Tag Archives: Basic Education

Finding Mary Younger’s Mitochondrial DNA – 52 Ancestors #219

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Ah, the blessings of cousins.

The Y and mitochondrial DNA of our ancestors can provide us with a smorgasbord of information. Unfortunately, we only carry the Y and mitochondrial DNA of one or two lines. If you’re a female, you carry the mitochondrial DNA (mtDNA) of your matrilineal line only, and if you’re a male, you carry the paternal (patrilineal meaning surname) Y DNA line (blue squares) in addition to your mother’s matrilineal line (red circles.) You can read about the difference between maternal versus matrilineal and paternal versus patrilineal here.

Y and mito

Therefore, to collect the rest of the haplogroups and match information about our ancestral lines, meaning those with no color above, we must depend on cousins who descend from those ancestors in such a way that they carry the desired Y or mtDNA.

For men, their surname is generally reflective of the Y DNA inheritance path, presuming that neither the surname nor the Y DNA was changed, intentionally or otherwise – meaning adoption or name changes, for example.

Women contribute their mitochondrial DNA to both genders of their children, but only females pass it on to the next generation.

This inheritance path assures that neither the Y nor mitochondrial DNA is admixed with the DNA of the other parent, meaning the DNA changes little if at all generation to generation and we can see back a very long distance into the past by following the stair-step mutations that have accumulated over hundreds and thousands of years.

Think of it as your genetic periscope!

Recently a press article reported that in very limited cases with a medically co-presenting mitochondrial disease, the father’s mitochondrial DNA is found in children. Blaine Bettinger explained further here. It’s actually not new news and you really don’t need to worry about this in regard to genealogy.

Mary Younger

When I originally wrote Mary Younger’s 52 Ancestors article, I didn’t know anything about her mitochondrial DNA because no one from that line had yet tested.

In that article, I detailed her descendants as best I could, and of those descendants, who would carry Mary’s mitochondrial DNA.

A cousin, Lynn, read the article and replied that indeed, she descends from Mary through all females – and was willing to DNA test. Thank you Lynn!!!

Mary’s mtDNA Dispells a Myth

Lynn’s results came back and told us that Mary Younger’s mitochondrial DNA is haplogroup H1a3a.

Often in early genealogy research, when a colonial lineage brick wall was encountered, the comment that “maybe she was Indian,” was made. Sometimes those comments fanned the flames of myths that took hold like wildfire and are reflected today in many online trees. The “maybe” became quickly omitted and the comment was elevated from the realm of speculation to gospel.

Mary Younger was born about 1766, probably in either Essex or King and Queen County to Marcus Younger and his wife, Susannah whose surname we don’t know. Therefore, Susannah would have been born between 1720 and 1746.

There’s a persistent rumor that Susannah’s surname was Hart and there is some reason to suspect that it may have been, but the bottom line is that we don’t know.

If Susannah’s surname IS Hart, we don’t know which Hart individual was her father, although Anthony Hart (1755-1832) and Marcus Younger were both associated with one Robert Hart, believed to be Anthony’s father, but that too is unproven. The King and Queen County courthouse burned and that’s where the Hart land was located, so most records are gone. Bummer.

There is some amount of suspicion that Anthony Hart and Susannah that married Marcus Younger were siblings. To make matters even worse, Marcus and Susannah Younger’s son, John Younger married Lucy Hart – so autosomal DNA from that line will match the Hart line and not (necessarily) because of Susannah. Therefore, John Younger’s line can’t be used for comparisons to the Hart line for either mitochondrial or autosomal. However, cousin Lynn’s DNA as Mary Younger’s direct matrilineal descendant can be utilized for both mitochondrial and autosomal comparisons.

What we do know, from Mary Younger’s mitochondrial DNA alone is that Susannah through her matrilineal line was NOT Native American. Haplogroup H1a3a is European, unquestionably European.

We can dispel that Native American myth forever, at least about this particular line.

Lynn’s H1a3a Matches

What can we tell about haplogroup H1a3a and in particular, Lynn’s matches?

Mary Younger matches map

None of Lynn’s three exact matches have completed their geographical information for their most distant known ancestor. These match maps are such powerful tools if people would only complete the information.

Other than the three with no information, so aren’t shown on the map – the matches on the map in the US aren’t terribly relevant unless specific clusters suggest a particular migration path. In this case, nothing of note, although those 3 Canadian maritime matches are curious. I don’t know if there is any useful information there or not.

However, Europe is different, because those matches are fairly tightly clustered.

All of Lynn’s matches are either in the British Isles or in Scandinavia. This could suggest either that descendants of her ancestors, hundreds or thousands of years ago migrated to both locations, or it could mean that the English locations are perhaps showing a Viking influence.

Lynn’s matches themselves are unremarkable other than the fact that her only rare mutation occurs in the coding region, which means that we really do need the full sequence test to make use of this information. She has 107 full sequence matches, of which three are exact, providing the following most distant ancestor information.

  • Martha Patsy Terry was born in 1805 in North Carolina and died after 1865 in Alabama
  • Sarah Emma Doyle was born in 1824 in Fayette County, TN and died in 1890 in Cass Co., Texas.
  • The third match says “information needed.” Well, me too😊

The only person with one mutation difference shows their most distant ancestor with a name and birth of 1534. They apparently misunderstood what was being asked, because if you look at their tree, their most distant matrilineal ancestor is Margaret Moore born in NC, died in Texas, and who had daughter Dicie Moore in 1830 in Tennessee.

Unfortunately, these matches aren’t terribly helpful either, at least not today.

Two of the three exact matches have trees which I checked for the surname of Hart and Younger and looked for geographic proximity.

Checking advanced matches by selecting both Family Finder and the Full Sequence mitochondrial matches shows no individual who matches on both tests.

Haplogroup H1a3a

If Lynn’s mtDNA matches aren’t being productive, what can I tell about haplogroup H1a3a itself?

Doron Behar in his 2012 paper placed the age of H1a3a at 3859 years, give or take 1621 years, so therefore haplogroup H1a3a was born between 1238 and 6480 years ago. An exact match with no additional mutations could be from long ago. Fortunately, Lynn does have a few additional mutations, so her exact matches share mutations since the birth of haplogroup H1a3a.

Using the Family Tree DNA mitochondrial tree and searching for H1a3a, we discover the following information.

Mary Younger H1a3a

Haplogroup H1a3a is found in a total of 21 countries. The most common location is Germany, which isn’t reflected in Lynn’s matches.

Mary Younger mtDNA countries

This is especially interesting, because it suggests that the haplogroup itself may have spread from the Germanic region of Europe into both England and Sweden. Lynn’s matches are only found in those diaspora regions, not in Germany itself. To me, this also suggests that the people still in Germany have accrued several mutations as compared to Mary Younger’s DNA. They are no longer considered a match since their common ancestor is far enough back in time that they have accumulated several mutations difference from cousin Lynn today. Conversely, the people closer in time that share some of those mutations do qualify as matches.

And no, haplogroup H1a3a is not Native American, in spite of the one person who had indicated such (the feather icon.) Many people record “American” or “Native American” because they believe, before testing, that they have Native American on “that side,” as opposed in that specific line. Of course, the maternal side could mean any one of many ancestors – as opposed to the matrilineal line which is directly your mother’s mother’s mother’s line until you run out of direct line mothers in your tree.

What we know now is that sometime between 1200 and 6500 years ago, the haplogroup defining mutations between H1a3 and H1a3a occurred, probably someplace in Germanic Europe. From there, people migrated to both the British Isles and portions of Scandinavia.

Given that we find Susannah in the early 1700s in King and Queen County, Virginia, it would be a reasonable working hypothesis that she was English (or at least from the British Isles) and not Scandinavian. Alexander Younger, the grandfather of Marcus Younger was from Scotland and many of the early era colonial settlers in that region were English.

Hopefully, time and more DNA testers will eventually tell more of Susannah’s tale – either through mitochondrial or autosomal DNA matches, or both.

What About You?

If you haven’t yet tested your mitochondrial DNA, now would be a great time. In fact, you can click here to order the mtFull test. Who knows what you might learn. Are there specific questions you’d like to answer about dead end female lines? Mitochondrial DNA is one way to circumvent a surname/genealogical blockade – at least partially.

If you don’t carry the mitochondrial DNA line that you need, sponsor a test for a cousin. You’ll get to meet a really cool person to share information with, like Lynn, and learn about your common genealogical bond as well as your ancestor’s DNA.

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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.

AutoClustering by Genetic Affairs

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The company Genetic Affairs launched a few weeks ago with an offer to regularly visit your vendor accounts at Family Tree DNA, Ancestry and 23andMe, and compile a spreadsheet of your matches, download it, and send it to you in an e-mail. They then update your match list at regular intervals of your choosing.

I didn’t take advantage of this, mostly because Ancestry doesn’t provide me with segment information and while 23andMe and Family Tree DNA both do, I maintain a master spreadsheet that the new matches wouldn’t integrate with. Granted, I could sort by match date and add only the new ones to my master spreadsheet, but it was never a priority. That was yesterday.

