Naia – Oldest Native American Facial Reconstruction

Naia, named affectionately for the ancient water nymphs of Greek mythology is actually the face of the oldest Native American.  At least, the oldest one whose skull is complete and whose face we can reconstruct.  Naia was a teenager when she died between 12,000 and 13,000 years ago by falling into a cave in the Yukatan. In 2007, her remains were found in a submerged cavern, and history was about to be made, after waiting some 12,000+ years.

A scientific team would study her remains, sample her DNA and reconstruct her face.  The January 2015 issue of National Geographic magazine has an absolutely wonderful article and the online magazine version does as well.

nat geo naia

Start by reading the wonderful story, of course, but don’t miss the video about how they recovered the remains and the subsequent analysis.  There is also a photo gallery and several other links, across the top of the article – all worth seeing.

One of the unexpected findings was how different Naia looks than what we would have expected based on what Native people look like today.  She had a more African and Polynesian facial structure than later Native people, and she was much smaller.  Be sure to check out Nat Geo’s “clues to an ancient mystery.”

Naia’s mitochondrial DNA confirms that indeed, her matrilineal line originated in Asia, a common base haplogroup found in Native Americans todayhaplogroup D1.

The accompanying academic paper was published in the May 2014 issue of the Journal Science, titled “Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans” by James Chatters et al.

The article is behind a paywall, but the abstract is as follows:

Abstract:

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

A second article, published in Science, also in May 2014, “Bones from a Watery “Black Hole” Confirm First American Origins” by Michael Balter discuss the fact that the earlier skeletons of Native people often don’t resemble contemporary Native people.

Also behind a paywall, the summary states:

Summary:

Most researchers agree that the earliest Americans came over from Asia via the Bering Strait between Siberia and Alaska, beginning at least 15,000 years ago. But many have long puzzled over findings that some of the earliest known skeletons—with long skulls and prominent foreheads—do not resemble today’s Native Americans, who tend to have rounder skulls and flatter faces. Some have even suggested that at least two migrations into the Americas were involved, one earlier and one later. But the discovery of a nearly 13,000-year-old teenage girl in an underwater cave in Mexico’s Yucatán Peninsula argues against that hypothesis. The girl had the skull features of older skeletons, but the genetic profile of some of today’s Native Americans—suggesting that the anatomical differences were the result of evolutionary changes after the first Americans left Asia, rather than evidence of separate ancestry.

Of course, the fact that Naia was found so early in such a southern location has spurred continuing debate about migration waves and paths, land versus water arrivals.  Those questions won’t be resolved until we have a lot more data to work with – but they do make for lively debate.  Dienekes wrote a short article about this topic when the paper was first released, and the comments make for more interesting reading than the article.

Cultural Footprints

I was recently corresponding with a descendant of Valentine Collins, one of the Melungeon families of mixed race found in and nearby Hawkins County, Tennessee in the 1800s.

Here’s what he had to say.

When I first started looking into my Collins’ family history, I realized very early this was going to be a real adventure. What I did was set up a system to look at different aspects of their lives/history. I call it ‘cultural footprints’. I have those foot prints broken down as:

  • Religion
  • The Table (food)
  • Music
  • Language

Most of the data I’ve mined are based on these four Cultural Footprints. But I would have to say Genetic Genealogy provided the biggest breakthroughs, the best tool by far.

Well, obviously I liked his commentary about genetic genealogy, which gives us the ability to connect and to prove, or disprove, connections.  But as I looked at his list, I thought about my own ancestors.  Those of you who follow my blog regularly know that I love to learn about the history during the time that my ancestors were living – what happened to and near them and how it affected them.  But his commentary made me wonder what I’ve been missing.

As I think back, one of the biggest and most useful clues to one of my ancestral lines was an accidental comment made by my mother about her grandmother. She mentioned, in passing, “that little white hat that she always wore.”  I almost didn’t say anything, but then I thought, “little white hat, that’s odd.”  So I asked and my mother said something like, “you know, those religious hats.”  I asked if she meant Amish or Mennonite, given the context of where they lived and she said, “yes, a hat like that.”  Then, when questioned further, it turns out that the family didn’t drive, even though cars were certainly utilized by then.  My mother never thought about it.  Turns out that the family was actually Brethren, also one of the pietist faiths similar to Amish and Mennonite, but that hint sent me in the right direction.

How could my mother have been unaware of something that important, well, important to me anyway?  Easy.  It was, ahem, not discussed in the family.  You see, it was somewhat of a scandal.

My mother’s father had married outside the Brethren religion, so was rather ostracized from the family for his choice to marry a Lutheran. Then the family became, horror of horrors, Methodist.  So, I would add clothing to my friend’s list of cultural footprints as well.  Sometimes, like in my case, dress will lead you to religion.  In the photo below, my mother’s grandmother is the female in the middle back row.  If you look carefully, you can see that both she and her mother are wearing a prayer cap.

John David Miller Photo

I know the religion of many of my ancestors. Whatever their religious choice, it was extremely important to many.  I have 1709ers, Acadians, Brethren, Mennonites, Huguenots, fire and brimstone Baptists, Methodists and Presbyterians in my family line.  I always try to find their church and the church records if possible.  Some are quite interesting, like Joseph Bolton who was twice censured from the Baptist church in Hancock County, Tennessee.  Many of my ancestors made their life choices based on their faith.  In particular, the Huguenots, 1709ers, Brethren and Mennonites suffered greatly for their beliefs.  Conversely, some of my ancestors appear to never have set foot in a church.  I refer to them as the “free thinkers.”

Well, in one case, my ancestor was a bootlegger in the mountains of Kentucky. What the hey…every family has to have some color, and he was definitely colorful….and free thinking.

Most of us are a mixture of people, cultures and places. All of them are in us.  Their lives, culture, choices and  yes, their DNA, make us who we are.  If you have any doubt, just look at your autosomal ethnicity predictions.

Language of course is important, but more personally, local dialects that our ancestors may have spoken. In the US, every part of the country has their own way of speaking.

Here’s a YouTube video of a Louisiana Cajun accent. Many Acadians settled in that region after being forcibly removed from Nova Scotia in 1755.

Acadian-Cajun language, music and early homes in Louisiana

Here’s a wonderful video of Appalachian English. In my family, this is known as “hillbilly” and that is not considered a bad thing to be:)  In fact, we truthfully, all love Jeff Foxworthy, well, because he’s one of us.  I’m just sure if we could get him to DNA test, that we’d be related!

There are regional and cultural differences too.

Here’s a video about Lumbee English. The Lumbee are a Native American tribe found in North Carolina near the border with South Carolina.

Going further east in North Carolina, the Outer Banks has a very distinctive dialect.

What did your ancestor’s speech sound like?   What would it have sounded like in that time and place?

That, of course, leads to music. Sometimes music is the combination of speech and religion, with musical instruments added.  Sometimes it has nothing to do with religion, but moves us spiritually just the same.  Music is the voice of the soul.

Here’s Amazing Grace on the bagpipes. If you can get through this dry-eyed, well, then you’re not Scottish…just saying.  This connects me to my Scottish ancestors.  It was played at both my mother’s and my brother’s funerals.  Needless to say, I can’t get through it dry eyed!

Amazing Grace isn’t limited to bagpipes or musical instruments. The old “hardshell” Baptists didn’t utilize musical instruments, and still don’t, in their churches.  Listen to their beautiful voices, and the beautiful landscape of Kentucky.  This is the land, voices and religion of some of my people.

A hauntingly and sadly beautiful Negro Spiritual. Kleenex box warning.  This, too, is the music of my family.

Yeha – Noha – a Native American song by Sacred Spirit. One of my favorite music pieces.

Bluegrass gospel – Swing Low Sweet Chariot. Bet you can’t keep your foot from tapping!!!

Appalachian fiddle music. Speaks directly to my heart.  And my hands.  I just have to clap my hands.

Acadian music. This would be very familiar to my Acadian ancestors.

At this link, you can hear samples of Acadian folk songs by scrolling down and clicking on the track listing.

Moving a little closer in time. This is the official state song of Tennessee – one of my all-time favorites.  I can’t tell you how many times I’ve danced to this.  This just says “home” to me and I can feel my roots.

What kind of music did your ancestors enjoy? Did they play any musical instruments?  Can you find the music of the time and place in which they lived?  YouTube has a wide variety and the videos are an added benefit, bringing the reality of the life of our distant ancestors a little closer.

Now that you know what fed their souls, let’s look at what fed their bodies.  Along with regional speech and musical differences, the diet of our ancestors was unique and often quite different from ours of today.

On the Cumberland Gap Yahoo group, we often exchange and discuss regional recipes, especially around the holidays. Same on the Acadian rootsweb group.  Although this year we’ve been talking about deep fried turkeys.  Maybe in another couple hundred years that will be considered representative of our time.  Hopefully it’s not McDonalds!

The Smithsonian sponsors a website about Appalachian foods.  Let me share with you what I remember about my childhood.  We made do with what we had, whatever that was.  Some things were staples.  Like biscuits, with butter, or honey, or jam, or apple butter…whatever you had on hand that was in season.

biscuits

Chicken fried in bacon grease was for Sunday, or company, which usually came on Sunday.

fried chicken

We wasted nothing, ever, because you never knew when you might not have enough to eat. So, we ate leftovers until they were gone and we canned. Did we ever can.  Lord, we canned everything.  Mason jars in huge boiling kettles in the hottest part of summer.  Let’s just say that is not my favorite memory of growing up.  But green beans at Christmas time were just wonderful, and you couldn’t have those without canning in the August heat.

cans

Different areas have become known for certain types of cuisine. In North Carolina, they are known for their wood-fired BBQ.  In western North Carolina, they use a red, slightly sweet, tomato based BBQ sauce, but in eastern NC, they use a vinegar based BBQ sauce.  Want to start a fight?  Just say that the other one is better on the wrong side of the state:)

BBQ pit

Creole cuisine is found in the south, near the Mississippi Delta region and is from a combination of French, Spanish and African heritage.

creole

Jambalaya is a Louisiana adaptation of Spanish paella.

OLYMPUS DIGITAL CAMERA

Soul food is the term for the foods emanating from slavery.  When I looked up soul food on wiki, I found the foods my family ate every day.  When I think of food that we didn’t eat, but that my African American cousins did eat, I think of chitlins.  Yes, I know I didn’t spell that correctly, but that’s how we spelled it. And the chitlins we had were flowered and fried too, not boiled.  Maybe that is a regional difference or an adaptation.

chitterlings

Another “out of Africa” food is sorghum, used to make a sweet substance similar to molasses, used on biscuits in our family. Sorghum is an African plant, often called Guinea Corn, and arrived with slaves in colonial days.

sorghum

Native American cuisine varies by where the tribe lived, and originally, they lived across all of North and South America. Originally, the Native people had the three sisters, corn, squash and beans.  Hominy is Native, as is grits, a southern staple today.  I’m drooling now…

grits

Today, however, one of the signature Native American dishes is FryBread. Fried and seriously unhealthy, the lines at powwows are longer for frybread and a derivative, Indian Tacos, than anything else.

frybread

In many places, the settlers, slaves and Native people assimilated and the food their descendants ate reflected all three cultures, like Brunswick Stew.  Even Brunswick Stew varies widely by location as do the origin stories.  Many foods seems to have evolved in areas occupied by European settlers, Native people and slaves, to reflect ingredients from all three groups.

Brunswick stew

That’s the case in my family, on my father’s side. We didn’t know any differently, or where that particular type of food originated.  However, sometimes by looking at the foods families ate, we can tell something of their origins.

In marginalized populations, and by that, in the US I mean mixed race or descendants of enslaved people, it’s often very difficult to use traditional genealogical records because they didn’t own land or leave other records. Many of them spent a lot of time trying to make themselves transparent and didn’t want to attract any attention.

Often, it’s the DNA that unlocks the doors to their heritage, and after making that discovery, we can then look the cultural footprints they left for us to follow.

I’m starving. I’m going to eat something unhealthy and listen to some wonderful music!  How about grits with butter and Indian tacos for lunch along with powwow music?  Oh yeahhhhhh…….

Anzick Matching Update

In response to my article about haplogroup C3*, a regular contributor, Armando, left the following comment:

“Roberta, there was a problem with the way Felix was processing files and he had to change the Clovis Anzick file three times at Gedmatch. The last one is kit F999919 uploaded October 8, 2014. You can see his post on that at http://www.fc.id.au/2014/10/new-clovis-anzick-1-kit-in-gedmatch.html

If you do one-to-many matching on Clovis Anzick F999919 at Gedmatch there is not a single person that reports to have mtDNA M. Your extracts for Clovis Anzick are from September 24, 2014 and therefore are based on a bad file which was kit F999912. The older bad kits F999912 and F999913 have been deleted from Gedmatch. Felix mentions the updates at http://www.fc.id.au/2014/09/clovis-anzick-1-dna-match-living-people.html

This comment came in on Christmas Eve, and I replied that I would look into this after the holidays.

Given that it was Christmas Eve, I certainly wasn’t going to bother anyone over the holidays with questions, so I quickly ran a one to many compare for the current Anzick kit, F999919, and found at 5cM and below that there were 4 haplogroup M matches.

ancient match

As I did before, I sent emails to those who provided e-mail addresses asking about their matrilineal heritage.

The first thing I wanted to do, of course, was to check with Felix.  I knew that Felix had updated the kits, but my understanding was that he added SNPs from the various companies to create a single file with all the SNPs from all three testing companies, not that any file was bad, so to speak.

I asked Felix if the original files had problems or were bad, and here is his response.

“I can assure you none of the earlier/older versions uploaded to GEDmatch (kit# F999912 and F999913) of Clovis Anzick was bad.

  • F999912 – Contains only FTDNA SNPs extracted from VCF file provided by authors.
  • F999913 – Contains all SNPs used by DNA testing companies extracted from VCF file provided by authors.
  • F999919 – Contains all SNPs used by DNA testing companies processed from BAM file provided by authors.

Source files: 

I removed the earlier versions not because they are bad but only to avoid redundancy for the same sample kit, and processed BAM file (which is a 41 GB file) contains significantly more SNPs compared to VCF source. Because the latest file has more SNPs, it is possible that some missing SNPs in earlier uploads (which was assumed as matching in GEDmatch) may actually have mismatches in new file and thus, could fall below the thresholds or could break the previously matching segment.

The difference in matches between F999912 and F999919 kit for Clovis Anzick is similar to difference in matches between a 23andMe V4 kit and V3 kit for the same person.”

After thinking about this some, it occurred to me that perhaps GedMatch was treating different files from different vendors differently in their matching and sorting routines. That might account for a difference in matching. So, I asked John Olson at GedMatch.

John’s reply is as follows:

“At one time, I did use different thresholds depending on which vendor was being compared to which other vendor.  That was a holdover from when FTDNA had Affymetrix kits that were producing somewhat different results than Illumina kits.  I have since changed the one-to-many thresholds to 5cM/500 SNPs for all comparisons.  The one-to-one thresholds default to 7cm/700 SNPs.  I believe I made that change about a year ago, but it may have been longer.  At any rate, they are all the same now, and I’m pretty sure they are all the same since Felix has introduced the F9999xx kits.  Another change made within the past year is to treat A=T and C=G for all comparisons.  This was done to get rid of single SNP errors in the few cases where one vendor was reporting a different strand than another vendor.  In a few cases, I have observed that this “heals” some single-SNP breaks in otherwise continuous matching segments.

It is possible that older one-to-many comparisons may have been made under slightly different conditions than newer ones.  Older comparisons made with a 3cm/300 SNP threshold may show larger total segment match if they contained many very small matching segments.  This usually happens with endogamous populations.  Comparisons affected by the change to A=T, C=G may show a larger matching segment where 2 smaller matching segments existed previously.

Another issue to be aware of when comparing artificial kits is that there may be large gaps between the defined SNPs.  So, even if there is a gap of a million SNPs, the GEDmatch comparison algorithm will treat them as contiguous.  This works OK when everybody is using the same SNPs, but when the list of SNPs is significantly different, it may produce matches that are bogus.  This is particularly obvious when generating artificial kits that are missing large segments of data.  I have had to deal with this issue with phased kits and Lazarus kits by introducing the concept of a “hard break” that forces a break between smaller matching segments.”

I wanted to know how the three files that Felix prepared compared relative to the matches they produced.  I originally ran several comparisons with each of the first two versions, kits F999912 and F999913, and I didn’t save all of the original files, but I do have at least one file saved from each version.  Therefore, I dropped all three sets of results (F999912, F999913 and F999919) into a spreadsheet to see how matching compared between the three Anzick file versions.

Keep in mind that the first file (F999912) contained just the FTDNA SNPs, while the second (F999913) and third (F999919) files contain the SNPs from all of the testing companies.  This could potentially make the participant files appear to have missing segments when the matching routine at GedMatch sees SNPs in the Anzick file not in the participant files.  However, this shouldn’t be much different than comparing a file from two different vendors except that the Anzick file has the SNPs from all three vendors combined.

The first file from 9-23 at the default threshold had 491 matches, but I subsequently lowered the threshold so I could see as many matches as possible.

GedMatch only shows you your closest 1500 matches, although I now know that as of 12-31-2014, there were a total of 3442 Anzick matches at the 5cM threshold.

The second file from 9-29, run at 6cM had more than 1500 matches.  I ran the third kit at default settings on December 27th and it has 720 matches.

One would expect that the second and third files would have the effect of including more matches from both 23andMe and Ancestry since all of the SNPs utilized by those companies are included (if they are available in the Anzick sample.)  We also have to remember that there are new files being uploaded from all three vendor sites on a daily basis, so the total available to match is also increasing.  Of the 721 kit matches to F999919, 31 were shades of green which indicate that they have been uploaded during the last 30 days, so we could probably presume that about double that number were uploaded (and match) in two months or triple in three months, so probably about 100 new kits.  Those kits would show in the match extraction for this month but not for the first month and possibly not for the second.  However, all the kits that matched the first month at the highest threshold should still be showing in the second and third month.  Let’s see if that holds true.

I dropped all three sets of data into a spreadsheet and colorized the rows.

ancient match 1

  • Blue = F999912, first extraction, 9-23-2014
  • Yellow = F999913, second extraction, 9-29-2014
  • Pink = F999919, third extraction, 12-27-2014

Then I counted the number of blue rows, which are the first extraction, that had matches to both yellow and pink, or only yellow, the second extraction, or only pink, the third (current) extraction, or no matches at all.

You can see that the green grouping shows that all three match each other.  The match between A003479 in both the second and third extraction could be because the kit was not present when the first extraction was done.

All 3 match 1st to 2nd Only 1st  to 3rd Only No Match
Percent First Extraction Matches to Other Extractions 54% 36% 5% 5%

By percent, this is how the matching between kits worked.  About half of the kits in the first extraction continued to match kits in both subsequent extractions.  Of the remaining half, three quarters of the balance matches the second extraction only and a few match just the third extraction or no extraction at all.  For the most part, there is no evident reason upon inspection why the kits would not match the second or third extraction, so the cause has to be a result of the additional SNPs or the matching routine or both.  This is not to imply that the results are problematic, just that they are different than I would have expected.

A very low percentage of kits matched only between the first and third extracts and the same percentage had no matches in either the second or third extraction.

I took a closer look at the kits with no matches at all.  All of them had relatively low threshold total cM and largest segment size.  The smallest total cM was 7.1 and the largest was 8.2.  The smallest segment was 7.1 and the largest segment was also 8.2.  All of these entries had the total cM equal to the largest cM.  It appears that these simply slipped below the match threshold, but that doesn’t appear to be the case because in the current (pink) extract, a total of 171 entries were at or below 8.2 total cM and 8.2 largest cM and several kits had the exact same cM as the kits that didn’t show up from the first (blue) extract as a match – so obviously something truly was different in the SNPs or how the matching was done.

Is there any correlation to the kits in the original extract that didn’t match any other extract in terms of which testing company the participants utilized?

One Ancestry kit (4%), 18 23andMe kits (64%), 7 Family Tree DNA kits (25%) and 2 FN kits (7%) didn’t match anyone.  But how many kits were in the original extract from the various companies?

Original Kit Matches Second KitMatches Current Kit Matches
Ancestry Kits (A) 26 (5%) 438 (29%) 199 (28%)
FTDNA Kits (F) 94 (19%) 295 (20%) 121 (17%)
Other F+ Kits* 15 (3%) 35 (2%) 15 (2%)
23andMe Kits (M) 354 (72%) 732 (49%) 382 (53%)

*FB, FN, FE, FV

The effect of the additional SNPs in the kits seems to have been to increase the Ancestry kit matches significantly.

It was interesting to see how the same person’s kit from different vendors compared as well.  In this random example, the Family Finder kit has a higher total cM and largest segment than the 23andMe v3 kit.

ancient match 2

Here’s a kit from one person at all three vendors, but the 23andMe kit is version 4, in which 23andMe significantly reduced the number of SNPs tested by about one third, from about 900,000 to about 600,000.

ancient match 3

I wondered if there is a difference in what is reported based on the threshold selected.  Now at first glance, one would think, “well of course there is a difference,” but the difference should be on the bottom end of the list.  In other words, the top matches should be the top matches at 7cM, 6cM, 5cM, etc.  The top matches at 7cM would still be the top at 6cM, just more smaller matches appended to the end of the match list – or that is what I would expect.

Let’s see if this holds true with the current file.

I ran the “one to many” option for the current Anzick kit, F999919, at seven different levels, on the same day, one right after the other, as follows:

  • 7cM, 700 SNPs
  • 6cM, 600 SNPs
  • 5cM, 500 SNPs
  • 4cM, 400 SNPs
  • 3cM, 300 SNPs
  • 2cM, 200 SNPs
  • 1cM, 100 SNPs

The first extract produced 719 records.  The rest were all over the 1500 threshold, so we only see the first 1500.  Normally, for genealogy the 1500 threshold would certainly be adequate, but for research, the threshold is frustrating.

To make this easier let me say that the extracts from 5cM down through 1cM were exactly the same, but the extracts at 7, 6 and 5cM, respectively, were not.

Discussions with John Olson at GedMatch shed some light on why the 5cM through 1cM extracts were exactly the same.

 “For the past year or so, the database has only stored matches down to 5 cM.”

I sure wish I had known that BEFORE I did all of those extracts.

I combined and color coded all 7 extractions into a spreadsheet.

Most of the grouping look like this where blue=7cm, pink=6cM, grn=5cM, purple=4cm, teal=3cm,apricot=2cm, yellow=1cm.  Nice rainbows.

ancient match 4

All of the matches from the 7cM extraction, with the exception of a few X matches at the end, some of which have no matches on chromosomes 1-22, are included in the 6cM and 5cM extractions, but after the first several records, they are not in the same position.  In other words, they are not the top 719, in the same order, in either the 5 or 6cM extraction, but the 5cM through 1cM extractions are identical.  Of course, now we know why the 5cM through 1cM matches are exact. From here forth in the article, I won’t mention the 4cM-1cM extracts because they are the same as the 5cM extract.

For example, looking at the kit in position 712, the last non-X match in the 7cM extract – you find this same kit at row 1140 in the 6cM extract and row 1489 in the 5cM extract.

The 6cM extract appears to have some issues.  I ran this twice with the same parameters to be sure there wasn’t an error in how it was set up, and the two runs were identical.

There are about 350 individuals who show up in the 6cM extract who should  show up in the 5cM extract as well, but who don’t show in the 5cM extract.  They are under the threshold for the 7cM extract, so that is correct, but why are these 350 individuals not appearing as matches at the 5cM threshold?

ancient match 5

The kits noted above are the largest non-matching total cM and largest cM that don’t show up in the 5cM extract.  The smallest matches are 6.1 and 6.1, respectively.

Checking the 5cM extract, below, there are files with smaller total cMs and a smaller largest segment that are showing as matches.

ancient match 6

However, looking at the kits with the smallest cMs at the 5cM level, the smallest total cMs is 6.9 and it is combined with the largest segment of 6.9 as well, so that is above the 6.8 and 6.8 shown above.  The smallest individual segment is 5.1 but the total cM for that individual is 10.1.  So obviously the matching threshold at GedMatch is some combination of both the total cM and the largest segment.  This is somewhat unexpected, but doesn’t seem to be a red flag, just how this system works.

So, where are we?

I am glad to have Felix confirm that the files weren’t “bad,” only truly “new and improved,” and that the matching between the various files is pretty much as expected – and from various tests run, everything pretty much looks kosher.  The newer files with all of the SNPs utilized by the companies seem to level the playing field, allowing Ancestry kits a better chance of matching.

Aside from my intense interest due to the Native American connection, this is also how I’ve been extracting potential Native American mitochondrial haplogroups from the Anzick matches, including haplogroup M, for my research notes.  M is potentially a Native American haplogroup, but is as yet unproven.  With haplogroup M showing up in these people who are often heavily Native, and often from Mexico, Central and South America where 80% of the mitochondrial population is believed to be of Native American heritage, it seems prudent to add them to my research notes for further research and possible proof in the future.  I contact individuals and ask about their matrilineal heritage.  If they don’t have Asian or genealogically proven heritage elsewhere, and their families emerge from the areas with high Native frequencies, I include them on the research list.

In the three days between the two extracts this past week, three of the four haplogroup M individuals were pushed below the match threshold and are no longer visible at the default level.  Yes, I have confirmed hat they are still there just not visible at the 1500 match threshold.

I have contacted the individuals with e-mail addresses, asking about their matrilineal heritage.  One person said the tester’s mother’s heritage was from India, so that haplogroup M is not on the research list, of course, because it is proven to be from elsewhere – a place where haplogroup M and subgroups are quite common.

In total, there were 15 new potentially Native DNA mitochondrial DNA haplogroups listed in the 12-27 extract.  I’ll be adding those to my research notes as soon as I have the opportunity to contact these folks and ask about their known matrilineal genealogy.

I didn’t really anticipate that there would be so much change, nor so quickly, so it looks like I’m going to have to check the Anzick matches for potential Native mitochondrial haplogroups much more often.

Since it looks like there may be lots of additions over time, far more than I expected, I’ll also be going back and making better notes in my research file.  I will, for example, note the kit number and date for all of the extractions.  For this and future extractions, I’ll also be listing the number of results per haplogroup.  I think that would be valuable information as well.

I’d like to thank Armando for raising this topic.  The research into matching with a kit that has the entire spectrum of SNPs from all three of the companies has been quite interesting.  In fact, unless Felix has added all of the SNPs to the other ancient kits, this is the only kit in existence that has all of the SNPs from all of the companies included.

My thanks to Felix Immanuel (formerly Felix Chandrakumar) and John Olson for assistance with research for this article.

2014 Top Genetic Genealogy Happenings – A Baker’s Dozen +1

It’s that time again, to look over the year that has just passed and take stock of what has happened in the genetic genealogy world.  I wrote a review in both 2012 and 2013 as well.  Looking back, these momentous happenings seem quite “old hat” now.  For example, both www.GedMatch.com and www.DNAGedcom.com, once new, have become indispensable tools that we take for granted.  Please keep in mind that both of these tools (as well as others in the Tools section, below) depend on contributions, although GedMatch now has a tier 1 subscription offering for $10 per month as well.

So what was the big news in 2014?

Beyond the Tipping Point

Genetic genealogy has gone over the tipping point.  Genetic genealogy is now, unquestionably, mainstream and lots of people are taking part.  From the best I can figure, there are now approaching or have surpassed three million tests or test records, although certainly some of those are duplicates.

  • 500,000+ at 23andMe
  • 700,000+ at Ancestry
  • 700,000+ at Genographic

The organizations above represent “one-test” companies.  Family Tree DNA provides various kinds of genetic genealogy tests to the community and they have over 380,000 individuals with more than 700,000 test records.

In addition to the above mentioned mainstream firms, there are other companies that provide niche testing, often in addition to Family Tree DNA Y results.

In addition, there is what I would refer to as a secondary market for testing as well which certainly attracts people who are not necessarily genetic genealogists but who happen across their corporate information and decide the test looks interesting.  There is no way of knowing how many of those tests exist.

Additionally, there is still the Sorenson data base with Y and mtDNA tests which reportedly exceeded their 100,000 goal.

Spencer Wells spoke about the “viral spread threshold” in his talk in Houston at the International Genetic Genealogy Conference in October and terms 2013 as the year of infection.  I would certainly agree.

spencer near term

Autosomal Now the New Normal

Another change in the landscape is that now, autosomal DNA has become the “normal” test.  The big attraction to autosomal testing is that anyone can play and you get lots of matches.  Earlier in the year, one of my cousins was very disappointed in her brother’s Y DNA test because he only had a few matches, and couldn’t understand why anyone would test the Y instead of autosomal where you get lots and lots of matches.  Of course, she didn’t understand the difference in the tests or the goals of the tests – but I think as more and more people enter the playground – percentagewise – fewer and fewer do understand the differences.

Case in point is that someone contacted me about DNA and genealogy.  I asked them which tests they had taken and where and their answer was “the regular one.”  With a little more probing, I discovered that they took Ancestry’s autosomal test and had no clue there were any other types of tests available, what they could tell him about his ancestors or genetic history or that there were other vendors and pools to swim in as well.

A few years ago, we not only had to explain about DNA tests, but why the Y and mtDNA is important.  Today, we’ve come full circle in a sense – because now we don’t have to explain about DNA testing for genealogy in general but we still have to explain about those “unknown” tests, the Y and mtDNA.  One person recently asked me, “oh, are those new?”

Ancient DNA

This year has seen many ancient DNA specimens analyzed and sequenced at the full genomic level.

The year began with a paper titled, “When Populations Collide” which revealed that contemporary Europeans carry between 1-4% of Neanderthal DNA most often associated with hair and skin color, or keratin.  Africans, on the other hand, carry none or very little Neanderthal DNA.

http://dna-explained.com/2014/01/30/neanderthal-genome-further-defined-in-contemporary-eurasians/

A month later, a monumental paper was published that detailed the results of sequencing a 12,500 Clovis child, subsequently named Anzick or referred to as the Anzick Clovis child, in Montana.  That child is closely related to Native American people of today.

http://dna-explained.com/2014/02/13/clovis-people-are-native-americans-and-from-asia-not-europe/

In June, another paper emerged where the authors had analyzed 8000 year old bones from the Fertile Crescent that shed light on the Neolithic area before the expansion from the Fertile Crescent into Europe.  These would be the farmers that assimilated with or replaced the hunter-gatherers already living in Europe.

http://dna-explained.com/2014/06/09/dna-analysis-of-8000-year-old-bones-allows-peek-into-the-neolithic/

Svante Paabo is the scientist who first sequenced the Neanderthal genome.  Here is a neanderthal mangreat interview and speech.  This man is so interesting.  If you have not read his book, “Neanderthal Man, In Search of Lost Genomes,” I strongly recommend it.

http://dna-explained.com/2014/07/22/finding-your-inner-neanderthal-with-evolutionary-geneticist-svante-paabo/

In the fall, yet another paper was released that contained extremely interesting information about the peopling and migration of humans across Europe and Asia.  This was just before Michael Hammer’s presentation at the Family Tree DNA conference, so I covered the paper along with Michael’s information about European ancestral populations in one article.  The take away messages from this are two-fold.  First, there was a previously undefined “ghost population” called Ancient North Eurasian (ANE) that is found in the northern portion of Asia that contributed to both Asian populations, including those that would become the Native Americans and European populations as well.  Secondarily, the people we thought were in Europe early may not have been, based on the ancient DNA remains we have to date.  Of course, that may change when more ancient DNA is fully sequenced which seems to be happening at an ever-increasing rate.

http://dna-explained.com/2014/10/21/peopling-of-europe-2014-identifying-the-ghost-population/

Lazaridis tree

Ancient DNA Available for Citizen Scientists

If I were to give a Citizen Scientist of the Year award, this year’s award would go unquestionably to Felix Chandrakumar for his work with the ancient genome files and making them accessible to the genetic genealogy world.  Felix obtained the full genome files from the scientists involved in full genome analysis of ancient remains, reduced the files to the SNPs utilized by the autosomal testing companies in the genetic genealogy community, and has made them available at GedMatch.

http://dna-explained.com/2014/09/22/utilizing-ancient-dna-at-gedmatch/

If this topic is of interest to you, I encourage you to visit his blog and read his many posts over the past several months.

https://plus.google.com/+FelixChandrakumar/posts

The availability of these ancient results set off a sea of comparisons.  Many people with Native heritage matched Anzick’s file at some level, and many who are heavily Native American, particularly from Central and South America where there is less admixture match Anzick at what would statistically be considered within a genealogical timeframe.  Clearly, this isn’t possible, but it does speak to how endogamous populations affect DNA, even across thousands of years.

http://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Because Anzick is matching so heavily with the Mexican, Central and South American populations, it gives us the opportunity to extract mitochondrial DNA haplogroups from the matches that either are or may be Native, if they have not been recorded before.

http://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Needless to say, the matches of these ancient kits with contemporary people has left many people questioning how to interpret the results.  The answer is that we don’t really know yet, but there is a lot of study as well as speculation occurring.  In the citizen science community, this is how forward progress is made…eventually.

http://dna-explained.com/2014/09/25/ancient-dna-matches-what-do-they-mean/

http://dna-explained.com/2014/09/30/ancient-dna-matching-a-cautionary-tale/

More ancient DNA samples for comparison:

http://dna-explained.com/2014/10/04/more-ancient-dna-samples-for-comparison/

A Siberian sample that also matches the Malta Child whose remains were analyzed in late 2013.

http://dna-explained.com/2014/11/12/kostenki14-a-new-ancient-siberian-dna-sample/

Felix has prepared a list of kits that he has processed, along with their GedMatch numbers and other relevant information, like gender, haplogroup(s), age and location of sample.

http://www.y-str.org/p/ancient-dna.html

Furthermore, in a collaborative effort with Family Tree DNA, Felix formed an Ancient DNA project and uploaded the ancient autosomal files.  This is the first time that consumers can match with Ancient kits within the vendor’s data bases.

https://www.familytreedna.com/public/Ancient_DNA

Recently, GedMatch added a composite Archaic DNA Match comparison tool where your kit number is compared against all of the ancient DNA kits available.  The output is a heat map showing which samples you match most closely.

gedmatch ancient heat map

Indeed, it has been a banner year for ancient DNA and making additional discoveries about DNA and our ancestors.  Thank you Felix.

Haplogroup Definition

That SNP tsunami that we discussed last year…well, it made landfall this year and it has been storming all year long…in a good way.  At least, ultimately, it will be a good thing.  If you asked the haplogroup administrators today about that, they would probably be too tired to answer – as they’ve been quite overwhelmed with results.

The Big Y testing has been fantastically successful.  This is not from a Family Tree DNA perspective, but from a genetic genealogy perspective.  Branches have been being added to and sawed off of the haplotree on a daily basis.  This forced the renaming of the haplogroups from the old traditional R1b1a2 to R-M269 in 2012.  While there was some whimpering then, it would be nothing like the outright wailing now that would be occurring as haplogroup named reached 20 or so digits.

Alice Fairhurst discussed the SNP tsunami at the DNA Conference in Houston in October and I’m sure that the pace hasn’t slowed any between now and then.  According to Alice, in early 2014, there were 4115 individual SNPs on the ISOGG Tree, and as of the conference, there were 14,238 SNPs, with the 2014 addition total at that time standing at 10,213.  That is over 1000 per month or about 35 per day, every day.

Yes, indeed, that is the definition of a tsunami.  Every one of those additions requires one of a number of volunteers, generally haplogroup project administrators to evaluate the various Big Y results, the SNPs and novel variants included, where they need to be inserted in the tree and if branches need to be rearranged.  In some cases, naming request for previously unknown SNPs also need to be submitted.  This is all done behind the scenes and it’s not trivial.

The project I’m closest to is the R1b L-21 project because my Estes males fall into that group.  We’ve tested several, and I’ll be writing an article as soon as the final test is back.

The tree has grown unbelievably in this past year just within the L21 group.  This project includes over 700 individuals who have taken the Big Y test and shared their results which has defined about 440 branches of the L21 tree.  Currently there are almost 800 kits available if you count the ones on order and the 20 or so from another vendor.

Here is the L21 tree in January of 2014

L21 Jan 2014 crop

Compare this with today’s tree, below.

L21 dec 2014

Michael Walsh, Richard Stevens, David Stedman need to be commended for their incredible work in the R-L21 project.  Other administrators are doing equivalent work in other haplogroup projects as well.  I big thank you to everyone.  We’d be lost without you!

One of the results of this onslaught of information is that there have been fewer and fewer academic papers about haplogroups in the past few years.  In essence, by the time a paper can make it through the peer review cycle and into publication, the data in the paper is often already outdated relative to the Y chromosome.  Recently a new paper was released about haplogroup C3*.  While the data is quite valid, the authors didn’t utilize the new SNP naming nomenclature.  Before writing about the topic, I had to translate into SNPese.  Fortunately, C3* has been relatively stable.

http://dna-explained.com/2014/12/23/haplogroup-c3-previously-believed-east-asian-haplogroup-is-proven-native-american/

10th Annual International Conference on Genetic Genealogy

The Family Tree DNA International Conference on Genetic Genealogy for project administrators is always wonderful, but this year was special because it was the 10th annual.  And yes, it was my 10th year attending as well.  In all these years, I had never had a photo with both Max and Bennett.  Everyone is always so busy at the conferences.  Getting any 3 people, especially those two, in the same place at the same time takes something just short of a miracle.

roberta, max and bennett

Ten years ago, it was the first genetic genealogy conference ever held, and was the only place to obtain genetic genealogy education outside of the rootsweb genealogy DNA list, which is still in existence today.  Family Tree DNA always has a nice blend of sessions.  I always particularly appreciate the scientific sessions because those topics generally aren’t covered elsewhere.

http://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

http://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

http://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

http://dna-explained.com/2014/10/15/tenth-annual-family-tree-dna-conference-wrapup/

Jennifer Zinck wrote great recaps of each session and the ISOGG meeting.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

I thank Family Tree DNA for sponsoring all 10 conferences and continuing the tradition.  It’s really an amazing feat when you consider that 15 years ago, this industry didn’t exist at all and wouldn’t exist today if not for Max and Bennett.

Education

Two educational venues offered classes for genetic genealogists and have made their presentations available either for free or very reasonably.  One of the problems with genetic genealogy is that the field is so fast moving that last year’s session, unless it’s the very basics, is probably out of date today.  That’s the good news and the bad news.

http://dna-explained.com/2014/11/12/genetic-genealogy-ireland-2014-presentations 

http://dna-explained.com/2014/09/26/educational-videos-from-international-genetic-genealogy-conference-now-available/

In addition, three books have been released in 2014.emily book

In January, Emily Aulicino released Genetic Genealogy, The Basics and Beyond.

richard hill book

In October, Richard Hill released “Guide to DNA Testing: How to Identify Ancestors, Confirm Relationships and Measure Ethnicity through DNA Testing.”

david dowell book

Most recently, David Dowell’s new book, NextGen Genealogy: The DNA Connection was released right after Thanksgiving.

 

Ancestor Reconstruction – Raising the Dead

This seems to be the year that genetic genealogists are beginning to reconstruct their ancestors (on paper, not in the flesh) based on the DNA that the ancestors passed on to various descendants.  Those segments are “gathered up” and reassembled in a virtual ancestor.

I utilized Kitty Cooper’s tool to do just that.

http://dna-explained.com/2014/10/03/ancestor-reconstruction/

henry bolton probablyI know it doesn’t look like much yet but this is what I’ve been able to gather of Henry Bolton, my great-great-great-grandfather.

Kitty did it herself too.

http://blog.kittycooper.com/2014/08/mapping-an-ancestral-couple-a-backwards-use-of-my-segment-mapper/

http://blog.kittycooper.com/2014/09/segment-mapper-tool-improvements-another-wold-dna-map/

Ancestry.com wrote a paper about the fact that they have figured out how to do this as well in a research environment.

http://corporate.ancestry.com/press/press-releases/2014/12/ancestrydna-reconstructs-partial-genome-of-person-living-200-years-ago/

http://www.thegeneticgenealogist.com/2014/12/16/ancestrydna-recreates-portions-genome-david-speegle-two-wives/

GedMatch has created a tool called, appropriately, Lazarus that does the same thing, gathers up the DNA of your ancestor from their descendants and reassembles it into a DNA kit.

Blaine Bettinger has been working with and writing about his experiences with Lazarus.

http://www.thegeneticgenealogist.com/2014/10/20/finally-gedmatch-announces-monetization-strategy-way-raise-dead/

http://www.thegeneticgenealogist.com/2014/12/09/recreating-grandmothers-genome-part-1/

http://www.thegeneticgenealogist.com/2014/12/14/recreating-grandmothers-genome-part-2/

Tools

Speaking of tools, we have some new tools that have been introduced this year as well.

Genome Mate is a desktop tool used to organize data collected by researching DNA comparsions and aids in identifying common ancestors.  I have not used this tool, but there are others who are quite satisfied.  It does require Microsoft Silverlight be installed on your desktop.

The Autosomal DNA Segment Analyzer is available through www.dnagedcom.com and is a tool that I have used and found very helpful.  It assists you by visually grouping your matches, by chromosome, and who you match in common with.

adsa cluster 1

Charting Companion from Progeny Software, another tool I use, allows you to colorize and print or create pdf files that includes X chromosome groupings.  This greatly facilitates seeing how the X is passed through your ancestors to you and your parents.

x fan

WikiTree is a free resource for genealogists to be able to sort through relationships involving pedigree charts.  In November, they announced Relationship Finder.

Probably the best example I can show of how WikiTree has utilized DNA is using the results of King Richard III.

wiki richard

By clicking on the DNA icon, you see the following:

wiki richard 2

And then Richard’s Y, mitochondrial and X chromosome paths.

wiki richard 3

Since Richard had no descendants, to see how descendants work, click on his mother, Cecily of York’s DNA descendants and you’re shown up to 10 generations.

wiki richard 4

While this isn’t terribly useful for Cecily of York who lived and died in the 1400s, it would be incredibly useful for finding mitochondrial descendants of my ancestor born in 1802 in Virginia.  I’d love to prove she is the daughter of a specific set of parents by comparing her DNA with that of a proven daughter of those parents!  Maybe I’ll see if I can find her parents at WikiTree.

Kitty Cooper’s blog talks about additional tools.  I have used Kitty’s Chromosome mapping tools as discussed in ancestor reconstruction.

Felix Chandrakumar has created a number of fun tools as well.  Take a look.  I have not used most of these tools, but there are several I’ll be playing with shortly.

Exits and Entrances

With very little fanfare, deCODEme discontinued their consumer testing and reminded people to download their date before year end.

http://dna-explained.com/2014/09/30/decodeme-consumer-tests-discontinued/

I find this unfortunate because at one time, deCODEme seemed like a company full of promise for genetic genealogy.  They failed to take the rope and run.

On a sad note, Lucas Martin who founded DNA Tribes unexpectedly passed away in the fall.  DNA Tribes has been a long-time player in the ethnicity field of genetic genealogy.  I have often wondered if Lucas Martin was a pseudonym, as very little information about Lucas was available, even from Lucas himself.  Neither did I find an obituary.  Regardless, it’s sad to see someone with whom the community has worked for years pass away.  The website says that they expect to resume offering services in January 2015. I would be cautious about ordering until the structure of the new company is understood.

http://www.dnatribes.com/

In the last month, a new offering has become available that may be trying to piggyback on the name and feel of DNA Tribes, but I’m very hesitant to provide a link until it can be determined if this is legitimate or bogus.  If it’s legitimate, I’ll be writing about it in the future.

However, the big news exit was Ancestry’s exit from the Y and mtDNA testing arena.  We suspected this would happen when they stopped selling kits, but we NEVER expected that they would destroy the existing data bases, especially since they maintain the Sorenson data base as part of their agreement when they obtained the Sorenson data.

http://dna-explained.com/2014/10/02/ancestry-destroys-irreplaceable-dna-database/

The community is still hopeful that Ancestry may reverse that decision.

Ancestry – The Chromosome Browser War and DNA Circles

There has been an ongoing battle between Ancestry and the more seasoned or “hard-core” genetic genealogists for some time – actually for a long time.

The current and most long-standing issue is the lack of a chromosome browser, or any similar tools, that will allow genealogists to actually compare and confirm that their DNA match is genuine.  Ancestry maintains that we don’t need it, wouldn’t know how to use it, and that they have privacy concerns.

Other than their sessions and presentations, they had remained very quiet about this and not addressed it to the community as a whole, simply saying that they were building something better, a better mousetrap.

In the fall, Ancestry invited a small group of bloggers and educators to visit with them in an all-day meeting, which came to be called DNA Day.

http://dna-explained.com/2014/10/08/dna-day-with-ancestry/

In retrospect, I think that Ancestry perceived that they were going to have a huge public relations issue on their hands when they introduced their new feature called DNA Circles and in the process, people would lose approximately 80% of their current matches.  I think they were hopeful that if they could educate, or convince us, of the utility of their new phasing techniques and resulting DNA Circles feature that it would ease the pain of people’s loss in matches.

I am grateful that they reached out to the community.  Some very useful dialogue did occur between all participants.  However, to date, nothing more has happened nor have we received any additional updates after the release of Circles.

Time will tell.

http://dna-explained.com/2014/11/18/in-anticipation-of-ancestrys-better-mousetrap/

http://dna-explained.com/2014/11/19/ancestrys-better-mousetrap-dna-circles/

DNA Circles 12-29-2014

DNA Circles, while interesting and somewhat useful, is certainly NOT a replacement for a chromosome browser, nor is it a better mousetrap.

http://dna-explained.com/2014/11/30/chromosome-browser-war/

In fact, the first thing you have to do when you find a DNA Circle that you have not verified utilizing raw data and/or chromosome browser tools from either 23andMe, Family Tree DNA or Gedmatch, is to talk your matches into transferring their DNA to Family Tree DNA or download to Gedmatch, or both.

http://dna-explained.com/2014/11/27/sarah-hickerson-c1752-lost-ancestor-found-52-ancestors-48/

I might add that the great irony of finding the Hickerson DNA Circle that led me to confirm that ancestry utilizing both Family Tree DNA and GedMatch is that today, when I checked at Ancestry, the Hickerson DNA Circle is no longer listed.  So, I guess I’ve been somehow pruned from the circle.  I wonder if that is the same as being voted off of the island.  So, word to the wise…check your circles often…they change and not always in the upwards direction.

The Seamy Side – Lies, Snake Oil Salesmen and Bullys

Unfortunately a seamy side, an underbelly that’s rather ugly has developed in and around the genetic genealogy industry.  I guess this was to be expected with the rapid acceptance and increasing popularity of DNA testing, but it’s still very unfortunate.

Some of this I expected, but I didn’t expect it to be so…well…blatant.

I don’t watch late night TV, but I’m sure there are now DNA diets and DNA dating and just about anything else that could be sold with the allure of DNA attached to the title.

I googled to see if this was true, and it is, although I’m not about to click on any of those links.

google dna dating

google dna diet

Unfortunately, within the ever-growing genetic genealogy community a rather large rift has developed over the past couple of years.  Obviously everyone can’t get along, but this goes beyond that.  When someone disagrees, a group actively “stalks” the person, trying to cost them their employment, saying hate filled and untrue things and even going so far as to create a Facebook page titled “Against<personname>.”  That page has now been removed, but the fact that a group in the community found it acceptable to create something like that, and their friends joined, is remarkable, to say the least.  That was accompanied by death threats.

Bullying behavior like this does not make others feel particularly safe in expressing their opinions either and is not conducive to free and open discussion. As one of the law enforcement officers said, relative to the events, “This is not about genealogy.  I don’t know what it is about, yet, probably money, but it’s not about genealogy.”

Another phenomenon is that DNA is now a hot topic and is obviously “selling.”  Just this week, this report was published, and it is, as best we can tell, entirely untrue.

http://worldnewsdailyreport.com/usa-archaeologists-discover-remains-of-first-british-settlers-in-north-america/

There were several tip offs, like the city (Lanford) and county (Laurens County) is not in the state where it is attributed (it’s in SC not NC), and the name of the institution is incorrect (Johns Hopkins, not John Hopkins).  Additionally, if you google the name of the magazine, you’ll see that they specialize in tabloid “faux reporting.”  It also reads a lot like the King Richard genuine press release.

http://urbanlegends.about.com/od/Fake-News/tp/A-Guide-to-Fake-News-Websites.01.htm

Earlier this year, there was a bogus institutional site created as well.

On one of the DNA forums that I frequent, people often post links to articles they find that are relevant to DNA.  There was an interesting article, which has now been removed, correlating DNA results with latitude and altitude.  I thought to myself, I’ve never heard of that…how interesting.   Here’s part of what the article said:

Researchers at Aberdeen College’s Havering Centre for Genetic Research have discovered an important connection between our DNA and where our ancestors used to live.

Tiny sequence variations in the human genome sometimes called Single Nucleotide Polymorphisms (SNPs) occur with varying frequency in our DNA.  These have been studied for decades to understand the major migrations of large human populations.  Now Aberdeen College’s Dr. Miko Laerton and a team of scientists have developed pioneering research that shows that these differences in our DNA also reveal a detailed map of where our own ancestors lived going back thousands of years.

Dr. Laerton explains:  “Certain DNA sequence variations have always been important signposts in our understanding of human evolution because their ages can be estimated.  We’ve known for years that they occur most frequently in certain regions [of DNA], and that some alleles are more common to certain geographic or ethnic groups, but we have never fully understood the underlying reasons.  What our team found is that the variations in an individual’s DNA correlate with the latitudes and altitudes where their ancestors were living at the time that those genetic variations occurred.  We’re still working towards a complete understanding, but the knowledge that sequence variations are connected to latitude and altitude is a huge breakthrough by itself because those are enough to pinpoint where our ancestors lived at critical moments in history.”

The story goes on, but at the bottom, the traditional link to the publication journal is found.

The full study by Dr. Laerton and her team was published in the September issue of the Journal of Genetic Science.

I thought to myself, that’s odd, I’ve never heard of any of these people or this journal, and then I clicked to find this.

Aberdeen College bogus site

About that time, Debbie Kennett, DNA watchdog of the UK, posted this:

April Fools Day appears to have arrived early! There is no such institution as Aberdeen College founded in 1394. The University of Aberdeen in Scotland was founded in 1495 and is divided into three colleges: http://www.abdn.ac.uk/about/colleges-schools-institutes/colleges-53.php

The picture on the masthead of the “Aberdeen College” website looks very much like a photo of Aberdeen University. This fake news item seems to be the only live page on the Aberdeen College website. If you click on any other links, including the link to the so-called “Journal of Genetic Science”, you get a message that the website is experienced “unusually high traffic”. There appears to be no such journal anyway.

We also realized that Dr. Laerton, reversed, is “not real.”

I still have no idea why someone would invest the time and effort into the fake website emulating the University of Aberdeen, but I’m absolutely positive that their motives were not beneficial to any of us.

What is the take-away of all of this?  Be aware, very aware, skeptical and vigilant.  Stick with the mainstream vendors unless you realize you’re experimenting.

King Richard

King Richard III

The much anticipated and long-awaited DNA results on the remains of King Richard III became available with a very unexpected twist.  While the science team feels that they have positively identified the remains as those of Richard, the Y DNA of Richard and another group of men supposed to have been descended from a common ancestor with Richard carry DNA that does not match.

http://dna-explained.com/2014/12/09/henry-iii-king-of-england-fox-in-the-henhouse-52-ancestors-49/

http://dna-explained.com/2014/12/05/mitochondrial-dna-mutation-rates-and-common-ancestors/

Debbie Kennett wrote a great summary article.

http://cruwys.blogspot.com/2014/12/richard-iii-and-use-of-dna-as-evidence.html

More Alike than Different

One of the life lessons that genetic genealogy has held for me is that we are more closely related that we ever knew, to more people than we ever expected, and we are far more alike than different.  A recent paper recently published by 23andMe scientists documents that people’s ethnicity reflect the historic events that took place in the part of the country where their ancestors lived, such as slavery, the Trail of Tears and immigration from various worldwide locations.

23andMe European African map

From the 23andMe blog:

The study leverages samples of unprecedented size and precise estimates of ancestry to reveal the rate of ancestry mixing among American populations, and where it has occurred geographically:

  • All three groups – African Americans, European Americans and Latinos – have ancestry from Africa, Europe and the Americas.
  • Approximately 3.5 percent of European Americans have 1 percent or more African ancestry. Many of these European Americans who describe themselves as “white” may be unaware of their African ancestry since the African ancestor may be 5-10 generations in the past.
  • European Americans with African ancestry are found at much higher frequencies in southern states than in other parts of the US.

The ancestry proportions point to the different regional impacts of slavery, immigration, migration and colonization within the United States:

  • The highest levels of African ancestry among self-reported African Americans are found in southern states, especially South Carolina and Georgia.
  • One in every 20 African Americans carries Native American ancestry.
  • More than 14 percent of African Americans from Oklahoma carry at least 2 percent Native American ancestry, likely reflecting the Trail of Tears migration following the Indian Removal Act of 1830.
  • Among self-reported Latinos in the US, those from states in the southwest, especially from states bordering Mexico, have the highest levels of Native American ancestry.

http://news.sciencemag.org/biology/2014/12/genetic-study-reveals-surprising-ancestry-many-americans?utm_campaign=email-news-weekly&utm_source=eloqua

23andMe provides a very nice summary of the graphics in the article at this link:

http://blog.23andme.com/wp-content/uploads/2014/10/Bryc_ASHG2014_textboxes.pdf

The academic article can be found here:

http://www.cell.com/ajhg/home

2015

So what does 2015 hold? I don’t know, but I can’t wait to find out. Hopefully, it holds more ancestors, whether discovered through plain old paper research, cousin DNA testing or virtually raised from the dead!

What would my wish list look like?

  • More ancient genomes sequenced, including ones from North and South America.
  • Ancestor reconstruction on a large scale.
  • The haplotree becoming fleshed out and stable.
  • Big Y sequencing combined with STR panels for enhanced genealogical research.
  • Improved ethnicity reporting.
  • Mitochondrial DNA search by ancestor for descendants who have tested.
  • More tools, always more tools….
  • More time to use the tools!

Here’s wishing you an ancestor filled 2015!

 

Haplogroup C3* – Previously Believed East Asian Haplogroup is Proven Native American

In a paper just released, “Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping,” by Mezzavilla et al, research shows that haplogroup C3* (M217, P44, Z1453), previously believed to be exclusively East Asian, is indeed, Native American.

Subgroup C-P39 (formerly C3b) was previously proven to be Native and is found primarily in the eastern US and Canada although it was also reported among the Na-Dene in the 2004 paper by Zegura et all titled “High-resolution SNPs and microsatellite haplotypes point to a single recent entry of Native American Y chromosomes into the Americas.”

The discovery of C3* as Native is great news, as it more fully defines the indigenous American Y chromosome landscape.  It also is encouraging in that several mitochondrial haplogroups, including variants of M, have also been found in Central and South America, also not previously found in North America and also only previously found in Asia, Polynesia and even as far away as Madagascar.  They too had to come from someplace and desperately need additional research of this type.  There is a great deal that we don’t know today that remains to be discovered.  As in the past, what is thought to be fact doesn’t always hold water under the weight of new discoveries – so it’s never wise to drive a stake too far in the ground in the emerging world of genetics.  It’s likely to get moved!

You can view the Y DNA projects for C-M217 here, C-P39 here, and the main C project here.  Please note that on the latest version of the ISOGG tree, M217, P44 and Z1453 are now listed as C2, not C3.  Also note that I added the SNP names in this article.  The Mezzavilla paper references the earlier C3 type naming convention which I have used in discussing their article to avoid confusion.

In the Messavilla study, fourteen individuals from the Kichwa and Waorani populations of South America were discovered to carry haplogroup C3*.  Most of the individuals within these populations carry variants of expected haplogroup Q, with the balance of 26% of the Kichwa samples and 7.5% of the Waorani samples carrying C3*.  MRCA estimates between the groups are estimated to be between 5.0-6.2 KYA, or years before present.

Other than one C3* individual in Alaska, C3* is unknown in the rest of the Native world including all of North American and the balance of Central and South America, but is common and widespread in East Asia.

In the paper, the authors state that:

We set out to test whether or not the haplogroup C3* Y chromosomes found at a mean frequency of 17% in two Ecuadorian populations could have been introduced by migration from East Asia, where this haplogroup is common. We considered recent admixture in the last few generations and, based on an archaeological link between the middle Jōmon culture in Japan and the Valdivia culture in Ecuador, a specific example of ancient admixture between Japan and Ecuador 6 Kya.

In a paper, written by Estrada et all, titled “Possible Transpacific Contact on the Cost of Ecuador”, Estrada states that the earliest pottery-producing culture on the coast of Ecuador, the Valdivia culture, shows many striking similarities in decoration and vessel shape to pottery of eastern Asia. In Japan, resemblances are closest to the Middle Jomon period. Both early Valdivia and Middle Jomon are dated between 2000 and 3000 B.C. A transpacific contact from Asia to Ecuador during this time is postulated.

This of course, opens the door for Asian haplogroups not found elsewhere to be found in Ecuador.

The introduction of the Mezzabilla paper states:

The consensus view of the peopling of the Americas, incorporating archaeological, linguistic and genetic evidence, proposes colonization by a small founder population from Northeast Asia via Beringia 15–20 Kya (thousand years ago), followed by one or two additional migrations also via Alaska, contributing only to the gene pools of North Americans, and little subsequent migration into the Americas south of the Arctic Circle before the voyages from Europe initiated by Columbus in 1492.

In the most detailed genetic analysis thus far, for example, Reich and colleagues identified three sources of Native American ancestry: a ‘First American’ stream contributing to all Native populations, a second stream contributing only to Eskimo-Aleut-speaking Arctic populations, and a third stream contributing only to a Na-Dene-speaking North American population.

Nevertheless, there is strong evidence for additional long-distance contacts between the Americas and other continents between these initial migrations and 1492. Norse explorers reached North America around 1000 CE and established a short-lived colony, documented in the Vinland Sagas and supported by archaeological excavations. The sweet potato (Ipomoea batatas) was domesticated in South America (probably Peru), but combined genetic and historical analyses demonstrate that it was transported from South America to Polynesia before 1000–1100 CE. Some inhabitants of Easter Island (Rapa Nui) carry HLA alleles characteristic of South America, most readily explained by gene flow after the colonization of the island around 1200 CE but before European contact in 1722. In Brazil, two nineteenth-century Botocudo skulls carrying the mtDNA Polynesian motif have been reported, and a Pre-Columbian date for entry of this motif into the Americas discussed, although a more recent date was considered more likely. Thus South America was in two-way contact with other continental regions in prehistoric times, but there is currently no unequivocal evidence for outside gene flow into South America between the initial colonization by the ‘First American’ stream and European contact.

The researchers originally felt that the drift concept, which means that the line was simply lost to time in other American locations outside of Ecuador, was not likely because the populations of North and Central America have in general experienced less drift and retained more diversity than those in South America.

The paper abstract states:

The colonization of Americas is thought to have occurred 15–20 thousand years ago (Kya), with little or no subsequent migration into South America until the European expansions beginning 0.5 Kya. Recently, however, haplogroup C3* Y chromosomes were discovered in two nearby Native American populations from Ecuador. Since this haplogroup is otherwise nearly absent from the Americas but is common in East Asia, and an archaeological link between Ecuador and Japan is known from 6 Kya, an additional migration 6 Kya was suggested.

Here, we have generated high-density autosomal SNP genotypes from the Ecuadorian populations and compared them with genotypes from East Asia and elsewhere to evaluate three hypotheses: a recent migration from Japan, a single pulse of migration from Japan 6 Kya, and no migration after the First Americans.

First, using forward-time simulations and an appropriate demographic model, we investigated our power to detect both ancient and recent gene flow at different levels. Second, we analyzed 207,321 single nucleotide polymorphisms from 16 Ecuadorian individuals, comparing them with populations from the HGDP panel using descriptive and formal tests for admixture. Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6 Kya ago could be detected.

However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere.

This graphic from the paper, shows the three hypothesis that were being tested, with recent admixture being ruled out entirely, and admixture 6000 years ago most likely being ruled out as well by utilizing autosomal DNA.

Mezzavilla Map crop

The conclusions from the paper states that:

Three different hypotheses to explain the presence of C3* Y chromosomes in Ecuador but not elsewhere in the Americas were tested: recent admixture, ancient admixture ∼6 Kya, or entry as a founder haplogroup 15–20 Kya with subsequent loss by drift elsewhere. We can convincingly exclude the recent admixture model, and find no support for the ancient admixture scenario, although cannot completely exclude it. Overall, our analyses support the hypothesis that C3* Y chromosomes were present in the “First American” ancestral population, and have been lost by drift from most modern populations except the Ecuadorians.

It will be interesting as additional people are tested and more ancient DNA is discovered and processed to see what other haplogroups will be found in Native people and remains that were previously thought to be exclusively Asian, or perhaps even African or European.

This discovery also begs a different sort of question that will eventually need to be answered.  Clearly, we classify the descendants of people who arrived with the original Beringian and subsequent wave migrants as Native American, Indigenous American or First Nations.  However, how would we classify these individuals if they had arrived 6000 years ago, or 2000 years ago – still before Columbus or significant European or African admixture – but not with the first wave of Asian founders?  If found today in South Americans, could they be taken as evidence of Native American heritage?  Clearly, in this context, yes – as opposed to African or European.  Would they still be considered only Asian or both Asian and Native American in certain contexts – as is now the case for haplogroup C3* (M217)?  This scenario could easily and probably will happen with other haplogroups as well.

Kostenki14 – A New Ancient Siberian DNA Sample

k14 skeleton

This week, published in Science, we find another ancient DNA full genome sequence from Siberia in an article titled “Genomic structure in Europeans dating back at least 36,200 years” by Seguin-Orlando et al.. This sample, partially shown above, is quite old and closely related to the Mal’ta child, also found in Siberia from about 24,000 years ago. Interestingly enough, K14 carries more Neanderthal DNA than current Europeans. This skeleton was actually excavated in 1954, but was only recently genetically analyzed.

k14 mapFrom the paper, this map above shows the locations of recently analyzed ancient DNA samples.  Note that even though K14 and Mal’ta child are similar, they are not located in close geographic proximity.

k14 population clusterAlso from the paper, this chart of population clusters is quite interesting, because we can see which of these ancient samples share some heritage with today’s indigenous American populations, shown in grey. UPGH=Upper Paleolithic Hunter-Gatherer, MHG=Mesolithic Hunter Gatherer, which is later in time that Paleolithic, and NEOL=Neolithic indicating the farming population that arrived in Europe approximately 7,000-10,000 years ago from the Middle East

You can see that the Neolithic samples show no trace of ancestry with today’s Native people, but both pre-Neolithic Hunter-Gatherer cultures show some amount of shared ancestry with Native people. However, to date, MA1, the Malta child is the most closely related and carries the most DNA in common with today’s Native people.

Felix Chandrakumar is currently preparing the K14 genome for addition to the ancient DNA kits at GedMatch.  It will be interesting to see if this sample also matches currently living individuals.

Also from the K14 paper, you can see on the map below where K14 matches current worldwide and European populations, where the warmer colors, i.e. red, indicated a closer match.

K14 population matches

Of interest to genealogists and population geneticists, K14’s mitochondrial haplogroup is U2 and his Y haplogroup is C-M130, the same as LaBrana, a late Mesolithic hunter-gatherer found in northern Spain. Haplogroup C is, of course, one of the base haplogroups for the Native people of the Americas.

The K14 paper further fleshes out the new peopling of Europe diagram discussed in my Peopling of Europe article.

This map, from the Lazardis “Ancient human genomes suggest three ancestral populations for present-day Europeans” paper published in September 2014, shows the newly defined map including Ancient North Eurasian in this diagram.

Lazaridis tree

K14 adds to this diagram in the following manner, although the paths are flipped right to left.

K14 tree

Blue represent current populations, red are ancient remains and green are ancestral populations.

Dienekes wrote about this find as well, here.

Paper Abstract:

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

You can read the full paper at the two links below.

http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114

http://www2.zoo.cam.ac.uk/manica/ms/2014_Seguin_Orlando_et_al_Science.pdf

It’s been a great year for ancient DNA analysis and learning about our ancestral human populations.

However, I have one observation I just have to make about this particular find.

What amazing teeth. Obviously, this culture did not consume sugar!

Peopling of Europe 2014 – Identifying the Ghost Population

Beginning with the full sequencing of the Neanderthal genome, first published in May 2010 by the Max Planck Institute with Svante Paabo at the helm, and followed shortly thereafter with a Denisovan specimen, we began to unravel our ancient history.

neanderthal reconstructed

Neanderthal man, reconstructed at the National Museum of Nature and Science in Tokyo

The photo below shows a step in the process of extracting DNA from ancient bones at Max Planck.

planck extraction

Our Y and mitochondrial DNA haplogroups take us back thousands of years in time, but at some point, where and how people were settling and intermixing becomes fuzzy. Ancient DNA can put the people of that time and place in context.  We have discovered that current populations do not necessarily represent the ancient populations of a particular locale.

Recent information discovered from ancient burials tells us that the people of Europe descend from a 3 pronged model. Until recently, it was believed that Europeans descended from Paleolithic hunter-gatherers and Neolithic farmers, a two-pronged model.

Previously, it was believed that Europe was peopled by the ancient hunter-gatherers, the Paleolithic, who originally settled in Europe beginning about 45,000 years ago. At this time, the Neanderthal were already settled in Europe but weren’t considered to be anatomically modern humans, and it was believed, incorrectly, that the two groups did not interbreed.  These hunter-gatherers were the people who settled in Europe before the last major ice age, the Younger Dryas, taking refuge in the southern portions of Europe and Eurasia, and repeopling the continent after the ice receded, about 12,000 years ago.  By that time, the Neanderthals were gone, or as we now know, at least partially assimilated.

This graphic shows Europe during the last ice age.

ice age euripe

The second settlement wave, the agriculturalist farmers from the Near East either overran or integrated with the hunter-gatherers in the Neolithic period, depending on which theory you subscribe to, about 8000-10,000 years ago.

2012 – Ancient Northern European (ANE) Hints

Beginning in 2012, we began to see hints of a third lineage that contributed to the peopling of Europe as well, from the north. Buried in the 2012 paper, Estimating admixture proportions and dates with ADMIXTOOLS by Patterson et al, was a very interesting tidbit.  This new technique showed a third population, referred to by many as a “ghost population”, because no one knew who they were, that contributed to the European population.

patterson ane

The new population was termed Ancient North Eurasian, or ANE.

Dienekes covered this paper in his blog, but without additional information, in the community in general, there wasn’t much more than a yawn.

2013 – Mal’ta Child Stirs Excitement

The first real hint of meat on the bones of ANE came in the form of ancient DNA analysis of a 24,000 year old Siberian boy that has come to be named Mal’ta (Malta) Child. In the original paper, by Raghaven et al, Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, he was referred to as MA-1.  I wrote about this in my article titled Native American Gene Flow – Europe?, Asia and the Americas.   Dienekes wrote about this paper as well.

This revelation caused quite a stir, because it was reported that the Ancestor of Native Americans in Asia was 30% Western Eurasian.  Unfortunately, in some cases, this was immediately interpreted to mean that Native Americans had come directly from Europe which is not what this paper said, nor inferred.  It was also inferred that the haplogroups of this child, R* (Y) and U (mtDNA) were Native American, which is also incorrect.  To date, there is no evidence for migration to the New World from Europe in ancient times, but that doesn’t mean we aren’t still looking for that evidence in early burials.

What this paper did show was that Europeans and Native Americans shared a common ancestor, and that the Siberian population had contributed to the European population as well as the Native American population.  In other words, descendants settled in both directions, east and west.

The most fascinating aspect of this paper was the match distribution map, below, showing which populations Malta child matched most closely.

malta child map

As you can see, MA-1, Malta Child, matches the Native American population most closely, followed by the northern European and Greenland populations. The further south in Europe and Asia, the more distant the matches and the darker the blue.

2013 – Michael Hammer and Haplogroup R

Last fall at the Family Tree DNA conference, Dr. Michael Hammer, from the Hammer Lab at the University of Arizona discussed new findings relative to ancient burials, specifically in relation to haplogroup R, or more specifically, the absence of haplogroup R in those early burials.

hammer 2013

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Based on the various theories and questions, ancient burials were enlightening.

hammer 2013-4

hammer 2013-5

In 2013, there were a total of 32 burials from the Neolithic period, after farmers arrived from the Near East, and haplogroup R did not appear. Instead, haplogroups G, I and E were found.

hammer 2013-7

What this tells us is that haplogroup R, as well as other haplogroup, weren’t present in Europe at this time. Having said this, these burials were in only 4 locations and, although unlikely, R could be found in other locations.

hammer 2-13-8

hammer 2013-9

hammer 2013-10

hammer 2013-11

Last year, Dr. Hammer concluded that haplogroup R was not found in the Paleolithic and likely arrived with the Neolithic farmers. That shook the community, as it had been widely believed that haplogroup R was one of the founding European haplogroups.

hammer 2013-12

While this provided tantalizing information, we still needed additional evidence. No paper has yet been published that addresses these findings.  The mass full sequencing of the Y chromosome over this past year with the introduction of the Big Y will provide extremely valuable information about the Y chromosome and eventually, the migration path into and across Europe.

2014 – Europe’s Three Ancient Tribes

In September 2014, another paper was published by Lazaridis et al that more fully defined this new ANE branch of the European human family tree.  An article in BBC News titled Europeans drawn from three ancient ‘tribes’ describes it well for the non-scientist.  Of particular interest in this article is the artistic rendering of the ancient individual, based on their genetic markers.  You’ll note that they had dark skin, dark hair and blue eyes, a rather unexpected finding.

In discussing the paper, David Reich from Harvard, one of the co-authors, said, “Prior to this paper, the models we had for European ancestry were two-way mixtures. We show that there are three groups. This also explains the recently discovered genetic connection between Europeans and Native Americans.  The same Ancient North Eurasian group contributed to both of them.”

The paper, Ancient human genomes suggest three ancestral populations for present-day Europeans, appeared as a letter in Nature and is behind a paywall, but the supplemental information is free.

The article summary states the following:

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1, 2, 3, 4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

This paper utilized ancient DNA from several sites and composed the following genetic contribution diagram that models the relationship of European to non-European populations.

Lazaridis tree

Present day samples are colored purple, ancient in red and reconstructed ancestral populations in green. Solid lines represent descent without admixture and dashed lines represent admixture.  WHG=western European hunter-gatherer, EEF=early European farmer and ANE=ancient north Eurasian

2014 – Michael Hammer on Europe’s Ancestral Population

For anyone interested in ancient DNA, 2014 has been a banner years. At the Family Tree DNA conference in Houston, Texas, Dr. Michael Hammer brought the audience up to date on Europe’s ancestral population, including the newly sequenced ancient burials and the information they are providing.

hammer 2014

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Dr. Hammer said that ancient DNA is the key to understanding the historical processes that led up to the modern. He stressed that we need to be careful inferring that the current DNA pattern is reflective of the past because so many layers of culture have occurred between then and now.

hammer 2014-2

Until recently, it was assumed that the genes of the Neolithic farmers replaced those of the Paleolithic hunter-gatherers. Ancient DNA is suggesting that this is not true, at least not on a wholesale level.

hammer 2014-3

The theory, of course, is that we should be able to see them today if they still exist. The migration and settlement pattern in the slide below was from the theory set forth in the 1990s.

hammer 2014-4

In 2013, Dr. Hammer discussed the theory that haplogroup R1b spread into Europe with the farmers from the Near East in the Neolithic. This year, he expanded upon that topic that based on the new findings from ancient burials.

hammer 2014-5

Last year, Dr. Hammer discussed 32 burials from 4 sites. Today, we have information from 15 ancient DNA sites and many of those remains have been full genome sequenced.

hammer 2014-6

Information from papers and recent research suggests that Europeans also have genes from a third source lineage, nicknamed the “ghost population of North Eurasia.”

hammer 2014-7

Scientists are finding a signal of northeast Asian related admixture in northern Europeans, first suggested in 2012.  This was confirmed with the sequencing of Malta child and then in a second sequencing of Afontova Gora2 in south central Siberia.

hammer 2014-8

We have complete genomes from nine ancient Europeans – Mesolithic hunter gatherers and Neothilic farmers. Hammer refers to the Mesolithic here, which is a time period between the Paleolithic (hunter gatherers with stone tools) and the Neolithic (farmers).

hammer 2014-9

In the PCA charts, shown above, you can see that Europeans and people from the Near East cluster separately, except for a bridge formed by a few Mediterranean and Jewish populations. On the slide below, the hunter-gatherers (WHG) and early farmers (EEF) have been overlayed onto the contemporary populations along with the MA-1 (Malta Child) and AG2 (Afontova Gora2) representing the ANE.

hammer 2014-10

When sequenced, separate groups formed including western hunter gathers and early european farmers include Otzi, the iceman.  A third group is the north south clinal variation with ANE contributing to northern European ancestry.  The groups are represented by the circles, above.

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Dr. Hammer said that the team who wrote the “Ancient Human Genomes” paper just recently published used an F3 test, results shown above, which shows whether populations are an admixture of a reference population based on their entire genome. He mentioned that this technique goes well beyond PCA.

hammer 2014-13

Mapped onto populations today, most European populations are a combination of the three early groups. However, the ANE is not found in the ancient Paleolithic or Neolithic burials.  It doesn’t arrive until later.

hammer 2014-14

This tells us that there was a migration event 45,000 years ago from the Levant, followed about 7000 years ago by farmers from the Near East, and that ANE entered the population some time after that. All Europeans today carry some amount of ANE, but ancient burials do not.

These burials also show that southern Europe has more Neolithic farmer genes and northern Europe has more Paleolithic/Mesolithic hunter-gatherer genes.

hammer 2014-15

Pigmentation for light skin came with farmers – blue eyes existed in hunter gatherers even though their skin was dark.

hammer 2014-16

Dr. Hammer created these pie charts of the Y and mitochondrial haplogroups found in the ancient burials as compared to contemporary European haplogroups.

hammer 2014-17

The pie chart on the left shows the haplogroups of the Mesolithic burials, all haplogroup I2 and subclades. Note that in the current German population today, no I2a1b and no I1 was found.  The chart on the right shows current Germans where haplogroup I is a minority.

hammer 2014-18

Therefore, we can conclude that haplogroup I is a good candidate to be identified as a Paleolithic/Mesolithic haplogroup.

This information shows that the past is very different from today.

hammer 2014-19

In 2014 we have many more burials that have been sequenced than last year, as shown on the map above.

Green represents Neolithic farmers, red are Mesolithic hunter-gatherers, brown at bottom right represents more recent samples from the Metallic age.

hammer 2014-20

There are a total of 48 Neolithic burials where haplogroup G dominates. In the Mesolithic, there are a total of six haplogroup I.

This suggests that haplogroup I is a good candidate to be the father of the Paleolithic/Mesolithic and haplogroup G, the founding father of the Neolithic.

In addition to haplogroup G in the Neolithic, one sample of both E1b1b1 (M35) and C were also found in Spain.  E1b1b1 isn’t surprising given it’s north African genesis, but C was quite interesting.

The Metal ages, which according to wiki begin about 3300BC in Europe, is where haplogroup R, along with I1, first appear.

diffusion of metallurgy

Please note that the diffusion of melallurgy map above is not part of Dr. Hammer’s presentation. I have added it for clarification.

hammer 2014-21

Nothing is constant in Europe. The Y DNA was very upheaved, as indicated on the graphic above.  Mitochondrial DNA shifted from pre-Neolithic to Neolithic which isn’t terribly different from the present day.

Dr. Hammer did not say this, but looking at the Y versus the mtDNA haplogroups, I wonder if this suggests that indeed there was more of a replacement of the males in the population, but that the females were more widely assimilated. This would certainly make sense, especially if the invaders were warriors and didn’t have females with them.  They would have taken partners from the invaded population.

Haplogroup G represents the spread of farming into Europe.

hammer 2014-22

The most surprising revelation is that haplogroup R1b appears to have emerged after the Neolithic agriculture transition. Given that just three years ago we thought that haplogroup R1b was one of the original European settlers thousands of years ago, based on the prevalence of haplogroup R in Europe today, at about 50%, this is a surprising turn of events.  Last year’s revelation that R was maybe only 7000-8000 years old in Europe was a bit of a whammy, but the age of R in Europe in essence just got halved again and the source of R1b changed from the Near East to the Asian steppes.

Obviously, something conferred an advantage to these R1b men. Given that they arrived in the early Metalic age, was it weapons and chariots that enabled the R1b men who arrived to quickly become more than half of the population?

hammer 2014-23

The Bronze Age saw the first use of metal to create weapons. Warrior identity became a standard part of daily life.  Celts ranged over Europe and were the most dominant iron age warriors.  Indo-European languages and chariots arrived from Asia about this time.

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The map above shows the Hallstadt and LaTene Celtic cultures in Europe, about 600BC. This was not a slide presented by Dr. Hammer.

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Haplogroup R1b was not found in an ancient European context prior to a Bell Beaker period burial in Germany 4.8-4.0 kya (thousand years ago, i.e. 4,800-4,000 years ago).  R1b arrives about 4.6 kya and is also found in a Corded Ware culture burial in Germany.  A late introduction of these lineages which now predominate in Europe corresponds to the autosomal signal of the entry of Asian and Eastern European steppe invaders into western Europe.

hammer 2014-28

Local expansion occurred in Europe of R1b subgroups U106, L21 and U152.

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A current haplogroup R distribution map that reflects the findings of this past year is shown above.

Haplogroup I is interesting for another reason. It looks like haplogroup I2a1b (M423) may have been replaced by I1 which expanded after the Mesolithic.

hammer 2014-31

On the slide above, the Loschbour sample from Luxembourg was mapped onto a current haplogroup I SNP map where his closest match is a current day Russian.

One of the benefits of ancient DNA genome processing is that we will be able to map current trees into maps of old SNPs and be able to tell who we match most closely.

Autosomal DNA can also be mapped to see how much of our DNA is from which ancient population.

hammer 2014-32

Dr. Hammer mapped the percentages of European Mesolithic/Paleolithic hunter-gatherers in blue, Neolithic Farmers from the Near East in magenta and Asian Steppe Invaders representing ANE in yellow, over current populations. Note the ancient DNA samples at the top of the list.  None of the burials except for Malta Child carry any yellow, indicating that the ANE entered the European population with the steppe invaders; the same group that brought us haplogroup R and possibly I1.

Dr. Hammer says that ANE was introduced to and assimilated into the European population by one or more incursions. We don’t know today if ANE in Europeans is a result of a single blast event or multiple events.  He would like to do some model simulations and see if it is related to timing and arrival of swords and chariots.

We know too that there are more recent incursions, because we’re still missing major haplogroups like J.

The further east you go, meaning the closer to the steppes and Volga region, the less well this fits the known models. In other words, we still don’t have the whole story.

At the end of the presentation, Michael was asked if the whole genomes sequenced are also obtaining Y STR data, which would allow us to compare our results on an individual versus a haplogroup level. He said he didn’t know, but he would check.

Family Tree DNA was asked if they could show a personal ancient DNA map in myOrigins, perhaps as an alternate view. Bennett took a vote and that seemed pretty popular, which he interpreted as a yes, we’d like to see that.

In Summary

The advent of and subsequent drop in the price of whole genome sequencing combined with the ability to extract ancient DNA and piece it back together have provided us with wonderful opportunities.  I think this is jut the proverbial tip of the iceberg, and I can’t wait to learn more.

If you are interested in other articles I’ve written about ancient DNA, check out these links: