Genetic Affairs: AutoPedigree Combines AutoTree with WATO to Identify Your Potential Tree Locations

July 2020 Update: Please note that Ancestry issues a cease-and-desist order against Genetic Affairs, and this tool no longer works at Ancestry. The great news is that it still works at the other vendors, and you can ask Ancestry matches to transfer, which is free.

If you’re an adoptee or searching for an unknown parent or ancestor, AutoPedigree is just what you’ve been waiting for.

By now, we’re all familiar with Genetic Affairs who launched in 2018 with their signature autocluster tool. AutoCluster groups your matches into clusters by who your matches match with each other, in addition to you.

browser autocluster

A year later, in December 2019, Genetic Affairs introduced AutoTree, automated tree reconstruction based on your matches trees at Ancestry and Family Finder at Family Tree DNA, even if you don’t have a tree.

Now, Genetic Affairs has introduced AutoPedigree, a combination of the AutoTree reconstruction technology combined with WATO, What Are the Odds, as seen here at DNAPainter. WATO is a statistical probability technique developed by the DNAGeek that allows users to review possible positions in a tree for where they best fit.

Here’s the progressive functionality of how the three Genetic Affairs tools, combined, function:

  • AutoCluster groups people based on if they match you and each other
  • AutoTree finds common ancestors for trees from each cluster
  • Next, AutoTree finds the trees of all matches combined, including from trees of your DNA matches not in clusters
  • AutoPedigree checks to see if a common ancestor tree meets the minimum requirement which is (at least) 3 matches of greater to or equal to 30-40 cM. If yes, an AutoPedigree with hypotheses is created based on the common ancestor of the matching people.
  • Combined AutoPedigrees then reviews all AutoTrees and AutoPedigrees that have common ancestors and combine them into larger trees.

Let’s look at examples, beginning with DNAPainter who first implemented a form of WATO.

DNA Painter

Let’s say you’re trying to figure out how you’re related to a group of people who descend from a specific ancestral couple. This is particularly useful for someone seeking unknown parents or other unknown relationships.

DNA tools are always from the perspective of the tester, the person whose kit is being utilized.

At DNAPainter, you manually create the pedigree chart beginning with a common couple and creating branches to all of their descendants that you match.

This example at DNAPainter shows the matches with their cM amounts in yellow boxes.

xAutoPedigree DNAPainter WATO2

The tester doesn’t know where they fit in this pedigree chart, so they add other known lines and create hypothesis placeholder possibilities in light blue.

In other words, if you’re searching for your mother and you were born in 1970, you know that your mother was likely born between 1925 (if she was 45 when she gave birth to you) and 1955 (if she was 15 when she gave birth to you.) Therefore, in the family you create, you’d search for parents who could have given birth to children during those years and create hypothetical children in those tree locations.

The WATO tool then utilizes the combination of expected cMs at that position to create scores for each hypothesis position based on how closely or distantly you match other members of that extended family.

The Shared cM Project, created and recently updated by Blaine Bettinger is used as the foundation for the expected centimorgan (cM) ranges of each relationship. DNAPainter has automated the possible relationships for any given matching cM amount, here.

In the graphic above, you can see that the best hypothesis is #2 with a score of 1, followed by #4 and #5 with scores of 3 each. Hypothesis 1 has a score of 63.8979 and hypothesis 3 has a score of 383.

You’ll need to scroll to the bottom to determine which of the various hypothesis are the more likely.

Autopedigree DNAPainter calculated probability

Using DNAPainter’s WATO implementation requires you to create the pedigree tree to test the hypothesis. The benefit of this is that you can construct the actual pedigree as known based on genealogical research. The down-side, of course, is that you have to do the research to current in each line to be able to create the pedigree accurately, and that’s a long and sometimes difficult manual process.

Genetic Affairs and WATO

Genetic Affairs takes a different approach to WATO. Genetic Affairs removes the need for hand entry by scanning your matches at Ancestry and Family Tree DNA, automatically creating pedigrees based on your matches’ trees. In addition, Genetic Affairs automatically creates multiple hypotheses. You may need to utilize both approaches, meaning Genetic Affairs and DNAPainter, depending on who has tested, tree completeness at the vendors, and other factors.

The great news is that you can import the Genetic Affairs reconstructed trees into DNAPainter’s WATO tool instead of creating the pedigrees from scratch. Of course, Genetic Affairs can only use the trees someone has entered. You, on the other hand, can create a more complete tree at DNAPainter.

Combining the two tools leverages the unique and best features of both.