AutoClustering

That changed this week. Genetic Affairs introduced a new AutoClustering tool that provides users with clustered matches. I’m salivating and couldn’t get signed up quickly enough.

Please note that I’ve cropped the names for this article – the Genetic Affairs display shows you the entire name.

In short, each tiny square node represents a three-way match, between you and both of the people in the intersection of the grid. This does NOT mean they are triangulated, but it does mean there’s a really good chance they would triangulate. Think of this as the Family Tree DNA matrix on steroids and automated.

This tool allows me by using my mother’s test as well to actually triangulate my matches. If they are on my mother’s side of the tree, match me and mother both, and are in the match matrix, they must triangulate on my mother’s side of my tree if they both match me on the same segment.

With this information, I can check the chromosome browser, comparing my chromosomes to those other two individuals in the matrix to see if we share a common segment – or I can simply sort the spreadsheet provided with the AutoCluster results. Suddenly that delivery service is extremely convenient!

No, this service is not free, but it’s quite reasonable. I’m going to step through the process. Note that at times, the website seemed to be unresponsive especially when moving from one step to another. Refreshing the page remedied the problem.

Account Setup

Go to www.geneticaffairs.com. Click on Register to set up your account, which is very easy.

After registering, move to step 2, “Add website.”

Add websites where you have accounts. All of your own profiles plus the other people’s that you manage at both Ancestry and 23andMe are included when you register that site in your profile.

You’ll need your signon information and password for each site.

At Family Tree DNA, you’ll need to add a new website for each account since every account has its own kit number and password.

I added my own account and my mother’s account since mother’s DNA is every bit as relevant to my genealogy as my own, AND, I only received half of her DNA which means she will have many matches that I don’t.

When you’re finished adding accounts, click on “Websites and Profiles” at the top to open the website tab of your choosing and click on the blue circular arrows AutoCluster link. You are telling the system to go out and gather your matches from the vendor and then cluster your matches together, generating an AutoCluster graphic file.

There are several more advanced options, but I’m going to run initially with Approach A, the default level. This will exclude my closest matches. Your closest matches will fall into multiple cluster groups, and the software is not set up to accommodate that – so they will wind up as a grey nonclustered square. That’s not all bad, but you’ll want to experiment to see which parameters are best for you.

If you have half-siblings, you may want to work with alternate settings because that half-sibling is important in terms of phasing your matches to maternal or paternal sides.

Asking me if “I’m sure” always causes me to really sit back and think about what I’ve done. Like, do I want to delete my account. In this case, it’s “overworry” because the system is just asking if you want to spend 25 credits, which is less than a dollar and probably less than a quarter. Right now, you’re using your free initial credits anyway.

The first time you set up an account, Genetic Affairs signs in to your account to assure that your login information is accurate.

I selected my profile and my mother’s profile at Family Tree DNA, plus one profile each at 23andMe and Ancestry. I have two profiles at both 23andMe (V3 and V4) and Ancestry (V1 and V2).

When making my selections, I wasn’t clear about the meaning of “minimum DNA match” initially, but it means fourth cousin and closer, NOT fourth and more distant.

My recommendation until you get the hang of things is to use the first default option, at least initially, then experiment.

Welcome

While I was busy ordering AutoClusters, Genetic Affairs was sending me a welcome e-mail.

Hello Roberta Estes,

Thank you for joining Genetic Affairs! We hope you will enjoy our services.

We have a manual available as well as a frequently asked questions section that both provide background information how to use our website.

You currently have 200 credits which can be supplemented using single payments and/or monthly subscriptions. Check out our prices page for more information concerning our rates.

Please let us know if anything is unclear, we can be reached using the contact form.

The great news is that everyone begins with 200 free credits which may last you for quite some time.  Or not. Consider them introductory crack from your new pusher.

Options

Genetic affairs will sign on your account at either Ancestry, 23andMe or Family Tree DNA, or all 3, periodically and provide you with match information about your new matches at each website. You select the interval when you configure your account. After each update, you can order a new AutoCluster if you wish.

Each update, and each AutoCluster request has a cost in points, sold as credits, associated with the service.

To purchase credits after you use your initial 200, you will need to enter your credit card information in the Settings Page, which is found in the dropdown (down arrow) right beside your profile photo.

You can select from and enroll in several plans.

Prices which varies by how often you want updates to be performed and for how many accounts. To see the various service offerings and cost, click here.

Here’s an example calculation for weekly updates:

This is exactly what I need, so it looks like this service will cost me $2.16 per month, plus any Autoclustering which is 25 credits each time I AutoCluster. Therefore, I’ll add another 100 credits for a total of $3.16 per month.

It looks like the $5 per month package will do for me. But don’t worry about that right now, because you’re enjoying your free crack, um, er, credits.

Ok, the e-mail with my results has just arrived after the longest 10 minutes on earth, so let’s take a look!

The Results E-mail

In a few minutes (or longer) after you order, an e-mail with the autoclustering results will arrive. Check your spam filter. Some of my e-mails were there, and some reports simply had to be reordered. One report never arrived after being ordered 3 times.

The e-mail when it arrives states the following:

Hello Roberta Estes,

For profile Roberta Estes: An AutoCluster analysis has been performed (access it through the attached HTML file).

As requested, cM thresholds of 250 cM and 50 cM were used. A total number of 176 matches were identified that were used for a AutoCluster analysis. There should be two CSV files attached to this email and if enough matches can be clustered, an additional HTML file. The first CSV file contains all matches that were identified. The second CSV file contains a spreadsheet version of the AutoCluster analysis. The HTML file will contain a visual representation of the AutoCluster analysis if enough matches were present for the clustering analysis. Please note that some files might be displayed incorrectly when directly opened from this email. Instead, save them to your local drive and open the files from there.

Attached I found 3 files:

  • Matches list
  • Autocluster grid csv file
  • Autocluster html file that shows the cluster itself

The Match Spreadsheet

The first thing that will arrive in your e-mail is a spreadsheet of your matches for the account you configured and ordered an AutoCluster for.

In the e-mail, your top 20 matches are listed, which initially confused me, because I wondered if that means they are not in the spreadsheet. They are.

At 23andMe, I initially selected 5th cousins and closer, which was the most distant match option provided. I had a total of 1233 matches.

23andMe caps your account at 2000 (unless you have communicated with people who are further than 2000 away, in which case they remain on your list), but you can’t modify the Genetic Affairs profile to include any people more distant than 5th cousins

Note that the 23andMe download shows you information about your match, but NOT the actual matching segment information☹

At Ancestry, I selected 4th cousin and closer and I received a total of 2698 matches. I could select “distant cousin” which would result in additional matches being downloaded and a different autoclustering diagram. I may experiment with this with my V2 account and compare them side by side.

This Ancestry information provides an important clue for me, because the matches I work with are generally only my Shared Ancestor Hints matches. If the Viewed field equals false, this tells  me immediately that I didn’t have a shared ancestor hint – but now because of the clustering, I know where they might fit.

At Family Tree DNA, I selected 4th cousin, but I could have selected 5th cousins. I have a total of 1500 matches.

This report does include the segment information (Yay!) and my only wish here would be to merge the two downloads available at Family Tree DNA, meaning the segment information and the match information. I’d like to know which of these are assigned to maternal or paternal buckets, or both.

AutoClustering

The Autocluster csv file is interesting in that it shows who matches whom. It’s the raw data used to construct the colored grid.

My matches are numbered in their column. For example, person M.B. is person 1. Every person that matches person 1 is noted at left with a 1 in that column.  Look at the second person under the Name column, C. W., who matches person 1 (M.B.), 2 (C.W.), 3 (T.F.), 4 (purple) and 5 (A.D.).

All of these people are in the same cluster, number 3, which you’ll see below.

The AutoCluster Graph

Finally, we get to the meat of the matter, the cluster graph.

Caveat – I experienced a significant amount of difficulty with both my account and my graph. If your graph does not display correctly, save the file to your system and click to open the file from your hard drive. Try Edge or Internet explorer if Chrome doesn’t work correctly. If it still doesn’t display accurately, notify GeneticAffairs at info@geneticaffairs.com. Consider this software release late alpha or early beta. Personally, I’m just grateful for the tool.

When you first open the html file, you’ll be able to see your matches “fly” into place. That’s pretty cool. Actually, that’s a metaphor for what I want all of my genealogy to do.

This grid shows the people who match me and each other as well, so a trio – although this does NOT mean the three of us match on the same segment.

The first person is Debbie, a known cousin on my father’s side. She and all of the other 12 people match me and each other as well and are shown in the orange cluster at the top left.

I know that my common ancestor couple with Debbie is Lazarus Estes and Elizabeth Vannoy, so it’s very likely that all of these same people share the same ancestral line, although perhaps not the same ancestral couple. For example, they could descend from anyone upstream of Lazarus and Elizabeth. Some may have known ancestors on either the Estes or Vannoy side, which will help determine who the actual oldest common ancestors are.

