RootsTech 2020: It’s a Wrap

Before sharing photos and details about the last three days at RootsTech, I want to provide some general observations.

I expected the attendance to be down this year because of the concern about the Novel Corona Virus. There was a lot of hand-washing and sanitizer, but no hand-wringing.

I don’t think attendance was lagging at all. In fact, this show was larger, based on how my feet feel and general crowd observation than ever before. People appeared to be more engaged too.

According to RootsTech personnel, 4 major vendors pulled out the week before the show opened; 23andMe, LivingDNA, FindMyPast and a book vendor.

I doubt there’s much of a refund policy, so surely something happened in these cases. If you recall, LivingDNA and FindMyPast have a business relationship. 23andMe just laid off a number of people, but then again, so did Ancestry but you’d never know it based on the size of their booth and staffing here.

Family Search has really stepped up their game to modernize, capture stories, scan books and otherwise make genealogy interesting and attractive to everyone.

We got spoiled last year with the big DNA announcements at RootsTech, but nothing of that magnitude was announced this year. That’s not to say there weren’t vendor announcements, there were.

FamilyTreeDNA announced:

  • Their myOrigins Version 3.0 which is significantly updated by adding several worldwide populations, increasing the number from 24 to 90. I wrote about these features here.
  • Adding a myOrigins chromosome browser painted view. I am SOOO excited about this because it makes ethnicity actually useful for genealogy because we can compare specific ethnicity segments with genealogical matches. I can hardly wait.

RootsTech 2020 Sunny Paul

Sunny Morton with Family Tree Magazine interviewing Dr. Paul Maier, FamilyTreeDNA’s population geneticist. You can see the painted chromosome view on the screen behind Dr. Maier.

  • Providing, after initial release, a downloadable ethnicity estimate segment file.
  • Sponsorship of The Million Mito Project, a joint collaborative citizen science project to rewrite the mitochondrial tree of womankind includes team members Dr. Miguel Vilar, Lead Scientist of the National Geographic Genographic Project, Dr. Paul Maier, Population Geneticist at FamilyTreeDNA, Goran Runfeldt, Head of Research and Development at FamilyTreeDNA, and me, DNAeXplain, scientist, genetic genealogist, National Geographic Genographic Affiliate Researcher.

RootsTech 2020 Million Mito

I was honored to make The Million Mito Project announcement Saturday morning, but it was hard for me to contain my enthusiasm until Saturday. This initiative is super-exciting and I’ll be writing about the project, and how you can participate, as soon as I get home and recover just a bit.

  • Michael Sager, aka Mr. Big Y, announced additions to the Y Tree of Mankind in the Demo Theater, including a particularly impressive haplogroup D split.

Rootstech 2020 Sager

RootsTech 2020 Sager 2

RootsTech 2020 Sager hap d

In case anyone is counting, as of last week, the Y tree has 26,600+ named branches and over half a million detected (private variant) SNPs at FamilyTreeDNA waiting for additional testers to be placed on the tree. All I can say is WOW!!! In 2010, a decade ago, there were only 441 Y DNA branches on the entire Y tree. The Y tree has shot up from a twig to an evergreen. I think it’s actually a Sequoia and we just don’t know how large it’s going to grow to be.

RootsTech 2020 FTDNA booth

FamilyTreeDNA stepped up their game with a way-cool new booth that incorporated a lovely presentation area, greatly improved, which featured several guest presenters throughout the conference, including Judy Russell, below.

RootsTech 2020 Judy Russell

Yes, in case anyone is wondering, I DID ask permission to take Judy’s picture, AND to publish it in my article. Just sayin’😊

MyHeritage announced their new photo colorization, MyHeritage in Color, just before RootsTech. I wrote about it, here. At RootsTech MyHeritage had more announcements, including:

  • Enhancements coming soon to the photo colorization program. It was interesting to learn that the colorization project went live in less than 2 months from inception and resulted from an internal “hack-a-thon,” which in the technology industry is a fun think-tank sort of marathon endeavor where ideas flow freely in a competitive environment. Today, over a million photos have been colorized. People LOVE this feature.

RootsTech 2020 MyHeritage booth

One of their booth giveaways was a magnet – of your colorized ancestor’s photo. Conference attendees emailed the photo to a special email address and came by the booth a few minutes later to retrieve their photo magnet.

The photos on the board in front, above, are the colorized photos waiting for their family to pick them up. How fun!!!

  • Fan View for family trees which isn’t just a chart, but dynamic in that you can click on any person and they become the “center.” You can also add to your tree from this view.

RootsTech 2020 MyHeritage fan tree

One of the views is a colorful fan. If you sign on to your MyHeritage account, you’ll be asked if you’d like to see the new fan view. You can read about the new tree features on their blog, here.

  • The release of a MASSIVE 100-year US city directory digitization project that’s more than just imaging and indexing. If you’ve every used city directories, the unique abbreviations in each one will drive you batty. MyHeritage has solved that problem by providing the images, plus the “translation.” They’ve also used artificial intelligence to understand how to search further, incorporating things like spouse, address and more to provide you with not just one year or directory, but linear information that might allow you to infer the death of a spouse, for example. You can read their blog article, here.

RootsTech 2020 MyHeritage city directories

The MyHeritage booth incorporated a very cool feature this year about the Mayflower. Truthfully, I was quite surprised, because the Mayflower is a US thing. MyHeritage is working with folks in Leiden, Netherlands, where some Mayflower family members remained while others continued to what would become Plymouth Colony to prove the connection.

Rootstech 2020 MyHeritage Mayflower virtual

MyHeritage constructed a 3D area where you can sail with the Pilgrims.

I didn’t realize at first, but the chair swivels and as you move, your view in the 3D “goggles” changes to the direction on board the ship where you are looking.

RootsTech 2020 MyHeritage Mayflower virtual 2

The voyage in 1620 was utterly miserable – very rough with a great deal of illness. They did a good job of portraying that, but not “too much” if you get my drift. What you do feel is the utter smallness of the ship in the immense angry ocean.

I wonder how many descendants “sailed with their ancestors” on the virtual Mayflower. Do you have Mayflower ancestors? Mine are William Brewster, his wife, Mary and daughter, Patience along with Stephen Hopkins and his son, Gyles.

Ancestry’s only announcements were:

  • That they are “making things better” by listening and implementing improvements in the DNA area. I’ll forego any commentary because it would be based on their failure to listen and act (for years) about the absence of segment information and a chromosome browser. You’ve guessed it, that’s not mentioned.
  • That the WWII young man Draft Registration cards are now complete and online. Truthfully, I had no idea that the collection I was using online wasn’t complete, which I actually find very upsetting. Ancestry, assuming you actually are listening, how about warning people when they are using a partially complete collection, meaning what portion is and is not complete.
  • Listing content record additions planned for 2020 including the NYC birth index and other state and international records, some of which promise to be very useful. I wonder which states the statewide digitization projects pertain to and what that means, exactly.

OK, now we’re done with vendor announcements, so let’s just take a walk around the expo hall and see who and what we find. We might run into some people you know!

Walking Around

I sandwiched my walking around in-between my sessions. Not only did I present two RootsTech classes, but hosted the ToolMaker Meetup, attended two dinners, two lunches, announced The Million Mito Project, did two booth talks, one for FamilyTreeDNA and one for WikiTree, and I think something else I’ve forgotten about. Plus, all the planned and chance meetings which were absolutely wonderful.

