Lazarus – Putting Humpty Dumpty Back Together Again

Recently, GedMatch introduced a tool, Lazarus, to figuratively raise the dead by combining the DNA of descendants, siblings and other relatives of long-dead ancestors to recreate their genome.  Kind of like piecing Humpty Dumpty back together again.

Humpty Dumpty

Blaine Bettinger wrote about using Lazarus here and here where he recreated the genome of his grandmother.  I’d like to use Lazarus to see how it works with one pair of siblings and a first cousin.  Blaine was fortunate to have 4 siblings.  I have a much smaller group of people to work with, so let’s see what we can do and how successful we are, or aren’t.  But first, lets talk about the basics and how we can reconstruct an ancestor.

The Basics

An individual has 6766.2 cM of DNA.  Both parents give half of their DNA to each child, but not exactly the same parental DNA is contributed to each child.  A random process selects which half of the parents’ DNA is given to each child.  Different children will have some of the same DNA from their parents, and some different DNA from each parent.

Obviously, the DNA contributed to each child from a parent is a combination of the DNA given to the parent by the grandparents.  Approximately half of the grandparent’s DNA is given to each child.  In many cases, the DNA contributed to the child from the grandparents is not actually divided evenly, and we receive all or nothing of individual segments, not half.  Half is an average that works pretty well most of the time.  It’s a statistic, and we all know about statistics…right???

Therefore, children carry 3383cM of each parent’s DNA.  Each sibling carries half of the same DNA from their parents.  From the ISOGG autosomal DNA statistics chart, each sibling actually carries 25% of exactly the same DNA from both parents, 50% where they inherited half of the same DNA from one parent and different DNA from the other parent, and 25% where the siblings don’t share any of the identical DNA from their parents. This averages 50%.

This chart, also from ISOGG, sums up what percentage of the same DNA different relatives can expect to carry.

cousin percents

Recreating Ferverda Brothers

I have a situation where I have a person, Barbara, and two of her first cousins, Cheryl and Don, who are siblings.  This is the same family we discussed in the Just One Cousin article.

Miller Ferverda chart

In this case, Cheryl and Don share 50% of Roscoe’s DNA.

Barbara shares 12.5% of Hiram and Evaline’s DNA with Cheryl and 12.5% with Don, but not the same 12.5%.  Since siblings share 50% of their DNA, Barbara should share about 12.5% of Cheryl’s DNA and an additional 6.25% that the Cheryl didn’t receive from Roscoe, but that Don did.

Translating that into cMs, Barbara should share about 850 cM with Cheryl and an additional 425 cM with Don, for an approximate total of 1275 cM.

At http://www.gedmatch.com, I selected the Tier 1 (subscription or donation) option of Lazarus and was presented with this menu.

lazarus menu

My first attempt was to recreate Barbara’s father, John W. Ferverda.  I allowed 100 SNPs and 4cM because I was hoping to be able to accumulate more than the required 1500cM of matching DNA for the kit to be utilized as a “real kit,” available for one-to-many matching.

100SNP 4cM 200SNP 4cM 300SNP 4cM 400SNP 4cM 500SNP 4cM 600SNP 4cM 700SNP 4cM
John W. Ferverda 1330.7 cM 1370.2 cM 1360.0 cM 1353.5 cM 1338.7 cM 1336.2 cM 1322.9 cM

I then experimented with the various SNP levels, leaving the cM at 4.

The resulting number of cM of just over 1300, no matter how you slice and dice it, is very near the expected approximation of 1275.

Using the Lazarus tool, I created “John Ferverda” by listing Barbara as his descendant and both Cheryl and Don as cousins.

To create “Roscoe Ferverda,” I reversed the positions of the individuals, listing Don and Cheryl as descendants and Barbara as the cousin.

Lazarus options

These two created individuals, “John” and “Roscoe” should be exactly the same, and, thankfully, they were.

Both recreated “John” and “Roscoe” represent a common set of DNA from the parents of both of these men, Hiram Ferverda and Evaline Miller based on the matching DNA of their descendants, Barbara, Cheryl and Don.

The way Lazarus works is that all kits in Group 1, the descendants, are compared with Group 2, other relatives but not descendants.  The descendants will carry some of Roscoe’s DNA, but also the DNA of Roscoe’s wife, the mother of Don and Cheryl.  By comparing against known relatives but not direct descendants, Lazarus effectively narrows the DNA to that contributed only by the common ancestor of group 1 and group 2.  In this case, that common ancestor would be John and Roscoe’s parents, Hiram Ferverda and Evaline Miller.  By comparing the descendant and non-descendant-but-otherwise-related groups, you effectively subtract out the mother’s DNA from the descendants – in this case meaning the DNA of John Ferverda’s wife and Roscoe Ferverda’s wife.

In other words, the descendants, above, are NOT compared to each other, but instead, to each one of the not-descendant-but-otherwise-related group.

Unfortunately, none of the kits generated was over the 1500 cM threshold.  I remembered that there is also a second cousin, Rex, whose DNA we can add because he descends from the parents of Evaline Miller.

Adding Rex to the mix brought the resulting “Roscoe” kit to 1589.7 cM and the resulting “John” kit to 1555.7 cM, both now barely over the 1500 threshold – but over just the same and that’s all that matters.  Soon, we’ll be able to utilize both of these kits for direct matching as a “person” at GedMatch.  Now how cool is that???

You receive four pieces of output information when you create a Lazarus kit.

First, a comparison between the descendants (Group 1 above, Kit 2 below) and each of the cousins and related-but-not-descendants individuals (Group 2 above, Kit 1 below), by chromosome.

John W. Ferverda

Processed: 2015/01/09 17:32:41
Name: John W. Ferverda
SNP threshold = 100 cM
Threshold = 4.0 cM
Batch processing will be performed if resulting kit achieves required threshold of 1500 cM.

Contributions:

Kit 1

Kit 2

Chr

Start

End

cM

F9141

M133930

1

72017

5703284

14.8

F9141

M133930

1

17271101

18589169

4.1

F9141

M133930

1

32804999

65722466

37.8

F9141

M133930

1

242601404

247174776

8.5

Obviously, these are only snippets of the output for chromosome 1.  You receive a chart of this same information for all of the chromosomes of the people being compared.

Second, a chart that shows the resulting matching segments.

Resulting Segments:

Chr

Start

End

cM

1

742429

5694404

14.8

1

17285357

18588145

4.1

1

38226163

43823334

7.2

1

43975578

54990495

8.0

1

55040097

62847030

12.1

1

76341094

85237614

8.7

1

242606491

247179501

8.5

At the bottom of this second set of numbers is the all-important total cM.  This is the only place you will find this number

Total cM: 1555.7

Third, a list of the original kits that have match results between the two groups.

Original Kits match with result:

Kit

Chr

Start

End

cM

F9141

1

742429

5700507

14.8

F9141

1

10899689

12530765

4.5

F9141

1

35075204

65714854

35.3

F9141

1

76334120

85252045

8.7

F9141

1

242606379

247169190

8.5

M133930

1

742429

5705356

14.8

M133930

1

35075956

65714854

35.3

M133930

1

242606491

247165725

8.5

F50000

1

10899689

12530765

4.5

F153785

1

742584

5700507

14.8

F153785

1

76337055

85252045

8.7

F153785

1

242606379

247169190

8.5

And finally, a summary.

196074 single allele SNPs were derived for the resulting kit.
37068 bi-allelic SNPs were derived for the resulting kit.
233142 total SNPs were derived for the resulting kit.
Kit number of Result: LX056148
Kit Name: John Ferverda 8
Your Lazarus file has been generated.

Is this as good as the real McCoy, meaning swabbing John and Roscoe?  Of course not, but John and Roscoe aren’t available for swabbing.  In fact, John and Roscoe are both probably finding this pretty amusing from someplace on the other side, watching their children “recreate” them!

I can hear them now, shaking their heads, “Well I never….”

They should have known if they left Cheryl and me here, together, unsupervised that we would do something like this!!!

What If You Die?

coffinWell, it’s not exactly a what-if question, it’s a given.  You’re going to.  The only real question is when, and will you be prepared?

By prepared, I’m not talking about your will, I’m talking about your DNA.

The unspeakable happened this past weekend.  A long time researcher and close friend, Aleda, died, rather unexpectedly.  She has been chronically ill for some time, but not critically.  On Saturday, she read my blog, worked with her research group on the Autosomal DNA Segment Analyzer and ordered Emily’s book.  Then, in the afternoon, she said she didn’t feel well and got into her chair to take a nap.  Nothing unusual about that.  Aleda didn’t feel well a lot, but she persevered anyway, always helping and guiding her research group.  But this time was different.  Aleda was gone.

Her research group is wandering around like a group of lost souls.  It’s like someone shot a hole through the middle of all of us.  This isn’t a large well organized group with an official structure, but a small group of closely and not so closely related researchers trying to figure out their DNA and genealogy connections.

If you are a significant contributor, you will be sorely missed.  If you are reading this, and have had your DNA tested, you are one of the contributors.

The research group members are already asking, “What next?  How do we access the DNA records of the people Aleda had tested?”  Good question.  Let’s talk about preparing for the inevitable.

Aleda had given the kit passwords to a friend, who is now so upset she can’t find them.  As the project administrator of one of the projects that includes one of Aleda’s family member’s kits, I can see some of the information.

E-Mail

I can see that Aleda set up a special DNA e-mail address which I’m presuming she used for all of the kits.  Unfortunately, there is no alternate e-mail address.

When Family Tree DNA, and virtually all the companies, do a password reset, they send the password information to the e-mail address on file.

Does anyone, other than Aleda, have the password to that e-mail account?

Project administrators cannot change primary e-mail addresses.  Only the kit owner can do that.

If you change your password to your e-mail account, you’ll need to remember to provide the new password to your trusted other as well.

Passwords

If you share your password with someone, that’s fine, but if they can’t find it, or if you change it and don’t tell them, that won’t be helpful.  You might want to add their e-mail as an alternate.  You might want to provide this information to multiple people, just in case your chosen person predeceases you, or some other unfortunate situation exists, like a fire, system crash or losing the passwords.

At 23andMe, to download a raw data file, a password isn’t enough.  You also have to know the answer to the secret question.

Beneficiary Information

Family Tree DNA goes one step further and provides people with a beneficiary form for situations just like this.

Unfortunately, Aleda’s family member’s form is blank, and she protected his information by changing the setting to prevent project administrators from completing this form.

beneficiary form

Covering all the Bases

Don’t forget about 3rd party sites like GedMatch where you may also be registered.

What to do?

1. Family Tree DNA is the only company to provide the option of beneficiary information.  Take advantage of this and complete the form.  It’s only 3 lines – name, phone and e-mail of your beneficiary.  You can find it under the “My Account” tab on the blue/black bar at the top of your personal page.

beneficiary dropdown

2. Add an alternate e-mail address.

3. Provide password and e-mail password information to a trusted other, and maybe a few trusted others.

4. Remember to notify password holders when you change passwords to either e-mail or DNA kits.

5. If you are a project administrator, try your best to find a co-administrator and share information, such as genealogy provided by participants.

6. Provide a notification list for your family that includes important genealogy and DNA contacts, including Family Tree DNA if you are a project administrator.  Many times I’ve received an e-mail from someone’s account with their name as the subject.  I’ve learned to cringe when I see them, because I know what’s coming…but at least the family has taken the trouble to notify those of us who communicate electronically with that person instead of leaving us to wonder forever what happened.

7. Preparing for the inevitable doesn’t just apply to DNA testing, but to all aspects of online life.  Think about Facebook, for example.  My brother died 2 years ago, today, and no one has his password.  We post to his page from time to time, but like a ghost ship, his Facebook account will sail off into the indefinite captainless future.

Picture This

Margaret Herrell, what did you look like?

Margaret died in 1892, but we don’t have a photo of her nor of her second husband Joseph Preston Bolton who died in 1887.  Her son, my great-grandfather, Joseph “Dode” Bolton died in 1920 and we don’t have a picture of him either, or his wife, Margaret Claxton/Clarkson who died just days later in the flu epidemic.  The closest I can get is this photo of Margaret Herrell’s daughter.

Smith-Martin

Pleasant Smith and Surelda Martin (1836-1890) – daughter of my ancestor Margaret Herrell with her first husband, Anson Cook Martin – Hancock County, Tennessee.

Today, there was an article in “abroad in the yard” by Lee Rimmer that discussed an academic paper published in PLOS Genetics this week by Liu et al titled “A Genome-Wide Association Study Identifies 5 Loci Influencing Facial Morphology in Europeans.”

We all know that facial characteristics are genetic.  Identical twins look more alike that fraternal twins, and fraternal twins look more alike that cousins or half-siblings.  But exactly which genes contribute to that structural composition of faces is unknown, or has been until now.  This recent paper identifies 5 genes that influence to some extent the morphology of the face by identifying specific facial landmarks and the genes that influence them.  Researchers expect to find hundreds or thousands more, but many of these may play small roles.

Already people are talking about forensic applications where from a drop of blood, a hair, spit or other body fluids or tissues, one could sequence the DNA, then create a 3D profile or image of the perpetrator of the crime.  Indeed, that is the holy grail of forensic genetics.

And yes, it’s a long way in the future.  However, the very definition of “long way” is certainly open to debate.  We’ve covered genetic ground in the past decade alone that we never thought possible.

This (future) application has other possibilities for genealogists.  We already know how to phase data, to attribute it to one parent or the other.  Using those and other comparative and triangulation tools, we also know how to determine genetic sequences that we share inherited from specific ancestors.  In fact, once that genetic segment is identified as inherited from a particular ancestral line, might it be possible in the future to indeed, reassemble enough of the DNA of that ancestor (by knowing the genes involved and the descendants who carry those genes today) to create an image of that long dead ancestor?

Maybe one day, not terribly far in the future, we’ll be able to submit a list of segments of DNA to a special processing “studio” online, that will in return provide us with what our ancestor looked like, long before the advent of cameras when only the images of royalty were preserved.  And maybe, just maybe, if you tell them the place and time your ancestor was born, and his or her occupation, if you know, you’ll also receive the “photo” of your ancestor dressed in period clothes and hairstyle.

And while it might not be exact, just like this “cleaned up” photo isn’t exact from an  original, shown below, it’s most assuredly better than nothing – and in that image we can certainly see something very similar to our ancestor – and in them we can see ourselves.

Smith-Martin orig

Let’s hope that this big genealogical dream of what today seems impossible happens in our lifetime so that we can complete our family tree by recreating images of ancestors from long ago.  Indeed, how much closer could one feel to an ancestor than to have their image resurrected by the DNA, their DNA, carried by their descendants. And what an incredible crowdsourcing project – it may take a virtual genealogical village.

Swabbing the (Recently) Deceased

Ezekiel EstesMeet Ezekiel Estes, son of Susanna Estes and ?  Ezekiel was born in 1814 in Halifax County, Virginia, and died in 1885, not terribly long after the camera was invented.  That is clearly when this photo was taken, at his death.

His great-grandchildren didn’t know that his father was ?  The family rumor had always been that Susanna, his mother, was apparently married to an Estes cousin, which explained why her surname as a “widow” was the same as her maiden name.  However, a lot of courthouse records research, reading of old depositions that still exist and DNA testing of a descendant proved that indeed, Ezekiel’s father was not an Estes man.

How many of you have a photo like this, or maybe one even better, with the casket showing?  Believe it or not, people made postcards of these kinds of photos.  In the early 1900s, there were photos of children who had died that were dressed and posed with the parents, as if they were still alive.  Can’t make it to the funeral, don’t worry…you get a picture.

But back then, once someone was dead, they were, well, dead forever… gone, except for that one photo.  Today, that’s not quite the case, because one can preserve DNA and part of that person will live forever through the information their DNA provides.  I mean, if we had Ezekiel’s actual DNA, we might be able to figure out who his father was.

So, what do you do if you meant to have Aunt Gladys swab at the family reunion this summer, but she had the bad judgment to pass away at Memorial Day?  Don’t just throw up your hands and show up at the funeral empty handed.  The funeral director is your friend.  They do a fine job of cheek swabbing.

Call Family Tree DNA (on the phone, not e-mail), tell the customer service representative the situation and ask for a kit to be overnighted to either the funeral director or a family member who can be counted on to take it to the funeral director the same day.  The funeral director will swab the cheek of the dearly departed and you will indeed still have the DNA information that Aunt Gladys meant to give you at the reunion.  Indeed, it’s a wonderful last gift and legacy for her to leave for you and the rest of her family and descendants.

Yes, and I know the next question that’s coming.  What about digging up the dead or testing things left behind?  Well, you’ll have to wait for a future article to discuss that in detail.  It’s much easier and infinitely less expensive to get a swab kit to the funeral director, let’s put it that way.  Plus, you’re pretty much guaranteed to get DNA from a cheek swab and attempting to retrieve DNA from personal items later is less than 50% successful, best case, and sometimes much less.  So, enlist the help of the funeral director, call Family Tree DNA or keep a swab kit handy at home at all times!