Tenth Annual Family Tree DNA Conference Wrapup

baber summary

This slide, by Robert Baber, pretty well sums up our group obsession and what we focus on every year at the Family Tree DNA administrator’s conference in Houston, Texas.

Getting to Houston, this year, was a whole lot easier than getting out of Houston. They had storms yesterday and many of us spent the entire day becoming intimately familiar with the airport.  Jennifer Zinck, of Ancestor Central, is still there today and doesn’t have a flight until late.

And this is how my day ended, after I finally got out of Houston and into my home airport. This isn’t at the airport, by the way.  Everything was fine there, but I made the apparent error of stopping at a Starbucks on the way home.  This is the parking lot outside an hour or so later.  What can I say?  At least I had my coffee, and AAA rocks, as did the tow truck driver and my daughter for getting out of bed to come and rescue me!!!  Hmmm, I think maybe things have gone full circle.  I remember when I used to go and rescue her:)

jeep tow

So far, today hasn’t improved any, so let’s talk about something much more pleasant…the conference itself.

Resources

One of the reasons I mentioned Jennifer Zinck, aside from the fact that she’s still stuck in the airport, is because she did a great job actually covering the conference as it happened. Since I had some time yesterday to visit with her since our gates weren’t terribly far apart, I asked her how she got that done.  I took notes too, and photos, but she turned out a prodigious amount of work in a very short time.  While I took a lightweight MacBook Air, she took her regular PC that she is used to typing on, and she literally transcribed as the sessions were occurring.  She just added her photos later, and since she was working on a platform that she was familiar with, she could crop and make the other adjustments you never see but we perform behind the scenes before publishing a photo.

On the other hand, I struggled with a keyboard that works differently and is a different size than I’m used to as well as not being familiar with the photo tools to reduce the size of pictures, so I just took rough notes and wrote the balance later.  Having familiar tools make such a difference.  I think I’ll carry my laptop from now on, even though it is much heavier.  Kudos to Jennifer!

I was initially going to summarize each session, but since Jen did such a good job, I’m posting her links. No need to recreate a wheel that doesn’t need to be recreated.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

ISOGG, the International Society of Genetic Genealogy is not affiliated with Family Tree DNA or any testing company, but Family Tree DNA is generous enough to allow an ISOGG meeting on Sunday before the first conference session.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

You can find my conference postings here:

http://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

http://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

http://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

Several people were also posting on a twitter feed as well.

https://twitter.com/search?q=%23FTDNA2014&src=tyah

Those of you where are members of the ISOGG Yahoo group for project administrators can view photos posted by Katherine Borges in that group and there are also some postings on the Facebook ISOGG group as well.

Now that you have the links for the summaries, what I’d like to do is to discuss some of the aspects I found the most interesting.

The Mix

When I attended my first conference 10 years ago, I somehow thought that for the most part, the same group of people would be at the conferences every year. Some were, and in fact, a handful of the 160+ people attending this conference have attended all 10 conferences.  I know of two others for certain, but there were maybe another 3 or so who stood up when Bennett asked for everyone who had been present at all 10 conferences to stand.

Doug Mumma, the very first project administrator was with us this weekend, and still going strong. Now, if Doug and I could just figure out how we’re related…

Some of the original conference group has passed on to the other side where I’m firmly convinced that one of your rewards is that you get to see all of those dead ends of your tree. If we’re lucky, we get to meet them as well and ask all of those questions we have on this side.  We remember our friends fondly, and their departure sadly, but they enriched us while they were here and their memories make us smile.  I’m thinking specifically of Kenny Hedgepath and Leon Little as I write this, but there have been others as well.

The definition of a community is that people come and go, births, deaths and moves.

This year, about half of the attendees had never attended a conference before. I was very pleased to see this turn of events – because in order to survive, we do need new people who are as crazy as we are…er….I mean as dedicated as we are.

isogg reception

ISOGG traditionally hosts a potluck reception on Saturday evening. Lots of putting names with faces going on here.

Collaboration

I asked people about their favorite part of the conference or their favorite session. I was surprised at the number of people who said lunches and dinners.  Trust me, the food wasn’t that wonderful, so I asked them to elaborate.  In essence, the most valuable aspect of the conference was working with and talking to other administrators.

bar talk

It’s not like we don’t talk online, but there is somehow a difference between online communications and having a group discussion, or a one-on-one discussion. Laptops were out and in use everyplace, along with iPads and other tools.  It was so much fun to walk by tables and hear snippets of conversations like “the mutation at location 309.1….” and “null marker at 425” and “I ordered a kit for my great uncle…..”

I agree, as well. I had pre-arranged two dinners before arriving in order to talk with people with whom I share specific interests.  At lunches, I either tried to sit with someone I specifically needed to talk to, or I tried to meet someone new.

I also asked people about their specific goals for the next year. Some people had a particular goal in mind, such as a specific brick wall that needs focus.  Some, given that we are administrators, had wider-ranging project based goals, like Big Y testing certain family groups, and a surprising number had the goal of better utilizing the autosomal results.

Perhaps that’s why there were two autosomal sessions, an introduction by Jim Bartlett and then Tim Janzen’s more advanced session.

Autosomal DNA Results

jim bartlett

Note the cool double helix light fixture behind the speakers.

tim janzen

Tim specifically mentioned two misconceptions which I run across constantly.

Misconception 1 – A common surname means that’s how you match.  Just because you find a common surname doesn’t mean that’s your DNA match.  This belief is particularly prevalent in the group of people who test at Ancestry.com.

Misconception 2 – Your common ancestor has to be within the past 6 generations.  Not true, many matches can be 6-10th cousins because there are so many descendants of those early ancestors, even as many as 15 generations back.

Tim also mentioned that endogamous relationships are a tough problem with no easy answer. Polynesians, Ashkenazi Jews, Low German Mennonites, Acadians, Amish, and island populations.  Do I ever agree with him!  I have Brethren, Mennonite and Acadian in the same parent’s line.

Tim has been working with the Mennonite DNA project now for many years.

Tim included a great resource slide.

tim slide1

Tim has graciously made his entire presentation available for download.

tim slide2

There are probably a dozen or so of us that are actively mapping our ancestors, and a huge backlog of people who would like to. As Tim pointed out with one of his slides, this is not an easy task nor is it for the people who simply want to receive “an answer.”

tim slide3

I will also add that we “mappers” are working with and actively encouraging Family Tree DNA to develop tools so that the mapping is less spreadsheet manual work and more automated, because it certainly can be.

Upload GEDCOM Files

If you haven’t already, upload your GEDCOM to Family Tree DNA.  This is becoming an essential part of autosomal matching.  Furthermore, Family Tree DNA will utilize this file to construct your surname list and that will help immensely determining common surnames and your common ancestor with your Family Finder matches.  If you have sponsored tests for cousins, then upload a GEDCOM file for them or at least construct a basic tree on their Family Tree DNA page.

Ethics

Family Tree DNA always tries to provide a speaker about ethics, and the only speakers I’ve ever felt understood anything about what we want to do are Judy Russell and Blaine Bettinger.  I was glad to see Blaine presenting this year.

blaine bettinger

The essence of Blaine’s speech is that ethics isn’t about law. Law is cut and dried.  Ethics isn’t, and there are no ethics police.

Sometimes our decisions are colored necessarily by right and wrong.  Sometimes those decisions are more about the difference between a better and a worse way.

As a community, we want to reduce negative press coverage and increase positive coverage. We want to be proactive, not reactive.

Blaine stresses that while informed consent is crucial, that DNA doesn’t reveal secrets that aren’t also revealed by other genealogical forms of research. DNA often reveals more recent secrets, such as adoptions and NPEs, so it’s possibly more sensitive.

Two things need to govern our behavior. First, we need to do only things that we would be comfortable seeing above the fold in the New York Times.  Second, understand that we can’t make promises about topics like anonymity or about the absence of medical information, because we don’t know what we don’t know.

The SNP Tsunami

One of my concerns has been and remains the huge number of new SNPs that have been discovered over the past year or so with the Big Y by Family Tree DNA and  corresponding tests from other vendors.

When I say concern, I’m thrilled about this new technology and the advances it is allowing us to make as a community to discover and define the evolution of haplogroups. My concern is that the amount of data is overwhelming.  However, we are working through that, thanks to the hours and hours of volunteer work by haplogroup administrators and others.

Alice Fairhurst, who volunteers to maintain the ISOGG haplotree, mentioned that she has added over 10,000 SNPs to the Y tree this year alone, bringing the total to over 14,000. Those SNPs are fully vetted and placed.  There are many more in process and yet more still being discovered.  On the first page of the Y SNP tree, the list of SNP sources and other critical information, such as the criteria for a SNP to be listed, is provided.

isogg tree3

isogg snps

isogg snps 2014

So, if you’re waiting for that next haplotree poster, give it up because there isn’t a printing press that big, unless you want wallpaper.

isogg new development 2014

These slides are from Alice’s presentation. The ISOGG tree provides an invaluable resource for not only the genetic genealogy community, but also researchers world-wide.

As one example of how the SNP tsunami has affected the Y tree, Alice provided the following summary of R-U106, one of the two major branches of haplogroup R.

From the ISOGG 2006 Y tree, this was the entire haplogroup R Y tree. You can see U106 near the bottom with 3 sub-branches.  While this probably makes you chuckle today, remember that 2006 was only 8 years ago and that this tree didn’t change much for several years.

2006 entire tree

2007 was the same.

2008 u106 tree

2008 shows 5 subclades and one of the subclades had 2 subclades.

2009 u106 tree

2009 showed a total of 12 sub-branches and 2010 added one more.

2011 however, showed a large change. U106 in 2011 had 44 subgroups total and became too large to show on one screen shot.  2012 shows 99 subclades, if I counted accurately.  The 2014 U106 tree is shown below.

before big y

after big y

u106 now

u106 now2

There’s another slide too, but I didn’t manage to get the picture.  You get the idea though…

As you can imagine, for Family Tree DNA, trying to keep up with all of the haplogroups, not just one subgroup like U106 is a gargantuan task that is constantly changing, like hourly. Their Y tree is currently the National Geographic tree, and while they would like to update it, I’m sure, the definition of “current tree” is in a constant state of flux.  Literally, Mike Walsh, one of the admins in the R-L21 group uploads a new tree spreadsheet several times every day.

In order to deal attempt to deal with this, and to encourage people who don’t want to do a Big Y discovery type test, but do want to ferret out their location on their assigned portion of the tree, Family Tree DNA is reintroducing the Backbone tests.

They are starting with M222, also known as the Niall of the 9 Hostages haplogroup which is their beta for the new product and new process. You can see the provisional tree and results in the two slides they provided, below.  I apologize for the quality, but it was the best I could do.

M222

m222 pie

Haplogroup administrators are going to be heavily involved in this process. Family Tree DNA is putting SNP panels together that will help further define the tree and where various SNPs that have been recently discovered, and continue to be discovered, will fall on the tree.

As Big Y tests arrive, haplogroup project administrators typically assemble a spreadsheet of the SNPS and provisionally where they fall on the tree, based on the Big Y results.

What Bennett asked is for the admins to work with Family Tree DNA to assemble a testing panel based on those results. The goal is for the cost to be between $1.50 and $2 (US) for each SNP in the panel, which will reduce the one-off SNP testing and provide a much more complete and productive result at a far reduced price as compared to the current $29 or $39 per individual SNP.

If you are a haplogroup administrator, get in touch with Family Tree DNA to discuss your desired backbone panels. New panels, when it’s your turn, will take about 2 weeks to develop.

Keep in mind that the following SNPs, according to Bennett, are not optimal for panels:

  • Palindromic regions
  • Often mutating regions designated as .1, .2, etc.
  • SNPs in STRs

Nir Leibovich, the Chief Business Officer, also addressed the future and the Big Y to some extent in his presentation.

nir leibovich

ftdna future 2014

Utilizing the Big Y for Genealogy

In my case, during the last sale, I ordered several Big Y tests for my Estes family line because I have several genealogically documented lines from the original Estes family in Kent, England through our common ancestor, Robert Estes born in 1555 and his wife Anne Woodward. The participants also agreed to extend their markers to 111 markers as well.  When the results are back, we’ll be able to compare them on a full STR marker set, and also their SNPs.  Hopefully, they will match on their known SNPs and there will be some new novel variants that will be able to suffice as line marker mutations.

We need more BIG Y tests of these types of genealogically confirmed trees that have different sons’ lines from a distant common ancestor to test descendant lines. This will help immensely to determine the actual, not imputed, SNP mutation rate and allow us to extrapolate the ages of haplogroups more accurately.  Of course, it also goes without saying that it helps to flesh out the trees.

I personally expect the next couple of years will be major years of discovery. Yes, the SNP tsumani has hit land, but it’s far from over.

Research and Development

David Mittleman, Chief Scientific Officer, mentioned that Family Tree DNA now has their own R&D division where they are focused on how to best analyze data. They have been collaborating with other scientists.  A haplogroup G1 paper will be published shortly which states that SNP mutation rates equate to Sanger data.

FTDNA wants to get Big Y data into the public domain. They have set up consent for this to be done by uploading into NCBI.  Initially they sent a survey to a few people that  sampled the interest level.  Those who were interested received a release document.  If you are interested in allowing FTDNA to utilize your DNA for research, be it mitochondrial, Y or autosomal, please send them an e-mail stating such.

Don’t Forget About Y Genealogy Research

It’s very easy for us to get excited about the research and discovery aspect of DNA – and the new SNPs and extending haplotrees back in time as far as possible, but sometimes I get concerned that we are forgetting about the reason we began doing genetic genealogy in the first place.

Robert Baber’s presentation discussed the process of how to reconstruct a tree utilizing both genealogy and DNA results. It’s important to remember that the reason most of our participants test is to find their ancestors, not, primarily, to participate in the scientific process.

Robert baber

edward baber

Robert has succeeded in reconstructing 110 or 111 markers of the oldest known Baber ancestor, shown above. I wrote about how to do this in my article titled, Triangulation for Y DNA.

Not only does this allow us to compare everyone with the ancestor’s DNA, it also provides us with a tool to fit individuals who don’t know specific genealogical line into the tree relatively accurately. When I say relatively, the accuracy is based on line marker mutations that have, or haven’t, happened within that particular family.

Jim illustrated how to do this as well, and his methodology is available at the link on his slide, below.

baber method

I had to laugh. I’ve often wondered what our ancestors would think of us today.  Robert said that that 11 generations after Edward Baber died, he flew over church where Edward was buried and wondered what Edward would have thought about what we know and do today – cars, airplanes, DNA, radio, TV etc..  If someone looked in a crystal ball and told Edward what the future held 11 generations later, he would have thought that they were stark raving mad.

Eleven generations from my birth is roughly the year 2280. I’m betting we won’t be trying to figure out who our ancestors were through this type of DNA analysis then.  This is only a tiny stepping stone to an unknown world, as different to us as our world is to Edward Baber and all of our ancestors who lived in a time where we know their names but their lives and culture are entirely foreign to ours.

Publications

When the Journal of Genetic Genealogy was active, I, along with other citizen scientists published regularly.  The benefit of the journal was that it was peer reviewed and that assured some level of accuracy and because of that, credibility, and it was viewed by the scientific community as such.  My co-authored works published in JOGG as well as others have been cited by experts in the academic community.  It other words, it was a very valuable journal.  Sadly, it has fallen by the wayside and nothing has been published since 2011.  A new editor was recruited, but given their academic load, they have not stepped up to the plate.  For the record, I am still hopeful for a resurrection, but in the mean time, another opportunity has become available for genetic genealogists.

Brad Larkin has founded the Surname DNA Journal, which, like JOGG, is free to both authors and subscribers. In case you weren’t aware, most academic journal’s aren’t.  While this isn’t a large burden for a university, fees ranging from just over $1000 to $5000 are beyond the budget of genetic genealogists.  Just think of how many DNA tests one could purchase with that money.

brad larkin

surname dna journal

Brad has issued a call for papers. These papers will be peer reviewed, similarly to how they were reviewed for JOGG.

call for papers

Take a look at the articles published in this past year, since the founding of Surname DNA Journal.

The citizen science community needs an avenue to publish and share. Peer reviewed journals provide us with another level of credibility for our work. Sharing is clearly the lynchpin of genetic genealogy, as it is with traditional genealogy. Give some thought about what you might be able to contribute.

Brad Larkin solicited nominations prior to the conference and awarded a Genetic Genealogist of the Year award. This year’s award was dually presented to Ian Kennedy in Australia, who, unfortunately, was not present, and to CeCe Moore, who just happened to follow Brad’s presentation with her own.

Don’t Forget about Mitochondrial DNA Either

I believe that mitochondrial DNA the most underutilized DNA tool that we have, often because how to use mitochondrial DNA, and what it can tell you, is poorly understood. I wrote about this in an article titled, Mitochondrial, The Maligned DNA.

Given that I work with mitochondrial DNA daily when I’m preparing client’s Personalized DNA Reports (orderable from your personal page at Family Tree DNA or directly from my website), I know just how useful mitochondrial can be and see those examples regularly. Unfortunately, because these are client reports, I can’t write about them publicly.

CeCe Moore, however, isn’t constrained by this problem, because one of the ways she contributes to genetic genealogy is by working with the television community, in particular Genealogy Roadshow and the PBS series, Finding Your Roots. Now, I must admit, I was very surprised to see CeCe scheduled to speak about mitochondrial DNA, because the area of expertise where she is best known is autosomal DNA, especially in conjunction with adoptee research.

cece moore

cece mtdna

During the research for the production of these shows, CeCe has utilized mitochondrial DNA with multiple celebrities to provide information such as the ethnic identification of the ancestor who provided the mitochondrial DNA as Native American.

Autosomal DNA testing has a broad but shallow reach, across all of your lines, but just back a few generations.  Both Y and mitochondrial DNA have a very deep reach, but only on one specific line, which makes them excellent for identifying a common ancestor on that line, as well as the ethnicity of that individual.

I have seen other cases, where researchers connected the dots between people where no paper trail existed, but a relationship between women was suspected.

CeCe mentioned that currently there are only 44,000 full sequence results in the Family Tree DNA data base and and 185K total HVR1, HVR2 and full sequence tests. Y has half a million.  We need to increase the data base, which, of course increases matches and makes everyone happier.  If you haven’t tested your mitochondrial DNA to the full sequence level, this would be a great time!

There are several lessons on how to utilize mitochondrial DNA at this ISOGG link.

I’m very hopeful that CeCe’s presentation will be made available as I think her examples are quite powerful and will serve to inspire people.  Actually, since CeCe is in the “movie business,” perhaps a short video clip could be made available on the FTDNA website for anyone who hasn’t tested their mitochondrial DNA so they can see an example of why they should!

myOrigins

I would be fibbing to you if I told you I am happy with myOrigins. I don’t feel that it is as sensitive as other methods for picking up minority admixture, in particular, Native American, especially in small amounts.  Unfortunately, those small amounts are exactly what many people are looking for.

If someone has a great-great-great-great grandparent that is Native, they carry about 1%, more or less, of the Native ancestor’s DNA today. A 4X great grandparent puts their birth year in the range of 1800-1825 – or just before the Trail of Tears.  People whose colonial American families intermarried with Native families did so, generally, before the Trail of Tears.  By that time, many tribes were already culturally extinct and those east of the Mississippi that weren’t extinct were fighting for their lives, both literally and figuratively.

We really need the ability to develop the most sensitive testing to report even the smallest amounts of Native DNA and map those segments to our chromosomes so that we can determine who, and what line in our family, was Native.

I know that Family Tree DNA is looking to improve their products, and I provided this feedback to them. Many people test autosomally only for their ethnicity results and I surely would love to have those people’s results available as matches in the FTDNA data base.

Razib Khan has been working with Family Tree DNA on their myOrigins product and spoke about how the myOrigins data is obtained.

razib kahn

my origins pieces

Given that all humans are related, one way or another, far enough back in time, myOrigins has to be able to differentiate between groups that may not be terribly different. Furthermore, even groups that appear different today may not have been historically.  His own family, from India, has no oral history of coming from the East, but the genetic data clearly indicates that they did, along with a larger group, about 1000 years ago.  This may well be a result of the adage that history is written by the victors, or maybe whatever happened was simply too long ago or unremarkable to be recorded.

Razib mentioned that depending on the cluster and the reference samples, that these clusters and groups that we see on our myOrigins maps can range from 1000-10,000 years in age.

relatedness of clusters

The good news is that genetics is blind to any preconceived notions. The bad news is that the software has to fit your results to the best population, even though it may not be directly a fit.  Hopefully, as we have more and better reference populations, the results will improve as well.

my origin components

pca chart

Razib showed a PCA (principal components analysis) graph, above. These graphs chart reference populations in different quadrants.  Where the different populations overlap is where they share common historic ancestors.  As you can see, on this graph with these reference populations, there is a lot of overlap in some cases, and none in others.

Your personal results would then be plotted on top of the reference populations. The graph below shows me, as the white “target” on a PCA graph created by Doug McDonald.

my pca chart

The Changing Landscape

A topic discussed privately among the group, and primarily among the bloggers, is the changing landscape of genetic genealogy over the past year or so.  In many ways I think the bloggers are the canaries in the mine.

One thing that clearly happened is that the proverbial tipping point occurred, and we’re past it. DNA someplace along the line became mainstream.  Today, DNA is a household word.  At gatherings, at least someone has tested, and most people have heard about DNA testing for genealogy or at least consumer based DNA testing.

The good news in all of this is that more and more people are testing. The bad news is that they are typically less informed and are often impulse purchasers.  This gives us the opportunity for many more matches and to work with new people.  It also means there is a steep learning curve and those new testers often know little about their genealogy.  Those of us in the “public eye,” so to speak, have seen an exponential spike in questions and communications in the past several months.  Unfortunately, many of the new people don’t even attempt to help themselves before asking questions.

Sometimes opportunity comes with work clothes – for them and us both.

I was talking with Spencer about this at the reception and he told me I was stealing his presentation.  He didn’t seem too upset by this:)

spencer and me

I had to laugh, because this falls clearly into the “be careful what you wish for, you may get it” category. The Genographic project through National Geographic is clearly, very clearly, a critical component of the tipping point, and this was reflected in Spencer’s presentation.  Although I covered quite a bit of Spencer’s presentation in my day 2 summary, I want to close with Spencer here.  I also want to say that if you ever have the opportunity to hear Spencer speak, please do yourself the favor and be sure to take that opportunity.  Not only is he brilliant, he’s interesting, likeable and very approachable.  Of course, it probably doesn’t hurt that I’ve know him now for 9 years!  I’ve never thought to have my picture taken with Spencer before, but this time, one of my friends did me the favor.

I have to admit, I love talking to Spencer, and listening to him. He is the adventurer through whom we all live vicariously.  In the photo below, Spencer along with his crew, drove from London to Mongolia.  Not sure why he is standing on the top of the Land Rover, but I’m sure he will tell us in his upcoming book about that journey,

spencer on roof

I’m warning you all now, if I win the lottery, I’m going on the world tour that he hosts with National Geographic, and of course, you’ll all be coming with me via the blog!

Spencer talked about the consumer genomics market and where we are today.

spencer genomics

Spencer mentioned that genetic genealogy was a cottage industry originally. It was, and it was even smaller than that, if possible.  It actually was started by Bennett and his cell phone.  I managed to snap a picture of Bennett this weekend on the stage looking at his cell, and I thought to myself, “this is how it all started 14 years ago.”  Just look where we are today.  Thank you Michael Hammer for telling Bennett that you received “lots of phone calls from crazy genealogists like you.”

bennett first office

So, where exactly are we today?  In 2013, the industry crossed the millionth kit line.  The second millionth kit was sold in early summer 2014 and the third million will be sold in 2015.  No wonder we feel like a tidal wave has hit.  It has.

Why now?

DNA has become part of national consciousness.  Businesses advertise that “it’s in our DNA.”  People are now comfortable sharing via social media like facebook and twitter.  What DNA can do and show you, the secrets it can unlock is spreading by word of mouth.  Spencer termed this the “viral spread threshold” and we’ve crossed that invisible line in the sand.  He terms 2013 as the year of infection and based on my blog postings, subscriptions, hits, reach and the number of e-mails I receive, I would completely agree.  Hold on tight for the ride!

Spencer talked about predictions for near term future and said a 5 year plan is impossible and that an 18 month plan is more realistic. He predicts that we will continue to see exponential growth over the next several years.  He feels that genetic genealogy testing will be primary driver of growth because medical or health testing is subject to the clinical utility trap being experienced currently by 23andMe.  The Big 4 testing companies control 99% of consumer market in US (Ancestry, 23andMe, Family Tree DNA and National Geographic.)

Spencer sees a huge international market potential that is not currently being tapped. I do agree with him, but many in European countries are hesitant, and in some places, like France, DNA testing that might expose paternity is illegal.  When Europeans see DNA testing as a genealogical tool, he feels they will become more interested.  Most Europeans know where their ancestral village is, or they think they do, so it doesn’t have the draw for them that it does for some of us.

Ancestry testing (aka genetic genealogy as opposed to health testing) is now a mature industry with 100% growth rate.

Spencer also mentioned that while the Genographic data base is not open access, that affiliate researchers can send Nat Geo a proposal and thereby gain research access to the data base if their proposal is approved. This extends to citizen scientists as well.

spencer near term

Michael Hammer

You’ll notice that Michael Hammer’s presentation, “Ancient and Modern DNA Update, How Many Ancestral Populations for Europe,” is missing from this wrapup. It was absolutely outstanding, and fascinating, which is why I’m writing a separate article about his presentation in conjunction with some additional information.  So, stay tuned.

Testing, More Testing

It’s becoming quite obvious that the people who are doing the best with genetic genealogy are the ones who are testing the most family members, both close and distant. That provides them with a solid foundation for comparison and better ways to “drop matches” into the right ancestor box.  For example, if someone matches you and your mother’s sister, Aunt Margaret, especially if your mother is not available to test, that’s a very important hint that your match is likely from your mother’s line.

So, in essence, while initially we would advise people to test the oldest person in a generational line, now we’ve moved to the “test everyone” mentality.  Instead of a survey, now we need a census.  The exception might be that the “child” does not necessarily need to be tested because both parents have tested.  However, having said that, I would perhaps not make that child’s test a priority, but I would eventually test that child anyway.  Why?  Because that’s how we learn.  Let me give you an example.

I was sitting at lunch with David Pike. were discussing autosomal DNA generational transmission and inheritance.  He pulled out his iPad, passed it to me, and showed me a chromosome (not the X) that has been passed entirely intact from one generation to the next.  Had the child not been tested, we would never have known that.  Now, of course, if you’ll remember the 50% rule, by statistical prediction, the child should get half of the mother’s chromosome and half of the father’s, but that’s not how it worked.  So, because we don’t know what we don’t know, I’m now testing everyone I can find and convince in my family.  Unfortunately, my family is small.

Full genome testing is in the future, but we’re not ready yet. Several presenters mentioned full genome testing in some context.  Here’s the bottom line.  It’s not truly full genome testing today, only 95-96%.  The technology isn’t there yet, and we’re still learning.  In a couple of years, we will have the entire genome available for testing, and over time, the prices will fall.  Keep in mind that most of our genome is identical to that of all humans, and the autosomal tests today have been developed in order to measure what is different and therefore useful genealogially.  I don’t expect big breakthroughs due to full genome testing for genetic genealogy, although I could be wrong.  You can, however, count me in, because I’m a DNA junkie.  When the full genome test is below $1000, when we have comparison tools and when the coverage won’t necessitate doing a second or upgrade test a few years later, I’ll be there.

Thank you

I want to offer a heartfelt thank you to Max Blankfeld and Bennett Grenspan, founders of Family Tree DNA, shown with me in the photo below, for hosting and subsidizing the administrator’s conference – now for a decade. I look forward to seeing them, and all of the other attendees, next year.

I anticipate that this next decade will see many new discoveries resulting in tools that make our genealogy walls fall.  I can’t help but wonder what the article I’ll be writing on the 20th anniversary looking back at nearly a quarter century of genetic genealogy will say!

roberta, max and bennett

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

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That Unruly X….Chromosome That Is

Iceberg

Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

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Genealogy Research

2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

Last year I wrote a column at the end of the year titled  “2012 Top 10 Genetic Genealogy Happenings.”  It’s amazing the changes in this industry in just one year.  It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen.  I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal.  Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention.  To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy!  I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order.  We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007.  This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested.  However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled.  The resolution to this tree shuffling hasn’t yet come out in the wash.  Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined.  That publication has been discussed and anticipated for some time now, but it has yet to materialize.  In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree.  While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company.  Kind of like Jekyll and Hyde.  See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg.  The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs.  This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

http://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

http://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera.  A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA.  One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed.  And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches.  We, as a community, suddenly woke up and started ordering these tests in droves.  A few months later, Family Tree DNA also began offering this type of testing as well.  The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy.  To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base.  For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease.  That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole.  Judy Russell, the Legal Genealogist, discussed this here.  It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent.  Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment.  But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013.  This made me decidedly uncomfortable.  Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal.  I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be.  And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it.  They did not say they won’t sell it.  This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using?  So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22nd cease and desist order) for several years.  The FDA wants assurances that what 23andMe is telling consumers is accurate.  Based on the letter issued to 23andMe on November 22nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc.  They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time.  However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company.  Period.  No excuses.  Something that critically important should be on the agenda of every executive management meeting.   Why?  In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them.  There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation.  The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them.  I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing.  However, in reality, the FDA was only meting out the consequences that 23andMe asked for.  My teenage kids knew this would happen.  If you do what you’re not supposed to….X, Y and Z will, or won’t, happen.  It’s called accountability.  Just ask my son about his prom….he remembers vividly.  Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me.  It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information.  I don’t think so, at least not in this case.  Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone.  The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information.  The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy.  The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be.  The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else.  But 23andMe didn’t, they decided to fight the fight, and we all supported their decision.  But they let us all down.  The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence.  This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA.  Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records.  In other cases, segments that previously matched are disappearing.  One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not.  They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year.  The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

http://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

http://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

http://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

http://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

http://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented.  Myriad Genetics held patents on two BRCA genes that predisposed people to cancer.  The cost for the tests through Myriad was about $3000.  Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995.  Other firms followed suit, and all were subsequently sued by Myriad for patent infringement.  I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything.  Making it stick is yet another matter.  Many firms settle to avoid long and very expensive legal battles.  Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive.  It potentially won’t be settled for a long time.

http://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

http://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results.  This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

http://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year.  More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests.  That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records.  Of course, the operative word here is “was” but that may revive when the FDA issue is resolved.  One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate.  They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies.  This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example.  Unfortunately, not enough people know about GedMatch, or are willing to download their files.  Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward.  For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect.  Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung.  In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

http://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

http://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

http://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

http://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

http://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

http://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

http://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible.  Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time.  This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately.  Multiple steps?  Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob.  Please remember that Rob’s site is free, meaning it’s donation based.  So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available.  GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools.  They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done.  When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release.  All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree.  The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other.  Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent.  And there wasn’t just one, not two, but three instances of this.  What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other.  In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection.  They have found a genealogical cousin, and it MIGHT be the genetic connection.  But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base.  No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions.  The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic.  See the Ethnicity Makeovers section for more on this.  The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising.  Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching.  I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now.  Ancestry has the funds to do development.  They are not a small company.  This is obviously not a priority because they don’t need to develop this feature.  Why is this?  Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed.  I’m reminded of an old joke.  The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet.  They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools.  One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

http://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

http://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable.  We have learned a great deal, and there are many more skeletal remains just begging to be sequenced.  One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA.  Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G.  It will be very interesting as the data bases of fully sequenced skeletons are built and compared.  The history of our ancestors is held in those precious bones.

http://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

http://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

http://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

http://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

http://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

http://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

http://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

http://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

http://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both.  Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this.  Sensationalist reporting, while irritating, can be dealt with if the science is sound.  However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

http://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years.  By this, I mean when citizen scientists work as part of a team on a significant discovery or paper.  Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model.  As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research.  JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication.  Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research.  This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

http://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

http://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

http://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

http://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

http://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other.  But I have to hand it to them, their marketing is amazing.  When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.”  Yea, a new me, based on Ancestry’s erroneous interpretation.  And by reversed, I’m serious.  I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different.  Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time.  My results at 23andMe are relatively accurate.  I saw very little change, but others saw more.  Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results.  In some cases, they are flat out wrong, as with Ancestry, and can be proven.  This does not engender a great deal of confidence.  I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.”  That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

http://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well.  Recently Family Tree DNA has also sponsored a series of free Webinars.  I know that at least one book is in process and very near publication, hopefully right after the first of the year.  We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014.  Genetic genealogy is going mainstream!!!  Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

http://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

http://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference.  All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators.  In addition, everyone who answers questions on a list or board or on Facebook is a volunteer.  Many donate their time to coordinate events, groups, or moderate online facilities.  Many speak at events or for groups.  Many more write articles for publications from blogs to family newsletters.  Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki.  Without our volunteer army, there would be no genetic genealogy community.  Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises.  And if there is one thing this industry is well known for….it’s surprises.  I can’t wait to see what 2014 has in store for us!!!  All I can say is hold on tight….

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2013 Family Tree DNA Conference Day 2

ISOGG Meeting

The International Society of Genetic Genealogy always meets at 8 AM on Sunday morning.  I personally think that 8AM meeting should be illegal, but then I generally work till 2 or 3 AM (it’s 1:51 AM now), so 8 is the middle of my night.

Katherine Borges, the Director speaks about current and future activities, and Alice Fairhurst spoke about the many updates to the Y tree that have happened and those coming as well.  It has been a huge challenge to her group to keep things even remotely current and they deserve a huge round of virtual applause from all of us for the Y tree and their efforts.

Bennett opened the second day after the ISOGG meeting.

“The fact that you are here is a testament to citizen science” and that we are pushing or sometimes pulling academia along to where we are.

Bennett told the story of the beginning of Family Tree DNA.  “Fourteen years ago when the hair that I have wasn’t grey,” he began, “I was unemployed and tried to reorganize my wife’s kitchen and she sent me away to do genealogy.”  Smart woman, and thankfully for us, he went.  But he had a roadblock.  He felt there was a possibility that he could use the Y chromosome to solve the roadblock.  Bennett called the author of one of the two papers published at that time, Michael Hammer.  He called Michael Hammer on Sunday morning at his home, but Michael was running out the door to the airport.  He declined Bennett’s request, told him that’s not what universities do, and that he didn’t know of anyplace a Y test could be commercially be done.  Bennett, having run out of persuasive arguments, started mumbling about “us little people providing money for universities.”  Michael said to him, “Someone should start a company to do that because I get phone calls from crazy genealogists like you all the time.”  Let’s just say Bennett was no longer unemployed and the rest, as they say, is history.  With that, Bennett introduced one of our favorite speakers, Dr. Michael Hammer from the Hammer Lab at the University of Arizona.

Bennett day 2 intro

Session 1 – Michael Hammer – Origins of R-M269 Diversity in Europe

Michael has been at all of the conferences.  He says he doesn’t think we’re crazy.  I personally think we’ve confirmed it for him, several times over, so he KNOWS we’re crazy.  But it obviously has rubbed off on him, because today, he had a real shocker for us.

I want to preface this by saying that I was frantically taking notes and photos, and I may have missed something.  He will have his slides posted and they will be available through a link on the GAP page at FTDNA by the end of the week, according to Elliott.

Michael started by saying that he is really exciting opportunity to begin breaking family groups up with SNPs which are coming faster than we can type them.

Michael rolled out the Y tree for R and the new tree looks like a vellum scroll.

Hammer scroll

Today, he is going to focus on the basic branches of the Y tree because the history of R is held there.

The first anatomically modern humans migrated from Africa about 45,000 years ago.

After last glacial maximum 17,000 years ago, there was a significant expansion into Europe.

Neolithic farmers arrived from the near east beginning 10,000 years ago.

Farmers had an advantage over hunter gatherers in terms of population density.  People moved into Northwestern Europe about 5,000 years ago.

What did the various expansions contribute to the population today?

Previous studies indicate that haplogroup R has a Paleolithic origin, but 2 recent studies agree that this haplogroup has a more recent origin in Europe – the Neolithic but disagree about the timing of the expansion.

The first study, Joblin’s study in 2010, argued that geographic diversity is explained by single Near East source via Anaotolia.

It conclude that the Y of Mesololithic hunger-gatherers were nearly replaced by those of incoming farmers.

In the most recent study by Busby in 2012 is the largest study and concludes that there is no diversity in the mapping of R SNP markers so they could not date lineage and expansion.  They did find that most basic structure of R tree did come from the near east.  They looked at P311 as marker for expansion into Europe, wherever it was.  Here is a summary page of Neolithic Europe that includes these studies.

Hammer says that in his opinion, he thought that if P311 is so frequent and widespread in Europe it must have been there a long time.  However, it appears that he and most everyone else, was wrong.

The hypothesis to be tested is if P311 originated prior to the Neolithic wave, it would predict higher diversity it the near east, closer to the origins of agriculture.  If P311 originated after the expansion, would be able to see it migrate across Europe and it would have had to replace an existing population.

Because we now have sequences the DNA of about 40 ancient DNA specimens, Michael turned to the ancient DNA literature.  There were 4 primary locations with skeletal remains.  There were caves in France, Spain, Germany and then there’s Otzi, found in the Alps.

hammer ancient y

All of these remains are between 6000-7000 years old, so prior to the agricultural expansion into Europe.

In France, the study of 22 remains produced, 20 that were G2a and 2 that were I2a.

In Spain, 5 G2a and 1 E1b.

In Germany, 1I G2a and 2 F*.

Otzi is haplogroup G2a2b.

There was absolutely 0, no, haplogroup R of any flavor.

In modern samples, of 172 samples, 94 are R1b.

To evaluate this, he is dropping back to the backbone of haplogroup R.

hammer backbone

This evidence supports a recent spread of haplogroup R lineages in western Europe about 5K years ago.  This also supports evidence that P311 moved into Europe after the Neolithic agricultural transition and nearly displaced the previously existing western European Neolithic Y, which appears to be G2a.

This same pattern does not extrapolate to mitochondrial DNA where there is continuity.

What conferred advantage to these post Neolithic men?  What was that advantage?

Dr. Hammer then grouped the major subgroups of haplogroup R-P3111 and found the following clusters.

  • U106 is clustered in Germany
  • L21 clustered in the British Isles
  • U152 has an Alps epicenter

hammer post neolithic epicenters

This suggests multiple centers of re-expansion for subgroups of haplogroup R, a stepwise process leading to different pockets of subhaplogroup density.

Archaeological studies produce patterns similar to the hap epicenters.

What kind of model is going on for this expansion?

Ancestral origin of haplogroup R is in the near east, with U106, P312 and L21 which are then found in 3 European locations.

This research also suggests thatG2a is the Neolithic version of R1b – it was the most commonly found haplogroup before the R invasion.

To make things even more interesting, the base tree that includes R has also been shifted, dramatically.

Haplogroup K has been significantly revised and is the parent of haplogroups P, R and Q.

It has been broken into 4 major branches from several individual lineages – widely shifted clades.

hammer hap k

Haps R and Q are the only groups that are not restricted to Oceana and Southeast Asia.

Rapid splitting of lineages in Southeast Asia to P, R and Q, the last two of which then appear in western Europe.

hammer r and q in europe

R then, populated Europe in the last 4000 years.

How did these Asians get to Europe and why?

Asian R1b overtook Neolithic G2a about 4000 years ago in Europe which means that R1b, after migrating from Africa, went to Asia as haplogroup K and then divided into P, Q and R before R and Q returned westward and entered Europe.  If you are shaking your head right about now and saying “huh?”…so were we.

Hammer hap r dist

Here is Dr. Hammer’s revised map of haplogroup dispersion.

hammer haplogroup dispersion map

Moving away from the base tree and looking at more recent SNPs, Dr. Hammer started talking about some of the findings from the advanced SNP testing done through the Nat Geo project and some of what it looks like and what it is telling us.

For example, the R1bs of the British Isles.

There are many clades under L 21.  For example, there is something going on in Scotland with one particular SNP (CTS11722?) as it comprises one third of the population in Scotland, but very rare in Ireland, England and Wales.

New Geno 2.0 SNP data is being utilized to learn more about these downstream SNPs and what they had to say about the populations in certain geographies.

For example, there are 32 new SNPs under M222 which will help at a genealogical level.

These SNPs must have arisen in the past couple thousand years.

Michael wants to work with people who have significant numbers of individuals who can’t be broken out with STRs any further and would like to test the group to break down further with SNPs.  The Big Y is one option but so is Nat Geo and traditional SNP testing, depending on the circumstance.

G2a is currently 4-5% of the population in Europe today and R is more than 40%.

Therefore, P312 split in western Eurasia and very rapidly came to dominate Europe

Session 2 – Dr. Marja Pirttivaara – Bridging Social Media and DNA

Dr. Pirttivaara has her PhD in Physics and is passionate about genetic genealogy, history and maps.  She is an administrator for DNA projects related to Finland and haplogroup N1c1, found in Finland, of course.

marja

Finland has the population of Minnesota and is the size of New Mexico.

There are 3750 Finland project members and of them 614 are haplogroup N1c1.

Combining the N1c1 and the Uralic map, we find a correlation between the distribution of the two.

Turku, the old capital, was full or foreigners, in Medieval times which is today reflected in the far reaching DNA matches to Finnish people.

Some of the interest in Finland’s DNA comes from migration which occurred to the United States.

Facebook and other social media has changed the rules of communication and allows the people from wide geographies to collaborate.  The administrator’s role has also changed on social media as opposed to just a FTDNA project admin.  Now, the administrator becomes a negotiator and a moderator as well as the DNA “expert.”

Marja has done an excellent job of motivating her project members.  They are very active within the project but also on Facebook, comparing notes, posting historical information and more.

Session 3 – Jason Wang – Engineering Roadmap and IT Update

Jason is the Chief Technology Officer at Family Tree DNA and recently joined with the Arpeggi merger and has a MS in Computer Engineering.

Regarding the Gene by Gene/FTDNA partnership, “The sum of the parts is greater than the whole.”  He notes that they have added people since last year in addition to the Arpeggi acquisition.

Jason introduced Elliott Greenspan, who, to most of us, needed no introduction at all.

Elliott began manually scoring mitochondrial DNA tests at age 15.  He joined FTDNA in 2006 officially.

Year in review and What’s Coming

4 times the data processed in the past year.

Uploads run 10 times faster.  With 23andMe and Ancestry autosomal uploads, processing will start in about 5 minutes, and matches will start then.

FTDNA reinvented Family Finder with the goal of making the user experience easier and more modern.   They added photos, profiles and the new comparison bars along with an advanced section and added push to chromosome browser.

Focus on users uploading the family tree.  Tools don’t matter if the data isn’t there.  In order to utilize the genealogy aspect, the genealogy info needs to be there.   Will be enhancing the GEDCOM viewer.  New GEDCOMs replace old GEDCOMs so as you update yours, upload it again.

They are now adding a SNP request form so that you can request a SNP not currently available.  This is not to be confused with ordering an existing SNP.

They currently utilize build 14 for mitochondrial DNA.  They are skipping build 15 entirely and moving forward with 16.

They added steps to the full sequence matches so that you can see your step-wise mutations and decide whether and if you are related in a genealogical timeframe.

New Y tree will be released shortly as a result of the Geno 2.0 testing.  Some of the SNPs have mutated as much as 7 times, and what does that mean in terms of the tree and in terms of genealogical usefulness.  This tree has taken much longer to produce than they expected due to these types of issues which had to be revised individually.

New 2014 tree has 6200 SNPS and 1000 branches.

  • Commitment to take genetic genealogy to the next level
  • Y draft tree
  • Constant updates to official tree
  • Commitment to accurate science

If a single sample comes back as positive for a SNP, they will put it on the tree and will constantly update this.

If 3 or 4 people have the same SNP that are not related it will go directly to the tree.  This is the reason for the new SNP request form.

Part of the reason that the tree has taken so long is that not every SNP is public and it has been a huge problem.

When they find a new SNP, where does it go on the tree?  When one SNP is found or a SNP fails, they have run over 6000 individual SNPs on Nat Geo samples to vet to verify the accuracy of the placement.  For example, if a new SNP is found in a particular location, or one is found not to be equivalent that was believe to be so previously, they will then test other samples to see where the SNP actually belongs.

X Matching

Matching differential is huge in early testing.  One child may inherit as little as 20% of the X and another 90%.  Some first cousins carry none.

X matching will be an advanced feature and will have their own chromosome browser.

End of the year – January 1.  Happy New Year!!!

Population Finder

It’s definitely in need of an upgrade and have assigned one person full time to this product.

There are a few contention points that can be explained through standard history.

It’s going to get a new look as well and will be easily upgradeable in the future.

They cannot utilize the National Geographic data because it’s private to Nat Geo.

Bennett – “Committed to an engineering team of any size it takes to get it done.  New things will be rolling out in first and second quarter of next year.”  Then Bennett kind of sighed and said “I can’t believe I just said that.”

Session 4 – Dr. Connie Bormans – Laboratory Update

The Gene by Gene lab, which of course processes all of the FTDNA samples is now a regulated lab which allows them to offer certain regulated medical tests.

  • CLIA
  • CAP
  • AABB
  • NYSDOH

Between these various accreditations, they are inspected and accredited once yearly.

Working to decrease turn-around time.

SNP request pipeline is an online form and is in place to request a new SNP be added to their testing menu.

Raised the bar for all of their tests even though genetic genealogy isn’t medical testing because it’s good for customers and increases quality and throughput.

New customer support software and new procedures to triage customer requests.

Implement new scoring software that can score twice as many tests in half the time.  This decreases turn-around time to the customer as well.

New projects include improved method of mtDNA analysis, new lab techniques and equipment and there are also new products in development.

Ancient DNA (meaning DNA from deceased people) is being considered as an offering if there is enough demand.

Session 5 – Maurice Gleeson – Back to Our Past, Ireland

Maurice Gleeson coordinated a world class genealogy event in Dublin, Ireland Oct. 18-20, 2013.  Family Tree DNA and ISOGG volunteers attended to educate attendees about genetic genealogy and DNA. It was a great success and the DNA kits from the conference were checked in last week and are in process now.  Hopefully this will help people with Irish ancestry.

12% of the Americans have Irish ancestry, but a show of hands here was nearly 100% – so maybe Irish descendants carry the crazy genealogist gene!

They developed a website titled Genetic Genealogy Ireland 2013.  Their target audience was twofold, genetic genealogy in general and also the Irish people.  They posted things periodically to keep people interested.  They also created a Facebook page.  They announced free (sponsored) DNA tests and the traffic increased a great deal.  Today ISOGG has a free DNA wiki page too.  They also had a prize draw sponsored by the Ireland DNA and mtdna projects. Maurice said that the sessions and the booth proximity were quite symbiotic because when y ou came out of the DNA session, the booth was right there.

2000-5000 people passed by the booth

500 people in the booth

Sold 99 kits – 119 tests

45 took Y 37 marker tests

56 FF, 20 male, 36 female

18 mito tests

They passed out a lot of educational material the first two days.  It appeared that the attendees were thinking about things and they came back the last day which is when half of the kits were sold, literally up until they threatened to turn the lights out on them.

They have uploaded all of the lectures to a YouTube channel and they have had over 2000 views.  Of all of the presentation, which looked to be a list of maybe 10-15, the autosomal DNA lecture has received 25% of the total hits for all of the videos.

This is a wonderful resource, so be sure to watch these videos and publicize them in your projects.

Session 6 – Brad Larkin – Introducing Surname DNA Journal

Brad Larkin is the FTDNA video link to the “how to appropriately” scrape for a DNA test.  That’s his minute or two of fame!  I knew he looked familiar.

Brad began a peer reviewed genetic genealogy journal in order to help people get their project stories published.  It’s free, open access, web based and the author retains the copyright..  www.surnamedna.com

Conceived in 2012, the first article was published in January 2013.  Three papers published to date.

Encourage administrators to write and publish their research.  This helps the publication withstand the test of time.

Most other journals are not free, except for JOGG which is now inactive.  Author fees typically are $1320 (PLOS) to $5000 (Nature) and some also have subscription or reader fees.

Peer review is important.  It is a critical review, a keen eye and an encouraging tone.  This insures that the information is evidence based, correct and replicable.

Session 7 – mtdna Roundtable – Roberta Estes and Marie Rundquist

This roundtable was a much smaller group than yesterday’s Y DNA and SNP session, but much more productive for the attendees since we could give individual attention to each person.  We discussed how to effectively use mtdna results and what they really mean.  And you just never know what you’re going to discover.  Marie was using one of her ancestors whose mtDNA was not the haplogroup expected and when she mentioned the name, I realized that Marie and I share yet another ancestral line.  WooHoo!!

Q&A

FTDNA kits can now be tested for the Nat Geo test without having to submit a new sample.

After the new Y tree is defined, FTDNA will offer another version of the Deep Clade test.

Illumina chip, most of the time, does not cover STRs because it measures DNA in very small fragments.  As they work with the Big Y chip, if the STRs are there, then they will be reported.

80% of FTDNA orders are from the US.

Microalleles from the Houston lab are being added to results as produced, but they do not have the data from the older tests at the University of Arizona.

Holiday sale starts now, runs through December 31 and includes a restaurant.com $100 gift card for anyone who purchases any test or combination of tests that includes Family Finder.

That’s it folks.  We took a few more photos with our friends and left looking forward to next year’s conference.  Below, left to right in rear, Marja Pirttivaara, Marie Rundquist and David Pike.  Front row, left to right, me and Bennett Greenspan.

Goodbyes

See y’all next year!!!

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Family Tree DNA Research Center Facilitates Discovery of Ancient Root to Y Tree

The genetic genealogy community has been abuzz for months now with the discovery of the new Root of the Y tree.  First announced last fall at the conference for DNA administrators hosted by Family Tree DNA, this discovery has literally changed the landscape of early genetic genealogy and our understanding of the timeframe of the origins of mankind.  While it doesn’t make much difference in genetic genealogy in the past few generations, since the adoption of surnames, it certainly makes a difference to all of us in terms of our ancestors and where we came from – our origins.  After all, the only difference between current genetic genealogy and the journey of mankind is a matter of generations – and all of our ancestors were there, and survived to reproduce, or we wouldn’t be here.

One of the important aspects of this discovery is the collaboration of citizen scientists with academic institutions and corporations.  In this case, the citizen scientist was Bonnie Schrack, a volunteer haplogroup project administrator, Dr. Michael Hammer of the University of Arizona, National Geographic’s Genographic Project, and Thomas Krahn and Astrid Krahn, both with the Gene by Gene Genomics Research Center.  Without any one of these players, and Family Tree DNA’s support of projects, this discovery would not have been made.  This discovery of the “new root” legitimizes citizen science in the field of genetic genealogy and ushers in a new day in scientific research in which crowd sourced samples, in this case, through Family Tree DNA projects, provide clues and resources for important scientific discoveries.

Today Gene by Gene released a press release about the discovery of the new root.  In conjunction, Family Tree DNA has lowered their Y DNA test price to $39 for the introductory 12 marker panel for the month of March, hoping to attract new participants and to eliminate price as a factor.  On April 1, the price will increase to $49, still a 50% discount from the previous $99.  Who knows where that next discovery lies.  Could it be in your DNA?

Family Tree DNA’s Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

HOUSTON, March 26, 2013 /PRNewswire/   — Gene By Gene, Ltd., the Houston-based   genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic’s Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years.  This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report “An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree” in The   American Journal of Human Genetics earlier this month.  The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of   the University of Arizona, who currently serves on Gene By Gene’s advisory board, and two of the company’s staff scientists, Drs.Thomas and Astrid-Maria Krahn.

The DNA sample had originally been submitted to National Geographic’s Genographic Project, the world’s largest “citizen science” genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA’s database for genealogical research.  Once in Family Tree DNA’s database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

“This whole discovery began, really, with a citizen scientist – someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products,” said Gene By Gene President Bennett Greenspan.  “While reviewing samples in our database, she recognized that this specific sample was unique and  brought it to the attention of our scientists to do further testing.  The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution.”

The discovery took place at Family Tree DNA’s Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project.  Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company’s Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations.  Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

“Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago,” said Dr. Michael Hammer.  “Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade.  This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise.”

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%.  By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research.  They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd. 
Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic  tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients   worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

SOURCE Gene By Gene, Ltd.

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Projects, Administrators and Expectations

projects fireside

One of the reasons  I wanted to start a blog was to be able to chat about genetic genealogy topics that interest people.  I can tell what’s on your mind by the questions I receive.  For some reason, I’ve received several questions and some complaints about projects and administrators recently, and I think a fireside chat might clarify things a lot.

A few questions arrived in my in-box this past week that I’d like to paraphrase and address.  The first question is from a male and the second from a female.

Question 1 –  I’m in a number of projects.  One of the administrators contacted me and suggested I do some additional SNP testing.  But my surname project administrator has never said anything about this.  If I needed more testing, why wouldn’t my surname project administrator tell me about this?  Is this legitimate?

Question 2 – I’m so upset.  I tried to join the XYZ surname project and the administrator told me that I couldn’t.  Why can’t they be more flexible and realize I’m related to that family?  This project is listed by Family Tree DNA as one I should join, but the administrator won’t let me.

I see confusion, misunderstanding and frustration in both of these questions, for both the participants and the administrators.  I’d like to talk a little bit about projects, why they are formed, administrators, participants and expectations.

Projects

There are four types of projects at Family Tree DNA.

1.  Surname Projects – The earliest projects formed were surname projects.  Those are based on surnames, like Estes, and typically focus on the paternal lines and the Y chromosome and only that specific surname.  Herein lies the first point of confusion.  Because these projects were formed to sort out male family lines of a particular surname, they are typically restricted to males who carry that surname, or sometimes males who match that surname through adoptions of some sort.

Question 2 relates to this problem.  From her perspective, she “should be” allowed to join, because she is related.  But from a scientific perspective, there is no benefit for a female to join a male focused project.  However, from a public relations perspective, it won’t hurt to let her join.  Because women’s surnames change every generations, she could theoretically join all the surname projects for all of her ancestors.  None of it would benefit her for matching etc., but it won’t hurt anything either.

From an administrator’s perspective, having people in a project that can’t advance the goals of the project is simply clutter.  Not only that, but we have to do something with them, categorize them somehow, or leave them ungrouped.  It’s also confusing to people looking at a Y-line project to see other surnames and apparently unrelated or unconnected people.  Conversely, I want people to be happy with genetic genealogy and since she is related and very interested, perhaps she can contribute something in the way of research.angel devil

If this sounds a bit like the angel and devil, one on each shoulder talking to each other…..well, that’s because it is and there is no one right answer.

There is an exception, of course, to what I just said.  It seems there is always an exception to everything.

Family Finder

Recently with the Family Finder tests, more and more administrators are including people in their surname projects who are related to that family but who do not carry the surname because it’s the only way we have today of including Family Finder participants and grouping them.  I have begun to do this myself as a project administrator.

The alternative to this is to begin lineage projects, such as the Johann Michael Miller Descendants project, just for descendants who have taken the Family Finder test.  This is a way to know who they are, to group them so that you can work with their results.  The challenge is that projects are not set up to function this way.  They are set up to display Yline (males) and mitochondrial DNA results, only, or both for a kit, and in this case, the Yline and mitochondrial DNA results are both irrelevant and misleading if they are displayed as valid results.  Administrators are trying to figure out the best way to deal with this.

The work-around I’ve implemented is a grouping within the surname project labeled Family Finder where those who are related but don’t carry the particular surname are grouped.  I am actively recruiting descendants for these groupings as Family Finder holds great promise in finding those elusive unidentified wives, unnamed children…..but I digress.

Here’s what my Crumley project looks like.  You can see that the grouping of Family Finder is entirely irrelevant to the rest of the project, but it’s the best we can do under the current project structure.

Projects 1

2.  Haplogroup Projects – The second type of project formed was haplogroup projects.  These are for both Y-line and mitochondrial.  Some haplogroups have only one project, like mitochondrial haplogroup K, for example.  Others, like mitochondrial haplogroup H or Y-line R have many subprojects.  These projects are a function of who wants to study what – and who is willing to do the work.

Haplogroup projects, by and large, are research projects.  This means that they are arranged quite differently than surname projects.  Surname projects are generally arranged by family and within family, by line, when possible.  Haplogroup projects aren’t concerned with surnames, but with deep ancestry and location, and they are arranged by haplogroup and sub-haplogroup.

A great deal of the progress in understanding haplogroups, their history, migration patterns and the discovery of subgroups has come from the haplogroup projects.  They are very important, make no mistake.  Family Tree DNA is the only place in the world where there are groups of people grouped by haplogroup in public projects.  This is citizen science at it’s best.

The haplogroup Q project had made significant scientific contributions.  You can see that participants are grouped by haplogroup, meaning by SNP.  In some cases, administrators also group participants by the tests needed to further refine their haplogroups.  When you refine your haplogroup with further testing, you also refine your personal story and contribute to science as well.

projects 2

Haplogroup Q groups participants by their haplogroup, above, but when they need additional testing, they are grouped with others who need that test, below.  Why do they need additional testing?  That’s how we learn about haplogroups.  Every additional SNP that you test positive or negative for tells us more about migrations, about where your ancestors lived and what they did.  The power of this isn’t just in one test, but in many tests combined that write the story of our ancestors.

Projects 3

To illustrate the power of many versus one, the mapping function comes to mind.  Each project administrator can enable or disable mapping.  Mapping can be very useful to surname projects, but it’s crucial to haplogroup projects.

Here’s the map for all of haplogroup Q.   Interesting, but all that this really tells us is that it’s pretty universal.  It’s one of two Native American haplogroups, but sub-groups are found throughout Asia and Europe as well.  Want to know if you’re Native?  Then you’ll have to do SNP testing.

Projects 4

The map below shows the oldest known ancestors for those who carry SNP M25.  Looking at this map tells you immediately that these people aren’t Native American.  But if you live in the US and you’re looking for Native ancestry, and you don’t test to this level, you can be left with the erroneous impression that your haplogroup Q result IS Native when it isn’t.

Projects 5

Ah, the power of maps.  Most project administrators enable maps.

The administrators of haplogroup projects are focused very differently than surname project administrators.  This explains the confusion in question 1 about why the surname admin didn’t suggest SNP testing, but the haplogroup project admin did.

Administrators Are Different People

Ok, stop laughting!

This introduces a bit of a different topic and that is what motivates haplogroup administrators.  I mean, let’s face it, why WOULD you volunteer for this?  The answer is simple – passion combined with a smidgen of insanity!

Surname administrators are most often the family genealogist.  We all know them.  We probably are them.  It’s what attracted us to genetic genealogy in the first place.  They may or may not be terribly familiar with the science of genetics, with SNPs, and may or may not be aware of the benefits of SNP testing.  They can, however, recite the details of the original immigrant who arrived in Virginia in 1683 and all their children!

Haplogroup project administrators tend to be scientists.  I’m very fortunate that my co-admin on the haplogroup E1b1a project is a population geneticist.  Yes, they are interested in their surname family, but they are also very focused on their ancient ancestry too – in making that connection between the two and unraveling their story.  To them, haplogroup projects represent opportunities not otherwise available.

This brings us to the third and fourth kinds of projects, lineage and geographic projects, whose administrators are passionate about their project’s subject.

3.  Lineage Projects – Not many of these exist today and most that do are maternal (mitochondrial) DNA lineage projects, such as the descendants of Jane Doe, but I expect as we sort through how to best address lineage with Family Finder tests, lineage projects will become more widely utilized.

4.  Geographic projects, the fourth type of project, are all projects other than above.  These include many special interest projects, such as the Hatteras Island project, the Cumberland Gap project, the Mothers of Acadia project, the Lumbee project, the Lost Colony project, and many more.

These projects are as different as the people who founded them.  Some projects are research projects and some are what I term courtesy projects.

My Cumberland Gap Project is a courtesy project.  This means I formed it to allow people from a particular region to interact and to share.  There is an associated Yahoo group that is very active. I do not have to approve membership. It’s open for all

The Lost Colony projects (and there are three, Y-line, mitochondrial and Family) are research projects.  This means that the membership is restricted to people with specific qualifications.  I don’t do this to be mean, it’s critical to the research goals of the project.  Let me illustrate.  The goal of the Lost Colony Y-line project is to test people with a specific set of surnames (the Lost Colonists surnames) who are found in very early eastern North Carolina counties.  The project description says this and so does the FAQ.  However, 99% of the requests to join the projects say something like this: “I want to compare my results with that of the Lost Colonists.”  Well, guess what folks…..we’re trying to figure out what the Lost Colonists’ DNA looks like too.

Right now, the people in the Lost Colony Y-line project are good candidates to be descended from the colonists.  We’re working to find the colonist families in England to confirm.  However, if I let everyone who wants to compare their DNA to these people into the project, how would we ever know who is a true colonist candidate and who is just a comparer???

People get really upset when I explain this to them.  And I have to say this…I can’t resist….had they read the project background and goals in the first place….they could have saved themselves and me both some time because they would have known that they don’t qualify, and why.  They can support the project in other ways if they are interested.

As a project administrator, my largest frustration by far is with people who don’t read what is available for them.

I finally set up the Lost Colony Family project as a courtesy project for everyone who wants to test and compare their results to each other.  Now there is a place for the frustrated people who can’t join the Lost Colony Y-line or mitochondrial projects.

Some geographic (and surname) projects require pedigree charts and a specific genealogy to join.  For example, both the Lumbee and Cherokee projects have this requirement.  Of course, for a Y-line or mtDNA project, your connection must be through either the paternal line or the maternal line.  We receive requests to join daily from people who are connected, but not by Y-line or mtDNA, and they are terribly frustrated and sometimes quite angry when they are told they aren’t qualified to join.  It’s not a judgment, it’s the way DNA works.

Project administrators are the gatekeepers to be sure the project retains focus and stays on track, which is only fair to the people hoping to learn and gain information by being project members.  Project administrators are not there to simply be difficult to random applicants.  Most of us really dislike having to decline a join request, even if we do explain.  We know that some people simply won’t understand and will be upset or angry with us personally.  Not fun.

This begs the question of why people are trying to join projects that aren’t good fits for them anyway???

Picking the Right Project

The good news and the bad news is that Family Tree DNA tries to help people find relevant projects.  Unfortunately, it’s easy to misinterpret this if you don’t understand the source of this information.  Below is an example.  I’ve entered my surname, Estes, and these are the “associated projects” that are shown.  Many people interpret these to be “recommended” by Family Tree DNA, and they join each and every one of them.  That’s not the goal, nor are all projects appropriate for everyone.

Projects 6

Since I’m a female, none of the Y projects are relevant to me, and neither is the Estes surname project, generally.  However, a new person wouldn’t have the experience to know this, so administrators need to help educate people.  I wrote about this in the article, “What Project Do I Join?”

These projects are on this list because their administrator included the surname in their project profile, meaning they are interested in attracting people, or at least some people, with that surname.  However, they may not be interested in attracting all people with that surname.  If your surname is Estes and your family never set foot in America, then obviously the Cumberland Gap group, focused on the convergence of states Kentucky, Tennessee and Virginia, is not likely to be of interest to you.  Since it is a courtesy project, you can join if you want, but if it was a project like the Lost Colony projects, then you would need to provide some evidence that your family fits the criteria for those the project is seeking.

Ok, so now we’ve talked about the four kinds of projects and how to select the right one for you.  Let’s talk a little bit about what you can expect from an administrator and what they expect from you.

Administrators

First of all, administrators are volunteers.  They receive no compensation of any sort, no discounts, nothing, except they are eligible to attend the annual DNA Conference in Houston.  Eligible to attend does not mean the conference is free.  I don’t bring this up as a complaint, it’s just that there has been a persistent rumor that refuses to entirely die that administrators receive some percentage of sales or compensation of some sort for running projects.  They don’t and never have.

Because they are volunteers, their administration and personal communication styles vary widely.  Many don’t have any co-administrators so have no backup or assistance.  Some are prompt at answering e-mails, some not.  Genetic genealogy and projects are now more than 10 years old.  People age, they die, they get distracted and some just haven’t kept up.  This field moves very rapidly.  If you see a project in trouble, consider offering to help.  If that doesn’t work, notify Family Tree DNA.

There are published guidelines for administrators.  Mostly these deal with privacy and what they can and can’t do.  Most of this is intuitive, but maybe not to everyone so it is in writing.

A good project administrator:

  • Communicates with members, especially if contacted
  • Keeps the project groups current
  • Assists members equally and fairly
  • Is honest, but sensitive, especially in difficult situations like undocumented adoptions (NonParental Events)
  • Is courteous

Sounds kind of like the scouts doesn’t it?

Every project is different.  As an administrator, every time I send group messages to large projects, my e-mail address gets blacklisted as a spammer.  So I set up a Yahoo group for each of these projects, plus have provided my blog address.  Every person receives this information when they join in an automated e-mail which explains explicitly how to join the Yahoo groups and subscribe to my blog.  Still, last week, someone left one of these projects with the comment “no communication.”  Sigh.  Remember what I said about reading???

A few very poorly run projects do exist.  In one case, the administrator does not use Family Tree DNA’s public website, nor a private one, and the only way you can obtain project information is by signing up with My Family.  In another case, the administrator keeps the results private, much like above, but wrote a book about the surname a couple years ago.  That seems to call into question the motivation for the project.  These are sad and frustrating experiences for the participants.

Project admins cannot:

  • Charge a fee to join a project
  • Share or change private information (in fact, the Family Tree DNA website blocks that for admins)
  • Share the identity or personal information of participants without permission
  • Move members from one project to another
  • Use member information for any commercial purpose without authorization
  • Use member information and e-mails for spamming, etc.
  • Use a DNA project to advocate a personal or political agenda

Notify family tree DNA is you feel something is wrong or you have a concern.  Consider offering to help if you notice a project languishing.

Project Members

We’ve talked about projects, why they are different and what you can expect from an administrator, but what do they expect from you as a participant, or potential participant?

1. Courtesy – I’ve met many lovely people through genetic genealogy, but I’ve also met my share of real dooseys.  I see increasingly more “entitlement attitude” relative to projects with join criteria.  In the words of one person who did not meet the criteria, “I deserve to be in this project.  I have the right.”  I strongly suspect that only the nice people who want to learn will have gotten this far in this article, so I won’t expound further:)  For you folks, I don’t need to!

2. READ – Please, please read what is provided relative to the project goals and join criteria.  Now this is a double edged sword, because it means the admin needs to be sure to provide this information and keep it current.  Maybe I need to look at my project verbiage to see if it needs to be bolded, highlighted or in red!

3. Information – If information is requested, especially in a specific format, please comply as best you can.  There is generally a reason for the request.  Most admins don’t want to make extra work for you or themselves.  Not all projects require information.  I ask for a pedigree chart for everyone in my surname projects, and you would be amazed at how many people join the project and then never reply to any of my e-mails – probably about 50%.  This is why some admins have gone to requiring a pedigree chart of some sort before people are allowed to join. And providing a pedigree chart does not mean sending a link to your tree at Ancestry.  At Ancestry, all the admin can do is write everything down, by hand, IF they can find your line of the family in the chart.  Remember, current and recent generations are “private” at Ancestry, so finding the right family line is almost impossible without additional information.  I provide a mini-genealogy form for my project members that has them complete only the direct line directly back from them.  Here’s the one for mitochondrial and the one for Y-line is the same except the word mother is changed to father.

Projects 7

Our Fireside Chat

I hope this has helped dispel some of the confusion surrounding projects, administrators, participants and expectations.  This field started out to be quite simple, with only Y surname projects, but as the field has developed and evolved over the last decade, so have projects and with that has come some level of complexity.  Joining the correct projects for you, your family and your DNA can be one of the most beneficial aspects of genetic genealogy, allowing you to find family and collaborate your research efforts with others.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

2012 Top 10 Genetic Genealogy Happenings

2012 has been a very busy year for genetic genealogists.  There have been lots of discoveries and announcements that affect everyone, now and in the future.  The watchwords for 2012 would be “churn” and “explosive growth.”  Let’s take a look at the 10 most important events, why they are important and what they mean for the future of genetic genealogy.

These items are in what I think are relatively good order, ranked by their importance, although I had a very difficult time deciding between number 1 and 2.

1. The New Root – Haplogroup A00

At the Family Tree DNA conference in November, Michael Hammer, Bonnie Schrack and Thomas Krahn announced that they had made a monumental discovery in the age of modern man known as Y-line Adam.  The discovery of Haplogroup A00 pushes the “birth” of mankind back from about 140,000 years ago to an amazing 338,000 years ago.  Utterly amazing.  The DNA came from an American family from South Carolina.  This discovery highlights the importance of citizen science.  Bonnie is a haplogroup administrator who recognized the potential importance of one of her participants’ DNA.  Thomas Krahn of course is with Family Tree DNA and ran the WTY test, and Michael Hammer is at the University of Arizona.  So you have the perfect blend here of participant, citizen scientist, commercial lab and academia.  What was never thought possible a decade or so ago is not only working, it’s working well and changing the face of both science and humanity.

http://dna-explained.com/2012/11/16/the-new-root-haplogroup-a00/

http://www.haplogroup-a.com./

2. Geno 2.0

Geno 2.0 is the Nickname for the National Geographic Society’s Genographic Project version 2.0.  That mouthful is why it has a nickname.

This amazing project has leveraged the results of the past 7 years of research from the original Genographic project into a new groundbreaking product.  Geno 2.0, utilizing the GenoChip, a sequencing chip created specifically for Nat Geo, offers the most complete Y tree in the world today, expanding the SNP tree from just over 800 SNPs to over 12,000.  They are in essence redrawing the Y chromosome tree as I write this.  In addition, the person who purchases Geno 2.0 will receive a mitochondrial DNA haplogroup assignment.  Over 3300 new mitochondrial mutations were discovered. A brand new anthropological “percentages of ethnicity” report is featured based on over 75,000 Ancestry Informative Markers, many only recently discovered by the Genographic project.  Additionally, participants will receive their percentage of both Neanderthal and Denisovan ancestry based on 30,000 SNPs identified that signal interbreeding between the hominids.  A new website will also facilitate social networking and uploading information to Family Tree DNA.

The wonderful news is that there is a massive amount of new information here that will change the landscape of genetic genealogy.  The difficulty is that we are struggling a bit under the load of that massive amount of information that is just beginning to descend upon us.  It’s a great problem to have!

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/07/31/geno-2-0-wty-mtdna-full-sequence-participants-and-more/

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

http://dna-explained.com/2012/10/16/geno-2-0-the-kit-arrives/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

3. Reconstructed Sapiens Reference Sequence (RSRS)

In July, Family Tree DNA implemented the RSRS that in effect reconstructs the genetic profile of Mitochondrial Eve and bases the comparison of our DNA today against the RSRS sequence as opposed to the Cambridge Reference Sequence (rCRS) created in 1981 that is or was the current standard.  The RSRS is a result of the watershed paper published in April 2012 by Dr. Doron Behar and 8 other authors titled “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root.”  A complementary research website, www.mtdnacommunity.org, accompanies the paper.

http://dna-explained.com/2012/07/14/what-happened-to-my-mitochondrial-dna/

http://dna-explained.com/2012/07/15/the-crs-and-the-rsrs/

http://dna-explained.com/2012/07/16/the-mtdna-community/

http://dna-explained.com/2012/12/02/little-a-big-a-mitochondrial-dna/

4. Full Genome and Exome Sequence Offered Commercially by Gene by Gene

It was announced at the November DNA conference that Gene by Gene, the parent company of Family Tree DNA, through their division titled DNA DTC is offering full genomic sequencing for the amazing price of $5495 for the full genome and $695 for the exome.  This is a first in the consumer marketspace.  Today, this doesn’t have a lot of application for genetic genealogy, but as the price continues to drop, and utilities are built to process the full genomic data, certainly a market and applications will emerge.  This is an important step forward in the industry with a product that still cost 3 million dollars in 2007.

http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/

5. Neanderthal and Denisovan DNA

It’s official – they did it.  Yep, they interbred and well, they are not them anymore, they are us.  Given that everyone in Asia and Europe carries a part of them, but not people from Africa, it would appear that two populations admixed rather thoroughly in Eurasia and/or the populations were small.  The amount of Neanderthal and Denisovan DNA will continue at approximately the proportions seen today in Europe (2% Neanderthal) and Asia unless a significant amount of admixture from a population (Africa) that does not carry this admixture is introduced.  So if you’re European, you carry both Neanderthal and Denisovan DNA.  They are your ancestors.  The good news is that you can find how much of each through  the Geno 2.0 test.  23andMe results give you the percentage of Neanderthal, but not Denisovan.

http://dna-explained.com/2012/08/31/denisovan-dna-tells-a-story/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

6. Ancestral Genome Reconstruction Begins,  Led by Falling Autosomal Prices and the Ability to Fish in Multiple Ponds

2012 has been the year of autosomal testing price reductions and a great deal of churn in this marketspace.  Companies are playing leap-frog with one another.  However, sometimes things are not all that they seem.

Initially, 23andMe opted for an initial payment plus monthly subscription model, which they abandoned for a one time payment price of $299 in early 2012.  Family Tree DNA was slightly less, at $289.

Ancestry led the price war by giving away kits, then selling them for $99, then $129 plus a subscription as an entrance into this market.  However, looking at the Ancestry consent form hints at possible reasons why they were selling below the cost of the tests.  You are in essence giving them permission to sell your DNA and associated information.  In addition, to gain full access to your results and matches, you must maintain some level of subscription to Ancestry.com, increasing the total effective price.

Next came Family Tree DNA’s sale where they dropped their autosomal price to $199, but they were shortly upstaged by 23andMe whose price has now dropped to $99 permanently, apparently, a result of a 50 million dollar investment in order to reach 1 million customers.  They currently have about 180,000.  23andMe has always been in the medical/health business, so their clients have always understood what they were consenting to and for.

Not to be outdone, Family Tree DNA introduced the ability earlier in 2012 to upload your data files from 23andMe to FamilyTree DNA for $89, far less than a second test, which allows you to fish in a second pond where genealogists live for matches.  The challenge at 23andMe is that most of their clients test for the health traits and either don’t answer inquiries or match requests, or know little about their genealogy if they do.  At Family Tree DNA, matches don’t have to answer and allow a match, testers are automatically matched with all participants who take the Family Finder test (or upload their 23andMe results) and testers are provided with their matches’ e-mail address.

Of course, Geno 2.0 was also introduced in the midst of this, in July, for $199 with the additional lollipop of new SNPS, lots of them, that others simply don’t have access to yet.

The good news is that consumers have benefitted from this leapfrogging, I think.  Let’s hope that the subsidized tests at Ancestry and 23andMe don’t serve long term to water down the demand to the point where unsubsidized companies (who don’t selling participants genetic results to others) have problems remaining viable.

Personally, I’ve tested at all of these companies.  I’ll be evaluating the results shortly in detail on my blog at www.dna-explained.com.

The tools provided by most testing companies, plus GedMatch, and multiple ponds to fish in are allowing the serious genetic genealogist to “reconstruct” their genome, attributing segments to specific ancestors.  Conversely, we will also be able to “reconstruct” specific ancestral family lines as well by identifying autosomal segments in multiple descendants.  This new vision of autosomal genetic genealogy will allow much more accurate ancestral line matching, and ancestor identification in the not-so-distant future.

http://www.yourgeneticgenealogist.com/2012/01/family-tree-dna-now-accepting-23andme.html

http://www.yourgeneticgenealogist.com/2012/05/23andme-eliminates-subscription-model.html

http://www.yourgeneticgenealogist.com/2012/10/clarification-of-what-is-available-to.html

http://www.yourgeneticgenealogist.com/2012/12/23andme-receives-50-million-and-drops.html

http://www.thegeneticgenealogist.com/2012/12/26/23andme-and-labcorp-sued-for-patent-infringement/

7. Ethnicity Tests Mature – Minus 1

The good news is that the various ethnicity tests (known as BGA or biogeographical ancestry tests) that provide participants with their percentages of various world populations are improving.  The bad news is that there is currently one bad apple in the card with very misleading percentages – and that is Ancestry.com.

23andMe introduced a new version of their ethnicity product in December, expanding from only 3 geographic categories to several.  The Geno 2.0 test results are just beginning to be returned which include ethnicity predictions and references to several base populations.

Family Tree DNA finally has some competition in this arena where for years they have been the only serious player, although opinions differ widely about which of these three organizations results are the most accurate.  All four are Illumina chip based, using hundreds of thousands of locations, as compared with the previous CODIS type tests which used between 15 and 300 markers and are now outdated.  All companies use different reference populations which, of course, provide somewhat different results to participants.  All companies, except Ancestry, have documented and shared their reference population information.

Outside of these companies, Doug McDonald offers a private analysis and Gedmatch offers a series of BGA comparisons written by third parties.

While this industry continues to grow and mature, I’m thinking about just averaging the autosomal ethnic results and calling it good:)

http://dna-explained.com/2012/07/21/ethnicity-finders/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

http://dna-explained.com/2012/09/09/doug-mcdonald-on-biogeograpical-analysis/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://www.yourgeneticgenealogist.com/2012_12_01_archive.html

8. Finding Your Roots PBS Series with Henry Louis Gates

PBS sponsored a wonderful series in the spring of 2012 hosted by Henry Louis “Skip” Gates, the chair of African American Studies at Harvard.  This series followed a lesser known 2010 series.  The 2012 inspirational series reached tens of thousands of people and increased awareness of genetic genealogy as well as sparked an interest in genealogy itself, especially for mixed race and African American people.  I was disappointed that the series did not pursue the Native American results unexpectedly obtained for one participant.  It seemed like a missed opportunity.  Series like this bring DNA testing for genealogy into the mainstream, making it less “strange” and frightening and more desirable for the average person.  These stories were both inspirational and heartwarming.  I hope we can look forward to similar programs in the future.

http://en.wikipedia.org/wiki/Finding_Your_Roots

CeCe Moore covered this series in March and April on her blog.

http://www.yourgeneticgenealogist.com/2012/03/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_09.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_16.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_23.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_30.html

9. Ancestry, GeneTree and Sorenson

GeneTree, a for profit company and Sorenson, a non-profit company were both purchased by Ancestry.com.  This was about the same time as Ancestry introduced their autosomal AncestryDNA product.  Speculation was that the autosomal results at Sorenson might be the foundation for the new autosomal test comparisons, although there has been no subsequent evidence of this.

Ancestry initially gave away several thousand kits in order to build their data base, then sold thousands more for $99 before raising the price to what appears to be a normalized price of $129 plus an annual ancestry subscription.

While GeneTree was never a major player in the DNA testing marketspace, Sorenson Molecular Genealogical Foundation played an important role for many years as a nonprofit research institute.  There was significant distress in the genetic genealogy community related to the DNA contributed to Sorenson for research being absorbed by Ancestry as a “for profit” company.  Ancestry is maintaining the www.smgf.org website, but no additional results will be added.  Sorenson has been entirely shuttered.  Many of the Sorenson/GeneTree employees appear to have moved over to Ancestry.

The initial AncestryDNA autosomal product offering is poor, lacks tools and the ethnicity portion has significant issues. It’s strength is that many people who test are already Ancestry subscribers and have attached their trees.  So you can’t see how you connect genetically to your matches (lack of tools), but you can see the trees, if they are attached and not marked as private, of those with whom you match.  Ancestry provides “hints” relative to matching individuals or surnames.

Eventually, if Ancestry improves its products, provides tools and releases the raw data to consumers, this may be a good thing.  It’s an important event in 2012 because of the massive size of Ancestry, but the product is mediocre at best.  Ancestry seems unwilling to acknowledge issues unless their feet are held to the fire publicly as illustrated with a “lab error” erroneous match for an adoptee caught by the consuming public and ignored by Ancestry until CeCe Moore exposed them in her blog.  Whether Ancestry ultimately helps or hurts the genetic genealogy industry is a story yet to be told.  There is very little positive press in the genetic genealogy community surrounding the Ancestry product, but with their captive audience, they are clearly going to be a player.

http://www.yourgeneticgenealogist.com/2012/05/ancestrycom-buys-genetree-and-launches.html

http://dna-explained.com/2012/07/12/did-you-test-at-genetree/

http://dna-explained.com/2012/08/30/is-history-repeating-itself-at-ancestry/

http://dna-explained.com/2012/07/18/the-trouble-with-ancestry-com-matches/

http://dna-explained.com/2012/08/14/y-dna-family-tree-dna-vs-ancestry/

http://dna-explained.com/2012/08/16/ancestrys-consent-form-for-ancestrydna-autosomal-test/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://dna-explained.com/2012/10/15/ancestrys-dna-survey/

http://dna-explained.com/2012/10/23/ancestry-to-release-array-data-in-2013/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://www.thegeneticgenealogist.com/2012/06/19/problems-with-ancestrydnas-genetic-ethnicity-prediction/

http://www.yourgeneticgenealogist.com/2012/08/ancestrydna-confusing-relationship.html

http://www.yourgeneticgenealogist.com/2012/08/follow-up-on-ancestrydna-and-adoptees.html

http://www.yourgeneticgenealogist.com/2012/09/23andme-says-no-match-for-adoptees.html

10. GedMatch

GedMatch, www.gedmatch.com, created by John Olson and Curtis Rogers, isn’t new in 2012, but it’s maturing into a tool that is becoming the defacto workhorse of the serious autosomal community.  People who test at either 23andMe or Family Tree DNA download their raw results and other match information and then use a variety of tools at GedMatch to look at results in different ways and using different thresholds. GedMatch is currently working to accept the newly arriving Geno 2.0 data files.  Ancestry does not at this time allow their customers access to their raw data files, so there is nothing to upload. The bad news is that not everyone downloads/uploads their information.  Only the most savvy users, and the download/upload is not always a smooth process, often necessitating several attempts, a magic wand and some fairy dust for luck.

GedMatch is a volunteer effort funded by donations on the GedMatch site.  The magnitude of this project came to light when they needed new servers this year because the amount of traffic disabled their internet service provider.  It may be a volunteer effort, but it has mainstream requirements.  Therefore, while occasionally frustrating, it’s easy to understand why it’s light on documentation and one has to poke around a bit to figure things out.  I would actually prefer that they make it a subscription site, clean up the bugs, add the documentation and take it to the next level.  It would also be very nice if they could arrange something with the major players in terms of a seamless data transfer for clients.  All told, it’s an amazing contribution as a volunteer site.  Hats off to Curtis and John for their ongoing contribution to genetic genealogists!!!

www.gedmatch.com

http://www.legalgenealogist.com/blog/2012/08/12/gedmatch-a-dna-geeks-dream-site/

______________________________________________________________

Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

The New Root – Haplogroup A00

Now that things have calmed down a bit from the whirlwind of the Family Tree DNA Conference, I’d like to write in a little more comprehensive and sane manner about the revelation that we have a new root on the human tree.

I’m referring to the session given by Bonnie Schrack, Thomas Krahn and Michael Hammer titled “In Search of the Root: Discovery of a Highly Divergent Y Chromosome Lineage.”

Bonnie has posted her slides from the presentation as well as her speaking notes on her new haplogroup A webpage.  She contacted me with some corrections to my original Blog posting about that session at the conference as well as provided additional information.  Thank you Bonnie, not just for this info, but for your work with haplogroup A that has been such a key part of this momentous discovery.  This isn’t just a once-in-a-lifetime event, it’s a once-in-the-history-of-mankind event.  Watch the haplogroup A website for more information from Bonnie about this exciting discovery and project.

Understandably, Bonnie, Thomas and Michael are somewhat restricted in what they can say until such time as the resulting academic paper in the works is published.

We all know that male humans arise from a person we call Y-line Adam, just like we call the first woman Mitochondrial Eve.  Before a 2011 paper, it was believed that shortly after Adam, haplogroup A and B were formed about the same time and were brother haplogroups.  Fulvio Cruciani’s 2011 paper, “A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa” reorganized that tree and showed that indeed, haplogroup A formed from the root of all humanity with B forming from haplogroup A.

Cruciani showed his newly organized tree with haplogroup A1b, A1a and then A2, A3 and BT as brother haplogroups.  Cruciani did not use STR data, only SNP data in his study.

A second recent study, also in 2011, “Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages” by Chiara Batini et al, did include some STR marker that matched some of the haplogroup A samples.  Batini did not use SNP testing, so did not realize the potential of these STR samples.  These did not match the new A00 root, but other rare haplogroup A samples in subgroups.

The 7 marker STR samples that did match the new A00 sample were from a private database at the Center for Genetic Anthropology who very graciously worked with Michael Hammer and provided small amounts of those samples for further analysis.

In my conference blog posting, I asked how this discovery was previously missed, and Bonnie Schrack responded as follows:

“The reasons we had never heard about A00 before would be:

  • Very scanty research and sample collection in Africa, in proportion to the size and diversity of the population, compared to Europe and other more developed countries
  • Only recently has large-scale Y sequencing become practical and affordable; Cruciani’s 2011 paper was a breakthrough precisely because for the first time they were able to sequence a few samples on the scale of a WTY, resulting in a lot of new SNPs, and we’ve been able to make even more progress because we had a larger pool of (customer) samples from which I could cherry-pick the most divergent samples, and then our genetic genealogy/anthropology community made it possible to raise enough funds for us to sequence the most important three of them (after that point, Hammer and FTDNA found the other samples and funds).”

Before the WTY program, this type of analysis simply wasn’t being done.  This monumental discovery was a combination of citizen science, the haplogroup A project, an innovative scientific program, the WTY at Family Tree DNA, academic partnership, Michael Hammer’s lab at the University of Arizona and other institutions, along with that crucial public participation.  Without the public participation aspect, the rest would be a moot point.

Haplogroup A research at Family Tree DNA discovered not only one, but two new branches of haplogroup A, one of which was actually a new base root that needed to be inserted before, upstream of, the current root.  The locations where these new branches/roots needed to be inserted required the renaming of the current branches, hence, the newly discovered branch A00 and Cruciani’s branch, formerly A1b, is now A0.

Thomas Krahn’s A00 discovery presentation slides are also available online.  You can tell he’s a scientist from the nature of his presentation.  You can see the actual process of discovery, in essence, what he saw as this new root was unearthed.  It’s fun to walk along with him, even if you don’t understand everything you see.

As part of this process, Thomas also sequenced the DNA of a chimp and a gorilla.  You can see the results at www.ysearch.org for the chimp at 6RCUU, the gorilla at 9ED3A and the new root, A00, at 6M5JA.  You can breathe easy, humans are far distant from chimps and gorillas, but maybe closer to Neanderthals or other archaic humans than we thought.

Update: As of 2019, Ysearch is no longer available.

At the end of Thomas’s presentation, he included the image of a tree with a new root and lots of interesting branches.

Zooming in on the branches, you can see all of the DNA sequencing paraphernalia, microplates, readouts and results.  Maybe there is a little artist buried someplace in Thomas amid those scientific genes!

This work was no small feat, and the significance is mind-boggling.  This new discovery pushed the date of Y-Adam back a whopping 67% in one fell swoop.  Cruciani’s birth age for haplogroup A1b was 140,000 years ago and A00, compared to Cruciani’s sample, falls at 237,000 years ago.