You’ll notice people in grey squares that aren’t in the cluster, but match me and Debbie both. This means that they would fall into two different clusters and the software can’t accommodate that. You may find your closest relatives in this grey never-never-land. Don’t ignore the grey squares because they are important too.

The second green cluster is also on my father’s side and represents the Vannoy line. My common ancestor with several matches is Joel Vannoy and Phoebe Crumley.

Working my way through each cluster, I can discern which common ancestor I match by recognizing my cousins or people who I’ve already shared genealogy with.

The third red cluster is on my mother’s side and I know that it’s my Jacob Lentz and Fredericka Ruhle line. I can verify this by looking at my mother’s AutoCluster file to see if the same people appear in her cluster.

You can also view this grid by name, # of shared matches and the # of shared cMs with the tester. Those displays are nice but not nearly as informative at the AutoClusters.

Scroll for More Match Information

Be sure to scroll down below the grid (yes, there is something below the grid!) and read the text where you’re provided a list of people who qualify to be included in the clusters, but don’t match anyone else at the criteria selection level you chose – so they aren’t included in the grid. This too is informative.  For example, my cousin Christine is there which tells me that our mutual line may not be represented by a cluster. This isn’t surprising, since our common ancestor immigrated in the 1850s – so not a lot of descendants today.

You’re also provided with AutoCluster match information, including whether or not your match has a tree. I do have notes on my matches at Family Tree DNA for several of these people, but unfortunately, the file download did not pick those notes up.

However, the fact that these matches are displayed “by cluster” is invaluable.

You can bet your socks that I’m clicking on the “tree” hotlink and signing on to FTDNA right now to see if any of these people have recognizable ancestors (or surnames) of either Elizabeth Vannoy or Lazarus Estes, or upstream. Some DO! Glory be!

Better yet, their DNA may descend from one of my dead-ends in this line, so I’ll be carefully recording any genealogical information that I can obtain to either confirm the known ancestors or break through those stubborn walls.

Dead ends would become evident by multiple people in the cluster sharing a different ancestor than one you’re already familiar with. Look carefully for patterns. Could this be the key to solving the mystery of who the mother of Nancy Ann Moore is? Or several other brick walls that I’d love to fall, just in time for Christmas. Who doesn’t have brick walls?

By signing on to Family Tree DNA and looking carefully at the trees and surnames of the people in each group, I was able to quickly identify the common line and assign an ancestor to most of the matching groups.

This also means I’ll now be able to make notes on these matches at Family Tree DNA paint these in DNAPainter! (I’ve written several articles about using DNAPainter which you can read by entering DNAPainter into the search box on this blog.)

Mom’s Acadian Cluster

Endogamy is always tough and this tool isn’t any different. Lots of grey squares which mean people would fit into multiple clusters. That’s the hallmark of endogamy.

My Mom’s largest clustered group is Acadian, which is endogamous, and her orange cluster has a very interesting subgroup structure.

If you look, the larger loosely connected orange group extends quite some way down the page, but within that group, there seems to be a large, almost solid orange group in the lower right. I’m betting that almost solid group to the right lower part of the orange region represents a particular ancestral line within the endogamous Acadian grouping.

Also of interest, my Mom’s green cluster is the same as my red Jacob Lentz/Frederica Ruhle cluster group, with many of the same individuals. This confirms that these people match me and that other person on Mom’s side, so whoever in this group matches me and any other person on the same segment is triangulated to my Mom’s side of my genealogy.

You can also use this information in conjunction with your parental bucketing at Family Tree DNA.

In Summary

I’m still learning about this tool, it’s limitations and possibilities. The software is new and not bug-free, but the developer is working to get things straightened out. I don’t think he expected such a deluge of desperate genealogists right away and we’ve probably swamped his servers and his inbox.

I haven’t yet experimented with changing the parameters to see who is included and who isn’t in various runs. I’ll be doing that over the next several days, and I’ll be applying the confirmed ancestral segments I discover in DNAPainter!

This is going to be a lot of fun. I may not surface again until 2019😊

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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.

Whole Genome Sequencing – Is It Ready for Prime Time?

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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.

I wrote about Helix here. 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?

_____________________________________________________________________

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:

Veterans Day Ancestor Lineup

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This Veterans Day stands apart from the rest, marking the 100th anniversary of the end of WWI.

I wondered how many of my direct line male ancestors served in some capacity.

I decided to make a chart tracking what I know of their service along with their Y DNA which represents that surname lineage. This was a fun project and will provide a discussion topic with family members at that not-too-distant holiday dinner.

Do you know how many ancestors you have that served their country?

Creating and sharing a chart like this just might result in a male descended from that same ancestor, or ancestral line who carries the surname today and is willing to Y DNA test. What a wonderful way to fill in that missing portion of your ancestor’s history.

If you are a male, carry the surname and descend from one of the men (or direct paternal lines) below, I have a DNA testing scholarship for you!

Name Birth Death Service Y DNA
William Sterling Estes October 1, 1901, 2 or 3 August 27, 1963 Army, WWI, 3 tours of duty R-ZS3700
John Y. Estes Dec. 29, 1818 September 19, 1895 Civil War, CSA, POW R-ZS3700
Samuel Claxton June 6, 1827 Dec. 5, 1876 Civil War, North, died as a result of injuries R-JFS2001
Jacob Kirsch May 1, 1841 July 23, 1917 Civil War, unproven, wife applied for pension Believe we have a tester
John R. Estes Mar-June, 1787 May 30, 1885 War of 1812, bounty land R-ZS3700
George Estes Feb. 3, 1763 July 1859 Revolutionary War, 3 enlistments R-ZS3700
Moses Estes 1711 1787 French and Indian War R-ZS3700
Marcus Younger Before 1740 1816 Revolutionary War Contributor I1-M253
Jacob Dobkins 1751 Augusta Co., VA March 4, 1833 Claiborne Co., TN Revolutionary War DNA Testing Scholarship Available
Lazarus Dodson 1760 1826 Claiborne Co., TN Revolutionary War R-P25
Capt. John Dobkins After 1787 Augusts Co., VA Revolutionary War DNA Testing Scholarship Available
William McNiel 1760/61 1830 Revolutionary War R-DF104
Rev. George McNiel 1720 June 7, 1805 Revolutionary War, unproven, Battle of King’s Mountain R-DF104
William Crumley III 1788 Feb. 18, 1859 War of 1812 I-M223
Henry Bolton 1759 Nov. 24, 1846 Revolutionary War, Pennsylvania Militia R-BBY69454
William Harrell 1789/90 October 8, 1859 War of 1812 I-P37
John Harrold 1761 1828/30 Revolutionary War I-P37
Michael McDowell 1747 After 1840 Revolutionary War R-Z16432
James Lee Clarkson/Claxton about 1775 Feb. 20, 1815, Fort Decatur, GA War of 1812, died in service R-JFS2001
Samuel Muncy 1740 ? Dunsmore’s War I-Y92887
Col. Robert Craven 1696 May 1782 French and Indian War R-M269
Abraham Workman April 27, 1708 1813 Militia I-M253
Jan Derik Woertman 1665 Revolutionary War I-M253
Nicholas Speak March 3, 1782 August 4, 1804 War of 1812 I-BY14004
Gideon Faires Before 1748 March 1821 Revolutionary War, Campaign Against the Cherokees DNA Testing Scholarship Available
Philip Jacob Miller 1726 September 1799 Rev War Militia R-CTS7822
Johann Nicholas Schaeffer Jan. 3, 1736 Jan. 20, 1796 Revolutionary War R-U106
William Hall June 8, 1651 July 11, 1727 Militia Uncertain if descendant has tested

I was surprised that there were 28 veterans. One, James Lee Claxton, died in the War of 1812 and Samuel Claxton, his grandson, died as a result of his service in the Civil War.

Philip Jacob Miller was a Brethren and managed to serve in the militia in spite of that.

Several men served in frontier forts.

Two men, my father and George Estes served 3 terms each.

Furthermore, all men in colonial times were militia members, so in essence, they all served in some capacity.

I’m sure there are more veterans whose service records I just haven’t discovered yet.

Discovering Your Veterans’ Haplogroups

If you would like to compile the Y haplogroups of your service veterans, or any other male lines, first check the Y DNA projects at Family Tree DNA to see if anyone has tested in your line by clicking here and scrolling down until you see the area to enter the surname you’re searching for.

Check the surname project to determine if any of the most distant ancestors listed are yours.

Then, find a male who carries that surname in your family line to Y DNA test to confirm a match to your surname line. No one listed from your line yet? Not everyone joins projects, so be sure to test. You’ll never know what you’ll learn.

I’m upgrading several of my Y lines to Big Y tests one by one. As genealogists, we want every scrap of information about our ancestors and what better tool to tell stories about the past than their own DNA.

____________________________________________________________________

Standard Disclosure

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

Hot links are provided to companies with whom I have an affiliate relationship. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication 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 my affiliate link if you are interested in products from the following companies.

Affiliate links are limited to:

Family Tree DNA’s New Chromosome Browser

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39

Family Tree DNA has released their new, updated chromosome browser with a completely new look and feel. It’s quite different from the previous version, so let’s take a test drive.

The first thing you notice is a new link on your personal page in the Family Finder section.

You can access the chromosome browser in one of two ways.

  • Matches button
  • Clicking on the Chromosome Browser button

Either way, you eventually get to the same place.

Matches

By viewing your matches, you can now select a total of 7 people, increased from 5 previously, to compare to you in the chromosome browser.

After selecting the people you want to view in the chromosome browser, click on the Chromosome Brower button above your matches, just like before.

Note that on your Matches page, the other tools, such as In Common With (ICW), Not In Common With (NICW), Search by name, Search by ancestral surname, the list of ancestral surnames for each match and other information is exactly where it has always been located. Nothing else changed on the Match page except your ability to select 7 people instead of just 5.

The Chromosome Browser

The new chromosome browser tool looks different. A lot different. It’s also much more intuitive.

If you make match selections on your match page and click the chromosome browser button, you see the following page reflecting your choices. The link no longer immediately compares the individuals in the chromosome browser.

Your match list is shown to the right of the selected individuals, shown at left.

This is also the page where you land if you click the Chromosome Browser button on your dashboard.

From Your Dashboard

If you don’t click on your Matches button first, and click directly on the Chromosome Browser button, this is what you’ll see.

Your matches are shown at right, and when you select them, they will appear on the list at left.

Select as many as 7. You’ll see them appear to the left as you make your selections.

Features

To aid in your selection, you can utilize the filter above the matches to view only specific levels of matches.

The “name search,” at upper right, searches for an individual match with that first or last name.

However, if you enter the full name, it finds that individual person, so if you know you want to compare Uncle Rex Doe’s kit, you just search for his name as Rex, Doe or Rex Doe.

This page does NOT search the ancestral surnames. If you want to do that, you need to work from the matches page which does search for people with that ancestral surname in their Ancestral Surname List.

I’m very glad to see this new search feature for matches at the browser level. It makes searching for a particular match a LOT easier.

Notice that not all of the match information is available on this page. X matching, match date, linked relationships and ancestral surnames are only available on the Matches page.

The icons for contacting matches, notes and the tree are also only available on the Matches page.

However, a new field is available here, the number of shared segments. This number includes segments to the 1cM level so long as they are 500 SNPs or larger. For most (nonresearch) purposes, I generally use segments of 7cM or larger, although I do sometimes want to see smaller segments.

At right, the In Common With and Not In Common With functions are available by clicking on the three dots:

In Common With and Not In Common With

The In Common With (ICW) and Not In Common With (NICW) features have been greatly improved.

By selecting an individual, such as William Sterling Estes in this example, then clicking the In Common With (ICW) link, I see all of the people I match in common with William Sterling Estes. Furthermore, the system now automatically puts William Sterling Estes into my match list. By making additional selections from that ICW list and adding them to the list, I can then easily compare my DNA, that of William Sterling Estes and the people that we both match to determine if we have common matching chromosome segments.

The Not In Common With feature works exactly the same way.

Compare

To view the new chromosome browser, click on the orange compare button at the bottom of the list. It’s so large you can’t miss it!

Chromosome Browser Format

The new chromosome browser itself looks a LOT different. To begin with, the color and design of the chromosomes themselves has changed. There is now space for 7 people in the comparison on each chromosome, plus you as the “background” person that those 7 are being compared to.

Chromosomes 1-5 with 7 matches being compared to me are shown below. At the top of the page, the colors of the segments are coded by the colors at the top of the profile placards of the matches I selected.

You can view information about any individual by clicking on their profile button.

By clicking on the Update Selected Matches button, at right above the chromosomes, you can change the individuals being compared.

Now, let’s take a look at how to interpret these matches.

Reading the Results

As before, the centromere is notated by the little white “waists” in each chromosome, and the light grey represents regions not tested, so you won’t see matches there.

Please note that you can click any image to enlarge.

Notice Charlene, the navy blue person match on my chromosome 1.

Reading left to right, we have:

  • At the beginning of the chromosome, dark grey tested region with no match
  • Beginning with the red box, navy blue match region
  • Light grey untested region, crossing centromere and continuing until small navy blue region
  • The entire small tested region is navy blue, indicating a match
  • Small light grey untested region
  • Dark grey tested region that does not match
  • Navy blue region that does match to the end of the red box
  • Dark grey tested region that does not match to the end of the chromosome

We would read this as 2 matching segments, not 3, with the first large navy segment and the tiny middle navy segment forming one contiguous segment across the centromere and untested regions. The third navy part of that chromosome is a separate matching segment, because it’s separated from the first two by a darker grey area that is tested but does not match.

By positioning your cursor over the colored portions of the chromosome, and waiting for a second or so, the information about that specific segment will appear.

Please note that you can click to enlarge any graphic.

Downloading Just These Matching Segments

Clicking on Download Segments, the blue link at right just above chromosome 1 downloads just the information in a csv file for the people currently being compared in the browser. It does not download all of your matches. That feature is elsewhere.

Options

The default minimum centiMorgans display view is still 5, and you can select 1, 5, 7 or 10. All matches displayed are 500 SNPs or larger.

Detailed Segment Data

Another new feature is the Detailed Segment Data tab. Click to view.

In essence, this is the same information as the csv download file, except you don’t have to download the file and you don’t have to know anything about Excel. However, you can’t sort this data by chromosome like you can in a spreadsheet.

You can select which DNA match you wish to view, one by one.

I hope that Family Tree DNA will add the feature of being able to sort each column.

Downloading All Matches

For those interested in downloading all matches, not just the matches displayed, you can perform that function at the bottom of your matches page:

Or at the bottom of the initial Chromosome Browser selection page, but BEFORE you click on compare.

Quick Reference Feature Navigation Chart

I’m always grateful for new features and updates, but sometimes new features feel a bit like someone rearranged the furniture in the room while you were sleeping. I’ve created a quick reference chart to show you what’s available where and to help you navigate.

Summary

I like the updated chromosome browser as well as the new In Common With feature. The new browser facilitates 7 comparisons at once and is a LOT more user friend with new ease-of-use features. The new ICW page eliminates several steps and confusion that exists when trying to use the function from the Matches page.

I’m hoping that this update is a new skin in preparation for more nifty new features, such as triangulation. Hint, hint, Family Tree DNA. Christmas is coming😊

_____________________________________________________________________

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 Mitochondrial Haplotree

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41

On September 27th, 2018 Family Tree DNA published the largest Y haplotree in the world, based on SNP tests taken by customers. Now, less than two weeks later, they’ve added an exhaustive mitochondrial DNA (mtDNA) public haplotree as well, making this information universally available to everyone.

Family Tree DNA’s mtDNA Haplotree is based on the latest version of the mtDNA Phylotree. The new Family Tree DNA tree includes 5,434 branches derived from more than 150,000 full sequence results from 180+ different countries of origin. Family Tree DNA‘s tree has SIX TIMES more samples than the Phylotree. Furthermore, Family Tree DNA only includes full sequence results, where Phylotree includes partial results.

This new tree is a goldmine! What does it provide that that’s unique? Locations – lots of locations!

The Official Phylotree

Unlike the Y DNA tree, which is literally defined and constructed by the genetic community, new mitochondrial DNA branches cannot be added to the official mitochondrial Phylotree by Family Tree DNA. Haplogroups, meaning new branches in the form of SNPs are added to the Y tree as new SNPs are discovered and inserted into the tree in their proper location. The mitochondrial DNA phylotree can’t be expanded by a vendor in that manner.

The official mitochondrial Phylotree is maintained at www.phylotree.org and is episodically updated. The most recent version was mtDNA tree build 17, published and updated in February 2016. You can view version history here.

Mitochondrial Phylogenic Tree Version 17

Version 17 of the official mitochondrial tree consists of approximately 5,400 nodes, or branches with a total of 24,275 samples uploaded by both private individuals and academic researchers which are then utilized to define haplogroup branches.

Individuals can upload their own full sequence results from Family Tree DNA, but they must be in a specific format. I keep meaning to write detailed instructions about how to submit your full sequence test results, but so far, that has repeatedly slipped off of the schedule. I’ll try to do this soon.

In a nutshell, download your FASTA file from Family Tree DNA and continue with the submission process here. The instructions are below the submission box, so scroll down.

In any case, the way that new branches are added to the phylotree is when enough new results with a specific mutation are submitted and evaluated, the tree will have a new branch added in the next version. That magic number of individuals with the same mutation was 3 in the past, but now that so many more people are testing, I’m not sure if that number holds, or if it should. Spontaneous mutations can and do happen at the same location. The Phylotree branches mean that the haplogroup defining mutations indicate a common ancestor, not de novo separate mutations. That’s why analysis has to be completed on each candidate branch.

How do Mitochondrial DNA Branches Work?

If you are a member of haplogroup J1c2f today, and a certain number of people in that haplogroup have another common mutation, that new mutation may be assigned the designation of 1, as in J1c2f1, where anyone in haplogroup J1c2f who has that mutation will be assigned to J1c2f1.

While the alternating letter/number format is very easy to follow, some problems and challenges do exist with the alternating letter/number haplogroup naming system.

The Name of the Game

The letter number system works fine if not many new branches are added, branches don’t shuffle and if the growth is slow. However, that’s not the case anymore.

If you recall, back in July of 2012, which is equivalent to the genetic dark ages (I know, right), the Y tree was also represented with the same type of letter number terminology used on the mitochondrial tree today.

For example, Y DNA haplogroup R-M269 was known as R1b1a2, and before that the same haplogroup was known as R1b1c. The changes occurred because so many new haplgroups were being discovered that a new sprout wasn’t added from time to time, but entire branches had to be sawed off and either discarded or grafted elsewhere. It became obvious that while the R1b1a2 version was nice, because it was visually obvious that R1b1a2a was just one step below R1b1a2, that long term, that format just wasn’t going to be able to work anymore. New branches weren’t just sprouting, wholesale shuffling was occurring. Believe it or not, we’re still on the frontier of genetic science.

In 2012, the change to the SNP based haplogroup designations was introduced by Family Tree DNA, and adopted within the community.

The ISOGG tree, the only tree that still includes the older letter/number system and creates extended letter number haplogroup names as new SNPs are added provides us with an example of how much the Y tree has grown.

You can see that the letter/number format haplogroups to the far right are 19 locations in length. The assigned SNP or SNPs associated with that haplogroup are shown as well. Those 19-digit haplogroup names are just too unwieldy, and new haplogroups are still being discovered daily.

It’s 2012 All Over Again

That’s where we are with mitochondrial DNA today, but unlike Y DNA naming, a vendor can’t just make that change to a terminal SNP based naming system because all vendors conform to the published Phylotree.

However, in this case, the vendor, Family Tree DNA has more than 6 times the number of full sequence mitochondrial results than the mitochondrial reference model Phylotree. If you look at the haplogroup projects at Family Tree DNA, you’ll notice that (some) administrators routinely group results by a specific mutation that is found within a named haplogroup, meaning that the people with the mutation form a subgroup that they believe is worthy of its own haplogroup subgroup name. The problem is that unless enough people upload their results to Phylotree, that subgroup will never be identified, so a new haplogroup won’t be added.

If the entire Family Tree DNA data base were to be uploaded to Phylotree, can you imagine how many new haplogroups would need to be formed? Of course, Family Tree DNA can’t do that, but individual testers can and should.

Challenges for Vendors

The challenge for vendors is that every time the phylotree tree is updated and a new version is produced, the vendors must “rerun” their existing tester samples against the new haplogroup defining mutations to update their testers’ haplogroup results.

In some cases, entire haplogroups are obsoleted and branches moved, so it’s not a simple matter of just adding a single letter or digit. Rearranging occurs, and will occur more and more, the more tests that are uploaded to Phylotree.

For example, in the Phylotree V17 update, haplogroup A4a1 became A1a. In other words, some haplogroups became entirely obsolete and were inserted onto other branches of the tree.

In the current version of the Phylotree, haplogroup A4 has been retired.

Keep in mind that all haplogroup assignments are the cumulative combination of all of the upstream direct haplogroups. That means that haplogroup A4a1, in the prior version, had all of the haplogroup defining mutations shown in bold in the chart below. In the V17 version, haplogroup A1a contains all of the mutations shown in bold red. You might notice that the haplogroup A4 defining mutation T16362C is no longer included, and haplogroup A4, plus all 9 downstream haplogroups which were previously dependent on T16362C have been retired. A4a1 is now A1a.

Taking a look at the mitochondrial tree in pedigree fashion, we can see haplogroup A4a1 in Build 15 from September 2012, below.

Followed by haplogroup A1a in the current Build 17.

Full Sequence Versus Chip Based Mitochondrial Testing

While Family Tree DNA tests the full sequence of their customers who purchase that level of testing, other vendors don’t, and these changes wreak havoc for those vendors, and for compatibility for customer attempting to compare between data bases and information from different vendors.

That means that without knowing which version of Phylotree a vendor currently uses, you may not be able to compare meaningfully with another user, depending on changes that occurred that haplogroup between versions. You also need to know which vendor each person utilized for testing and if that vendor’s mitochondrial results are generated from an autosomal style chip or are actually a full mitochondrial sequence test. Utilizing the ISOGG mtDNA testing comparison chart, here’s a cheat sheet.

Vendor No Mitochondrial Chip based haplogroup only mitochondrial Full Sequence mitochondrial
Family Tree DNA No Yes – V17
23andMe Yes – Build V7 No
Ancestry None
LivingDNA Yes – Build V17 No
MyHeritage None
Genographic V2 Yes – Build V16 No

Of the chip-based vendors, 23andMe is the most out of date, with V7 extending back to November of 2009. The Genographic Project has done the best job of updating from previous versions. LivingDNA entered the marketplace in 2016, utilizing V17 when they began.

Family Tree DNA’s mitochondrial test is not autosomal chip based, so they don’t encounter the problem of not having tested needed locations because they test all locations. They have upgraded their customers several times over the years, with the current version being V17.

Family Tree DNA’s mitochondrial DNA test is a separate test from their Family Finder autosomal test while the chip-based vendors provide a base-level haplogroup designation that is included in their autosomal product. However, for chip-based vendors, updating that information can be very challenging, especially when significant branch changes occur.

Let’s take a closer look.

Challenges for Autosomal Chip-Based Vendors Providing Mitochondrial Results

SNP based mitochondrial and Y DNA testing for basic haplogroups that some vendors include with autosomal DNA is a mixed blessing. The up side, you receive a basic haplogroup. The down aide, the vendor doesn’t test anyplace near all of the 16,569 mitochondrial DNA SNP locations.

I wrote in detail about how this works in the article, Haplogroup Comparisons Between Family Tree DNA and 23andMe. Since that time, LivingDNA has also added some level of haplogroup reporting through autosomal testing.

How does this work?

Let’s say that a vendor tests approximately 4000 mitochondrial DNA SNPs on the autosomal chip that you submit for autosomal DNA testing. First, that’s 4000 locations they can’t use for autosomal SNPs, because a DNA chip has a finite number of locations that can be utilized.

Secondly, and more importantly, it’s devilishly difficult to “predict” haplogroups at a detailed level correctly. Therefore, some customers receive a partial haplogroup, such as J1c, and some receive more detail.

It’s even more difficult, sometimes impossible, to update haplogroups when new Phylotree versions are released.

Why is Haplogroup Prediction and Updating so Difficult?

The full mitochondrial DNA sequence is 16,569 locations in length, plus or minus insertions and deletions. The full sequence test does exactly what that name implies, tests every single location.

Now, let’s say, by way of example, that location 10,000 isn’t used to determine any haplogroup today, so the chip-based vendors don’t test it. They only have room for 4000 of those locations on their chip, so they must use them wisely. They aren’t about to waste one of those 4000 spaces on a location that isn’t utilized in haplogroup determination.

Let’s say in the next release, V2, that location 10,000 is now used for just one haplogroup definition, but the haplogroup assignment still works without it. In other words, previously to define that haplogroup, location 9000 was used, and now a specific value at location 10,000 has been added. Assuming you have the correct value at 9,000, you’re still golden, even if the vendor doesn’t test location 10,000. No problem.

However, in V3, now there are new haplogroup subgroups in two different branches that use location 10,000 as a terminal SNP. A terminal SNP is the last SNP in line that define your results most granularly. In haplogroup J1c2f, the SNP(s) that define the f are my terminal SNPs. But if the vendor doesn’t test location 10,000, then the mutation there can’t be used to determine my terminal SNP, and my full haplogroup will be incomplete. What now?

If location 10,000 isn’t tested, the vendor can’t assign those new haplogroups, and if any other haplogroup branch is dependent on this SNP location, they can’t be assigned correctly either. Changes between releases are cumulative, so the more new releases, the further behind the haplogroup designations become.

Multiple problems exist:

  • Even if those vendors were to recalculate their customer’s results to update haplogroups, they can’t report on locations they never tested, so their haplogroup assignments become increasingly outdated.
  • To update your haplogroup when new locations need to be tested, the vendor would have to actually rerun your actual DNA test itself, NOT just update your results in the data base. They can’t update results for locations they didn’t test.
  • Without running the full mitochondrial sequence, the haplogroup can never be more current than the locations on the vendor’s chip at the time the actual DNA test is run.
  • No vendor runs a full sequence test on an autosomal chip. A full mitochondrial sequence test at Family Tree DNA is required for that.
  • Furthermore, results matching can’t be performed without the type of test performed at Family Tree DNA, because people carry mutations other than haplogroup defining mutations. Haplogroup only information is entertaining and can sometimes provide you with base information about the origins of your ancestor (Native, African, European, Asian,) but quickly loses its appeal because it’s not specific, can’t be used for matching and can’t reliably be upgraded.