Oh yes, and I attended a couple of sessions myself as an attendee and a few in the vendors booths too.

The great thing, or at least I think its great, is that most of the major vendors also have booth educational learning opportunities with presentation areas at their booths. Unfortunately, there is no centralized area where you can find out which booths have sessions, on what topics, when. Ditto for the Demo Theater.

Of course, that means booth presentations are also competing for your time with the regular sessions – so sometimes it’s really difficult to decide. It’s sort of like you’re awash in education for 4 days and you just can’t absorb enough. By Saturday, you’re physically and emotionally exhausted and you can’t absorb another iota, nor can you walk another step. But then you see someone you know and the pain in your feet is momentarily forgotten.

Please note that there were lots of other people that I saw and we literally passed, hugged and waved, or we were so engrossed in conversation that I didn’t realize until later that I had failed to take the photo. So apologies to all of those people.

RootsTech 2020 Amy Mags

I gave a presentation in the WikiTree booth about how to incorporate WikiTree into your 52 Ancestor stories, both as a research tool and as a way to bait the hook for cousins. Not to mention seeing if someone has already tested for Y or mtDNA, or candidates to do so.

That’s Amy Johnson Crow who started the 52 Ancestors challenge years ago, on the left and Mags Gaulden who writes at Grandma’s Genes and is a WikiTree volunteer (not to mention MitoY DNA.) Amy couldn’t stay for the presentation, so of course, I picked on her in her absence! I suspect her ears were burning. All in a good way of course.

RootsTech 2020 Kevin Borland

Kevin Borland of Borland Genetics, swabbing at the Family Tree DNA  booth, I hope for The Million Mito Project.

RootsTech 2020 Daniel Horowitz

Daniel Horowitz with MyHeritage at the blogger dinner. How about that advertising on his laptop lid. I need to do that with DNAexplain. Wonder where I can get one of those decals custom made.

RootsTech 2020 Hasani

Hasani Carter who I know from Facebook and who I discovered volunteering in a booth at RootsTech. I love to see younger people getting involved and to meet people in person. Love your dreads, Hasani.

RootsTech 2020 Randy Seaver

Cousin Randy Seaver who writes at Genea-Musings, daily, and has for YEARS. Believe it or not, he has published more than 13,000 articles, according to the Lifetime Achievement Award presented by Dear Myrtle at RootsTech. What an incredible legacy.

If you don’t already subscribe (it’s free), you’re missing out. By the way, I discovered Randy was my cousin when I read one of his 52 Ancestors articles, recognizing that his ancestor and my ancestor had the same surname in the same place. He knew the connection. Those articles really work. Thanks Randy – it was so good to see you again.

RootsTech 2020 univ dundee

The University of Dundee booth, with Sylvia Valentine and Pat Whatley, was really fun.  As part of their history and genealogy curriculum (you an earn certificates, bachelors and masters degrees,) they teach paleography, which, in case you are unaware is the official word for deciphering “ancient handwriting.” You didn’t know that’s what you’d been doing did you?

RootsTech 2020 paleography

They provided ink and quills for people to try their own hand.

RootsTech 2020 Paleography 2

The end of the feather quill pen is uneven and scratchy. Pieces separate and splatter ink. You can’t “write,” you draw the letters very, very carefully and slowly. I must say, my “signature” is more legible than normal.

Rootstech 2020 scribe

I now have a lot more empathy for those scribes. It’s probably a good thing that early records are no worse than they are.

RootsTech 2020 Gilad Japhet

Gilad Japhet at the MyHeritage luncheon. I have attended other vendor sponsored (but paid by the attendee) lunches at RootsTech in the past and found them disappointing, especially for the cost. Now MyHeritage is the only sponsored lunch that I attend and I always enjoy it immensely. Yes, I arrived early and sat dead center in front.

I also have a confession to make – I was so very excited about being contacted by Mary Tan Hai’s son that I was finishing colorizing the photos part of the time while Gilad was talking. (I did warn him so he didn’t think I was being rude.) But it’s HIS fault because he made these doggone photos so wonderful – and let’s just say time was short to get the photos to Mary’s family. You can read this amazing story, here.

Gilad always shares part of his own personal family story, and this time was no different. He shared that his mother is turning 85 soon and that the family, meaning her children and grandchildren all teamed up to make her a lovely video. Trust me, it was and made us all smile.

I’m so grateful for a genealogy company run by a genealogist. Speaking of that, Gilad’s mother was a MyHeritage board member in the beginning. That beginning also included a story about how the MyHeritage name came to be, and how Gilad managed to purchase the domain for an unwilling seller. Once again, by proxy, his mother entered into the picture. If you have the opportunity to hear Gilad speak – do – you won’t be disappointed. You’ll hear him speak for sure if you attend MyHeritage LIVE in Tel Aviv this October.

RootsTech 2020 Paul Woodbury

Paul Woodbury who works for Legacy Tree Genealogists, has a degree in both family history and genetics from BYU. He’s standing with Scott Fisher (left). Paul’s an excellent researcher and the only way you can put him to work on your brick wall is through Legacy Tree Genealogists. If you contact them for a quote, tell them I referred you for a $50 discount.

Rootstech 2020 Toolmaker meetup

From The ToolMaker’s Meetup, at far left, Jonny Pearl of DNAPainter, behind me, Dana Leeds who created The Leeds Method, and at right, Rob Warthen, the man behind DNAGedcom. Thanks to Michelle Patient for the photo.

RootsTech 2020 Toolmaker meetup 2

The meetup was well received and afforded people an opportunity to meet and greet, ask questions and provide input.

RootsTech 2020 Campbell baby

In fact, we’re working on recruiting the next generation. I have to say, my “grandma” kicked in and I desperately wanted to hold this beautiful baby girl. What a lovely family. Of course, when I noticed the family name is Campbell, we had a discussion of a different nature, especially since my cousin, Kevin Campbell and I were getting ready to have lunch. We will soon find out if Heidi’s husband is our relative, which makes her and her daughter our relative too!

Rootstech 2020 Kevin Campbell

It was so much fun to sit and develop a research plan with Kevin Campbell. We’re related, somehow on the Campbell line – we just have to sort out when and where.

Bless Your Heart

The photo I cherish most from RootsTech 2020 is the one that’s not pictured here.

A very special gentleman told me, when I asked if we could take a picture together, after he paid me the lovely compliment of saying that my session was the best one he had ever attended, that he doesn’t “do pictures.” Not in years, literally. I thought he was kidding at first, but he was deadly seriously.

The next day, I saw him again a couple of times and we shares stories. Our lives are very different, yet they still intersected in amazing ways. I feel like I’ve known him forever.

Then on the last day, he attended my Million Mito presentation and afterwards came up and told me a new story. How he had changed his mind, and what prompted the change of heart. Now we have a wonderful, lovely photo together which I will cherish all the more because I know how special it is – and how wonderful that makes me feel.

To my friend – you know who you are – thank you! You have blessed my heart. Bless yours😊

The Show Floor

I think I actually got all the way through the show floor, but I’m not positive. In some cases, the “rows” weren’t straight or had dead ends due to large booths, and it was possible to miss an area. I didn’t get to every booth I wanted to. Some were busy, some I simply forgot to take photos.

RootsTech 2020 everything

You can literally find almost anything.

I focused on booths related to genetic genealogy, but not exclusively.

RootsTech 2020 DNAPainter

Jonny Perl and the DNAPainter booth. I’ve written lots of articles, here, about using DNAPainter, one of my very favorite tools.

RootsTech 2020 Rootstech store

The RootsTech store was doing a brisk business.

RootsTech 2020 DNA basics

The RootsTech show area itself had a DNA Basics area which I thought was brilliant in its simplicity.

Inheritance is show by jellybeans.

Rootstech 2020 dNA beans

Put a cup under the outlet and pull the lever.

Rootstech 2020 beans in cup

How many of which color you receive in your cup is random, although you get exactly the same number from the maternal and paternal side.

Now you know I wanted to count these, don’t you?

Rootstech 2020 JellyGenes

And they are of course, called, “JellyGenes.” Those must be deletions still laying in the bin.

RootsTech 2020 Wikitree

WikiTree booth and volunteers. I love WikiTree – it’s “one great tree” is not perfect but these are the people, along with countless others that inject the “quality” into the process.

RootsTech 2020 MitoYDNA

MitoYDNA with Kevin Borland standing in front of the sign.

RootsTech 2020 Crossley

This amazing artist whose name I didn’t get. I was just so struck by her work, painting her ancestor from the picture on her phone.

RootsTech 2020 painter

I wish I was this talented. I would love to have some of my ancestor’s painted. Hmm….

Rootstech 2020 GeneaCreations

Jeanette at GeneaCreations makes double helix zipper pulls, along with lots of other DNA bling, and things not so blingy for men. These are just SOOO cool.

RootsTech 2020 zipper pull

I particularly love my “What’s Your Haplogroup” t-shirt and my own haplogroup t-shirt. Yes, she does custom work. What’s your haplogroup? You can see those goodies here.

Around the corner, I found CelebrateDNA.

RootsTech 2020 Celebrate DNA

Is that a Viking wearing a DNA t-shirt?

Rootstech 2020 day of the dead

CelebrateDNA has some very cool “Day of the Dead” bags, t-shirts and mouse pads, in addition to their other DNA t-shirts. I bought an “Every day is Day of the Dead for Genealogists” mouse pad which will live permanently in my technology travel bag. You can see their other goodies, here.

RootsTech 2020 skeleton

Hey, I think I found a relative. Can we DNA test to see?

Rootstech 2020 Mayflower replica

The Mayflower Society had a fun booth with a replica model ship.

RootsTech 2020 Mayflower passengers

Along with the list of passengers perched on a barrel of the type that likely held food or water for the Pilgrims.

RootsTech 2020 Webinar Marathon

Legacy Family Tree Webinars is going to have a 24-hour Genealogy Webinar Marathon March 12-13. So, who is going to stay up for this?Iit’s free and just take a look at the speakers, and topics, here. I’m guessing lots of people will take advantage of this opportunity. You can also subscribe for more webinars, here.

On March 4th, I’m presenting a FREE webinar, “3 Genealogy DNA Case Studies and How I Solved Them,” so sign up and join in!

Rootstech 2020 street art

Food at RootsTech falls into two categories. Anything purchased in the convention center meaning something to stave off starvation, and some restaurant with friends – the emphasis being on friends.

A small group went for pizza one evening when we were too exhausted to do anything else. Outside I found this interesting street art – and inside Settebello Pizzeria Napoletana I had the best Margarita Pizza I think I’ve ever had.

Then, as if I wasn’t already stuffed to the gills, attached through a doorway in the wall is Capo Gelateria Italiana, creators of artisan gelato. I’ve died and gone to heaven. Seriously, it’s a good thing I don’t live here.

Rootstech 2020 gelatto

Who says you can’t eat ice cold gelato in the dead of winter, outside waiting for the Uber, even if your insides are literally shivering and shaking!! It was that good.

This absolutely MUST BE a RootsTech tradition.

Rootstech 2020 ribbons

That’s it for RootsTech 2020. Hope you’ve enjoyed coming along on this virtual journey and that you’ve found something interesting, perhaps a new hint or tool to utilize.

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Thank you so much.

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Y DNA: Part 2 – The Dictionary of DNA

After my introductory article, Y DNA: Part 1 – Overview, I received several questions about terminology, so this second article will be a dictionary or maybe more like a wiki. Many terms about Y DNA apply to mitochondrial and autosomal as well.

Haplogroup – think of your Y or mitochondrial DNA haplogroup as your genetic clan. Haplogroups are assigned based on SNPs, specific nucleotide mutations that change very occasionally. We don’t know exactly how often, but the general schools of thought are that a new SNP mutation on the Y chromosome occurs someplace between every 80 and 145 years. Of course, those would only be averages. I’ve as many as two mutations in a father son pair, and no mutations for many generations.

Dictionary haplogroup.png

Y DNA haplogroups are quite reliably predicted by STR results at Family Tree DNA, meaning the results of a 12, 25, 37, 67 or 111 marker tests. Haplogroups are only confirmed or expanded from the estimate by SNP testing of the Y chromosome. Predictions are almost always accurate, but only apply to the upper level base haplogroups. I wrote about that in the article, Haplogroups and the Three Brothers.

Haplogroups are also estimated by some companies, specifically 23andMe and LivingDNA who provide autosomal testing. These companies estimate Y and mitochondrial haplogroups by targeting certain haplogroup defining locations in your DNA, both Y and mitochondrial. That doesn’t mean they are actually obtaining Y and mtDNA information from autosomal DNA, just that the chip they are using for DNA processing targets a few Y and mitochondrial locations to be read.

Again, the only way to confirm or expand that haplogroup is to test either your Y or mitochondrial DNA directly. I wrote about that in the article Haplogroup Comparisons Between Family Tree DNA and 23andMe and Why Different Haplogroup Results?.

Nucleotide – DNA is comprised of 4 base nucleotides, abbreviated as T (Thymine), A (Adenine), C (Cytosine) and G (Guanine.) Every DNA address holds one nucleotide.

In the DNA double helix, generally, A pairs with T and C pairs with G.

Dictionary helix structure.png

Looking at this double helix twist, green and purple “ladder rungs” represent the 4 nucleotides. Purple and green and have been assigned to one bonding pair, either A/T or C/G, and red and blue have been assigned to the other pair.

When mutations occur, most often A or T are replaced with their paired nucleotide, as are C and G. In this example, A would be replaced with T and vice versa. C with G and vice versa.

Sometimes that’s not the case and a mutation occurs that pairs A with C or G, for example.

For Y DNA SNPs, we care THAT the mutation occurred, and the identity of the replacing nucleotide so we know if two men match on that SNP. These mutations are what make DNA in general, and Y DNA in particular useful for genealogy.

The rest of this nucleotide information is not something you really need to know, unless of course you’re playing in the jeopardy championship. (Yes, seriously.) The testing lab worries about these things, as well as matching/not matching, so you don’t need to.

SNP – Single nucleotide polymorphism, pronounced “snip.” A mutation that occurs when the nucleotide typically found at a particular location (the ancestral value) is replaced with one of the other three nucleotides (the derived value.) SNPs that mutate are called variants.

In Y DNA, after discovery and confirmation that the SNP mutation is valid and carried by more than one man, the mutation is given a name something like R-M269 where R is the base haplogroup and M269 reflects the lab that discovered and named the SNP (M = Peter Underhill at Stanford) and an additional number, generally the next incremental number named by that lab (269).

Some SNPs were discovered simultaneously by different labs. When that happens, the same mutation in the identical location is given different names by different organizations, resulting in multiple names for the name mutation in the same DNA location. These are considered equivalent SNPs because they are identical.

In some cases, SNPs in different locations seem to define the same tree branching structure. These are functionally equivalent until enough tests are taken to determine a new branching structure, but they are not equivalent in the sense that the exact same DNA location was named by two different labs.

Some confusion exists about Y DNA SNP equivalence.

Equivalence Confusion How This Happens Are They the Same?
Same exact DNA location named by two labs Different SNP names for the same DNA location, named by two different labs at about the same time Exactly equivalent because SNPs are named for the the exact same DNA locations, define only one tree branch ever
Different DNA locations and SNP names, one current tree branch Different SNPs temporarily located on same branch of  the tree because branches or branching structure have not yet been defined When enough men test, different branches will likely be sorted out for the non-equivalent SNPs pointing to newly defined branch locations that divide the tree or branch

Let’s look at an example where 4 example SNPs have been named. Two at the same location, and two more for two additional locations. However, initially, we don’t know how this tree actually looks, meaning what is the base/trunk and what are branches, so we need more tests to identify the actual structure.

Dictionary SNPs before branching.png

The example structure of a haplogroup R branch, above, shows that there are three actual SNP locations that have been named. Location 1 has been given two different SNP names, but they are the same exact location. Duplicate names are not intentionally given, but result from multiple labs making simultaneous discoveries.

However, because we don’t have enough information yet, meaning not enough men have tested that carry at least some of the mutations (variants,), we can’t yet define trunks and branches. Until we do, all 4 SNPs will be grouped together. Examples 1 and 2 will always be equivalent because they are simply different names for the exact same DNA location. Eventually, a branching structure will emerge for Examples 1/2, Example 3 and Example 4..

Dictionary SNP branches.png

Eventually, the downstream branches will be defined and split off. It’s also possible that Example 4 would be the trunk with Examples 1 and 2 forming a branch and Example 3 forming a branch. Branching tree structure can’t be built without sufficient testers who take the NGS tests, specifically the Big Y-700 which doesn’t just confirm a subset of existing named SNPs, but confirms all named SNPs, unnamed variants and discovers new previously-undiscovered variants which define the branching tree structure.

SNP testing occurs in multiple ways, including:

  • NGS, next generation sequencing, tests such as the Big Y-700 which scans the gold standard region of the Y chromosome in order to find known SNPs at specific locations, mutations (variants) not yet named as SNPs, previously undiscovered variants and minimally 700 STR mutations.
  • WGS, whole genome sequencing although there currently exist no bundled commercial tools to separate Y DNA information from the rest of the genome, nor any comparison methodology that allows whole genome information to be transferred to Family Tree DNA, the only commercial lab that does both testing and matching of NGS Y DNA tests and where most of the Y DNA tests reside. There can also be quality issues with whole genome sequencing if the genome is not scanned a similar number of times as the NGS Y tests. The criteria for what constitues a “positive call” for a mutation at a specific location varies as well, with little standardization within the industry.
  • Targeted SNP testing of a specific SNP location. Available at Family Tree DNA  and other labs for some SNP locations, this test would only be done if you are looking for something very specific and know what you are doing. In some cases, a tester will purchase one SNP to verify that they are in a particular lineage, but there is no benefit such as matching. Furthermore, matching on one SNP alone does not confirm a specific lineage. Not all SNPs are individually available for purchase. In fact, as more SNPs are discovered at an astronomical rate, most aren’t available to purchase separately.
  • SNP panels which test a series of SNPs within a certain haplogroup in order to determine if a tester belongs to a specific subclade. These tests only test known SNPs and aren’t tests of discovery, scanning the useable portion of the Y chromosome. In other words, you will discern whether you are or are not a member of the specific subclades being tested for, but you will not learn anything more such as matching to a different subclade, or new, undiscovered variants (mutations) or subclades.

Subclade – A branch of a specific upstream branch of the haplotree.

Dictionary R.png

For example, in haplogroup R, R1 and R2 are subclades of haplogroup R. The graphic above conveys the concept of a subclade. Haplogroups beneath R1 and R2, respectively, are also subclades of haplogroup R as well as subclades of all clades above them on the haplotree.

Older naming conventions used letter number conventions such as R1 and R2 which expanded to R1b1c and so forth, alternating letters and numbers.

Today, we see most haplogroups designated by the haplogroup letter and SNP name. Using that notation methodology, R would be R-M207, R1 would be R-M173 and R2 would be R-M479.

Dictionary R branches.png

ISOGG documents Y haplogroup naming conventions and their history, maintaining both an alphanumeric and SNP tree for backwards compatibility. The reason that the alphanumeric tree was obsoleted was because there was no way to split a haplogroup like R1b1c when a new branch appeared between R1b and R1b1 without renaming everything downstream of R1b, causing constant reshuffling and renaming of tree branches. Haplogroup names were becoming in excess of 20 characters long. Today, the terminal SNP is used as a person’s haplogroup designation. The SNP name never changes and the individual’s Y haplogroup only changes if:

  • Further testing is performed and the tester is discovered to have an additional mutation further downstream from their current terminal SNP
  • A SNP previously discovered using the Big Y NGS test has since been named because enough men were subsequently discovered to carry that mutation, and the newly named SNP is the tester’s terminal SNP

Terminal SNP – It’s really not fatal. Used in this context, “terminal” means end of line, meaning furthest down and closest to present in the haplotree.

Depending on what level of testing you’ve undergone, you may have different haplogroups, or SNPs, assigned as your official “end of line” haplogroup or “terminal SNP” at various times.

If you took any of the various STR panel tests (12, 25, 37, 67 or 111) at Family Tree DNA your SNP was predicted based on STR matches to other men. Let’s say that prediction is R-M198. At that time, R-M198 was your terminal SNP. If you took the Big Y-700 test, your terminal SNP would almost assuredly change to something much further downstream in the haplotree.

If you took an autosomal test, your haplogroup was predicted based on a panel of SNPs selected to be informative about Y or mitochondrial DNA haplogroups. As with predicted haplogroups from STR test panels, the only way to discover a more definitive haplogroup is with further testing.

If you took a Y DNA STR test, you can see by looking at your match list that other testers may have a variety of “terminal SNPs.”

Dictionary Y matches.png

In the above example, the tester was originally predicted as R-M198 but subsequently took a Big Y test. His haplogroup now is R-YP729, a subclade of R-M198 several branches downstream.

Looking at his Y DNA STR matches to view the haplogroups of his matches, we see that the Y DNA predicted or confirmed haplogroup is displayed in the Y-DNA Haplogroup column – and several other men are M198 as well.

Anyone who has taken any type of confirming SNP test, whether it’s an individual SNP test, a panel test or the Big Y has their confirmed haplogroup at that level of testing listed in the Terminal SNP column. What we don’t know and can’t tell is whether the men whose Terminal SNP is listed as R-M198 just tested that SNP or have undergone additional SNP testing downstream and tested negative for other downstream SNPs. We can tell if they have taken the Big Y test by looking at their tests taken, shown by the red arrows above.

If the haplogroup has been confirmed by any form of SNP testing, then the confirmed haplogroup is displayed under the column, “Terminal SNP.” Unfortunately, none of this testers’ matches at this STR marker level have taken the Big Y test. As expected, no one matches him on his Terminal SNP, meaning his SNP farthest down on the tree. To obtain that level of resolution, one would have to take the Big Y test and his matches have not.

Dictionary Y block tree.png

Looking at this tester’s Big Y Block Tree results, we can see that there are indeed 3 people that match him on his terminal SNP, but none of them match him on the STR tests which generally produce genealogical matches closer in time. This suggests that these haplogroup level matches are a result of an ancestor further back in time. Note that these men also have an average of 5 variants each that are currently unnamed. These may eventually be named and become baby branches.

SNP matches can be useful genealogically, depending on when they occurred, or can originate further back in time, perhaps before the advent of surnames.

Our tester’s paternal ancestors migrated from Germany to Hungary in the late 1700s or 1800s, settling in a region now in Croatia, but he’s brick-walled on his paternal line due to record loss during the various wars.

The block tree reveals that the tester’s Big Y SNP match is indeed from Germany, born in 1718, with other men carrying this same terminal SNP originating in both Hungary and Germany even though they aren’t shown as a STR marker match to our tester.

You can read more about the block tree in the article, Family Tree DNA’s New Big Y Block Tree.

Haplotype – your individual values for results of gene sequencing, such as SNPs or STR values tested in the 12, 25, 37, 67 and 111 marker panels at Family Tree DNA. The haplotype for the individual shown below would be 13 for location DYS393, 26 for location DYS390, 16 for location DYS19, and so forth.

Dictionary panel 1.png

The values in a haplotype tend to be inherited together, so they are “unique” to you and your family. In this case, the Y DNA STR values of 13, 26, 16 and 10 are generally inherited together (unless a new mutation occurs,) passed from father to son on the Y chromosome. Therefore, this person’s haplotype is 13, 26, 16 and 10 for these 4 markers.

If this haplotype is rare, it may be very unique to the family. If the haplotype is common, it may only be unique to a much larger haplogroup reaching back hundreds or thousands of years. The larger the haplotype, the more unique it tends to be.

STR – Short tandem repeat. I think of a short tandem repeat as a copy machine or a stutter error. On the Y chromosome, the value of 13 at the location DYS393 above indicates that a series of DNA nucleotides is repeated a total of 13 times.

Indel example 1

Starting with the above example, let’s see how STR values accrue mutations.

STR example

In the example above, the value of CT was repeated 4 times in this DNA sequence, for a total of 5, so 5 would be the marker value.

Indel example 3

DNA can have deletions where the DNA at one or more locations is deleted and no DNA is found at that location, like the missing A above.

DNA can also have insertions where a particular value is inserted one or more times.

Dictionary insertion example.png

For example, if we know to expect the above values at DNA locations 1-10, and an insertion occurs between location 3 and 4, we know that insertion occurred because the alignment of the pattern of values expected in locations 4-10 is off by 1, and an unexpected T is found between 3 and 4, which I’ve labeled 3.1.

Dictionary insertion example 1.png

STR, or copy mutations are different from insertions, deletions or SNP mutations, shown below, where one SNP value is actually changed to another nucleotide.

Indel example 2

Haplotree – the SNP trees of humanity. Just a few years ago, we thought that there were only a few branches on the Y and mitochondrial trees of humanity, but the Big Y test has been a game changer for Y DNA.

At the end of 2019, the tree originating in Africa with Y chromosome Adam whose descendants populated the earth is comprised of more than 217,277 variants divided into 24,838 individual Y haplotree branches

A tree this size is very difficult to visualize, but you can take a look at Family Tree DNA’s public Y DNA tree here, beginning with haplogroup A. Today, there 25,880 branches, increased by more than 1000 branches in less than 3 weeks since year end. This tree is growing at breakneck speed as more men take the Big Y-700 test and new SNPs are discovered.

On the Public Y Tree below, as you expand each haplogroup into subgroups, you’ll see the flags representing the locations of where the testers’ most distant paternal ancestor lived.

Dictionary public tree.png

I wrote about how to use the Y tree in the article Family Tree DNA’s PUBLIC Y DNA Haplotree.

The mitochondrial tree can be viewed here. I wrote about to use the mitochondrial tree in the article Family Tree DNA’s Mitochondrial Haplotree.

Need Something Else?

I’ll be introducing more concepts and terms in future articles on the various Y DNA features. In the mean time, be sure to use the search box located in the upper right-hand corner of the blog to search for any term.

DNAexplain search box.png

For example, want to know what Genetic Distance means for either Y or mitochondrial DNA? Just type “genetic distance” into the search box, minus the quote marks, and press enter.

Enjoy and stay tuned for Part 3 in the Y DNA series, coming soon.

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Whole Genome Sequencing – Is It Ready for Prime Time?

Dante Labs is offering a whole genomes test for $199 this week as an early Black Friday special.

Please note that just as I was getting ready to push the publish button on this article, Veritas Genetics also jumped on the whole sequencing bandwagon for $199 for the first 1000 testers Nov. 19 and 20th. In this article, I discuss the Dante Labs test. I have NOT reviewed Veritas, their test nor terms, so the same cautions discussed below apply to them and any other company offering whole genome sequencing. The Veritas link is here.

Update – Veritas provides the VCF file for an additional $99, but does not provide FASTQ or BAM files, per their Tweet to me.

I have no affiliation with either company.

$199 (US) is actually a great price for a whole genome test, but before you click and purchase, there are some things you need to know about whole genome sequencing (WGS) and what it can and can’t do for you. Or maybe better stated, what you’ll have to do with your own results before you can utilize the information for genealogical purposes.

The four questions you need to ask yourself are:

  • Why do you want to consider whole genome testing?
  • What question(s) are you trying to answer?
  • What information do you seek?
  • What is your testing goal?

I’m going to say this once now, and I’ll say it again at the end of the article.

Whole genome sequencing tests are NOT A REPLACEMENT FOR GENEALOGICAL DNA TESTS for mitochondrial, Y or autosomal testing. Whole genome sequencing is not a genealogy magic bullet.

There are both pros and cons of this type of purchase, as with most everything. Whole genome tests are for the most experienced and technically savvy genetic genealogists who understand both working with genetics and this field well, who have already taken the vendors’ genealogy tests and are already in the Y, mitochondrial and autosomal comparison data bases.

If that’s you or you’re interested in medical information, you might want to consider a whole genome test.

Let’s start with some basics.

What Is Whole Genome Sequencing?

Whole Genome Sequencing will sequence most of your genome. Keep in mind that humans are more than 99% identical, so the only portions that you’ll care about either medically or genealogically are the portions that differ or tend to mutate. Comparing regions where you match everyone else tells you exactly nothing at all.

Exome Sequencing – A Subset of Whole Genome

Exome sequencing, a subset of whole genome sequencing is utilized for medical testing. The Exome is the region identified as the portions most likely to mutate and that hold medically relevant information. You can read about the benefits and challenges of exome testing here.

I have had my Exome sequenced twice, once at Helix and once at Genos, now owned by NantOmics. Currently, NantOmics does not have a customer sign-in and has acquired my DNA sequence as part of the absorption of Genos. I’ll be writing about that separately. There is always some level of consumer risk in dealing with a startup.

Helix sequences your Exome (plus) so that you can order a variety of DNA based or personally themed products from their marketplace, although I’m not convinced about the utility of even the legitimacy of some of the available tests, such as the “Wine Explorer.”

On the other hand, the world-class The National Geographic Society’s Genographic Project now utilizes Helix for their testing, as does Spencer Well’s company, Insitome.

You can also pay to download your Exome sequence data separately for $499.

Autosomal Testing for Genealogy

Both whole genome and Exome testing are autosomal testing, meaning that they test chromosomes 1-22 (as opposed to Y and mitochondrial DNA) but the number of autosomal locations varies vastly between the various types of tests.

The locations selected by the genealogy testing companies are a subset of both the whole genome and the Exome. The different vendors that compare your DNA for genealogy generally utilize between 600,000 and 900,000 chip-specific locations that they have selected as being inclined to mutate – meaning that we can obtain genealogically relevant information from those mutations.

Some vendors (for example, 23andMe and Ancestry) also include some medical SNPs (single nucleotide polymorphisms) on their chips, as both have formed medical research alliances with various companies.

Whole genome and Exome sequencing includes these same locations, BUT, the whole genome providers don’t compare the files to other testers nor reduce the files to the locations useful for genealogical comparisons. In other words, they don’t create upload files for you.

The following chart is not to scale, but is meant to convey the concept that the Exome is a subset of the whole genome, and the autosomal vendors’ selected SNPs, although not the same between the companies, are all subsets of the Exome and full genome.

I have not had my whole genome sequenced because I have seen no purpose for doing so, outside of curiosity.

This is NOT to imply that you shouldn’t. However, here are some things to think about.

Whole Genome Sequencing Questions

Coverage – Medical grade coverage is considered to be 30X, meaning an average of 30 scans of every targeted location in your genome. Some will have more and some will have less. This means that your DNA is scanned thirty different times to minimize errors. If a read error happens once or twice, it’s unlikely that the same error will happen several more times. You can read about coverage here and here.

Genomics Education Programme [CC BY 2.0 (https://creativecommons.org/licenses/by/2.

Here’s an example where the read length of Read 1 is 18, and the depth of the location shown in light blue is 4, meaning 4 actual reads were obtained. If the goal was 30X, then this result would be very poor. If the goal was 4X then this location is a high quality result for a 4X read.

In the above example, if the reference value, meaning the value at the light blue location for most people is T, then 4 instances of a T means you don’t have a mutation. On the other hand, if T is not the reference value, then 4 instances of T means that a mutation has occurred in that location.

Dante Labs coverage information is provided from their webpage as follows:

Other vendors coverage values will differ, but you should always know what you are purchasing.

Ownership – Who owns your data? What happens to your DNA itself (the sample) and results (the files) under normal circumstances and if the company is sold. Typically, the assets of the company, meaning your information, are included during any acquisition.

Does the company “share, lease or sell” your information as an additional revenue stream with other entities? If so, do they ask your permission each and every time? Do they perform internal medical research and then sell the results? What, if anything, is your DNA going to be used for other than the purpose for which you purchased the test? What control do you exercise over that usage?

Read the terms and conditions carefully for every vendor before purchasing.

File Delivery – Three types of files are generated during a whole genome test.

The VCF (Variant Call Format) which details your locations that are different from the reference file. A reference file is the “normal” value for humans.

A FASTQ file which includes the nucleotide sequence along with a corresponding quality score. Mutations in a messy area or that are not consistent may not be “real” and are considered false positives.

The BAM (Binary Alignment Map) file is used for Y DNA SNP alignment. The output from a BAM file is displayed in Family Tree DNA’s Big Y browser for their customers. Are these files delivered to you? If so, how? Family Tree DNA delivers their Big Y DNA BAM files as free downloads.

Typically whole genome data is too large for a download, so it is sent on a disc drive to you. Dante provides this disc for BAM and FASTQ files for 59 Euro ($69 US) plus shipping. VCF files are available free, but if you’re going to order this product, it would be a shame not to receive everything available.

Version – Discoveries are still being made to the human genome. If you thought we’re all done with that, we’re not. As new regions are mapped successfully, the addresses for the rest change, and a new genomic map is created. Think of this as street addresses and a new cluster of houses is now inserted between existing houses. All of the houses are periodically renumbered.

Today, typically results are delivered in either of two versions: hg19(GRVH37) or hg38(GRCH38). What happens when the next hg (human genome) version is released?

When you test with a vendor who uses your data for comparison as a part of a product they offer, they must realign your data so that the comparison will work for all of their customers (think Family Tree DNA and GedMatch, for example), but a vendor who only offers the testing service has no motivation to realign your output file for you. You only pay for sequencing, not for any after-the-fact services.

Platform – Multiple sequencing platforms are available, and not all platforms are entirely compatible with other competing platforms. For example, the Illumina platform and chips may or may not be compatible with the Affymetrix platform (now Thermo Fisher) and chips. Ask about chip compatibility if you have a specific usage in mind before you purchase.

Location – Where is your DNA actually being sequenced? Are you comfortable having your DNA sent to that geographic location for processing? I’m personally fine with anyplace in either the US, Canada or most of Europe, but other locations maybe not so much. I’d have to evaluate the privacy policies, applicable laws, non-citizen recourse and track record of those countries.

Last but perhaps most important, what do you want to DO with this file/information?

Utilization

What you receive from whole genome sequencing is files. What are you going to do with those files? How can you use them? What is your purpose or goal? How technically skilled are you, and how well do you understand what needs to be done to utilize those files?

A Specific Medical Question

If you have a particular question about a specific medical location, Dante allows you to ask the question as soon as you purchase, but you must know what question to ask as they note below.

You can click on their link to view their report on genetic diseases, but keep in mind, this is the disease you specifically ask about. You will very likely NOT be able to interpret this report without a genetic counselor or physician specializing in this field.

Take a look at both sample reports, here.

Health and Wellness in General

The Dante Labs Health and Wellness Report appears to be a collaborative effort with Sequencing.com and also appears to be included in the purchase price.

I uploaded both my Exome and my autosomal DNA results from the various testing companies (23andMe V3 and V4, Ancestry V1 and V2, Family Tree DNA, LivingDNA, DNA.Land) to Promethease for evaluation and there was very little difference between the health-related information returned based on my Exome data and the autosomal testing vendors. The difference is, of course, that the Exome coverage is much deeper (and therefore more reliable) because that test is a medical test, not a consumer genealogy test and more locations are covered. Whole genome testing would be more complete.

I wrote about Promethease here and here. Promethease does accept VCF files from various vendors who provide whole genome testing.

None of these tests are designed or meant for medical interpretation by non-professionals.

Medical Testing

If you plan to test with the idea that should your physician need a genetics test, you’re already ahead of the curve, don’t be so sure. It’s likely that your physician will want a genetics test using the latest technology, from their own lab, where they understand the quality measures in place as well as how the data is presented to them. They are unlikely to accept a test from any other source. I know, because I’ve already had this experience.

Genealogical Comparisons

The power of DNA testing for genealogy is comparing your data to others. Testing in isolation is not useful.

Mitochondrial DNA – I can’t tell for sure based on the sample reports, but it appears that you receive your full sequence haplogroup and probably your mutations as well from Dante. They don’t say which version of mitochondrial DNA they utilize.

However, without the ability to compare to other testers in a database, what genealogical benefit can you derive from this information?

Furthermore, mitochondrial DNA also has “versions,” and converting from an older to a newer version is anything but trivial. Haplogroups are renamed and branches sawed from one part of the mitochondrial haplotree and grafted onto another. A testing (only) vendor that does not provide comparisons has absolutely no reason to update your results and can’t be expected to do so. V17 is the current build, released in February 2016, with the earlier version history here.

Family Tree DNA is the only vendor who tests your full sequence mitochondrial DNA, compares it to other testers and updates your results when a new version is released. You can read more about this process, here and how to work with mtDNA results here.

Y DNA – Dante Labs provides BAM files, but other whole genome sequencers may not. Check before you purchase if you are interested in Y DNA. Again, you’ll need to be able to analyze the results and submit them for comparison. If you are not capable of doing that, you’ll need to pay a third party like either YFull or FGS (Full Genome Sequencing) or take the Big Y test at Family Tree DNA who has the largest Y Database worldwide and compares results.

Typically whole genome testers are looking for Y DNA SNPs, not STR values in BAM files. STR (short tandem repeat) values are the results that you receive when you purchase the 37, 67 or 111 tests at Family Tree DNA, as compared to the Big Y test which provides you with SNPs in order to resolve your haplogroup at the most granular level possible. You can read about the difference between SNPs and STRs here.

As with SNP data, you’ll need outside assistance to extract your STR information from the whole genome sequence information, none of which will be able to be compared with the testers in the Family Tree DNA data base. There is also an issue of copy-count standardization between vendors.

You can read about how to work with STR results and matches here and Big Y results here.

Autosomal DNA – None of the major providers that accept transfers (MyHeritage, Family Tree DNA, GedMatch) accept whole genome files. You would need to find a methodology of reducing the files from the whole genome to the autosomal SNPs accepted by the various vendors. If the vendors adopt the digital signature technology recently proposed in this paper by Yaniv Erlich et al to prevent “spoofed files,” modified files won’t be accepted by vendors.

Summary

Whole genome testing, in general, will and won’t provide you with the following:

Desired Feature Whole Genome Testing
Mitochondrial DNA Presumed full haplogroup and mutations provided, but no ability for comparison to other testers. Upload to Family Tree DNA, the only vendor doing comparisons not available.
Y DNA Presume Y chromosome mostly covered, but limited ability for comparison to other testers for either SNPs or STRs. Must utilize either YFull or FGS for SNP/STR analysis. Upload to Family Tree DNA, the vendor with the largest data base not available when testing elsewhere.
Autosomal DNA for genealogy Presume all SNPs covered, but file output needs to be reduced to SNPs offered/processed by vendors accepting transfers (Family Tree DNA, MyHeritage, GedMatch) and converted to their file formats. Modified files may not be accepted in the future.
Medical (consumer interest) Accuracy is a factor of targeted coverage rate and depth of actual reads. Whole genome vendors may or may not provide any analysis or reports. Dante does but for limited number of conditions. Promethease accepts VCF files from vendors and provides more.
Medical (physician accepted) Physician is likely to order a medical genetics test through their own institution. Physicians may not be willing to risk a misdiagnosis due to a factor outside of their control such as an incompatible human genome version.
Files VCF, FASTQ and BAM may or may not be included with results, and may or may not be free.
Coverage Coverage and depth may or may not be adequate. Multiple extractions (from multiple samples) may or may not be included with the initial purchase (if needed) or may be limited. Ask.
Updates Vendors who offer sequencing as a part of a products that include comparison to other testers will update your results version to the current reference version, such as hg38 and mitochondrial V17. Others do not, nor can they be expected to provide that service.
Version Inquire as to the human genome (hg) version or versions available to you, and which version(s) are acceptable to the third party vendors you wish to utilize. When the next version of the human genome is released, your file will no longer be compatible because WGS vendors are offering sequencing only, not results comparisons to databases for genealogy.
Ownership/Usage Who owns your sample? What will it be utilized for, other than the service you ordered, by whom and for what purposes? Will you we able to authorize or decline each usage?
Location Where geographically is your DNA actually being sequenced and stored? What happens to your actual DNA sample itself and the resulting files? This may not be the location where you return your swab kit.

The Question – Will I Order?

The bottom line is that if you are a genealogist, seeking genetic information for genealogical purposes, you’re much better off to test with the standard and well know genealogy vendors who offer compatibility and comparisons to other testers.

If you are a pioneer in this field, have the technical ability required to make use of a whole genome test and are willing to push the envelope, then perhaps whole genome sequencing is for you.

I am considering ordering the Dante Labs whole genome test out of simple curiosity and to upload to Promethease to determine if the whole genome test provides me with something potentially medically relevant (positive or negative) that autosomal and Exome testing did not.

I’m truly undecided. Somehow, I’m having trouble parting with the $199 plus $69 (hard drive delivery by request when ordering) plus shipping for this limited functionality. If I was a novice genetic genealogist or was not a technology expert, I would definitely NOT order this test for the reasons mentioned above.

A whole genome test is not in any way a genealogical replacement for a full sequence mitochondrial test, a Y STR test, a Y SNP test or an autosomal test along with respective comparison(s) in the data bases of vendors who don’t allow uploads for these various functions.

The simple fact that 30X whole genome testing is available for $199 plus $69 plus shipping is amazing, given that 15 years ago that same test cost 2.7 billion dollars. However, it’s still not the magic bullet for genealogy – at least, not yet.

Today, the necessary integration simply doesn’t exist. You pay the genealogy vendors not just for the basic sequencing, but for the additional matching and maintenance of their data bases, not to mention the upgrading of your sequence as needed over time.

If I had to choose between spending the money for the WGS test or taking the genealogy tests, hands down, I’d take the genealogy tests because of the comparisons available. Comparison and collaboration is absolutely crucial for genealogy. A raw data file buys me nothing genealogically.

If I had not previously taken an Exome test, I would order this test in order to obtain the free Dante Health and Wellness Report which provides limited reporting and to upload my raw data file to Promethease. The price is certainly right.

However, keep in mind that once you view health information, you cannot un-see it, so be sure you do really want to know.

What do you plan to do? Are you going to order a whole genome test?

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Glossary – Terminal SNP

What is a Terminal SNP?

It sounds fatal doesn’t it, but don’t worry, it’s not.

The phrase Terminal SNP is generally used in conjunction with discussing Y DNA testing and haplogroup identification.

SNPs Define Haplogroups

In a nutshell, SNPs, single nucleotide polymorphisms, are the mutations that define different haplogroups. Haplogroups reach far back in time on the direct paternal, generally the surname, line.

SNPs, mutations that define haplogroups are considered to be “once in the lifetime of mankind” events that divide one haplogroup into two subgroups, or branches.

A haplogroup can be thought of as the ancient genetic clan of males – specifically their Y DNA. You might want to read the article, What is a Haplogroup?

If you test your Y DNA with Family Tree DNA, you’ll notice that you receive an estimated haplogroup with the regular Y DNA tests which test STR, or short tandem repeat, markers. STRs are the markers tested in the 37, 67 or 111 marker tests. You can read about the difference between STRs and SNPs in the article, STRs vs SNPs, Multiple DNA Personalities.

STR markers are used for more recent genealogical testing and comparison, while haplogroups reach further back in time.

An estimated haplogroup as provided by Family Tree DNA is based on STR matches to people who have done SNP testing. Estimated haplogroups are quite accurate, as far as they go. However, by necessity, they aren’t deep haplogroups, meaning they aren’t the leaves on the end of the twigs of the branch of your haplotree. Estimated haplogroups are the big branches.

In essence, what a haplogroup provided with STR testing tells you is the name of the town and the main street through town. To get to your house, you may need to turn on a few side streets.

Haplotree

The haplotree, back in the ancient days of 2002 used to hold less than 100 haplogroups, each main branch called by a different letter of the alphabet. The main branches or what is referred to as the core backbone is shown in this graphic from Wikipedia.

Today, the haplotree shown for each Y DNA tester on their personal page at Family Tree DNA, has tens of thousands of branches. No, that’s not a misprint.

The haplotree is the phylogenetic tree that defines all of the branches of mankind and groups them into increasingly refined “clans” or groups, the further down the tree you go.

In other words, Y Adam is at the root, then his “sons” who, due to specific mutations, formed different base haplogroups. As more mutations occurred in the son’s descendants’ lines, more haplogroups were born. Multiply that over tens of thousands of years, and you have lots of branches and twigs and even leaves on the branches of this tree of humanity.

Let’s look at the terminal SNP of my cousin, John, on his Haplotree and SNP page at Family Tree DNA.

John’s terminal SNP is R-BY490. R indicates the main branch and BY490 is the name of the SNP that is the further down the tree – his leaf, for lack of a better definition.

In John’s case, we know this is the smallest leaf on his branch, because he took the Big Y test which reads all of his SNPs on the Y chromosome.

Haplogroup R is quite large with thousands of branches and leaves – each one with its own distinct history that is an important part of your genealogy. Tracking where and when these mutations happened tells you the migration history of your paternal ancestor.

How else would you ever know?

How Do I Discover My Terminal SNP?

Sometimes “terminal SNP” is used to mean the SNP for which a man has most recently tested. It may NOT mean that he has tested for all of the available SNPs. What this really means is that when someone gives you a terminal SNP name, or you see one listed someplace, you’ll need to ask about the depth of the testing undergone by the man in question.

Let’s look at an example.

I’ve condensed John’s tree into only the SNPs for which he tested positive. The entire tree includes SNPs that John tested negative for, and their branches which are not relevant to John – although we certainly didn’t know that they weren’t relevant before he tested. However, he may want to reference the large and accurate scientific tree, so all information is provided to John. It’s like seeing a map that includes all roads, not just the one you’re traveling.

I’ve created a descendant chart style tree below. Y line Adam is the first male. Some several thousands of years later, his descendant had a mutation that created haplogroup R defined by the SNP M207, in yellow.

John, based on his STR matches, was predicted to be R-M269. On his results page, that’s the estimated haplogroup that was showing when his results were first returned.

If you had asked John about his terminal SNP, he would have probably told you R-M269. At that time, to the best of his knowledge, that WAS his terminal SNP – but it wasn’t really.

John could choose three ways to test for additional SNPs to discover his actual terminal SNP.

  • One by One

John could selectively test one SNP at a time to see if he was positive, meaning that he has that mutation. SNPs cost $39 each to test, as of the time this article was written. Of course, John could also be negative for that SNP, meaning he doesn’t have the SNP, and therefore does not descend from that line. That’s good information too, but then John would have to select another branch to test by purchasing the SNP associated with that new branch.

If John had selected any of the SNPs on the list above to test, he would have tested positive. So, let’s say John decided to test L21, a major branch. If he tested positive, that means that all of the branches directly above L21, between L21 and M207, are also positive, by inference.

At that point, John would tell you that his terminal SNP is L21, but it isn’t actually.

  • SNP Packs

Now, John wants to purchase a more cost-effective SNP pack, because he can test 100 or more SNP locations by purchasing one SNP pack for $99. That’s a great value, so John purchases the SNP pack offered on his personal page. A SNP pack tests selective SNPs all over the relevant portion of the tree in an attempt to place a man on a relatively low branch. These SNPs are selected to find an appropriate branch, not the appropriate leaf. They confirm (or disprove) SNPs that have already been discovered.

Let’s say, in John’s case, the SNP pack moves him down to R-ZP21. If you asked him now about his terminal SNP, he would probably tell you R-ZP21, but it still isn’t actually.

SNP packs are great and do move people down the tree, but the only way to move to the end of the twigs is the Big Y test.

  • The Big Y Test

The Big Y test tests for all known SNPs as well as what were called Novel Variants and are now called Unnamed Variants which are new SNPs discovered that are as yet unnamed. You may have a new SNP in your line waiting to be discovered. The Estes family has one dating from sometime before 1495 that, to date, has only been found in Estes descendant males from that common ancestor who was born in 1495.

The Big Y test scans virtually the entire Y chromosome in order to place testers on the lowest leaf of the tree. You can’t get there any other way with certainty and you’ll never know if you have any as yet undiscovered SNPs or leaves unless you take the Big Y.

In John’s case, that leaf was 4 more branches below R-ZP21, at R-BY490.

Why Does a Terminal SNP Matter?

Haplogroup R-M269 is the most common haplogroup of European men.

Looking at the SNP map, you can see that there are so many map locations as to color the map of the UK entirely red.

Genealogically, this isn’t helpful at all.

However, looking now at DF49, below, we see many fewer locations, suggesting perhaps that men with this terminal SNP are clustered in particular areas.

SNPS further down John’s personal haplotree tell an increasingly focused and granular story, each step moving closer in time.

Summary

Men generally want to discover their terminal SNP with the hope that they can learn something interesting about the migration of their ancestors before the genesis of surnames.

Perhaps they will discover that they match all men with McSurnames, suggesting perhaps a Scottish origin. Or maybe their terminal SNP is only found in a mountainous region of Germany, or perhaps their Big Y matches all have patronymic surnames from Scandinavia.

Big Y testing is also a community sourced citizen science effort to expand the Y haplotree – and quite successfully. The vast majority of SNPs on the publicly available ISOGG Y tree today are from individual testers, not from academic studies.

Haplogroups, and therefore terminal SNPs are the only way we have to peek back behind the veil of time.

If you’re interested in discovering your terminal SNP, you’ll be money ahead to simply purchase the Big Y up front and skip individual SNP testing along with SNP packs. In addition to discovering your terminal SNP, you are also matched to other men who have taken the Big Y test.

You can order the Big Y, individual SNPs or SNP packs by clicking on this link, signing on to your account, and then clicking on the blue “Upgrade” button, either in the Y DNA section, shown below, or in the upper right hand corner of your personal page.

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