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!

______________________________________________________________

Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

 

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

hammer 2013-1

hammer 2013-2

hammer 2013-3

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

hammer 2014-1

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.

hammer 2014-11

hammer 2014-12

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.

hammer 2014-24

hammer 2014-25

hammer 2014-26

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

hammer 2014-27

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.

hammer 2014-29

hammer 2014-30

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:

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Disclosure

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

Thank you so much.

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Genealogy Services

Genealogy Research

Anzick (12,707-12,556), Ancient One, 52 Ancestors #42

anzick burial location

His name is Anzick, named for the family land, above, where his remains were found, and he is 12,500 years old, or more precisely, born between 12,707 and 12,556 years before the present.  Unfortunately, my genealogy software is not prepared for a birth year with that many digits.  That’s because, until just recently, we had no way to know that we were related to anyone of that age….but now….everything has changed ….thanks to DNA.

Actually, Anzick himself is not my direct ancestor.  We know that definitively, because Anzick was a child when he died, in present day Montana.

anzick on us map

Anzick was loved and cherished, because he was smeared with red ochre before he was buried in a cave, where he would be found more than 12,000 years later, in 1968, just beneath a layer of approximately 100 Clovis stone tools, shown below.  I’m sure his parents then, just as parents today, stood and cried as the laid their son to rest….never suspecting just how important their son would be some 12,500 years later.

anzick clovis tools

From 1968 until 2013, the Anzick family looked after Anzick’s bones, and in 2013, Anzick’s DNA was analyzed.

DNA analysis of Anzick provided us with his mitochondrial haplogroup,  D4h3a, a known Native American grouping, and his Y haplogroup was Q-L54, another known Native American haplogroup.  Haplogroup Q-L54 itself is estimated to be about 16,900 years old, so this finding is certainly within the expected range.  I’m not related to Anzick through Y or mitochondrial DNA.

Utilizing the admixture tools at GedMatch, we can see that Anzick shows most closely with Native American and Arctic with a bit of east Siberian.  This all makes sense.

Anzick MDLP K23b

Full genome sequencing was performed on Anzick, and from that data, it was discovered that Anzick was related to Native Americans, closely related to Mexican, Central and South Americans, and not closely related to Europeans or Africans.  This was an important discovery, because it in essence disproves the Solutrean hypothesis that Clovis predecessors emigrated from Southwest Europe during the last glacial maximum, about 20,000 years ago.

anzick matches

The distribution of these matches was a bit surprising, in that I would have expected the closest matches to be from North America, in particular, near to where Anzick was found, but his closest matches are south of the US border.  Although, in all fairness, few people in Native tribes in the US have DNA tested and many are admixed.

This match distribution tells us a lot about population migration and distribution of the Native people after they left Asia, crossed Beringia on the land bridge, now submerged, into present day Alaska.

This map of Beriginia, from the 2008 paper by Tamm et all, shows the migration of Native people into (and back from) the new world.

beringia map

Anzick’s ancestors crossed Beringia during this time, and over the next several thousand years, found their way to Montana.  Some of Anzick’s relatives found their way to Mexico, Central and South America.  The two groups may have split when Anzick’s family group headed east instead of south, possibly following the edges of glaciers, while the south-moving group followed the coastline.

Recently, from Anzick’s full genome data, another citizen scientist extracted the DNA locations that the testing companies use for autosomal DNA results, created an Anzick file, and uploaded the file to the public autosomal matching site, GedMatch.  This allowed everyone to see if they matched Anzick.  We expected no, or few, matches, because after all, Anzick was more than 12,000 years old and all of his DNA would have washed out long ago due to the 50% replacement in every generation….right?  Wrong!!!

What a surprise to discover fairly large segments of DNA matching Anzick in living people, and we’ve spent the past couple of weeks analyzing and discussing just how this has happened and why.  In spite of some technical glitches in terms of just how much individual people carry of the same DNA Anzick carried, one thing is for sure, the GedMatch matches confirm, in spades, the findings of the scientists who wrote the recent paper that describes the Anzick burial and excavation, the subsequent DNA processing and results.

For people who carry known Native heritage, matches, especially relatively large matches to Anzick, confirm not only their Native heritage, but his too.

For people who suspect Native heritage, but can’t yet prove it, an Anzick match provides what amounts to a clue – and it may be a very important clue.

In my case, I have proven Native heritage through the Micmac who intermarried with the Acadians in the 1600s in Nova Scotia.  Given that Anzick’s people were clearly on a west to east movement, from Beringia to wherever they eventually wound up, one might wonder if the Micmac were descended from or otherwise related to Anzick’s people.  Clearly, based on the genetic affinity map, the answer is yes, but not as closely related to Anzick as Mexican, Central and South Americans.

After several attempts utilizing various files, thresholds and factors that produced varying levels of matching to Anzick, one thing is clear – there is a match on several chromosomes.  Someplace, sometime in the past, Anzick and I shared a common ancestor – and it was likely on this continent, or Beringia, since the current school of thought is that all Native people entered the New World through this avenue.  The school of thought is not united in an opinion about whether there was a single migration event, or multiple migrations to the new word.  Regardless, the people came from the same base population in far northeast Asia and intermingled after arriving here if they were in the same location with other immigrants.

In other words, there probably wasn’t much DNA to pass around.  In addition, it’s unlikely that the founding population was a large group – probably just a few people – so in very short order their DNA would be all the same, being passed around and around until they met a new population, which wouldn’t happen until the Europeans arrived on the east side of the continent in the 1400s.  The tribes least admixed today are found south of the US border, not in the US.  So it makes sense that today the least admixed people would match Anzick the most closely – because they carry the most common DNA, which is still the same DNA that was being passed around and around back then.

Many of us with Native ancestors do carry bits and pieces of the same DNA as Anzick.  Anzick can’t be our ancestor, but he is certainly our cousin, about 500 generations ago, using a 25 year generation, so roughly our 500th cousin.  I had to laugh at someone this week, an adoptee who said, “Great, I can’t find my parents but now I have a 12,500 year old cousin.”  Yep, you do!  The ironies of life, and of genealogy, never fail to amaze me.

Utilizing the most conservative matching routine possible, on a phased kit, meaning one that combines the DNA shared by my mother and myself, and only that DNA, we show the following segment matches with Anzick.

Chr Start Location End Location Centimorgans (cM) SNPs
2 218855489 220351363 2.4 253
4 1957991 3571907 2.5 209
17 53111755 56643678 3.4 293
19 46226843 48568731 2.2 250
21 35367409 36761280 3.7 215

Being less conservative produces many more matches, some of which are questionable as to whether they are simply convergence, so I haven’t utilized the less restrictive match thresholds.

Of those matches above, the one on chromosomes 17 matches to a known Micmac segment from my Acadian lines and the match on chromosome 2 also matches an Acadian line, but I share so many common ancestors with this person that I can’t tell which family line the DNA comes from.

There are also Anzick autosomal matches on my father’s side.  My Native ancestry on his side reaches back to colonial America, in either Virginia or North Carolina, or both, and is unproven as to the precise ancestor and/or tribe, so I can’t correlate the Anzick DNA with proven Native DNA on that side.  Neither can I associate it with a particular family, as most of the Anzick matches aren’t to areas on my chromosome that I’ve mapped positively to a specific ancestor.

Running a special utility at GedMatch that compared Anzick’s X chromosome to mine, I find that we share a startlingly large X segment.  Sometimes, the X chromosome is passed for generations intact.

Interestingly enough, the segment 100,479,869-103,154,989 matches a segment from my mother exactly, but the large 6cM segment does not match my mother, so I’ve inherited that piece of my X from my father’s line.

Chr Start Location End Location Centimorgans (cM) SNPs
X 100479869 103154989 1.4 114
X 109322285 113215103 6.0 123

This tells me immediately that this segment comes from one of the pink or blue lines on the fan chart below that my father inherited from his mother, Ollie Bolton, since men don’t inherit an X chromosome from their father.  Utilizing the X pedigree chart reduces the possible lines of inheritance quite a bit, and is very suggestive of some of those unknown wives.

olliex

It’s rather amazing, if you think about it, that anyone today matches Anzick, or that we can map any of our ancestral DNA that both we and Anzick carry to a specific ancestor.

Indeed, we do live in exciting times.

Honoring Anzick

On a rainy Saturday in June, 2014, on a sagebrush hillside in Montana, in Native parlance, our “grandfather,” Anzick was reburied, bringing his journey full circle.  Sarah Anzick, a molecular biologist, the daughter of the family that owns the land where the bones were found, and who did part of the genetic discovery work on Anzick, returns the box with his bones for reburial.

anzick bones

More than 50 people, including scientists, members of the Anzick family and representatives of six Native American tribes, gathered for the nearly two-hour reburial ceremony. Tribe members said prayers, sang songs, played drums and rang bells to honor the ancient child. The bones were placed in the grave and sprinkled with red ocher, just like when his parents buried him some 12,500 years before.

Participants at the reburial ceremony filled in the grave with handfuls, then shovelfuls of dirt and covered it with stones. A stick tied with feathers marks Anzick’s final resting place.

Sarah Anzick tells us that, “At that point, it stopped raining. The clouds opened up and the sun came out. It was an amazing day.”

I wish I could have been there.  I would have, had I known.  After all, he is part of me, and I of him.

anzick grave'

Welcome to the family, Anzick, and thank you, thank you oh so much, for your priceless, unparalleled gift!!!

tobacco

If you want to read about the Anzick matching journey of DNA discovery, here are the articles I’ve written in the past two weeks.  It has been quite a roller coaster ride, but I’m honored and privileged to be doing this research.  And it’s all thanks to an ancient child named Anzick.

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Tenth Annual Family Tree DNA Conference Wrapup

baber summary

This slide, by Robert Baber, pretty well sums up our group obsession and what we focus on every year at the Family Tree DNA administrator’s conference in Houston, Texas.

Getting to Houston, this year, was a whole lot easier than getting out of Houston. They had storms yesterday and many of us spent the entire day becoming intimately familiar with the airport.  Jennifer Zinck, of Ancestor Central, is still there today and doesn’t have a flight until late.

And this is how my day ended, after I finally got out of Houston and into my home airport. This isn’t at the airport, by the way.  Everything was fine there, but I made the apparent error of stopping at a Starbucks on the way home.  This is the parking lot outside an hour or so later.  What can I say?  At least I had my coffee, and AAA rocks, as did the tow truck driver and my daughter for getting out of bed to come and rescue me!!!  Hmmm, I think maybe things have gone full circle.  I remember when I used to go and rescue her:)

jeep tow

So far, today hasn’t improved any, so let’s talk about something much more pleasant…the conference itself.

Resources

One of the reasons I mentioned Jennifer Zinck, aside from the fact that she’s still stuck in the airport, is because she did a great job actually covering the conference as it happened. Since I had some time yesterday to visit with her since our gates weren’t terribly far apart, I asked her how she got that done.  I took notes too, and photos, but she turned out a prodigious amount of work in a very short time.  While I took a lightweight MacBook Air, she took her regular PC that she is used to typing on, and she literally transcribed as the sessions were occurring.  She just added her photos later, and since she was working on a platform that she was familiar with, she could crop and make the other adjustments you never see but we perform behind the scenes before publishing a photo.

On the other hand, I struggled with a keyboard that works differently and is a different size than I’m used to as well as not being familiar with the photo tools to reduce the size of pictures, so I just took rough notes and wrote the balance later.  Having familiar tools make such a difference.  I think I’ll carry my laptop from now on, even though it is much heavier.  Kudos to Jennifer!

I was initially going to summarize each session, but since Jen did such a good job, I’m posting her links. No need to recreate a wheel that doesn’t need to be recreated.

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

ISOGG, the International Society of Genetic Genealogy is not affiliated with Family Tree DNA or any testing company, but Family Tree DNA is generous enough to allow an ISOGG meeting on Sunday before the first conference session.

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

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

You can find my conference postings here:

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/

Several people were also posting on a twitter feed as well.

https://twitter.com/search?q=%23FTDNA2014&src=tyah

Those of you where are members of the ISOGG Yahoo group for project administrators can view photos posted by Katherine Borges in that group and there are also some postings on the Facebook ISOGG group as well.

Now that you have the links for the summaries, what I’d like to do is to discuss some of the aspects I found the most interesting.

The Mix

When I attended my first conference 10 years ago, I somehow thought that for the most part, the same group of people would be at the conferences every year. Some were, and in fact, a handful of the 160+ people attending this conference have attended all 10 conferences.  I know of two others for certain, but there were maybe another 3 or so who stood up when Bennett asked for everyone who had been present at all 10 conferences to stand.

Doug Mumma, the very first project administrator was with us this weekend, and still going strong. Now, if Doug and I could just figure out how we’re related…

Some of the original conference group has passed on to the other side where I’m firmly convinced that one of your rewards is that you get to see all of those dead ends of your tree. If we’re lucky, we get to meet them as well and ask all of those questions we have on this side.  We remember our friends fondly, and their departure sadly, but they enriched us while they were here and their memories make us smile.  I’m thinking specifically of Kenny Hedgepath and Leon Little as I write this, but there have been others as well.

The definition of a community is that people come and go, births, deaths and moves.

This year, about half of the attendees had never attended a conference before. I was very pleased to see this turn of events – because in order to survive, we do need new people who are as crazy as we are…er….I mean as dedicated as we are.

isogg reception

ISOGG traditionally hosts a potluck reception on Saturday evening. Lots of putting names with faces going on here.

Collaboration

I asked people about their favorite part of the conference or their favorite session. I was surprised at the number of people who said lunches and dinners.  Trust me, the food wasn’t that wonderful, so I asked them to elaborate.  In essence, the most valuable aspect of the conference was working with and talking to other administrators.

bar talk

It’s not like we don’t talk online, but there is somehow a difference between online communications and having a group discussion, or a one-on-one discussion. Laptops were out and in use everyplace, along with iPads and other tools.  It was so much fun to walk by tables and hear snippets of conversations like “the mutation at location 309.1….” and “null marker at 425” and “I ordered a kit for my great uncle…..”

I agree, as well. I had pre-arranged two dinners before arriving in order to talk with people with whom I share specific interests.  At lunches, I either tried to sit with someone I specifically needed to talk to, or I tried to meet someone new.

I also asked people about their specific goals for the next year. Some people had a particular goal in mind, such as a specific brick wall that needs focus.  Some, given that we are administrators, had wider-ranging project based goals, like Big Y testing certain family groups, and a surprising number had the goal of better utilizing the autosomal results.

Perhaps that’s why there were two autosomal sessions, an introduction by Jim Bartlett and then Tim Janzen’s more advanced session.

Autosomal DNA Results

jim bartlett

Note the cool double helix light fixture behind the speakers.

tim janzen

Tim specifically mentioned two misconceptions which I run across constantly.

Misconception 1 – A common surname means that’s how you match.  Just because you find a common surname doesn’t mean that’s your DNA match.  This belief is particularly prevalent in the group of people who test at Ancestry.com.

Misconception 2 – Your common ancestor has to be within the past 6 generations.  Not true, many matches can be 6-10th cousins because there are so many descendants of those early ancestors, even as many as 15 generations back.

Tim also mentioned that endogamous relationships are a tough problem with no easy answer. Polynesians, Ashkenazi Jews, Low German Mennonites, Acadians, Amish, and island populations.  Do I ever agree with him!  I have Brethren, Mennonite and Acadian in the same parent’s line.

Tim has been working with the Mennonite DNA project now for many years.

Tim included a great resource slide.

tim slide1

Tim has graciously made his entire presentation available for download.

tim slide2

There are probably a dozen or so of us that are actively mapping our ancestors, and a huge backlog of people who would like to. As Tim pointed out with one of his slides, this is not an easy task nor is it for the people who simply want to receive “an answer.”

tim slide3

I will also add that we “mappers” are working with and actively encouraging Family Tree DNA to develop tools so that the mapping is less spreadsheet manual work and more automated, because it certainly can be.

Upload GEDCOM Files

If you haven’t already, upload your GEDCOM to Family Tree DNA.  This is becoming an essential part of autosomal matching.  Furthermore, Family Tree DNA will utilize this file to construct your surname list and that will help immensely determining common surnames and your common ancestor with your Family Finder matches.  If you have sponsored tests for cousins, then upload a GEDCOM file for them or at least construct a basic tree on their Family Tree DNA page.

Ethics

Family Tree DNA always tries to provide a speaker about ethics, and the only speakers I’ve ever felt understood anything about what we want to do are Judy Russell and Blaine Bettinger.  I was glad to see Blaine presenting this year.

blaine bettinger

The essence of Blaine’s speech is that ethics isn’t about law. Law is cut and dried.  Ethics isn’t, and there are no ethics police.

Sometimes our decisions are colored necessarily by right and wrong.  Sometimes those decisions are more about the difference between a better and a worse way.

As a community, we want to reduce negative press coverage and increase positive coverage. We want to be proactive, not reactive.

Blaine stresses that while informed consent is crucial, that DNA doesn’t reveal secrets that aren’t also revealed by other genealogical forms of research. DNA often reveals more recent secrets, such as adoptions and NPEs, so it’s possibly more sensitive.

Two things need to govern our behavior. First, we need to do only things that we would be comfortable seeing above the fold in the New York Times.  Second, understand that we can’t make promises about topics like anonymity or about the absence of medical information, because we don’t know what we don’t know.

The SNP Tsunami

One of my concerns has been and remains the huge number of new SNPs that have been discovered over the past year or so with the Big Y by Family Tree DNA and  corresponding tests from other vendors.

When I say concern, I’m thrilled about this new technology and the advances it is allowing us to make as a community to discover and define the evolution of haplogroups. My concern is that the amount of data is overwhelming.  However, we are working through that, thanks to the hours and hours of volunteer work by haplogroup administrators and others.

Alice Fairhurst, who volunteers to maintain the ISOGG haplotree, mentioned that she has added over 10,000 SNPs to the Y tree this year alone, bringing the total to over 14,000. Those SNPs are fully vetted and placed.  There are many more in process and yet more still being discovered.  On the first page of the Y SNP tree, the list of SNP sources and other critical information, such as the criteria for a SNP to be listed, is provided.

isogg tree3

isogg snps

isogg snps 2014

So, if you’re waiting for that next haplotree poster, give it up because there isn’t a printing press that big, unless you want wallpaper.

isogg new development 2014

These slides are from Alice’s presentation. The ISOGG tree provides an invaluable resource for not only the genetic genealogy community, but also researchers world-wide.

As one example of how the SNP tsunami has affected the Y tree, Alice provided the following summary of R-U106, one of the two major branches of haplogroup R.

From the ISOGG 2006 Y tree, this was the entire haplogroup R Y tree. You can see U106 near the bottom with 3 sub-branches.  While this probably makes you chuckle today, remember that 2006 was only 8 years ago and that this tree didn’t change much for several years.

2006 entire tree

2007 was the same.

2008 u106 tree

2008 shows 5 subclades and one of the subclades had 2 subclades.

2009 u106 tree

2009 showed a total of 12 sub-branches and 2010 added one more.

2011 however, showed a large change. U106 in 2011 had 44 subgroups total and became too large to show on one screen shot.  2012 shows 99 subclades, if I counted accurately.  The 2014 U106 tree is shown below.

before big y

after big y

u106 now

u106 now2

There’s another slide too, but I didn’t manage to get the picture.  You get the idea though…

As you can imagine, for Family Tree DNA, trying to keep up with all of the haplogroups, not just one subgroup like U106 is a gargantuan task that is constantly changing, like hourly. Their Y tree is currently the National Geographic tree, and while they would like to update it, I’m sure, the definition of “current tree” is in a constant state of flux.  Literally, Mike Walsh, one of the admins in the R-L21 group uploads a new tree spreadsheet several times every day.

In order to deal attempt to deal with this, and to encourage people who don’t want to do a Big Y discovery type test, but do want to ferret out their location on their assigned portion of the tree, Family Tree DNA is reintroducing the Backbone tests.

They are starting with M222, also known as the Niall of the 9 Hostages haplogroup which is their beta for the new product and new process. You can see the provisional tree and results in the two slides they provided, below.  I apologize for the quality, but it was the best I could do.

M222

m222 pie

Haplogroup administrators are going to be heavily involved in this process. Family Tree DNA is putting SNP panels together that will help further define the tree and where various SNPs that have been recently discovered, and continue to be discovered, will fall on the tree.

As Big Y tests arrive, haplogroup project administrators typically assemble a spreadsheet of the SNPS and provisionally where they fall on the tree, based on the Big Y results.

What Bennett asked is for the admins to work with Family Tree DNA to assemble a testing panel based on those results. The goal is for the cost to be between $1.50 and $2 (US) for each SNP in the panel, which will reduce the one-off SNP testing and provide a much more complete and productive result at a far reduced price as compared to the current $29 or $39 per individual SNP.

If you are a haplogroup administrator, get in touch with Family Tree DNA to discuss your desired backbone panels. New panels, when it’s your turn, will take about 2 weeks to develop.

Keep in mind that the following SNPs, according to Bennett, are not optimal for panels:

  • Palindromic regions
  • Often mutating regions designated as .1, .2, etc.
  • SNPs in STRs

Nir Leibovich, the Chief Business Officer, also addressed the future and the Big Y to some extent in his presentation.

nir leibovich

ftdna future 2014

Utilizing the Big Y for Genealogy

In my case, during the last sale, I ordered several Big Y tests for my Estes family line because I have several genealogically documented lines from the original Estes family in Kent, England through our common ancestor, Robert Estes born in 1555 and his wife Anne Woodward. The participants also agreed to extend their markers to 111 markers as well.  When the results are back, we’ll be able to compare them on a full STR marker set, and also their SNPs.  Hopefully, they will match on their known SNPs and there will be some new novel variants that will be able to suffice as line marker mutations.

We need more BIG Y tests of these types of genealogically confirmed trees that have different sons’ lines from a distant common ancestor to test descendant lines. This will help immensely to determine the actual, not imputed, SNP mutation rate and allow us to extrapolate the ages of haplogroups more accurately.  Of course, it also goes without saying that it helps to flesh out the trees.

I personally expect the next couple of years will be major years of discovery. Yes, the SNP tsumani has hit land, but it’s far from over.

Research and Development

David Mittleman, Chief Scientific Officer, mentioned that Family Tree DNA now has their own R&D division where they are focused on how to best analyze data. They have been collaborating with other scientists.  A haplogroup G1 paper will be published shortly which states that SNP mutation rates equate to Sanger data.

FTDNA wants to get Big Y data into the public domain. They have set up consent for this to be done by uploading into NCBI.  Initially they sent a survey to a few people that  sampled the interest level.  Those who were interested received a release document.  If you are interested in allowing FTDNA to utilize your DNA for research, be it mitochondrial, Y or autosomal, please send them an e-mail stating such.

Don’t Forget About Y Genealogy Research

It’s very easy for us to get excited about the research and discovery aspect of DNA – and the new SNPs and extending haplotrees back in time as far as possible, but sometimes I get concerned that we are forgetting about the reason we began doing genetic genealogy in the first place.

Robert Baber’s presentation discussed the process of how to reconstruct a tree utilizing both genealogy and DNA results. It’s important to remember that the reason most of our participants test is to find their ancestors, not, primarily, to participate in the scientific process.

Robert baber

edward baber

Robert has succeeded in reconstructing 110 or 111 markers of the oldest known Baber ancestor, shown above. I wrote about how to do this in my article titled, Triangulation for Y DNA.

Not only does this allow us to compare everyone with the ancestor’s DNA, it also provides us with a tool to fit individuals who don’t know specific genealogical line into the tree relatively accurately. When I say relatively, the accuracy is based on line marker mutations that have, or haven’t, happened within that particular family.

