Goodbye to a 30 Year Friend – PAF to RootsMagic

When I first installed PAF back in the 1980s on my old CPM machine, everyone at the local Family History Center was cautiously curious. I worked in the computer industry and they wanted to see how this new-fangled computer software thing worked.

I loved PAF. It allowed me to organize my information.  I probably didn’t use it exactly correctly, because I typed everything into the notes field which was, thankfully, of unlimited size.

I later discovered I should have been using source fields and such, but I’m not even sure there was a source field initially.

When the Mormon Church discontinued support for PAF in 2013, I was greatly saddened, not because the software had been free and I was now going to have to purchase software, but because I knew that software so well and was so comfortable using it. I didn’t want to have to take the time to evaluate and learn anything else.  To me, software is only a tool and the tool I had was fine.

So, I’ve used it for the past 2+ years unsupported, but I know full well that with the advent of new operating systems, one day it’s not going to work anymore and I surely don’t want to have a crisis and have to adapt on top of a crisis situation.  I knew it was better to be proactive.

Recently, I had a forced upgrade to Window 10 with the purchase of a new laptop, and I need my genealogy on my laptop. I mean, you never know when you’re going to need to refer to your genealogy!  If you think I’m kidding, I met one my closest cousins, Kathy, at a client site about 15 years ago (how can it have been that long???) completely by accident and yes, we compared our family trees on my laptop.  I just remember wondering if our unknown “cousinhood” was the reason we got along so well.  We went on to become and remain very close friends.

I evaluated several software packages, but it came down to two, Legacy and its competitor, RootsMagic.  I selected RootsMagic for a few reasons.

  1. I asked several people with large data bases if they had problems when they converted. Specifically, anyone with large notes files, if the entire notes file came over, or they lost data. The reviews were unanimously and overwhelmingly positive for RootsMagic, with data bases far larger than mine with its 37,000+ records.
  2. RootsMagic had everything that I wanted but without being overly complex, cluttered or busy.
  3. RootsMagic was intuitive to use.
  4. RootsMagic felt very PAFlike to me in terms of screen layout and functions, just PAF on steroids.
  5. RootsMagic offers a “RootsMagic for PAF Users Guide” which made me feel better.

paf bye

So, here’s my last look at PAF on my computer. I feel a bit guilty, like I’m abandoning an old friend or an old car that has served me so well for a very long time.

paf tombstone

I imported my file into RootsMagic which took an amazingly short time, so short that I was sure there was a problem. There wasn’t.  I checked notes, they were there.  Now obviously I can’t check all 37,000+ records individually, but some of the larger ones are there and intact – all of the records I checked were fine.

rootsmagic hello

Here’s my first look at the equivalent screen in Rootsmagic. I was very pleased to see that my all-caps first names for my direct line ancestors had come over as all-caps.

And guess what, the first I thing I see to do is something that has been bugging me forever. I discovered that my grandparents had a child that died, but when I added the child, PAF put them at the end of the list.  Yes, that could have been changed, but it wasn’t easy nor intuitive, so I never did.

rootsmagic rearrange children

Well, it’s easy and intuitive now and I fixed it with ‘move up’ and ‘move down’ arrows. Yes, I like this software already.  Little triangles pop up, discretely, if there is something you need to look at.  I clicked on the one for this child.

rootsmagic problem list

It told me I hadn’t added the sex for the child, and I hadn’t because I don’t know the sex of the child.  Thank goodness not many of my entries have problem lists, and the ones that do are short.

But hey, look, I’m already using two new features I didn’t have before.  I think I like RootsMagic.

Next, I printed RootsMagic for PAF Users which equates PAF functions to RootsMagic functions in the lingo of the PAF user, and went through this document step by step.

All in all, less than an hour and I’m up and running and feeling confident. I have changed the children’s birth orders in several families, edited a few things and now all I have to do is to keep myself from going back and looking at PAF, out of habit.  Goodbye really needs to be goodbye.  Goodbye old friend!

Charting Companion from Progeny Software

I’ve got to tell you, I love Charting Companion.  I’ve used it for many years now with my PAF software, although it is compatible with virtually every genealogy software program on the market, as well as Family Search.

Recently, the owners updated the software to include a wonderful new feature where appropriate on reports.  They map and color the X chromosome inheritance path.  I did have to upgrade my Charting Companion software, but at $29.95, it certainly won’t break the bank….and it’s worth every penny.

If you’re jumping up and down, doing the happy dance and hollering “WooHoooo,” I certainly understand.  I did the same thing.

This option is available for all charts that have ancestors: Ancestor, Fan, Hourglass and Bowtie.

There are several ways to select charts in this software, but the most comprehensive selection in one place is on the menu bar.

chart companion

Select the type of chart you want to produce.  Click through the various options and select the information you want to include on your chart.

To select the X-chromosome option, the user simply selects “X-chromosome” in the Color option tab:

Ancestor chart options

When finished, click preview to be sure it’s what you want.  Here are a couple examples of my reports with the X chromosome selected.

X with Fan

x fan

This fan chart can’t reasonably be made much larger than this, in terms of generations.  If you need more, shift to the Ancestor chart which can span pages.  I would suggest providing at least 10 generations when sending information to people you match on autosomal DNA tests.  I include 12 generations to at least get every ancestor off of US soil and back into the old country – or as many as I can get off of US soil:)

Ancestor – X Pedigree

x pedigree 1

x pedigree 2

I love these X reports.  When you match someone on the X, you can send them one of these and they can visually see which of your lines are available for X matching.  These, utilized in conjunction with the regular Charting Companion Pedigree Chart report are a powerful combinational tool.

My Favorite Report

I generate a pedigree chart for each “side” of my tree, Moms and my Dad’s.  Often, based on my matches, I immediately know which side the new match is from, so I only send them the relevant information.  If need be, I just send both files.

I’ve been a long time user of this software.  I do have a tree at Ancestry but I hate to refer anyone there.  Conversely, I hate receiving links to Ancestry trees.  I much prefer Rootsweb/WorldConnect.

All trees have some inherent problems.  First, how would a match even begin to know what surname to search for or where to find it on my tree.  Secondly, every time I view someone’s tree, Ancestry does me the favor of forever mailing me after that with their updates and such by attaching their tree to my account.  I hate that.  And yes, I know I can go in and one-by-one, undo Ancestry’s favor, but why should I have to do that?  And I certainly don’t want to make anyone else do that either.  Sending a pedigree chart provides them with only the relevant information without being invasive, problematic or being a “forever” thing with an attached tree.  We’re only looking here, not getting married:)

So, I send a pedigree chart of 12 generations in a pdf file with an index at the end.

If you select 4 generations per page, each item will have the associated location information.  5 generations per page makes the 5th generation default to only date information, meaning they won’t be able to see locations, so don’t do that.

Select the index option to add the index at the end.  This makes it easy for people to skim quickly for surnames that look familiar.

Lastly, when you have your selection in order, you can preview, and then the “publish” button saves this to a file on your system.

Please note that if you include submitter information, it includes everything including your address and phone number in the lower left hand corner.  I do not include that information in the pdf file I send to matches.  I wish the software had a submitter name/e-mail only option.  That’s it though, my only suggestion for this software.  I love it!

pedigree chart

Chart above, index below.

pedigree index

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.

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

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

https://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.

https://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/

https://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/

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

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

https://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.

https://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/

https://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.

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

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

https://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.

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

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

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

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

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

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

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

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

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

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

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

https://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.

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

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

https://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.

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

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

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

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

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

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

https://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

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

https://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.

https://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.

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

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

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

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

https://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.

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

https://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

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

https://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.

https://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

https://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….

One Chromosome, Two Sides, No Zipper – ICW and the Matrix

ZipperThe questions I’ve received most often since the release of the new Family Finder Matrix from Family Tree DNA has to do with matches.  Specifically, what the “In Common With” feature is telling you versus what the Family Finder “Matrix” is telling you and how to utilize all of this information together.  At the bottom of this confusion is often a fundamental lack of understanding of how matching occurs and what it means in different contexts.

Let’s talk about this, step by step.

The “in common with” function (called triangulation for a few weeks, but now labeled “run common matches” ) shows you every person that you and one of your matches, match with in common.  I’ll be running this option for my matches with cousin David, shown below.

zipper 1

Here’s an example of my matches in common with my cousin, David.

Zipper 2

The Family Finder Matrix takes this information a bit further and shows you whether or not the people involved with this match, match each other as well.

In this case, I happen to know that my cousins Harold, Carl and Dean will match each other on my father’s side, as will my cousin David.  Warren doesn’t have firm genealogy, but from this, we can tell that he is indeed connected to this family group because he matches me, David, Harold and Carl, but not Dean and not Nova.  We have no idea how Nova connects to this line, if she does.  Notice that Nova does not match any of the other people in this group in the matrix below.  That means that my and David’s common ancestor with her is likely not from this same ancestral line shared by Harold, Carl and Dean.

zipper 3

From this point forward, I would drop back to my trusty downloaded full match spreadsheet that I maintain to see if indeed any of these people match me and my known cousins on the same segments.  If so, that confirms a family/ancestor relationship.   On the snipped from my spreadsheet below, you can see that Warren indeed matches both Buster and David and I, but not on the same segments.  Nova didn’t match any grouping on the same segments.  However, Buster and David both match me on the same portion of chromosome 19, so this confirms that we do share a common ancestor.  In this case, we also know, from our genealogy that the common ancestor is Lazarus Estes and wife, Elizabeth Vannoy.  Based on our multiple cousin matches, we can say that Warren is somehow connected to this line, but we can’t say how.

Zipper 4

I’ve had comments like “I have everything I need on my spreadsheet – I can see where all of my matches match me.”  And indeed, you can, but it’s not everything you need.  Here’s why.

Without additional information, you can’t tell, by just looking at your spreadsheet whether two people who match you on the same segment are matching on your Mom or Dad’s side.  For example, above, I know that both David and Buster are from my Dad’s line, but if I didn’t know that, one of them could be from Mom’s line and one could be from Dad’s, and while they are both related to me, on the same chromosome, they would, in that case, not be related to each other.  So, my spreadsheet of matches tells me clearly THAT people match me, and where, but it doesn’t tell me HOW or on which side.  For that, I need additional tools like ICW, the Matrix and plain old genealogy research.

This is the fundamental concept of matching and in a nutshell, why it’s so difficult.

Every Chromosome Has Two Sides

There are two sides to every chromosome, Mom’s side and Dad’s side.  Except nature has played a cruel trick on us and not installed a zipper.  There are no Mom and Dad labels.  There is no dividing that DNA or those matches in half magically, except by determing who they match, and how they do or don’t match each other.

When we match ourselves against our parents, for example, we then know immediately which half of our DNA came from which parent, but if you don’t have any parents available to match against, then you have to use genealogy or cousin matches to figure that out.

I talk about that in the Chromosome Mapping aka Ancestor Mapping article.

I’m going to use spreadsheets as examples here.  It think they are easier to see and understand, plus, I can manipulate them easily to reflect different situations.

Example 1 – The Very Basics of Matching

At each DNA location, or address, you have two alleles, one from each parent.  These alleles can have one of 4 values, or nucleotides, at each location, represented by the abbreviations T, A, C and G, short for Thymine, Adenine, Cytosine and Guanine.  That’s it, you’re done with all the science words now, so keep reading:)

On any given chromosome, from locations 1-20, you have the following DNA, in our example.

From Mom, you received all As and from Dad, all Cs.  You know that because I’m telling you, but remember, the matching software doesn’t know that because there is no zipper in your DNA.  All the software sees are that you have both an A and an C in location 1 and either an A or C is considered a match.

Zipper 5

In fact, this is what the software sees.  Be aware that in this case, AC=CA.

Zipper 6

Easy so far, right?

Example Two – Mom’s Known Cousin and Dad’s Known Cousin

Now you have two cousins, Mary and Myrtle.  You know, from having known them all of your life and sharing lots of Thanksgiving turkey that they are your family and you know clearly which side of your family they descend from.  Both of your cousins, Mary and Myrtle match you at the same locations on this chromosome, from 5-15.

But Mary is your mother’s cousin, and Myrtle is your Dad’s cousin.  So even though they both match you on the same exact chromosome and the same location, they do not match each other.  Well, let’s put it this way, if they also match each other, then you have an entirely different family genetic genealogy problem, called endogamy, and yes, you might be your own grandpa…but I digress.  But we’re going to assume for this discussion that your mother and father are not related to each other and do not share common ancestors.

Zipper 7

Still easy, right?

Example Three – An Unknown Cousin

Next, we have Martha.  You don’t know Martha, and you don’t know how she is related, but she obviously is.  Martha matches you, but she does not match Myrtle at all, and she doesn’t match Mary on enough overlapping chromosomes to be considered a match to her.  You can see their common match here between Mary and Martha in location 5.  In this case, as it turns out, Martha IS a cousin to Mary on Mom’s side, but we can’t tell that from this information because they don’t match in enough common locations to be above the matching threshold.  With this information, you can’t draw any conclusions.  You will have to wait to see who else Martha matches and look on your spreadsheet to see if Martha matches any of your known cousins and you on common segments which would confirm a common ancestor.  Your download spreadsheet will contain much more detailed information because once you match on any segment above the match threshold of about 7.7cM (plus a few other factors,) all matching segments of 1cM or above are downloaded – so you have a lot of information to work with.

But using both the ICW and matrix tools, Mary might cluster with other cousins on Mom’s side which would provide us with clues as to her relationship.  In fact, the first thing I’d do is to run an ICW with Mary and then utilize the Matrix tool to further define those relationships.

Zipper 8

Still not difficult.

Example Four – A “False Match”

Next we have Jeremy who is also a match to you.

Zipper 9

If you look at how Jeremy matches, you can see that he is actually matching on both sides, Mom’s and Dad’s side, but randomly.  Technically, he is a match to you, because he does match one or the other of your nucleotides at each location, A or C, but without a zipper, we have no idea HOW that DNA is divided in you between Mom and Dad.  In other words, the software doesn’t know that Mom was all A and Dad was all C, unless we’ve phased the data against your parents AND the software knows how to utilize that information.

However, if your parents are one of your matches, you can immediately see which side the match falls on, if either.  In this case, Jeremy doesn’t fall on either side because he is simply a circumstantial match, also known as a match my convergence or a false match.  This is also called IBS, or identical by state, as opposed to IBD, identical by descent.  The smaller the segment you show as a match, especially if there is no clustering, the more likely the match is to be IBS instead of the genealogically desirable IBD.

When people ask how someone can match a child but not a parent, this is the answer.  He matches you on 11 segments, circumstantially, but he only matches your parents on 5 and 6 segments, respectively, which often (but not always) puts him under the matching threshold.  Jeremy may also match Mary, depending on the thresholds.

This is also how someone can match in the “in common with” tool, but not be a match to anyone on the match list in the Matrix.  In fact, this is the power of these multiple tools.

This also doesn’t mean this match is entirely useless, because you DO match.  It may simply not be relevant genealogically.  In “The Autosomal Me” series, I’ve utilized very small match segments that in fact very probably ARE reflective of a common population and not of recent ancestry.  In my Native American research, this is exactly what I was looking for.  You may not be able to utilize this information today, but don’t entirely discount it either.  Just set it aside and move on to a more productive match.

Example Five – Common Matches, Different Ancestors

This situation provides clues, but no proof.

Mary and Joyce both match me on Mom’s segments, but they do not match each other.  They don’t match me on the same segments, so this indicates that they are probably from different ancestors in my Mother’s lines.  As more matches appear, the clusters of people and their genealogy will make this more apparent.

In order to determine which ancestors, I’ll need to work on the genealogy of both Mary and Joyce and see who else they also match on the same segments.  Sometimes the secret of the genealogy match is in the genealogy research or descent of your matches.

Zipper 10

Example Six – Clusters of Cousins

In this example, no one matches Dad, so he’s just out for now.  Susie and Mary match mom on the same segment, which proves that the three of these people share a common ancestor.  Mom and Joyce match each other too, but Joyce doesn’t match Mary and Susie, so they won’t cluster together on the matrix.  However, on the ICW tool, all three women, Joyce, Mary and Susie will match me and Mom.

Using the ICW tool if I were to ICW with Mom, you would see this list:

  • Joyce
  • Mary
  • Susie

The question then becomes, are Joyce, Mary and Susie related to each other, or not.  If so, and to me and Mom, then that indicates a common ancestor within the match group, like me, Joyce and Mom.  The second group doesn’t match the first group – me, Mary, Mom and Susie.  Using these tools together, these people clearly fall into two match groups, the green and blue on the spreadsheet below.  But remember, the match routine doesn’t know which side your As and Cs came from.  All it knows is that you match these people.  But based on these groups and my download spreadsheet common segment matches, I can tell that I’m working with two ancestral lines.

Zipper 11

My matrix for these people would look like this:

Zipper 12

My master matching spreadsheet would now look like this.

zipper 13

When we started, all I would have been able to see is that all of these people matched Mom and Dad and I on the same segments. By utilizing the various tools, I was able to sort into groups and eventually, subgroups.

In fact, you can see below that within Mom’s pink group, there is also the smaller cluster of Mary, Susie, me and Mom.

Zipper 14

For Jeremy and Martha, we can’t do any more right now, so I’ve recorded what we do know and set them aside.

Here, you can see the matches sorted by chromosome, start and end segment.

zipper 16

It looks a lot different than where we started, shown below, when all we had was a list of people who matched each other with no additional information.  We’ve added a lot!

zipper 17

In Summary – Creating the Zipper

So, where are we with this?

By utilizing all of the tools at your disposal, including the ICW tool, the Family Finder Matrix, your matching spreadsheet and your genealogical information, you’re in essence creating that zipper that divides half of your DNA into Mom’s side and Dad’s side.  Then into grandma’s and grandpa’s side, and on up the pedigree chart.

Each of these tools can tell you something unique and important.

The ICW tool tells you who matches you and another person, in common.  It doesn’t tell you if they also match each other.  This tool can provide extremely important clustering information.  For example, if I see unknown cousin Martha clustered with a whole group of known Estes descendants, then that’s a pretty good clue about how I’m related to Martha.  If, on the other hand, I find Martha clustered with people from both sides of my family, well, my Mom and Dad just might be related to each other or their ancestors went to or came from the same places.

By utilizing the Matrix tool, I can tell which of my matches are actually matching each other too, so that puts Martha in a much smaller group, or maybe eliminates her from certain groups.

By then utilizing my downloaded match spreadsheet, on which I record every known tidbit of genealogy information, even generalities like, “family from NC” if that’s the best I can get, I can then see where Martha matches me and others on the same segments, and based on the information in the ICW and the Matrix and my genealogy info, I may be able to slot Martha into a family group.  On a great day – I’ll be able to be more specific and tell her which family group – like we were able to do with my newly found cousin, Loujean.

So, I hope you’ve enjoyed learning how to install a chromosome zipper.  Now you can happily go about unzipping all of that genealogy information held in your DNA, that piece by piece, we’re slowing revealing.

zipper final

Family Tree DNA Listens, and Acts

During and after the 9th Conference hosted by Family Tree DNA in Houston, TX November 8-10, several administrators collectively submitted a list of “wants and needs” that the genetic genealogy community felt could improve their experience and Family Tree DNA’s product.  A small team worked diligently together afterward to refine the plans and help prioritize.  Today, the fruits are already ripening on the tree.  Thank you Family Tree DNA!!!

During the conference, Bennett Greenspan said he was committing “whatever resources it takes,” followed by a groan (his), and the statement “I can’t believe I just said that.”  Of course, all of us heard it…and Family Tree DNA is indeed coming through, very quickly.  Two weeks ago there were some changes and additions, and again, today, more.

I’m personally very glad to see the common matches ”crossover” link on the main screen now as well as the much requested,”download all matches,” item 6 below.

ftdna 12-4

Here’s a note from Bennett Greenspan about today’s six new features.

Today we are releasing some great updates that were requested during our 9th International Conference on Genetic Genealogy.  Here is a quick summary with some screen shots of what to expect.

1. The timeout for myFTDNA has been increased from 30 min to 2 hrs.  This will benefit everyone but will especially be appreciated by our Group Admins when they are impersonating into a kit.

2. Changed the word “Triangulation” to “Common Matches” for Family Finder matching.

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3. Instead of using the word “Steps” on the matching pages we will now use “Genetic Distance.”  This will effect both the Y-DNA and mtDNA matching pages.

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4. Fixed the Interactive Tour.  It was getting stuck at the Family Finder section but will now complete.

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5. Updated the Profile Pop up on matching pages with a new design and restored the “About Me” section and badges.  This profile is available on all matching pages:  Y-DNA, mtDNA, Family Finder, and Advanced Matching.

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6. Added the ability for a user to download chromosome browser data for all of their matches.  This new option is towards the top right side of the chromosome browser page and will be in Excel format.

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WikiTree and DNA

Several years ago, at a DNA conference, I found myself sitting next to Peter Roberts at lunch.  We discovered common ground – how can you NOT discover common ground at a genetic genealogy conference?  We’ve kept in touch ever since.  One of the things we discussed is the daunting task of managing multiple “stories” about the same ancestor, and now, DNA information that relates to that ancestor.  Or maybe, the DNA information doesn’t relate to that ancestor, but “should.”  How do we handle all of these challenges, separately or together?  Peter, an archivist by trade, has a special interest in organizing records, of course, and has been working on this topic.  I asked him to share his recent experience with WikiTree, and he has been gracious enough to do so.  Here’s what he had to say.

We know how personal computers changed the genealogy landscape by allowing us to build our own genealogy databases.  The next step was the Internet which provided easier communication and convenient access to family history information.  Then came DNA which allowed us to confirm if our genealogies were indeed correct.  Now there is a new genetic genealogy tool, WikiTree, that puts it all together for free!
wikitree 1

Peter Roberts originally tested in 2003 and has been not-so-patiently waiting since then for one collaborative online ancestral tree where we can all hang our results.  First he tried uploading a large GEDCOM in WikiTree but faced the daunting task of trying to merge his records with so many of his ancestors among the 6.1 million already in WikiTree.  He opted for a manual approach and focused on DNA tested lines for himself and cousins.

Fortunately, WikiTree has addressed and includes DNA testing.  In Peter’s public profile under “DNA” WikiTree asked, “Has Peter taken a DNA test for genealogy?”  Well yes! As many as he could afford.  He clicked through to an “Add a New Test” page where he selected one of the Y-DNA test options from a drop down menu which generated entry fields for Haplogroup, Number of Markers, YSearch ID, and Kit Number.  He did the same for his mtDNA and atDNA tests and entered his MitoSearch and GEDmatch IDs.  And for good measure he added the ancestry and Y-DNA results for a distant paternal line cousin (whose test kit he manages) who he listed as “Anonymous Roberts” to wikitree 2protect the man’s privacy.  For that easy work WikiTree awarded each test taker a handsome DNA Tested badge which can be displayed on the tester’s public profile.

Like magic (but it actually took about 24 hours) in the public profiles of Peter’s direct line ancestors, WikiTree automatically provided links to corresponding results in YSearch and MitoSearch.  And cousin Anonymous was there also.  Here’s the screen shot from WikiTree regarding DNA testing relevant to this ancestor, Bennie Roberts.

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Now anyone can see Peter’s DNA test list and compare his results with those of his direct line cousins to determine if their DNA is a close enough match.  If not, then the mis-matching DNA is pointing out a problem in that direct line.

Peter’s crotchety cousin Rufus refuses to DNA test and his WikiTree profile notes by default “…there are no known yDNA or mtDNA test-takers in the same direct paternal or maternal line.”  It’s a reminder that perhaps someday Rufus’ son will do that honor.

The profile of Peter’s paternal grandfather, Bennie Roberts, http://www.wikitree.com/wiki/Roberts-7102 illustrates many beneficial features.  Under the DNA heading are the known Y-DNA testers in WikiTree who share his direct paternal line and the mtDNA tester who shares his direct maternal line.  These names link to their public WikiTree profiles.  Here is Peter’s page via the “person who DNA tested” link on his grandfather’s page.  Please note that while WikiTree is “free,” there is no such thing as a “free lunch” so Ancestry ads are plastered all over every page in strategically placed locations.  Peter has no control over this, and neither will you.

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To the right of the tester’s name is the testing company and the type of test (Y-DNA or mtDNA).  This links to a more descriptive Test Connections overview page.  A key feature on these test connections pages is the earliest known direct line ancestor is highlighted and followed by a link to a descendant chart of carriers of the type of DNA tested (Y-DNA http://www.wikitree.com/treewidget/Roberts-7104/890 or mtDNA http://www.wikitree.com/treewidget/Unknown-205578/890).  Unlike many other online genealogy databases, these charts have a web addresses (urls) which facilitates sharing.

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Peter is now joyously (joyfully?) decorating his ancestral tree with haplogroup ornaments and haplotype garlands as well as project badges. His tree is growing in an aspen forest and there is something special about aspen forests.

Aside from the obvious “tree” challenges, in terms of results that might not match the expected line and are not part, genetically, of the aspen forest, there are also other challenges to be addressed.  Over time, the naming of haplogroups has become confusing.  This is because haplogroups are defined by SNPs that are given names like M-269.  M-269 happens to define haplogroup R1b1a2, which used to be R1b1c.

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Genealogists have tried to fit the SNPs into a tree-like structure, shown above (tree compliments of Family Tree DNA) because we understand trees and haplogroups are like trees (trunk, branches, leaves) – but the problem occurred when newly discovered branches needed to be inserted in-between already existing branches that already had names.  Every downstream branch’s name shifted, for example, from R1b1c to R1b1a2, and confusion resulted.  Today, we are moving away from haplogroup names like R1b1a2 and using only the SNP name, M269, which will never change.  Of course, the problem with this is that the name doesn’t give you any idea of where the SNP falls on the tree, where the old nomenclature did – R1b1a2 was downstream from R1b1a which was downstream from R1b1, etc.

When entering information into WikiTree, Y chromosome (Y-DNA) haplogroups should be labeled with the first letter of the major haplogroup branch followed by a dash and the name of the final (downstream or most recent) SNP. For example: R-M269 which is the SNP for R1b1a2.  Because separate labs have reported different labels over time for haplogroups and their subclades, and because there is no verification process for how haplogroups are entered in WikiTree, there will be inconsistencies in haplogroup labeling.  So in the note field it is important to explain how you came up with that haplogroup (eg. Estimated haplogroup R-CTS241, aka R1b1a2a1a2c1 per ISOGG Y-DNA Haplogroup Tree, 17 Jul 2013).  Also, remember to update your information at WikiTree if you take more DNA tests or upgrade.

The source and the date for the Mitochondrial (mtDNA) haplogroups should be entered as reported by the genetic genealogy testing lab, along with which lab did the testing. An example is: L3f. If you have additional knowledge of your more precise subclade (e.g. from full sequence results) then use the more precise haplogroup label.

Peter notes that more features are revealed once you are a registered WikiTree user.

For more information and guidelines see the help pages at

http://www.wikitree.com/wiki/Project:DNA

http://www.wikitree.com/wiki/DNA

Thanks much to Peter Roberts for sharing with us.  Think you might be related or have questions?  You can contact Peter directly at peterebay@yahoo.com.

The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines

holy grail

Sangreal – the Holy Grail.  We are finally here, Part 9 and the final article in our series.  The entire purpose of The Autosomal Me series has been to use our DNA and the clues it holds to identify minority admixture, in this case, Native American, and by identifying those Native segments, and building chromosomal clusters, to identify the family lines that contributed that Native admixture.  Articles 1-8 in the series set the stage, explained the process and walked us through the preparatory steps.  In this last article, we apply all of the ingredients, fasten the lid, shake and see what we come up with.  Let’s take a minute and look at the steps that got us to this point.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we  extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes.  We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

In this final segment, Part 9, we will be applying the chromosomal information we’ve gathered to our matches and determine which of our lines are the most likely to have Native Ancestry.  This, of course, has been the goal all along.  So, drum roll…..here we go.

In Part 8, we ended by entering the start and stop locations of both Strong Native and Blended Asian clusters into a table to facilitate easy data entry into the chromosome match spreadsheet downloaded from either 23andMe or Family Tree DNA.  If you downloaded it previously, you might want to download it again if you haven’t modified it, or download new matches since you last downloaded the spreadsheet and add them to the master copy.

My goal is to determine which matches and clusters indicate Native ancestry, and how to correlate those matches to lineage.  In other words, which family lines in my family were Native or carry Native heritage someplace.

The good news is that my mother’s line has proven Native heritage, so we can use her line as proof of concept.  My father’s family has so many unidentified wives, marginalized families and family secrets that the Native line could be almost any of them, or all of them!  Let’s see how that tree shakes out.

Finding Matches

So let’s look at a quick example of how this would work.  Let’s say I have a match, John, on chromosome 4 in an area where my mother has no Native admixture, but I do.  Therefore, since John does not match my mother, then the match came from my father and if we can identify other people who also match both John and I in that same region on that chromosome, they too have Native ancestry.  Let’s say that we all also share a common ancestor.  It stands to reason at that point, that the common ancestor between us indicates the Native line, because we all match on the Native segment and have the same ancestor.  Obviously, this would help immensely in identifying Native families and at least giving pointers in which direction to look.  This is a “best case’ example.  Some situations, especially where both parents contribute Native heritage to the same chromosome, won’t be this straightforward.

Based on our findings, the maximum range and minimum (least common denominator or “In Common” range is as follows for the strongest Native segments on chromosomes 1 and 2.

  Chromosome 1 Chromosome 2
Largest   Range 162,500,000   – 180,000,000 79,000,000   – 105,000,000
Smallest   Range 165,658,091   – 171,000,000 90,000,000   – 103,145,425

At GedMatch

At GedMatch, I used a comparison tool to see who matched me on chromosome 1.  Only 2 people outside of immediate family members matched, and both from Family Tree DNA.  Both matched me on the critical Native segments between about 165-180mg.  I was excited.  I went to Family Tree DNA and checked to see if these two people also matched my mother, which would confirm the Native connection, but neither did, indicating of course that these two people matched me on my father’s side.  That too is valuable information, but it didn’t help identify any common Native heritage with my mother on chromosome 1.  It did, however, eliminate them as possibilities which is valuable information as well.

DNAGedcom

I used a new tool, DNAGedcom, compliments of Rob Warthen who has created a website, DNA Tools, at www.dnagedcom.com.  This wonderful tool allows you to download all of your autosomal matches at Family Tree DNA and 23andMe along with their chromosomal segment matches.  Since my mother’s DNA has only been tested at Family Tree DNA, I’m limiting the download to those results for now, because what I need is to find the people who match both she and I on the critical segments of chromosome 1 or 2.

Working with the Download Spreadsheet

It was disappointing to discover that my mother and I had no common matches that fell into this range on chromosome 1, but chromosome 2 was another matter.  Please note that I have redacted match surnames for privacy.

step 9 table 1

The spreadsheet above shows the comparison of my matches (pink) and Mother’s (white).  The Native segment of chromosome 2 where I match Mother is shaded mustard.  I shaded the chromosome segments that fell into the “common match” range in green.  Of those matches, there is only one person who matches both Mother and I, Emma.  The next step, of course, is to contact Emma and see if we can discover our common ancestor, because whoever it is, that is the Native line.  As you might imagine, I am chomping at the bit.

There are no segments of chromosome 2 that are unquestionably isolated to my father’s line.

Kicking it up a Notch

Are you wondering about now how something that started out looking so simple got so complex?  Well, I am too, you’re not alone.  But we’ve come this far, so let’s go that final leg in this journey.  My mom always used to say there was no point in doing something at all if you weren’t going to do it right.  Sigh….OK Mom.

The easiest way to facilitate a chromosome by chromosome comparison with all of your matches and your Strong Native and Blended Asian segments is to enter all of these segment groups into the match spreadsheet.  If you’re groaning and your eyes glaze over right after you do one big ole eye roll, I understand.

But let’s take a look at how this helps us.

On the excerpt from my spreadsheet below, for a segment of chromosome 5, I have labeled the people and how they match to me.  The ones labeled “Mom” in the last column are labeled that way because these people match both Mom and I.  The ones labeled “Dad” are labeled that way because I know that person is related on my father’s side.

Using the information from the tables created in Step 8, I entered the beginning and end of all matching segment clusters into my spreadsheet.  You can see these entries on lines 7, 8, 22, 23 and 24.  You then proceed to colorize your matches based on the entry for either Mom or Dad – in other words the blue row or the purple row, line 7, 22 or 24.  In this example, actually, line 5 Rex, based on the coloration, should have been half blue and half purple, but we’ll discuss his case in a minute.

The you can then sort either by match name or by chromosome to view data in both ways.  Let’s look at an example of how this works.

Legend:

  • White Rows:  Mother’s matches.  When Mother and I both match an individual, you’ll see the same matches for me in pink.  This double match indicates that the match is to Mother’s side and not Father’s side.
  • Pink Rows:  My matches.
  • Purple “Mom” labels in last column:  The individual matches both me and Mom.  This is a genetic match.
  • Teal “Dad” labels in last column: Genealogically proven to be from my father’s side.  This is a genealogical, not a genetic label, since I don’t have Dad’s DNA and can only infer these genetically when they don’t also match Mother.
  • Dark Pink Rows labeled “Me Amerind Only” are Strong Native or Blended Asian segments from Chromosome Table that I have entered.  My segments must come from one of my parents, so I’ve either colored them purple, if the match is someone who matches Mother and I both, or teal, if they don’t match both Mom and I, so by inference they come from my father’s line.
  • Dark Purple Rows labeled “Mom Amerind Only” are Mom’s segments from the Chromosome Table.
  • Dark Teal Rows labeled “Dad Amerind Only” are inferred segments belonging to my father based on the fact that Mother and I don’t share them.

Inferred Relationships

This is a good place to talk for just a minute about inferred relationships in this context.  Inference gets somewhat tenuous or weak.  The inferred matches on my father’s side began with the Native segments in the admix tools.  Some inferences are very strong, where Mother has no Native at all in that region.  For example, Mom has European and I have Native American.  No question, this had to come from my father.  But other cases are much less straightforward.

In many cases, categorization may be the issue.  Mom has West Asian for example and I have Siberian or Beringian.  Is this a categorization issue or is this a real genetic difference, meaning that my Siberian/Beringian is actually Native and came from my father’s side?

Other cases of confusion arise from segment misreads, etc.  I’ve actually intentionally included a situation like this below, so we can discuss it.  Like all things, some amount of common sense has to enter the picture, and known relationships will also weigh heavily in the equation.  How known family members match on other chromosome segments is important too.  Do you see a pattern or is this match a one-time occurrence?  Patterns are important.

Keep in mind that these entries only reflect STRONG Asian or Native signals, not all signals.  So even if Mother doesn’t have a strong signal, it doesn’t mean that she doesn’t have ANY signal in that region.  In some cases, start and stop segments for Mom and Dad overlapped due to very long segments on some matches.  In this case, we have to rely on the fact that we do have Mother’s actual DNA and assume that if they aren’t also a match to Mother, that what we are seeing is actually Dad’s lines, although this may not in actuality always be true.  Why?  Because we are dealing with segments below the matching threshold limit at both Family Tree DNA and 23andMe, and both of my parents carry Native heritage.  We can also have crossed a transitional boundary where the DNA that is being matched switches from Mom’s side to Dad’s side.

Ugh, you say, now that’s getting messy.  Yes, it is, and it has complicated this process immensely.

The Nitty-Gritty Data Itself

step 9 table 2

Taking a look at this portion of chromosome 5, we have lots going on in this cluster.  Most segments will just be boring pink and white (meaning no Native), but this segment is very busy.  Mom and I match on a small segment from 52,000,000 to 53,000,000.  Indeed, this is a very short segment when compared to the entire chromosome, but it is strongly Native.  We both also match Rex, our known cousin.  I’ve noted him with yellow in the table. Please note that Mom’s white matches are never shaded.  I am focused on determining where my own segments originate, so coloring Mother’s too was only confusing.  Yes, I did try it.

You can see that Mother actually shares all or any part of her segment with only me and Rex.  This simplifies matters, actually.  However, also note that I carry a larger segment in this region than does Mother, so either we have a categorization issue, a misread, or my father also contributed.  So, a conundrum.  This very probably implies that my father also carried Native DNA in this region.

Let’s see what Rex’s DNA looks like on this same segment of chromosome 5, from 52-53 using Eurogenes.  In the graph below, my chromosome is the top bar, Rex’s the middle and the bottom bar shows common DNA with the black nonmatching.  Yellow is Native American, red is South Asian, putty is Siberian, lime green is Mediterranean, teal is North Europe, orange is Caucus.

Step 9 item 3

This same comparison is shown to Mother’s DNA (top row) below.

step 9 item 4

It’s interesting that while Mother doesn’t have a lot of yellow (Native), she does have it throughout the same segment where Rex’s occurs, from about 52 through 53.5.

Does this actually point to a Native ancestor in the common line between Rex, Mom and I, which is the Swiss/German Johann Michael Miller line which does include an unidentified wife stateside, or does this simply indicate a common ancient population long ago in Asia?  It’s hard to say and is deserving of more research.  I feel that it is most likely Native because of the actual yellow, Native segment. If this was an Asian/European artifact, it would be much less likely to carry the actual yellow segment.

Is Rex also genealogically related to my father?  As I’ve worked through this process with all of my chromosomes and matches, I’ve really come to question if one of my father’s dead ends is also an ancestral line of my mother’s.

The key to making sense of these results is clusters.

Clusters vs Singleton Outliers

The work we’ve already done, especially in Step 8, clusters the actual DNA matching segments.  We’ve now entered that information into the spreadsheet and colored the segments of those who match.  What’s next?

The key is to look for people with clusters.  Many matches will have one segment, of say, 10 that match, colored.  Unless this is part of a large chromosome cluster, it’s probably simply an outlier.  Part of a large chromosome cluster would be like the large Strong Native segments on chromosome 1 or 2, for example.  How do we tell if this is a valid match or just an outlier?

Sort the spreadsheet by match name.  Take a look at all of the segments.

The example we’ll use is that of my cousin, Rex.  If you recall, he matches both me and Mother, is a known first cousin twice removed to me, (genetically equal to a second cousin), and is descended from the Miller line.

In this example, I also colored Mother’s segments because I wanted to see which segments that I did not receive from her were also Native. You can see that there are many segments where we all match and several of those are Native.  These also match to other Miller descendants as well, so are strongly indicative of a Native connection someplace in our common line.

If we were only to see one Native segment, we would simply disregard this as an outlier situation.  But that’s not the case.  We see a cluster of matches on various segments, we match other cousins from the same line on these segments, and reverting back to the original comparison admixture tools verifies these matches are Native for Rex, Mom and me.

step 9 item 5

Hmmmm…..what is Dad’s blue segment color doing in there?  Remember I said that we are only dealing with strong match segments?  Well, Mom didn’t have a strong segment at that location and so we inferred that Dad did.  But we know positively that this match does come from Mother’s side.  I also mentioned that I’ve come to wonder if my Mom and Dad share a common line.  It’s the Miller line that’s in question.  One of Johann Michael Miller’s children, Lodowick, moved from Pennsylvania to Augusta County, Virginia in the 1700s and his line became Appalachian, winding up in many of the same counties as my father’s family.  I’m going to treat this as simply an anomaly for now, but it actually could be, in this case, an small indication that these lines might be related.  It also might be a weak “Mom” match, or irrelevant.  I see other “double entries” like this in other Miller cousins as well.

What is the pink row on chromosome 12?  When I grouped the Strong Native and Asian Clusters, sometimes I had a strong grouping, and Mom had some.  The way I determined Dad’s inferred share was to subtract what Mom had in those segments from mine.  In a few cases, Mom didn’t have enough segments to be considered a cluster but she had enough to prevent Dad from being considered a cluster either, so those are simply pink, me with no segment coloring for Mom or Dad.

Let’s say I carry Strong Native/Mixed Asian at the following 8 locations:

10, 12, 14, 16, 18, 20, 22, 24

This meets the criteria for 8 of 15 ethno-geographic locations (in the admix tools) within a 2.5 cM distance of each other, so this cluster would be included in the Mixed Asian for me.  It could also be a Strong Native cluster if it was found in 3 of 4 individual tools.  Regardless of how, it has been included.

Let’s now say that Mom carries Native/Mixed Asian at 10, 12 and 14, but not elsewhere in this cluster.

Mom’s 3 does not qualify her for the 8/15 and it only leaves Dad with 5 inferred segments, which disqualifies him too.  So in this case, my cluster would be listed, but not attributable directly to either parent.

What this really says is that both of my parents carry some Native/Blended Asian on this segment and we have to use other tools to extrapolate anything further.  The logic steps are the same as for Dad’s blue segment.  We’re going to treat that as an outlier.  If I really need to know, I can go back to the actual admixture tools and see whether Mom or Dad really match me strongly on which segments and how we compare to Rex as well.  In this case, it’s obvious that this is a match to my Mother’s side, so I’m leaving well enough alone.

Let’s see what the matches reveal.

Matches

Referring back to the Nitty Gritty Data spreadsheet, Mom’s match to Phyllis on row 15 confirms an Acadian line.  This is the known line of Mother’s Native ancestry.  This makes sense and they match on Native segments on several other chromosomes as well.  In fact, many of my and Mother’s matches have Acadian ancestry.

My match to row 19, Joy, is a known cousin on my father’s side with common Campbell ancestry.  This line is short however, because our common ancestor, believed to be Charles Campbell died before 1825 in Hawkins County, TN.  He was probably born before 1750, given that his sons were born about 1770 and 1772.  Joy and I descend from those 2 sons.  Charles wife and parents are unknown, as is his wife.

My match to row 20, inferred through my father’s side, is to a Sizemore, a line with genetically proven Native ancestry.  Of course, this needs more research, but it may be a large hint.  I also match with several other people who carry Sizemore ancestors.  This line appears to have originated near the NC/VA border.

I wanted to mention rows 4 and 17.  Using our rules for the spreadsheet, if I match someone and they don’t also match Mother on this segment, I have inferred them to be through my father.  These are two instances that this is probably incorrect.  I do match these people through Mother, but Mother didn’t carry a strong signal on this segment, so it automatically became inferred to Dad.  Remember, I’m only recording the Strong Native or the Blended Asian segments, not all segments.  However, I left the inferred teal so that you can see what kinds of judgment calls you’ll have to make.  This also illustrates that while Mom’s genetic matches are solid, Dad’s inferred matches are less so and sometimes require interpretation.  The proper thing to do in this instance would be to refer back to the original admixture tools themselves for clarification.

Let’s see what that shows.

step 9 item 6

Using HarrappaWorld, the most pronounced segment is at about 52.  Teal is American.  You can see that Mother has only a very small trace between 53 and 54, almost negligible.  Mother’s admixture at location 52 is two segments of purple, brown and cinnamon which translate to Southwest Asian (lt purple), Mediterranean (dk purple), Caucasian (brown) and Balock (cinnamon), from Pakistan.

Checking Dodecad shows pretty much the same thing, except Mother’s background there is South Asian, which could be the same thing as Caucus and Pakistan, just different categorizations.

In this case, it looks like the admixture is not a categorization issue, but likely did come from my father.  Each segment will really be a case by case call, with only the strongest segments across all tools being the most reliable.

It’s times like this that we have to remember that we have two halves of each chromosome and they carry vastly different information from each of our parents.  Determining which is which is not always easy.  If in doubt, disregard that segment.

Raw Numbers

So, what, really did I figure out after all of this?

First, let’s look at some numbers.

I was working with a total of 292 people who had at least one chromosomal segment that matched me with a Strong Native or Blended Asian segment.  Of those, 59 also matched Mom’s DNA.  Of those, 18 had segments that matched only Mom.  This means that some of them had segments that also matched my father.  Keep in mind, again, that we are only using “strong matches” which involves inferring Dad’s segments and that referring back to the original tools can always clarify the situation.  There seems to be some specific areas that are hotspots for Native ancestry where it appears that both of my parents passed Native ancestry to me.

Many of my and my mother’s 59 matches have Acadian ancestry which is not surprising as the Acadians intermarried heavily with the Native population as well as within their own ethnic group.

Several also have Miller Ancestry.  My Miller ancestor is Johann Michael Miller (1692-1771) who immigrated in the colonial period and settled on the Pennsylvania frontier.  His son, Philip Jacob Miller’s (1726-1799) wife was a woman named Magdalena whose last name has been rumored for years to be Rochette, but no trace of a Rochette family has ever been found in the county where they lived, region or Brethren church history…and it’s not for lack of looking.  Several matches point to Native Ancestry in this line.  This also begs the question of whether this is really Native or whether it is really the Asian heritage of the German people.  Further analysis, referring back to the admixture tools, suggests that this is actually Native. It’s also interesting that absolutely none of Mother’s other German or Dutch lines show this type of ancestry.

There is no suggestion of Native ancestry in any of her other lines.  Mother’s results are relatively clean.  Dad’s are anything but.

Dad’s Messy Matches

My father’s side of the family, however, is another story.

I have 233 matches that don’t also match my mother.  There can be some technical issues related to no-calls and such, but by and large, those would not represent many.  So we need to accept that most of my matches are from my Father’s side originating in colonial America.  This line is much “messier” than my mother’s, genealogically speaking.

Of those 233 matches, only 25 can be definitely assigned to my father.  By definitely assigned, I mean the people are my cousins or there is an absolutely solid genealogical match, not a distant match.  Why am I not counting distant matches in this total?  We all know by virtue of the AncestryDNA saga that just because we match family lines and DNA does NOT mean that the DNA match is the genealogical line we think it is.  If you would like to read all about this, please refer to the details in CeCe Moore’s blog where she discussed this phenomenon.  The relevant discussion begins just after the third photo in this article where she shows that 3 of 10 matches at Ancestry where they “identify” the common DNA ancestor are incorrect.  Of course, they never SAY that the common ancestor is the DNA match, but it’s surely inferred by the DNA match and the “leaf” connecting these 2 people to a common ancestor.  It’s only evident to someone who has tested at least one parent and is savvy enough to realize that the individual whose ancestor on Mom’s side that they have highlighted, isn’t a match to Mom too.  Oops.  Mega-oops!!!

However, because we are dealing in our project, on Dad’s side, with inferences, we’re treading on some of the same ground.  Also, because we are dealing with only “strong clustered” segments, not all Native or Asian segments and because it appears that my parents both have Native ancestry.  To make matters worse, they may both have Algonquian, Iroquoian or both.

I have also discovered during this process that several of my matches are actually related to both of my parents.  I told you this got complex.

Of the people who don’t match Mother, 32 of them have chromosomal matches only to my father, so those would be considered reliable matches, as would the closest ones of the 25 that can be identified genealogically as matching Dad.  Many of these 25 are cousins I specifically asked to test, and those people’s results have been indispensable in this process.

In fact, it’s through my close circle of cousins that we have been able to eliminate several lines as having Native ancestry, because it doesn’t’ show as strong and they don’t have it either.

Many of these lines group together when looking at a specific chromosome.  There is line after line and cousin after cousin with highlighted data.

Dad’s Native Ancestors

So what has this told me?  This information strongly suggests that the following lines on my father’s side carry Native heritage.  Note the word “carry.”  All we can say at this point is that it’s in the soup – and we can utilize current matches at our testing company and at GedMatch, genealogy research and future matches to further narrow the branches of the tree.  Many of these families are intermarried and I have tried to group them by marriage group.  Obviously, eventually, their descendants all intermarried because they are all my ancestors on my father’s side.  But multiple matches to other people who carry the Native markers but aren’t related to my other lines are what define these as lines carrying Native heritage someplace.

  • Campbell – Hawkins County, Tn around 1800, missing wife and parents, married into the Dodson family
  • Dodson – Hawkins County, Tn, Virginia – written record of Lazarus Dodson camping with the Cherokee – missing wife, married into the Campbell and Estes family
  • Claxton/Clarkson – Russell Co., Va, Claiborne and Hancock Co., Tn – In NC associated with the known Native Hatcher family.  Possibly a son-in-law.  Missing family entirely.
  • Cook – Russell Co., Va. – daughter married Claxton/Clarkson – missing wives
  • Harrold, Harrell, Herrell – Hancock Co., Tn., Wilkes Co., NC – missing wives
  • McDowell – Hancock Co. Tn, Wilkes Co., NC, Augusta Co., Va – married into the Harrell family, missing wife
  • McNeil, McNiel – Wilkes Co., NC – missing wives, married into the Vannoy family
  • Vannoy – Wilkes County – some wives unaccounted for pre-1800
  • Crumley – Greene County, Tn., Lee Co., Va. – oral history of Native wife, married into the Vannoy family
  • Brown – Greene County, Tn, Montgomery Co., Va – married into the Crumley family, missing wives

While this looks like a long list, the list of families that don’t have any Native ancestry represented is much longer and effectively serves to eliminate all of those lines.  While I don’t have “THE” answer, I certainly know where to focus my research.  Maybe there isn’t the one answer.  Maybe there are multiple answers, in multiple lines.

The Take Away

Is this complex?  Yes!  Is it a lot of work?  You bet it is!  Is everything cast in concrete?  Never!  You can see that by the differences we’ve found in data interpretation, not to mention issues like no-calls (areas that for some reason in the test don’t read) and cross overs where your inheritance switches from your mom’s side to your dad’s side.  Is there any other way to do this?  No, not if your minority admixture is down in that weedy area around 1%.

Is it worth it?  You’ll have to decide.  It guess it depends on how desperately you want to know.

Part of the reason this is difficult is because we are missing tools in critical locations.  It’s an intensively laborious manual process.  In essence, using various tools, one has to figure out the locations of the Native and Asian chromosome segments and then use that information to infer Native matches by a double match (genetic match at DNA company plus match with Strong Native/Blended Asian segment) with the right parent.  It becomes even more complex if neither parent is available for testing, but it is doable although I would think the reliability could drop dramatically.

Tidbits and Trivia

I’ve picked up a number of little interesting tidbits during this process.  These may or may not be helpful to you.  Just kind of file them away until needed:)

  • Matches at testing companies come and go….and sometimes just go.  At Family Tree DNA, I have some matches that must be trembling on the threshold that come and go periodically.  Now you see them, now you don’t.  I lost matches moving from the Affy chip to the Illumina chip and lost additional matches between Build 36 and 37.  Some reappeared, some haven’t.
  • The start and stop boundaries changed for some matches between build 36 and build 37.  I did not go back and readjust, as most of these, in the larger scheme of things, were minor.  Just understand that you are looking for  patterns here that indicate Native heritage, not exact measurements.  This process is a tool, and unfortunately, not a magic wand:)
  • The centromere locations change between builds.  If you have matches near or crossing the middle of the chromosome, called the centromere, there may be breaks in that region.  I enter the centromere start and stop locations in my spreadsheet so that if I notice something odd going on in that region, the centromere addresses are right there to alert me that I’m dealing with that “odd” region.  You can find the centromere addresses in the FAQ at Family Tree DNA for their current build.
  • At 23andMe, when you reach the magic 1000 matches threshold, you start losing matches and the matching criteria is elevated so that you can stay under 1000 matches.  For people with colonial American or Jewish heritage, in other words those with high numbers of matches, this is a problem.
  • Watch for matches that are related to both sides of your family.  If your family lived in colonial America, you’re going to have a lot of matches and many are probably related to each other in ways you aren’t aware of.
  • If your parents are related to each other, this process might simply be too complex and intertwined to provide enough granular data to be useful.
  • Endogamous groups are impossible to sort through as to where, meaning which ancestor, the DNA came from.  This is because the original group founders’ DNA is just getting passed around and around, with little or no new DNA being introduced.  The effect of this on downstream generations relative to genetic genealogy is that matches appear to be more closely related than they are because of the amount of matching DNA they carry.  For my Brethren and my Acadian groups of people, I just list them by the group name, since, as the saying goes, “if you’re related to one Acadian, you’re related to all Acadians.”
  • If you’re going to follow this procedure, save one spreadsheet copy with the Strong Native only and then a second one with both the Strong Native and Blended Asian.  I’m undecided truthfully whether the Mixed Asian adds enough resolution for the extra work it generates.
  • When in question, refer back to the original tools.  The answer will always be found there.
  • Unfortunately, tools change.  You may want to take screen shots.  During this process, FTDNA went from build 36 to 37, match thresholds changed, 23andMe introduced a new user interface (which I find much less intuitive) and GedMatch has made significant changes.  The net-net of this is when you decide to undertake this project, commit to it and do it, start to finish.  Doing this little by little makes you vulnerable to changes that may make your data incompatible midstream – and you may not even realize it.
  • This entire process is intensively manual.  My spreadsheet is over 5500 rows long.  I won’t be doing it again…although I will update my spreadsheet with new matches from time to time.  The hard work is already done.
  • This same technique applies to any minority ancestry, not just Native, although that’s what I’ve been hunting for and one of the most common inquiries I receive.
  • I am hopeful that in the not too distant future many of these steps and processes will be automated by the group of bright developers that contribute to GedMatch or via other tools like DNAGedcom. HINT – HINT!!!

I would like to follow this same process to identify the source of my African heritage, but I’m thinking I’ll wait for the tools to become automated.  The great irony is that it’s very likely in the same lines as my Native ancestors.

If You Want to Test

What does it take to do this for yourself using the tools we have today, as discussed?

If your parents are living, the best gift you can give yourself is to test them, now, while you still can.  My mother has been gone for several years, but her DNA archived at Family Tree DNA was still viable.  This is not always the case.  I was fortunate.  Her DNA is one of the best gifts she gave me.  Not just by inheritance, but by having hers tested.  I thank her every single day, for both!  I could not have written this article without her DNA results.  The gift that keeps on giving.

If you don’t have a parent to test, you can test several other family members who will provide some information, but clearly won’t carry the same amounts of common DNA with you as your parents.  These would include your aunts and uncles, your parents’ siblings and what I’ve referred to as your close cousin circle.  Attempt to test at least someone from each line.  Yes, it gets expensive, but as one of my cousins said, as she took her third or 4th DNA test.  “It’s only money.  This is about family.”

You can also test your own siblings as well to obtain more information that you can use to match up to your family lines. Remember, you only receive half of your parents DNA, and your siblings will received some DNA from your parents that you didn’t.

I don’t have any other siblings to test, but I have tested cousins from several lines which have proven invaluable when trying to discern the sources of certain segments. For example, one of these Native segments fell on a common segment with my cousin Joy.  Therefore, I know it’s from the Campbell line, and because I have the Campbell paternal Y-DNA which is European, I know immediately the Native admixture would have had to be from a wife.

Much of this puzzle is deductive, but we now have the tools, albeit manual, to do this type of work that was previously impossible.  I am somewhat disappointed that I can’t pinpoint the exact family lines, yet, but hopefully as more people test and more matches provide genealogical information, this will improve.

If you want to play in this arena, you need to test at either Family Tree DNA, 23andMe, or both.  Right now, the most cost effective way to achieve this is to purchase a $99 kit from 23andMe, test there, then download your results from 23andMe and upload them to Family Tree DNA for $99.  That way, you are fishing in both pools.  Be aware that less than half of the people who test at either company download results to GedMatch, so your primary match locations are with the testing companies.  GedMatch is auxiliary, but critical for this analysis.  And the newest tool, DNAGedcom is a Godsend.

Also note that transferring your result to Family Tree DNA is NOT the same thing as actually testing there.  Why does this matter?  If you want a future test at Family Tree DNA, who is the premiere genetic genealogy testing company, offering the most variety and “deepest” commercial tests, they archive your DNA for 25 years, but if you transfer results, they don’t have your DNA to archive, so no future products can be ordered.  All I can say is thank Heavens Mom’s DNA was there.

Ancestry.com doesn’t provide any tools such as the chromosome browser or even the basic information of matching segments.  All you get is a little leaf that says you’re related, but the questions of which segment or how are not answerable today at Ancestry and as CeCe’s experience proved, its unreliable.  It’s  possible that you share the same surnames and ancestor, but your genetic connection is not through that family line.  Without tools, there is no way to tell.  Ancestry released raw data files a few weeks ago and very recently, GedMatch has implemented the ability to upload them so that Ancestry participants can now utilize the additional tools at GedMatch.

Although this has been an extraordinarily long and detailed process, I can’t tell you how happy I am to have developed this new technique to add to my toolbox.  My Native and African ancestors have been most elusive.  There are no records, they didn’t write and probably didn’t even speak English, certainly not initially.  The only clues to their existence, prior to DNA, were scant references and family lore.  The only prayer of actually identifying them is though these small segments of our DNA – yep – down in the weeds.  Are there false starts perhaps, and challenges and maybe a few snakes down there?  Yes, for sure, but so is the DNA of your ancestors.

Happy gardening and rooting around in the weeds.  Just think of it as searching for the very best buried treasure!  It’s down there, just waiting to be found.  Keep digging!

I hope you’ve enjoyed this series and that it leads you to your own personal genealogical treasure trove!

treasure chest