New Y DNA Haplogroup Naming Convention

In late 2012, the way haplogroups were being named and referenced began changing.  Before the introduction of the Geno 2.0 test in July 2012, there were approximately 850 SNPs identified on the haplotree, meaning 850 haplogroup names that all began with the letter of the haplogroup, but then had alternating numbers and letters that were added as new haplogroup branches were discovered.

The most common one in Europe is R1b1a2.  This means that after haplogroup R itself was discovered, then another haplogroup, R1 was discovered, then R1b, and so forth.  But now, for the fly in the ointment.  Let’s say that a new haplogroup has been discovered and it needs to be inserted between haplogroup R1 and haplogroup R1b.  What happens?  This naming methodology is not conducive to insertions.  It’s only been a couple of years that the tree was entirely rewritten, redrawn.  Haplogroups that were previously called E3a became E1b1a.  To say it was a large and very disconcerting shift is an understatement.  Add to this that all of the academic papers on which we depend are written in the lingo of the time.  So something that references haplogroup J1a in 2002 may not be talking about the same J1a, as defined by a SNP, in 2013 or some time in the future.

Now for the jolt.  The Genographic project utilized over 10,000 new SNPs not before known or utilized for a total of over 12,000 Y DNA SNPs in their Geno 2.0 test introduced in July of 2012 .  Therefore, the tree was going to have to be entirely drawn with the haplogroup branches renamed, once again.  This was going to be a much bigger shift than before, simply due to the sheer magnitude, and more SNPs are being discovered almost daily.  Therefore, a new methodology was needed.

Every haplogroup, such as R1b1a2, is defined by a specific SNP, in this case, M269.  This SNP and haplogroup name have a specific location on the haplotree.  The SNP locations can change without a problem, but the names of the haplogroups that need to change are the problem.  This has already led to different trees maintained by different organizatiosn being out of sync with each other.

Today, at Family Tree DNA, this is what the top part of the haplogroup R tree looks like.

new hap name

As new SNPs are discovered and inserted into the tree, there will no longer be a name assigned, shown in the right hand column.  As the names are obsoleted because of shuffling of branches on the tree, they will not be renamed.  Already, at Family Tree DNA, they are using just the SNP name as the haplogroup indicator, as you can see in the top bar where is says “Your confirmed haplogroup R-L21.  This means haplogroup R, SNP L21, which occurs further down on the tree.

Today,  R-L21 is still shown on the tree with its name, R1b1a2a1a1b4, but as the tree branches shuffle and this name no longer applies to R-L21, the name will be obsoleted and the haplogroup will only referenced as R-L21.

new hap name 1

Max Blankfeld and Bennett Greenspan of Family Tree DNA recently wrote this explanation which is found on the haplogroup pages at Family Tree DNA.

Long time customers of Family Tree DNA have seen the YCC-tree of Homo Sapiens evolve over the past several years as new SNPs have been discovered. Sometimes these new SNPs cause a substantial change in the “longhand” explanation of your terminal Haplogroup. Because of this confusion, we introduced a shorthand version a few years ago that lists the branch of the tree and your terminal SNP, i.e. J-L147, in lieu of J1c3d. Therefore, in the very near term, Family Tree DNA will discontinue showing the current “longhand” on the tree and we will focus all of our discussions around your terminal defining SNP.

This changes no science – it just provides an easier and less confusing way for us all to communicate.

Obviously, more than a decade’s worth of information exists that references the haplogroups in both formats.  Other companies in this space are not doing this level of testing and do not yet need to address this type of issue, so their data bases and references will likely stay the same, at least for the time being.  For some time to come, we will be dealing in a dual world where both methodologies are utilized and yes, some amount of confusion will certainly result.  In preparation, I wanted you to understand what has happened in the past, the recent changes, what the future holds, and why.

Family Tree DNA Research Center Facilitates Discovery of Ancient Root to Y Tree

The genetic genealogy community has been abuzz for months now with the discovery of the new Root of the Y tree.  First announced last fall at the conference for DNA administrators hosted by Family Tree DNA, this discovery has literally changed the landscape of early genetic genealogy and our understanding of the timeframe of the origins of mankind.  While it doesn’t make much difference in genetic genealogy in the past few generations, since the adoption of surnames, it certainly makes a difference to all of us in terms of our ancestors and where we came from – our origins.  After all, the only difference between current genetic genealogy and the journey of mankind is a matter of generations – and all of our ancestors were there, and survived to reproduce, or we wouldn’t be here.

One of the important aspects of this discovery is the collaboration of citizen scientists with academic institutions and corporations.  In this case, the citizen scientist was Bonnie Schrack, a volunteer haplogroup project administrator, Dr. Michael Hammer of the University of Arizona, National Geographic’s Genographic Project, and Drs. Thomas Krahn and Astrid Krahn, both with the Gene by Gene Genomics Research Center.  Without any one of these players, and Family Tree DNA’s support of projects, this discovery would not have been made.  This discovery of the “new root” legitimizes citizen science in the field of genetic genealogy and ushers in a new day in scientific research in which crowd sourced samples, in this case, through Family Tree DNA projects, provide clues and resources for important scientific discoveries.

Today Gene by Gene released a press release about the discovery of the new root.  In conjunction, Family Tree DNA has lowered their Y DNA test price to $39 for the introductory 12 marker panel for the month of March, hoping to attract new participants and to eliminate price as a factor.  On April 1, the price will increase to $49, still a 50% discount from the previous $99.  Who knows where that next discovery lies.  Could it be in your DNA?

Family Tree DNA’s Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

HOUSTON, March 26, 2013 /PRNewswire/   — Gene By Gene, Ltd., the Houston-based   genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic’s Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years.  This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report “An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree” in The   American Journal of Human Genetics earlier this month.  The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of   the University of Arizona, who currently serves on Gene By Gene’s advisory board, and two of the company’s staff scientists, Drs.Thomas and Astrid-Maria Krahn.

The DNA sample had originally been submitted to National Geographic’s Genographic Project, the world’s largest “citizen science” genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA’s database for genealogical research.  Once in Family Tree DNA’s database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

“This whole discovery began, really, with a citizen scientist – someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products,” said Gene By Gene President Bennett Greenspan.  “While reviewing samples in our database, she recognized that this specific sample was unique and  brought it to the attention of our scientists to do further testing.  The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution.”

The discovery took place at Family Tree DNA’s Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project.  Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company’s Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations.  Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

“Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago,” said Dr. Michael Hammer.  “Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade.  This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise.”

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%.  By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research.  They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd. 
Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic  tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients   worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

SOURCE Gene By Gene, Ltd.

Ancestry Needs Another Push – Chromosome Browser

ancestry push

It seems that the genetic genealogy community is constantly doing battle with Ancestry in regards to Ancestry’s mediocre and at times, outright faulty autosomal DNA product, AncestryDNA.  AncestryDNA, similar to Family Finder at Family Tree DNA and the 23andMe test, matches you against others who have taken the test for “relatedness” across all of your ancestral lines.  I wrote a primer about autosomal testing in an earlier article, another comparing the various company offerings and a third comparing the actual results.

While we were excited this week that Ancestry has finally lived up to their promise to provide our raw data files for download, albeit many months later,  they have made a decision apparently to NOT provide a chromosome browser, their logic being, according to genetic genealogists who spoke to Kenny Freestone, Ancestry’s product development manager this week at Rootstech, that their primary focus is to keep things simple for the newer users.  Just so you know, if you’re an Ancestry user, not only have they just called you “stupid” but they also insinuated that you are unable to learn and to be anything other than stupid.  Are you insulted?  I surely am.

Ok, let’s forget, for the moment, about the fact that Ancestry just insulted us and let’s look at why having a chromosome browser is important.

This is very simple.

Just because you have a paper genealogy match with someone, especially a distant DNA match, does NOT mean that is how you’re related to them. 

Ancestry does a good job of linking up people who match by connecting people in their trees.  But that doesn’t mean that connection is how they are genetically related.  Plus, we all know about the, ahem, “quality” of Ancestry trees.

ancestry push 1

Here’s an example.  This is a match to someone through my ancestor, James Claxton and his wife Sarah Cook.  However, what if I’m also related to this person through the Estes family too?  Or an unknown line?  Just because the paper connection is to James Claxton doesn’t mean the genetic connection is to him as well.  This person has over 11,000 people in his tree.  If we are from the same geography, it’s likely that we match on multiple lines.  What if we match on paper on two or three lines?  How do we know how we are genetically related – through which line or lines?

At Ancestry, you don’t – you can’t – because they want to “keep things simple.”   Let me translate – they would rather leave you with a vague “feel good” notion about who you are related to, even if it’s not true, than give you the tools to discover the truth.

We need a chromosome browser to let us see how and if the DNA we share with these people is really from the Clarkson/Claxton family or the Cook family, or if maybe it’s from another line that isn’t shown on the pedigree chart being displayed by Ancestry.

Let’s move to Family Tree DNA to see what a chromosome browser does for you.  At Family Tree DNA, three of my Vannoy cousins have tested.  By using the chromosome browser to look at their DNA compared to mine, we can identify some segments as “Vannoy” segments – meaning they unquestionably come from that line.  We do that by using triangulation. It’s easy.  Using 3 or more relatives from a particular line, if three or more match on a particular segment, you know that segment is from that family line.

ancestry push 2

I’ve selected three cousins to compare to my results, above, and their results will be displayed using these colors.  Below, you can see that on chromosome 15, all 4 of us match on a significant sized matching segment.  That means that this segment is definitely “Vannoy.”  How does this benefit us?

ancestry push 3

Well, it benefits us in two ways.  Let’s say an adoptee, or someone who has hit a brick wall also matches us on this segment.  It tells us that they are also “Vannoy” or perhaps ancestors of Vannoys.  Ancestors of Vannoys?

ancestry push 4

Yes, Vannoy is of course made up of their ancestral names and lineages too, so in time, let’s say that a Hickerson matches this segment too.  Then we’ll know that this segment comes from Daniel Vannoy’s wife, Sarah Hickerson’s line.  Do you have any wives surnames in your lines that need to be identified?  This is one way to do it, but you can’t without a chromosome browser.  And you could be the one who is brickwalled with the answer just waiting…..if there was a chromosome browser.  Do you see why this is so important, especially given the number of people who have tested at Ancestry?

Pretty simple stuff, right?  Well, Ancestry doesn’t think so.  They think you’re not capable of understanding this.  Funny, both Family Tree DNA and 23andMe provide this capability and people use it and depend upon it daily.  If you don’t want to use it, you certainly don’t have to, but to deprive all of us of an absolutely critical component of genetic genealogy is unconscionable. It’s simply not acceptable.

What can we do about this?  CeCe Moore, Tim Janzen and Dave Dowell were at Rootstech this week where they spoke with Kenny Freestone, among others.  He’s says he does personally read the information submitted through the “Feedback” button.  That is apparently how Ancestry gauges what needs to be done and prioritizes items.  Of course, if most of their novice clients don’t know what they are missing, they won’t be able to ask for what they don’t know about.  They are living under the illusion that they ARE genetically connected to everyone whose tree shows, and through the common paper line, and that’s it.  They don’t know that Ancestry is intentionally leaving them in their “feel good” cocoon and intentionally withholding “the rest of the story” and with it, their ability to discover even more.

But we know better and we were all “new users” at one time.  Use the feedback button.

ancestry push 5

It’s at the top right of your DNA pages at Ancestry.  Send Kenny the message…..”Kenny, we need a chromosome browser.”

Pssst….pass it on.  Everyone needs to provide this feedback.  This is how we got the raw data released and it’s the only way we’ll ever convince Ancestry to implement a chromosome browser.  Facebook this posting, Tweet it, post it on groups and forums.  Get the word out.  Send Feedback!!!

ancestry push

Judy Russell, the Legal Genealogist blogged about this today as well.

Downloading Ancestry’s Autosomal DNA Raw Data File

Well, the big day has finally arrived.  Ancestry has at last allowed us to download our raw data files.  To download yours, sign on to your Ancestry account and fly over the DNA tab.  You’ll see the selection, “Your DNA Home Page,”  Click on that.

ancestry download

Then click on “Manage Test Settings” to the right of the orange “View Results” box.  You’ll see the following screen.

ancestry download 1Click on “Get Started” in the right hand box under “Download your raw DNA data.”  You will then be prompted to enter your password to receive an e-mail to allow the download.

ancestry download 2

The e-mail will arrive, and you will need to click the link in the e-mail, shown below, to activate the download.

ancestry download 3

Clicking on the e-mail link “Confirm Data Download” takes you to the next step on Ancestry’s website, below.

ancestry download 4

Clicking on the green “Download DNA Raw Data” link shows the following:

ancestry download 5

Shortly, your browser will do whatever it does to ask you if you want to save or display the file.

ancestry download 6

I use Internet Explorer and download files are automatically saved in the “download” folder.  I renamed it and moved it to someplace where I can find it, hopefully.  The good news is that if I “lose” it on my computer, it’s easy to repeat this process.

Now, what can you do with this file today?  Not a lot.  You can compare raw data segments with others who might download their files too, but life will be a lot easier when tools like GedMatch can accept these files and do something with them.  There were also rumors last fall that Family Tree DNA would support uploads as well when Ancestry released these files, the same as they do with 23andMe raw data files.  Let’s hope so.

However, today will be the first day these organizations see the raw data too, so expect a bit of lag time before anyone can process or incorporate this information.  Of course, it goes without saying that we have to address issues pertaining to file layout and compatibility.

I’m hopeful that since Ancestry has the raw data files for everyone who has tested there, that they will do what the other two major players have done and create a chromosome browser where you can see who matches you on which segments and download that comparative information as well.  It’s not just the raw data we need, it’s the integrated tools to use it.  Hopefully we’re at the crawl before you walk stage and we’ll be walking soon!

The Autosomal Me – Start, Stop, Go – Identifying Native Chromosome Segments

This is Part 7 of a multi-part series.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7 – “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, takes a deeper dive and focusing on the two chromosomes with proven Native heritage, begins by comparing those chromosome segments using the 4 GedMatch admixture tools.  In addition, we’ll be extracting Native segment chromosomal start and stop addresses that we’ll be using in a future segment.

Using Doug McDonald’s tool and the 23andMe results, we can begin with the following two Native segments, one each on chromosome 1 and 2.  These will be our reference points, because according to both sources, these are the largest and most pronounced Native segments, the strongest indicators, so they will be our best yardsticks.

  Chromosome 1 Chromosome 2
23andMe

165,658,091 to 175,711,116

86,316,174 to 103,145,426

McDonald

165,000,000 to 180,000,000

90,000,000 to 105,000,000

On all of these admixture graphs, my results are shown first, then mother’s, then the comparison between the two where the colored regions show common ancestry and the black shows nonmatching segments – in other words those contributed by my father.

Please note that Native contribution in this analysis is being evaluated by a combination of geographies.  In some cases, one individual will show as “Native” meaning in the case of MDLP “North Amerindian” and the parent (or child) will show as something similar, like “Actic,” “South American” or “MesoAmerican.”  In order to normalize this, I have combined all of the geographies that are Native indicators.

MDLP

On the MDLP graph below, the legend indicates that these 4 regions are relevant to Native ancestry.

  • Army green – Mesoamerican
  • Lime Green – Arctic
  • Emerald – South American Indian
  • Grey – North Amerindian

Chromosome 1 – Native Segment

On the graph below, you can see that mother has more grey than I do from about 162-165, but then I have some grey that she does not at about 170.

step 7

A detailed analysis of the segment of chromosome 1 between 158-173 shows the following admixture:

On my results, the putty green, MesoAmerican, is scattered between about 158 and 173, in three segments.  The putty green in my mother’s segments are from 159-160.5 and then 167-170.5.  Therefore, my father, by inference has a segment from about 162-165 and from about 170.5 to 173.

My teal, North Siberian, ranges from 162-163 and from 168-171.  My mother carries no teal in these segments, so this is inferred to be contributed from my father.

My dark grey, North Amerind, ranged from 162-165.5 and then from 168-169.5.  My mother’s range is from 161-165.5.  Therefore my grey segment at 168-169.5 is either recognized as MesoAmerican or Arctic Amerind in my mother.

Chromosome 2 – Native Segment

step 7 - 1

Chromosome 2 is quite interesting.  You can see that on my chromosome, the North Siberian begins at about 80.  Mom has none at that location.  My North Amerind begins at about 95 and extends to 105, where Mom’s begins in the same location but then transitions to a large segment of MesoAmerican which I do not carry.  I do have MesoAmerican, but mine begins about where hers ends and extends to about 105.  Mom’s North Amerind ends about 101, while mine continues to about 105.  She looks to have trace amounts beginning about 105 and extending through 115.

Eurogenes

The next graph shows the same chromosomes using Eurogenes.  Regions relevant to Native ancestry include:

  • Red – South Asian
  • Brown – Southwest Asian
  • Yellow – North Amerindian and Arctic
  • Putty – Siberian
  • Emerald – East Asian

Chromosome 1 – Native Segment

step 7 - 2

The difference between my chromosome 1 and my mother’s in this region is quite pronounced.  My mother’s is drenched in beautiful red South Asian, while I have absolutely none.  Some of the area where I have North Amerindian shows as South Asian on hers, but in other areas, there is no correlation.  It is expected of course, that there are areas where she has some ancestry and I have none, due to the fact that I only inherit half of her DNA, but she has a significant segment of East Asian between 163 and 164, and I look to have received only a very small portion.  The same is true of her Siberian segments at 163-164, but then I have Siberian that she does not at 169-170 and she has some that I don’t at 160-161.5.  Some of this difference can likely be explained, especially between the yellow North Amerindian and the red South Asian by slight differences in the DNA read and how it is categorized, but in other cases, the difference is real.  Looking at mother’s red segments from about 166.5 to about 168 and then looking at my corresponding region, you can see that I have nothing that hints at Native.  In that region, I clearly inherited from my father as well as my mother’s North European.

Chromosome 2 – Native Segment

step 7 - 3

As different as our chromosomes 1 were, one wouldn’t expect chromosome 2 to be so similar.  In the graph, I included my large South Asian segment surrounding 80, where Mom has a trace, although that is beyond the area indicated as Native by 23andMe and Doug McDonald.  In the range of interest, beginning at about 80, we find nothing until about 94 where mother and I both have North Amerindian segments that stretch through about 105.  Mom’s goes slightly further than mine, to about 105.5.  It’s interesting to note that in part of this region, on either side of 101, her Siberian and my North Amerindian are the same shape at the same location, so obviously the same DNA is being read and categorized as two different regions, probably due to my father’s admixture.

Dodecad

On the Dodecad graph of the Native segment, you can see the Native colors are in shades of green.

  • Putty – West Asian
  • Yellow-green – South Asian
  • Emerald – Northeast Asian
  • Light Green – Southeast Asian

To use Dodecad in an equivalent manner as the rest of the tools, it looks like Northeast Asian is the closest we would get to Native American since that is where Native Americans lived just prior to crossing Beringia, so the greens should probably be evaluated as a group.  As can be seen on chromosome 1, they do clump together.  Even though West Asian is also found with this group, it seems to be outside the range, so I am not including it in the evaluation.

Chromosome 1 – Native Segment

You can see another example here of one segment being called South Asian in Mom’s and Northeast Asian in mine at about 170mb.

step 7-4

The Native, or in this case, Northeast Asian/Southeast Asian begins at about 162.5 where Mom’s and mine are very similar.  However, we diverge at about 164.5 where Mom begins with large segments of South Asian.  I have a little bit, but not much.  Beginning about 168, I have a large Northeast Asian segment, but she shows with South Asian there, although the segments are not exact.

Chromosome 2 – Native Segment

step 7 - 5

Chromsome 2 is quite simple using Dodecad.  Only two of the three groups appear.  Southeast Asian is absent, South Asian is present only in trace amounts except for one small area between 79.5 and 80 on my chromosome.  As expected, Northeast Asia is more prominent.  Mother has a few areas that I don’t, which is to be expected.

HarrappaWorld

Last, we have HarrappaWorld.  American and Beringian are the Native American categories here.  Regions relevant to Native American heritage would be:

  • Teal – American
  • Periwinkle – Beringian
  • Lime Green – Siberia
  • Emerald – Northeast Asia

Chromosome 1 – Native Segment

You can see both Beringian and American embedded again at about location 169.  In mine, this entire block reads as American.

step 7 - 6

There is one large chunk of Northeast Asian showing for both results, but part of that region of my chromosome, between 163-164 shows as American instead of Northeast Asian.  The Beringian is scattered through the American, which I would expect.  The American runs either strongly or weakly through this entire segment from 163 to 175 in mine or to 179 in mother’s.  Surprisingly there is no Siberian at all.  I would have expected to see Siberian before Northeast Asian.

Chromosome 2 – Native Segment

step 7 - 7

Where on chromosome 1, we saw no Siberian, on chromosome 2, we find Siberian instead of Northeast Asian.  I have no Beringian, but mother has 4 segments.  Three of her 4 segments are embedded with American segments.  Two may simply be categorized differently in my results, but two, I did not inherit.

Analysis Discussion

What have we learned?

When we are dealing with small amounts of minority admixture, they may or may not be able to be picked up directly by the testing companies.  Of course, part of this has to do with their thresholds for what is “real” and reportable, and what isn’t.  Aside from that, lack of identification of minority admixture probably has to do with which segments were inherited and their size, if they have been isolated and identified as Native by population geneticists, and the robustness of the data base sources the data is being compared against.

We can also see how difficult it is to sort through threshold matches, meaning what is Native, Asian, central Asian, etc.  Many of these differences are probably not actually differences between groups, but similarities with slight categorization differences.  Of course, it’s those differences we seek to identify our ancestral heritage.  Combining similar geographies may help reveal relationships masked my reporting and categorization differences.

Given that multiple sources have indicated Native ancestry, and on the same two chromosomes, I have no doubt that it exists.  Had any doubt remained, the exercises creating the MDLP Chromosome Map Table and reviewing the segments on chromosome 1 between 160 and 180mb would have removed any residual concerns.

The following table shows the results for the Native segments of chromosomes 1 and 2 beginning with the 23andMe and McDonald results, and adding the start and stop segments from each of the 4 admixture tools we used.

  Chromosome 1 Chromosome 2
23andMe

165,658,091 to 175,711,116

86,316,174 to 103,145,426

McDonald

165,000,000 to 180,000,000

90,000,000 to 105,000,000

MDLP

162,000,000 to 173,000,000

80,000,000 to 105,000,000

Eurogenes

162,500,000 to 171,500,000

79,000,000 to 105,000,000

Dodecad?

162,500,000 to 171,000,000

79,500,000 to 105,000,000

Harrappaworld

163,000,000 to 180,000,000

79,000,000 to 104,000,000

In Common

165,658,091 to 171,000,000

90,000,000 to 103,145,426

Although the start and end (or stop) segments vary a bit, all resources above confirm that the region on chromosome 1 between 165,658,091 and 171,000,000 is Native and on chromosome 2, between 90,000,000 and 103,145,426.  Those are the areas “in common” between all resources, which is shown in the last table entry.

The concept of “in common” is important, because while any one resource may report something differently, or not at all, when all or most of the resources report something the same way, it is less likely to be a fluke or reporting issue, and is much more likely to be real.  We’ll be using this methodology throughout the rest of the articles in “The Autosomal Me” series.

In the next segment, Part 8, we’ll be extracting the actual start and stop addresses of the Native only segments, referred to as the “Strong Native” method, and the combined Native indicator segments, referred to as the “Blended Asian” method and looking at how we can use those results.

Is the Family Tree DNA 12 Marker Test Worthwhile?

There has been quite a bit of discussion about the 12 marker test at Family Tree DNA.  Some people would like to see this discontinued, mostly administrators who would very much like people to test at higher marker levels out the door.  However, sometimes that just doesn’t happen, and the 12 marker test is still quite valuable for a number of reasons:

  • Removes cost as a constraint to DNA testing at $39
  • Allows relatives to pay for tests – I’ve purchased 4 in the past couple of weeks
  • Can often exclude some family lines (no more barking up the wrong tree) – but may need more testing if common haplogroup like R1b1a2 to determine exact family line
  • Provides tester with haplogroup which can be very enlightening (European, African, Asian or Native American)
  • Provides tester with matches
  • DNA is stored for 25 years, so tests can be performed at a later date
  • Let’s people stick their toe in the pool for $39 – they can upgrade later

The question was then asked whether the $39 12 marker test at Family Tree DNA really saves money by ordering the 12 marker test and upgrading later to a higher marker count.  The hardest part of answering this question was finding someone in my projects who had only tested to 12 markers so I could look at the upgrade pricing.

The answer is yes.  Here’s the breakdown.

Upgrade cost from 12 markers to other levels:

12 to 25 – $49

12 to 37 – $99

12 to 67 – $189

111 markers was not listed as an upgrade from 12 markers, so I did not use the 111 marker tests in this comparison.

Total with $39 plus Upgrade, above:

25 markers – $88

37 markers – $138

67 markers – $228

Ordering Higher Marker Level Within Project (no $39 entry level test – just order the higher marker level out the gate):

12 – $39 (same price)

25 – $124 ($36 savings to upgrade separately)

37 – $149 ($11 savings to upgrade separately)

67 – $238 ($10 savings to upgrade separately)

Ordering Higher Marker Level Outside of Project (no $39 entry level test, order higher marker level out the gate):

12 – $39 (same price)

25 – not offered outside of projects

37 – $169 ($31 savings to upgrade separately)

67 – $268 ($1 savings to upgrade separately)

So your best value would be to purchase the $39 kit and upgrade to higher marker levels separately.

The Autosomal Me – DNA Analysis – Splitting Up

DNA Analysis purchased 1-24-2013This is Part 6 of a multi-part series.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In this segment, Part 6, “DNA Analysis – Splitting Up” we’re going to focus on specific aspects of those tools and begin our analysis of our minority ancestry.

Analysis.  Sounds like I’m climbing on the shrink’s couch.  But I’m not, I’m saving all my dollars for DNA kits!  Besides, I don’t want to stop!  This analysis, we’ll do by putting several pieces of data together and sorting the wheat from the chaff.  And yes, we’ll be splitting up…well…splitting our DNA up into pieces contributed by our father and mother.

Let’s start with looking at the DNA segments that mother and I share that are Native.

According to Doug McDonald, we have significant Native matches on chromosomes 1 and 2, with third party tools confirm that finding.  Unfortunately, the only company where Mom’s DNA resides is Family Tree DNA whose test did not reveal the Native ancestry.  23andMe did confirm Native segments in my DNA in those locations.

I’ve used several third party tools at GedMatch to see where Mom and I both have Native heritage, where she has it and I don’t, and equally as important, where I have it and she doesn’t?  What is that so important?  Simple, it means my father had Native heritage too, and tells me on which chromosomes his Native DNA is located  This could, when matching people in the future, on particular segments, help to isolate who our common Native ancestor was, or at least which line.  That is the ultimate goal we are working towards with this entire process.

In this case, to identify my father’s Native lines, if Mom and I neither or both have Native markers at a particular chromosome location, the values are irrelevant, because the Native lineage came from mother.  I did notice in a few cases that I had more than mother, and of course, in that situation, it means that my father contributed some too, or my mother had a misread in that region or a categorization issue exists.  For that reason, I am looking for patterns, not single instances.  We’ll discuss using patterns in a future segment.

Using the MDLP chromosome mapping tool, as MDLP appears to be the most comprehensive, I created a spreadsheet using my results as a base.  I then added mother’s values in the spaces where I had no values, and then I highlighted my results in the locations where mother had no value.  The essence of this is that the red, bold, underscore values mean Mom had a Native result here, but I didn’t receive it.  A yellow highlighted cell means I got the entire amount from my father, because my mother has no percentage showing.  In other cases, of course, it’s possible that both mother and father contributed Native ancestry on some adjacent chromosome segments.  The MDLP mapping tool with my additions is shown below for chromosomes one through eight.  Chromosomes 9-22 are similar, but the chart is too big to display as a whole.  This provides an example of how to do this analysis with your own results.

MDLP Chromosome Map Table

The results were very interesting.

My two primary regions, North-East-Europe and Atlantic-Mediterranean-Neolithic, were represented on every chromosome for both my mother and myself.  No surprises there.  The other regions would be considered minority admixture.

In 2 categories, North-European-Mesolithic and East Siberian, only my father contributed genetic material on some chromosomes and there were no chromosomes where my mother alone contributed.

In 1 category, Melanesia, only my mother contributed genetic material on some chromosomes and there were no chromosomes where my father alone contributed.

In all other categories, both parents contributed on some chromosomes where the other didn’t.  This is important, because it will allow me to associate a match with a particular segment of a chromosome on a particular parent’s side with Native ancestry.

In the minority categories for Native American, Mesoamerican, Arctic-Amerind, South America Amerind and North Amerind, grouped together, both parents contributed on some chromosomes where the other didn’t, and in two categories, on 3 chromosomes, I carry more than my mother, indicating an additional contribution from my father.

This is a repeated occurrence, with Native ancestry for my parents and I combined showing on a total of 42 chromosome locations across 4 geographic/ethnic categories, and in at least three cases, both parents contributed.

In the African categories, South African, Sub-Saharan and Pygmy, I had contributions from both parents on a combined total of 18 chromosome segments.  The African admixture, in total, was less than the Native, and they are assuredly below 5% combined.  If they were present at higher levels, I wouldn’t need to go through these genetic gyrations to prove or disprove the heritage and which parent contributed, because it would be evident in the testing results of all companies.

In our next segment, Step 7, we will be further scrutinizing Chromosomes 1 and 2 for additional information about Native heritage and assigning specific Native segments that I carry on various chromosomes  to either my mother or father’s lineage.