What is a Haplogroup?

Posted on January 24, 2013 by Roberta Estes

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Sometimes we’ve been doing genetic genealogy for so long we forget what it’s like to be new. I’m reminded, sometimes humorously, by some of the questions I receive.

When I do DNA Reports for clients, each person receives a form to complete with a few questions designed to give them the opportunity to tell me what their testing goals are and to ask any questions they might have. One woman asked, “Can you tell me about my psychogroup?”

I thought that psychogroup was particularly appropriate for a cluster of genealogists, especially genetic genealogists, but decided I had better let that one go.

Then there was the person who wanted to know about their hologroup. I wondered if I needed 3D glasses for that one.

Someone else wondered about their helpgroup. I couldn’t help but think of introducing myself, “Hello, my name is Roberta and I’m a member of haplogroup J.” Kinda gives new meaning to “what’s your sign?”

Then there was the person who though it was a Biblical reference, Holygroup and wanted to know how they connected to Biblical folks. Well, we do talk about Y-line Adam and Mitochondrial Eve, so why wouldn’t someone ask that?

My favorite, though is the person who gave this reason for leaving a haplogroup project, “not my glopo.” Hey, at least they realized that, as opposed to the person who called me a member of the KKK for suggesting that they did not belong in a particular project. I found that to be particularly humorous, given my ethnic mix, heritage and family.

But today, when my cousin asked me if a haplogroup follows the mitochondrial DNA, I decided it was time to talk about what a haplogroup is, a little history, and why we use them. And Shanen, thanks for asking!

Think of a haplogroup as an ancestral clan, a large family, like the Celts, or Vikings. These would be larger than Native American tribes, encompassing members of many tribes. There are two male Native American haplogroups that include all Native American males. There are a few more African clans, or haplogroups, but not many.

There are clans for the Y chromosome, which is of course tested by the Y DNA test at Family Tree DNA and generally follows the paternal surname up and down the tree. Y DNA is passed from father to son, only, through the Y chromosome which only males possess.

There are also clans for mitochondrial DNA, tested by the mtDNA tests at Family Tree DNA, which follows the direct maternal line up your family tree. This means your mother, her mother, her mother, etc. Woman give their mitochondrial DNA to all of their offspring, males and females, but only females pass it on.

You can see the Y-line, paternal (blue) and mitochondrial, maternal (red), lines on the pedigree chart below.

Companies like 23andMe and the Geno 2.0 project provide haplogroups for both Y-line and mitochondrial DNA, but neither of them test personal mutations that allow you to compare your mutations against those of other people for genealogical matches. The regular Y-line and mitochondrial tests at Family Tree DNA do that. In addition, both also provide your haplogroup or clan designation.

A new haplogroup is born when a very specific new mutation occurs. All descendants will carry that mutation. That mutation defines that haplogroup. So if a new haplogroup is born today, we wouldn’t know it was a haplogroup until hundreds or thousands of years later when we see that lots of people have this same mutation from a single individual. As you might imagine, many haplogroups over the ages have died out, but some have been very successful as evidenced by the fact that we are all here today! Roughly half of the European men carry Y haplogroup R and mitochondrial haplogroup H is found in nearly 50% of all Europeans – both descending, respectively, from one single person tens of thousands of years ago.

Since all of humanity, both male and female, sprang initially from Africa, the earliest haplogroups were found there. As some people moved further away and crossed into Asia and Europe, they developed unique mutations that would give rise to the European, Asian and Native American haplogroups we know today. There are 4 main groupings, African, European, Asian and Native American, but there are several subgroups within most of those main groups, except for Native Americans who only have two male haplogroups.

So in essence, haplogroups are a pedigree chart of the clans of humanity. Family Tree DNA displays a haplogroup chart with the main haplogroups shown on everyone’s personal page for Y-line DNA. They were simply named alphabetically with no connection to a word. So no, A is not A because it’s African, even though it happens to be. N is not Native American. E is not European. You get the drift. Any resemblance is purely coincidental.

Your clan, in this example, haplogroup I, is shown with an arrow. Every clan, male and female, has subclans, often known as subclades for Y DNA or subgroups for mitochondrial DNA. To see the various subgroups of I, click on the tab and voila, there they are, the subgroups of haplogroup I. Yours is the lowest one on the tree that is green, in this case I2b1a1.

Because of the dramatic new number of haplogroups recently discovered, future versions of the haplotree will be moving away from the letter based names like I2b1a1 and will only use the terminal, or lowest branch, SNP to identify a haplogroup. In this case, that would be L126 or L137 which are equivalent SNPs. So in the future this person’s haplogroup will be called I-L126 instead of I2b1a1 because L126 will never change, but the name I2b1a1 changes every time a new upstream haplogroup is discovered between the root of haplogroup I and I2b1a1 and needs to be inserted into its proper place in the tree.

As we learn more about the subgroups, each one has its own story which is somewhat different than the stories of the other subgroups. Some are evident, such as Jewish clusters, some not so much. Each clan story involves how that haplogroup came to be found where it is today. For example, haplogroup E is African, but within haplogroup E, there are two major divisions with very different stories for their clans. One group is found only in Sub-Saharan African and one is found mostly in the Middle East and the Mediterranean basin and is known colloquially as the Berber haplogroup. We’re still learning about subgroups, and with the Geno 2.0 test, the haplotree is growing exponentially.

