2018 – The Year of the Segment

Looking in the rear view mirror, what a year! Some days it’s been hard to catch your breath things have been moving so fast.

What were the major happenings, how did they affect genetic genealogy and what’s coming in 2019?

The SNiPPY Award

First of all, I’m giving an award this year. The SNiPPY.

Yea, I know it’s kinda hokey, but it’s my way of saying a huge thank you to someone in this field who has made a remarkable contribution and that deserves special recognition.

Who will it be this year?

Drum roll…….

The 2018 SNiPPY goes to…

DNAPainter – The 2018 SNiPPY award goes to DNAPainter, without question. Applause, everyone, applause! And congratulations to Jonny Perl, pictured below at Rootstech!

Jonny Perl created this wonderful, visual tool that allows you to paint your matches with people on your chromosomes, assigning the match to specific ancestors.

I’ve written about how to use the tool  with different vendors results and have discovered many different ways to utilize the painted segments. The DNA Painter User Group is here on Facebook. I use DNAPainter EVERY SINGLE DAY to solve a wide variety of challenges.

What else has happened this year? A lot!

Ancient DNA – Academic research seldom reports on Y and mitochondrial DNA today and is firmly focused on sequencing ancient DNA. Ancient genome sequencing has only recently been developed to a state where at least some remains can be successfully sequenced, but it’s going great guns now. Take a look at Jennifer Raff’s article in Forbes that discusses ancient DNA findings in the Americas, Europe, Southeast Asia and perhaps most surprising, a first generation descendant of a Neanderthal and a Denisovan.

From Early human dispersals within the Americas by Moreno-Mayer et al, Science 07 Dec 2018

Inroads were made into deeper understanding of human migration in the Americas as well in the paper Early human dispersals within the Americas by Moreno-Mayer et al.

I look for 2019 and on into the future to hold many more revelations thanks to ancient DNA sequencing as well as using those sequences to assist in understanding the migration patterns of ancient people that eventually became us.

Barbara Rae-Venter and the Golden State Killer Case

Using techniques that adoptees use to identify their close relatives and eventually, their parents, Barbara Rae-Venter assisted law enforcement with identifying the man, Joseph DeAngelo, accused (not yet convicted) of being the Golden State Killer (GSK).

A very large congratulations to Barbara, a retired patent attorney who is also a genealogist. Nature recognized Ms. Rae-Venter as one of 2018’s 10 People Who Mattered in Science.

DNA in the News

DNA is also represented on the 2018 Nature list by Viviane Slon, a palaeogeneticist who discovered an ancient half Neanderthal, half Denisovan individual and sequenced their DNA and He JianKui, a Chinese scientist who claims to have created a gene-edited baby which has sparked widespread controversy. As of the end of the year, He Jiankui’s research activities have been suspended and he is reportedly sequestered in his apartment, under guard, although the details are far from clear.

In 2013, 23andMe patented the technology for designer babies and I removed my kit from their research program. I was concerned at the time that this technology knife could cut two ways, both for good, eliminating fatal disease-causing mutations and also for ethically questionable practices, such as eugenics. I was told at the time that my fears were unfounded, because that “couldn’t be done.” Well, 5 years later, here we are. I expect the debate about the ethics and eventual regulation of gene-editing will rage globally for years to come.

Elizabeth Warren’s DNA was also in the news when she took a DNA test in response to political challenges. I wrote about what those results meant scientifically, here. This topic became highly volatile and politicized, with everyone seeming to have a very strongly held opinion. Regardless of where you fall on that opinion spectrum (and no, please do not post political comments as they will not be approved), the topic is likely to surface again in 2019 due to the fact that Elizabeth Warren has just today announced her intention to run for President. The good news is that DNA testing will likely be discussed, sparking curiosity in some people, perhaps encouraging them to test. The bad news is that some of the discussion may be unpleasant at best, and incorrect click-bait at worst. We’ve already had a rather unpleasant sampling of this.

Law Enforcement and Genetic Genealogy

The Golden State Killer case sparked widespread controversy about using GedMatch and potentially other genetic genealogy data bases to assist in catching people who have committed violent crimes, such as rape and murder.

GedMatch, the database used for the GSK case has made it very clear in their terms and conditions that DNA matches may be used for both adoptees seeking their families and for other uses, such as law enforcement seeking matches to DNA sequenced during a criminal investigation. Since April 2018, more than 15 cold case investigations have been solved using the same technique and results at GedMatch. Initially some people removed their DNA from GedMatch, but it appears that the overwhelming sentiment, based on uploads, is that people either aren’t concerned or welcome the opportunity for their DNA matches to assist apprehending criminals.

Parabon Nanolabs in May established a genetic genealogy division headed by CeCe Moore who has worked in the adoptee community for the past several years. The division specializes in DNA testing forensic samples and then assisting law enforcement with the associated genetic genealogy.

Currently, GedMatch is the only vendor supporting the use of forensic sample matching. Neither 23anMe nor Ancestry allow uploaded data, and MyHeritage and Family Tree DNA’s terms of service currently preclude this type of use.

MyHeritage

Wow talk about coming onto the DNA world stage with a boom.

MyHeritage went from a somewhat wobbly DNA start about 2 years ago to rolling out a chromosome browser at the end of January and adding important features such as SmartMatching which matches your DNA and your family trees. Add triangulation to this mixture, along with record matching, and you’re got a #1 winning combination.

It was Gilad Japhet, the MyHeritage CEO who at Rootstech who christened 2018 “The Year of the Segment,” and I do believe he was right. Additionally, he announced that MyHeritage partnered with the adoption community by offering 15,000 free kits to adoptees.

In November, MyHeritage hosted MyHeritage LIVE, their first user conference in Oslo, Norway which focused on both their genealogical records offerings as well as DNA. This was a resounding success and I hope MyHeritage will continue to sponsor conferences and invest in DNA. You can test your DNA at MyHeritage or upload your results from other vendors (instructions here). You can follow my journey and the conference in Olso here, here, here, here and here.

GDPR

GDPR caused a lot of misery, and I’m glad the implementation is behind us, but the the ripples will be affecting everyone for years to come.

GDPR, the European Data Protection Regulation which went into effect on May 25,  2018 has been a mixed and confusing bag for genetic genealogy. I think the concept of users being in charge and understanding what is happened with their data, and in this case, their data plus their DNA, is absolutely sound. The requirements however, were created without any consideration to this industry – which is small by comparison to the Googles and Facebooks of the world. However, the Googles and Facebooks of the world along with many larger vendors seem to have skated, at least somewhat.

Other companies shut their doors or restricted their offerings in other ways, such as World Families Network and Oxford Ancestors. Vendors such as Ancestry and Family Tree DNA had to make unpopular changes in how their users interface with their software – in essence making genetic genealogy more difficult without any corresponding positive return. The potential fines, 20 million plus Euro for any company holding data for EU residents made it unwise to ignore the mandates.

In the genetic genealogy space, the shuttering of both YSearch and MitoSearch was heartbreaking, because that was the only location where you could actually compare Y STR and mitochondrial HVR1/2 results. Not everyone uploaded their results, and the sites had not been updated in a number of years, but the closure due to GDPR was still a community loss.

Today, mitoydna.org, a nonprofit comprised of genetic genealogists, is making strides in replacing that lost functionality, plus, hopefully more.

On to more positive events.

Family Tree DNA

In April, Family Tree DNA announced a new version of the Big Y test, the Big Y-500 in which at least 389 additional STR markers are included with the Big Y test, for free. If you’re lucky, you’ll receive between 389 and 439 new markers, depending on how many STR markers above 111 have quality reads. All customers are guaranteed a minimum of 500 STR markers in total. Matching was implemented in December.

These additional STR markers allow genealogists to assemble additional line marker mutations to more granularly identify specific male lineages. In other words, maybe I can finally figure out a line marker mutation that will differentiate my ancestor’s line from other sons of my founding ancestor😊

In June, Family Tree DNA announced that they had named more than 100,000 SNPs which means many haplogroup additions to the Y tree. Then, in September, Family Tree DNA published their Y haplotree, with locations, publicly for all to reference.

I was very pleased to see this development, because Family Tree DNA clearly has the largest Y database in the industry, by far, and now everyone can reap the benefits.

In October, Family Tree DNA published their mitochondrial tree publicly as well, with corresponding haplogroup locations. It’s nice that Family Tree DNA continues to be the science company.

You can test your Y DNA, mitochondrial or autosomal (Family Finder) at Family Tree DNA. They are the only vendor offering full Y and mitochondrial services complete with matching.

2018 Conferences

Of course, there are always the national conferences we’re familiar with, but more and more, online conferences are becoming available, as well as some sessions from the more traditional conferences.

I attended Rootstech in Salt Lake City in February (brrrr), which was lots of fun because I got to meet and visit with so many people including Mags Gaulden, above, who is a WikiTree volunteer and writes at Grandma’s Genes, but as a relatively expensive conference to attend, Rootstech was pretty miserable. Rootstech has reportedly made changes and I hope it’s much better for attendees in 2019. My attendance is very doubtful, although I vacillate back and forth.

On the other hand, the MyHeritage LIVE conference was amazing with both livestreamed and recorded sessions which are now available free here along with many others at Legacy Family Tree Webinars.

Family Tree University held a Virtual DNA Conference in June and those sessions, along with others, are available for subscribers to view.

The Virtual Genealogical Association was formed for those who find it difficult or impossible to participate in local associations. They too are focused on education via webinars.

Genetic Genealogy Ireland continues to provide their yearly conference sessions both livestreamed and recorded for free. These aren’t just for people with Irish genealogy. Everyone can benefit and I enjoy them immensely.

Bottom line, you can sit at home and educate yourself now. Technology is wonderful!

2019 Conferences

In 2019, I’ll be speaking at the National Genealogical Society Family History Conference, Journey of Discovery, in St. Charles, providing the Special Thursday Session titled “DNA: King Arthur’s Mighty Genetic Lightsaber” about how to use DNA to break through brick walls. I’ll also see attendees at Saturday lunch when I’ll be providing a fun session titled “Twists and Turns in the Genetic Road.” This is going to be a great conference with a wonderful lineup of speakers. Hope to see you there.

There may be more speaking engagements at conferences on my 2019 schedule, so stay tuned!

The Leeds Method

In September, Dana Leeds publicized The Leeds Method, another way of grouping your matches that clusters matches in a way that indicates your four grandparents.

I combine the Leeds method with DNAPainter. Great job Dana!

Genetic Affairs

In December, Genetic Affairs introduced an inexpensive subscription reporting and visual clustering methodology, but you can try it for free.

I love this grouping tool. I have already found connections I didn’t know existed previously. I suggest joining the Genetic Affairs User Group on Facebook.

DNAGedcom.com

I wrote an article in January about how to use the DNAGedcom.com client to download the trees of all of your matches and sort to find specific surnames or locations of their ancestors.

However, in December, DNAGedcom.com added another feature with their new DNAGedcom client just released that downloads your match information from all vendors, compiles it and then forms clusters. They have worked with Dana Leeds on this, so it’s a combination of the various methodologies discussed above. I have not worked with the new tool yet, as it has just been released, but Kitty Cooper has and writes about it here.  If you are interested in this approach, I would suggest joining the Facebook DNAGedcom User Group.

Rootsfinder

I have not had a chance to work with Rootsfinder beyond the very basics, but Rootsfinder provides genetic network displays for people that you match, as well as triangulated views. Genetic networks visualizations are great ways to discern patterns. The tool creates match or triangulation groups automatically for you.

Training videos are available at the website and you can join the Rootsfinder DNA Tools group at Facebook.

Chips and Imputation

Illumina, the chip maker that provides the DNA chips that most vendors use to test changed from the OmniExpress to the GSA chip during the past year. Older chips have been available, but won’t be forever.

The newer GSA chip is only partially compatible with the OmniExpress chip, providing limited overlap between the older and the new results. This has forced the vendors to use imputation to equalize the playing field between the chips, so to speak.

This has also caused a significant hardship for GedMatch who is now in the position of trying to match reasonably between many different chips that sometimes overlap minimally. GedMatch introduced Genesis as a sandbox beta version previously, but are now in the process of combining regular GedMatch and Genesis into one. Yes, there are problems and matching challenges. Patience is the key word as the various vendors and GedMatch adapt and improve their required migration to imputation.

DNA Central

In June Blaine Bettinger announced DNACentral, an online monthly or yearly subscription site as well as a monthly newsletter that covers news in the genetic genealogy industry.

Many educators in the industry have created seminars for DNACentral. I just finished recording “Getting the Most out of Y DNA” for Blaine.

Even though I work in this industry, I still subscribed – initially to show support for Blaine, thinking I might not get much out of the newsletter. I’m pleased to say that I was wrong. I enjoy the newsletter and will be watching sessions in the Course Library and the Monthly Webinars soon.

If you or someone you know is looking for “how to” videos for each vendor, DNACentral offers “Now What” courses for Ancestry, MyHeritage, 23andMe, Family Tree DNA and Living DNA in addition to topic specific sessions like the X chromosome, for example.

Social Media

2018 has seen a huge jump in social media usage which is both bad and good. The good news is that many new people are engaged. The bad news is that people often given faulty advice and for new people, it’s very difficult (nigh on impossible) to tell who is credible and who isn’t. I created a Help page for just this reason.

You can help with this issue by recommending subscribing to these three blogs, not just reading an article, to newbies or people seeking answers.

Always feel free to post links to my articles on any social media platform. Share, retweet, whatever it takes to get the words out!

The general genetic genealogy social media group I would recommend if I were to select only one would be Genetic Genealogy Tips and Techniques. It’s quite large but well-managed and remains positive.

I’m a member of many additional groups, several of which are vendor or interest specific.

Genetic Snakeoil

Now the bad news. Everyone had noticed the popularity of DNA testing – including shady characters.

Be careful, very VERY careful who you purchase products from and where you upload your DNA data.

If something is free, and you’re not within a well-known community, then YOU ARE THE PRODUCT. If it sounds too good to be true, it probably is. If it sounds shady or questionable, it’s probably that and more, or less.

If reputable people and vendors tell you that no, they really can’t determine your Native American tribe, for example, no other vendor can either. Just yesterday, a cousin sent me a link to a “tribe” in Canada that will, “for $50, we find one of your aboriginal ancestors and the nation stamps it.” On their list of aboriginal people we find one of my ancestors who, based on mitochondrial DNA tests, is clearly NOT aboriginal. Snake oil comes in lots of flavors with snake oil salesmen looking to prey on other people’s desires.

When considering DNA testing or transfers, make sure you fully understand the terms and conditions, where your DNA is going, who is doing what with it, and your recourse. Yes, read every single word of those terms and conditions. For more about legalities, check out Judy Russell’s blog.

Recommended Vendors

All those DNA tests look yummy-good, but in terms of vendors, I heartily recommend staying within the known credible vendors, as follows (in alphabetical order).

For genetic genealogy for ethnicity AND matching:

  • 23andMe
  • Ancestry
  • Family Tree DNA
  • GedMatch (not a vendor because they don’t test DNA, but a reputable third party)
  • MyHeritage

You can read about Which DNA Test is Best here although I need to update this article to reflect the 2018 additions by MyHeritage.

Understand that both 23andMe and Ancestry will sell your DNA if you consent and if you consent, you will not know who is using your DNA, where, or for what purposes. Neither Family Tree DNA, GedMatch, MyHeritage, Genographic Project, Insitome, Promethease nor LivingDNA sell your DNA.

The next group of vendors offers ethnicity without matching:

  • Genographic Project by National Geographic Society
  • Insitome
  • LivingDNA (currently working on matching, but not released yet)

Health (as a consumer, meaning you receive the results)

Medical (as a contributor, meaning you are contributing your DNA for research)

  • 23andMe
  • Ancestry
  • DNA.Land (not a testing vendor, doesn’t test DNA)

There are a few other niche vendors known for specific things within the genetic genealogy community, many of whom are mentioned in this article, but other than known vendors, buyer beware. If you don’t see them listed or discussed on my blog, there’s probably a reason.

What’s Coming in 2019

Just like we couldn’t have foreseen much of what happened in 2018, we don’t have access to a 2019 crystal ball, but it looks like 2019 is taking off like a rocket. We do know about a few things to look for:

  • MyHeritage is waiting to see if envelope and stamp DNA extractions are successful so that they can be added to their database.
  • www.totheletterDNA.com is extracting (attempting to) and processing DNA from stamps and envelopes for several people in the community. Hopefully they will be successful.
  • LivingDNA has been working on matching since before I met with their representative in October of 2017 in Dublin. They are now in Beta testing for a few individuals, but they have also just changed their DNA processing chip – so how that will affect things and how soon they will have matching ready to roll out the door is unknown.
  • Ancestry did a 2018 ethnicity update, integrating ethnicity more tightly with Genetic Communities, offered genetic traits and made some minor improvements this year, along with adding one questionable feature – showing your matches the location where you live as recorded in your profile. (23andMe subsequently added the same feature.) Ancestry recently said that they are promising exciting new tools for 2019, but somehow I doubt that the chromosome browser that’s been on my Christmas list for years will be forthcoming. Fingers crossed for something new and really useful. In the mean time, we can download our DNA results and upload to MyHeritage, Family Tree DNA and GedMatch for segment matching, as well as utilize Ancestry’s internal matching tools. DNA+tree matching, those green leaf shared ancestor hints, is still their strongest feature.
  • The Family Tree DNA Conference for Project Administrators will be held March 22-24 in Houston this year, and I’m hopeful that they will have new tools and announcements at that event. I’m looking forward to seeing many old friends in Houston in March.

Here’s what I know for sure about 2019 – it’s going to be an amazing year. We as a community and also as individual genealogists will be making incredible discoveries and moving the ball forward. I can hardly wait to see what quandaries I’ve solved a year from now.

What mysteries do you want to unravel?

I’d like to offer a big thank you to everyone who made 2018 wonderful and a big toast to finding lots of new ancestors and breaking down those brick walls in 2019.

Happy New Year!!!

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Disclosure

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

Thank you so much.

Big Y-500 Flash Sale

Beginning today, Big Y prices at Family Tree DNA will be reduced FURTHER to the following levels:

  • Big Y-500 with no prior Y STR tests: $449 – this test includes all 500 STR markers plus the Big Y itself.

This is an amazing price given that the 111 panel itself is normally $359 alone. For just $90 more, you get the full 500 STR markers, including those 111, and the Big Y. This provides you with matches on 111 STR markers, your most refined haplogroup, and Big Y matching as well. Pricing has never been better.

Upgrades to Big Y-500:

  • Y12: $449 – normally $629 – save $180
  • Y25: $449 – normally $599 – save $150
  • Y37: $429 – normally $569 – save $140
  • Y67: $379 – normally $499 – save $130
  • Y111: $329 – normally $449 – save $130

Updated Testing Strategy 

Initially, I was testing only one man per family line, but I’ve revised that practice now because we’ve discovered new SNPs in different lines of the same family within a genealogical timeframe. This is exciting news, because it allows us to combine STRs and SNPs to define and sort family lines.

This is particularly useful when the tester knows they descend from a specific surname line, but has no idea how. The Big Y can solve that mystery when other methods don’t. I have two ancestral lines that have line-defining SNPs where STRs failed to make the division. I hope you have some of the same success – and the price sure is right.

My new strategy is to test minimally two men who descend from different sons of the oldest known ancestor of the line. In some family lines, several men have taken the Big Y, and downstream branches have been discovered. SNP mutations are much more common than we once believed.

These are great prices but the sale ends August 31st, so you only have 2 days!  Click here to purchase or upgrade.

_____________________________________________________________________

Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

I provide Personalized DNA Reports for Y and mitochondrial DNA results for people who have tested through Family Tree DNA. I provide Quick Consults for DNA questions for people who have tested with any vendor. I would welcome the opportunity to provide one of these services for you.

Hot links are provided to Family Tree DNA, where appropriate.  If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase.  Clicking through the link does not affect the price you pay.  This affiliate relationship helps to keep this publication, with more than 900 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc.  In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received.  In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product.  I only recommend products that I use myself and bring value to the genetic genealogy community.  If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA, or one of the affiliate links below:

Affiliate links are limited to:

Should I Upgrade My Y DNA Test?

I’m often asked about the benefits of upgrading Y DNA tests at Family Tree DNA, and if people should order an upgrade.

The answer to this, like just about everything else DNA is “it depends.”

Yes – Upgrade!

The answer IS YES if:

  • You have tested less than 37 markers. You really need 37 or 67 markers minimally today for genealogy.
  • You want to obtain all of the information possible about your ancestral lineage and where it came from. (That’s me!)
  • You want to participate in family as well as scientific research by upgrading to the Big Y. Why the Big Y? I wrote about that here.
  • You want the most refined haplogroup possible in order to see who you match the most closely that might not be a match on the STR (12-111) panels. This is particularly useful in terms of looking for clan overlap and relatedness further back in time in Scotland, for example.
  • You have lots of matches at your current level and you wish to eliminate the ones that aren’t relevant.
  • You have (your own) surname matches at levels higher than you’ve tested and you want to further determine which matches are closer genealogically.
  • You have no matches at your current level. Sometimes you pick up matches at higher levels because they allow more mutations and your mutations (or their mutations) may simply fall in the lower panels.
  • You want to leave a legacy for future genealogists by providing as much information as possible. This is especially important if you are the last of your line, or males with surname from your family line are in short supply.

No – Maybe Not Now

The answer IS NO if none of the above applies and:

  • You’ve already tested to 37 markers, don’t have matches at lower levels, and you don’t care.
  • You’ve tested to 37 markers, don’t have matches and have to choose between a Y upgrade and a different kind of test, like autosomal or mitochondrial that you haven’t yet taken. You’ll probably learn more by testing an untapped resource.
  • You’ve tested to 37 markers and have to choose between a Y upgrade and a new test for a relative that will provide information about one of your paternal ancestral lines that hasn’t been tested. Hint, look at the surname project in question to be sure your lines aren’t already present.

Surname Project Search

You can search for the surname and projects on the main Family Tree DNA page by scrolling down until you see the surname search box.

Of course, if your ancestor is represented in a public surname project, and you have someone available to test, it’s always a good idea to test that person…well…because you never know if there was an adoption or some hanky panky – or your genealogy is wrong. Better to find out now that to go on blissfully doing genealogy on the wrong line.

Summer Sale is in Full Swing

The great news is that the Family Tree DNA Summer Sale is in full swing, and unlike last year’s sale, upgrades ARE included.

Plus, as an added bonus, when you upgrade to the Big Y-500 test, the markers between where you’ve already tested and the Big Y-500 are included in the price. So if you’ve tested to 37 markers and order the Big Y 500, you receive:

  • 67 marker upgrade
  • 111 marker upgrade
  • Big Y test
  • Additional markers to total 500 above the 111 marker panel – that’s 389 extra markers for free with the Big Y

In essence, this upgrade is 4 tests bundled into one and it’s on sale for less than the Big Y itself used to cost on sale, a year ago, at about $500. This has never been a better value than it is now.

Upgrade prices are shown above and you can order by clicking here and signing on to your account. Then, just click on the blue upgrade button by your Y DNA results.

Need to order a new test, not an upgrade? Great! Click here to view the sale prices. The sale lasts until August 31st.

_____________________________________________________________________

Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

I provide Personalized DNA Reports for Y and mitochondrial DNA results for people who have tested through Family Tree DNA. I provide Quick Consults for DNA questions for people who have tested with any vendor. I would welcome the opportunity to provide one of these services for you.

Hot links are provided to Family Tree DNA, where appropriate.  If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase.  Clicking through the link does not affect the price you pay.  This affiliate relationship helps to keep this publication, with more than 900 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc.  In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received.  In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product.  I only recommend products that I use myself and bring value to the genetic genealogy community.  If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA, or one of the affiliate links below:

Affiliate links are limited to:

Why Different Haplogroup Results?

“Why do vendors give me different haplogroups?”

This questions often comes up when people test with different vendors and receive different haplogroup results for both Y and mitochondrial DNA.

If you need a quick refresher on who carries which types of DNA, read 4 Kinds of DNA for Genetic Genealogy.

You’re the same person, right, so why would you receive different answers from different testing companies, and which answer is actually right?

The answer is pretty straightforward, conceptually – having to do with how vendors test and interpret your DNA.

Different companies test different pieces of your DNA, depending on:

  • The type of chip the company is using for testing
  • The way they have programmed the chip
  • The version of the reference “tree” they are using to assign haplogroups
  • The level they have decided to report

Therefore, their haplogroups reported may vary, and some may be more exact than others. Occasionally, a vendor outside the major testers is simply wrong.

Not All Tests are Created Equal

All haplogroups carry interesting information and can be at least somewhat genealogically useful. For example, haplogroups alone can tell you if your direct line DNA (paternal or matrilineal) is probably European, Asian, African or Native American. Note the word probably. This too may be subject to interpretation.

A basic haplogroup can rule out a genealogical match through a specific branch, but can’t confirm a genealogical match. You need to compare specific DNA locations not provided with haplogroup testing alone for genealogical matching. Plus you’ll need to add genealogical records where possible.

Let’s look at two examples.

Mitochondrial DNA

Your mitochondrial DNA is inherited from your mother’s direct line, on up you tree until you run out of mothers.  So, you, your mother, her mother, her mother…etc.

The red circles show the mitochondrial lineage in the pedigree chart, below.

If your mitochondrial haplogroup is H1a, for example, then your base haplogroup is “H”, the first branch is “1” and the next smaller branch is “a.”

Therefore, if you don’t match at H, your base haplogroup, you aren’t a possible match on that genealogical line. In other words, if you are H1a, or H plus anything, you can’t match on the direct matrilineal line of someone who is J1a, or J plus anything. H and J are different base haplogroups who haven’t shared a common ancestor in tens of thousands of years.

You can, however, potentially be related on any other line – just not on this specific line.

If your haplogroup does match, even exactly, that doesn’t mean you are related in a genealogically relevant timeframe. It means you share an ancestor, but that common ancestor may be back hundreds, thousands or even tens of thousands of years.

The further downstream, the younger the branches.  “H” is the oldest, then “1,” then “a” is the youngest.

Some companies might just test the locations for H, some for H1 and some for H1a.  Of course, there are even more haplogroups, like H1a2a. New, more refined haplogroups are discovered with each new version of the mitochondrial reference tree.

The only company that tests your haplogroup all the way to the end, meaning the most refined test possible to give you your complete haplogroup and all mutations, is Family Tree DNA with their mtFull Sequence test.

A quick comparison of my mitochondrial DNA at the following three vendors shows the following:

23andMe Living DNA Family Tree DNA Full Seqence
J1c2 J1c J1c2f

With Family Tree DNA’s full sequence test, you’ll receive your full haplogroup along with matching to other people who have taken mitochondrial DNA tests. They are the only vendor to offer Y and mitochondrial matching, because they are the only vendor that tests at that level.

Y DNA

Y DNA operates on the same principle. Specific locations called SNPs are tested by companies like 23andMe and Living DNA to provide customers with a branch level haplogroup. You don’t receive matching with these types of tests.

Just like with mitochondrial DNA, a basic branch level test can eliminate a match on the direct paternal (surname) branch but can’t confirm the genealogical match.

If your haplogroup branch is E-M2 and someone else’s is R-M269, you can’t share a common paternal ancestor because your base haplogroups don’t match, meaning E and R.

You can share an ancestor on any other line, just not on the direct Y line.

The blue squares show the Y DNA lineage on the pedigree chart below.

Family Tree DNA predicts your haplogroup for free if you take the 37, 67 or 111 marker Y-DNA STR test, but if you take the Big Y-500, your Y chromosome is completely tested and your haplogroup defined to the most refined level possible (often called your terminal SNP) – including mutations that may exist in only very few people. You also receive matching to other testers (with any Y test) which can be very genealogically relevant, plus bonus Y STR markers with the Y-500.

OK, But Why Do Different Companies Give Me Different Haplogroup Results?

Great question.

For this example, let’s say your haplogroup is H1a2a.

Let’s say that Company 1 uses a chip that they’ve programmed to test to the H1a level of haplogroup H1a2a.

Let’s say that Company 2 uses a chip that they’ve programmed to test to the H1 level of haplogroup H1a2a.

Let’s say that you take the full sequence test with Family Tree DNA and they fully test all 15,659 locations of your mitochondria and determine that you are H1a2a.

Company 1 will report your mitochondrial haplogroup as H1a, Company 2 as H1 and Family Tree DNA as H1a2a.

With mitochondrial DNA, you can at least see some consist pathway in naming practices, meaning H, H1, H1a, etc., so you can tell that you’re on the same branch.

With Y DNA, the only consistent part is the base haplogroup.

With Y DNA, let’s say that Company 1 programs their chip to test for specific SNP  locations, and they return a Y DNA haplogroup of R-L21.

Company 2 programs their chip to test for fewer or different locations and they return a Y DNA haplogroup of R-M269.

You purchase a Big Y-500 test at Family Tree DNA, and they return your haplogroup as R-CTS3386.

All three haplogroups can be correct, as far as they go. It’s just that they don’t test the same distance down the Y chromosome tree.

R-M269, R-L21 and R-CTS3386 are all increasingly smaller branches on the Y haplotree.

Furthermore, for both Y and mitochondrial DNA, there is always a remote possibility that a critical location won’t be able to be read in your DNA sample that might affect your haplogroup.

Obtaining Your Haplogroup

I strongly encourage people to test with and upload to only well-known major companies or organizations. Some companies provide haplogroup information that is simply wrong.

Companies that I am comfortable with relative to haplogroups include:

Neither MyHeritage nor Ancestry provide Y or mitochondrial haplogroups.

The chart below shows the various vendor offerings, including Y and mitochondrial DNA matching.

Company Offerings Matching
Family Tree DNA – Y DNA Y haplogroup is estimated with STR test. Haplogroup provided to most refined level possible with Big Y-500 test. Individual SNP tests also available. Yes
Family Tree DNA – mitochondrial At least base haplogroup provided with mtPlus test, plus more if possible, but full haplogroup plus additional mutations provided with mtFull Sequence test. Yes
Genographic Project More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No
23andMe More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No
Living DNA More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No

Want More Detail?

If you’d like to read a more detailed answer about how haplogroups are determined, take a look at the article, Haplogroup Comparisons Between Family Tree DNA and 23andMe.

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Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

I provide Personalized DNA Reports for Y and mitochondrial DNA results for people who have tested through Family Tree DNA. I provide Quick Consults for DNA questions for people who have tested with any vendor. I would welcome the opportunity to provide one of these services for you.

Hot links are provided to Family Tree DNA, where appropriate.  If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase.  Clicking through the link does not affect the price you pay.  This affiliate relationship helps to keep this publication, with more than 900 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc.  In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received.  In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product.  I only recommend products that I use myself and bring value to the genetic genealogy community.  If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA, or one of the affiliate links below:

Affiliate links are limited to:

Family Tree DNA’s Y-500 is Free for Big Y Customers

Did you notice something new on your Y DNA results page at Family Tree DNA this week? If not quite yet, you will soon if you have taken the Big Y test. There’s a surprise waiting for you. You can sign in here to take a look.

The first thing you might notice is that the Big Y has been renamed to the Big Y500. However, the results I want you to take a look at aren’t under the Big Y500 tab, but on your regular Y DNA Y-STR Results tab. Click to take a look

In the past, 5 panels of Y DNA STR markers have been available:

  • Panel 1 – 1-12 markers
  • Panel 2 – 13-25 markers
  • Panel 3 – 26-37 markers
  • Panel 4 – 38-67 markers
  • Panel 5 – 68-111 markers

Now, a 6th panel has been added:

  • Panel 6 – 112-550 markers

However, there is a difference between the first 5 panels and the 6th panel.

Why is it Called the Y500?

If there is a total of 550 markers reported, why is this product called the Y500?

That’s a great question with an even greater answer.

Family Tree DNA actually tests for a total of 550 markers. Values for markers between 112 and 550 are provided FOR FREE when you take a Big Y test.

Family Tree DNA guarantees that you will receive at least a total of 500 markers, or they will rerun your Big Y test at no cost to you to obtain enough additional markers to reach 500. (The 500 number assumes that you have all 111 STR markers. If you have not tested all of the STR panels, the number will be lower by the number of STR values you haven’t tested. This means that if you took the Y67, but not the Y111, your 500 guarantee number would be 500-44, where 44 is the number of markers in the Y111 panel that you have not yet ordered.)

The best part?

The markers above 111 are ENTIRELY FREE with a Big Y test – for both existing customers who have already taken that test, and all future customers too. Yes, you read that right. If you took the Big Y previously, you are receiving the markers in panel 6, 112-550 absolutely free.

How does it get better than free?

The Big Y Uses a Different Technology

There is a difference between the first 111 markers and the markers from 112-550, meaning that they are read using different technologies

The results for the first 111 STR markers are produced using a technology that targets these specific areas and is very accurate.

The results for the 112-550 markers is produced using next generation sequencing (NGS) on a different testing platform than the Y-111 results. NGS, utilized for the Big Y, scans the Y chromosome rather than targeting specific locations. This scanning process is repeated several times, with values at specific locations recorded.

Scanning

Using NGS technology, your DNA is scanned multiple times, with the number of scans, such as 25 or 30, referred to as the coverage level. The goal is for multiple/most/all scans to find the same value at the same location consistently. Because of the nature of scanning technology, this sometimes doesn’t happen, for various reasons, including “no-calls” which is when for some reason, the scans simply can’t get a reliable read at that location in your DNA. No calls are typical and occur at low levels in everyone’s scan.

Here’s an example from a Big Y scan viewing the actual results using the Big Y chromosome browser.

The blue bars are forward reads and the green bars are reverse reads. Dark blue and dark green bars indicate high quality scans. Medium blue and green are medium quality scans and faintly colored bars indicate poor quality. If you take a look at where the little black arrow at the top is pointing, you can see that a T is the expected value at that location.

When the expected value as determined in the human reference genome is found at that location, nothing is recorded in that column. However, when a different result is discovered, like A in this case, it’s noted and highlighted with pink. We can see that there are 5 As on forward and reverse strands of high quality, then a low quality read, 6 more high quality reads, followed by two reads that show the expected value (nothing recorded) and then three more high quality A reads.

The goal is to determine what actual value resides at that location, and when that value is determined, it’s referred to as a “call.”

For a “call” to be made, meaning the determination of the actual value in that position, the person or software making the call must take several quality factors into consideration.

In this case, the number of high quality reads indicating the derived (mutation) value of “A” allows this location to be definitively called as “A.” Because several other men previously tested have A at this location, a SNP name has already been assigned to this mutation – in this case, A126 in haplogroup R.

However, if you look to the right and left of the arrow to the next two browser locations that contain mutations, you can see in both cases that there are less than half of the column locations that are marked as pink with derived values (mutations), meaning those not expected when compared to the reference model.

These types of locations which are neither clearly ancestral (reference model) nor derived values are when value judgements come into play in terms of deciding which value, the ancestral or derived, is actually present in the DNA of the person being tested.

Some people will call a SNP with only one mutation reported out of 20 or 30 scans. Some people will call a SNP with 2 scans; some with 5, and so forth. Generally, Family Tree DNA uses a minimum threshold of 5 high quality scans to call a mutation value.

Now, let’s talk about how STR values, meaning results displayed in those locations between 112-550, are found in your Big Y NGS data file. You can read about the difference between SNPs and STRs in the article, STRs vs SNPs, Multiple DNA Personalities.

STRs

Short tandem repeats, known as STR values, are the numbers reported in your STR panels. These are stutters of DNA, kind of like the copy machine got stuck in that one area for a few copies.

For example, in haplogroup R, for this person, the value of 13, meaning 13 repeats of a particular sequence, is found at marker DYS393.

Repeated sequences are in essence inserted in-between SNPs in some DNA regions, and the number of repeats reported in STR marker panels is the number of stutters, or repeats, of a particular repeated sequence.

That sounds simpler than it is, because how to count a sequence isn’t always the same. Let’s look at an example showing 20 consecutive DNA positions.

The actual values are shown in the value row. However, these values can be counted in a number of different ways. I’ve also added a “stray read” at location 13 which causes confusion.

At location 13, we show a value of G which does not fit into the repeat pattern. How do we interpret that, and what do we do with it?

The repeat pattern itself is a matter of where you start counting, and how you count.

I’ve color coded the repeats with blue and yellow. Incomplete repeats are red. The stray G in location 13 is green, because it breaks the repeat sequence.

In example 1, we start counting with T in position 1, and there are clearly 3 repeated groups of TACG before we hit our stray G in position 13, which stops the repeat pattern. However, after the stray G, there is one more full repeat sequence of TACG. Do we ignore the G and count the 4th TACG as part of the group, or do we count only the first 3 complete TACG sequences? The total number of repeats could be counted as either 3 or 4, depending on how we interpret the stray G in location 13.

In example 2, we start counting with the GTAC, because I was simulating a reverse read where we start at the end and work backwards. In this case, we clearly have 2 reads, then our stray G which occurs in the middle of a read. Do we ignore that stray G and call the rest of the blue GTAC surrounding the G as a repeat? That blue repeat group is followed by another yellow group. Do we count it at all, or do we simply stop with the marker count of 2 because the G is in the way and breaks the sequence? This repeat sequence could be counted as either 2, 3 or 4, depending on what you do with the G and the following sequence group, both.

Examples 3 and 4 follow the same concept and have the same questions.

All STR sequences face the issue of where to start reading. Where you begin reading can affect the number of repeat counts you wind up with, even without our stray G in position 13.

STR markers obtained from NGS sequencing face this same challenge, but it’s complicated by the issue of no-reads and the call variance that we saw in the chromosome browser where the same location is sometimes called differently on different scans, meaning we really can’t tell which is the actual value. What do we do with those?

All of this is complicated by the fact that some regions of the Y chromosome simply do not produce valid or reliable information. Different (groups of) people define this unreliable region as starting and ending in different locations. Therefore different people analyzing the same information often arrive at different answers to the same question or use marker locations that others don’t.

I suspect all of this may fall into the category of trivia you never wanted to know, but now you’ll understand why you may find different (sometimes strongly held) opinions of what is “right” when two geeky types are arguing strongly about a particular STR value as your eyes glaze over…

Here’s the bottom line – if you’re using results called by the same vendor, you don’t have to worry about whether you and someone else are being accurately compared. You and everyone else at that vendor will have your results reported using the same technology and calling methodology.

Family Tree DNA has always taken a more conservative approach, because they only want to report to customers what they know to be accurate.

You will not see low confidence values on your reports, nor calls from an unreliable region. Genealogists cannot reach reliable genealogical conclusions using unreliable data.

The Big Y 500

Because of the nature of scanned STR results, Family Tree DNA can’t guarantee that you will have a reliable read at every location. In fact, few people will have values at every location. The technology for the Y-111 markers provides a very high level of accuracy and Family Tree DNA will provide results for every 1-111 location unless you actually have a deletion, meaning no DNA in that location. However, the values of markers 112-550 are taken from the Big Y NGS scan.

Therefore, some Big Y customers will have a few markers above 111 that show a “-“ instead of results, such as FTY945 and FTY1025, shown below. A value of “0” found in markers 1-111 means that there is actually no DNA in that location, and it’s not a read error. No DNA at a specific location is heritable, meaning it can serve as a line-marker mutation, while a “no call” means that the scan couldn’t read that genetic address. No calls cannot be compared to others and should be ignored.

Before someone starts to complain about having markers with “no reads,” remember that Family Tree DNA is providing up to 439 additional markers available FOR FREE to customers who have taken (or will take) the Big Y test.

That’s right, there is no charge for these new markers. You are guaranteed 389 additional markers, but you may actually receive as many as 439, depending on how well your DNA reads. The kits I’ve checked have only been missing a couple of marker values, so these kits received 437 additional markers, far above the guaranteed 389.

Right now, matching is not included for the 112-550 markers. Matching above 111 markers may be challenging because while Family Tree DNA does guarantee that you’ll have at least 389 new marker values, those won’t be the same markers above 111 for everyone. In a worst-case scenario, you could mismatch with someone on as many as 100 markers above 111 panel, simply because both you and the person you are matching against are both missing 50 different markers each, for a total of 100 markers mismatching.

Additionally, not everyone has tested all 111 STR markers, and you will receive your 112-550 values if you have taken the Big Y test regardless of whether or not you’ve tested all 111 STR markers.

Matching

Matching on the first 111 markers is reliable because you will have an accurate value, even if the value is 0. Having no DNA at a specific location is a valid result and can be compared to other testers.

With different markers between 112 and 550 missing for different men, matching becomes very tricky. Specifically, how do we interpret mismatches? How many mismatches to we allow to still be considered a reasonable match?

Matching is an entirely different prospect when integrating the markers between 112 and 550 into the equation with a potential of up to 100 mismatching locations in that range simply from no-reads.

I had presumed that Family Tree DNA would offer matching on these additional markers. Presume is a dangerous word, I know. Matching is not offered right now, and given the complexities, I don’t know if matching as we know it will be the future or not, how reliable it would be, or how Family Tree DNA would compensate for the missing STR information that differs with each person’s test.

Furthermore, I’m not quite sure what they would do with two men who haven’t both tested to the same STR level, meaning panels 1-5, but have taken the Big Y so have values for 112-550.

Big Y Purchases

Here’s the status of Big Y tests, today:

  • New Big Y purchase if you have done no Y DNA testing at all – you will now be able to purchase a Big Y without having to previously purchase any STR markers. The 111 STR markers are now bundled into the Big Y purchase, which makes the Big Y appear more expensive than before when the STR markers had to be purchased separately before you could order a Big Y test. The Big Y plus all 111 STR markers is now $649 during the DNA Day Sale, regularly $799.
  • Already tested through 111 STRs – the Big Y is only $349 on sale right now, and $449 regularly, both significantly discounted from just a few months ago.
  • Existing customers who have taken some level of Y STR test but not the Big Y – will have to upgrade their STR test to the 111 level when ordering the Big Y. Those tests are discounted appropriately, shown in the table below.
  • Existing customers who have not tested their STR markers to 111, but have already taken the Big Y – will receive marker values from 112-550. However, they will only receive the Y STR markers below 112 for panels they have paid for. This means that if you have only tested to 37 markers, you will have results for locations 1-37, not for 38-111, but will have results for locations that read from 112-550. This would be the perfect time to upgrade so that you have a complete marker set.

Right now, Family Tree DNA is having their DNA Day Sale and it’s a great time to purchase a Big Y or to upgrade your STR markers if you don’t have the full 111. The sale pricing shown is valid through April 28th. You can click here to order.

____________________________________________________________________

Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 900 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA, or one of the affiliate links below:

Affiliate links are limited to: