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Author Topic: What do we know about YCC?  (Read 2008 times)
Mike Walsh
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« on: October 12, 2012, 11:42:38 AM »

It's hard to find much about them other than just looking at their research papers.

I used to think that the Y Chromosome Consortium (YCC) was important. I still think it could be, but their record just hasn't supported that. Here is what I mean.

The YCC hasn't maintained currency of their Y DNA tree. I believe their last update was in early 2011 or maybe even late 2010.

I'm not sure there is much consensus in the scientific community behind YCC. I don't think ScottishDNA, Oxford, etc., etc. are in it, but it is not really clear how broad YCC's support is.

FTDNA will tell you at http://www.familytreedna.com/understanding-haplogroups.aspx
Quote from: FTDNA
The Y Chromosome Consortium (YCC) developed a naming system for the Y-DNA haplogroups designed to easily accommodate expansion as new groups are discovered. The YCC has defined 20 major haplogroups, called A through T, which represent the major divisions of human diversity based on SNPs on the Y-chromosome.
All Family Tree DNA explanations and terminology, including our haplogroup database, use the standard system developed by the YCC and defined in the YCC paper. The Y Chromosome Consortium scientific paper, which describes the Haplogroup naming system, can be found at the link below:
YCC Nomenclature System
The link to the YCC is broken. Broken links are a bad sign as it relates to business or institutional health.

If you try to google them they are hard to get information on. That's not good either. Someone, not the YCC, was kind enough to write a Wiki article on the YCC. That's about the only place I can find a link that works to something that might be a YCC home page. http://ycc.biosci.arizona.edu/
Go ahead and look at that and see what you can find. This is at the University of Arizona which makes sense because that's where Dr. Mike Hammer is and he is FTDNA's Chief Scientist as well as a member of the YCC, at least in the past.

Maybe something is changing. This was just posted today on Rootsweb.
Quote from: Jane Murtishaw Lindsey
In questioning
FTDNA we received the following:...
"Family Tree DNA has had a longstanding partnership with the University of
Arizona, which has been a testing partner with FTDNA for nearly 12 years.
However, this partnership has recently come to a close
, as we have decided
to move all of our testing into our in-house lab."
http://archiver.rootsweb.ancestry.com/th/read/Y-DNA-PROJECTS/2012-10/1350054445
« Last Edit: October 12, 2012, 11:43:38 AM by Mikewww » Logged

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razyn
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« Reply #1 on: October 12, 2012, 01:29:09 PM »

That's kind of big news, isn't it?
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rms2
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« Reply #2 on: October 12, 2012, 01:56:01 PM »

I think that's been coming for quite some time, ever since Thomas Krahn came on board with FTDNA.

Maybe FTDNA will switch to a y tree developed and maintained by Thomas Krahn?
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gtc
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« Reply #3 on: October 12, 2012, 10:51:06 PM »

As I said in another thread, it seems that the YCC has quietly disbanded itself.

It wasn't an organization, it was a coalition of scientists most (all?) of whom headed up testing labs. Its main purpose was to establish standards for nomenclature for the field back when most SNP discovery was in the hands of academics.

That time has long passed.

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« Reply #4 on: October 13, 2012, 09:35:23 AM »

I'm not sure the YCC has disbanded itself.

The ISOGG Wiki article on the YCC lists its "Key people" as "Michael Hammer, Peter Underhill, Peter Forster, Tatiana Karafet, et al". Those are some heavy hitters. I don't know who the "et al" refers to, however. It would be nice to know.

How extensive is the YCC? What sort of weight do its pronouncements carry in the world of genetic science?

Of course, "the world of genetic science" can't even seem to agree on a single set of names for y-dna SNPs, so it doesn't look like there is any single organization or consortium making binding decisions on nomenclature.

« Last Edit: October 13, 2012, 09:44:43 AM by rms2 » Logged

Mike Walsh
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« Reply #5 on: October 13, 2012, 09:44:11 AM »

... Of course, "the world of genetic science" can't even seem to agree on a single set of names for y-dna SNPs, so it doesn't look like there is any single organization or consortium making binding decisions on nomenclature.