Genetic Affairs AutoPedigree Options

Recently, Genetic Affairs released AutoPedigree, their new tool that utilizes the reconstructed AutoTrees+WATO to place the tester in the most likely region or locations in the reconstructed tree.

Let’s take a look at an example. I’m using my own kit to see what kind of results and hypotheses exist for where I fit in the tree reconstructed from my matches and their trees.

If you actually do have a tree, the AutoTree portion will simply be counted as an equal tree to everyone else’s trees, but AutoPedigree will ignore your tree, creating hypotheses as if it doesn’t exist. That’s great for adoptees who may have hypothetical trees in progress, because that tree is disregarded.

First, sign on to your account at Genetic Affairs and select the AutoPedigree option for either Ancestry or Family Tree DNA which reconstructs trees and generates hypotheses automatically. For AutoPedigree construction, you cannot combine the results from Ancestry and FamilyTreeDNA like you can when reconstructing trees alone. You’ll need to do an AutoPedigree run for each vendor. The good news is that while Ancestry has more testers and matches, FamilyTreeDNA has many testers stretching back 20 years or so in the past who passed away before testing became available at Ancestry. Often, their testers reach back a generation or two further. You can easily transfer Ancestry (and other) results to Family Tree DNA for free to obtain more matches – step-by-step instructions here.

At Genetic Affairs, you should also consider including half-relations, especially if you are dealing with an unknown parent situation. Selecting half-relationships generates very large trees, so you might want to do the first run without, then a second run with half relationships selected.

AutoPedigree options

Results

I ran the program and opened the resulting email with the zip file. Saving that file automatically unzips for me, displaying the following 5 files and folders.

Autopedigree cluster

Clicking on the AutoCluster HTML link reveals the now-familiar clusters, shown below.

Autopedigree clusters

I have a total of 26 clusters, only partially shown above. My first peach cluster and my 9th blue cluster are huge.

Autopedigree 26 clusters

That’s great news because it means that I have a lot to work with.

autopedigree folder

Next, you’ll want to click to open your AutoPedigree folder.

For each cluster, you’ll have a corresponding AutoPedigree file if an AutoPedigree can be generated from the trees of the people in that cluster.

My first cluster is simply too large to show successfully in blog format, so I’m selecting a smaller cluster, #21, shown below with the red arrow, with only 6 members. Why so small, you ask? In part, because I want to illustrate the fact that you really don’t need a lot of matches for the AutoPedigree tool to be useful.

Autopedigree multiple clusters

Note also that this entire group of clusters (blue through brown) has members in more than one cluster, indicated by the grey cells that mean someone is a member of at least 2 clusters. That tells me that I need to include the information from those clusters too in my analysis. Fortunately, Genetic Affairs realizes that and provides a combined AutoPedigree tool for that as well, which we will cover later in the article. Just note for now that the blue through brown clusters seem to be related to cluster 21.

Let’s look at cluster 21.

autopedigree cluster 21

In the AutoPedigree folder, you’ll see cluster files when there are trees available to create pedigrees for individual clusters. If you’re lucky, you’ll find 2 files for some clusters.

autopedigree ancestors

At the top of each cluster AutoPedigree file, Genetic Affairs shows you the home couple of the descendant group shown in the matches and their corresponding trees.

Autopedigree WATO chart

Image 1 – click to enlarge

I don’t expect you to be able to read everything in the above pedigree chart, just note the matches and arrows.

You can see three of my cousins who match, labeled with “Ancestry.” You also see branches that generate a viable hypothesis. When generating AutoPedigrees, Genetic Affairs truncates any branches that cannot result in a viable hypothesis for placing the tester in a viable location on the tree, so you may not see all matches.

Autopedigree hyp 1

Image 2 – click to enlarge

On the top branch, you’ll see hyp-1-child1 which is the first hypothesis, with the first child. Their child is hyp-2- child2, and their child is hyp-3-child3. The tester (me, in this case) cannot be the persons shown with red flags, called badges, based on how I match other people and other tree information such as birth and death dates.

Think of a stoplight, red=no, green are your best bets and the rest are yellow, meaning maybe. AutoPedigree makes no decisions, only shows you options, and calculated mathematically how probable each location is to be correct.

Remember, these “children,” meaning hypothesis 1-child 1 may or may not have actually existed. These relationships are hypothetical showing you that IF these people existed, where the tester could appear on the tree.

We know that I don’t fit on the branch above hypothesis 1, because I only match the descendant of Adam Lentz at 44.2 cM which is statistically too low for me to also inhabit that branch.