The lack of complete testing also means that while Family Tree DNA can publish this type of tree and contribute to science, the other vendors can’t.

Let’s take a look at Family Tree DNA’s new tree.

Finding the Tree

To view the tree, click here, but do NOT sign in to your account. Simply scroll to the bottom of the page where you will see the options for both the Y DNA Haplotree and the mtDNA Haplotree under the Community heading.

Click on mtDNA Haplotree.

If you are a Family Tree DNA customer, you can view both the Y and mitochondrial trees from your personal page as well. You don’t have to have taken either the Y or mitochondrial DNA tests to view the trees.

Browsing the mtDNA Tree

Across the top, you’ll see the major haplogroups.

I’m using haplogroup M as an example, because it’s far up the tree and has lots of subgroups. Only full sequence results are shown on the tree.

The basic functionality of the new mitochondrial tree, meaning how it works, is the same as the Y tree, which I wrote about in the Family Tree DNA’s PUBLIC Y DNA Haplotree.

You can view the tree in two formats, countries or variants, in the upper left-hand corner. View is not the same thing as search.

When viewing the mitochondrial DNA phylotree by country, we see that haplogroup M has a total of 1339 entries, which means M and everything below M on the tree.

However, the flags showing in the M row are only for people whose full mitochondrial sequence puts them into M directly, with no subgroup.

As you can see, there are only 12: 6 people in Australia, and one in 5 other countries. These are the locations of the most distant known ancestor of those testers. If they have not completed the maternal Country of Origin on the Earliest Known Ancestor tab, nothing shows for the location.

Viewing the tree by variant shows the haplogroup defining mutations, but NOT any individual mutations beyond those that are haplogroup defining.

For each haplogroup, click on the three dots to the right to display the country report for that haplogroup.

The Country Report

The Country Report provides three columns.

The column titled Branch Participants M shows only the total of people in haplogroup M itself, with no upstream or downstream results, meaning excluding M1, M2, etc. Just the individuals in M itself. Be sure to note that there may be multiple pages to click through, at bottom right.

The second column, Downstream Participants – M and Downstream (Excluding other Letters) means the people in haplogroup M and M subclades. You may wonder why this column is included, but realize that branches of haplogroup M include haplogroups G, Q, C, Z, D and E. The middle column only includes M and subgroups that begin with M, without the others, meaning M, M10, M11 but not G, Q, etc.

Of course the final column, All Downstream Participants – M and Downstream (Including other Letters) shows all of the haplogroup M participants, meaning M and all subclades, including all other haplogroups beneath M, such as M10, G, Q, etc..

What Can I Do with This Information?

Unlike the companion Y tree DNA, since surnames change every generation for maternal lineages, there is no requirement to have multiple matching surnames on a branch to be displayed.

Therefore, every person who includes a location for a most distant known ancestor is included in the tree, but surnames are not.

I want to see, at a glance, where the other people in my haplogroup, and the haplogroups that are the “direct ancestral line” of mine are found today. Clusters may mean something genealogically or are at least historically important – and I’ll never be able to view that information any other way. In fact, before this tree was published, I wasn’t able to see this at all. Way to go Family Tree DNA!!

It’s very unlikely that I’ll match every person in my haplogroup – but the history of that haplogroup and all of the participants in that haplogroup are important to that historical lineage of my family. At one time, these people all shared one ancestor and determining when and where that person lived is relevant to my family story.

Searching for Your Haplogroup

I’m searching for haplogroup J1c2f by entering J1c2f in the “Go to Branch Name.”

There it is.

I can see that there are 17 people in Sweden, 13 in Norway, 5 in Germany, 3 in Russia, etc. What’s with the Scandinavian cluster? My most distant known ancestor was found in Germany. There’s something to be learned here that existing records can’t tell me!

The mother branch is J1c2 which shows the majority of individuals in Ireland followed by England. This probably suggests that while J1c2f may have been born in Scandinavia, J1c2 probably was not. According to the supplement to Dr. Doron Behar’s paper, A “Copernican” Reassessment of the Human Mitochondrial DNA tree from its Root, which provides ages for some mitochondrial DNA haplogroups:

Haplogroup How Old Standard Deviation Approximate Age Range in Years
J1c2 9762 2010 7,752 – 11,772
J1c2f 1926 3128 500 – 5,054

I happen to know from communicating with my matches that the haplogroup J1c2f was born more than 500 years ago because my Scandinavian mito-cousins know where their J1c2f cousin was then, and so do I. Mine was in Germany, so we know our common ancestor existed sometime before that 500 year window, and based on our mutations and the mutation tree we created, probably substantially before that 500 year threshold.

Given that J1c2, which doesn’t appear to have been born in Scandinavia is at least 7,700 years old, we can pretty safely conclude that my ancestor wasn’t in Scandinavia roughly 9,000 years ago, but was perhaps 2,000 years, ago when J1c2f was born. What types of population migration and movement happened between 2,000 and 9,000 years ago which would have potentially been responsible for the migration of a people from someplace in Europe into Scandinavia.

The first hint might be that in the Nordic Bronze Age, trade with European cultures became evident, which of course means that traders themselves were present. Scandinavian petroglyphs dating from that era depict ships and art works from as far away as Greece and Egypt have been found.

The climate in Scandinavia was warm during this period, but later deteriorated, pushing the Germanic tribes southward into continental Europe about 3000 years ago. Scandinavian influence was found in eastern Europe, and numerous Germanic tribes claimed Scandinavian origins 2000 years ago, including the Bergundians, Goths, Heruls and Lombards.

Hmmm, that might also explain how my mitochondrial DNA, in the form of my most distant known ancestor arrived in Germany, as well as the distribution into Poland.

Is this my family history? I don’t know for sure, but I do know that the clustering information on the new phylotree provides me with clustering data to direct my search for a historical connection.

What Can You Do?

  • Take a full mitochondrial DNA test. Click here if you’d like to order a test or if you need to upgrade your current test.
  • Enter your Earliest Known Ancestor on the Genealogy tab of your Account Information, accessed by clicking the “Manage Personal Information” beneath your profile photo on your personal page.

The next few steps aren’t related to actually having your results displayed on the phylotree, but they are important to taking full advantage of the power of testing.

  • While viewing your account information, click on the Privacy and Sharing tab, and select to participate in matching, under Matching Preferences.

  • Also consent to Group Project Sharing AND allow your group project administrators to view your full sequence matches so that they can group you properly in any projects that you join. You full sequence mutations will never be shown publicly, only to administrators.

Of course, always click on save when you’re finished.

  • Enter your most distant ancestor information on your Matches Map page by clicking on the “Update Ancestor’s Location” beneath the map.

  • Join a project relevant to your haplogroup, such as the J project for haplogroup J. To join a project, click on myProjects at the top of the page, then on Join Projects.

  • To view available haplogroup projects, scroll down to the bottom of the screen that shows you available projects to join, and click on the letter of your haplogroup in the MTDNA Haplogroup Projects section.

  • Locate the applicable haplogroup, then click through to join the project.

These steps assure that you’ve maximized the benefits of your mitochondrial results for your own research and to your matches as well. Collaborative effort in completing geographic and known ancestor information means that we can all make discoveries.

The article, Working with Mitochondrial DNA Results steps you through you all of the various tools provided to Family Tree DNA testers.

Now, go and see who you match, where your closest matches cluster, and on the new mtDNA Haplotree, what kind of historical ancestral history your locations may reveal. What’s waiting for you?

_____________________________________________________________________

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:

MyHeritage Step by Step Guide: How to Upload-Download DNA Files

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In this Upload-Download Series, we’ll cover each major vendor:

  • How to download raw data files from the vendor
  • How to upload raw data files to the vendor, if possible
  • Other mainstream vendors where you can upload this vendor’s files

Uploading TO MyHeritage

Upload Step 1

To upload your DNA to MyHeritage, click here and then click on the purple “Start” button.

Upload Step 1 If You Already Have an Account at MyHeritage

If you already have an account, click here to sign in and then click on the DNA tab to display the “Upload DNA Data” option which displays the graphic above. Click on the purple “Start” button. This is the same process you’ll use whether it’s the first time you’ve uploaded a kit, or you’re uploading subsequent kits to your account that you’ll be managing.

Upload Step 2

You’ll be prompted to create a free account by entering your name, e-mail and password, and from there you can upload your autosomal DNA file.

You’ll be asked whose DNA you’re uploading and prompted to read and agree to the terms of service and consent.

Click the purple upload button.

Then click done when the file is finished uploading.

You’ll be notified by e-mail within a couple days when the file is finished processing.

Downloading FROM MyHeritage

Download Step 1

Sign on to your MyHeritage account.

Click on DNA on the upper toolbar.

The dropdown menu includes “Manage DNA Kits”

Download Step 2

At the right of the kit you wish to download, click on the three small buttons which will include an option for “Download,” as shown in the graphics below from the MyHeritage blog article.

Download Step 3

You’ll be presented with a box titled “Learn more about DNA data files.” Click the purple “Continue” button.

Download Step 4

You’ll need to confirm that you want to download your data, and that you understand that the download is outside of MyHeritage and their protection. Click the purple “Continue” button.

Download Step 5

You’ll receive a confirmation e-mail. Click on “Click here to continue with download.”

This e-mail link is only valid for 24 hours.

Download Step 6

Enter your password again, and click on the purple “Download” button.

Download Step 7

Save the file as a recognizable file name on your computer.

MyHeritage File Transfers TO Other Vendors

You can upload your MyHeritage file to other vendors, as follows.

From below to >>>>>>>>>>> Family Tree DNA Accepts Ancestry Accepts 23andMe Accepts GedMatch Accepts
MyHeritage Yes No No Yes

Neither Ancestry nor 23andMe accepts uploads from any vendor.

MyHeritage File Transfers FROM Other Vendors

You can upload files from other vendors to MyHeritage, as follows:

  From Family Tree DNA From Ancestry From 23andMe From LivingDNA
To MyHeritage Yes Yes Yes Yes

Testing and Transfer Strategy

Transferring to MyHeritage is always free. You can view your ethnicity, your matches and their trees, and utilize the DNA tools, but you won’t receive the full benefit of SmartMatching and other records without a subscription. You will be limited to building a tree of 250 people for free, but you can upload a Gedcom file of any size, although you do need to subscribe to change anything in that file if it contains more than 250 individuals.

Until December 1, 2018, all DNA tools will be and remain free for anyone who uploads before that date. After December 1st, matching will remain free, but the advanced tools such as ethnicity, the chromosome browser, triangulation and more will require payment. MyHeritage has not yet indicated how that will work, so upload now to receive free DNA tools forever.

My testing/transfer recommendations are as follows relative to MyHeritage:

Have fun!

_____________________________________________________________________

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:

Ancestry 2018 Ethnicity Update

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165

When ethnicity estimates were first produced by vendors, they tended to resemble the wild west.

Today, results are becoming more refined and hopefully, more accurate as reference populations grow and become more reliable.

The Ancestry ethnicity update has been in beta for several months, but this week, Ancestry rolled out the ethnicity update for everyone.

Checking Your New Results

To see your updated results, sign on and click on the DNA Story to the left with Ethnicity Estimates.

Ancestry then explains that while your DNA doesn’t change, the estimates (pay attention to that word) do as the science improves.

Ethnicity Estimate Aren’t Precise

I’ve said this before, and I want to say it again. Ethnicity is the least precise and the least accurate of DNA tools for genetic genealogy. Ethnicity estimates are the most accurate at a continental level. Within continents, like Europe, Asia and Africa, there has been a lot of population movement and intermixing over time making the term “ethnicity” almost meaningless.

I know, I know – ethnicity estimates are also the simplest because there isn’t much learning curve and they’re easy to understand at a glance. This deceptive “ease of use” also makes them interesting to people who have only a passing curiosity. That’s why they attract so many test takers who either love of hate their results, but never fully understand the true message or utilize any other genetic genealogy tools.

Let’s take a look at how ethnicity estimates have changed over time and if they have improved with the latest version.

Ethnicity Estimate Changes

In my case, my original Ancestry ethnicity estimate in 2012 was:

  • British Isles 80%
  • Scandinavia 12%
  • Uncertain 8%

To say it was really bad is an understatement.

In 2013, Ancestry introduced their ethnicity V2 version which provided a lot more granularity.

Version 2 was dramatically different, with the British Isles moving from 80% to a total of 6%. Like a pendulum swinging, neither was accurate.

Ancestry introduced new features and combined their Genetic Communities with their ethnicity estimates in 2017.

In this new 2018 version, Ancestry has divided and recombined the British Isles and Western Europe differently and the resulting differences are significant.

My mystery Scandinavian is entirely gone now, but sadly, so is my Native American.

The New Results

I just got really boring – but the question is whether or not the new results are more accurate as compared to my proven genealogy. Boring doesn’t matter. Accuracy does.

Various Ancestry Ethnicity Versions Compared to Proven Genealogy

I created a chart that reflects the three Ancestry ethnicity versions as compared to my proven genealogy.

For the current version, I also included the ranges as provided by Ancestry.

As you can see, generally, the results are much more accurate, but the regions are also fairly broad which makes accuracy easier to achieve.

Until this current version, Ancestry didn’t show any Germanic, but now the Germanic estimate is exact at 25%.  The Germanic range is also very tight at 24-26%, right where it should be.

The England, Wales & Northeast Europe category is somewhat high, but that could be accurate because I do have some ancestry that is unknown.

Unfortunately, my Native is proven, both through Y and mtDNA and by triangulating the Native segments to others descending from the same Native ancestors. That portion is now missing in my Ancestry ethnicity.

Ancestry V1 Test Versus the V2 Test

For the record, I’m using my Ancestry V1 test because I’ve used that test version for all previous ethnicity comparisons.  My Ancestry V2 test ethnicity results are approximately the same, as follows:

  • England, Wales and Northeast Europe – 76%
  • Germanic – 22%
  • Ireland and Scotland – 2%

The same tree is attached to both tests.

On my V2 test, which I seldom use, I had to answer a couple of question regarding my expectations about ethnicity testing changes and how accurate my previous results were perceived to be before I could access my updated results.

Regions Changed

In Ancestry’s FAQ, they provided this list of how the regions were and are defined.

Previous Region New Regions
Scandinavia Norway, Sweden
Iberian Peninsula Spain, Portugal, Basque
Europe South Italy, Greece and the Balkans, Sardinia
Europe East Baltic States, Eastern Europe and Russia
Caucasus Turkey and the Caucasus, Iran/Persia
Europe West Germanic Europe, France
Native American Native America—North, Central, South; Native America—Andean
Asia South Southern Asia, Western and Central India, Balochistan, Burusho
Asia East Japan, Korea and Northern China, China, Southeast Asia—Dai (Tai), Southeast Asia—Vietnam, Philippines

Ancestry has addressed lots of other questions in their FAQ as well, and I suggest taking a look. I particularly like their comment, “Some places are complicated.” Indeed, that’s true with population churn both in historical times along with unknown pre-history and that complexity is exactly what makes intra-continental ethnicity estimates so difficult. Of course, people whose ancestors are from Europe, for example, want as much granularity as possible.

Previous Ethnicity Versions

For the first time, Ancestry explains what happened between versions, at least at a high level.

Click on the little “i” in the upper right hand corner of your ethnicity estimate box.

You’ll see more information.

Click on “View Previous Estimate” at the bottom.

Your previous ethnicity estimate is shown.

To see how your estimate changed, click on “Compare these results to your most recent Ancestry DNA estimate.”

This display shows you the differences compared to the previous version. In my case, England, Wales and NE Europe increased by 69%, but that’s because Ancestry redefined the regions. Note the little slide box underneath the regions on the map. You can slide back and forth from previous to current (update.).

I do wish Ancestry had told us where the “Scandinavian” went, what category it fell into. Are those segments, as a group, included in another region? Was the previous estimate simply flat out wrong? Was Scandinavian a vestige of Vikings who invaded much of Europe? What happened?

New Regions and Reference Samples

By clicking on “See other regions tested” at the bottom of your Ethnicity Estimate box, you can view the locations of Ancestry’s current reference populations.

The regions tested in which you have results are colored, and the regions where you aren’t showing results are shades of grey. This is an improvement over the previous version which people routinely misinterpreted to mean that they had results in those tested regions.

Best Features

In my opinion, the best feature of the combined ethnicity and Genetic Communities is the combined mapping. For example, the screenshot below combines the ethnicity regions with the ancestors from my tree who immigrated from that region in that timeframe.

By clicking on the 1700 box, the people from that time period in my tree are displayed. I can enlarge the map to make the display larger, until finally individual “people” icons are displayed, as shown with Johann Peter Koehler, below. Clicking on the individual person pin shows that individual in the box at right.

By clicking on the “Lower Midwest and Virginia Settlers,” I see this region and Ancestry tells me where those settlers likely originated.

You can then scroll down to the bottom of the information box where you see “Ancestry DNA Members.”

Click on the 1000+ link and you will then see the people who match you in a specific region or migration.

It’s worth noting that this isn’t always accurate. My 2nd cousin match is showing as a “Lower Midwest and Virginia” match and our ancestors came from the Netherlands directly to Northern Indiana. Ironically, she shows up in three of the 4 regions I can select from. This feature is not 100%, but it’s still nice to be able to see where that match is grouped in terms of ethnicity and Genetic Communities, according to Ancestry.

Given this combined functionality, I do wonder if Ancestry’s new ethnicity isn’t simply population genetics, but a combination of population genetics, ancestors in my tree, my matches and corresponding DNA Circles with their associated history. If so, that would make sense, both in terms of what I’m seeing as my new ethnicity results and the map functionality as well. Could that be where my Germanic came from, and why it’s so precise at 25% which matches by tree exactly?