Yes, that's too bad. I use to have greater hope in YCC and I never understood the value of ISOGG, but it is now apparent. Since ISOGG is all volunteer from the get go, they are "self-funded." They also have a singularity in purpose, the benefit of the community.

The academic folks have to deal with funding and their careers. Not that that is bad, just that we can't expect them to work together or to even necessarily have continuity. Testing companies have to worry about making a profit and staying in business and our competitive with each other. That's okay too and in fact I like that, but we definitely can't expect them to work together. They also may not provide continuity as they go out of business, combine or switch marketplaces.

The only well funded entity, other than ISOGG's form of "self-funding" is the National Genographic Project. The last I've read, they get a ton of money from IBM and the Waitt Family Foundation. ..... this leaves us in the hands of Dr. Spencer Wells.
« Last Edit: October 13, 2012, 09:55:18 AM by Mikewww » Logged

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rms2
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« Reply #6 on: October 13, 2012, 09:56:57 AM »

The nice thing about the YCC, or at least the idea of a YCC, is that fairly well known geneticists comprise it, so its opinions and pronouncements carry the weight of their expertise. That's something ISOGG lacks, although by that I mean no disrespect to ISOGG or the expertise of its officers.

I think our main complaint against the YCC right now is that they don't update their y tree often enough. There have been quite a few advances in y-dna knowledge since their last update, and we would like to see those reflected in the "Haplotree" in use by FTDNA. All of us (or most of us, anyway) would also like to see an update in the green, SNP-tested haplogroup indicators in the various FTDNA projects, as well, even if the longhand version is replaced with the shorthand. I know I would like for my DF41 terminal SNP to be displayed, whether in the longhand or the shorthand.

I would also like to see terminal SNPs more strongly indicated in Ysearch. That would sure make life easier for purposes of project recruitment and research.
« Last Edit: October 13, 2012, 09:58:40 AM by rms2 » Logged

Mike Walsh
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« Reply #7 on: October 13, 2012, 10:35:39 AM »

.... I know I would like for my DF41 terminal SNP to be displayed, whether in the longhand or the shorthand.

I would also like to see terminal SNPs more strongly indicated in Ysearch. That would sure make life easier for purposes of project recruitment and research.

I was thinking about that. On that R1b group someone came up with idea of publishing modals to help people evaluate if stand-alone SNP testing was an option for them, versus Geno 2.0.

My initial reaction was lets make sure we a strong set of Ysearch modals, but as I think about it, what's important are just what you said, the terminal haplogroup modals.

Essentially, we can pretty well identify the permanent (although nothing is permanent) terminal SNPs. There are things fencing them in. Of course relative to each other the younger SNP is always the terminal (even if only temporarily so) SNP. However, on the other side is a definition that if you less than 15% diversity then an SNP is private.   So, any SNPs that are less than 20% diversity but at least 15% might be strong candidates for a "permanent" terminal SNP list.  Those would be the one we definitely one to capture and publish. Over time this list will grow, but if a novice comes in with a question of Geno 2.0 versus stand-alone testing, it would be logical for them to try a terminal SNP stand-alone test as long as it was on the "permanent" (low diversity) list.
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gtc
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« Reply #8 on: October 13, 2012, 11:41:48 AM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

Quote
The ISOGG Wiki article on the YCC lists its "Key people" as "Michael Hammer, Peter Underhill, Peter Forster, Tatiana Karafet, et al". Those are some heavy hitters. I don't know who the "et al" refers to, however. It would be nice to know.

From what I can gather, dating back from its foundation in 1994, the participant list of the YCC waxed and waned depending on who attended YCC meetings, gave presentations, etc.

In 2002, when they published "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups" the nomenclature committee was stated as comprising:

Peter Forster
Michael Hammer
Matthew E Hurles
Mark Jobing
Peter de Knijff
Chris Tyler-Smith
Peter Underhill

Quote
How extensive is the YCC?

