Louis Kessler’s Behold Blog

Lots has been happening on the DNA analysis front in the past few months. Lots of very divergent opinions on a whole bunch of issues.

Here are my opinions. You are free to agree or disagree, but these are mine.

AncestryDNA

• Ancestry has had performance issues. Couldn’t they have been more honest to say performance is the reason for their cease and desist orders to the 3rd party screen scrapers who have been providing useful utilities.
• I just hate the endless scrolling screens. Bring back paging, please.
• The 6 and 7 total cM matches that Ancestry will be deleting definitely include people who have a higher probability of being related, but not because of the small DNA match which is likely false and too distant a match to ever track.
• The 6 and 7 total cM matches are also being deleted because of their performance issues.   
• I in no way trust Ancestry’s Timber algorithm, especially with the longest segment length being labeled as pre-Timber to explain why it’s longer than the post-Timber total cM. Now none of their numbers make sense.
• Longest segment length is not as helpful if you have to look at it one by one. Why didn’t they show it in the match list and let us sort by it?
• Let us download our match list, please.
• Thinking Ancestry will ever give us a chromosome browser is a pipe dream.

23andMe

• I love that they show your ethnicity on a chromosome map. This is in my opinion, a very underutilized feature by DNA testers.
• Their Family Tree generated from just your DNA matches is a fantastic innovation.
• A month ago, some people were able to add any of their DNA matches to that family tree. They’ve never announced this and it still hasn’t rolled out to me yet. What’s the problem here? Release it, please!
• If my matches don’t opt in, I don’t want to know that. Please give me 2000 matches rather than 1361 matches that I can see and 639 that I can’t.

FamilyTreeDNA

• Lot’s of innovation that they don’t get enough credit for, e.g. their assignment of Paternal / Maternal / Both to your matches based on the Family Tree you build.
• Keeps your DNA for a looooooong time! Will be useful for future tests that don’t exist now on your relatives who passed away.
• Best Y-DNA and mtDNA analysis for those who can make use of it.
• Take advantage of their Projects if you can!
• Nobody should see segment matches down to 1 cM, or have them included in your match totals. Pick a more reasonable cutoff, please.

MyHeritage DNA

• I hate, hate, hate, did I say hate, imputation and splicing.
• As a result of the aforementioned, I believe MyHeritage has the most inaccurate matching and ethnicities of the major services.
• Showing triangulations on their chromosome browser is their best advanced feature that no one else has. 
• I love that you are working with 3rd parties, and include features that others won’t such as AutoClusters.
• How about some features to connect your DNA matches to your tree, like Ancestry and 23andMe and Family Tree DNA have?

Living DNA

• They’ve missed out on a golden opportunity. They had the whole European market available.
• Three years ago they launched and promised shared matches and a chromosome browser, which they’ve still not implemented.
• Your ethnicity in no way works for me unless you add a Jewish category.

GEDmatch

• I feel so sorry for GEDmatch’s recent troubles. They are trying so hard.
• Great tools. Love the new Find Common Ancestors from DNA Matches tool that compares your GEDCOM with the GEDCOM files of your matches. Would love it more if I had any results from it.
• They let you analyze anyone’s DNA, but don’t let you download your own tool-manipulated raw data.  Doesn’t that seem backwards?
• Over 100 cold cases have been solved using DNA to identify the suspect. I loved CeCe Moore’s Genetic Detective series. I can’t figure why more people won’t opt-in their DNA for police use.

ToTheLetter DNA and KeepSake DNA

• C’mon guys. We all want the stamps and envelopes our ancestors licked analyzed. This sounded so promising a couple of years ago. What’s taking so long?

Whole Genome Sequencing (WGS)

• Sorry, but today’s WGS technology will never improve relative matching the way some people think it will. Current chip-based testing already does as good a job you can do when you’re dealing with unphased data.
• Today’s WGS short read technology is too short. Today’s WGS long read technology is too inaccurate.
• The breakthrough will come once accurate long reads can sequence and phase the entire genome with a single de novo assembly (no reference required) for $100.
• PacBio is leading the way with their unbiased accurate long read SMRT technology that is not subject to repeat errors. It just needs to be about 100 times longer and remain accurate and we’re there. Optimistically: 5 years for the technology and 10 years for the price to come down.

Have you heard the big hubbub going on in genetic genealogy circles?  Ancestry will be dropping your 6 and 7 cM matches from your match list.

In my case, I have 192,306 DNA matches at Ancestry. Of those, 54,498 matches are below 8 cM meaning Ancestry will drop over 28% of the the people on my match list.

The Proof Corner

Many of the DNA experts understand that a 6 or 7 cM segment is small and is rarely useful for proof of anything. That is totally true. As Blaine Bettinger states, small segment are “poison”. They are often false matches. When they are not, those segments are usually too many generations back to be used as “proof” of the connection.

I am not talking about Y-DNA or mtDNA here. Those have provable qualities in them. I’m talking about autosomal matching, you know, the DNA where the amount of DNA you share with a cousin reduces with each generation and you can be a 3rd cousin with someone and not share anything.

The only reasonable way to use autosomal segment matches as a “proof” is to use the techniques Jim Bartlett developed for Walking an Ancestor Back. This technique uses combinations of MRCAs on the same ancestral line, e.g. a 2C, a 3C, a 5C and a 7C all matching on the same segment who are on the same line. Jim has been able to do this successfully only because he has an extensive family tree and has rigorously mapped all his matches into triangulation groups over his whole genome. This is something that 99.9% of us will never attempt.

Note that Jim only includes matches that triangulate that are at least 7 cM. He is also aware that small segments may be false even when triangulated, so he excludes them.

But too often, people find through a DNA match a new 7th cousin, and find a family tree connection to them, and then claim that the DNA match proves the connection. This is so untrue on so many fronts.

Or people find two relatives who have a segment match that starts and/or ends at the same position as another DNA match. They then use this as proof of their connection to Charlemagne. Now doesn’t that sound ridiculous?

The Hint Corner

So why the worry of eliminating these mostly false, poison matches that can’t prove anything from your Ancestry DNA match list? It’s because they are hints.

As genealogists, we are using our DNA matches to find possible relatives that have common ancestors with us. We do that to extend our tree outwards and up. Any person who may have researched a part of our tree and have information about our relatives and ancestors that we don’t have is a very welcome find. (Hopefully they’ll respond to our email!)

So of my 192,306 matches, the closest 1% are the best candidates for me to research and see if I can connect them.

What about the other 99%? Surely, some of them might turn up to be a closer cousin than expected, or be along a line that I have researched deeper.

Obviously, none of us can spend the rest of our lives researching 190,000 matches one by one. So what do we do. We filter them to get interesting candidates, via:

1. A match who shares a common ancestor.

2. Match name who matches a surname in our tree

3. Surname in matches’ tree who matches one of ours

4. Birth location in matches’ tree that is a place our ancestors were from, or our relatives now live.

5. Shared matches who match with some of our DNA matches who we already have in our tree.

6. ThruLines, which compares the trees of our DNA matches for us and gives us possible family connections that we can investigate.

The people we find through any of these 6 methods (and other similar methods) is a way to take an unmanageable list of 192,000 people and select a subset for us to look at. Our hope (we don’t know this for sure) is that this will include more people who we’ll be able to connect to our family, and exclude the ones who are less likely.

So what most people are lamenting is not the loss of 28% of their DNA matches, but a loss of 28% of the hints they might be able to use.

Recommendation

If you want, there are ways to save some of the 6 and 7 cM matches that Ancestry will soon be eliminating. I won’t describe them here since many others already have. See Randy Seaver’s summary.

But please, don’t spend the next few weeks robotically marking the tens of thousands of small matches so that you don’t lose them. Yes, maybe one of them will turn out to be a hint one day. But you’ve got all your other matches to work with as well. You won’t run out of things to do, I guarantee it.

Addendum:  July 29, 2020:

If small DNA matches of 6 or 7 cM at Ancestry DNA cannot be used to prove a connection, because they are either false matches, or are too many generations back to confirm their ancestral path, then why can they be used as hints?

Answer: Simply because if you take a random selection of, say, 20,000 DNA testers at Ancestry, some of them will be relatives of yours. They may not actually share DNA with you, since 3rd cousins and further need not, but they could be people whose family tree connects to yours.

Basically, Ancestry DNA is giving you hints by simply giving you a large random selection of DNA testers. Their filtering tools (surname, place) may narrow those down to possible relatives, who don’t necessarily share any actual DNA with you.    
   
But these hints are better than just random hints. They will likely be people who share more ethnicity with you than a random DNA tester at Ancestry would.

For example, Ancestry has me at 100% European Jewish. If I compare myself with my first 6 cM match at Ancestry, I get this:

This 6 cM match of mine also has 100% European Jewish ethnicity.

To see if this was generally the case, I took my closest 20 matches, and my first 20 matches at 40 cM, at 20 cM, 15 cM, 10 cM, 9 cM, 8 cM, 7 cM and 6 cM. I marked down what percentage of European Jewish they had. Then I sorted each group of 20 highest to lowest. I get this:

Of the 180 matches I checked 179 had some European Jewish Ancestry. Over half of the matches also had 100% European Jewish ethnicity and many of them have 50% or more.

There is a much greater chance that I might find a connection to someone with European Jewish ancestry than someone without any, so these are good hints. Using ancestral surname and place filtering tools, I might find that some of these people are relatives and they can help me extend my family tree.

Does that mean that we share DNA?  Not necessarily. The matches, especially the small ones, may be false matches.,

Or we may actually share DNA. but the segments we share may not be coming from the common ancestor we found, but may be from another more distant line that we’ll never find, or it may be (especially in my case) general background noise from distant ancestors due to endogamy. We don’t know and cannot tell.

None-the-less, these matches are hints that might connect you to a relative.

A very exciting day for me today, as most of you reading this will relate to. A second cousin of mine who I know showed up on my 23andMe match list. She matched me with 3.1% = 234 cM on 19 segments, which is exactly where she should be according to The Shared cM Project tool.

I have 9 other cousins who have have tested at 23andMe and match me. What makes this newly tested cousin different from the other 9 is that she’s on my mother’s side! All my previous known matches at 23andMe were on my father’s side.

So now I can finally get some maternal information from my 23andMe matches. A second cousin is perfect because we share great-grandparents and she will allow me to cluster my maternal matches into my mother’s father’s side, the side she is on.

23andMe’s Family Tree

I last looked at 23andMe’s Family Tree last September in my article: 23andMe’s Family Tree Beta.

My tree as calculated by 23andMe back then included 13 of my DNA matches. It placed 8 on my father’s side and 5 on my mother’s side.

My automated tree today has two more of my matches included, so there are now 15. The 8 circled matches at the left are on my father’s side. The 7 circled matches at the right are on my mother’s side. The people circled in blue are the 5 relatives in the tree that I know how I’m related to. One is a 1C1R who is the granddaughter of my uncle, so she shares both my paternal grandparents with me and I show her above the “F”. The other 4 are all on my father’s father’s side, and they are in the “FF” section. I do have a few relatives on my father’s mother’s side that tested, but 23andMe decided not to include them in my automated tree. There are 10 matches that I don’t know how they are related to me. But the tree hypothesizes that 1 is on my father’s father’s side, 2 are on my father’s mother’s side, and 7 are on my mother’s side. (Click the image below for a larger version)

23andMe has not yet included my new mother-side match on my tree. They only recalculate the tree from time to time and I’d have to wait until they do it again to see if they add my cousin to it.

Of those 7 people hypothesized to be on my mother’s side, 3 are with one parent and 4 are with the other. So once my cousin is added, presumably the group of 3 or the group of 4 would be with her on my mother’s father’s side and the other group would be on my mother’s mother’s side.

But then I saw that I don’t have to wait for 23andMe’s recalculation.

At the top left of the tree is this symbol:

When I click on it, it brings up this box with unplaced relatives:

I have 5 people shown at the bottom. You have to scroll to the right to see the other two. The person on the left is my newly tested cousin. The other 4 are people I don’t know how I’m related to.

Clicking on the little info symbol next to the “Unplaced Relatives” text gives:

Clicking on the “Learn more” link gives:

Well 5 minutes doesn’t sound so bad. Let’s see what happens when I reset my tree.

Recalculating the 23andMe Family Tree

I press the “Yes, delete my edits and recalculate my tree” button, and it gives this:

Okay. 5 to 10 minutes isn’t so bad either.  Back at the tree, they actually show progress:

Now it’s saying less than 1 minute. Sheesh!  After about what turns out to be 3 minutes, I get this message:

I’m doing this on a Thursday evening at 7 p.m. CDT. Is this a busy time?

I wait a couple of minutes and of course I don’t believe them and don’t want to wait until tomorrow, so I go back up to the 23andMe main menu, and under Family & Friends, select “Family Tree”

Sure enough, I didn’t have to wait a day. It displays my new tree:

Now it only shows 6 of my DNA matches. Pressing the symbol in the top left, it now shows this:

So it moved 9 of my previously placed matches into the Unplaced Relatives list. That list now has those 9 plus the 5 that I had before I had them recalculate the tree, plus the 8 non-tested relatives (e.g. my parents, grandparents, uncle, cousin, etc.) that I had previously manually added to my tree.