In Summary

For me, Ancestry’s ethnicity estimates are significantly improved with the exception that my Native disappeared. I’ve worked long and hard on the Native aspect of my genealogy, and I know that part of my ethnicity mix is valid. However, that is a very small percentage overall (about 2%), and the combined improvements certainly outshine that one negative.

Of course, your mileage may vary. What are you seeing in terms of your new ethnicity estimates as compared to your known genealogy? Better? Worse? Did you lose any categories that you know are valid? What about small amounts of minority heritage?

MyHeritage Now Accepts Living DNA and 23andMe V5 Transfer Results and Partners with European Retailer

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MyHeritage has been busy – making two major announcements this week.

European Retail Market Penetration

I was very encouraged a few days ago when I received an email from MyHeritage stating that they have partnered with British Retailer WHSmith to sell their tests in retail stores in Europe. The new in-store products will be called the MyHeritage Family History Discovery Kit which will bundle the DNA test with a 3 month subscription of the Complete MyHeritage plan which combines Premium Plus, Data Subscription including historical records and DNA integration.

MyHeritage has not yet released the price, but I expect it will be competitive. I’m very grateful for the MyHeritage push into Europe and look forward to new European matches. My mother carries a very high percentage of both German and Dutch and matches from those countries have been slim. Retail marketing and an in-store presence may signal the end of that problem – at least I hope so.

The great news is that MyHeritage DNA matching supports filtering DNA matches by location.

MyHeritage Accepts Illumina GSA Chip Transfers

I’ve written before about the Illumina GSA chip and compatibility issues between the that chip and existing data produced on the other Illumina chips, including the chip utilized by both MyHeritage and Family Tree DNA.  However, MyHeritage also just announced that they are accepting GSA file transfers, which means that people who have tested at the following vendors can now transfer their raw autosomal data results to MyHeritage for free.

  • 23andMe began utilizing the Illumina GSA V5 chip in August 2017, so if you have tested since that time, you haven’t been able, until now, to upload to MyHeritage.
  • LivingDNA launched with the Illumina GSA chip, so if you have ever tested at LivingDNA, you haven’t been able to upload your raw data files. Now you can!

The good news is that the upload to MyHeritage, along with the MyHeritage DNA tools are free until December 1st, and will remain free for those who upload before that date. After that, MyHeritage will begin charging a fee or subscription for advanced features such as ethnicity estimates, the chromosome browser and other features. The $$ amount will be announced closer to December.

Of course, you can also upload results from Family Tree DNA, Ancestry and earlier versions of the 23andMe test.

So, don’t wait, click here to upload now, while the upload is totally free.

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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:

In the Beginning – First Steps in Genealogy

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Everyone starts someplace in their genealogy. A lucky few have the opportunity to springboard from another family member who has documented the family carefully. Most of us, me included, began in the simplest of ways – asking family members.

Thank goodness I did that while there were at least a few family members left of older generations. I wish I had begun sooner, but that’s probably the most common lament of genealogists.

The next most common lament, today, would be that we wish we had DNA tested every single person in the older generations. If you haven’t, please do, immediately, while you can – and be sure they are in at least in the Family Tree DNA, Ancestry and MyHeritage databases. I also recommend uploading to GedMatch as well which will catch genealogists that test at 23andMe. Generally, only genealogists upload  to GedMatch.

I didn’t start out to be a genealogist. I was simply interested in my family. I didn’t even really grasp what a genealogist was. One day someone said to me, “Oh, so you’re a genealogist,” and I replied, “No, I’m just curious about my family.”

Famous last words.

I didn’t know there was such a thing as a pedigree chart, and my notes for the first few years were on plain paper with little organization other than a page or folder for each person. I then advanced to a green bookkeeping columnar pad to keep track of what was in the folders.

Eventually, some poor soul took pity on me and gave me a pedigree chart. I started filling in what I knew and it would be another decade before I made my first “genealogical” find in the local Family History Center. I refer to that as my first genealogical find because I wasn’t talking to a family member and had begun researching through records. My curiosity had gotten the best of me!

I remember the thrill of that obsession-defining moment well.

It was my first visit to the Center, following a brief introductory session that I had discovered in the local newspaper, and I was filled with trepidation. I didn’t want someone trying to convert me, but I was also very curious. I needn’t have worried. In all the years I visited the local FHC at the Mormon Church, no one ever tried to convert me and I visited regularly, making discovery after discovery.

The first discovery that life-changing evening, the marriage of Lazarus Estes to Elizabeth Vannoy, is what hooked me. We found it in an index, and I was terribly disappointed to discover that I had to order a microfiche and wait until it arrived from some distant location to find out WHEN Lazarus married Elizabeth. Oh, the torture!

But hooked I was, and I anxiously awaited the call from the FHC librarian telling me that my fiche had arrived. I drove to the church in record time!

I had taken my daughter with me on the first trip to the church, just in case I needed a quick “escape.” Kids are always great for “not feeling well” and she was always having stomach aches. Obviously, no escape was needed – except maybe for her.

Recently, while going through some papers, I discovered my very first pedigree chart. My first reaction was, “ahhh, how sweet,” which quickly turned to mortification when I realized how much was blank or worse, incorrect.

Let’s just bask in the “oh so sweet” for a moment.

We all start with the information we gather from family. You can see by the different ink and white-out (you do remember, white-out, right?) that I gleefully added to this pedigree as new information was discovered. Some is written in pencil, with question marks. People weren’t sure about some things, but I made notes anyway. Thankfully!

The blank spaces aren’t blank anymore, today, but that information was revealed slowly, like peeling an onion, through records research. I had talked to my mother and my great-aunt on my maternal side, and my father’s sister on my paternal side, and I gathered all that they knew. From that point forward, I had to do the research. It fell to me.

When I looked at this pedigree chart and realized how much was wrong, my initial reaction was horror – BUT – we all have to start with what we have available. If there was ever a textbook example of why verification and documentation is essential – this is it.

Much to my embarrassment, the red arrows point to information that was wrong. I’ve sized the arrows relative to the magnitude of the inaccuracy.

For example, the biggest error is that Rebecca Rosenberg or Rosenbaum was NOT the mother of Margaret Clarkson/Claxton. For the record, Elizabeth Speaks was, but she was related to the Rosenbaums through her father’s sister’s marriage. My aunt had her in the right neighborhood and family, but attributed the wrong person as her mother.

Of course, if I hadn’t figured it out through records, eventually DNA might have revealed the problem. BUT, since the Rosenbaum descendants were related to the Speaks family, autosomal DNA might not have divulged the problem since the Rosenbaums would have matched some Speaks too. However, mitochondrial DNA would have immediately showed a discrepancy because their matrilineal ancestors weren’t the same. Don’t forget to utilize all tools available.

Oh, and based on the Rosenbaum/Rosenburg surname, my aunt informed me that we were Jewish. Also that the Bolton’s were German, and that my great-grandmother Elizabeth Vannoy was Cherokee, all of which were subsequently proven to be incorrect by using historical records plus DNA, but I digress. Point being that I believed my aunt at the time, because surely she knew – and she obviously knew more than I did which was absolutely nothing.

Notice that several of the dates have smaller arrows. Those are off by one or two years, so again, the right ballpark but the wrong information. At least the information for my parents was accurate! (humor)

It’s also interesting that on my mother’s side, much more was known about the female side of the family. But then again, my great-aunt who I was able to interview was my maternal grandmother’s sister.

My Aunt Margaret on my father’s side didn’t grow up in Tennessee and most of what she knew was second hand. For example, she told me that her Bolton grandparents, Joseph and Margot (Margaret) had both died a day or so apart in the 1918 flu epidemic. He died first and the family put him in the barn waiting for her to die the next day so they could bury them in the same coffin. I didn’t know if that was romantic or simply expeditious for the survivors, under the circumstances, especially if many were ill and coffin-makers and grave-diggers were in short supply.

Well, Aunt Margaret was close. Joseph died on February 23, 1920, not during the 1918 flu epidemic. Still, they did both die of pneumonia following the flu, according to their death certificates, which certainly weren’t available to me in the 1970s or 1980s. Joseph’s wife died on March 11, 1920. Of course, there’s no way to know if they were buried at the same funeral, or in the same coffin. Their deaths were separated by more than two weeks.

I’m certainly glad I recorded every tidbit that I did. I’ve returned to my original notes years later and found extremely valuable hints that I had originally forgotten about or didn’t understand the value of the hint initially.

How could I forget something important? It wasn’t important then or we’re human and we do forget.

Every piece of family information needs to be viewed as a hint, not as gospel. As well-meaning as our family members are, and lovely for sharing, they can only provide us with the information they know or have been provided by others. Who’s to say if it has been conveyed or remembered accurately? The most reliable information is first person, but even that is subject to lapses of memory or the softening of time.

Don’t believe it? Just remember how often you forget what you went into the other room for😊

Documenting every piece of information is up to us and seldom does that documentation process and subsequent review not provide some new tidbit or surprise.

How accurate was your original pedigree chart?

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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: