103-DS7F050475FC12528C11C14C8560@phx.gbl>

These comparisons are "apples vs. oranges." The Henry system, Dewey decimal
system, and the Library of Congress system are not hierarchical and certainly
not phylogenetic. In these systems, the contents of the groupings and the order
of the groupings in the system are both entirely arbitrary. There is nothing
inherent in the objects being classified that determines their classification.

In contrast, the subclades of the Y-DNA cladogram (haplotree) are not arbitrary
groupings, nor is the order of the groupings arbitrary. The evolutionary
sequence of SNP mutations forces the ordering of each subclade and determines
the contents of each subclade. The phylogenetic classification of evolutionary
organisms is inherent within the organisms -- exactly the opposite of an
arbitrary system like the organization of books in a library.

The hierarchical naming system used in the labeling of the Y-DNA cladogram has
been arrived at through decades of experience by literally thousands of
scientists to be the most logical, most objective, most concise, most
informative, and most easily understood way for such a cladogram to be labeled.
To substitute an arbitrary, un-informative naming system for an objective,
informative one would be a monumental step backwards -- and truly chaotic.


P.S. The mtDNA haplotree is also a cladogram, the subclades of which are also
named hierarchically.
The only difference in the nomenclature is that the main mtDNA haplogroups were
named alphabetically as they were discovered, rather than being labeled
alphabetically in the order of their evolutionary appearance, so the main
branches of the mtDNA haplotree are not in alphabetical order they way they are
in the Y-DNA haplotree.
But, otherwise, there's no fundamental difference in the way the two trees are
named. If the mtDNA tree seems more complex, it's probably because the
cladogram appears to have more nodes (I haven't actually counted the nodes on
either tree, but my impression is that the mtDNA tree has more).

> -----Original Message-----
> From: On Behalf Of RICHARD KENYON
> Sent: Thursday, May 21, 2009 11:29 PM
> To:
> Subject: Re: [DNA] Haplogroup naming conventions (was NPE)
> As I've understood it, the Y haplogroup naming system is a
> Henry system, as is the Dewey decimal system used by many
> libraries. It seems to me your scheme is like giving
> classification numbers 1 through N to the books in a library
> of N books. That's chaos! Do you suggest that we also discard
> the Dewey decimal scheme and the alternate LC classification
> schemes? If you want to find something to complain about,
> take a look at the classification scheme for mitochondrial
> DNA. That's much more complex for a number of reasons. I
> certainly wish MT classification could be as simple as Y is
> (but I don't even think it can happen).
> ----- Original Message -----
> From: Peter A. Kincaid<mailto:>
> To: <mailto:>
> Sent: Thursday, May 21, 2009 8:04 PM
> Subject: Re: [DNA] Haplogroup naming conventions (was NPE)
> I think one has to step back and try to look
> from the perspective of a newbie versus
> someone who has been using the current
> system for sometime. There is nothing
> really intuitive or hierarchial about something
> like R1b1b2a1a. One only understands
> something like this after the system has
> been explained to them. Furthermore, with
> different conventions for naming SNPs and
> their position in the hierarchy subject to change,
> everyone at some point has to go back and
> review the currect tree to reset their bearings.
> The point I was trying to make was that
> numbers are easier on the eyes and easier
> to remember than what we have now. I
> will concede the point that people also like
> hierarchial systems.
> That said, since this is a genealogy group why
> isn't a standard genealogical numbering systems
> being used rather than the corrupted version we
> have now. What we are dealing with here is a
> descending numbering system. The Henry system
> is perhaps more used/understood. If one can't shake
> the initial A-T grouping, we could at least use the
> Henry system for the subsequent generations. For
> example, R1428 would translate as the last point being
> the 8th branch of the 2nd branch of the 4th branch
> of the 1st branch of R group (for rare occasion
> where there are more than 9 branches in a generation
> than 10 is represented by X, 11 by A, 12 by B, 13
> by C, etc.).
> Instead of having a long accepted system like the
> Henry system people here have put together
> a corrupted Pama system that really is no help and
> should be changed.
> Peter
> ----- Original Message -----
> <<mailto:>>
> To: <<mailto:>>
> Sent: Thursday, May 21, 2009 7:39 PM
> Subject: [DNA] Haplogroup naming conventions (was NPE)
> > Your idea for labeling haplogroups would certainly be
> non-intuitive,
> > showing nothing of the hierarchial structure. Your
> suggested labels could
> > move to new positions on the tree as the phylogenetic
> tree develops in the
> > future. To determine one's position on the tree, a copy
> of the latest
> > version would have to be at hand. You must agree that
> this would be a real
> > pain. I think we all hope the tree will continue to grow
> and develop new
> > branches with occasional moving of some twigs to
> different branches. It is
> > hoped by many as subclades get further subdivided we will
> more accurately
> > understand migration patterns and our origins.
> >
> > As you may know, the YCC long ago suggested an alternate,
> abbreviated
> > notation. Thus, taking your example R1b1b2a1a is simply
> R-M467. Here M467
> > is the furtherest downstream derived SNP. This seems far
> more meaningful
> > than your arbitrary numbering suggestion. However SNP
> naming is arbitrary
> > and are not always unique. For example, M467 is also
> named S29 and U198.
> > So with the abbreviated YCC notation, it's necessary to
> have something
> > such as the ISOGG document handy to determine the
> explicit name. I prefer
> > the "long" notation as it explicitly specifies the
> location on the tree.
> > ----- Original Message -----
> > From: Peter A.
> Kincaid<mailto:<mailto:
> > To:
> <mailto:<m
> ailto:%3Cmailto:>>
> > Sent: Thursday, May 21, 2009 2:51 PM
> > Subject: Re: [DNA] NPE
> >
> >
> > I don't see where you got the notion I was interested in
> > stability. I have been an advocate of terminology that
> > that is accurate/representative/understandable/concise.
> >
> > I think the R1b1b2a1a type scheme is a mess also.
> > As more subsets come on board we will likely see
> > something like R1b1b2a1a2a1a1a2a ... How is
> > that helpful? I think it would have been better to
> > have a numbering scheme once the intial letters were
> > used up. In the R group for example, initial subsets
> > could have been assigned R0, R10, R20 ... R90.
> > Then there could be 9 more breakdowns of the
> > initial group (ie. R0 gets R1-R9). When this initial
> > allottment runs out 10 more can be taken from the
> > next 100, and then the next 100, etc (ie. R0 group
> > gets R100-R109 then R200-R209, then R300-R309,
> > etc.). There is no limit to this and your get more
> > appealing labels (i.e. something like R5500 is better
> > than R1b1b2a1a2a1a1a2a...
> >
> > Peter. A. Kincaid
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