The recalculation placed some of my paternal cousins at the wrong generational level. But that’s no problem. Since the beta 10 months ago, 23andMe has added the ability to move people in the tree, and even move a whole branch of the tree:

The link the often show that says “View our guide:” takes you to 23andMe’s illustrative guide of How to build and edit your Family Tree, which is worth a read. In there, you’ll see that you not only can add people to your tree, but you can include their date and place of birth and death and add a photo. I’m not sure why entering the birth and death information is currently useful, since that information doesn’t show up in the tree. But maybe 23andMe has planned a use for it that they’ve not implemented yet.

Unfortunately, the one person I really wanted automatically added, my new DNA testing relative on my mother’s side, was not placed. That would have separated out my maternal sides. But now it wouldn’t have helped anyway, because the 7 people they previously placed on my maternal side were now all with the Unplaced Relatives. So placing my 2nd cousin without those 7 on the tree no longer will allow me to divide them up into my MF and MM sides.

My New 23andMe’s Family Tree

I can easily add my new cousin, because I know where she goes. But I can’t add the people that the recalculation removed from the tree because I don’t know how I’m related to them. It would have been nice if 23andMe could have left them in. The algorithm must have changed somewhat. Maybe those people were previously placed inaccurately.

So be aware. You may lose some of 23andMe’s theories if you recalculate. Make sure you record how everyone is connected before you get it to do the recalculation.

Now my tree has 6 DNA relatives whose relationship I know. There is only one theory remaining. My tree now looks like this, with my father’s side now being on the right side.

I’ve circled in green the 6 relatives I have that I know are placed correctly. Circled in red is the one relative that remains as 23andMe’s theory.

23andMe has left me with 13 people in my Unplaced Relatives that I cannot place.

I also have 5 relatives among my matches that I know how I’m related, but 23andMe’s Family Tree chose not to include them. I could add them to the correct place on 23andMe’s Family Tree. But they would not be connected to their DNA match information. It would be nice if 23andMe would allow you to select people from your match list. I think I’ll suggest that to them via their survey at the bottom of Your Family Tree page.

Updating My Double Match Triangulator 23andMe Results

I last tried DMT on my 23andMe data last October:  Using DMT, Part 1: My 23andMe Data. Since I only had paternal matches back then, DMT couldn’t do much with my maternal side other than classifying which matches it calculated were maternal. What it gave me back then was this:

So now I’ll just do this exercise again. I’ll use DNAGedcom Client to download a new set of segment match files from 23andMe (see DMT’s help file for how to do this).

The segment match files I’ll download will be for myself and the 10 relatives I know how I’m related to. Each takes about 10 minutes for DNAGedcom to gather, so I’ll do them while I’m working on something else.

Two Hours Later

I put the 11 segment match files into a folder. I start DMT and select my own segment match file as File A. I have DMT create my People file with all my matches. Now I go through and add the MRCA for my 10 known relatives (9 of which are shown below):

Now I set Folder B to the folder containing all the match files and I let ‘er rip.

Double Match Triangulator clusters my matches into these groups. Compare this to the table above:

I have 199 more matches than I did last October.  The percentages are about the same as they used to be with the exception that DMT was able to pick out 201 of the maternal matches and associate them with my mother’s father’s cluster, due to their segment matches with my newly tested cousin.

Also, last October, I was only able to paint grandparents or further over 46.1% of my paternal DNA and none of my maternal side.  Now with my new data including my newly tested cousin, I’m able to paint 46.8% of my paternal side and 25.6% of my maternal side as well.

Uploading the DNA Painter file that DMT produces with this latest run into DNA Painter now gives this:

This is very similar to what I got 10 months ago, but now a significant amount of my maternal grandfather’s side (MF, in red) also gets painted. That’s a nice chunk of additional painting that DMT was able to add.

That one person whose relationship that I don’t know that 23andMe added to my tree (see the last tree above, red circle, far right) they included as a second cousin once removed on my father’s father’s mother’s side. DMT puts that person in my FF (father’s father’s) cluster. DMT cannot work this any further back because I don’t have any cousins tested who I know are on either my FFF or FFM side for it to use. So 23andMe’s estimation of FFM is a good theory and could be correct. Now I’ll just have to trace his family tree and see if we can connect.