Dr. Michael Hammer at the University of Arizona reanalyzed the haplogroup A tree and root with the new information available, and his new ages are even more amazing.  Cruciani’s A1b/A0 sample is now at 200,000 years old and A00 is at 338,000, with a 98% confidence level.

These dates pre-date all human fossils, although there are some archaic fossils that have been found and dated after this time in neighboring Nigeria.  This new information provides us with glimpses through the keyhole of time into ancient human origins, and begs even more questions that will be answered in time, with more genetic and anthropology research.  We all descend from this common root, and we may all be more closely related to archaic man that we knew.

The A00 participant descends from a former slave family in South Carolina.  The closest matches are found in western Cameroon near the Gulf of Guinea, a prime location in the slave trade.

There appears to be about 500 years between the participant and the samples from Cameroon, an age that speaks to the beginning of the slave trade.

Having worked closely with Lenny Trujillo, the man whose WTY sample provided us with haplogroup-changing and defining information for haplogroup Q, and understanding what a moving experience this journey has been for Lenny, I wondered about how the family involved with this revolutionary discovery must feel.

As luck would have it, I have worked with this family in one of my projects as well, and they contacted me after seeing my blog about the conference.

I asked how they felt, how they were reacting to this history-changing event in which their family was the keystone.  I have extracted pieces from e-mails back and forth, and with the families permission, am sharing what they had to say.  Clearly, without them and their active and supportive participation, this discovery would not have been made.  We all owe them a debt of gratitude.

“I have a B.S. in Mathematics. I love science and learning. I recently retired, but I spent a lot of that time working with research scientists on cutting edge technology and methods so it is very exciting to me to be a part of such a scientific discovery. My family would say I was the right one chosen.  This is the family line I know the most about so I am glad it was this part of my family.

I don’t yet have the formal results from Family Tree DNA concerning the Y-DNA sample they tested in the Walk Through the Y, I did know that the discovery was monumental from some preliminary results from Thomas.

I wanted to see the tie back to Africa, looks like GOD did exceedingly, abundantly more than I could ever ask or think. Just think of how long HE has preserved this Y-lineage just for such a time as this.”

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Family Tree DNA Conference 2012 – Nits and Grits

First things first!  I want to thank Max and Bennett for graciously hosting the 8th Annual Genetic Genealogy Conference in Houston, Texas!  This is actually the 9th year, but a pesky hurricane interfered one year.  Max and Bennett are very generous with their time and resources and heavily subsidize this conference for us.  We’re registering in the photo above.

Georgia Kinney Bopp said it best.  At some point during this amazing conference, someone tweeted an earlier quote from a conversation between Ann Turner and Georgia:

“it’s hard to realize you’re living history while it happens…”

This was ever so true this weekend.  Even my husband (who is not genetic genealogy crazy) realized this.  I’m not sure everyone at the conference did, or realized the magnitude of what they were hearing, as we did have a lot of newbies.  Newbies are a good thing.  It means our obsessive hobby and this industry have staying power and there will be people to pass the torch to someday.

I’ve already covered the Native American focus meeting in an earlier blog.

For those of you who want the nitty gritty play by play as it happened at the conference, go to www.twitter.com and search for hashtag #ftdna2012.  If you want some help with Twitter, I blogged about that too.  Twitter is far from perfect, but it is near-realtime as things are happening.

As always, Family Tree DNA hosts a reception on Friday evening.  This helps break the ice and allows people to put faces with names.  So many of us “know” each other by our e-mail name and online presence alone.

We had a special guest this year too, Nina, a little puppy who was rescued by Rebekah Canada just a few days before the conference.  Nina behaved amazingly well and many of us enjoyed her company. 

Bennett opened the conference this year, and in the Clint Eastwood political tradition, spoke to his companion, the chair named Max.  The real Max, it turns out, was losing his voice, but that didn’t prevent him from chatting with us and answering questions from time to time.

While Bennett was very low key with this announcement, it was monumental.  He indicated that the parent company of Family Tree DNA has reorganized a bit.  It has changed its name to Gene by Gene and now has 4 divisions.  You can check this out at www.genebygene.com.  This isn’t the monumental part.

The new division, DNADTC’s new products are the amazing parts.  Through this new division, they are the first commercial company to offer a full genome sequence test.  The price, only $5495.  For somewhat less, $695, they are offering the exome, which are your 20,000 genes.  Whoever though it would be a genetic genealogy company who would bring this to the public.  Keep in mind that the human genome was only fully sequenced in 2003 at a cost of 3 billion dollars.

The amazing part is that a full genome sequence cost about 3 million in 2007 and the price will continue to fall.  While consumers will be able to order this, if they want, it comes with no tools, as it is focused at the research community who would be expected to have their own analytical tools.  However, genetic genealogists being who and what they are, I don’t expect the research market will outweigh the consumer market for long, especially when the price threshold reaches about $1000.

Bennett also said that he expects that National Geographic will, in 2013 sometime, decide to allow upgrades from Family Tree DNA clients for the Geno 2.0 product.  This will allow those people who cannot obtain a new sample to participate as well.  However, an unopened vial will be required.  No promises as to when, and the decision is not his to make.

The first session was Spencer Wells via Skype from Italy.  Spencer has just presented at two conferences within the week, one in San Francisco and one in Florence, Italy.  Fortunately, he was able to work us into his schedule and he didn’t even sound tired.

Of course, his topic was the Geno 2.0 test which is, of course, run on the new GenoChip.  The first results are in the final stages of testing, so we should see them shortly.  Sometime between the 19th and the end of the month.

This product comes with all new migration maps.  He showed one briefly, and I noticed that one of the two Native Y-lines are now showing different routes than before.  One across Siberia, which hasn’t changed, and one up the pacific rim.  Hmmm, can’t wait for that paper.

The new maps all include heat maps which show frequency by color.  The map below is a haplogroup Q heat map, but it is NOT from the Geno project.  I’m only using it as an example.

Spencer indicated that the sales of the 2.0 product rival those of the 1.0 product and that they have sold substantially more than 10K and substantially less than 100K kits so far.  In total, they have sold more than 470,000 kits in over 130 countries.  And that’s just the public participation part, not the indigenous samples.  They have collected over 75,000 indigenous samples from more than 100 populations resulting in 36 publications to date with another half dozen submitted but not yet accepted.  Academic publication is a very long process.

Nat Geo has given 62 legacy grants to indigenous communities that have participated totaling more than 1.7 million dollars.  That money comes in part from the public participation kits, meaning Geno 1.0 and now 2.0.

Geno 2.0 continues to be a partnership between National Geographic and Family Tree DNAFamily Tree DNA is running all of their samples in the expanded Houston lab.  Also added to the team is Dr. Eran Elhaik at Johns Hopkins University who has developed a new tool, AIMSFINDER, that locates never before identified Ancestral Informative Markers to identify population specific markers.  This is extremely important because it allows us to read our DNA and determine if we carry the markers reflective of any specific population.  Well, we don’t do the reading, they do with their sophisticated software.  But we are the recipients with the new deep ancestral ethnicity results which are more focused on anthropology than genealogy.  Spencer says that if you have 2% or more Native American, they can see it.  They have used results from both public and private repositories in developing these tools.

This type of processing power combined with a new protocol that tests all SNPS in a sequence, not just selected ones, promises to expand the tree exponentially and soon. It has already been expanded 7 fold from 863 branches of the Y tree to 6153 and more have already been discovered that are not on the GenoChip, but will be in the next version.

The National Geographic project will also be reaching out to administrators and groups who may have access to populations of interest.  For example, an ex-pat group in an American city.  Keep this in mind as you think of projects.

Another piece of this pie is a new educational initiative in schools called Threads.

This isn’t all, by any means, on this topic, I really do encourage you to go and use Twitter hashtag #ftdna2012.  Several of us were tweeting and the info was coming so fast and furious that no one could possibly get it all.

The future with Nat Geo looks exceedingly bright.  We have gone from the Barney Rubble age to the modern era and now there is promise for a rosy and as yet undiscovered future.

Judy Russell was next.  I have to tell you, when I saw where they positioned her, I was NOT envious.  I mean, who wants to follow Spencer Wells, even if he’s not there in person.  Well, if anyone was up to this, it certainly was Judy.  For those who don’t know, she blogs as The Legal Genealogist.

Judy is one of us.  That means she actually understands our industry, what drives genealogists and why.  In addition to being a lawyer, she is a certified genealogist and a genetic genealogy crazy too.  Maybe I shouldn’t call a lawyer crazy….well…it was meant as a compliment:)

Judy has the perspective to help us, not just criticize us remotely.  She reviewed several areas where we might make mistakes.  After all, we’re all volunteers coming from quite varied backgrounds.  She suggests that we all put some form of disclosure on our projects explaining what participants can expect in terms of use.  She used the Core Melungeon project as a good example, along with the Fox project.

“The goal of this project is to use DNA to better understand the origins of the Melungeon people, and this will be done by comparing the DNA with other project members, those outside of projects, and will incorporate relevant genealogical and historical research. All participants will be included in the ongoing studies and by joining the project, you are giving consent for your information to be anonymously included in ongoing genetic genealogy research. Your personal identity will not be revealed, but your results will be used to better understand the Melungeons as a people and their ancestors.”

From the Fox project:

“The exact function of these STR markers is not yet known and they have no known medical function but recent research shows they have some sort of regulatory function on the genes. While there is no medical information in these numbers, the absence of a certain few markers near a fertility gene could indicate sterility – something that would certainly already be known.

The results do provide a partial means of personal identification and, for this reason, our haplotype tables list only the FTDNA kit number and the most distant known male line ancestor. Within the project, however, the administrators feel free to disclose identities, particularly when a close match occurs.”

Judy’s stressed that we not tell people that there is no medical information revealed.  Partially, because we’ve discovered in rare cases that’s not true, and partially because we can’t see into the future.

Judy talked about regulation and that while we fear what it might intentionally or inadvertently do to genetic genealogy, it’s important to have regulations to get rid of the snake oil salesman, and yes, there are a couple in genetic genealogy.  They give us all a black eye and a bad name when people discover they’ve been hoodwinked. However, without regulation of some sort, we have no legal tools to deal with them.

Regulation certainly seems to be a double-edged sword.

I hope that Judy writes in her blog about what she covered in her session, because I think her message is important to all administrators and participants alike.  And just to be clear, the sky is not falling and Judy is not Chicken Little.  In fact, Judy is the most interesting attorney I have ever heard speak, and amazingly reasonable too.  She actually makes you WANT to listen, so if you ever get the chance to see one of her webcasts or attend one of her sessions, take the opportunity.

Following the break, breakout sessions began.  CeCe Moore ran one about “Family Finder,” Elise Friedman about “Group Administration” and Thomas Krahn provided the “Walk the Y Update.”  Bennett called this the propeller head session.  Harumph Bennett.  Guess you know which one I attended.  All sessions were offered a second time on Sunday.

Thomas said that they have once again upgraded their equipment, doubling their capacity again.  This gives 4 times the coverage of the original Walk the Y, covering more than 5 million bases.  To date, they have run 494 pre-qualified participants and of those, 198 did not find a new SNP.

There are changes coming in how the palindromic region is scored which will change the matches shown.  Palindromic mismatches will now be scored as one mutation event, not multiples.  Microalleles will able be reported in the next rollout version, expected probably in January.  The problem with microalleles is not the display, but the matching routine.

Of importance, there has not been an individual WTY tested from haplogroups B, M, D or S, and we need one.  So if you know of anyone, please contact Thomas.

Thomas has put his Powerpoint presentation online at  http://www.dna-fingerprint.com/static/FTDNA-Conference-2012-WalkThroughY.pdf

The next session by Dr. Tyrone Bowes was “Pinpointing a Geographical Location Using Reoccurring Surnames Matches.”  For those of us without a genetic homeland, this is powerful medicine.  Dr. Bowes has done us the huge favor of creating a website to tell us exactly how to do this.  http://www.irishorigenes.com/

He uses surnames, clan maps, matches, history and census records to reveal surname clusters.  One tidbit he mentioned is that if you don’t know the family ethnicity, look at the 1911 census records and their religion will often tell you.  Hmm, never thought of that, especially since our American ancestors left the homeland long ago.  But those remaining in the homeland are very unlikely to change, at least not in masse.  I’m glad he gave this presentation, or I would never have found his webpage and I can’t wait to apply these tools to some of my sticky-wickets.

This ended Saturday’s sessions, but at the end of every day, written questions are submitted for that day’s presenters or for Family Tree DNA.

Bennett indicated that another 3000 or 4000 SNPs will be added to the Family Finder calculations and a new version based on reference samples from multiple sources will be released in January.

Bennett also said that if and when Ancestry does provide the raw downloadable data to their clients, they will provide a tool to upload so that you can compare 23andMe and Ancestry both with your Family Finder matches.

Saturday evening is the ISOGG reception, also called the ISOGG party.  Everyone contributes for the room and food, and a jolly good time is had by all.  There is just nothing to compare with face to face communications.

For me, and for a newly found cousin, this was an amazing event.  A person named Z. B. Stroud left me a message that she was looking for me.  When I found her, along with her friend and cousin Revis, she tells me that she matches me autosomally, at 23andMe, and that she had sent me a sharing request that I had ignored.  I am very bad about that, because unless someone says they are related, I presume they aren’t and I don’t like to clutter up my list with non-related people.  It makes comparisons difficult.  My bad.  In fact, I’m going right now to approve that sharing request!!!

I will blog about this in the future, but without spilling too many beans….we had a wonderful impromptu family reunion.  We think our common ancestor is from the Halifax and Pittsylvania County region of Virginia, but of course, it will take some work to figure this out.

I’m also cousins with Revis Leonard (second from left).  We’ve known that for a long time, but Z.B. whose first name is Brisjon (second from right) is new to genealogy, DNA and cousin matching. I’m on the right above.  The Stroud project administrator, Susan Milligan, also related to Brisjon is on the left end.  In the center are Brisjon’s two cousins who came to pick her up for dinner and whom she was meeting for the first time.

But that’s not all all, cousin Brisjon also matches Catherine Borges.  Let me tell you, I know who got the tall genes in this family, and I’m not normally considered short.  Brisjon’s genealogical journey is incredibly amazing and she will be sharing it with us in an upcoming book.  Suffice it to say, things are not always what you think they are and Brisjon is living proof.  She also met her biological father for the first time this weekend!  I’m sure Houston and her 2012 visit where she met so many family members is a watershed event in her lifetime!  She is very much a lovely lady and I am so happy to have met her.  Cousins Rule!

ISOGG traditionally has its meeting on Sunday morning before the first session.  Lots of sleepy people because everyone has so much fun at the ISOGG party and stays up way too late.

Alice Fairhurst, who has done a remarkable job with the ISOGG Y SNP tree (Thank you Alice!) knows an avalanche is about to descend on her with the new Geno 2.0 chip.  They are also going to discontinue the haplogroup names, because they pretty much have to, but will maintain an indented tree so you can at least see where you are.  The names are becoming obsolete because everytime there is an insertion upstream, everything downstream gets renamed and it makes us crazy.  It was bad enough before, but going from 860+ branches to  6150+ in one fell swoop and knowing it’s probably just the beginning confirms the logic in abandoning the names.  However, we have to develop or implement some sort of map so you can find your relative location (no pun intended) and understand what it means.

Alice also mentioned that they need people to be responsible for specific haplogroups or subhaplogroups and they have lost people that have not been replaced, so if anyone is willing or knows of anyone….please contact Alice.

Alice also makes wonderful beaded double helix necklaces.

Brian Swann (sorry, no picture) is visiting from England this year and he spoke just a bit about British records.  He said it’s imperative to learn how they work and to use some of the British sites where they have been indexed.  He also reminded us to check GOONS (Guild of One Name Studies) for our surnames and that can help us localize family groups for recruiting.  He said that you may have to do family reconstructions because to get a Brit to test you have to offer them something.  That’s not terribly different from over here.  He also mentioned that today about half of the British people having children don’t marry, so in the next generation, family reconstruction will be much more difficult.  That too isn’t so terribly different than here, although I’m not sure about the percentages.  It’s certainly a trend, as are varying surname practices even within marriage.

Dr. Doron Behar began the official Sunday agenda with a presentation about the mtCommunity and a discussion of his recently published paper “A ‘Copernican’ Reassesement of the Human Mitochondrial DNA Tree from its Root.”  This paper has absolutely revolutionized the mitochondrial DNA community.  I blogged about this when the paper was first released and our home pages were updated.    One point he made is that it is important to remember is that your mutations don’t change.  The only thing that changes between the CRS (Cambridge Reference Sequence) and the RSRS (Reconstructed Sapiens Reference Sequence)  model is what your mutations are being compared to.  Instead of being compared to someone from Europe who live in 1981 (the CRS) we are now comparing to the root of the tree, Mitochondrial Eve (RSRS) as best we can reconstruct what her mitochondrial DNA looked like.

He also said that when people join the mtCommunity, their results are not automatically being added to GenBank at NCBI.  That is a separate authorization check box.

A survey was distributed to question participants as to whether they want results, when they select the GenBank option, to be submitted with their kit number.  Now, they are not, and they are under Bennett’s name, so any researcher with a question asks Bennett who has no “track back” to the person involved.  About 6000 of the 16,000 submissions today at GenBank are from Family Tree DNA customers.  Dr. Behar said that by this time next year, he would expect it to be over half.  Once again, genetic genealogy pioneers are leading the way!

At these conferences, there is always one session that would be considered the keynote.  Normally, it’s Spencer Wells when he is on the agenda, and indeed, his session was wonderful.  But at the 2012 conference, this next session absolutely stole the show.  Less public by far, and much less flashy, but at the core root of all humanity.

You can’t really tell from the title of this session what is coming.  Michael Hammer with Thomas Krahn and Bonnie Schrack, one of our own citizen scientists, presented something called “A Highly Divergent Y Chromosome Lineage.”  Yawn.  But the content was anything but yawn-material.  We literally watched scientific discovery unfold in front of our eyes.

Bonnie Schrack is the haplogroup A project administrator.  Haplogroup A is African and is at the root of the entire haplotree.  One of Bonnie’s participants, an African American man from South Carolina agreed to participate in WTY testing.  In a nutshell, when Thomas and Astrid began scoring his results, they continued and continued and continued, and wound up literally taking all night.  At dawn’s first light, Thomas told Astrid that he thought they had found an entirely new haplogroup that preceded any known today.  But he was too sleep deprived to be sure. Astrid, equally as sleep deprived, replied with “Huh?” in disbelief.  It’s certainly not a statement you expect to hear, even once in your lifetime.  This is a once in the history of mankind event.

Dr. Michael Hammer confirmed that indeed, they had discovered the new root of the human Y tree.  And not by a little either, but by a lot.  For those who want to take a look for yourself, Ysearch ID 6M5JA.  Hammer’s lab did the age projection on this sample, and it pushed the age of hominid men back by about 100,000 years, from 140,000 years ago to 237,000 years ago.  They then reevaluated the aging on all of the tree and have moved the prior date to about 200,000 years ago and the new one to about 338,000 years ago with a 98% confidence level.  This is before the oldest fossils that have been found, and also before the earliest mitochondrial DNA estimate, which previously had been twice as old as the Yline ancestor.

The previous root, A1b has been renamed A0 and the new root, just discovered is now A00.  Any other new roots discovered will simply get another zero appended.

How is it that we’ve never seen this before?  Well, it turns out that this line nearly went extinct.  Cruciani published a paper in 2012 that included some STR values that matched this sample, but fortunately, Michael Hammer’s lab held the actual samples.  A search of academic data bases reveals only a very few close matches, all in western Cameroon near the Gulf of Guinea.  Interestingly, next door, in Nigeria, fossils have been found younger than this with archaic features.  This is going to cause us to have to reevaluate the source of this lineage and with it the lineage of all mankind.  We must now ask the question about whether perhaps we really have stumbled upon a Neanderthal or other archaic lineage that of course “became” human.  Like many scientific discoveries, this answer only begs more questions.  My husband says this is like Russian tea dolls where ever smaller ones are nested in larger ones.

This discovery changes the textbooks, upsets the proverbial apple cart in a good way, and will keep scientists’ thinking caps on for years.  And to think, this was a result of one of our projects, an astute project administrator (Bonnie) and a single project member.  I wonder what the man who tested thinks of all of this. He is making science and all he thought he was doing was testing for genealogy.  You just never know where the next scientific breakthrough will come from.  Congrats to all involved, Bonnie, Thomas, Michael and to Bennett and Max for having this evolution revolution happen right in their lab!

If I felt sorry for Judy following Spencer, I really felt sorry for the breakout sessions following Thomas, Michael and Bonnie’s session.  Thankfully at least we had a break in-between, but most people were wandering around with some degree of stunned disbelief on their faces.  We all found it hard to fathom that we had been among the first to know of this momentous breakthrough.

I had a hard time deciding which session to attend, CeCe’s “Family Finder” session or Elise’s.  I decided to attend Elise’s “Advanced Admin Techniques” because I work with autosomal DNA with my clients and I tend to keep more current there.  Elise’s session was great for newer admins and held tips and hints for us old-timers too.  I realized I really need to just sit down and play with all of the options.

There are some great new features built in that I’ve never noticed.  For example, did you know that you can group people directly from the Y results chart without going to the subgrouping page?  It’s much easier too because it’s one step.  However, the bad news is that you still can’t invite someone who has already tested to join your project.  Hopefully that feature will be added soon.

The next session was “A Tale of Two Families” given by Rory Van Tuyl detailing how he used various techniques to discern whether individuals who did not show up as matches, meaning they were beyond the match threshold, were actually from the same ancient family or not.  Rory is a retired engineer and it shows in his attention to detail and affinity for math.

We always tell people that mutations can and do happen at any time, but Rory proved this.  He ran a monte-carlo simulation and showed that in one case, it was 50 generations between mutations, but in others, there was one mutation for three generations in a row.  Mutations by no means happen at a constant rate.  Of course, this means that our TIP calculator which has no choice but to use means and averages is by definition “not calibrated” for any particular family.

He also mentioned that his simulation shows that by about 150 generations, there are a couple of back mutations taking place.

The final session before the ending Q&A was Elliott speaking about IT, which really translates into new features and functions.  Let’s face it, today everything involves IT.

Again, I was having trouble typing fast enough, so you might want to check the Twitter feed.

They added the SNP maps (admins, please turn them on) and the interactive tour this year.  The tour isn’t used as much as it should be, so everyone, encourage your newbies to do this.

They have also added advanced matching, which I use a lot for clients, but many people didn’t realize it.  So maybe a quick tour through the website options might be in order for most of us.

They are handling 50 times more data now that a year ago.  Just think what next year will bring.  Wow.

They are going to update the landing page again with more color and more visible options for people to do things.  I hope they prompt people through things, like oldest ancestor mapping, for example.  Otherwise, if it isn’t easy, most don’t.

They are upgrading Population Finder and the Gedcom viewer.  They are adding a search feature.  Thank you!!  Older Gedcome will still be there but not searchable.

But the best news is that they are adding phasing (parent child) and an advanced capability to “reconstruct” an ancestor using more distant relatives, then the ability to search using that ancestral profile against Family Finder.  Glory be!  We are finally getting there.  Maybe my dreaming big wasn’t as far away as I thought.

They will also remove the 5 person autosomal download restriction and the “in common with” requirement to see additional information.  All good news.  They are also upgrading the Chromosome browser to add more filtering options.

They are also going to offer a developer “sandbox” area for applications.

The final Q&A session began with Bennett saying that their other priorities preclude upgrading Y search to 111 markers.

They are not planning to drop the entry level tests, 12 or 25 markers or the HVR1. If they do, lots of people will never take that plunge.  I was very glad to hear this.

And by way of trivia, Family Tree DNA has run more than 5 million individual tests.  Wow, not bad for a company that didn’t exist, in an industry that didn’t exist, 12 years ago!

It’s an incredible time to be alive and to be a genetic genealogist!  Thank you Family Tree DNA for making all of this possible.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

What the Heck is WTY?

Update: The WTY has been superceded by the Big Y test, but I’m leaving this article for historical continuity.

What the heck is WTY….and why do I care?

One of the reasons I started a blog is to continue what I do for my clients when I write their DNA reports. I make DNA understandable and fun for the normal air-breathing genealogist.

The past few days has been a whirlwind of information and announcements, some which tend to leave folks who don’t have a lot of experience in the dust.

For that, I do apologize.  However, I’d like to tackle a much easier topic now, and that’s the WTY test.  What is it and why is it so important?

WTY is short for Walk the Y, as in walk down the Y chromosome.

The tests we all order and love, at Family Tree DNA, that would be the 12, 25, 37, 67 and 111 marker tests, tell us about genealogy – who we are related to in the past several hundred years.

Deeper ancestry, anthropological in nature, a line I draw about the time when surnames were being adopted, is different and little information of that nature is exposed by the STR (short tandem repeat) genealogy markers.

By the way, short tandem repeat means those locations in our DNA that are prone to develop repeated sequences.  Think of them as genetic stutters.  They are important to us as genealogists, because on the Y chromosome, we count the number of those stutters and that is the marker value reported.

For example, below, we see that for marker 393, we have a value of 13.  That means there were 13 repeats of the same sequence.  Obviously, combining all of these sequences, or marker values, together creates our own genealogical genetic profile or fingerprint.  This, of course, is what we use to compare to others to see whom we match.

However, deep ancestry, identified by our haplogroup, is determined by a different kind of mutation, called a SNP, a single nucleotide polymorphism.

These are mutations that happen in only one location, and they are considered to be once in the lifetime of man mutations.  In actuality, these mutations sometimes happen independently in different haplogroups, but the cumulative sequence of SNP mutations defines our haplogroup.

You can see, for example, below, a haplotree from a Family Tree DNA client’s results page.

This person tested positive for the light green SNP, M417.  The plus means that they have this specific mutation.  In his case, this is his terminal SNP, meaning the one furthest down the tree that defines his haplogroup, as we know it today.  That would be R1a1a1.

The SNPs shown in red, below M417 are ones that he has also been tested for, but does not have, so he knows he is not a member of those haplogroups.  These are shown with a minus sign, such as M56-.

Now for the problem that WTY has been helping to solve.

If your STR markers take you back about 500 years, in round numbers, and your haplogroup tells you where your ancestors were between 3000 and 4500 years ago, in this case, where were they in-between?  What were they doing?  Where did they live and how did they get from where they were 4500 years ago to where you find them 300 or 400 years ago, if you’re a lucky genealogist and can go back that far?

There is a significant gap in the timeframe between STR genealogy markers and haplogroup SNP markers.  Finding additional SNPs will eventually close the gap between STR genealogy markers and haplogroups.  We will have a complete timeline of our ancestors.  In some cases, we’re even finding family-specific SNPs, known as “personal SNPs.”  How cool is that?  A new haplogroup is born in your family!

Did you notice on the tree above that some of the SNP markers begin with L?  Every SNP discovered is prefaced with a letter that tells people which lab or university discovered the SNP.  The L SNPs have all been discovered at Family Tree DNA’s Genomics Lab in Houston, Texas, run by Thomas Krahn.  They are the product of the WTY discovery process.

When there is reason to believe that a SNP might be lurking undiscovered in the DNA of a person or a group, then the WTY becomes an option.  Generally, the clue would be STR markers that are significantly different than any previously seen, or part of a small and quite unusual cluster.

Today, we test all of the known downstream SNPS, the ones in red above, and then if none are found, we would apply to Family Tree DNA to do a WTY test.  This test is quite labor intensive.  In essence, they manually look at between 450,000 and 500,000 positions to see if they spy any new mutations.

If they do, they begin the SNP naming process and the process of getting the SNP officially added onto the tree.  You can see the most current haplotree (Y SNP tree) at the ISOGG site.  Because of the long naming and authentication process, sometimes trees at different locations aren’t quite in sync.  The ISOGG tree, maintained by volunteer genetic genealogists, has become what most people look to and use as the gold standard today.

In any case, this process is how new SNPs are discovered.  The Geno 2.0 project includes 12,000 SNPs for the Y chromosome, an exponential growth from the current 862, or so.  At least some of these SNPs were discovered at Family Tree DNA, as a result of savvy project administrators and others who are familiar enough with DNA results to suspect that a new SNP might exist, and who advocated with the tester and Family Tree DNA for WTY testing.

Hopefully, you now understand better about the WTY and why WTY tests are so critically important.

How might you know if you or a family member is a good candidate?

If you have tested to 67 or more markers and have no matches, you may be a candidate.  You would need to do a deep clade test, which tests all relevant downstream SNPS at this point.  In the past this has been the Deep Clade test, but today it would be the Geno 2.0 test.  If you think you might be a candidate, you’ll want to work with your haplogroup administrator to see if there are any experimental SNPS to test for after the deep clade/Geno 2.0 is completed.

The WTY is the perfect example of collaborative citizen science.  Participants fund part of the testing, haplogroup administrators identify good candidates, Family Tree DNA underwrites part of the testing fee and of course performs the test, and everyone benefits.  Before you know it, you’ve got 12,000 new SNPs combined with new technology that promises to do more than we’ve ever dared dream before!!!

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