A Short History

The night before Christmas -Waiting for Santa to arrive -Opening -All tired out -Until next year -

Merry Christmas

Click on these gifts to open -

The Need for Standardized Y-STR Terminology

Public release date: 23-Dec-2008

Contact: Michael E. Newman
michael.newman@nist.gov
301-975-3025
National Institute of Standards and Technology (NIST)

NIST guides genetic genealogy labs toward improved accuracy
Anyone who has watched crime dramas on TV knows that forensic scientists can use DNA “profiling” to identify people from evidence gathered at a crime scene, establish a paternity link or help free an innocent person who has been wrongly jailed.    A lesser known but rapidly growing application of DNA profiling is tracing a person’s paternal ancestry — a process known as genetic genealogy.    The laboratories performing this testing often differ in their results, making data comparison between labs difficult and casting doubt on reported genetic matches.    Researchers at the National Institute of Standards and Technology (NIST) recently published a paper* with recommendations for genealogy testing that they hope will improve the accuracy and reliability of the product.

A man’s paternal lineage can be traced using the DNA on his Y chromosome (Y-DNA), which, like many European surnames, passes from father to son.    DNA profiling provides a genetic path that follows the surname through the years.    Women who wish to know their ancestry can ask their father, brother, paternal uncle or paternal grandfather to take the test for them.

Genetic genealogy works by studying the sequences of repeating nucleotide (the base components of DNA) patterns on the Y chromosome known as short tandem repeats (STRs).    Each STR is considered a separate marker for potential genetic matching because the number of times it is repeated will be the same for related males.    For example, a person may have one STR sequence that repeats 12 times, another 11 times, a third 17 times and so on.    If another male has a Y chromosome with a high percentage of the same STRs, it is considered likely that they share a common ancestor.    Accurately counting the number of repeats is a tricky task and the source of much of the error in genetic genealogy tests, causing genealogists to make incorrect matches or miss family connections altogether.

In their paper, the NIST researchers explain the basis for the differing interpretations and recommend a solution using the agency’s certified reference material for human Y-chromosome DNA profiling (Standard Reference Material 2395), a collection of Y-STR markers that can serve as a means for genetic labs to calibrate their testing equipment.    The researchers “strongly encourage [SRM 2395’s] use to enable compatible and calibrated measurements to be made between different Y-STR testing laboratories.”

Their sentiment is echoed by an editorial in the Journal of Genetic Genealogy that says of the NIST paper, “The advantages of having industry-wide standards are compelling for both buyers and sellers of genetic genealogy services.”

###
* J.M. Butler, M.C. Kline and A.E. Decker. Addressing Y-chromosome short tandem repeat (Y-STR) allele nomenclature. J. Genetic Genealogy 4:125-148 (2008).

I'm getting a rash . . .

We seem to be getting a rash of new results from FTDNA.    This is especially good since none were expected before January.    Either the FTDNA folks have been overcome by the Christmas spirit  .  .  .  .  or they want to take some time off.    Either way, here's what has just come in.

Joe's, #109, Y-DNA13-25 markers.    Joe's 12 marker panel didn't match anyone and, unfortunately, as expected, this panel didn't bring him any closer to anyone.    Joe is still waiting for his Y-DNA26-37 panel and, while that won't bring him any closer to anyone, it will ensure that when a match does come along it will be a related person.

Samuel's, #139, Y-DNA13-25 markers had some questionable matches at 12 markers some of which seem to be firming up at 25 markers and seem to indicate that Samuel is a member of the Faires Berrys Family.    37 markers will give us a better picture but Samuel may be a bit of an outlier, not really closely related.    We'll see.

What?    That's not a rash?    Well, FTDNA also reported the Y-DNA1-12 markers for a fellow named Sammy Berry, but Sammy only ordered 12 markers, has never bothered to respond to our welcome sent when he first ordered, and isn't close to matching anyone anyway   --   so I'm just ignoring him.

Maybe more tomorrow . . . . ?

A Reminder

12 more days . . . . .This offer is good thru FTDNA until December 31st, 2008 for kits ordered and paid for by that time.

New participant

Yes, we have a new participant  -  Samuel Tilton Berry, #139.    Sam's Y-DNA1-12 panel came back today.    Sam's yAncestry is posted with 'unassigned' in case anyone would like to take a look to see if you recognize any names in it.

No one should get excited about 12 marker matches, particularly a GD of 1 at 12 markers.    But - - - these folks who are a GD of 1 from Sam may want to be sure to look at his yAncestry:   Laurence, #9; Paul, #36, David, #59; C.E., #77; Bill, #79; Henry, #108; Edward, #110, Paul, #111; and John, #114.

And, we do have a pretty good pipeline now, at least for next month.

The Sinister Problem of Convergence

As you know from my last post, Charles Hayes, #138, matches all the English Colony Berrys 25/25, and is 36/37 with Robert, #43 (DYS456), and Alan, #112 (CDYb), the only other two who have tested 37 markers.

Lawrence Mayka, has just posted the following note to the Rootsweb DNA list:

In a highly populated haplogroup such as R1b1b2, almost every possible combination of values on fast-changing markers is occupied by _someone_, usually from the British Isles.    A member of R1b1b2 is thus almost entirely dependent on the slower markers for differentiation.    If, sadly, that member happens to have modal values for almost all the slower markers, he may very well get coincidentally convergent matches at 37 markers.    Luckily, of the additional 30 markers in a 67-marker upgrade, 28 of them are slow, and they generally do a good job of widening the gap.

An excellent example on Ysearch is that of 4ZKEU of Poland and M6PHZ of England.    At 37 markers, their GD is 3; at 67 markers, the GD is 16.    The Englishman has a relative who is even closer to the Pole:   a GD of 2 at 37 markers, a GD of 15 at 67 markers.

Coincidental convergence at 37 markers is not restricted to R1b1b2.    It can occasionally happen in other haplogroups, even G2a.    In one spectacular G2a example, a GD of 7 on 37 markers became a GD of 28 on 67 markers.

This is why:

- A putative cross-surname match at 37 markers must _always_ be extended to 67 for verification.

- At larger genetic distances, it is generally best to ignore the faster-changing markers and focus on the 54 slower markers.    Otherwise, your closest matches will be those (usually British Isles) individuals whose fast-changing markers _happen_ to match yours, purely due to coincidental convergence.

For the reasons stated, I would encourage each of you English Colony Berrys to expand your test results to 67 markers for the purpose of minimizing 'The Problem of Convergence'.

New English Colony Berry Hayes

Yes, we have a bonafied verified new English Colony Hayes member!    Charles Hayes, #138, is a lineal GGrandson of Stephen F. Berry, 1829-1911.

The English Colony Berry family now has five members with a complex testing history, One tested at Relative Genetics, one at DNA Heritage and three at FTDNA.    Only Charles, however, has tested 67 markers so they're difficult to compare beyond 25 markers and they are all exactly the same to 25 markers!    Their haplotypes can be see here.

This should be of particular interest to Lawrence Berry, #61, also a GGrandson of Stephen F. Berry, 1829-1911.

Madison's turn

Another of my neglected families during the time I couldn't manage to generate cladograms are the Madison Co. Berrys.    So here are your tables and diagrams.

First, the haplotypes of all the Madison Co. Berrys -and their genetic distances from one another -Don't put a lot of faith in this table, and be cognizant that these numbers represent not a fact but a 75% PROBABILITY -
So, finally, the cladograms.    Here's one for all those who have tested at least 25 markers -You'll remember that I told you that we can only generate a cladagram by using the same markers for all the folks compared?    Well, if you'll look at the haplotype table you will see that the last five folks there tested at DNAHeritage and SMGF so to include them beyond 25 markers I've used 7 additional common markers for a 32 marker cladogram -And a regular 37 marker one -and those Madison Co. Berrys who have tested 67 markers -
Yours to interpret.

Two new participants!

Over the past weekend we've added two more participants, our 145th and 146th, Brandon, #136, and Dave, #137.    Brandon expects to match the Barry/Berrys and David, the Faires Berrys.

Dave's Y-DNA37 results may finally show us enough differences to be able to generate a Faires cladagram to puzzle over, while Brandon may need all his Y-DNA67 markers to differentiate at all from the 'seeming twins' C.E., #77, and Bill, #79, who, you will recall, are exactly the same at 67 markers.    If you fellows are up for an experiment, because I have no real idea that it will show anything, you might both try something like the Panel 5 Palindromic Pack from the Advanced Orders section of your FTDNA Personal Page.

It would be nice if FTDNA were to offer a sale on Advanced Orders sometime.

Orange redux

Benjamin Berry Henderson has redrawn our cladogram by family groups, and these are his commments:

The Family lines of William, David, and Thomas group nicely.
The Robert Jr and Joshua Lines are fragmented.
Our documentation of the family lines is pretty good with Billy # 8 being connected to Robert Jr being our weakest link .
The documentation connecting #8 is still pretty sound however.I think the middle cladogram best describes our root DNA values. I say this because out of 10 samples of CDYa values, 6 of them are a value of 37 and 4 are a value of 36. This is my best guess based only on this fact only. Ben

Faires Berrys

I've just learned that we may soon be getting a new Faires Berry Project member so I thought I ought to bring the family up to date with what we have.

Here's their haplotypes.Difficult to see the differences here, though.    For a better view, take a look here.

Their genetic distance table -
And their Time to Most Recent Common Ancestor -

But, you ask, what about cladograms?    Well, here's the difficulty.    Cladograms require that equal length haplotypes be compared to one another.    So, for these folks we can compare five 25 marker haplotypes and three 37 marker haplotypes.    But, if you'll take a look at the first 25 markers you'll see that they're exactly the same except for a difference of 1 at DYS388 and 1 at DYS 392 for Dennis, #31.    So essentially what we have are four identical haplotypes and one different.    Unfortunately, another requirement for generating cladograms is that you have at least three different sequences.    So we can't do a 25 marker cladogram.

But, even three is pretty unexciting.    This family does have three different 37 marker haplotypes.    Here's their cladogram -

Mostly filler

A few shots up the Columbia Gorge from Portland to my home town, Bingen, Washington, a distance of about 70 miles -looking east, Mt. Hood in the distance.
The beginning of the gorge -

Looking west from Cascade Locks bridge -

This is it!    In the foreground, along the Columbia, hidden behind those lumber mills, the town of Bingen, pop. about 670, then and now.
Can you imagine these days admonishing your kids as they go out to play, "Don't go above the second bluff"?

Because I can

No sooner had I posted my Augusta/Washington Co. Berry cladogram the other day than Thurman's, #131, result came in.    Carol will be as interested as anyone in Thurman's position on this cladogram.I hope it helps continue her warm and fuzzy feeling.

Orange Co., NC Berrys

At various times I've postulated that Billy, #8, is the ancestral haplotype for this family, and at other times I've suggested Wiley, #18.    Click here.

I've just run new 37 marker cladograms and I want to show you two results.

First, using Dean McGee's Y-Utility to generate the .ych file, our cladogram looks like this:

However, when I direct Dean's Utility to create a modal for the family, the modal coincides with Wiley and the resulting cladogram looks like this:

Perhaps it should be shown as -
(The top left guy is 83, not 3)
Any of you Orange folks have an opinion on this?    Not the aesthetics of which presentation is better, but which of these folks might represent the ancestral haplotype for this family, and why?

CyberMonday

You'll recall that I've been having a problem getting my Parallels app to run properly so that I could transfer files back and forth between its virtual Windows computer and my 'real' MacBook.    Yesterday (CyberMonday) I saw the $80 VMWare Fusion (virtual Windows on a Mac) application on sale for half off with a $30 mail-in rebate offer.    Sweet.   

Oh, maybe you don't recall that and wonder why a Macintosh guy would care about running a Windows application.    Well, it seems that the fluxus engineering free Phylogenetic Network software only runs on Windows.    And it's how I generate my cladograms.

A case in point - that long overdue Augusta/Washington Co. Berry 37 marker cladogram -

So, as you see, I hit the PayPal button and downloaded the application.    Fusion works great.    To transfer between the real computer and the virtual computer you just drag and drop, just like another folder or window.