National Geographic – Geno 2.0 Announcement – The Human Story

Posted on July 25, 2012 by Roberta Estes

Have you ever dealt with something so massive and overwhelming it took a few days just to get your head wrapped around it? Well, that’s how I’ve been feeling about the new National Geographic Geno 2.0 announcement. It’s not just what has been announced, but the utterly massive amount of scientific research behind the scenes, and what it means to the rest of us.

If you think of all of the discoveries and progress that has been made in the 12 years since the advent of genetic genealogy, what you’re about to hear today dwarfs it all. Hold on tight – this is a white knuckle ride of a lifetime. The day I heard about this, I wandered around somewhat starry-eyed in amazement and kept muttering something terribly intelligent like “Wow, oh Wow.”

I’d like to share with you some of today’s big news and hope that you too share my sense of awe to be alive in such an exciting time, and to have not only a front row seat, but participating in making history. This isn’t a movie, it’s the real McCoy!

Let’s start with a bit of history about Nat Geo 1.0, the Genographic Project. Fasten your seatbelt, your E ticket ride starts here and now!

Nat Geo 1.0

Eight years ago, in April 2005, the National Geographic Genographic project was announced. The goal was to sell a total of 100,000 kits over 5 years to help fund the indigenous part of the project, which was to collect samples from indigenous peoples around the world to better understand population migration.

According to Nat Geo, this has been the most successful program they have ever undertaken. That in and of itself it an amazing statement, especially considering that there was a lively debate within Nat Geo prior to the project launch.

Someone opined to Spencer Wells that they wouldn’t even sell 10,000 kits, let alone 100,000. Well, they were wrong, 10,000 kits were sold the first day alone. I’m guessing that Bennett and Max at Family Tree DNA, whose test kits Nat Geo uses, has a sense of controlled panic about that time. The 100,000 kits were sold in the first 8 months and they still sell between 40,000 and 50,000 kits per year today.

How is that project doing? Well, it was scheduled to run for 5 years, and it’s now into its 7^th year. They have collected over 75,000 samples from indigenous people and on the public side, over 750,000 people in over 130 countries have bought kits to help fund the research. 32 publications either have been released or will be shortly. Of the 45 million dollars the project has grossed, National Geographic has contributed more than 1.7 million dollars to the Legacy Fund for investment back into the indigenous communities that participated in the Genographic project.

You might recall that the original Nat Geo project only tested 12 markers for men and the HVR1 region on the maternal side. At that time, 7 years ago, $99 for each of those was a great deal and the projects received a lot of new participants. About 20% of the Nat Geo participants transferred their result to Family Tree DNA, for free, so they could join projects and participate in genetic genealogy.

Today, 12 markers is quite light and so is HVR1 testing alone. Project administrators cringe when we see those, because we know it’s really not enough to do much with today. We’ve learned so much in the past 7 years. You don’t realize how much things have changed until you take a minute to look back.

At the same time we were learning, technology was also advancing. Seven years ago, running autosomal tests was simply cost prohibitive. If you consider that computer technology has decreased in price and doubled in speed every year or two (Moore’s Law), the advances in DNA sequencing technology and understanding are moving in the same directions (increased capability and decreased costs) by a factor of 5 as compared to computer technology. Literally, we are moving at the speed of light. See, I told you to hold on. I meant it!

Geno 2.0 – The Big Announcement

It’s amazing that something this big has been kept this quiet. Those of us involved have been bursting at the seams with excitement, and today is the big day. Last night about 9 o’clock we received word that the countdown had begun.

For a look at the new National Geographic webpage, go to www.genographic.com. This is the heart of the new Geno 2.0.

Geno 2.0 is still comprised of the 3 core components as before, the indigenous portion, the Legacy fund and the public participation portion. However the technology is changing, dramatically, and the public participation arena is expanding. Public participation will now include some “citizen science” projects, grants, an educational segment meaning kits in classrooms, and community based projects. All of this is made possible by advances in the core sciences and technology. This, plus the focus of the “Dream Team” of genetic genealogy and population genetics.

Thankfully, Spencer Wells at National Geographic and Bennett Greenspan and Max Blankfeld at Family Tree DNA prepared us in advance for what was coming, as much as you can prepare for a technological tsunami!

Let’s take a look at the technology and scientific advances that have occurred and what it means to us today.

New Chips and New Partnerships

The days of sequencing 12 markers in the lab are gone forever, replaced by high-speed sequencing that looks at half a million markers, or more, at a time, and for the same price as a 12 marker test and the mitochondrial DNA test, together, would have cost in Nat Geo 1.0.

However, when you’re looking at just the Y DNA and the mitochondrial, you’re missing 98% of the human genome, the part that isn’t Y or mitochondrial DNA. And that 98% holds many secrets, the secrets of our ancestors.

The National Geographic Society recruited one of the top geneticists in the world at Johns Hopkins, focused on autosomal genetic markers. He has spent the past two years identifying every known marker relevant to ancestry or population genetics that is NOT medically relevant. This includes the X and Y chromosomes, mitochondrial DNA and the balance of the autosomal markers.

Are you sitting down? Here’s the first of several bombs!

Relative to Y-line DNA, in 2010, just 2 years ago, the YCC SNP 2010 tree had a total of just over 800 SNPs that has been discovered. Today it still hasn’t reached 900. You can see the current tree at http://www.isogg.org/tree/index.html. Notice that all of the L SNPs were discovered by Thomas Krahn in the Family Tree DNA lab with the assistance of Family Tree DNA’s customers and project administrators. This is truly “crowd-science” in the flash mob sense.

Today, after a concerted effort of discovery involving many people, there are a total of 12,000 Y SNPS and of that, 10,000 of them are unique and new and have never been seen or published before. This means that your haplogroup will automatically be determined to the furthest branch of the tree with no additional SNPs to be tested. As this test becomes available to Family Tree DNA clients as an upgrade, it will signal the demise of the deep clade test.

If there is a project administrator sitting next to you, they have just fainted. The magnitude of this is simply mind-boggling.

Relative to mitochondrial DNA, 3352 unique (non-haplogroup defining) mutations have been discovered. To measure all of the relevant mitochondrial DNA mutations, including insertions and deletions, over 31,000 probes (locations) are needed on the new high density chips. Before this new approach, chip technology was unable to account for insertions and deletions, but that has been remedied by a new approach to an old problem. This means that haplogroups will be determined to their deepest level and they will be accurate, including insertions and deletions critical to haplogroup assignment.

Relative to autosomal DNA, over 75,000 Ancestrally Informative Markers (AIMs) have been discovered and included on the new chip, and that’s after removing any that might be considered medically informative. This astronomical number of SNPs will allow us to detect ethnicity and improve accuracy on a scale that we’ve never even dreamed about before. I specifically asked Spencer Wells if this will help resolve those “messy” situations where we have European, Native American and African admixture, and he indicated that it would. I can hardly wait. For those of us what have been waiting patiently, and some not so patiently, to be able to identify small amounts of admixture, this is the best news you could ever hope to hear! I told you that something wonderful was on the way!

Relative to admixture with Neanderthal, Denisovan and Melanesian man, meaning interbreeding, more than 30,000 SNPs have been identified that will signal interbreeding where it occurred between modern humans and ancient hominids. And yes, this means that it did occur! So indeed once again, you can begin wondering about your brother-in-law. He’s probably wondering about you too.

Relative to the X chromosome, it’s included. The X chromosome, because of its special inheritance pattern, gives us an additional, special tool when working with genetic genealogy. We’ll cover this in a future blog.

The New Chip

In total, the new SNP count to be included on the new Nat Geo 2.0 chip (photo above) includes both new and known existing SNPs in the following amounts:

Autosomal including X – 147,000
Neanderthal – 26,000
Denisovan – 1,500
Aboriginal – 13,000
Eskimo – 12,000
Chimpanzee – 1,100
Y Chromosome – 12,000
mtDNA – 31,000

This chip has been designed to distinguish between populations.

OMG – What Happened to the Haplotree?

We’re not done yet with bombshells.

After this new chip was created by Illumina specifically for National Geographic, about 1200 samples were run as proof of concept, including 400 WTY (Walk the Y), 350 mitochondrial full sequence and 500 Y samples. All of the samples run are checked and tested for all of the SNPs on the chip. Of course, females’ samples will fail on all of the Y haplogroup locations, etc.

Just based on this test run alone of 900 Y chromosome kits, the haplotree expanded from 862 SNPs to a total of 6153. If you’ve just said something akin to “Holy Cow,” you’re on the right track. Imagine what it will do with another 1000 or 10,000 or 100,000 tests. Right now, we’re making discoveries so fast we can hardly deal with them.

What Does This Mean?

In reality, what this means is that we will very soon use SNPs to determine heritage down to a genealogical meaningful timeframe, meaning 500 to maybe 1000 years. The standard STR (Short Tandem Repeat) markers we know and love will become the leaves on the branches of the tree and these will likely be used when there are no more SNPs to determine family groupings and line marker mutations within families.

New National Geographic Geno 2.0 Website

Needless to say, all of this discovery has prompted National Geographic to redo their website entirely. New maps are forthcoming. Yeah!! New maps include the migration maps as well as new haplogroup “heat maps” where the colors are graduated based on frequency.

There are entirely new capabilities too. The new website will show you as the center of a circle and you’ll be able to contact people who have tested at Nat Geo who are located near to you in the circle. Those closest to you, you’re most closely related to. Further away, more distantly related. Before, there was no matching between Nat Geo participants.

And yes, Geno 2.0 participants will still be able to transfer into Family Tree DNA for free. I hope they make that option much more visible or interactive.

A New Test Kit

Anyone wanting to participate in Geno 2.0 will have to order a new kit from National Geographic. The previous Nat Geo kits, if you recall, were anonymous unless you chose to transfer to Family Tree DNA, plus the permission you gave was specifically for mtdna or Y-line, not autosomal testing.

Furthermore, the DNA in many kits will be too old and will have degraded too much to use. Everyone ordering the new Geno 2.0 kit will receive a new swab kit, in an heirloom box. The comprehensive Y-line (haplogroup only), mtdna (haplogroup only) and autosomal testing will cost $199.

For Family Tree DNA clients who will be offered the upgrade in the late summer or fall, you will be able to upgrade if your DNA is less than 4 or 5 years old. Otherwise, you’ll receive a new swab kit too.

All processing will be done at the Family Tree DNA Houston facility.

New Results Pages

The new test of course requires all new results pages for participants.

Take a look at a few of the pages you can expect.

The results will be presented as a personal story.

Your story will also include information such as maps of where your ancestors lived and where they migrated.

I asked Spencer if participants will be able to download their results so that we can continue to compare them as we do today, using various phasing tools. Spencer replied, “Yes, raw results WILL be available for download. In the Genographic Project, you will always own your DNA results, and the genotype data will be yours to do with as you please. I feel very strongly that this is a cornerstone of ethical DTC genetic testing.” Way to go Spencer!!

As Geno 2.0 moves forward, additional analytical tools will be added.

Ordering

National Geographic is accepting pre-orders now. They will ship before the end of October, and they expect to be shipping significantly before that.

In Summary

Our world is changing, rapidly, and for the better. The door we’ve been peeking through for a decade now is swinging wide open. More brick walls will fall. We’ll find and meet new cousins. Ethnicities will be identified at a level never before possible. We’ll learn about our ancestors and the story of our past through their DNA that we carry today. It is the frontier within. DNA is truly the gift that keeps on giving!

“One small step for man, one giant leap for mankind.”

Neil Armstrong, July 20, 1969

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The Dreaded “Middle East” Autosomal Result

Posted on July 24, 2012 by Roberta Estes

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One of our blog followers, Ron, asked this question:

“My late father and his brother were born and raised on Hatteras Island which was a very isolated community until relatively recent times. Curious about their genetic ancestry, I had my uncle do the Family Tree DNA Family Finder test. His results for the Family (Population) Finder were:

Europe (Western European) – Orcadian 91.37% ±2.82%

Middle East – Palestinian, Bedouin, Bedouin South, Druze, Jewish, Mozabite 8.63% ±2.82%

The 8.63% Middle East was surprising since most if not all of his ancestors, going back 4 or more generations, were born on the OBX (Outer Banks). Most of the original families on Hatteras Island trace their roots back to the British Isles and western Europe.

Since my mother’s parents were immigrants from eastern Europe, I thought it would be interesting to know what contributions my maternal grandparents added to my genetic ancestry, so I submitted my DNA samples for the same test. The Population Finder test showed that I was Europe Orcadian 100.00% ±0.00%. I was shocked that some other population did not show in the results.

Can you help me understand how the representative populations are determined and why Middle East didn’t show in my sample?”

Yes, indeed, the dreaded “Middle Eastern” result. I’ve seen this over and over again. Let’s talk about what this is and why it might happen. As it happens, the fact that Ray is from Hatteras Island provides us with a wonderful research opportunity, because it’s a population I’m quite familiar with.

Given that Dawn Taylor and I administer the Hatteras Families DNA Projects (Y-line, mtDNA and autosomal), I have a good handle on the genealogy of the Hatteras Island Families. They are of particular interest because Hatteras Island is where Sir Walter Raleigh’s Lost Colonists are rumored to have gone and amalgamated with the Hatteras Indians. The Hatteras Indians in turn appear to have partly died off, and partly married into the European Island population. Both the Lost Colony Project and the Hatteras DNA Projects at http://www.familytreedna.com/public/HatterasFathers and http://www.rootsweb.ancestry.com/~molcgdrg/hatteras/hifr-index.htm are ongoing and all Hatteras families are included.

As part of the Hatteras families endeavor, Dawn and I have assembled a data base of the Hatteras families with over 5000 early settlers and their descendants to about the year 1900 included. What Ron says is accurate. Most of the Hatteras Island families settled on the island quite early, beginning about 1710. Nearly all of them came from Virginia, some directly and others after having settled on the NC mainland first for a generation or so in surrounding counties. By 1750, almost all of the families found there in 1900 were present. So indeed, this isolated island was settled by a group of people from the British Isles and a few of them intermarried with the local population of Hatteras Indians.

Once on the island, it was unusual to marry outside of the island population, so we have the situation known as endogamy, which is where an isolated population marries repeatedly within itself. Other examples of this are the Amish and Jewish populations. When this happens, the founding group of people’s DNA gets passed around in circles, so to speak, and no new DNA is introduced.

Typically what happens is that in each generation, 50% “new” DNA is introduced by the other parent. When the new DNA is from someone nonrelated, it’s relatively easy to sort out using today’s DNA phasing tools. But when the “new” DNA isn’t new at all, but comes from the same ancestral stock as the other parent, it has the effect of making relationships look “closer” in time.

Let’s look at an example.

You carry the following average percentages of DNA from these relatives:

Parents 50% from each parent
Grandparents 25%
Great-grandparents 12.5%
Great-great-grandparents 6.5%

As you can see, the percentage is divided in each generation. However, if two of your great-grandparents are the same person, then you actually carry 25% of the DNA from that person, not 12.5. When you’re looking at matches to other people in an endogamous community, nearly everyone looks more closely related than they are on paper due to the cumulative effect of shared ancestors. In essence, genetically, they are much closer than they look to be on a genealogy pedigree chart.

Ok, back to the question at hand. Where did the Middle Eastern come from?

Looking at the percentages above, you can see that if Ray’s Uncle was in fact 8% (plus or minus about 2%, so we’ll just call it 8%) Middle Eastern, his Middle Eastern relative would be either a great-grandparent or a great-great-grandparent. Given that generational length is typically 25 to 30 years, assuming Ray’s birth in 1960 and his uncles in 1940, this means that this Middle Eastern person would have been living on Hatteras Island between 1835 and 1860 using 25 year generations and between 1810 and 1840 using 30 year generations. Having worked with the original records extensively, I can assure you that there were no Middle Eastern people on Hatteras Island at that time. Furthermore, there were no Middle Eastern people on Hatteras earlier in the 1800s or in the 1700s that are reflected in the records. This includes all existent records, deed, marriages, court, tax, census, etc.

What we do find, however, are both Native Americans, slaves and free people of color who may be an admixture of either or both with Europeans. In fact, we find an entire community adjacent to the Indian village that is admixed.

We published an article in the Lost Colony Research Group Newsletter that discusses this mixed community when we identified the families involved. It’s titled, “Will the Real Scarborough, Basnett and Whidbee Please Stand Up” and details our findings.

These families were present on the island and were recorded as being “of color” before 1790, so the intermarriage occurred early in the history of the island.

Furthermore, these families continued to intermarry and they continued to live in the same community as before. In fact, in May and June of 2012, we visited with a woman who still owns the Indian land sold by the Indians to her family members in 1788! And yes, Ray’s surname is one of the surnames who intermarried with these families. In fact, it was someone with his family surname who bought the land that included the Indian village in 1788 from a Hatteras Indian woman.

So what does this tell us?

Having worked with the autosomal results of people who are looking for small amounts of Native American ancestry, I often see this “Middle Eastern” admixture. I’ve actually come to expect it. I don’t believe it’s accurate. I believe, for some reason, tri-racial admixture is being measured as “Middle Eastern.” If you look at the non-Jewish Middle East, this actually makes some sense. There is no other place in the world as highly admixed with a combination of African, European (Caucasian) and Asian. I’m not surprised that early admixture in the US that includes white, African and Native American looks somewhat the same as Middle Eastern in terms of the population as a whole. Regardless of why, this is what we are seeing on a regular basis.

New technology is on the horizon which will, hopefully, resolve some of this ambiguous minority admixture identification. As new discoveries are made, as we discussed when we talked about “Ethnicity Finders” in the blog a few days ago, we learn more and will be able to more acutely refine these minority amounts of trace admixture.

If Ray’s ancestor in 1750 was a Hatteras Indian, and if there was no Lost Colonist European admixture already in the genetic mix, then using a 25 year generation, we would see the following percentages of ethnicity in subsequent generations, assuming marriage to a 100% Caucasian in each generation, as follows:

1750 – 100% Indian
1775 – next generation, married white settler – 50% Indian
1800 – 25% Indian
1825 – 13.5% Indian
1850 — 6.25% Indian
1875 — 3.12% Indian
1900 – 1.56% Indian
1925 – 0.78% Indian
1950 – 0.39% Indian

Remember, however, about endogamy. This group of people were neighbors and lived in a relatively isolated community. They married each other. Every time they married someone else who descended from someone who was a Hatteras Indian in 1750, their percentage of Native Heritage in the subsequent generation doubled as compared to what it would have been without double inheritance. So if Ray’s Uncle is descended several times from Hatteras Indians due to intermarriage within that community, it’s certainly possible that he would carry 6-10% Native admixture. There are also records that suggest possible African admixture early in the Native community.

So now to answer Ray’s last question about inheritance.

Ray wanted to know why he didn’t show any “Middle Eastern” admixture when his uncle did.

Remember that Ray’s Uncle has two “genetic transmission events” that differ from Ray’s line. Ray’s Uncle, even though he had the same parents as Ray’s father, inherited differently from his parents. Children inherit half of their DNA from each parents, but not necessarily the same half. Maybe Ray’s father inherited little or none of the Native admixture. In the next generation, Ray inherited half of his father’s DNA and half of his mother’s. We have no way of knowing in which of these two transmission events Ray lost the Native admixture, or whether it’s there, but in such small pieces that the technology today can’t detect it.

Hopefully the new technology on the horizon will improve all aspects of autosomal admixture analysis and ethnicity detection. But for today, if you see the dreaded “Middle East” result appear as one of your autosomal geographic locations and your family isn’t Jewish and has been in the states since colonial times, think to yourself ‘racial admixture’ and revisit this topic as the technology improves. In other words, as far as I’m concerned, the jury is still out!

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Racial Admixture in Elizabethan London

Posted on July 22, 2012 by Roberta Estes

We typically don’t think of Africans in London in the 1500s, but they were there, as proven in parish and other records. Thankfully, they were rare enough that when there was a record pertaining to them, their ethnicity is recorded. But by 1600, after the Queen’s legendary decades-long conflict with Spain where galley slaves from Spanish ships were “rescued” when the ships were captured, the number of Africans and other “Moorish” people were becoming problematic, at least to the Queen, and she sought to repatriate at least some of them to “Barbary.”

Recently, the BBC ran a wonderful story about this which you can find at this link: http://www.bbc.co.uk/news/magazine-18903391

In the haplogroup E1b1a project, it’s not uncommon for a person who knows their family to be “white” to discover their haplogroup is of African origin. Many times, one can account for this by more fully researching the early colonial records of America, but not always. Perhaps we need to extend the research net a bid wider to include both London and Bristol records.

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