Monthly Archives: November 2012

Gene by Gene Announces Landmark DNA DTC Full Genome Sequence

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Gene by Gene, the parent company of Family Tree DNA, formally announced it’s direct to consumer (DTC) offering of full sequence human genome testing.

Testing will be performed in their state of the art research center, shown above, in Houston, Texas.  You can read more about Gene by Gene and their 4 divisions, DNA DTC, Family Tree DNA, DNA Traits and DNA Findings at www.genebygene.com.

Family Tree DNA was established 12 years ago to service the Genetic Genealogy market space, which didn’t yet exist at that time.  Family Tree DNA was an innovator in that field, and has brought the same innovative and entrepreneurial spirit to their other companies established since.

This new offering, the first of it’s kind, reaches out to researchers and others in need of “research only” next generation full genomic sequencing.

“Given the explosive demand for accurate, timely, and large-scale next
generation sequencing, we’re pleased to make our Genomics Research Center
available to investigators exploring the cutting edge of research to pioneer and
enhance treatment of disease, enhance quality of life, break new ground in
genealogical inquiry and otherwise advance the science of genomics,” Gene By
Gene President Bennett Greenspan said. “The launch of DNA DTC is the perfect
complement to our other divisions, through which we make genetic testing
advances every day in the fields of ancestry, health and relationship testing.”

Using the Illumina platform, DNA DTC will offer both full genomic sequence and full exome testing, adding these two items to their menu of over 200 types of DNA tests performed.  Gene by Gene’s lab has already processed more than 5 million discrete DNA tests for more than 700,000 individual clients.  Their institutional clients include the National Geographic Society’s Genographic project and other clients such as France’s Institut Pasteur, Israel’s Rabin Medical Center and the University of Utah.

By bringing full genomic sequencing to the public, they have broken the sound barrier in personal genetics, the veritable X-factor.  The full humane genome was first sequenced in 2003 at a cost of about 3 billion dollars.

A full genome sequence still cost about 3 million in 2007, but DNA DTC is offering it today for an amazing $5495.

While consumers will be able to order the full genome (or exome) test, if they want, it comes with no tools, as it is focused at the research community who would be expected to have their own analytical tools.  However, genetic genealogists being who and what they are, I don’t expect the research market will outweigh the consumer market for long, especially when the price threshold reaches about $1000.  For years the “$1000 genome” has been bantered about, and I expect with the next generation of technology, we may see it sooner than later.  The fact that it has dropped from 3 million to $5495 in 5 years is astounding.

Aside from DNA DTC and Family Tree DNA, the other two  Gene by Gene divisions are DNA Traits (www.dnatraits.com)  which provides CLIA Regulated Diagnostic tests for genetic diseases and DNA Findings (www.dnafindings.com)  which provides AABB certified paternity and relationship testing.

Way to go Max and Bennett and everyone at Gene by Gene!  Congratulations!

So, who is going to be the first in the genetic genealogy community to order this test???

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Disclosure

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

Thank you so much.

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Averages, TIP Calculator and One Size Fits All

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Averages.  We all know what that means, conceptually.  You add a group of numbers together and divide by the total of the numbers you added together.  For example, 9 number locations that have a value of 10 each totals 90.  If you divide 90 by the number of number locations, 9, you get 10 as the average.  Of course, that’s a very simple example, but the concept applies no matter how many number locations or how big or small the numbers.

Often, we don’t grasp a good working knowledge of how to apply that math concept as it relates to our DNA results.

What I’m referring to here is the TIP calculator provided by Family Tree DNA, but this concept applies equally as well to any TMRCA (Time to Most Recent Common Ancestor) calculation, regardless of who is calculating it.  The underpinnings, are, by necessity, the same.

At Family Tree DNA, the TIP calculator, the little orange button above, is available to you to compare Y-line results to matches and it will give you a rough idea of how long ago you can expect to have a common ancestor.

One of the most common questions I receive reads something like this:

“The TIP calculator says that we should be related at 99% within 12 generations, but my genealogy shows that it should be 8 generations.  What is wrong?”

Or something like this:  “The TIP calculator says we are related, but I have no idea how to interpret any of these numbers.”

The answer is that nothing is wrong and these are ranges of possibilities, based on average mutation rates of individual markers.  Having said that, we know absolutely that mutations are random events.  You can see this demonstrated in the Estes project where Abraham Estes (born 1647) who had 12 sons produced one line who has several people with no mutations as compared to Abraham, and another descendant whose line from another son has 8 mutations in the same  timeframe.  Now it’s obvious that both of these are on the outer bands of the spectrum, and the average is 4, which really is not reflective of either of these lines, but is dead center accurate for two of Abraham’s other sons’ lines.

Recently, I was working with the Nemaha Half-Breed Allottee, a list of names of mixed European/Native American individuals who received individual land allotments in 1860 in Nebraska from the government as a result of an 1830 treaty.  When analyzing the 365 people who had European names, I realized that this is the perfect example of averages and how they do, and don’t, work.  So let’s visit the Nemaha for a minute.

There are 122 different surnames represented, and the average then is that 2.99 people should carry each surname.  365 divided by 122=2.99.  So let’s say 3 people, as it’s very close.

In reality, here’s how the surname distribution breaks down.

Number of People Carrying Surname Number of Surnames
1 54
2 18
3 10
4 12
5 8
6 6
7 4
8 3
9 2
10 0
11 1
12 0
13 0
14 0
15 1
16 0
17 0
18 1

You can see that only 10 surnames actually have 3 people who carry them, for a total of 30 people, or about 12%.  For the remainder, 90 surnames have fewer than 3 people, for a total of 25%, and 63% of the surnames have more than 3 people who carry that surname.

Stated a little differently, this average is accurate for 12% of the people, and inaccurate for 88%. It is close for many.  About 23% fall directly on either side, meaning 2 people or 4 people carry that surname.

So what is the message here?  Averaging tools, TIP included, do the best with what they have, which includes results at both ends of the spectrum.  In this case, it includes the 54 surnames with only one person each, and the 3 surnames who each have over 10 people each, 11, 15 and 18, totaling 44 people.  If these people were trying to make sense of these averages, 3 people per surname, these numbers would be totally irrelevant to them.

So the lesson here is to use these tools as a guideline, and nothing more. You could be in the middle and these tools could apply to your family exactly, or you could be in the family who has 18 people carrying one surname instead of the “average” of 3.

This reminds me very much of the ‘one size fits all” nightshirt that got passed around for some years at home when I was a kid.  “One size fits all” really meant “fits no one” and translated into “no one was happy.”  Of course, if you don’t understand the meaning of “one size fits all” and averages, you might be happy and think you have an answer that you don’t.

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Disclosure

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

Thank you so much.

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Bigfoot is Real???

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If a new paper yet to be published and currently undergoing peer review is valid, it appears that Bigfoot, also known as Sasquatch, is indeed, real and a hominid mix, meaning that Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.

Following five years of research, a team of scientists has sequenced several Sasquatch genomes.  Results show that Bigfoot is a mixture between a human female, about 15,000 years ago, and a male, a previously unknown hominin related to Homo sapiens and other primate species.  Wow.  What a discovery!

This begs several questions.  Is all of the mitochondrial DNA the same, inferring a single maternal ancestor?  They have sequenced 20 different mitochondrial samples.  Given that the mitochondrial DNA is reportedly identical to that of modern humans, we can presume, one would think, that the mitochondrial DNA is Native American, so a member of haplogroup A, B, C, D or X.  Hopefully the forthcoming paper will be more specific.

The scientists fully sequenced three Bigfoot nuclear DNA samples and the results are stunning.  The male is not a contemporary human and they have eliminated both Neanderthal and Denisovian males as possible founders.

Dr. Melba Ketchum, one of the paper’s authors, states that, “The male progenitor that contributed the unknown sequence to this hybrid is unique as its DNA is more distantly removed from humans than other recently discovered hominins like the Denisovan individual. Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA. Genetically, the Sasquatch are a human hybrid with unambiguously modern human maternal ancestry.”

There are subtle and not so subtle messages buried here as well.  Obviously, for the team to acquire 20 samples to process, there has to be a population of these creatures living in North America.  Of course, everyone has heard of Sasquatch and seen photos and videos, but until this, nothing has been terribly convincing.  There has been no smoking gun.  If this research is valid and passes peer review, it not only confirms that Sasquatch is real, it vindicates many of the people who have had “sightings” over the years.  It becomes the smoking gun.  But as with much science, it raises more  questions than it answers.

For example, are there any non-admixed Sasquatch progenitors left, meaning the males that founded the Sasquatch line with the human female?  How would we tell the difference?  This of course implies that some sort of pre-hominid species existed on this continent before Native Americans arrived from Asia and had existed separate from hominids for a long time.  Is there other evidence of this creature in North America?

Where were these samples collected?  Are the Sasquatch samples studied from across North America or from one region only?  Are all of the Sasquatch related to each other, and how closely?  In other words, were there multiple founder events?  Was the Y-line DNA sequenced and what does it tell us? Were there multiple male founders or did the Sasquatch line arise from a “one time” event?  Do any of the Native tribes in these regions have oral history regarding either Sasquatch or interbreeding with Sasquatch type creatures?

Are there “Sasquatch” in other parts of the world as well?  The Yeti or Abominal Snowman of Nepal seems to be similar, and a scalp purportedly exists from that creature.  If DNA samples outside of North American have been sequenced, are they related to the North American Sasquatch or did they arise separately, assuming they too exist?

And finally, do these creatures have “rights” and are they the same “rights” as humans?  Given that they carry human mitochondrial DNA, and many Native tribes are maternally based, would they be considered “Native American?”  How do we, as humans, deal with this?  Are we learning that humanity is really a continuum?

Indeed, I look forward to seeing this published paper and I hope it is legitimate and not pseudo-science of some sort.  The mere fact that the scientiests have opted for academic publication versus a book or TV documentary certainly alludes to the fact that it is legitimate research.  You can read more about this announcment at these links.  I’ll let you know when the paper becomes available.

http://www.prweb.com/releases/prweb2012/11/prweb10166775.htm

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Disclosure

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

Thank you so much.

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Facebook Link

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We’re on Facebook now at www.facebook.com/DNAexplain.

I’m hopeful that reaching out through Facebook will attract some new people to genealogy.

You can also visit the Native Heritage Project Facebook page at www.facebook.com/NativeHeritageProject.

Facebook requires 25 “likes” before they will issue a direct link, so thank to everyone who “liked” these pages.

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Disclosure

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

Thank you so much.

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Thanksgiving, Spilling the Beans and Reaching Out

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Everyone in the US and Canada celebrates the holiday of Thanksgiving, although on different dates.  Traditionally, as all children learn in grade school, in the US this holiday celebrates the Pilgrims being helped by the Indians to survive and a feast they jointly held in Plymouth, Massachusetts in 1621.  There is a lot of debate about that event, whether it happened or not, but I think it’s actually irrelevant.  More important is what Thanksgiving has morphed into, what it is today.

It’s a family day, often more so than Christmas, especially in the northern climates.  In my family, and many others, at Thanksgiving you see more extended family than at Christmas, where Christmas is more immediate family.  In the North, travel has become difficult or iffy at best by the end of December, but the end of November generally is still safe.  Now that I’ve said that of course we’ll have a blizzard.

Thanksgiving is the time when my Aunt Verma inadvertently spilled the beans on the “skeleton in the closet” at the dinner table.  You could have heard a pin drop.  Well, before the gasps.

Thanksgiving is the time to ask about those ancestors or family members, even if you think you know the answer.  Because, you may not.  Often, it’s for lack of asking the question or introducing the subject that you don’t learn those stories.

Probably the number one regret of genealogists is that they never reached out when they could.

Today, reaching out isn’t just across the dinner table or while doing dishes, a favorite time to pick the brains of your relatives, it’s about reaching out using new technology.

If you could make contact with someone who has photos of your great-grandmother, wouldn’t you want to do that?  How about someone who has a copy of the family Bible owned by your Revolutionary War ancestor?  Maybe a tin type and journal of your Civil War ancestor.  Who has those today?  Maybe you don’t even know they exist.

If they aren’t in your family, it will take a new form of reaching out to find them.  I’ve celebrated Thanksgiving this week by reaching out to the younger generation.  I don’t mean to stereotype, but let’s face it, you’ll never meet these people on Rootsweb. Where do you find them?  Facebook, that’s where.  Want to find out what pictures their grandma has in the attic?  Well, you have to make contact with them so they will ask their grandma, or tell their grandma to check out your Facebook page.  And yes, more and more, grandma is using Facebook.

Now stop groaning.  I can hear you from here!  I know, I groaned too.  But I did it anyway.  We need to interest young people.  They can DNA test and someday, maybe one  of them will be who you pass the proverbial family torch to.  If you’re like me, it’s not one of your kids, no matter how badly you want it to be. I think I burned them out in courthouses at the copy machine when they were kids.  My bad.

This is not difficult.  If you are not on Facebook, summon up your courage and go to www.facebook.com and sign up.  If you are already on Facebook, skip down 2 or 3 paragraphs to the section on setting up pages and groups.

If you’re really uncertain, you can google about how to get started using Facebook, but it’s actually really easy and intuitive.  You want to be on Facebook because your kids and grandkids are there and you’re going to lose touch with them and how they communicate if you don’t join.  Just do it.

Once you join, just type names into the top bar to look for your friends and family, where it says “search for people, places and things.”  Then send them a friend request.  You’ll see the “Friend” button, just click on it.  This isn’t difficult, you just need to get used to it.  Here are the results when I searched for Jim.

Once you are a friend, you will see what they put on their timeline and their status posts.  These include photos and such.  I see new photos of my grandkids just about every day.  Your news feed aggregates all of the people and projects that you are following.

Of course, you’ll want to post something, eventually, yourself.  The best way to get a conversation started is to ask questions, just like at Thanksgiving.

On Facebook, you do that by typing something in the field that says “What’s on  your mind?”  Facebook is one big informal conversation.

After you get at least a little comfortable with Facebook and your News Feed, you’ll want to set up either a project group or a page.

Here’s what I did.  And by the way, I am not “comfortable” with Facebook but I just did this anyway.  The only way to get comfortable is to work with the software.

I set up two pages and I’m going to set up project groups.  My new pages are ”DNAexplain” and “Native Heritage Project.”  You will have to type those names (minus the quotes) in the search bar at the top of the page at Facebook to find them.  That’s how Facebook works.  Then you click on the image and then click on “like” to connect yourself to them.  So please, do me a favor and “like” both of them.  Facebook requires 25 likes for a new group or page to be recognized as legitimate.

Pages are public.  They are generally for entities, meaning businesses and organizations.  You might want to put a family association there.  ISOGG (International Society of Genetic Genealogists) is there, for example, as is the Lost Colony Research Group.  Everything posted on these pages is available for everyone to see.

Groups can be set up to be entirely public, private or secret, meaning by invitation only.   Facebook has a help page that discusses these differences.  Groups are generally for more personal discussions.  For example, you might choose to form a “by invitation only” intimate family group.  You might choose to set up a Page to advertise your family association and to attract people who are interested in addition to a group for more private discussions.  Remember, the whole point of this exercise it to reach out, so the more public your presence, the better chance you’ll have of attracting interested people.  Be aware however, that these pages are not text searchable and do not have archives like Yahoo Groups or Rootsweb.  But then again, this is for reaching out, not archiving.

To create a page, which is what I recommend for surname projects, scroll all the way down to the bottom of your Facebook page and click where it says, “create a page.”  From there on, Facebook guides you.

To create a group, on the left hand banner, Facebook will show you any groups you are a member of, and at the bottom of the list, it says “create groups.”  Click there and again, Facebook guides you through the rest.

Here is my commitment.  If a Facebook page or group does not exist for each one of my DNA surname or other pet projects, I’ll create one by year end.   Yes, this year, 2012.  There is nothing like the present moment.  I’m reaching out to the next generation.  After all, the old folks are gone now, so I need new information targets:)  Who knows what I’ll find, but if I don’t reach out and try, I’ll find absolutely nothing!  I want more family information to be thankful for by next Thanksgiving!!!  I want to honor those who have gone before by preserving the information about their life.  That is what heritage is.

How about you?  How can you reach out and what do you hope to find?

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Disclosure

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

Thank you so much.

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Otzi Was A Brown Eyed, Left Handed Farmer

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Otzi, the mummified man found in 1991 in the Italian alps has provided a huge amount of information to science for one man, especially one who has been dead for more than 5300 years.  Otzi was killed by an arrow to the back, probably bleeding to death, although maybe not right away.  Based on blood analysis, he may have had companions with him who were also injured.

He was an old man at the time, 45.  Most didn’t survive that long.  Surrounding the mummy was his quiver, copper ax, interpreted as a status symbol, knife and other belongings, which were nearly missed when the body was recovered.  He was dressed in hides from multiple species of animals, sported a bear-skin hat and a woven grass cloak.  He had eaten unleavened bread, fruit and deer meat only a couple of hours before his death.  He had also taken herbal medicine suggesting that perhaps his meal didn’t set too well with him.  He had tattoos which may have been related to a healing ritual since they were on or near body parts which showed wear, knees and ankles, which were probably painful to him.  Hair on his clothes tells us he herded cows, sheep and goats.  He was diminutive compared to today’s people at 5’3″ and 110 pounds.

If you think about it, Europe didn’t have a large population then.  Otzi may be an ancestor of many of us. But then again, maybe not, because genetic analysis tells us that he may have suffered from reduced fertility.  But we could easily still be related in some way, as the population was fairly small and the large population of Europe grew from the founders.  Otzi and his family clearly were founders of the European population.

When Otzi was first discovered, the National Geographic Society did a facial reconstruction of Otzi, depicting him as a robust, healthy relatively young-looking man.  More recent cranial imaging capabilities combined with genetic analysis and other fields of research have shown us that indeed, he wasn’t quite so healthy.  Robust Otzi is shown below.  Perhaps this resembled a younger Otzi.

Otzi, at his death, looked like the more recent reconstruction at the top of this blog.

Most recently, last week, at the American Society of Human Genetics meeting, scientists reported that Otzi was a farmer.  While this may not sound remarkable, it is, just the fact that they can determine this, and what his DNA and other similar DNA reveals about migration and settlement patterns.  It turns out that Otzi most closely resembles people from Sardinia, a large island off the west coast of Italy, not the hunter gatherers in the Alps where he was found.

Isotope analysis of his teeth tell us that Otzi did not grow up in the Alps where he died (red balloon), but south about 50 km near the village of Feldthurns (blue balloon).  But he didn’t grow up in Sardinia (yellow balloon), so that connection is further back in time.

In addition, his DNA also resembled the DNA of the farmers of Bulgaria and Sweden, but again, not the hunter-gatherer population.  Not only does this tell us that Otzi was a farmer, but it tells us how and where the farming population settled, and who they were.

http://www.huffingtonpost.com/2012/11/09/otzi-the-icemans-genes-central-europe_n_2099809.html

More interesting info here:

http://www.livescience.com/24666-otzi-iceman-mummy-life-death.html

Otzi, it appears, was left handed, was probably lactose intolerant and had Lyme disease, making him the earliest known case.  He was also more closely related to Neanderthals than Europeans today.  Today’s Europeans uniformly carry roughly between 2% and 4% Neanderthal ancestry.

Otzi’s mitochondrial DNA line may well be extinct.  If not extinct, then no others have yet been discovered.  He is a subgroup of the K1 lineage, named K1o (that is O for Otzi, not a zero.) His Y-line DNA is haplogroup G2a2b.

http://en.wikipedia.org/wiki/%C3%96tzi

National Geographic has funded significant research on Otzi and has provided additional information and reconstruction photos here:

http://news.nationalgeographic.com/news/2011/02/pictures/110225-otzi-iceman-new-face-science-mummy-oetzi/#/iceman-oetzi-otzi-reconstructed-new_32525_600x450.jpg

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Smith and Jones

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I just love a good mystery – don’t you?  To be good, it has to have some romance of course, a villain, an interesting plot with a twist, a couple red herrings and an unexpected outcome.  Personally, I like happy endings too – I just don’t want them to be too predictable.

Well, welcome to the Smith and Jones mystery.  And no, those names have not been changed to protect anybody.  They are quite real.

When I receive an order for a Personalized DNA Report, I send the client a short questionnaire to complete.  They have the opportunity to tell me why they tested their DNA, their goals, ask any specific questions, and to provide their genealogy so I have something to work with.  In addition, I customize the cover of their report with their family photos if they so desire.

When Mr. Jones returned his questionnaire, in answer to the questions about why he tested, he gave this response:

“My paternal grandfather was the son of an unwed mother.  So my paternal line doesn’t go back very far.  I really hope the DNA can help me find out who my paternal ancestors were.  So far, the indicators are they are Smiths from Bladen County, North Carolina.”

I cringed when I saw this.  Here’s a Jones who thinks he’s a Smith.  How am I ever going to straighten this out with these extremely common surnames?

In the genealogy section, he gave me a little more information.

His paternal grandfather, William Hobson Jones, below, was born in 1902 in Bladenboro, NC to unwed mother Emma Elizabeth Jones.

Those are all the facts I had to work with, other than his DNA results themselves, of course.

To begin, I checked the haplogroup hoping for something exotic that will serve as a differentiator.  R1b1a2-U106 – so no luck there.  However, when I prepared his marker frequency chart, he did have 3 very rare marker values.  Great.  Now we are getting someplace.

I divide marker values into three categories.  Very rare marker values occur in 6% or less of the haplogroup population, rare markers in less than 25%, and the balance are just unremarkable.  It’s the rare and very rare markers that give me something to work with, because they form a very specific genetic family surname “fingerprint.”  In this case, Mr. Jones’ marker 458 carried a value of 15 which occurs in 2% of the haplogroup R1b population, 576 with a value of 16 which occurs 6% of the time and 444 with 14 that occurs only 1% of the time.  These are the litmus paper tests of a real match.  In addition to these very rare marker values, he had 9 additional rare markers that can be used to refine the match criteria.  We’re in good shape for matching.

Mr. Jones had tested at 67 markers, but he had no matches at that level.  However, at 37 markers, he had 3 matches, and they were all to Smith men, none of whom had tested at 67 markers.  Now there’s a good indicator that he was right, that his genetic line is indeed Smith.  His exact match listed his oldest ancestor as being from Germany, but gave no name.  His one mutation match showed his oldest ancestor as Jeremiah Smith born 1795 NC and his 2 mutation match showed no information at all.  None of these matches had uploaded GEDCOM files.  Disappointing. With more information, this would have been much easier, but it wouldn’t be a good mystery without some glitches!

At 25 markers, he only had 7 matches, but at 12 markers, he had a whopping 536.  Obviously his first panel was too vanilla to be very useful, but of course, I did check for additional Smith men.  None to be found.  Just the 3, but those 3 are all very solid.

Sometimes, at this point, projects are a saving grace.  Project administrators are amazing people and put forth a lot of work, sort families, collect genealogies, etc.  The Smith DNA project does not have a public website at Family Tree DNA, but they do have a private site.

http://www.smithsworldwide.org/wwtestcomparisongrp.asp?kitno=’231289‘

At their site, I found a group of Smiths who match Mr. Jones, descended from one Moses Jones of Bladen County.  Huh?  This stopped me in my tracks for a minute, until I realized that this is my client’s kit number, and the Jones family, meaning Emma’s father’s line, indeed, does go back to a Moses Jones.  This would be irrelevant were it not incorrect, because Moses Jones’ male Y-line does not match the Smiths.  The only Jones line that matches a Smith is the one descended from his daughter Emma who had a child outside of wedlock, apparently by a Smith.

By this time, I was chomping at the bit to work with the genealogy records.  William Hobson Jones was born in 1902, so I was hopeful I could find his mother, Emma Jones, in the 1900 census.  The first rule in begetting is that the begetters must have physical proximity to each other – and the traveling salesman is the exception, not the rule.

Sure enough, in the 1900 census, there was Emma, right with her parents Nathan and Elizabeth Jones.  Emma was much older than I had expected, age 36.  She would have been considered a spinster in that time and place, and was probably considered a burden to her family.  Having a child would not have improved that situation any.

However, we have hit the proverbial jackpot here.  Take a closer look…..at the next door neighbor.

Claudius Smith is the neighbor….but wait….with his wife Glenora Smith.  Ok, let’s see if any of their sons are old enough to be the father of Emma’s child.  Nope, the oldest son is only 13, but Claudius himself is 38, just 2 years older than Emma.  Hmmm…..looks like maybe Claudius is the father, or at least he’s our best candidate right now.  Now Claudius might not be the father, but I’d wager that it is someone in his family, like a brother or uncle perhaps, if it is not him.  This Smith family is the best candidate due to the old begetters proximity rule.

This also might explain why Emma didn’t marry the father.  I wonder if she ever told anyone the identity of the father.  The family today certainly didn’t know.

Simple morbid curiosity got the best of me at this point.  I just had to look in the 1910 census to see if Claudius Smith and the Jones family were still neighbors. Was there a feud?  Did someone move?  Imagine my surprise to see Claudius married to Emma who had borne 4 children by this point.  What happened to Glenora?  And why did my client not tell me about this?  Surely he must have known.  Looking closer, this Emma is all of age 28 and her oldest child is 4….and flipping the census page, Emma Jones, along with her son Willie, age 6, indeed are still living next door, now in her brother’s household.  It seems that perhaps Claudius liked woman named Emma.  Maybe he was a widower when Emma Jones became pregnant.

I wondered if I could connect Claudius Smith with the Jeremiah Smith born in 1795 in NC shown as the oldest ancestor of one of Mr. Jones’ Smith matches.  I checked various sources, and Ancestry had a tree that pushed this particular Smith family back another generation, but not to Jeremiah.  This could probably be done, but not with the time alloted for genealogy in a DNA report.  I needed to look for other tools.  http://trees.ancestry.com/owt/person.aspx?pid=19139247

Chess Smith is shown as Claudius’s father and Elizabeth Ann Blackburn as his mother.  And yes, I’m fully aware that online trees should not be taken at face value, but they are good starting points and cannot be presumed to be incorrect either, especially if they confirm a suspected fact.  In this case, that didn’t happen – no Jeremiah.

Fortunately, Mr. Jones had also taken a Family Finder test.  He of course had Smith matches.  Who doesn’t?  But he also had three Blackburn matches.  The addition of this single female line surname gave me something concrete to look for.  I suggested that Mr. Jones contact his Blackburn autosomal matches to see if they can connect to the Chess Smith line.

So, at the end of the day that began with some level of apprehension that I might not be able to help Mr. Jones identify his genetic paternal line, we had a great research plan in hand.

We had discovered that the neighbor’s name was Smith, and he was married with 11 children in 1900, which might just explain why Emma never married the father of her child.  Of course, there might be other reasons too, like the father wasn’t Claudius, but another Smith relative.  It looks very promising, using autosomal tools to find Chess Smith’s wife’s surname, Blackburn, that this is indeed the correct Smith family.

Mr. Jones has some genealogy homework to do on the Chess Smith line, and some contact homework to do with his Blackburn matches, but now he does indeed have the information along with the tools he needs to solve the Jones-Smith mystery and break down that brick wall!

And thank you, Mr. Jones for permission to share your exciting family story!

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The New Root – Haplogroup A00

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Now that things have calmed down a bit from the whirlwind of the Family Tree DNA Conference, I’d like to write in a little more comprehensive and sane manner about the revelation that we have a new root on the human tree.

I’m referring to the session given by Bonnie Schrack, Thomas Krahn and Michael Hammer titled “In Search of the Root: Discovery of a Highly Divergent Y Chromosome Lineage.”

Bonnie has posted her slides from the presentation as well as her speaking notes on her new haplogroup A webpage.  She contacted me with some corrections to my original Blog posting about that session at the conference as well as provided additional information.  Thank you Bonnie, not just for this info, but for your work with haplogroup A that has been such a key part of this momentous discovery.  This isn’t just a once-in-a-lifetime event, it’s a once-in-the-history-of-mankind event.  Watch the haplogroup A website for more information from Bonnie about this exciting discovery and project.

Understandably, Bonnie, Thomas and Michael are somewhat restricted in what they can say until such time as the resulting academic paper in the works is published.

We all know that male humans arise from a person we call Y-line Adam, just like we call the first woman Mitochondrial Eve.  Before a 2011 paper, it was believed that shortly after Adam, haplogroup A and B were formed about the same time and were brother haplogroups.  Fulvio Cruciani’s 2011 paper, “A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa” reorganized that tree and showed that indeed, haplogroup A formed from the root of all humanity with B forming from haplogroup A.

Cruciani showed his newly organized tree with haplogroup A1b, A1a and then A2, A3 and BT as brother haplogroups.  Cruciani did not use STR data, only SNP data in his study.

A second recent study, also in 2011, “Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages” by Chiara Batini et al, did include some STR marker that matched some of the haplogroup A samples.  Batini did not use SNP testing, so did not realize the potential of these STR samples.  These did not match the new A00 root, but other rare haplogroup A samples in subgroups.

The 7 marker STR samples that did match the new A00 sample were from a private database at the Center for Genetic Anthropology who very graciously worked with Michael Hammer and provided small amounts of those samples for further analysis.

In my conference blog posting, I asked how this discovery was previously missed, and Bonnie Schrack responded as follows:

“The reasons we had never heard about A00 before would be:

  • Very scanty research and sample collection in Africa, in proportion to the size and diversity of the population, compared to Europe and other more developed countries
  • Only recently has large-scale Y sequencing become practical and affordable; Cruciani’s 2011 paper was a breakthrough precisely because for the first time they were able to sequence a few samples on the scale of a WTY, resulting in a lot of new SNPs, and we’ve been able to make even more progress because we had a larger pool of (customer) samples from which I could cherry-pick the most divergent samples, and then our genetic genealogy/anthropology community made it possible to raise enough funds for us to sequence the most important three of them (after that point, Hammer and FTDNA found the other samples and funds).”

Before the WTY program, this type of analysis simply wasn’t being done.  This monumental discovery was a combination of citizen science, the haplogroup A project, an innovative scientific program, the WTY at Family Tree DNA, academic partnership, Michael Hammer’s lab at the University of Arizona and other institutions, along with that crucial public participation.  Without the public participation aspect, the rest would be a moot point.

Haplogroup A research at Family Tree DNA discovered not only one, but two new branches of haplogroup A, one of which was actually a new base root that needed to be inserted before, upstream of, the current root.  The locations where these new branches/roots needed to be inserted required the renaming of the current branches, hence, the newly discovered branch A00 and Cruciani’s branch, formerly A1b, is now A0.

Thomas Krahn’s A00 discovery presentation slides are also available online.  You can tell he’s a scientist from the nature of his presentation.  You can see the actual process of discovery, in essence, what he saw as this new root was unearthed.  It’s fun to walk along with him, even if you don’t understand everything you see.

As part of this process, Thomas also sequenced the DNA of a chimp and a gorilla.  You can see the results at www.ysearch.org for the chimp at 6RCUU, the gorilla at 9ED3A and the new root, A00, at 6M5JA.  You can breathe easy, humans are far distant from chimps and gorillas, but maybe closer to Neanderthals or other archaic humans than we thought.

Update: As of 2019, Ysearch is no longer available.

At the end of Thomas’s presentation, he included the image of a tree with a new root and lots of interesting branches.

Zooming in on the branches, you can see all of the DNA sequencing paraphernalia, microplates, readouts and results.  Maybe there is a little artist buried someplace in Thomas amid those scientific genes!

This work was no small feat, and the significance is mind-boggling.  This new discovery pushed the date of Y-Adam back a whopping 67% in one fell swoop.  Cruciani’s birth age for haplogroup A1b was 140,000 years ago and A00, compared to Cruciani’s sample, falls at 237,000 years ago.

Dr. Michael Hammer at the University of Arizona reanalyzed the haplogroup A tree and root with the new information available, and his new ages are even more amazing.  Cruciani’s A1b/A0 sample is now at 200,000 years old and A00 is at 338,000, with a 98% confidence level.

These dates pre-date all human fossils, although there are some archaic fossils that have been found and dated after this time in neighboring Nigeria.  This new information provides us with glimpses through the keyhole of time into ancient human origins, and begs even more questions that will be answered in time, with more genetic and anthropology research.  We all descend from this common root, and we may all be more closely related to archaic man that we knew.

The A00 participant descends from a former slave family in South Carolina.  The closest matches are found in western Cameroon near the Gulf of Guinea, a prime location in the slave trade.

There appears to be about 500 years between the participant and the samples from Cameroon, an age that speaks to the beginning of the slave trade.

Having worked closely with Lenny Trujillo, the man whose WTY sample provided us with haplogroup-changing and defining information for haplogroup Q, and understanding what a moving experience this journey has been for Lenny, I wondered about how the family involved with this revolutionary discovery must feel.

As luck would have it, I have worked with this family in one of my projects as well, and they contacted me after seeing my blog about the conference.

I asked how they felt, how they were reacting to this history-changing event in which their family was the keystone.  I have extracted pieces from e-mails back and forth, and with the families permission, am sharing what they had to say.  Clearly, without them and their active and supportive participation, this discovery would not have been made.  We all owe them a debt of gratitude.

“I have a B.S. in Mathematics. I love science and learning. I recently retired, but I spent a lot of that time working with research scientists on cutting edge technology and methods so it is very exciting to me to be a part of such a scientific discovery. My family would say I was the right one chosen.  This is the family line I know the most about so I am glad it was this part of my family.

I don’t yet have the formal results from Family Tree DNA concerning the Y-DNA sample they tested in the Walk Through the Y, I did know that the discovery was monumental from some preliminary results from Thomas.

I wanted to see the tie back to Africa, looks like GOD did exceedingly, abundantly more than I could ever ask or think. Just think of how long HE has preserved this Y-lineage just for such a time as this.”

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Family Tree DNA Conference 2012 – Nits and Grits

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First things first!  I want to thank Max and Bennett for graciously hosting the 8th Annual Genetic Genealogy Conference in Houston, Texas!  This is actually the 9th year, but a pesky hurricane interfered one year.  Max and Bennett are very generous with their time and resources and heavily subsidize this conference for us.  We’re registering in the photo above.

Georgia Kinney Bopp said it best.  At some point during this amazing conference, someone tweeted an earlier quote from a conversation between Ann Turner and Georgia:

“it’s hard to realize you’re living history while it happens…”

This was ever so true this weekend.  Even my husband (who is not genetic genealogy crazy) realized this.  I’m not sure everyone at the conference did, or realized the magnitude of what they were hearing, as we did have a lot of newbies.  Newbies are a good thing.  It means our obsessive hobby and this industry have staying power and there will be people to pass the torch to someday.

I’ve already covered the Native American focus meeting in an earlier blog.

For those of you who want the nitty gritty play by play as it happened at the conference, go to www.twitter.com and search for hashtag #ftdna2012.  If you want some help with Twitter, I blogged about that too.  Twitter is far from perfect, but it is near-realtime as things are happening.

As always, Family Tree DNA hosts a reception on Friday evening.  This helps break the ice and allows people to put faces with names.  So many of us “know” each other by our e-mail name and online presence alone.

We had a special guest this year too, Nina, a little puppy who was rescued by Rebekah Canada just a few days before the conference.  Nina behaved amazingly well and many of us enjoyed her company. 

Bennett opened the conference this year, and in the Clint Eastwood political tradition, spoke to his companion, the chair named Max.  The real Max, it turns out, was losing his voice, but that didn’t prevent him from chatting with us and answering questions from time to time.

While Bennett was very low key with this announcement, it was monumental.  He indicated that the parent company of Family Tree DNA has reorganized a bit.  It has changed its name to Gene by Gene and now has 4 divisions.  You can check this out at www.genebygene.com.  This isn’t the monumental part.

The new division, DNADTC’s new products are the amazing parts.  Through this new division, they are the first commercial company to offer a full genome sequence test.  The price, only $5495.  For somewhat less, $695, they are offering the exome, which are your 20,000 genes.  Whoever though it would be a genetic genealogy company who would bring this to the public.  Keep in mind that the human genome was only fully sequenced in 2003 at a cost of 3 billion dollars.

The amazing part is that a full genome sequence cost about 3 million in 2007 and the price will continue to fall.  While consumers will be able to order this, if they want, it comes with no tools, as it is focused at the research community who would be expected to have their own analytical tools.  However, genetic genealogists being who and what they are, I don’t expect the research market will outweigh the consumer market for long, especially when the price threshold reaches about $1000.

Bennett also said that he expects that National Geographic will, in 2013 sometime, decide to allow upgrades from Family Tree DNA clients for the Geno 2.0 product.  This will allow those people who cannot obtain a new sample to participate as well.  However, an unopened vial will be required.  No promises as to when, and the decision is not his to make.

The first session was Spencer Wells via Skype from Italy.  Spencer has just presented at two conferences within the week, one in San Francisco and one in Florence, Italy.  Fortunately, he was able to work us into his schedule and he didn’t even sound tired.

Of course, his topic was the Geno 2.0 test which is, of course, run on the new GenoChip.  The first results are in the final stages of testing, so we should see them shortly.  Sometime between the 19th and the end of the month.

This product comes with all new migration maps.  He showed one briefly, and I noticed that one of the two Native Y-lines are now showing different routes than before.  One across Siberia, which hasn’t changed, and one up the pacific rim.  Hmmm, can’t wait for that paper.

The new maps all include heat maps which show frequency by color.  The map below is a haplogroup Q heat map, but it is NOT from the Geno project.  I’m only using it as an example.

Spencer indicated that the sales of the 2.0 product rival those of the 1.0 product and that they have sold substantially more than 10K and substantially less than 100K kits so far.  In total, they have sold more than 470,000 kits in over 130 countries.  And that’s just the public participation part, not the indigenous samples.  They have collected over 75,000 indigenous samples from more than 100 populations resulting in 36 publications to date with another half dozen submitted but not yet accepted.  Academic publication is a very long process.

Nat Geo has given 62 legacy grants to indigenous communities that have participated totaling more than 1.7 million dollars.  That money comes in part from the public participation kits, meaning Geno 1.0 and now 2.0.

Geno 2.0 continues to be a partnership between National Geographic and Family Tree DNA.  Family Tree DNA is running all of their samples in the expanded Houston lab.  Also added to the team is Dr. Eran Elhaik at Johns Hopkins University who has developed a new tool, AIMSFINDER, that locates never before identified Ancestral Informative Markers to identify population specific markers.  This is extremely important because it allows us to read our DNA and determine if we carry the markers reflective of any specific population.  Well, we don’t do the reading, they do with their sophisticated software.  But we are the recipients with the new deep ancestral ethnicity results which are more focused on anthropology than genealogy.  Spencer says that if you have 2% or more Native American, they can see it.  They have used results from both public and private repositories in developing these tools.

This type of processing power combined with a new protocol that tests all SNPS in a sequence, not just selected ones, promises to expand the tree exponentially and soon. It has already been expanded 7 fold from 863 branches of the Y tree to 6153 and more have already been discovered that are not on the GenoChip, but will be in the next version.

The National Geographic project will also be reaching out to administrators and groups who may have access to populations of interest.  For example, an ex-pat group in an American city.  Keep this in mind as you think of projects.

Another piece of this pie is a new educational initiative in schools called Threads.

This isn’t all, by any means, on this topic, I really do encourage you to go and use Twitter hashtag #ftdna2012.  Several of us were tweeting and the info was coming so fast and furious that no one could possibly get it all.

The future with Nat Geo looks exceedingly bright.  We have gone from the Barney Rubble age to the modern era and now there is promise for a rosy and as yet undiscovered future.

Judy Russell was next.  I have to tell you, when I saw where they positioned her, I was NOT envious.  I mean, who wants to follow Spencer Wells, even if he’s not there in person.  Well, if anyone was up to this, it certainly was Judy.  For those who don’t know, she blogs as The Legal Genealogist.

Judy is one of us.  That means she actually understands our industry, what drives genealogists and why.  In addition to being a lawyer, she is a certified genealogist and a genetic genealogy crazy too.  Maybe I shouldn’t call a lawyer crazy….well…it was meant as a compliment:)

Judy has the perspective to help us, not just criticize us remotely.  She reviewed several areas where we might make mistakes.  After all, we’re all volunteers coming from quite varied backgrounds.  She suggests that we all put some form of disclosure on our projects explaining what participants can expect in terms of use.  She used the Core Melungeon project as a good example, along with the Fox project.

“The goal of this project is to use DNA to better understand the origins of the Melungeon people, and this will be done by comparing the DNA with other project members, those outside of projects, and will incorporate relevant genealogical and historical research. All participants will be included in the ongoing studies and by joining the project, you are giving consent for your information to be anonymously included in ongoing genetic genealogy research. Your personal identity will not be revealed, but your results will be used to better understand the Melungeons as a people and their ancestors.”

From the Fox project:

“The exact function of these STR markers is not yet known and they have no known medical function but recent research shows they have some sort of regulatory function on the genes. While there is no medical information in these numbers, the absence of a certain few markers near a fertility gene could indicate sterility – something that would certainly already be known.

The results do provide a partial means of personal identification and, for this reason, our haplotype tables list only the FTDNA kit number and the most distant known male line ancestor. Within the project, however, the administrators feel free to disclose identities, particularly when a close match occurs.”

Judy’s stressed that we not tell people that there is no medical information revealed.  Partially, because we’ve discovered in rare cases that’s not true, and partially because we can’t see into the future.

Judy talked about regulation and that while we fear what it might intentionally or inadvertently do to genetic genealogy, it’s important to have regulations to get rid of the snake oil salesman, and yes, there are a couple in genetic genealogy.  They give us all a black eye and a bad name when people discover they’ve been hoodwinked. However, without regulation of some sort, we have no legal tools to deal with them.

Regulation certainly seems to be a double-edged sword.

I hope that Judy writes in her blog about what she covered in her session, because I think her message is important to all administrators and participants alike.  And just to be clear, the sky is not falling and Judy is not Chicken Little.  In fact, Judy is the most interesting attorney I have ever heard speak, and amazingly reasonable too.  She actually makes you WANT to listen, so if you ever get the chance to see one of her webcasts or attend one of her sessions, take the opportunity.

Following the break, breakout sessions began.  CeCe Moore ran one about “Family Finder,” Elise Friedman about “Group Administration” and Thomas Krahn provided the “Walk the Y Update.”  Bennett called this the propeller head session.  Harumph Bennett.  Guess you know which one I attended.  All sessions were offered a second time on Sunday.

Thomas said that they have once again upgraded their equipment, doubling their capacity again.  This gives 4 times the coverage of the original Walk the Y, covering more than 5 million bases.  To date, they have run 494 pre-qualified participants and of those, 198 did not find a new SNP.

There are changes coming in how the palindromic region is scored which will change the matches shown.  Palindromic mismatches will now be scored as one mutation event, not multiples.  Microalleles will able be reported in the next rollout version, expected probably in January.  The problem with microalleles is not the display, but the matching routine.

Of importance, there has not been an individual WTY tested from haplogroups B, M, D or S, and we need one.  So if you know of anyone, please contact Thomas.

Thomas has put his Powerpoint presentation online at  http://www.dna-fingerprint.com/static/FTDNA-Conference-2012-WalkThroughY.pdf

The next session by Dr. Tyrone Bowes was “Pinpointing a Geographical Location Using Reoccurring Surnames Matches.”  For those of us without a genetic homeland, this is powerful medicine.  Dr. Bowes has done us the huge favor of creating a website to tell us exactly how to do this.  http://www.irishorigenes.com/

He uses surnames, clan maps, matches, history and census records to reveal surname clusters.  One tidbit he mentioned is that if you don’t know the family ethnicity, look at the 1911 census records and their religion will often tell you.  Hmm, never thought of that, especially since our American ancestors left the homeland long ago.  But those remaining in the homeland are very unlikely to change, at least not in masse.  I’m glad he gave this presentation, or I would never have found his webpage and I can’t wait to apply these tools to some of my sticky-wickets.

This ended Saturday’s sessions, but at the end of every day, written questions are submitted for that day’s presenters or for Family Tree DNA.

Bennett indicated that another 3000 or 4000 SNPs will be added to the Family Finder calculations and a new version based on reference samples from multiple sources will be released in January.

Bennett also said that if and when Ancestry does provide the raw downloadable data to their clients, they will provide a tool to upload so that you can compare 23andMe and Ancestry both with your Family Finder matches.

Saturday evening is the ISOGG reception, also called the ISOGG party.  Everyone contributes for the room and food, and a jolly good time is had by all.  There is just nothing to compare with face to face communications.

For me, and for a newly found cousin, this was an amazing event.  A person named Z. B. Stroud left me a message that she was looking for me.  When I found her, along with her friend and cousin Revis, she tells me that she matches me autosomally, at 23andMe, and that she had sent me a sharing request that I had ignored.  I am very bad about that, because unless someone says they are related, I presume they aren’t and I don’t like to clutter up my list with non-related people.  It makes comparisons difficult.  My bad.  In fact, I’m going right now to approve that sharing request!!!

I will blog about this in the future, but without spilling too many beans….we had a wonderful impromptu family reunion.  We think our common ancestor is from the Halifax and Pittsylvania County region of Virginia, but of course, it will take some work to figure this out.

I’m also cousins with Revis Leonard (second from left).  We’ve known that for a long time, but Z.B. whose first name is Brisjon (second from right) is new to genealogy, DNA and cousin matching. I’m on the right above.  The Stroud project administrator, Susan Milligan, also related to Brisjon is on the left end.  In the center are Brisjon’s two cousins who came to pick her up for dinner and whom she was meeting for the first time.

But that’s not all all, cousin Brisjon also matches Catherine Borges.  Let me tell you, I know who got the tall genes in this family, and I’m not normally considered short.  Brisjon’s genealogical journey is incredibly amazing and she will be sharing it with us in an upcoming book.  Suffice it to say, things are not always what you think they are and Brisjon is living proof.  She also met her biological father for the first time this weekend!  I’m sure Houston and her 2012 visit where she met so many family members is a watershed event in her lifetime!  She is very much a lovely lady and I am so happy to have met her.  Cousins Rule!

ISOGG traditionally has its meeting on Sunday morning before the first session.  Lots of sleepy people because everyone has so much fun at the ISOGG party and stays up way too late.

Alice Fairhurst, who has done a remarkable job with the ISOGG Y SNP tree (Thank you Alice!) knows an avalanche is about to descend on her with the new Geno 2.0 chip.  They are also going to discontinue the haplogroup names, because they pretty much have to, but will maintain an indented tree so you can at least see where you are.  The names are becoming obsolete because everytime there is an insertion upstream, everything downstream gets renamed and it makes us crazy.  It was bad enough before, but going from 860+ branches to  6150+ in one fell swoop and knowing it’s probably just the beginning confirms the logic in abandoning the names.  However, we have to develop or implement some sort of map so you can find your relative location (no pun intended) and understand what it means.

Alice also mentioned that they need people to be responsible for specific haplogroups or subhaplogroups and they have lost people that have not been replaced, so if anyone is willing or knows of anyone….please contact Alice.

Alice also makes wonderful beaded double helix necklaces.

Brian Swann (sorry, no picture) is visiting from England this year and he spoke just a bit about British records.  He said it’s imperative to learn how they work and to use some of the British sites where they have been indexed.  He also reminded us to check GOONS (Guild of One Name Studies) for our surnames and that can help us localize family groups for recruiting.  He said that you may have to do family reconstructions because to get a Brit to test you have to offer them something.  That’s not terribly different from over here.  He also mentioned that today about half of the British people having children don’t marry, so in the next generation, family reconstruction will be much more difficult.  That too isn’t so terribly different than here, although I’m not sure about the percentages.  It’s certainly a trend, as are varying surname practices even within marriage.

Dr. Doron Behar began the official Sunday agenda with a presentation about the mtCommunity and a discussion of his recently published paper “A ‘Copernican’ Reassesement of the Human Mitochondrial DNA Tree from its Root.”  This paper has absolutely revolutionized the mitochondrial DNA community.  I blogged about this when the paper was first released and our home pages were updated.    One point he made is that it is important to remember is that your mutations don’t change.  The only thing that changes between the CRS (Cambridge Reference Sequence) and the RSRS (Reconstructed Sapiens Reference Sequence)  model is what your mutations are being compared to.  Instead of being compared to someone from Europe who live in 1981 (the CRS) we are now comparing to the root of the tree, Mitochondrial Eve (RSRS) as best we can reconstruct what her mitochondrial DNA looked like.

He also said that when people join the mtCommunity, their results are not automatically being added to GenBank at NCBI.  That is a separate authorization check box.

A survey was distributed to question participants as to whether they want results, when they select the GenBank option, to be submitted with their kit number.  Now, they are not, and they are under Bennett’s name, so any researcher with a question asks Bennett who has no “track back” to the person involved.  About 6000 of the 16,000 submissions today at GenBank are from Family Tree DNA customers.  Dr. Behar said that by this time next year, he would expect it to be over half.  Once again, genetic genealogy pioneers are leading the way!

At these conferences, there is always one session that would be considered the keynote.  Normally, it’s Spencer Wells when he is on the agenda, and indeed, his session was wonderful.  But at the 2012 conference, this next session absolutely stole the show.  Less public by far, and much less flashy, but at the core root of all humanity.

You can’t really tell from the title of this session what is coming.  Michael Hammer with Thomas Krahn and Bonnie Schrack, one of our own citizen scientists, presented something called “A Highly Divergent Y Chromosome Lineage.”  Yawn.  But the content was anything but yawn-material.  We literally watched scientific discovery unfold in front of our eyes.

Bonnie Schrack is the haplogroup A project administrator.  Haplogroup A is African and is at the root of the entire haplotree.  One of Bonnie’s participants, an African American man from South Carolina agreed to participate in WTY testing.  In a nutshell, when Thomas and Astrid began scoring his results, they continued and continued and continued, and wound up literally taking all night.  At dawn’s first light, Thomas told Astrid that he thought they had found an entirely new haplogroup that preceded any known today.  But he was too sleep deprived to be sure. Astrid, equally as sleep deprived, replied with “Huh?” in disbelief.  It’s certainly not a statement you expect to hear, even once in your lifetime.  This is a once in the history of mankind event.

Dr. Michael Hammer confirmed that indeed, they had discovered the new root of the human Y tree.  And not by a little either, but by a lot.  For those who want to take a look for yourself, Ysearch ID 6M5JA.  Hammer’s lab did the age projection on this sample, and it pushed the age of hominid men back by about 100,000 years, from 140,000 years ago to 237,000 years ago.  They then reevaluated the aging on all of the tree and have moved the prior date to about 200,000 years ago and the new one to about 338,000 years ago with a 98% confidence level.  This is before the oldest fossils that have been found, and also before the earliest mitochondrial DNA estimate, which previously had been twice as old as the Yline ancestor.

The previous root, A1b has been renamed A0 and the new root, just discovered is now A00.  Any other new roots discovered will simply get another zero appended.

How is it that we’ve never seen this before?  Well, it turns out that this line nearly went extinct.  Cruciani published a paper in 2012 that included some STR values that matched this sample, but fortunately, Michael Hammer’s lab held the actual samples.  A search of academic data bases reveals only a very few close matches, all in western Cameroon near the Gulf of Guinea.  Interestingly, next door, in Nigeria, fossils have been found younger than this with archaic features.  This is going to cause us to have to reevaluate the source of this lineage and with it the lineage of all mankind.  We must now ask the question about whether perhaps we really have stumbled upon a Neanderthal or other archaic lineage that of course “became” human.  Like many scientific discoveries, this answer only begs more questions.  My husband says this is like Russian tea dolls where ever smaller ones are nested in larger ones.

This discovery changes the textbooks, upsets the proverbial apple cart in a good way, and will keep scientists’ thinking caps on for years.  And to think, this was a result of one of our projects, an astute project administrator (Bonnie) and a single project member.  I wonder what the man who tested thinks of all of this. He is making science and all he thought he was doing was testing for genealogy.  You just never know where the next scientific breakthrough will come from.  Congrats to all involved, Bonnie, Thomas, Michael and to Bennett and Max for having this evolution revolution happen right in their lab!

If I felt sorry for Judy following Spencer, I really felt sorry for the breakout sessions following Thomas, Michael and Bonnie’s session.  Thankfully at least we had a break in-between, but most people were wandering around with some degree of stunned disbelief on their faces.  We all found it hard to fathom that we had been among the first to know of this momentous breakthrough.

I had a hard time deciding which session to attend, CeCe’s “Family Finder” session or Elise’s.  I decided to attend Elise’s “Advanced Admin Techniques” because I work with autosomal DNA with my clients and I tend to keep more current there.  Elise’s session was great for newer admins and held tips and hints for us old-timers too.  I realized I really need to just sit down and play with all of the options.

There are some great new features built in that I’ve never noticed.  For example, did you know that you can group people directly from the Y results chart without going to the subgrouping page?  It’s much easier too because it’s one step.  However, the bad news is that you still can’t invite someone who has already tested to join your project.  Hopefully that feature will be added soon.

The next session was “A Tale of Two Families” given by Rory Van Tuyl detailing how he used various techniques to discern whether individuals who did not show up as matches, meaning they were beyond the match threshold, were actually from the same ancient family or not.  Rory is a retired engineer and it shows in his attention to detail and affinity for math.

We always tell people that mutations can and do happen at any time, but Rory proved this.  He ran a monte-carlo simulation and showed that in one case, it was 50 generations between mutations, but in others, there was one mutation for three generations in a row.  Mutations by no means happen at a constant rate.  Of course, this means that our TIP calculator which has no choice but to use means and averages is by definition “not calibrated” for any particular family.

He also mentioned that his simulation shows that by about 150 generations, there are a couple of back mutations taking place.

The final session before the ending Q&A was Elliott speaking about IT, which really translates into new features and functions.  Let’s face it, today everything involves IT.

Again, I was having trouble typing fast enough, so you might want to check the Twitter feed.

They added the SNP maps (admins, please turn them on) and the interactive tour this year.  The tour isn’t used as much as it should be, so everyone, encourage your newbies to do this.

They have also added advanced matching, which I use a lot for clients, but many people didn’t realize it.  So maybe a quick tour through the website options might be in order for most of us.

They are handling 50 times more data now that a year ago.  Just think what next year will bring.  Wow.

They are going to update the landing page again with more color and more visible options for people to do things.  I hope they prompt people through things, like oldest ancestor mapping, for example.  Otherwise, if it isn’t easy, most don’t.

They are upgrading Population Finder and the Gedcom viewer.  They are adding a search feature.  Thank you!!  Older Gedcome will still be there but not searchable.

But the best news is that they are adding phasing (parent child) and an advanced capability to “reconstruct” an ancestor using more distant relatives, then the ability to search using that ancestral profile against Family Finder.  Glory be!  We are finally getting there.  Maybe my dreaming big wasn’t as far away as I thought.

They will also remove the 5 person autosomal download restriction and the “in common with” requirement to see additional information.  All good news.  They are also upgrading the Chromosome browser to add more filtering options.

They are also going to offer a developer “sandbox” area for applications.

The final Q&A session began with Bennett saying that their other priorities preclude upgrading Y search to 111 markers.

They are not planning to drop the entry level tests, 12 or 25 markers or the HVR1. If they do, lots of people will never take that plunge.  I was very glad to hear this.

And by way of trivia, Family Tree DNA has run more than 5 million individual tests.  Wow, not bad for a company that didn’t exist, in an industry that didn’t exist, 12 years ago!

It’s an incredible time to be alive and to be a genetic genealogist!  Thank you Family Tree DNA for making all of this possible.

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Disclosure

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

Thank you so much.

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Family Tree DNA Conference 2012 – Native American Focus Meeting

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Wow.  Talk about drinking from a firehose.  From the minute we arrived in the lobby Friday afternoon until we got back to the airport Sunday evening, we barely had time to breathe.

This was an amazing conference in many ways.  I’ll try to hit the high points in a separate blog, but in this posting, I want to cover the Native American Focus meeting and talk a little bit about the interests of the different attendees.

The first event, at 4 on Friday afternoon, was a small meeting of people who are admins or have a specific interest in Native American heritage.   Rebekah Canada, haplogroup Q project administrator, coordinated this meeting and a hearty thank you goes to her for her efforts.  We have never attempted this type of event before, and we all agreed, we need to do it again.

Unfortunately, many projects that are focused on or include Native results did not have a project administrator here and were not represented.

Peter Roberts is the administrator of the Bahamas project.  The Bahamas are rich with Native history, but evidence they existed in the DNA record is slim.  The Lucayan Indians were removed from the Island by the Spanish.  While we know they existed, their results, surprisingly, are not showing up directly in the yline or mtdna results.  We also know that some Seminoles arrived later from Florida and others came from the mainland as well.  Low levels of Native heritage are showing up in autosomal testing.

David Pike discovered his Native heritage quite by accident.  His father turned out to be 3.4% Native.  He believes it is probably MicMac (Mi’kmaq) or perhaps Beothuk, a now extinct tribe, in Newfoundland, but is still researching.  Dave mentioned an opportunity for tribal membership in Canada for those who can prove Micmac heritage and will be providing that information.  I will blog it when that arrives.

Marie Rundquist is the administrator of the AmerIndian Ancestors out of Acadia project which began in 2006.  I love this project, somewhat from a selfish perspective, since I’ve connected so many of my Acadian ancestors, and Native ancestors, through this project.  This is also one the most successful mitochondrial DNA projects, if not the most successful, there is.  Marie’s project has served to prove or disprove several Native rumors, and has found other Native people quite by accident.  She wrote a book, titled Revisiting Anne Marie and I’ve blogged about her success with the Doucet results.  This project is not just for Acadians in Canada, but reaches to Louisiana, and families with Acadian heritage outside of the primary relocation areas.

Kathy Johnson’s cousin came back with a haplogroup Q results.  Subsequent testing revealed 4 new SNPS in her sample.  This Pembrook family is believed to be from the Mohawk River area in New York.

Georgia and Tom Bopp, administrators of the Hawaii project, from Hawaii, attended.  Frankly, I had never thought about them and Native ancestry, but certainly Hawaii did have a Native population.  They had a very interesting situation where one of their early tester’s mitochondrial results came back as haplogroup B.  They were told they were Native American, then they were told they were Polynesian.  Native was reasonable, but Polynesian somewhat confounding given that their ancestor was a slave in Maryland.  Eventually, it was discovered their maternal ancestor was from Matagascar.  Georgia will send the information and we’ll do a blog about this in the future.  How very interesting.

Rob and Dyann Noles administer the Lumbee Tribe and Wiregrass Georgia projects.  Rob maintains a data base of over 250,000 individuals related to these projects.  While the Lumbee project is named as such, it is not endorsed by the Lumbee tribe itself.  However, numerous individuals descended from those who are early tribal founders have tested.

As haplogroup Q project administrator, Rebekah has been instrumental in the ongoing testing of haplogroup Q individuals.  Many members have been SNP tested and more than a few have participated in the WTY (Walk the Y)) which has resulted in many new haplogroup subgroups being discovered.  We’ve made more progress in the past two years than in the previous 10 in haplogroup Q.  Someday, I hope we’ll be able to identify at least members of different Native language groups by results.  Maybe I’m dreaming here, but goals are good!

I shared my work with the Native Heritage project and my ongoing transcriptions into the Native Names data base.  We now have over 8,000 different surnames and well over 30,000 people, and I’m no place near “done.”  Of course, it’s always a great day when I find a proven Native surname of someone who has tested Native in our haplogroup Q project.

We discussed the reluctance of recognized tribes to test and their concerns.  We all respect their decisions, although from a genetic genealogy perspective, we are glad when descendants test.

I suspect that many of the Native genetic lines have become extinct.  The Native people, aside from having to survive in a harsh, cold climate upon arriving from Asia, have had to endure multiple genocidal attempts (Native as well as European) in addition to many epidemics.  Some epidemics wiped out entire tribes.  In 1838, a smallpox epidemic took half of the powerful Cherokee.  No one was immune.  That combined with intermarriage, assimilation, and adoption through either traditional cultural means or kidnapping have caused the “Native” DNA results to not always be what we expect.

We are hopeful that ancient DNA will shed a light on extinct lines as well as answer the ever-present question about whether European or perhaps African DNA was present in the Native population before the traditional dates of European contact

I want to thank everyone who attended for their participation and sharing, and encourage anyone else who is interested to let either Rebekah or I know.

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research