I think that should read "was the YCC" as I feel that YCC no longer exists.

The list of contributors to the 2002 paper reads like a Who's Who of scientists in genetics and related fields.

Quote
What sort of weight do its pronouncements carry in the world of genetic science?

I think that would be measured by the number of times their publications are referenced in papers, especially recent ones. (Anybody like to count?)

Quote
Of course, "the world of genetic science" can't even seem to agree on a single set of names for y-dna SNPs, so it doesn't look like there is any single organization or consortium making binding decisions on nomenclature.

I agree, although an expanded and more formalized ISOGG may well fill the vacuum.

We live in interesting times.
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« Reply #9 on: October 13, 2012, 12:01:35 PM »

I would also like to see terminal SNPs more strongly indicated in Ysearch. That would sure make life easier for purposes of project recruitment and research.

There are many things about Ysearch that I'd like to see improved (frankly I think it needs a ground up rewrite), but I won't be holding my breath until Ysearch upgrade gets a priority on FTDNA's IT job list.

I'd be delighted if somebody independent of a test lab built a new and improved Ysearch.
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« Reply #10 on: October 13, 2012, 04:33:17 PM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

I wouldn't know if it were meeting or not meeting, but I did send an email to FTDNA about the YCC. If I don't get an answer early next week, I'll write Bennett Greenspan himself.


. . .

I think that should read "was the YCC" as I feel that YCC no longer exists.

 . . .

You might be right, but how do we know that it doesn't exist anymore?
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rms2
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« Reply #11 on: October 13, 2012, 05:12:44 PM »

Of course, by "terminal SNP", I mean the SNP furthest downstream for which the individual has tested positive. For some guys who quit upgrading after the old "Deep SNP-R1b" test, that would be M269.

We have guys in our projects now, however, who have tested L513+ or DF41+, or what-have-you, but who still show a red "R1b1a2" on their projects' Y-DNA Results pages, just as if they were simply sporting a "prediction" and had done no SNP testing at all. Most of us are still showing the green "R1b1a2a1a1b4" of someone only tested as far as L21+, even when things are actually otherwise. An update to FTDNA's Haplotree should clear all that up, whether it comes via the YCC or from some other source, like Thomas Krahn.

I would like to see FTDNA automatically generate a Ysearch page for each of its y-dna customers, one that automatically shows the terminal SNP for a customer who has been SNP tested. The privacy part could come into play through giving the customer the choice of whether or not to activate his Ysearch page and make it public. A customer who doesn't want an active Ysearch page could simply click a button making it private.
« Last Edit: October 13, 2012, 05:13:21 PM by rms2 » Logged

razyn
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« Reply #12 on: October 13, 2012, 05:32:28 PM »

Of course, by "terminal SNP", I mean the SNP furthest downstream for which the individual has tested positive. For some guys who quit upgrading after the old "Deep SNP-R1b" test, that would be M269.

We have guys in our projects now, however, who have tested L513+ or DF41+, or what-have-you, but who still show a red "R1b1a2" on their projects' Y-DNA Results pages, just as if they were simply sporting a "prediction" and had done no SNP testing at all.

Their own a la carte SNP testing is invisible to the creaky software of their "My haplotype" page -- which has had a facelift, but still shows whatever it thought was current two years ago.  I think it does show the Deep Clade test results, and that's what turns a red prediction to a green proven SNP... but only one that was known in early 2011.  (And its 2011 rutabaga name hasn't been, and can't be, made compatible with ISOGG's current one.)

Quote
I would like to see FTDNA automatically generate a Ysearch page for each of its y-dna customers, one that automatically shows the terminal SNP for a customer who has been SNP tested.

That would be way cool.  Is there any conceivable profit motive for them, to make it come to pass?
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« Reply #13 on: October 13, 2012, 05:39:31 PM »

Of course, by "terminal SNP", I mean the SNP furthest downstream for which the individual has tested positive. For some guys who quit upgrading after the old "Deep SNP-R1b" test, that would be M269.

We have guys in our projects now, however, who have tested L513+ or DF41+, or what-have-you, but who still show a red "R1b1a2" on their projects' Y-DNA Results pages, just as if they were simply sporting a "prediction" and had done no SNP testing at all.

Their own a la carte SNP testing is invisible to the creaky software of their "My haplotype" page -- which has had a facelift, but still shows whatever it thought was current two years ago.  I think it does show the Deep Clade test results, and that's what turns a red prediction to a green proven SNP... but only one that was known in early 2011.  (And its 2011 rutabaga name hasn't been, and can't be, made compatible with ISOGG's current one.)

It's only invisible if the a la carte SNP isn't on FTDNA's YCC Haplotree. Guys who tested L21+ a la carte, for example, get the green, longhand, R1b1a2a1a1b4 full "rutabaga" treatment.

An upgrade to FTDNA's Haplotree should fix that.

Quote from: rms2
I would like to see FTDNA automatically generate a Ysearch page for each of its y-dna customers, one that automatically shows the terminal SNP for a customer who has been SNP tested.

That would be way cool.  Is there any conceivable profit motive for them, to make it come to pass?

Hmmm . . . I don't know. I hadn't really thought in terms of profit, just of benefits for the rest of us. That is certainly a consideration, though, since there probably would be some additional cost to FTDNA involved.
« Last Edit: October 13, 2012, 05:39:59 PM by rms2 » Logged

gtc
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« Reply #14 on: October 14, 2012, 12:04:58 AM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

I wouldn't know if it were meeting or not meeting, but I did send an email to FTDNA about the YCC. If I don't get an answer early next week, I'll write Bennett Greenspan himself.

Good idea.

Meanwhile, I think there may be a hint of what's going on here:

"Then in 2010, FTDNA came out with a YCC-sanctioned tree which was distributed at the FTDNA conference and, as a result, ISOGG promptly did a major update to stay in alignment with the YCC.  Since then, no updates have come from the YCC.

Undaunted, the ISOGG Y Haplogroup Tree Committee has continued to add information as it becomes available from various sources and is now the most up-to-date source of this information. 

In November 2011 at the FTDNA Project Administrator's Conference, Spencer Wells of National Geographic, Michael Hammer of the University of Arizona, Thomas Krahn and Bennett Greenspan of FTDNA and Alice Fairhurst of ISOGG, reportedly agreed to all stay in alignment with the most current Y-DNA nomenclature to the best of their abilities.

As always, there is new research that has not yet become public. As it is released, ISOGG will again align its tree with the most current information and will continue to add updates as they become available. With the upcoming launch of Geno 2.0, the ISOGG Committee will have their work cut out for them!"


I've added white space for better readability, and the bolding is mime.

Given that Hammer was the driving force behind YCC, and Wells is the spokesperson for Geno 2 and is reportedly about to publish, perhaps a new YCC-type coalition is in the works.

http://www.yourgeneticgenealogist.com/2012/09/lets-all-start-using-terminal-snp.html
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« Reply #15 on: October 25, 2012, 09:20:48 PM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

I wouldn't know if it were meeting or not meeting, but I did send an email to FTDNA about the YCC. If I don't get an answer early next week, I'll write Bennett Greenspan himself.

Any word back from FTDNA on this?
« Last Edit: October 25, 2012, 09:21:11 PM by gtc » Logged

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« Reply #16 on: October 26, 2012, 04:06:18 AM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

I wouldn't know if it were meeting or not meeting, but I did send an email to FTDNA about the YCC. If I don't get an answer early next week, I'll write Bennett Greenspan himself.

Any word back from FTDNA on this?

Yes, but it wasn't satisfactory. The person I wrote did not know anything about the YCC and referred me to someone else, who has not emailed me. I have been so busy lately, I haven't followed up on it.

I will send Mr. Greenspan an email today when and if I get the chance.
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« Reply #17 on: October 26, 2012, 06:12:36 AM »

I'm not sure the YCC has disbanded itself.

Well, if it doesn't meet and publish minutes, and if it doesn't publish articles, then for mine it essentially doesn't exist anymore.

I wouldn't know if it were meeting or not meeting, but I did send an email to FTDNA about the YCC. If I don't get an answer early next week, I'll write Bennett Greenspan himself.

Any word back from FTDNA on this?

Yes, but it wasn't satisfactory. The person I wrote did not know anything about the YCC and referred me to someone else, who has not emailed me. I have been so busy lately, I haven't followed up on it.

I will send Mr. Greenspan an email today when and if I get the chance.

Thanks.

On a similar track, on Oct 14 I emailed Alice Fairhurst, ISOGG's Y tree coordinator, pointing out that the YCC link on their page is now effectively invalid, and asking if the YCC has essentially dissolved itself.

I have received no reply.

I hope you are more successful with BG.
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« Reply #18 on: October 27, 2012, 11:25:38 AM »

I emailed Bennett Greenspan about the YCC last night. He probably won't see the email until Monday at the earliest, since last night was Friday night.
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« Reply #19 on: October 27, 2012, 11:33:49 AM »

I emailed Bennett Greenspan about the YCC last night. He probably won't see the email until Monday at the earliest, since last night was Friday night.
Thanks.

It would be nice if at least two testing companies AND National Genographic would work jointly to help fund an international consortium to set standards.
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« Reply #20 on: October 27, 2012, 12:41:31 PM »

It would be nice if at least two testing companies AND National Genographic would work jointly to help fund an international consortium to set standards.

Something in my bones makes me feel that there's currently a sort of mutually agreed embargo on discussing the YCC pending a big announcement.

If I had to guess, I'd say that Hammer, FTDNA, ISOGG and interested others are jointly beavering away at a new tree management arrangement and an associated update/revision protocol which will better keep up with developments from all quarters, not just from academia. This may become known as YCC II and have a much smaller nomenclature committee membership at the center than YCC as we know (knew) it.

And I could be 100% wrong.
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« Reply #21 on: October 27, 2012, 01:22:11 PM »


Something in my bones makes me feel that there's currently a sort of mutually agreed embargo on discussing the YCC pending a big announcement.

If I had to guess, I'd say that Hammer, FTDNA, ISOGG and interested others are jointly beavering away

Hammer is on the program at the FTDNA conference for project admins in a couple of weeks.  Don't know if that's relevant to this topic, but they haven't gone their separate ways.
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« Reply #22 on: October 27, 2012, 08:54:05 PM »


Something in my bones makes me feel that there's currently a sort of mutually agreed embargo on discussing the YCC pending a big announcement.

If I had to guess, I'd say that Hammer, FTDNA, ISOGG and interested others are jointly beavering away

Hammer is on the program at the FTDNA conference for project admins in a couple of weeks.  Don't know if that's relevant to this topic, but they haven't gone their separate ways.

Even though FTDNA has stopped using Hammer's Lab, according to their website:
"Mike Hammer is FTDNA's Chief Scientist, and member of the Scientific Advisory Board" and I would expect that situation to continue going forward.

Hammer was the driving force behind the YCC and getting the nomenclature standardized. I can't see him walking away from that.
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« Reply #23 on: October 28, 2012, 07:40:48 AM »

I heard from Mr. Greenspan, but his answer was brief. He said Dr. Hammer is the head of the YCC and approved the current shorthand FTDNA is using. I hate to pester Bennett, but I think I will write him again and ask for some clarification.

He did say they want to drop the longhand entirely because it will be "changing SO much with the introduction of the Nat Geo Geno 2.0 product" (his words, including the caps).
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« Reply #24 on: October 28, 2012, 10:42:52 AM »

It would be interesting to put the question "What happened to the YCC?" on Rootsweb. I venture that there are folks on there who know the story.
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