Family Tree DNA predicts your clan, or haplogroup, with any Y-DNA test as long as you match exactly at 12 markers to someone who has been SNP tested. SNP testing is what tests for the special haplogroup defining mutations. If you don’t match, they will SNP test you for free to establish your primary haplogroup.

Many people purchase additional SNP tests to further define their Y haplogroup so that they can learn about where their ancestors were, when, and what they were doing. For example, we know that SNP M222 equates to Niall of the 9 Hostages in history. How cool is that to know!

Some years ago, Dr. Doug McDonald assembled this wonderful map of the basic haplogroups of the world. Although we’ve discovered subgroups for each haplogroup, it’s still quite valid. E3b has since been renamed E1b1b and ExE3b means haplogroup E1b1a. RxR1 means haplogroup R except R1a and R1b which have their own legend.

Mitochondrial DNA also has haplogroups, which are clans. On the drawing below, compliments of Dr. Whit Athey, it’s easier to see how the daughter clans arose, were born, and were named. Because of the naming pattern, this looks a little less like a pedigree chart and a little more like stars, planets and moons.

One difference between Y-line DNA and mitochondrial DNA clans is that although they are all currently named alphabetically, the mitochondrial clans have names. That is thanks to Dr. Bryan Sykes who wrote the book, “The Seven Daughters of Eve” published in 2001. For example, he named haplogroup H, Helena because Helena is Greek for light. He told somewhat accurate stories about each clan and although quite scientifically dated now, described the life that each clan would have lived in post-glacial Europe. This book was the first book about DNA to reach the popular reading public, and was a huge success because he humanized science and normal air-breathing humans could relate. I ordered my first mitochondrial DNA test through his company and received one page with a Sunday School gold star on the red dot for haplogroup J.

I was thrilled at the time, but times have changed a lot. Due to advances in research and new subclades being defined, thanks in large part to citizen scientists like you, I now know that I’m haplogroup J1c2f as a result of my full sequence mitochondrial DNA test.

Unlike Y-line DNA, no additional SNP test is required to fully determine your mitochondrial DNA haplogroup. When you take the full mitochondrial sequence test (mtFullSequence) at Family Tree DNA, you receive your most detailed, full haplogroup designation automatically. With the HVR1 (mtDNA) and HVR2 (mtDNAPlus) tests, you receive at least your base haplogroup. The full sequence is required to determine your full haplogroup.

To put this in perspective, think of your mitochondrial DNA as a clock face. There are a total of 16,569 locations in your mitochondrial DNA. The HVR1 test tests the number of locations from 11:55 to noon and the HVR2 test tests the number of locations between noon and 12:05PM. The full sequence test tests the rest, the balance of the 50 minutes of the hour.

Family Tree DNA is the only commercial testing company that offers the full sequence test.

As more discoveries are made for both male and female haplogroups, the subgroup names sometimes change within the clan or main haplogroup because new branches get inserted in the tree as they are discovered.

For example, from a scientific paper, here’s an early version of the haplogroup H mitochondrial phylotree which is what the haplotree is called for mitochondrial DNA.

Here’s a later version.

You wouldn’t even be able to see today’s version, because the print would have to be miniscule to fit it on the page. In Dr. Behar’s paper, “A ‘Copernican’ Reassessment of the Human Mitochondrial DNA Tree from its Root” published in April 2012, the supplemental material records haplogroup H87. Most of those subgroups have subgroups of their own, like you can see above, and those that don’t today soon will as new discoveries are made.

Now that you know what a haplogroup is, there’s a lot you can do with both mitochondrial and Y-line DNA results.

Even if you do nothing more, it’s fun to identify your clan. It’s the only way of extending our genealogy back in time beyond surnames. For me, to connect my last known maternal ancestor, Elisabetha Mehlheimer, born in or near Goppsmannbuhl, Germany around 1800 to the cave paintings in Chauvet, France created about 12,000 years ago was a magical moment, a reach across time through a tenuous umbilical strand allowing me to identify and touch my 12,000 year-old ancestor. In my wildest genealogist dreams, I never dreamed this could or would ever be possible and indeed, it wouldn’t be, were it not for the genetic genealogy tools we have today.

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Hackers and Your Genetic Secrets

Posted on January 20, 2013 by Roberta Estes

Did that title get your attention? Well, it was meant to, just like it was meant to in this NBC article titled “Scientists Demonstrate How Hackers Could Unlock Your Genetic Secrets.” Or how about this one in the New York Times, “Web Hunt for DNA Sequences Leaves Privacy Compromised?” Sensationalism sells….and so does fear. Don’t panic, the sky is not falling.

I’ve had several people forward me a variety of links to several articles about this expressing concern. Most people didn’t really understand what was going on…and since “family tree databases” were mentioned in the first paragraph, it frightened them.

This article says that the “security cracking trick relies on the availability of genetic information linked to surnames in a variety of public family-tree databases.” Well, that’s sort of true, but not exactly true. The issue is not the family tree databases, it’s the fact that the researchers in The Thousand Genomes Project, while keeping the names of those 1000 people “anonymous,” provided enough information that these scientific researchers, not hackers, were able to data mine the 1000 Genomes participants information to determine their Y-DNA marker values, then compared those haplotypes (marker values) just like we do in databases such as Ysearch and Sorenson. And yes, they likely had matches to several surnames, like most of us do.

Individuals in the 1000 Genomes Project signed a release indicating that they knew that their data was to be used publicly, although their identity would not be revealed but that researchers could not guarantee their privacy. The 1000 Genomes Project, unfortunately, posted the ages of the participants, which at the time seemed innocuous enough, and it was common knowledge within the scientific community that they all lived in Utah. With these three pieces of information, their age, their location, and from the scientists data mining, a possible surname, the scientists were then able, if the surname wasn’t something like Smith or Jones, to use publicly available Google and “white pages” types of searches to find people in that state, of that age, by that surname, and then using obituaries and such, connect them through online family trees to their more distant families. They did this with Craig Venter, for example.

This technique is nothing new to genealogists, as we’ve been finding cousins that way for years – the difference being of course that we didn’t data mine, otherwise in this case more aptly referred to as “scientific hacking,” the 1000 Genomes Project in order to find their Y-line DNA markers to determine a possible surname for them. That is the issue and the point of this article and ironically, it’s scientists who did it, then published the “how-to” manual.

Any genetic genealogist knows, especially anyone dealing with adoptees, that you can only reveal a biological surname about 30% of the time. In fact the scientists success rate was lower, 12%. But that’s actually irrelevant in the bigger context of the article. Their point was that they succeeded at all.

This is sort of like putting personal information on the internet, except your name, and then being surprised that someone could connect the dots and put the pieces together. No one would be surprised today if that were to happen. In fact, I’m sure we all have received cautions and warnings about putting too much info on Facebook because burglars were robbing homes when people were vacationing. Many people have their hometown, their high school and their birthday and year publicly available on Facebook. Now how many “security questions” does that answer right there? Combine that with your dog’s name and your mother’s maiden name and you’ve got almost all of the common ones.

Aside from the fear-mongering, I have three issues with these reports as a whole.

1. Statements like “they traced those three family tree pedigrees to find other connections between relatives and sensitive genetic data.” Whoa, stop right there. Just because you share a surname or even if you are a direct and immediate relative, that says nothing, absolutely nothing, about whether or not you inherited some genetically disposed health issue. Remember, children inherit half of their DNA from each parent. So unless they are finding identical twins or parents, one cannot infer that an entire family tree of people share frightening health traits. It’s irresponsible to suggest otherwise.

2. “For years, experts have worried that sensitive genetic data could be used to discriminate against patients, potential employees or would-be insurance customers. Such discrimination is illegal when it comes to employment or health insurance, but the law doesn’t’ cover life insurance, disability insurance or long-term care insurance. Theoretically an insurer could search through genetic records and turn you down because you have a genetic predisposition to, say, Alzheimer’s disease.”

Discrimination is an issue, and laws have been put in place to prohibit discrimination in the workplace. But insurers aren’t going to sift through genetic data like a private investigator. Suggesting this is unnecessary fear-mongering. Insurers don’t do that, they simply tell you that a blood test is a pre-requisite of obtaining insurance. I know, I bought life insurance and they sent a nurse to my house to verify my identity and take a blood sample. At that time, they were looking for diabetes, AIDs and probably a whole lot more. Today, they might be looking for genetic pre-dispositions. I don’t know, but I do know they have a direct method of obtaining that information and it’s not spending untold hours sifting through someone else’s data that likely isn’t relevant to you anyway.

3. This “research” project was inspired at Whitehead Institute, an affiliate of MIT, a publicly funded institution. When Yaniv Erlich dreamed up this new hacking technique, he said he couldn’t resist trying it, so instead of simply discovering a potential issue and privately and quietly working with the proper people to resolve the issue, he decided to exploit it publicly, obtaining, I suppose, his 15 minutes of fame. So yes, your tax dollars did indeed likely pay for some or all of this “research.”

In one of the articles, Dr. Jeffrey R. Botkin, associate vice president for research integrity at the University of Utah, which collected the genetic information of some research participants whose identities were breached, cautioned about overreacting. “Genetic data from hundreds of thousands of people have been freely available online,” he said, “yet there has not been a single report of someone being illicitly identified.” He added that “it is hard to imagine what would motivate anyone to undertake this sort of privacy attack in the real world.” But he said he had serious concerns about publishing a formula to breach subjects’ privacy. By publishing, he said, the investigators “exacerbate the very risks they are concerned about.”

Well, it’s obvious that these folks at Whitehead institute don’t live in the real world and clearly don’t have enough real scientific research to do.

So, what is the take home of all of this?

You are not at risk of having anything exposed in this incident unless you are one of the 1000 people in the 1000 Genomes Project. If you are part of the 1000 Genomes Project, and male, there is a 12% risk that they figured out your last name and using other tools, possibly who you are, along with your family. If you are related to someone in the 1000 Genomes Project, the researchers might have figured out that you are related to them. So now the risk is that they’ll do what with that information??? Guaranteed, someone will figure out the same information and much more quickly, without your DNA and without government funding if you simply stop paying your bills.

If you participate in a research project, such as the 1000 Genomes Project, where your full results are made publicly available, you sign a release, and that release indicates that your privacy may not be able to be protected. You are aware of the risks before you begin.

We, as a community, have been warned for years not to put information that might be medically informative on the internet, such as full sequence mitochondrial DNA information. Anyone who does so, does it at their own risk. The people in the 1000 Genomes Project knowingly took that risk.

If you stay within the confines of the genealogy and DTC mainstream testing companies, you are fairly well protected. Having said that, reading the consent forms of any of the companies makes it clear that your identity is never entirely protected. We’re genealogists after all. What good is genealogical testing if you can’t contact people you match?

Inferred health risks are not the issue they are being portrayed to be in these articles. Your cousins health risks are not necessarily yours. Genetic inheritance is a complex and individual event.

Insurers who can use health information to restrict or deny insurance are simply going to request a blood sample. They are not going to act like a blood hound on the scent of a rabbit and sort through tons of information for inferences. Why would they when they can obtain the information they seek, directly and much less expensively?

For those researchers involved with information made publicly available, such at the 1000 Genomes Project, this is a wake-up call that perhaps less information available publicly is better. Some information, such as ages and location should perhaps be available only to legitimate researchers, which would still have included the Whitehead Institute people, but would have taken away much of their thunder. I understand this change has already been implemented, but that doesn’t entirely mitigate the issue of genetic data mining publicly available full genomic sequence information for identity, only makes it a little more difficult and less likely to succeed.

I clearly understand why hackers want my bank account information, and why identity thieves want my personal information, but why, in the real world, not at Whitehead institute, would anyone ever spend the time and effort to do this? The motivation for these researchers was clearly to publish, but I can think of no reason other than that or simply “because they could” to spend the time doing something like this. Who would want to and for what purpose?

The sky is not falling

It’s behind a paywall, but you can access the scientific article here that started all of this hubbub.

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Transferring Results from National Geographic to Family Tree DNA

Posted on January 13, 2013 by Roberta Estes

There are several reasons why you might want to transfer your National Geographic Genographic Geno version 1.0 and 2.0 results to Family Tree DNA.

Please note these are only valid for the Geno 2.0 version, prior to the Helix tests that began in November of 2016.

If you’re not a Family Tree DNA client, there is a whole new genetic genealogy world just waiting on you, and transferring your results is free. National Geographic test version 1.0, which is no longer available, included a 12 marker Y DNA test, and version 2.0, currently available, includes extensive haplogroup (clan) information that complements the 12-111 marker tests at Family Tree DNA, as well as other information. If you haven’t yet taken the 12 marker or other Y DNA tests at Family Tree DNA, you will be offered that opportunity in order to find your matches. After transferring your results to Family Tree DNA, you will be able to order additional tests, contact your matches via e-mail and share your genealogy information. It’s an exciting time in genetic genealogy!

YDNA SNPs

If you are already a Family Tree DNA customer, then you’ll want to download your data for a different reason. The Geno 2.0 chip includes an extensive list of Y DNA SNPs that are tested, far beyond what Family Tree DNA offers, and you will want to integrate this data into your results pages at Family Tree DNA.

Mitochondrial DNA

If you have not yet tested your mitochondrial DNA, Geno 2.0 provides you with your haplogroup, your deep ancestral clan information. The markers required to define your haplogroup will transfer to Family Tree DNA. If you want, you can then order the mtDNA, mtDNAPlus or the full mitochondrial sequence test to see what personal mutations you carry, and who you match.

If you have taken any mitochondrial DNA test at Family Tree DNA, none of the Geno 2.0 information will transfer, including updated haplogroup information. The Full Mitochondrial Sequence test at Family Tree DNA is more extensive than the Geno 2.0 haplogroup only test.

Autosomal Results

The two autosomal tests, the one provided by Family Tree DNA (Family Finder) and the one included in the Geno 2.0 product are entirely different beasts. The Family Finder test provides you with a list of cousin matches with numerous matching tools and an ethnicity report.

The Geno 2.0 product also provides an ethnicity report but uses different comparison populations and markers than Family Tree DNA, so they serve different purposes, the Family Tree DNA Family Finder product being more focused towards genealogy and the National Geographic product being more focused towards anthropology or deep ancestry. I mean, let’s face it, you’re probably not going to be able to go back far enough in time to tack a pure Neanderthal or a pure Denisovan on your family tree, your favorite brother-in-law excepted:)

How to Transfer Your Results

In order to facilitate the transfer, you’ll need to set up an account at National Geographic, and you’ll need your National Geographic kit numbers. So find those before you start. If all else fails, find that lovely black box your Geno 2.0 test kit arrived in. Your participant number is on the inside of the front cover. And you thought it was just another pretty box!

You’ll also need your Family Tree DNA kit number and password for the kit you want these results to transfer into.

Go to the Genographic website at http://www.genographic.com and click on
“Check Results.” You’ll be prompted through setting up your account at National Geographic. Whether or not you want to transfer data, you need to set up your account because if you don’t, and you lose your Nat Geo kit number, you’re toast.

After you enter your kit ID and set up your account, you’ll see the main results screen. This is mine, and no, my paternal results aren’t missing…there aren’t any because as a female, I don’t carry a Y chromosome!

Now click on “Profile” in the upper right hand corner of the screen. You’ll see the profile screen below.

You’ll see your profile, along with your kit numbers. You’ll need these for the next step so you’ll want to be sure to write them down. I’ve greyed mine above, but you can see where they were. Note that if you have already transferred your Geno 1.0 results previouisly, adding that kit number here has been reported to generate an error. If so, then try again without the 1.0 kit number.

Next, click on “Expert Options” at the top right of the screen. You’ll see “Download Data” and “Transfer Data to Family Tree DNA.”

Click on “Transfer Data to Family Tree DNA.” You’re almost done!!! You will be transferred to a screen on the Family Tree DNA site.

The kit numbers that you need are the numbers are displayed in your National Geographic account settings screen that I suggested you write down – plus – of course – your Family Tree DNA kit number and password that you want your National Geographic results associated with.

Complete this and click on next. You will see an order screen that looks like you are placing an order. Don’t worry, the order is free, but you do need to complete the form. Click through the options and at the end, the free order for your transfer will be complete.

It takes about 24 hours before you can see your results on your personal page at Family Tree DNA.

Y SNPs

Currently, as of January 12, 2013, you will be able to see your terminal SNP on your Haplotree and SNP tab if your terminal SNP is one that Family Tree DNA tests for in their lab.

However, if your SNP is new on the Geno 2.0 chip, then you won’t be able to see your terminal SNP on your personal page at Family Tree DNA, yet, so be sure to make note of your terminal SNP from your National Geographic results. Some Geno 2.0 results at Family Tree DNA today show an upstream SNP, and others show no SNP at all.

This is one of those good news/bad news situations. The good news is that we are functioning on the leading, sometimes bleeding edge of science and get to play a very important role, which is exciting. The bad news is that we’re bleeding a bit right now. Family Tree DNA really can’t fix this problem until a new haplotree is in place.

The problem is that haplogroup/subgroup discoveries are being made so rapidly that the haplotree is in a bit of a state of flux….OK, a big state of flux, which will take some time to sort through. More, many more, discoveries than ever expected continue to be made as more kits are run through the process. Let’s just say we’re having some minor growing pains. But what a great problem to have. We already knew that Geno 2.0 would change the tree dramatically, but we really had no idea HOW dramatically. Now I’m wondering if we’ll even recognize it! What we thought was a tree was only a sprout. And it’s still growing!

Why I do believe, why yes, I do hear….In the Valley of the Jolly, Ho, Ho. Ho…

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Out of Eden – Retracing the Steps of Humanity

Posted on January 11, 2013 by Roberta Estes

So how long would it take a human, today, to walk the path that humanity traveled? Paul Salopek, a prize-winning journalist, (including a Pulitzer for his article about the Human Genome Diversity Project) and National Geographic fellow is going to find out, if it’s even possible.

According to Paul’s calculations, it will take him about 7 years to walk from the Garden of Eden, Herto Bouri, a village in Ethiopia’s Middle Awash valley, which has the longest and most continuous record of human evolution of any place on Earth, to the southern-most tip of South America. Paul left yesterday, January 10, 2013, so only another roughly 6 years and 364 days until his arrival. But then again, I’m thinking it’s not so much about the destination as the journey.

The map, below, released by National Geographic, documents the path Paul will take.

This same path, taken in essence by ancient humans, took 30,000 to 40,000 years, depending on the timeframe used for humans leaving Africa and arriving at the tip of South America. Of course, they didn’t have a nifty map, most of them didn’t make it, as the path then was entirely by trial and error. What Paul will accomplish in 7 years, it took ancient people between 1200 and 1600 generations to complete.

You can read more about Paul’s journey and see some great National Geographic photos at this link: http://news.yahoo.com/man-begins-7-walk-path-ancient-humans-170907164.html

Better yet, you can follow his progress at this link: http://www.outofedenwalk.com/
Click on the “follow” tab to sign up for e-mail notifications when Paul posts something interesting.

Under “The Storytelling” tab, be sure to watch the short video about Paul’s inspiration for making this epic journey.

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Decoding and Rethinking Neanderthals

Posted on January 10, 2013 by Roberta Estes

On January 9, 2013, PBS ran a wonderful documentary, Decoding Neanderthals, about Neanderthals, what we have recently discovered about them, and what it means to us as humans. There has been a lot of discussion about this topic spurred by both the 23andMe and the Geno2.0 tests that provide a percentage of Neanderthal to participants. Geno2.0 also provides a percentage of Denisovan.

Program Description:
Over 60,000 years ago, the first modern humans—people physically identical to us today—left their African homeland and entered Europe, then a bleak and inhospitable continent in the grip of the Ice Age. But when they arrived, they were not alone: the stocky, powerfully built Neanderthals had already been living there for hundreds of thousands of years. So what happened when the first modern humans encountered the Neanderthals? Did we make love or war? That question has tantalized generations of scholars and seized the popular imagination. Then, in 2010, a team led by geneticist Svante Paabo announced stunning news. Not only had they reconstructed much of the Neanderthal genome—an extraordinary technical feat that would have seemed impossible only a decade ago—but their analysis showed that “we” modern humans had interbred with Neanderthals, leaving a small but consistent signature of Neanderthal genes behind in everyone outside Africa today. In “Decoding Neanderthals,” NOVA explores the implications of this exciting discovery. In the traditional view, Neanderthals differed from “us” in behavior and capabilities as well as anatomy. But were they really mentally inferior, as inexpressive and clumsy as the cartoon caveman they inspired? NOVA explores a range of intriguing new evidence for Neanderthal self-expression and language, all pointing to the fact that we may have seriously underestimated our mysterious, long-vanished human cousins.

I’m going to share some of the highlights of the program, but this is in no way a spoiler, as the program contains lots of visual information that just can’t be conveyed by a review.

Chris Stringer from the Natural History Museum in London introduced us to the Neanderthals. It turns out that our perception of what a Neanderthal looks like is a result in large part of skeleton that was reconstructed improperly due to advanced arthritis, causing the individual to appear to walk hunched over, much like, well, our stereotypical view of a caveman. Just goes to show what bad PR can cause.

Neanderthal skeletons can be positively identified. Their facial structure is different than that of modern man, with an identifiable brow ridge and bones that push forward in the nose and mouth region, as compared to our flatter faces today.

Neanderthals lived a short life, most were dead by age 30. They were large and strong. They participated in up-close and personal hunting, using spears, which meant they had to come in close contact with their prey.

Neanderthals began living in Europe about 300,000 years ago, having exited from Africa. They evolved to fit the European, colder, climate. It had been thought up until recently that they lacked the brainpower of humans, had no spoken language, or the ability for such, no personal ornamentation, art or evidence of ritual or religion. These are the functions that make us uniquely human and separate us from the non-human world, and we fully believed that Neanderthals lacked these defining characteristics.

We have learned differently, much as a result of genetic discoveries that tell a different story of Neanderthals.

Homo sapiens left African about 40,000 years ago, and within 10,000 years, Neanderthals, who had spread throughout most of Europe and much of Asia were gone. The map below shows the locations where fossilized Neanderthal remains have been found.

The assumption has been made that Homo Sapiens were responsible for the Neanderthals demise, either by killing them off or providing too much competition for scarce resources, outnumbering them 10 to 1.

Svante Paabo, a Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology forever changed the genetic world, how we perceive Neanderthals, and paradoxically, how we think of ourselves.

Pääbo is known as one of the founders of paleogenetics, a discipline that uses the methods of genetics to study early humans and other ancient populations.

In August 2002, Paabo published findings about the “language gene”, FOXP2, which is lacking or damaged in some individuals with language disabilities. This research would prove critical, later, in the humanization of the Neanderthal.

In 2006, he announced a plan to reconstruct the entire genome of Neanderthals. In 2007, Pääbo was named one of TIME Magazine’s 100 most influential people of the year.

In February 2009, at the Annual Meeting of the American Association for the Advancement of Science (AAAS), it was announced that the Max Planck Institute for Evolutionary Anthropology had completed the first draft version of the Neanderthal genome. Over 3 billion base pairs were sequenced in collaboration with the 454 Life Sciences Corporation. This project, led by Pääbo, shed and will continue to shed new light on the recent evolutionary history of modern humans.

In March 2010, Pääbo and his coworkers published a report about the DNA analysis of a finger bone found in the Denisova Cave in Siberia; the results suggest that the bone belonged to an extinct member of the genus Homo that had not yet been recognized, the Denisova hominin.

In May 2010, Pääbo and his colleagues published a draft sequence of the Neanderthal genome in the journal Science. Below, a scientist at Max Plank extracting Neanderthal DNA.

Paabo shared in the program that many times during the Neanderthal sequencing project, he himself “despaired many times of being able to do it”, doubting that it could be done. It took a total of 4 years. The team found good candidates, 3 well-preserved female bone fragments from the Vindija Cave in Croatia.

Because of the age of the fragments, and because they had been in the ground for so long, much of the DNA recovered wasn’t Neanderthal, but that of bacterial organisms and fungus. The team developed a method to eliminate the bacteria, leaving only Neanderthal DNA. However, those genetic fragments still had to be reassembled, piece by piece, like a huge jigsaw puzzle with no picture on the box, into the Neanderthal genome.

Four long years later, the puzzle was finished. I hope the team had a very big celebratory party!

Ed Green, a scientist on Paabo’s team said that the first thing the scientists looked for was to determine whether or not Neanderthals had the FOXP2 gene for language, and if so, is it identical to the human version, or is it different. The answer was that it was identical to the language gene carried by Homo Sapiens, modern humans. This tells us not only that Neanderthals had the capabilities for language, but that this gene evolved in Africa, before Neanderthals left, 300,000 years ago.

The next question, of course, was whether or not modern humans carried any DNA that could be labeled as Neanderthal. In other words, the question of inter-species breeding arose. It was believed that this was impossible, because two different species cannot have fertile offspring. This was proven to be an inaccurate assumption relative to Neanderthal and Homo Sapiens.

Paabo’s team sequenced the DNA of 5 individuals from different parts of the world. They isolated parts of the Neanderthal DNA that were measurably different from that of modern humans. In other words, those sequences could be positively identified as Neanderthal. Compared against the DNA of the 5 contemporary individuals, only the person from Africa had none of the Neanderthal DNA.

Paabo didn’t believe the results, thought they might be an artifact of statistical error or the result of not enough data, so he had his team repeat the exercise with different people, again, and again, and again, and every time, the results came back the same. Neanderthals and humans inbred, and to the degree that there is Neanderthal DNA in every population on every continent outside of Africa today.

John Hawks, an anthropologist at the University of Wisconsin used jelly beans to illustrate Neanderthal DNA in worldwide populations today. It turns out that the Chinese have the least amount, with about 1% and the people of Tuscany have the most, with about 4%. So the mountainous areas of Europe and Italy were a hotbed of Neanderthal activity and human interbreeding.

This caused other experts to think again about the Neanderthals in what could be called a radical shift in perspective. All of a sudden, when we realized that they were part of us, they became more human to us. They could and probably did have speech, so they could and probably did other “human” things too.

Joao Zilhao, a paleolithic archaeologist at the University of Bristol, also a flintknapper, spent years reconstructing the process of making Neanderthal tools, what were once believed to be scraps of flint with sharp edges. He proved, among other things, that obtaining these “scraps” involved a complex process of very specific flintknapping strokes. This skill was far from the previously perceived unintelligent caveman, and furthermore, it likely required language instruction.

Another early technology, in use 250,000 years ago, involved a complex process to create a type of pitch to secure spearheads to spear shafts.

The Neanderthals began evolving before our very eyes.

Michael Walker, a professor of Zoology and Physical Anthropology at the University of Murcia, discovered indeed that Neanderthals likely did have ceremony and ritual, the hallmarks of religion, which involved the ability for complex thought and reasoning. Shells and bones, drilled or punched to be worn as ornaments have been identified, along with pigments believed to have been used as body paints.

We still do this today; look at the fans at any football game.

In addition, it appears that a burial may have been found in Spain, along with two panther paws. Michael mentioned them as a trophy, I thought more in terms of spiritual significance.

John Hawks discussed what the Neanderthal parts of our genome have done for humans. Many of the Neanderthal genes have no known purpose, but there is one significant exception. It’s somehow ironic that we may indeed have survived as a species in a foreign environment, colder Europe, thanks to inbreeding with the Neanderthals. Humans carry a very specific Neanderthal piece of DNA that is essential to the immune system’s ability to attack viruses and bacteria, the HLA or Human Leukocyte Antigen. Because individuals who carried HLA might well have survived when others didn’t, the HLA became naturally selected for, and therefore present in the descendant population, us, “saving lives to this day.’

As John said, we are just beginning to understand our debt to the Neanderthals. Not only that, we also are rethinking what extinction really meant. We have presumed that Neanderthals went extinct, or died out, because we could no longer find their remains in fossil evidence. Perhaps, as Mark Twain said “reports of my demise have been greatly exaggerated.”

Is the reason we could no longer find separate Neanderthals because they interbred and assimilated into the Homo Sapiens population who were probably the dominant species, outnumbering them ten to one? Was their extinction not a dying out at all, but an absorption? Perhaps that was simply the natural progression of things, or maybe they realized that their recipe for success, for long-term survival, was not to remain separate, but to become part of the larger population. In fact they do survive today in just that way, as a part of all of us outside of Africa.

Decoding Neanderthals is available to watch online at http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html

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Security and Privacy

Posted on January 9, 2013 by Roberta Estes

Did you really mean to say that you didn’t want to see your matches???? Have you accidentally done this?

At Family Tree DNA, you may notice that some of your matches, especially at the 12 marker or HVR1 levels, particularly if you have a lot of matches, may be marked “private” and greyed out, with no contact or other information. What does this mean and why would someone take a DNA test for genealogy, then mark their results as private?

Those are great questions and there are several answers. First, some people don’t realize that the selection they make in their “Account Settings” tab affects how their results are displayed, or not displayed, to their matches. They also don’t realize that it can suppress those matches for them as well.

You can see that for both Y-line and mitochondrial DNA, you can disable matches and e-mail notification. This means that you won’t receive match notifications for 12 marker matches, if you disable that level, nor will any of your information be shown to your matches. Furthermore, you won’t see those matches either. They will not appear on your match list. In fact, you won’t have a match list for the level you disable.

Some people only test at 12 markers, for example, so if you disable 12 marker matches, be absolutely sure that you really don’t want to be notified if you match someone with the same surname at 12 markers that did not test at a higher level. If you disable these notifications and matches, this is what your matches will see:

As you can see, your match will be able to see your surname only, how many mutations difference there is between you and them, no “most distant ancestor,” no haplogroup information and more importantly, no way to contact you. This is typically not what people mean to do, but this is the result.

In one case, a man was distraught because he had no matches, but had disabled matches at all levels of testing, so of course, none showed. He had matches, he just couldn’t see them and he didn’t notice the message that said he had disabled matching at that level. He thought that the only function he had disabled was the e-mail match messages, but that wasn’t the case. It’s all or nothing at each level. You can’t disable the messages without disabling the matches too.

There are other security options you can select as well. Some, are found under “Personal Profile” settings, others under “Account Settings,” and finally, a beneficiary designation in case something should happen to you. This is the only person that Family Tree DNA will allow to access your account. Please take a little time to click through these options so that you personalize your experience in such a way that best fits your testing goals.

Aside from your matches and project displays, the only other people who can see your information are the volunteer group administrators of the groups you join. You can control, by your selections, how much they can view. There are several items they can view, but not change, such as your e-mail address, for example. Group administrators have a set of guidelines that they must follow.

In the case of mitochondrial DNA, if you have tested at the full sequence level, the project administrators of haplogroup projects cannot see your full sequence level which is necessary to categorize your results into subgroups unless you specifically change your setting to allow them to view your mitochondrial full sequence results. This is found under “Account Settings” then “Results Display Settings.” Change the answer to yes for the appropriate projects.

The key, of course, to privacy and security is to have as much privacy as you wish, without actually hurting your chances of making genealogical connections, and contacts, which is, after all, the entire reason that you tested in the first place.

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Rethinking “Out of Africa”

Posted on January 6, 2013 by Roberta Estes

Neanderthals separated from humans, Homo Sapiens, about 400,000 years ago, but then, in Eurasia, the two species, who were believed to be unable to interbreed, came back together again, and did. We know this because every population in the world, except for Africa, carries both Neanderthal and/or Denisovan DNA, including aboriginal people from Australia. This information, newly discovered in the past year or so, raises a lot of thorny questions.

Neaderthals have been grouped as a separate species from Homo Sapiens, modern man, and members of two different species, by definition, are not supposed to be able to interbreed and have fertile offspring. So are Neanderthals and Homo Sapiens really the same species?

Neanderthals, as a separate species became physically extinct about 30,000 years ago, at least we can no longer find fossil records of them. But did they really, or did they simply assimilate and genetically, and physically, become the new us?

And if that wasn’t enough, there are the Denisovans and they too interbred with Homo Sapiens. In fact, Denisovan and Neanderthal bones have been discovered together, and Denisovans are believed to be an offshoot of Neanderthals. And what about the Hobbits of Flores Island? Where and how do they fit in?

And there are probably more surprises that await us, because there are more fossilized bones that we have not been able to obtain DNA from that don’t match any of the groups mentioned above. In the future, discoveries of fossilized bones will likely be made that from which we will be able to recover DNA, as the recovery techniques improve.

But what does all of this mean? How does it affect what we knew, or thought we knew, about the “Out of Africa” theory that says all contemporary man evolved in African, left Africa and subsequently killed off or replaced all of the other species, such as Neanderthals? If that’s not true, what is true? Did we evolve out of African several separate times, getting reacquainted some several 10s (or hundreds) of thousands of years later on another continent?

All of this unexpected mixture causes lots of questions, and today, we don’t have many answers. But maybe the biggest question is that of what, exactly, is a modern human?

CHRISTOPHER STRINGER is one of the world’s foremost paleoanthropologists. He is a founder and most powerful advocate of the leading theory concerning our evolution: Recent African Origin or “Out of Africa”. He has worked at The Natural History Museum, London since 1973, is a Fellow of the Royal Society, and currently leads the large and successful Ancient Human Occupation of Britain project (AHOB). His most recent book is The Origin of Our Species (titled Lone Survivors in the US).

Here’s what Christopher has to say:

“At the moment, I’m looking again at the whole question of a recent African origin for modern humans—the leading idea over the last 20 years. This argues that we had a recent African origin, that we came out of Africa, and that we replaced all of the other human forms that were outside of Africa. But we’re having to re-evaluate that now because genetic data suggest that the modern humans who came out of Africa about 60,000 years ago probably interbred with Neanderthals, first of all, and then some of them later on interbred with another group of people called the Denisovans, over in south eastern Asia.”

To read more of Christopher’s thoughts, click here. They are very interesting and enlightening indeed, from a man who has been in this field since the beginning, a mere 40 years ago.

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Autosomal Testing Comparison

Posted on January 3, 2013 by Roberta Estes

Currently, there are four different entities, 3 corporations and a nonprofit, that test autosomal DNA using the newest technology, the Illumina chip. There are different features and functions of each one.

I am describing them below in broad terms, and including links to articles where I and others have discussed their autosomal products.

23andMe – The first company to enter the chip based world of genetic processing by introducing a health traits and genealogy product that provided genealogists with cousin matches and percentages of ethnicity. They provide raw data files that can be downloaded and then uploaded to Family Tree DNA and GedMatch. In December 2012, after a significant capital investment, they dropped the price of their autosomal product to $99 with a goal to reach one million customers as a result. They currently have about 180,000.

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

Family Tree DNA – Clearly the leader in genetic genealogy testing, they offer the Family Finder test using the same chip based platform as 23andMe. Customers of 23andMe can upload their raw data file to Family Tree DNA for $89, effectively allowing them to fish in both pools for cousin matches and to obtain the ethnicity predictions from both companies. Family Tree DNA provides raw data files and numerous tools to assist the genealogist, including integrated searching of autosomal, Yline and mitochondrial matches. The Family Tree DNA Family Finder product is currently $199. Family Tree DNA customers are generally interested in genealogy, while 23andMe clients are often only interested in the health traits aspect of their test.

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

Ancestry – Ancestry introduced their AncestryDNA test in early 2012 by initially giving away tests, then selling tests for the reduced price of $99 to build their autosomal data base. Today, the tests range from $129 to $199 depending on whether or not you have an Ancestry.com subscription. Continued, complete access hinges upon maintaining a subscription at some level. Their test reports cousin matches and percentages of ethnicity. If your matches have attached their genealogy, and it’s not marked private, you can see if you share common ancestors by viewing their tree. Ancestry’s ethnicity predictions have significant issues, they provide no autosomal tools, such as a chromosome browser for cousin matching and they do not provide your raw data to download, although they have said they will provide that sometime in 2013.

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://www.isogg.org/wiki/AncestryDNA

National Geographic Genographic 2.0 – The latest autosomal test to be released is focused somewhat differently that the other tests. This test looks more at deep ancestry using the discoveries made within the Genographic project over the past 6 years. This test provides the deepest clade testing for the Y chromosome available from any test at any company. It also provides ethnicity percentages based on many newly discovered SNPs not in use elsewhere. The price is $199.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

In addition, Debbie Kennett has added a wiki page about comparing autosomal testing companies in the ISOGG Wiki at:

http://www.isogg.org/wiki/Autosomal_DNA_testing_comparison_chart

Thanks Debbie for your efforts to help everyone!

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2012 Blog in Review

Posted on January 1, 2013 by Roberta Estes

I want to take this opportunity to thank everyone for following and reading my blog this year. I launched www.dna-explained.com in July, so this annual report is only for 6 months. The blog had an amazing 85,000 views from 137 countries in 6 months. Not bad at all. If you’d like to see more, like which posts were the most popular and who posted the most comments, the WordPress.com stats helper monkeys prepared a 2012 annual report for my blog.

Here’s an excerpt:

19,000 people fit into the new Barclays Center to see Jay-Z perform. This blog was viewed about 85,000 times in 2012. If it were a concert at the Barclays Center, it would take about 4 sold-out performances for that many people to see it.

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