DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts

Not long ago, Jonny Perl introduced the free online tool, DNA Painter, designed to paint your chromosomes. I didn’t get around to trying this right away, but had I realized just how much fun I would have, I would have started sooner.

Fittingly, Jonny, pictured above, won the RootsTech Innovation award this year for DNA Painter – and I must say, it’s quite well-deserved.

Congratulations Jonny!

  • This is the first of four articles about DNA Painter. In this article, we’ll talk about how to use the tool, and how to get started.
  • The second article talks about mining your matches at the various vendors for paintable segments with instructions for how to do that accurately with each vendor.
  • In the third article, we’ll walk through an analysis of my painted segments, so you can too – and know how to spot revelations.
  • The fourth article explains how I solved a long-standing mystery that was driving me crazy. If you have a relatively close mystery person in your DNA match list that you can’t figure out quite where they fit, this article is written just for you!

I’ll tell you right now, I haven’t had this much fun in a long time!

Want to hear the best part? You don’t have to triangulate. DNA painting is “self-triangulating.” Yes, really!

Let’s get started!

Introducing DNA Painter

To begin to use DNA Painter, you’ll need to set up a free account at www.dnapainter.com.

Read the instructions and create your profile.

Jonny provides an overview.  Don’t get so excited that you skip this, or you won’t know how to paint correctly. You don’t need to be Picasso, but taking a few minutes up front will save you mistakes and frustration later.

Blaine Bettinger recorded a YouTube video discussing how to use DNA Painter to paint your chromosomes to identify and attribute particular segments to specific ancestors. It includes a mini-lesson on chromosome matching.

I strongly suggest you take time to watch Blaine’s video from the beginning. For some reason, this link drops into the video near the end, but just slide the red bar back to the beginning.

Get Started

Here’s my blank, naked chromosomes. Notice for every chromosome, you see a blue paternal “half” and a pink maternal “half.” That’s because everyone gets half of their autosomal DNA from their father, and the other half from their mother.

Looking at my own chromosome painting today, below, it’s incredibly exciting for me to see 57% of my DNA painted, attributed to 77 couples and one endogamous group, Acadians. This took me a month or so working off and on.

At the end of the day, this is often how I rewarded myself! The only problem it that it has been difficult to go to bed.

Comparatively, I’ve been working on my DNA match spreadsheet, attributing segments to ancestors now for 5 or 6 years, and I’ve never been able to see this information visually like this before. This view of my ancestrally painted chromosomes is so rewarding!

Who To Map

DNA Painter is not the kind of tool where you upload your results, it’s a tool where you selectively paint specific segments of matches – meaning segments on which you match particular people with known common ancestors.

How do you know who is a good candidate to map?

I began with painting my closest matches with whom I could identify the common ancestor.

Not only will painting your largest matches be rewarding as you harvest low-hanging-fruit, it will help you determine if you actually have identified the correct DNA for later matches being attributed to a specific genealogical line. In other words, mapping these larger known segments will help you identify false positives when you have no other yardstick.

Your First Painting

I’m opening a new profile in DNA Painter to demonstrate the steps in painting along with hints that I’ve learned along the way.

I’m going to utilize my cousin, Cheryl, whom I match closely at Family Tree DNA. If you don’t know how to use the Family Tree DNA autosomal tools, click here.

Cheryl is my first cousin once removed, so we share a significant amount of DNA.

I’ve selected Cheryl on my match list, checked her match box, and then clicked on the Chromosome Browser in order to view our segment matching information.

You can see on the chromosome browser that I share quite a bit of DNA with Cheryl.

At the top of the chromosome browser, click on “View this data in a table.”

Highlight and copy all of the segments for Cheryl. I only use 7cM segments or higher at DNA Painter, so you don’t have to copy the data in the rows below your last match at that level. DNA Painter takes care of stripping out all the extraneous stuff.

Paint a New Match

At DNA Painter, after you have your profile set up, click on “Paint a New Match.”

Simply paste the segment data into the box in the window that pops up. DNA Painter takes care of removing the header information as well as segments that are too small.

You can click on “overlay these segments” to “test” a fit, but I haven’t really found a good use for that, because I’m only painting segments I’m confident about and I know which side, maternal or paternal, the match is on based on the known relative.

Click on “save match now” in the bottom right corner.

In the Save Match popup, shown above, I utilize the fields as follows.

I enter the name of my DNA match, followed by their relationship to me, followed by the source of the match. In this case, “Cheryl <lastname>, 1C1R, FTDNA”

In the “Segment/Match Notes” I list how the match descends from the common ancestral couple, a GedMatch ID if known, and anything else pertinent including other potential ancestral lines in common. This means that I list every generation beginning with the common ancestral couple and ending with the tester.

Hiram Ferverda and Eva Miller, Roscoe, Cheryl, GedMatch Txxxxxx

You’ll wind up eventually rethinking some of your segment assignments to particular ancestors and you’ll want as much information here about this match as possible.

Moving to the next field, in the “Ancestors Name,” I utilize the couples name, because at this point, you can’t tell which of the two people actually contributed the DNA segment, or if part is from one ancestor of the couple and part is from the other. If the male ancestor is a Sr. or Jr., or is otherwise difficult to tell apart from your other ancestors, I suggest entering a birth year by his name. This is your selection list for later painting segments from the same ancestor, so you want to be sure you can tell the generations apart.

Next, you’ll select the maternal or paternal side of your family. Change the color if you don’t like the one pre-selected to assign to segments descending from that couple. Originally, I was going to have pinks or light colors for maternal, and blues or darker for paternal, but I quickly discovered that scheme didn’t work well, and I had more ancestors than I could ever have imagined whose DNA I am be able to map and paint.

Therefore, pick contrasting colors. You can use each color on each half, meaning maternal and paternal, since the segments will be painted on different halves of the chromosome.

In the “Notes for This Group,” I add more information for the couple such as birth and death dates and location if I know or am likely to forget.

Click “save.”

Here you go!  Isn’t this fun!!!! Cheryl’s segments that match mine are painted onto my chromosomes!

At the right, your ancestor key appears with each ancestor to whom you’ve assigned a color key.

So far, I only have one!

Want to paint another group of segments?

Let’s paint Cheryl’s brother.

Following the same sequence, I paint Donald’s DNA, but this time, I select “Or link these segments to an ancestor I’ve added before.”

I select Hiram Ferverda, Eva Miller and save. The segments that I have in common with Cheryl and/or Don will now be displayed on each chromosome.

Looking at chromosome 1, you can see that I match Cheryl and Don on the same segment at the beginning of the chromosome, but received two different segments of DNA on a different portion of chromosome 1, further to the right.

As one last example, I added the DNA from two known cousins, Rex and Maxine, who descend a couple generations further back in time through more distant ancestors in the same line – one maternal and one paternal.

Click on the chromosome number to expand to see all of the painted segments

You can see, looking at chromosome 3 that Cheryl and Don match me on a significant amount of the same large pink segment plus a smaller pink segment at the end

Rex (yellow) and Maxine (blue) both match me on different parts of the chromosome. It looks like there is a small amount of overlap between Rex and Maxine which is certainly feasible, because Jacob Lentz, the ancestor that Maxine descends from is ancestral to the couple that Rex descends from.

By utilizing known matches, and mapping, we can see segments that move us back in time, telling us from which ancestor that portion of the segment descends.

For example, if the blue segment was directly aligned with one of the pink segments, then we would know that the blue portion of the pink segment descended from Jacob Lentz and Fredericka Reuhl.

This is the most awesome, extremely addictive game of ancestor Sukoku ever.

Wanna play???

Here’s how to prepare for my next article where we’ll utilize the various vendor matches to begin painting.

Download and Upload Your Autosomal Files

You’ll want to have your DNA at the most vendor locations possible so you can find all your matches that can be attributed to known relatives and ancestors. You never know who is going to test at which vendor, and the only way to find out is to have your DNA there too.

For each vendor, I’ve provided a mini-tutorial on how to maximize your testing and transfers both monetarily and for maximum matching effect, or you can read an article here that explains more.

There’s also a cheat sheet for transfer strategies at the end of this article.

A technique called imputation is mentioned below, so you may want to read about imputation here. MyHeritage’s initial offering utilizing imputation was problem plagued but has since improved significantly.

Ancestry

To Ancestry – There’s no way to transfer files TO Ancestry, so you’ll need to test there to be in their database. You will also need at least a minimum subscription ($49) to utilize all of the Ancestry DNA features. You can see a with and without subscription feature comparison chart here.

From Ancestry – There is also no chromosome browser at Ancestry. In order to use DNA Painter, chromosome segment information is required, so if you test at Ancestry and want to paint your segments, you’ll need to download your DNA file to either or all of:

  • Family Tree DNA – partially compatible with the current Ancestry test chip format – transfer will provide you with your closest matches, 20-25% of the matches you would have if you tested at Family Tree DNA
  • MyHeritage – partially compatible, but uses imputation to infer additional genetic regions
  • GedMatch

My preference is to test at Ancestry, and then test at Family Tree DNA and upload the test results to MyHeritage. The Family Tree DNA and MyHeritage testing platforms are the same, so there is no incompatibility between the two.

Family Tree DNA

To Family Tree DNA – You can upload the following vendor files TO Family Tree DNA.  Matching is free, but to use the advanced tools, including ethnicity and the chromosome browser, you’ll need to pay the $19 unlock fee. That’s still significantly less than retesting, especially for files that are 100% compatible.

  • Ancestry – V1 files generated from before May 2016 are entirely compatible, V2 files from after May 2016 are partially compatible, providing between 20-25% of your matches, meaning your closest matches
  • 23andMe – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 platform file beginning in August 2017 is not compatible
  • MyHeritage – fully compatible

From Family Tree DNA – You can upload your Family Finder results to:

MyHeritage

To MyHeritage – You can upload the following files to MyHeritage:

  • Family Tree DNA – fully compatible
  • Ancestry – partially compatible but uses imputation to infer additional genetic regions
  • 23andMe – partially compatible but uses imputation to infer additional genetic regions

From MyHeritage – If you test at MyHeritage, you can upload your files to:

23andMe

To 23andMe – You cannot transfer TO 23andMe, so you’ll need to test there if you want to be in their database.

From 23andMe – If you tested at 23andMe, you can upload your files to the following vendors:

  • Family Tree DNA – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 chip beginning in August 2017 is not compatible
  • MyHeritage – 23andMe – partially compatible but uses imputation to infer additional genetic regions
  • GedMatch – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 chip beginning in August 2017 is only compatible in the Genesis sandbox area. V5 matching is not reliable. Files from other vendors are recommended for GedMatch unless you are matching against another V5 result.

GedMatch

GedMatch is a third-party site that accepts all of these vendors’ autosomal files, with a caveat that the 23andMe V5 kit matches very poorly and requires special handling. I don’t recommend using that kit at GedMatch unless you are matching against other 23andMe V5 kits.

I upload multiple kits to GedMatch and mark all but one for research only. This allows me to use my Ancestry kit to match with other Ancestry users for more accurate matches, my Family Tree DNA kit to other Family Tree DNA kits, and so forth. Not marking multiple kits for research means that you’ll appear more than once on other people’s match lists, and only your first 2000 matches are free. Marking all kits except one as research is a courtesy to others.

Recommended Testing Strategy for New Testers

  1. Test at Ancestry and download to GedMatch.
  2. Test at Family Tree DNA and upload to MyHeritage and GedMatch.
  3. Test at 23andMe and upload to GedMatch Genesis.
  4. At GedMatch, mark all except one kit as “research,” then utilize your kits from the same vendor for one-to-one comparisons.

Recommended Transfer Strategy

Of course, where you have, and haven’t already tested will impact your transfer strategy decision. I’ve prepared the following cheat sheet to be used in combination with the information discussed above.

*Unless you can transfer a 23andMe V3/V4 or an Ancestry V1 kit to Family Tree DNA, it’s better to test at Family Tree DNA. Ancestry V2 tests are only 20-25% compatible.

A transfer from Family Tree DNA to MyHeritage is best because those vendors are on the same platform and the tools at MyHeritage are free.

In my next article, we’ll discuss how to mine your matches at the various vendors to obtain accurate segments for chromosome painting – including a strategy for how to utilize Ancestry and Gedmatch together to identify at least some Ancestry segment matches.

So, for now, get ready by transferring your matches into whichever data bases they aren’t already in. The only data base where I couldn’t identify matches that I didn’t have elsewhere was at 23andMe. The rest were all there just waiting to be harvested!

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Day 2 RootsTech – Vendors, Visits and MyHeritage is Smokin’ Hot

This morning view just doesn’t get old!

Across the rooftop, you can see two churches in front of the mountain.

Day 2 was jam packed, and that’s without attending any sessions. I did hear through the RootsTech grapevine that some of the afternoon sessions did have a few seats available. Of course, you would need to select the right sessions.

There’s a lot of very unhappy rumbling here about the conference: lines, full sessions, lack of signage, etc.

I spent the day doing four things:

  • Visiting vendor booths
  • Talking to people
  • MyHeritage Lunch
  • Vendor appointments

Let’s take a look at each of the four.

Visiting Booths

There are probably hundreds of booths. Some quite large, of course, like FamilySearch (show sponsor), Ancestry and the other big players, to Mom and Pop shops.

I managed to visit maybe half of the booths today. I’ll try for the other half tomorrow. I am going to make myself absent for part of the day to visit the Family History Library.

I noticed a LOT of vendors offering products to digitize and catalog your photos. Others encouraged recording memories and of course, given that we’re in Salt Lake, there was lots of focus on the Mormon faith and many obviously local vendors.

In addition to the sessions, there was a vendor demo area in the rear of the hall. I wandered past a couple of times, but the two vendors I saw didn’t really catch my eye.

At the Legacy Tree Genealogists booth, I found Jessica Taylor (at left, beside me), Paul Woodbury and Amber Brown (far right). (I apologize for not getting the lady’s name at the far left.) Jessica is the owner and founder of Legacy Tree Genealogists, Paul Woodbury is the amazing genetic genealogist that specializes in adoptee and missing parent family reconstruction and Amber Brown is their marketing representative. They were kind enough to give me with a RootsTech survival basket. I’ve never been to a conference before where you needed one of these, and by the end of the day, I was extremely grateful.

A really big thank you Jessica and crew!

Next, I ran into my old friend, Peter Roberts, at the conference as a volunteer for WikiTree, a free site for you to upload your family tree and collaborate with other genealogists. I’ve known Peter for years from the Family Tree DNA annual conference where he is the project administrator for the Bahamas DNA Project.

Peter took the time to sit down with me and explain some of the new DNA features at WikiTree that include Y DNA, mitochondrial, autosomal and most recently, the ability to link your WikiTree tree to your DNAPainter profile. WikiTree utilizes various types of DNA information to support or disprove ancestral connections.

Peter and I also discussed that putting information like links to any articles or blog posting you have written about your ancestors into the description area about each ancestor would be a great idea! I was thinking about the 52 Ancestors series, of course.

I briefly met Chris Whitten, founder of WikiTree, but I wasn’t quick enough to grab a photo.

Speaking of DNAPainter, Jony Pearl, from England, won the Innovation Showcase with DNAPainter. I’ve been using this extremely useful tool for about a month now, and I have an article half written. I’ll be finishing it as soon as I get home. You’re going to love this tool!

Congratulations Jony! Well deserved.

This conference has lots of beginners. FamilySearch had a very large area called the Discovery Zone. Just walking past, I did notice people entirely engrossed and making discoveries.

One of the Discovery Zone areas encouraged you to take your photo, or a group photo, with a backdrop of your choice.

I couldn’t resist. Plus, it’s free and the results are messaged to your phone immediately.

I was amazed to find this backdrop, given that I have actually stood in exactly this place in Germany – in real life. In fact, I can tell you there are two lovely lace shops just past that clock tower arch, one on either side of the street, and a quilt shop just beyond. In fact it was right here that the quilt shop-owner’s husband came riding up on his bicycle to deliver our purchases at the end of the day.

A few minutes later, I came across MYndVault, a digital cloud storage solution that includes servers stores in the granite mountain.

To prove his point, the founder of MYndVault was giving little boxes of granite – well, chocolate that looked like granite anyway. The chocolate was great – and everyone needs to think about this type of “inheritance issue.” It’s not just cloud storage, but an electronic directive that lists your personal representative, things like social media accounts and passwords. Obviously, I suggested that he add a specific field for DNA results at vendors, but there is already ample room to include this in non-specific fields.

There were lots of “charts” vendors in attendance, but I particularly liked this one from BranchesArt.

I’ve been wanting to meet Lara Diamond, who blogs at Lara’s Jewnealogy. Lara is Jewish and specializes in endogamous DNA and the inherent frustrations therein.

The lovely thing about meeting in person is that you actually get to talk to the individual. Lara tested with 23andMe initially and it was that test (before the FDA restricted the information they could provide to consumers) that led her to discover she had both a mutation for cancer, and cancer itself. Take a minute and read Lara’s story here. DNA testing very literally saved her life!

Lara will be writing about a super-cool record find soon that defies all logic. Right, Lara, right???

Next was the MyHeritage lunch, where I was thrilled to meet Randy Seaver, finally, in person.

My joke is that I wake up each morning to Randy, because that’s when I read his blog, Genea-Musings, every day. Randy writes more quality content than any other blogger I know. In fact, he has a great compendium of RootsTech conference articles that you can check out on his blog yesterday and today.

The MyHeritage luncheon speaker was Gilad Japhet, founder and CEO of MyHeritage.

Gilad and I had a personal meeting later in the day, and he gave me permission to share the slides from the luncheon with my readers.

I must say, MyHeritage is making very big waves in the genealogy community.

For a company that just started DNA testing about 18 months ago, and had significant startup challenges with matching, they’ve come a very, very long way.

First, Gilad announced a new initiative to test 15,000 adoptees or those seeking unknown parents by donating free kits. You can read more about this program here or apply to receive a kit. Those with financial need will receive priority.

Second, they also announced Family Search Tree sync between Family Search and MyHeritage that allows collaborative syncing of trees between LDS members and MyHeritage.

Third, they announced the publication of a paper culminating from 7 years of research, published today, discussing 86 million family trees from Geni and the patterns that emerge from this much data about migration and families. For example, exceptional genetics only adds abut 5 years to life expectancy, but poor lifestyle habits can deduct 10.

They are on a tear, I’m telling you. They weren’t done yet.

Fourth, they announced that they are adding new records at an amazing pace. Three new collections, including the digitization and indexing of high school yearbooks from the US.

Fifth – new advancements in genetic genealogy.

MyHeritage has observed that many people don’t understand the details of genetic genealogy or how to use the tools. Additionally, many people don’t have or create family trees.

MyHeritage has created what they call “The Big Tree” where all of their customers are connected in one large “tree of humanity,” or at least as much of humanity as has tested or uploaded to MyHeritage. They then look at how your own node is connected to others in that large tree and distill the results into something useful for you.

The next step, Gilad calls the “Theory of Family Relativity,” where MyHeritage combines your DNA matches, their trees and documents from their collection to construct a theoretical tree between you and your matches.

The connection may need to go up and down other people’s trees a couple of times, and may be discovered in the tree of someone you both match.

In summary, “The Theory of Family Relativity” will provide a paper trail theory for how you match your DNA matches. That theory will be for you to confirm or disprove. Gilad says that it’s easier with a tree, but can be accomplished at some level even without one AND it will be released before year end 2018.

Sixth, a new triangulated chromosome browser that compared up to 7 people simultaneously.

Downloads are being added as well.

MyHeritage is focusing a marketing drive in Europe. Their market research revealed that in Germany (I think,) only 22% of the population had even heard of DNA testing. Their goal is to infiltrate that market space.

France Gilad…focus on France😊

Gilad has christened 2018 “The Year of the Segment.”

And as if that wasn’t enough, Gilad added even MORE items.

  • Paper trail theories and connections to explain DNA matches.
  • Theories genetically of how your matches connect to you.
  • Clustering of triangulated segments.
  • Automatic chromosome painting.
  • Identification and recreation of ancestors through the testing of multiple descendants by creating an “ancestral segment bank,” of sorts.
  • Resurrecting the DNA of dead ancestors which would be made into a kit for matching. For example, your grandfather.
  • Automatic tree building.

If you’re sitting there with your mouth hanging open in shock…well, so was I. This is what I’ve talked about for years, now coming to fruition.

Gilad credits these strides to a combination of vision, applied technology and very smart people!

All of these development items are either in beta or past proof of concept. Some are available now, some shortly, the “Tree of Family Relativity” by the end of 2018.

Truthfully, I don’t even know what to say after that massive announcement, except transfer your DNA results to MyHeritage.  If you ever had doubt, it’s gone now.

Finishing Up

In the Innovation Showcase competition, obviously DNAPainter won first place, but the rest of the entrants also deserve recognition. Rootsfinder and ItRunsInMyFamily took second and third. You may want to go and take a look for yourself.

I have not had a chance to review these myself, so you’ll have to let me know what you think.

Apparently LivingDNA made an announcement as well. Many vendors make private appointments with bloggers, movers and shakers at RootsTech. In the past few days I’ve been fortunate enough to have private meetings with Ancestry, Family Tree DNA and MyHeritage. Living DNA is not on that list. I did stop by their booth today, but the right people weren’t there.

We’ve known for some time that matching was to be released in 2018, but we didn’t know that LivingDNA planned to reconstruct trees from genetic data alone, with no trees or other information involved.

You can read the announcement for yourself here.

I don’t anticipate that I’ll have the opportunity to meet with a Living DNA representative to garner additional information, unfortunately.

I would be more comfortable with this goal if they had matching experience at all. MyHeritage, with their early out-the-door matching issues is proof of how difficult it can be to get matching right.

I also feel matching and tree reconstruction will be much more accurate with a blend of trees, documents and DNA.

However, Living DNA is giving it a shot, and everyone has to start someplace. I will be very interested in what their new product will look like and how well it will work.

On the way out the door this evening, I noticed a bunch of teenagers who had obviously been to the conference, having fun.

Various vendors give away ribbons to attach to the bottom of your badge.

These kids had obviously been very busy. I enjoy seeing young people having good clean fun, and especially if those young people are the future of genealogy!