I’ve included half relationships, so we see hyp-7-child1-half too, which is a half-sibling.

The rankings for hypotheses 1, 2, and 7 all have red badges, meaning not possible, so they have a score of 0. Hypothesis 3 and 8 are possible, with a ranking of 16, respectively.

autopedigree my location

Image 3 – click to enlarge

Looking now at the next segment of the tree, you see that based on how I match my Deatsman and Hartman cousins, I can potentially fit in any portion of the tree with green badges (in the red boxes) or yellow badges.

You can also see where I actually fit in the tree. HOWEVER, that placement is from AutoTree, the tree reconstruction portion, based on the fact that I have a tree (or someone has a tree with me in it). My own tree is ignored for hypothesis generation for the AutoPedigree hypothesis generation portion.

Had my first cousins once removed through my grandfather John Ferverda’s brother, Roscoe, tested AND HAD A TREE, there would have been no question where I fit based on how I match them.

autopedigree cousins

As it turns out they did test, but provided no tree meaning that Genetic Affairs had no tree to work with.

Remember that I mentioned that my first cluster was huge. Many more matches mean that Genetic Affairs has more to work with. From that cluster, here’s an example of a hypothesis being accurate.

autopedigree correct

Image 4 – click to enlarge

You can see the hypothetical line beneath my own line, with hypothesis 104, 105, 106, 107, 108. The AutoTree portion of my tree is shown above, with my father and grandparents and my name in the green block. The AutoPedigree portion ignores my own tree, therefore generating the hypothesis that’s where I could fit with a rank of 2. And yes, that’s exactly where I fit in the tree.

In this case, there were some hypotheses ranked at 1, but they were incorrect, so be sure to evaluate all good (green) options, then yellow, in that order.

Genetic Affairs cannot work with 23andMe results for AutoPedigree because 23andMe doesn’t provide or support trees on their site. AutoClusters are integrated at MyHeritage, but not the AutoTree or AutoPedigree functions, and they cannot be run separately.

That leaves Family Tree DNA and Ancestry.

Combined AutoPedigree

After evaluating each of the AutoPedigrees generated for each cluster for which an AutoPedigree can be generated, click on the various cluster combined autopedigrees.

autopedigree combined

You can see that for cluster 1, I have 7 separate AutoPedigrees based on common ancestors that were different. I have 3 AutoPedigrees also for cluster 9, and 2 AutoPedigrees for 15, 21, and 24.

I have no AutoPedigrees for clusters 2, 3, 5, 6, 7, 8, 14, 17, 18, and 22.

Moving to the combined clusters, the numbers of which are NOT correlated to the clusters themselves, Genetic Affairs has searched trees and combined ancestors in various clusters together when common ancestors were found.

Autopedigree multiple clusters

Remember that I asked you to note that the above blue through brown clusters seem to have commonality between the clusters based on grey cell matches who are found in multiple groups? In fact, these people do share common ancestors, with a large combined AutoPedigree being generated from those multiple clusters.

I know you can’t read the tree in the image that follows. I’m only including it so you’ll see the scale of that portion of my tree that can be reconstructed from my matches with hypotheses of where I fit.

autopedigree huge

Image 5 – click to enlarge

These larger combined pedigrees are very useful to tie the clusters together and understand how you match numerous people who descend from the same larger ancestral group, further back in time.

Integration with DNAPainter

autopedigree wato file

Each AutoPedigree file and combined cluster AutoPedigree file in the AutoPedigree folder is provided in WATO format, allowing you to import them into DNAPainter’s WATO tool.

autopedigree dnapainter import

You can manually flesh out the trees based on actual genealogy in WATO at DNAPainter, manually add matches from GEDmatch, 23andMe or MyHeritage or matches from vendors where your matches trees may not exist but you know how your match connects to you.

Your AutoTree Ancestors

But wait, there’s more.

autopedigree ancestors folder

If you click on the Ancestors folder, you’ll see 5 options for tree generations 3-7.

autopedigree ancestor generations

My three-generation auto-generated reconstructed tree looks like this:

autopedigree my tree

Selecting the 5th generation level displays Jacob Lentz and Frederica Ruhle, the couple shown in the AutoCluster 21 and AutoPedigree examples earlier. The color-coding indicates the source of the ancestors in that position.

Autopedigree expanded tree

click to enlarge

You will also note that Genetic Affairs indicates how many matches I have that share this common ancestor along with which clusters to view for matches relevant to specific ancestors. How cool is this?!!

Remember that you can also import the genetic match information for each AutoTree cluster found at Family Tree DNA into DNAPainter to paint those matches on your chromosomes using DNAPainter’s Cluster Auto Painter.

If you run AutoCluster for matches at 23andMe, MyHeritage, or FamilyTreeDNA, all vendors who provide segment information, you can also import that cluster segment information into DNAPainter for chromosome painting.

However, from that list of vendors, you can only generate AutoTrees and AutoPedigrees at Family Tree DNA. Given this, it’s in your best interest for your matches to test at or upload their DNA (plus tree) to Family Tree DNA who supports trees AND provides segment information, both, and where you can run AutoTree and AutoPedigree.

Have you painted your clusters or generated AutoTrees? If you’re an adoptee or looking for an unknown parent or grandparent, the new AutoPedigree function is exactly what you need.

Documentation

Genetic Affairs provides complete instructions for AutoPedigree in this newsletter, along with a user manual here, and the Facebook Genetic Affairs User Group can be found here.

I wrote the introductory article, AutoClustering by Genetic Affairs, here, and Genetic Affairs Reconstructs Trees from Genetic Clusters – Even Without Your Tree or Common Ancestors, here. You can read about DNAPainter, here.

Transfer your DNA file, for free, from Ancestry to Family Tree DNA or MyHeritage, by following the easy instructions, here.

Have fun! Your ancestors are waiting.

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Products and Services

Genealogy Research

 

Big Y News and Stats + Sale

I must admit – this past January when FamilyTreeDNA announced the Big Y-700, an upgrade from the Big Y-500 product, I was skeptical. I wondered how much benefit testers would really see – but I was game to purchase a couple upgrades – and I did. Then, when the results came back, I purchased more!

I’m very pleased to announce that I’m no longer skeptical. I’m a believer.

The Big Y-700 has produced amazing results – and now FamilyTreeDNA has decoupled the price of the BAM file in addition to announcing substantial sale prices for their Thanksgiving Sale.

I’m going to discuss sale pricing for products other than the Big Y in a separate article because I’d like to focus on the progress that has been made on the phylogenetic tree (and in my own family history) as a result of the Big Y-700 this year.

Big Y Pricing Structure Change

FamilyTreeDNA recently anounced some product structure changes.

The Big Y-700 price has been permanently dropped by $100 by decoupling the BAM file download from the price of the test itself. This accomplishes multiple things:

  • The majority of testers don’t want or need the BAM file, so the price of the test has been dropped by $100 permanently in order to be able to price the Big Y-700 more attractively to encourage more testers. That’s good for all of us!!!
  • For people who ordered the Big Y-700 since November 1, 2019 (when the sale prices began) who do want the BAM file, they can purchase the BAM file separately through the “Add Ons and Upgrades” page, via the “Upgrades” tab for $100 after their test results are returned. There will also be a link on the Big Y-700 results page. The total net price for those testers is exactly the same, but it represents a $100 permanent price drop for everyone else.
  • This BAM file decoupling reduces the initial cost of the Big Y-700 test itself, and everyone still has the option of purchasing the BAM file later, which will make the Big Y-700 test more affordable. Additionally, it allows the tester who wants the BAM file to divide the purchase into two pieces, which will help as well.
  • The current sale price for the Big Y-700 for the tester who has taken NO PREVIOUS Y DNA testing is now just $399, formerly $649. That’s an amazing price drop, about 40%, in the 9 months since the Big Y-700 was introduced!
  • Upgrade pricing is available too, further down in this article.
  • If you order an upgrade from any earlier Big Y to the Big Y-700, you receive an upgraded BAM file because you already paid for the BAM file when you ordered your initial Big Y test.
  • The VCF file is still available for download at no additional cost with any Big Y test.
  • There is no change in the BAM file availability for current customers. Everyone who ordered before November 1, 2019 will be able to download their BAM file as always.

The above changes are permanent, except for the sale price.

2019 has been a Banner Year

I know how successful the Big Y-700 has been for kits and projects that I manage, but how successful has it been overall, in a scientific sense?

I asked FamilyTreeDNA for some stats about the number of SNPs discovered and the number of branches added to the Y phylotree.

Drum roll please…

Branches Added This Year Total Tree Branches Variants Added to Tree This Year Total Variants Added to Tree
2018 6,259 17,958 60,468 132.634
2019 4,394 22.352 32,193 164,827

The tests completed in 2019 are only representative for 10 months, through October, and not the entire year.

Haplotree Branches

Not every SNP discovered results in a new branch being added to the haplotree, but many do. This chart shows the number of actual branches added in 2018 and 2019 to date.

Big Y 700 haplotree branches.png

These stats, provided by FamilyTreeDNA, show the totals in the bottom row, which is a cumulative branch number total, not a monthly total. At the end of October 2019, the total number of individual branches were 22,352.

Big Y 700 haplotree branches small.png

This chart, above, shows some of the smaller haplogroups.

Big Y 700 haplotree branches large.png

This chart shows the larger haplogroups, including massive haplogroup R.

Haplotree Variants

The number of variants listed below is the number of SNPs that have been discovered, named and placed on the tree. You’ll notice that these numbers are a lot larger than the number of branches, above. That’s because roughly 168,000 of these are equivalent SNPs, meaning they don’t further branch the tree – at least not yet. These 168K variants are the candidates to be new branches as more people test and the tree can be further split.

Big Y 700 variants.png

These numbers also don’t include Private Variants, meaning SNPs that have not yet been named.

If you see Private Variants listed in your Big Y results, when enough people have tested positive for the same variant, and it makes sense, the variants will be given a SNP name and placed on the tree.

Big Y 700 variants small.png

The smaller haplogroups variants again, above, followed by the larger, below.

Big Y 700 variants large.png

Upgrades from the Big Y, or Big Y-500 to Big Y-700

Based on what I see in projects, roughly one third of the Big Y and Big Y-500 tests have upgraded to the Big Y-700.

For my Estes line, I wondered how much value the Big Y-700 upgrade would convey, if any, but I’m extremely glad I upgraded several kits. As a result of the Big Y-700, we’ve further divided the sons of Abraham, born in 1747. This granularity wasn’t accomplished by STR testing and wasn’t accomplished by the Big Y or Big Y-500 testing alone – although all of these together are building blocks. I’m ECSTATIC since it’s my own ancestral line that has the new lineage defining SNP.

Big Y 700 Estes.png

Every Estes man descended from Robert born in 1555 has R-BY482.

The sons of the immigrant, Abraham, through his father, Silvester, all have BY490, but the descendants of Silvester’s brother, Robert, do not.

Moses, son of Abraham has ZS3700, but the rest of Abraham’s sons don’t.

Then, someplace in the line of kit 831469, between Moses born in 1711 and the present-day tester, we find a new SNP, BY154784.

Big Y 700 Estes block tree.png

Looking at the block tree, we see the various SNPs that are entirely Estes, except for one gentleman who does not carry the Estes surname. I wrote about the Block Tree, here.

Without Big Y testing, none of these SNPs would have been found, meaning we could never have split these lines genealogically.

Every kit I’ve reviewed carries SNPs that the Big Y-700 has been able to discern that weren’t discovered previously.

Every. Single. One.

Now, even someone who hasn’t tested Y DNA before can get the whole enchilada – meaning 700+ STRs, testing for all previously discovered SNPs, and new branch defining SNPs, like my Estes men – for $399.

If a new Estes tester takes this test, without knowing anything about his genealogy, I can tell him a great deal about where to look for his lineage in the Estes tree.

Reduced Prices

FamilyTreeDNA has made purchasing the Big Y-700 outright, or upgrading, EXTREMELY attractive.

Test Price
Big Y-700 purchase with no previous Y DNA test

 

$399
Y-12 upgrade to Big Y-700 $359
Y-25 upgrade to Big Y-700 $349
Y-37 upgrade to Big Y-700 $319
Y-67 upgrade to Big Y-700 $259
Y-111 upgrade to Big Y-700 $229
Big Y or Big Y-500 upgrade to Big Y-700 $189

Note that the upgrades include all of the STR markers as yet untested. For example, the 12-marker to Big Y-700 includes all of the STRs between 25 and 111, in addition to the Big Y-700 itself. The Big Y-700 includes:

  • All of the already discovered SNPs, called Named Variants, extending your haplogroup all the way to the leaf at the end of your branch
  • Personal and previously undiscovered SNPs called Private Variants
  • All of the untested STR markers inclusive through 111 markers
  • A minimum of a total of 700 STR markers, including markers above 111 that are only available through Big Y-700 testing

With the refinements in the Big Y test over the past few years, and months, the Big Y is increasingly important to genealogy – equally or more so than traditional STR testing. In part, because SNPs are not prone to back mutations, and are therefore more stable than STR markers. Taken together, STRs and SNPs are extremely informative, helping to break down ancestral brick walls for people whose genealogy may not reach far back in time – and even those who do.

If you are a male and have not Y DNA tested, there’s never been a better opportunity. If you are a female, find a male on a brick wall line and sponsor a scholarship.

Click here to order or upgrade!

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research