Jim illustrated how to do this as well, and his methodology is available at the link on his slide, below.

baber method

I had to laugh. I’ve often wondered what our ancestors would think of us today.  Robert said that that 11 generations after Edward Baber died, he flew over church where Edward was buried and wondered what Edward would have thought about what we know and do today – cars, airplanes, DNA, radio, TV etc..  If someone looked in a crystal ball and told Edward what the future held 11 generations later, he would have thought that they were stark raving mad.

Eleven generations from my birth is roughly the year 2280. I’m betting we won’t be trying to figure out who our ancestors were through this type of DNA analysis then.  This is only a tiny stepping stone to an unknown world, as different to us as our world is to Edward Baber and all of our ancestors who lived in a time where we know their names but their lives and culture are entirely foreign to ours.

Publications

When the Journal of Genetic Genealogy was active, I, along with other citizen scientists published regularly.  The benefit of the journal was that it was peer reviewed and that assured some level of accuracy and because of that, credibility, and it was viewed by the scientific community as such.  My co-authored works published in JOGG as well as others have been cited by experts in the academic community.  It other words, it was a very valuable journal.  Sadly, it has fallen by the wayside and nothing has been published since 2011.  A new editor was recruited, but given their academic load, they have not stepped up to the plate.  For the record, I am still hopeful for a resurrection, but in the mean time, another opportunity has become available for genetic genealogists.

Brad Larkin has founded the Surname DNA Journal, which, like JOGG, is free to both authors and subscribers. In case you weren’t aware, most academic journal’s aren’t.  While this isn’t a large burden for a university, fees ranging from just over $1000 to $5000 are beyond the budget of genetic genealogists.  Just think of how many DNA tests one could purchase with that money.

brad larkin

surname dna journal

Brad has issued a call for papers. These papers will be peer reviewed, similarly to how they were reviewed for JOGG.

call for papers

Take a look at the articles published in this past year, since the founding of Surname DNA Journal.

The citizen science community needs an avenue to publish and share. Peer reviewed journals provide us with another level of credibility for our work. Sharing is clearly the lynchpin of genetic genealogy, as it is with traditional genealogy. Give some thought about what you might be able to contribute.

Brad Larkin solicited nominations prior to the conference and awarded a Genetic Genealogist of the Year award. This year’s award was dually presented to Ian Kennedy in Australia, who, unfortunately, was not present, and to CeCe Moore, who just happened to follow Brad’s presentation with her own.

Don’t Forget about Mitochondrial DNA Either

I believe that mitochondrial DNA the most underutilized DNA tool that we have, often because how to use mitochondrial DNA, and what it can tell you, is poorly understood. I wrote about this in an article titled, Mitochondrial, The Maligned DNA.

Given that I work with mitochondrial DNA daily when I’m preparing client’s Personalized DNA Reports (orderable from your personal page at Family Tree DNA or directly from my website), I know just how useful mitochondrial can be and see those examples regularly. Unfortunately, because these are client reports, I can’t write about them publicly.

CeCe Moore, however, isn’t constrained by this problem, because one of the ways she contributes to genetic genealogy is by working with the television community, in particular Genealogy Roadshow and the PBS series, Finding Your Roots. Now, I must admit, I was very surprised to see CeCe scheduled to speak about mitochondrial DNA, because the area of expertise where she is best known is autosomal DNA, especially in conjunction with adoptee research.

cece moore

cece mtdna

During the research for the production of these shows, CeCe has utilized mitochondrial DNA with multiple celebrities to provide information such as the ethnic identification of the ancestor who provided the mitochondrial DNA as Native American.

Autosomal DNA testing has a broad but shallow reach, across all of your lines, but just back a few generations.  Both Y and mitochondrial DNA have a very deep reach, but only on one specific line, which makes them excellent for identifying a common ancestor on that line, as well as the ethnicity of that individual.

I have seen other cases, where researchers connected the dots between people where no paper trail existed, but a relationship between women was suspected.

CeCe mentioned that currently there are only 44,000 full sequence results in the Family Tree DNA data base and and 185K total HVR1, HVR2 and full sequence tests. Y has half a million.  We need to increase the data base, which, of course increases matches and makes everyone happier.  If you haven’t tested your mitochondrial DNA to the full sequence level, this would be a great time!

There are several lessons on how to utilize mitochondrial DNA at this ISOGG link.

I’m very hopeful that CeCe’s presentation will be made available as I think her examples are quite powerful and will serve to inspire people.  Actually, since CeCe is in the “movie business,” perhaps a short video clip could be made available on the FTDNA website for anyone who hasn’t tested their mitochondrial DNA so they can see an example of why they should!

myOrigins

I would be fibbing to you if I told you I am happy with myOrigins. I don’t feel that it is as sensitive as other methods for picking up minority admixture, in particular, Native American, especially in small amounts.  Unfortunately, those small amounts are exactly what many people are looking for.

If someone has a great-great-great-great grandparent that is Native, they carry about 1%, more or less, of the Native ancestor’s DNA today. A 4X great grandparent puts their birth year in the range of 1800-1825 – or just before the Trail of Tears.  People whose colonial American families intermarried with Native families did so, generally, before the Trail of Tears.  By that time, many tribes were already culturally extinct and those east of the Mississippi that weren’t extinct were fighting for their lives, both literally and figuratively.

We really need the ability to develop the most sensitive testing to report even the smallest amounts of Native DNA and map those segments to our chromosomes so that we can determine who, and what line in our family, was Native.

I know that Family Tree DNA is looking to improve their products, and I provided this feedback to them. Many people test autosomally only for their ethnicity results and I surely would love to have those people’s results available as matches in the FTDNA data base.

Razib Khan has been working with Family Tree DNA on their myOrigins product and spoke about how the myOrigins data is obtained.

razib kahn

my origins pieces

Given that all humans are related, one way or another, far enough back in time, myOrigins has to be able to differentiate between groups that may not be terribly different. Furthermore, even groups that appear different today may not have been historically.  His own family, from India, has no oral history of coming from the East, but the genetic data clearly indicates that they did, along with a larger group, about 1000 years ago.  This may well be a result of the adage that history is written by the victors, or maybe whatever happened was simply too long ago or unremarkable to be recorded.

Razib mentioned that depending on the cluster and the reference samples, that these clusters and groups that we see on our myOrigins maps can range from 1000-10,000 years in age.

relatedness of clusters

The good news is that genetics is blind to any preconceived notions. The bad news is that the software has to fit your results to the best population, even though it may not be directly a fit.  Hopefully, as we have more and better reference populations, the results will improve as well.

my origin components

pca chart

Razib showed a PCA (principal components analysis) graph, above. These graphs chart reference populations in different quadrants.  Where the different populations overlap is where they share common historic ancestors.  As you can see, on this graph with these reference populations, there is a lot of overlap in some cases, and none in others.

Your personal results would then be plotted on top of the reference populations. The graph below shows me, as the white “target” on a PCA graph created by Doug McDonald.

my pca chart

The Changing Landscape

A topic discussed privately among the group, and primarily among the bloggers, is the changing landscape of genetic genealogy over the past year or so.  In many ways I think the bloggers are the canaries in the mine.

One thing that clearly happened is that the proverbial tipping point occurred, and we’re past it. DNA someplace along the line became mainstream.  Today, DNA is a household word.  At gatherings, at least someone has tested, and most people have heard about DNA testing for genealogy or at least consumer based DNA testing.

The good news in all of this is that more and more people are testing. The bad news is that they are typically less informed and are often impulse purchasers.  This gives us the opportunity for many more matches and to work with new people.  It also means there is a steep learning curve and those new testers often know little about their genealogy.  Those of us in the “public eye,” so to speak, have seen an exponential spike in questions and communications in the past several months.  Unfortunately, many of the new people don’t even attempt to help themselves before asking questions.

Sometimes opportunity comes with work clothes – for them and us both.

I was talking with Spencer about this at the reception and he told me I was stealing his presentation.  He didn’t seem too upset by this:)

spencer and me

I had to laugh, because this falls clearly into the “be careful what you wish for, you may get it” category. The Genographic project through National Geographic is clearly, very clearly, a critical component of the tipping point, and this was reflected in Spencer’s presentation.  Although I covered quite a bit of Spencer’s presentation in my day 2 summary, I want to close with Spencer here.  I also want to say that if you ever have the opportunity to hear Spencer speak, please do yourself the favor and be sure to take that opportunity.  Not only is he brilliant, he’s interesting, likeable and very approachable.  Of course, it probably doesn’t hurt that I’ve know him now for 9 years!  I’ve never thought to have my picture taken with Spencer before, but this time, one of my friends did me the favor.

I have to admit, I love talking to Spencer, and listening to him. He is the adventurer through whom we all live vicariously.  In the photo below, Spencer along with his crew, drove from London to Mongolia.  Not sure why he is standing on the top of the Land Rover, but I’m sure he will tell us in his upcoming book about that journey,

spencer on roof

I’m warning you all now, if I win the lottery, I’m going on the world tour that he hosts with National Geographic, and of course, you’ll all be coming with me via the blog!

Spencer talked about the consumer genomics market and where we are today.

spencer genomics

Spencer mentioned that genetic genealogy was a cottage industry originally. It was, and it was even smaller than that, if possible.  It actually was started by Bennett and his cell phone.  I managed to snap a picture of Bennett this weekend on the stage looking at his cell, and I thought to myself, “this is how it all started 14 years ago.”  Just look where we are today.  Thank you Michael Hammer for telling Bennett that you received “lots of phone calls from crazy genealogists like you.”

bennett first office

So, where exactly are we today?  In 2013, the industry crossed the millionth kit line.  The second millionth kit was sold in early summer 2014 and the third million will be sold in 2015.  No wonder we feel like a tidal wave has hit.  It has.

Why now?

DNA has become part of national consciousness.  Businesses advertise that “it’s in our DNA.”  People are now comfortable sharing via social media like facebook and twitter.  What DNA can do and show you, the secrets it can unlock is spreading by word of mouth.  Spencer termed this the “viral spread threshold” and we’ve crossed that invisible line in the sand.  He terms 2013 as the year of infection and based on my blog postings, subscriptions, hits, reach and the number of e-mails I receive, I would completely agree.  Hold on tight for the ride!

Spencer talked about predictions for near term future and said a 5 year plan is impossible and that an 18 month plan is more realistic. He predicts that we will continue to see exponential growth over the next several years.  He feels that genetic genealogy testing will be primary driver of growth because medical or health testing is subject to the clinical utility trap being experienced currently by 23andMe.  The Big 4 testing companies control 99% of consumer market in US (Ancestry, 23andMe, Family Tree DNA and National Geographic.)

Spencer sees a huge international market potential that is not currently being tapped. I do agree with him, but many in European countries are hesitant, and in some places, like France, DNA testing that might expose paternity is illegal.  When Europeans see DNA testing as a genealogical tool, he feels they will become more interested.  Most Europeans know where their ancestral village is, or they think they do, so it doesn’t have the draw for them that it does for some of us.

Ancestry testing (aka genetic genealogy as opposed to health testing) is now a mature industry with 100% growth rate.

Spencer also mentioned that while the Genographic data base is not open access, that affiliate researchers can send Nat Geo a proposal and thereby gain research access to the data base if their proposal is approved. This extends to citizen scientists as well.

spencer near term

Michael Hammer

You’ll notice that Michael Hammer’s presentation, “Ancient and Modern DNA Update, How Many Ancestral Populations for Europe,” is missing from this wrapup. It was absolutely outstanding, and fascinating, which is why I’m writing a separate article about his presentation in conjunction with some additional information.  So, stay tuned.

Testing, More Testing

It’s becoming quite obvious that the people who are doing the best with genetic genealogy are the ones who are testing the most family members, both close and distant. That provides them with a solid foundation for comparison and better ways to “drop matches” into the right ancestor box.  For example, if someone matches you and your mother’s sister, Aunt Margaret, especially if your mother is not available to test, that’s a very important hint that your match is likely from your mother’s line.

So, in essence, while initially we would advise people to test the oldest person in a generational line, now we’ve moved to the “test everyone” mentality.  Instead of a survey, now we need a census.  The exception might be that the “child” does not necessarily need to be tested because both parents have tested.  However, having said that, I would perhaps not make that child’s test a priority, but I would eventually test that child anyway.  Why?  Because that’s how we learn.  Let me give you an example.

I was sitting at lunch with David Pike. were discussing autosomal DNA generational transmission and inheritance.  He pulled out his iPad, passed it to me, and showed me a chromosome (not the X) that has been passed entirely intact from one generation to the next.  Had the child not been tested, we would never have known that.  Now, of course, if you’ll remember the 50% rule, by statistical prediction, the child should get half of the mother’s chromosome and half of the father’s, but that’s not how it worked.  So, because we don’t know what we don’t know, I’m now testing everyone I can find and convince in my family.  Unfortunately, my family is small.

Full genome testing is in the future, but we’re not ready yet. Several presenters mentioned full genome testing in some context.  Here’s the bottom line.  It’s not truly full genome testing today, only 95-96%.  The technology isn’t there yet, and we’re still learning.  In a couple of years, we will have the entire genome available for testing, and over time, the prices will fall.  Keep in mind that most of our genome is identical to that of all humans, and the autosomal tests today have been developed in order to measure what is different and therefore useful genealogially.  I don’t expect big breakthroughs due to full genome testing for genetic genealogy, although I could be wrong.  You can, however, count me in, because I’m a DNA junkie.  When the full genome test is below $1000, when we have comparison tools and when the coverage won’t necessitate doing a second or upgrade test a few years later, I’ll be there.

Thank you

I want to offer a heartfelt thank you to Max Blankfeld and Bennett Grenspan, founders of Family Tree DNA, shown with me in the photo below, for hosting and subsidizing the administrator’s conference – now for a decade. I look forward to seeing them, and all of the other attendees, next year.

I anticipate that this next decade will see many new discoveries resulting in tools that make our genealogy walls fall.  I can’t help but wonder what the article I’ll be writing on the 20th anniversary looking back at nearly a quarter century of genetic genealogy will say!

roberta, max and bennett

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Generational Inheritance

Autosomal DNA testing has opened up the brave new world for genealogists.  Along with that opportunity comes some amount of frustration and sometimes desperation to wring every possible tidbit of information out of autosomal results, sometimes resulting in pushing the envelope of what the technology and DNA can tell us.

I often have clients who want me to take a look at DNA results from people several generations removed from each other and try to determine if the ancestors are likely to be brothers, for example.  While that’s fairly feasible in the first few generations, the further back in time one goes, the less reliably we can say much of anything about how DNA is transmitted.  Hence, the less we can say, reliably, about relationships between people.

The best we can ever do is to talk in averages.  It’s like a coin flip.  Take a coin out right now and flip it 10 times.  I just did, and did not get 5 heads and 5 tails, which the average would predict.  But averages are comprised of a large number of outcomes divided by the actual number of events.  That isn’t the same thing as saying if one repeats the event 10 times that you will have 5 heads and 5 tails, or the average.  Each of those 10 flips are entirely independent, so you could have any of 11 different outcomes:

  • 0 heads 10 tails
  • 1 head 9 tails
  • 2 heads 8 tails
  • 3 heads 7 tails
  • 4 heads 6 tails
  • 5 heads 5 tails
  • 6 heads 4 tails
  • 7 heads 3 tails
  • 8 heads 2 tails
  • 9 heads 1 tail
  • 10 heads 0 tails

What the average does say is that in the end, you are most likely to have an average of 5 heads and 5 tails – and the larger the series of events, the more likely you are to reach that average.

My 10 single event flips were 4 heads and 6 tails, clearly not the average.  But if I did 10 series of coin flips, I bet my average would be 5 and 5 – and at 100 flips, it’s almost assured to be 50-50 – because the population, or number of events, has increased to the point where the average is almost assured.

You can see above, that while the average does indeed map to 5-5, or the 50-50 rule, the results of the individual flips are no respecter of that rule and are not connected to the final average outcome.  For example, if one set of flips is entirely tails and one set of flips is entirely heads, the average is still 50/50 which is not at all reflective of the actual events.

And so it goes with inheritance too.

However, we have come to expect that the 50% rule applies most of the time.  We knowriffle shuffle that it does, absolutely, with parents.  We do receive 50% of our DNA from each parent, but which 50%?.  From there, it can vary, meaning that we don’t necessarily get 25% of each grandparent’s DNA.  So while we receive 50% in total from each parent, we don’t necessarily receive every other segment or location, so it’s not like a rifle card shuffle where every other card is interspersed.

If one parents DNA sequence is:

TACGTACGTACG

A child cannot be presumed to receive every other allele, shown in red below.

TACGTACGTACG

The child could receive any portion of this particular segment, all of it, or none of it.

So, if you don’t receive every other allele from a parent, then how do you receive your DNA and how does that 50% division happen?  The bottom line is that we don’t know, but we are learning.  This article is the result of a learning experience.

Over time, genetic genealogists have come to expect that we are most likely to receive 25% of our DNA from each grandparent – which is statistically true when there are enough inheritance events.  This reflects our expectation of the standard deviation, where about 2/3rds of the results will be within the closest 25% in either direction of the center.  You can see expected standard deviation here.

This means that I would expect an inheritance frequency chart to look like this.

expected inheritance frequency

In this graph above, about half of the time, we inherit 50% of the DNA of any particular segment, and the rest of the time we inherit some different amount, with the most frequently inherited amounts being closer to the 50% mark and the outliers being increasingly rare as you approach 0% and 100% of a particular segment.

But does this predictability hold when we’re not talking about hundreds of events….when we’re not talking about population genetics….but our own family genetics, meaning one transmission event, from parent to child?  Because if that expected 50% factor doesn’t hold true, then that affects DRAMATICALLY what we can say about how related we are to someone 5 or 6 generations ago and how can we analyze individual chromosome data.

I have been uncomfortable with this situation for some time now, and the increasing incidence of anecdotal evidence has caused me to become increasingly more uncomfortable.

There are repeated anecdotal instances of significant segments that “hold” intact for many generations.  Statistically, this should not happen.  When this does happen, we, as genetic genealogists, consider ourselves lucky to be one of the 1% at the end of spectrum, that genetic karma has smiled upon us.  But is that true?  Are we at the lucky 1% end of the spectrum?

This phenomenon is shown clearly in the Vannoy project where 5 cousins who descend from Elijah Vannoy born in 1786 share a very significant portion of chromosome 15.  These people are all 5 generations or more distantly related from the common ancestor, (approximate 4th cousins) and should share less than 1% of their DNA in total, and certainly no large, unbroken segments.   As you can see, below, that’s not the case.  We don’t know why or how some DNA clumps together like this and is transmitted in complete (or nearly complete) segments, but they obviously are.  We often call these “sticky segments” for lack of a better term.

cousin 1

I downloaded this chromosome 15 information into a spreadsheet where I can sort it by chromosome.  Below you can see the segments on chromosome 15 where these cousins match me.

cousin 2

Chromosome 15 is a total of 141 cM in length and has 17,269 SNPs.  Therefore, at 5 generations removed, we would expect to see these people share a total of 4.4cM and 540 SNPs, or less for those more distantly related.  This would be under the matching threshold at either Family Tree DNA or 23andMe, so they would not be shown as matches at all.  Clearly, this isn’t the case for these 5 cousins.  This DNA held together and was passed intact for a total of 25 different individual inheritance events (5 cousins times 5 events, or  generations, each.)  I wrote about this in the article titles “Why Are My Predicted Cousin Relationships Wrong?”

Finally, I had a client who just would not accept no for an answer, wanted desperately to know the genetically projected relationship between two men who lived in the 1700s, and I felt an obligation to look into generational inheritance further.

About this same time, I had been working with my own matches at 23andMe.  Two of my children have tested there as well, a son and a daughter, so all of my matches at 23andMe obviously match me, and may or may not match my children.  This presented the perfect opportunity to study the amount of DNA transmitted in each inheritance event between me and both children.

Utilizing the reports at www.dnagedcom.com, I was able to download all of my matches into a spreadsheet, but then to also download all of the people on my match list that all of my matches match too.

I know, that was a tongue twister.  Maybe an example will help.

I match John Doe.  My match list looks like this and goes on for 353 lines.

match list

I only match John Doe on one chromosome at one location.  But finding who else on my match list of 353 people that John Doe matches is important because it gives me clues as to who is related to whom and descends from the same ancestor.  This is especially true if you recognize some of the people that your match matches, like your first cousin, for example.  This suggests, below that John Doe is related to me through the same ancestor as my first cousin, especially if John matches me with even more people who share that ancestor.   If my cousin and I both match John Doe on the same segment, that is strongly suggestive that this segment comes from a common ancestor, like in the previous Vannoy example.

Therefore, I methodically went through and downloaded every single one of my matches matches (from my match list) to see who was also on their list, and built myself a large spreadsheet.  That spreadsheet exercise is a topic for another article.  The important thing about this process is that how much DNA each of my children match with John Doe tells me exactly how much of my DNA each of my children inherited from me, versus their father, in that segment of DNA.

match comparison

In the above example, I match John Doe on Chromosome 11 from 37,000,000-63,000,000.  Looking at the expected 50% inheritance, or normal distribution, both of my children should match John Doe at half of that.  But look at what happened.  Both of my children inherited almost exactly all of the same DNA that I had to give.  Both of them inherited just slightly less in terms of genetic distance (cM) and also in terms of the number of SNPs.

It’s this type of information that has made me increasingly skeptical about the 50% bell curve standard deviation rule as applied to individual, not population, genetics.  The bell curve, of course, implies that the 50% percentile is the most likely even to occur, with the 49th being next most likely, etc.

This does not seem to be holding true.  In fact, in this one example alone, we have two examples of nearly 100% of the data being passed, not 50% in each inheritance event.  This is the type of one-off anecdotal evidence that has been making me increasingly uncomfortable.

I wanted something more than anecdotal evidence.  I copied all of the match information for myself and my children with my matches to one spreadsheet.  There are two genetic measures that can be utilized, centimorgans (cM) or total SNPs. I am using cM for these examples unless I state otherwise.

In total, there were 594 inheritance events shown as matches between me and others, and those same others and my children.

Upon further analysis of those inheritance events, 6 of them were actually not inheritance events from me.  In other words, those people matched me and my children on different chromosomes.  This means that the matches to my children were not through me, but from their father’s side or were IBS, Inherited by State.

son daughter comparison

This first chart is extremely interesting.  Including all inheritance events, 55% of the time, my children received none of the DNA I had to give them.  Whoa Nellie.  That is not what I expected to see.  They “should have” received half of my DNA, but instead, half of the time, they received none.

The balance of the time, they received some of my DNA 23% of the time and all of my DNA 21% of the time.  That also is not what I expected to see.

Furthermore, there is only one inheritance event in which one of my children actually inherited exactly half of what I had to offer, so significantly less than 1% at .1%.  In other words, what we expected to see actually happened the least often and was vanishingly rare when not looking at averages but at actual inheritance events.

Let’s talk about that “none” figure for a minute.  In this case, none isn’t really accurate, but I can’t be more accurate.  None means that 23andMe showed no match.  Their threshold for matching is 7cM (genetic distance) and 700 SNPS for the first matching segment, and then 5cM and 700 SNPS for secondary matching segments.  However, if you have over 1000 matches, which I do, matches begin to “fall off,” the smallest ones first, so you can’t tell what the functional match threshold is for you or for the people you match.  We can only guess, based on their published thresholds.

So let’s look at this another way.

Of the 329 times that my children received none of my DNA, 105 of those transmissions would be expected to be under the 700cM threshold, based on a 50% calculation of how many cMs I matched with the individual.  However, not all of those expected events were actually under the threshold, and many transmissions that were not expected to be under that threshold, were.  Therefore, 224, or 68% of those “none” events were not expected if you look at how much of my DNA the child would be expected to inherit at 50%.

Another very interesting anomaly that pops right up is the number of cases where my children inherited more than I had to give them.  In the example below, you can see that I match Jane Doe with 15.2cM and 2859 SNPs, but my daughter matches Jane with 16.3cM and 2960 on the same chromosome.

spreadsheet layout

There are a few possibilities to explain this:

  • My daughter also matches this person on her father’s side at this transition point.
  • My daughter matches this person IBS at this point.
  • The 23andMe matching software is trying to compensate for misreads.
  • There are misreads or no calls in my file.

There of course may be a combination of several of these factors, but the most likely is the fact that she is IBS at this location and the matching software is trying to be generous to compensate for possible no-calls and misreads.  I suggest this because they are almost uniformly very small amounts.

Therefore when my children match me at 100% or greater, I simply counted it as an exact match.  I was surprised at how many of these instances there were.  Most were just slightly over the value of 2 in the “times expected” column.  To explain how this column functions, a value of 1 is the expected amount – or 50% of my DNA.  A value of 2 means that the child inherited all of the DNA I had to offer in that location.  Any value over 2 means that one or more of the bulleted possibilities above occurred.

Between both of my children, there were a total of 75, or 60% with values greater than 2 on cMs and 96, or 80%, on SNPs, meaning that my children matched those people on more DNA at that location than I had to offer.  The range was from 2 to 2.4 with the exception of one match that was at 3.7.  That one could well be a valid transition (other parent) match.

There has been a lot of discussion recently about X chromosome inheritance.  In this case, the X would be like any other chromosome, since I have two Xs to recombine and give to my children, so I did not remove X matches from these calculations.  The X is shown as chromosome 99 here and 23 on the graphs to enable correct column sorting/graphing.

In the chart below, inheritance events are charted by chromosome.  The “Total” columns are the combined events of both my son and daughter.  The blue and pink columns are the inheritance events for both of them, which equal the total, of course.

The “none” column reflects transmissions on that chromosome where my children received none of my DNA.  The “some” column reflects transmission events where my children received some portion of my DNA between 0 (none) and 100% (all).  The “all” column reflects events where my children received all of the DNA that I had to offer.

chromosomal comparison

I graphed these events.

total inheritance graph

The graph shows the total inheritance events between both of my children by chromosome.  Number 23 in these charts is the X chromosome.

son inheritance graph

daughter inheritance graph

These inheritance numbers cause me to wonder what is going on with chromosome 5 in the case of both my daughter and son, and also chromosome 6 with my son.  I wonder if this would be uniform across families relative to chromosome 5, or if it is simply an anomaly within my family inheritance events.  It seems odd that the same anomaly would occur with both children.

son daughter inheritance graph

What this shows is that we are not dealing with a distribution curve where the majority of the events are at the 50% level and those that are not are progressively nearer to the 50% level than either end.  In other words, the Expected Inheritance Frequency is not what was found.

expected inheritance frequency

The actual curve, based on the inheritance events observed here, is shown below, where every event that was over the value of 2, or 100%, was normalized to 2.  This graph is dramatically different than the expected frequency, above.

actual inheritance frequency

Looking at this, it becomes immediately evident that we inherit either all of nothing of our parents DNA segments 85% of the time, and only about 15% of the time we inherit only a portion of our parents DNA segments.  Very, very rarely is the portion we inherit actually 50%, one tenth of one percent of the time.

Now that we understand that individual generational inheritance is not a 50-50 bell curve event, what does this mean to us as genetic genealogists?

I asked fellow genetic genealogist, Dr. David Pike, a mathematician to look this over and he offered the following commentary:

“As relationships get more distant, the number of blocks of DNA that are likely to be shared diminishes greatly.  Once down to one block, then really there are three outcomes for subsequent inheritance:  either the block is passed intact, no part of it is passed on, or recombination happens and a portion of it is passed on.  If we ignore this recombination effect (which should rarely affect a small block) then the block is either passed on in an “all or nothing” manner.  There’s essentially no middle ground with small blocks and even with lots of examples it doesn’t really make sense to expect an average of 50%.  As an analogy, consider the human population:  with about half of us being female and about half of us being male, the “average” person should therefore be androgynous, and yet very few people are indeed androgynous.”

In other words, even if you do have a segment that is 10 cMs in length, it’s not 10 coin flips, it’s one coin flip and it’s going to either be all, nothing or a portion thereof, and it’s more than 6 times more likely to be all or nothing than to be a partial inheritance.

So how do we resolve the fact that when we are looking at the 700,000 or so locations tested at Family Tree DNA and the 600,000 locations tested at 23andMe, that we can in fact use the averages to predict relationships, at least in closely related individuals, but we can’t utilize that same methodology in these types of individual situations?  There are many inheritance events being taken into consideration, 600,000 – 700,000, an amount that is mathematically high enough to over overcome the individual inheritance issues.  In other words, at this level, we can utilize averages.  However, when we move past the larger population model, the individual model simply doesn’t fit anymore for individual event inheritance – in other words, looking at individual segments.

Dr. Pike was kind enough to explain this in mathematical terms, but ones that the rest of us can understand:

“I think that part of what is at stake is the distinction between continuous versus discrete events.  These are mathematical terms, so to illustrate with an example, the number line from 0 to 10 is continuous and includes *all* numbers between them, such 2.55, pi, etc.  A discrete model, however, would involve only a finite number of elements, such as just the eleven integers from 0 to 10 inclusive.  In the discrete model there is nothing “in between” consecutive elements (such as 3 and 4), whereas in the continuous model there are infinitely elements between them.

It’s not unlike comparing a whole spectrum against a finite handful of a few options.  In some cases the distinction is easily blurred, such as if you conduct a survey and ask people to rate a politician on a discrete scale of 0 to 10… in this case it makes intuitive sense to say that the politician’s average rating was 7.32 (for example) even though 7.32 was not one of the options within the discrete scale.

In the realm of DNA, suppose that cousins Alice and Bob share 9 blocks of DNA with each other and we ask how many blocks Alice is likely to share with Bob’s unborn son.  The answer is discrete, and with each block having a roughly 50/50 chance we expect that there will likely be 4 or 5 blocks shared by Alice and Bob Jr., although the randomness of it could result in anywhere from 0 to 9 of the blocks being shared.  Although it doesn’t make practical sense to say that “four and a half” blocks will likely be shared [well, unless we allow recombination to split a block and thereby produce a shared “half block”], there is still some intuitive comfort in saying that 4.5 is the average of what we would expect, but in reality, either 4 or 5 blocks are shared.

But when we get to the extreme situation of there being only 1 block, for which the discrete options are only 0 or 1 block shared, yes or no, our comfortable familiarity with the continuous model fails us.  There are lots of analogies here, such as what is the average of a coin toss, what is the average answer to a True/False question, what the average gender of the population, etc.

Discrete models with lots of options can serve as good approximations of continuous situations, and vice-versa, which is probably part of what’s to blame for confusion here.

Really DNA inheritance is discrete, but with very many possible segments [such as if we divided the genome up into 10 cM segments and asked how many of Alice’s paternal segments will be inherited by one of her children, we can get away with a continuous model and essentially say that the answer is roughly 50%.  Really though, if there are 3000 of these blocks, the actual answer is one of the integers:  0, 1, 2, …, 2999, 3000.  The reality is discrete even though we like the continuous model for predicting it.

However, discrete situations with very few options simply cannot be modelled continuously.”

Back to our situation where we are attempting to determine a relationship of 2 men born in the 1700s whose descendants share fragments of DNA today.  When we see a particularly large fragment of DNA, we can’t make any assumptions about age or how long it has been in existence by “reverse engineering” it’s path to a common ancestor by doubling the amount of DNA in every generation.  In other words, based on the evidence we see above, it has most likely been passed entirely intact, not divided.  In the case of the Vannoy DNA, it looks like the ends have been shaved a few times, but the majority of the segment was passed entirely intact.  In fact, you can’t double the DNA inherited by each individual 5 times, because in at least one case, Buster, doubling his total matching cM, 100, even once would yield a number of cM greater the size of chromosome 15 at 141 cM.

Conversely, when we see no DNA matches, for example, in people who “should be” distant cousins, we can’t draw any conclusions about that either.  If the DNA didn’t get passed in the first generation – and according to the numbers we just saw – 58% doesn’t get passed at all, and 26% gets passed in its entirety, leaving only about 15% to receive some portion of one parent’s DNA, which is uniformly NOT 50% except for one instance in almost 1000 events (.1%) – then all bets for subsequent generations are off – they can’t inherit their half if their half is already gone or wasn’t half to begin with.

Based on mathematical model, Probability of Recombination, Dr. Pike has this to say:

If I’m reading this right, a 10 cM block has a 10% chance of being split into parts during the recombination process of a single conception. Although 10% is not completely negligible, it’s small enough that we can essentially consider “all” or “nothing” as the two dominant outcomes.

This is the fundamental underlying reason why testing companies are hesitant to predict specific relationships – they typically predict ranges of relationships – 1st to 3rd cousin, for example, based on a combination of averages – of the percentages of DNA shared, the number of segments, the size of segments, the number of SNPs etc.  The testing company, of course, can have no knowledge of how our individual DNA is or was actually passed, meaning how much ancestral DNA we do or don’t receive, so they must rely on those averages, which are very reliable as a continuous population model, and apparently, much less so as discrete individual events.

I would suggest that while we certainly have a large enough sample of inheritance events between me and my two children to be statistically relevant, it’s not large enough study to draw any broad sweeping conclusions. It is, after all, only 3 people and we don’t know how this data might hold up compared to a much larger sample of family inheritance events.  I’d like to see 100 or 1000 of these types of studies.

I would be very interested to see how this information holds up for anyone else who would be willing to do the same type of information download of their data for parent/multiple sibling inheritance.  I will gladly make my spreadsheet with the calculations available as a template to anyone who wants to do the same type of study.

I wonder if we would see certain chromosomes that always have higher or lower generational inheritance factors, like the “none” spike we see on chromosome 5.  I wonder if we would see a consistent pattern of male or female children inheriting more or less (all or none) from their parents.  I wonder what other kinds of information would reveal itself in a larger study, and if it would enable us to “weight” match information by chromosome or chromosome/gender, further refining our ability to understand our genetic relationships and to more accurately predict relationships.

I want to thank Dr. David Pike for reviewing and assisting with this article and in particular, for being infinitely patient and making the application of the math to genetics understandable for non-mathematicians.  If you would like to see an example of Dr. Pike’s professional work, here is one of his papers.  You can find his personal web page here and his wonderful DNA analysis tools here.

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Cavendish Lab at Cambridge University

The old Cavendish Lab at Cambridge University, where Watson and Crick discovered DNA, is kind of like Mecca for people who love genetics.  So is the Eagle Pub where they ate lunch daily and announced their discovery.  I’m not convinced which is the more important.

Our family tour in September, 2013 was scheduled to visit Cambridge, England, after leaving London.  I’ve been truly blessed this trip with the most wonderful coincidences.  In London, our hotel was located just across Hyde Park from the Science Museum where Watson and Crick’s original DNA model is housed.  In Cambridge, we are staying right around the corner from the Cavendish Lab where Watson and Crick discovered DNA.  Talk about literally walking in the footsteps of the masters.

I was pleased when I discovered Cambridge on the itinerary, and I googled to find the Eagle Pub. I was excited to find that it was indeed within walking distance of the Cambridge City Hotel where we were staying.  Although I don’t drink, I would visit the pub and raise a non-alcoholic brew for Watson and Crick’s momentous discovery.  Problem is, I discovered, that they didn’t have any non-alcoholic brew.  In fact, most of England views non-alcoholic brew as “why bother.”  While I agree in concept, sometimes it’s not by choice.

Wondering why the Cavendish Lab is important?

Cavendish 1

The Cavendish Lab at Cambridge University was the birthplace of the discovery of DNA.  James Watson and Francis Crick discovered DNA in this lab in 1953.  This year of course is the 60th anniversary of that discovery and James Watson was interviewed in celebration.  Crick passed away in 2004.

Before visiting Cambridge, I tried to find the Cavendish Lab on a map and it looked to be entirely across the campus, which is not small.  That made no sense to me, since the Eagle Pub was close to the hotel, but I accepted that I might not be able to see the lab.  I’d have to be satisfied with the Eagle Pub.

Why is the Eagle Pub important?  It’s where Watson and Crick lunched and probably did a lot of brainstorming.  Pubs are like that in England.

Cavendish 2

On our day of arrival, a walking tour of the city with a guide, a retired professor, was scheduled for that afternoon.  After we began the tour, around the first corner, on a street that was only wide enough for one car, and then no cars, I remembered to ask the guide about the original Cavendish Lab.  Given that he was a retired professor, I figured if anyone knew, he would.

He smiled broadly, and said “I’m so glad you asked…it’s right up ahead.”  To say I was thrilled is an understatement.  In fact, this is one of the few locations I’m actually IN the photos, um, actually, in most all the photos.  My cousins were so excited because I was excited that they took pictures of me.  This was definitely “my day” on the trip.  This photo of me, taken in front of the Eagle Pub pretty much sets the mood.cavendish me laughing

The Cavendish Lab, it turns out, was on the right hand side, just about where the road narrowed too much for any vehicle.  There was a sign mounted on the wall of the building that this was indeed the old Cavendish Lab.  There is a new Cavendish Lab across campus, the one I had seen on the map.  So far, my luck on the DNA trail had been remarkably good.

I, of course, was thrilled to be where Watson and Crick began what would be a blooming industry 60 years later with a world of promise.  In another 50 years, DNA will be responsible for the cure of many diseases we feel are hopeless or nearly so today.  Like at the Science Museum in London, I was very disappointed to see it relegated to not even the footnotes.  I tried to find a DNA souvenir, t-shirt, hat, something to purchase and there was not one DNA thing in any store.  For shame!  Come on – Double Helix Ale anyone???

???????????????????????????????

Cambridge is an ancient medieval city and it’s evident everyplace.  The Cavendish Lab is arguably on the oldest “street,” or cartpath, in Cambridge.  I say this because the oldest church is right across that cartpath and dates from about the year 1000.  At that time, churches were always at the center of the village.  Today, that cart-path is not wide enough for a car, and there is no room to expand.

Today, the ancient church is of course physically tied into several other buildings and abuts others, as all buildings here generally are, especially old buildings.  This photo shows the oldest church constructed of chocolate brown stones, another very old church as well, and the spires of King’s College Chapel begun by Henry the 6th and finished by Henry the 8th in the distance to the far right.  Note that this is a one lane street at this point that shortly narrows to exclude vehicles.  To put this in perspective, the Eagle Pub is just about where the trees are on the far right, beside the King’s College Chapel spire.

Cavendish 4

In most of England, and assuredly in Cambridge, what we consider is the US to be old buildings, a hundred or two years old are considered to be rather new.  Their old buildings were constructed before Columbus “discovered” the Americas.

I can only imagine the nurturing quality of studying and working among such history.  I suppose one would get used to it, but I hope it would never be taken for granted.

There are two entrances to the lab.  One is through this door.

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Watson and Crick exited through this door, walked down this cartway every day for lunch and ate at the Eagle Pub, just a short walk away and around the corner in front of the church.  It’s here that they fined tuned their DNA research as do both students and professors yet today.

The second entrance to the lab is through this archway which actually forms a tunnel under the building.  Half way through the tunnel is an entrance to the buildings on both sides.

Cavendish 6

Walking a short distance down the cobblestone street, just past the chocolate colored church, you intersect a road and slightly to the left is the Eagle Pub, where Watson and Crick ate lunch most days and discussed their projects.  Rest assured that DNA was indeed a hot topic of conversation here. In fact, it’s reported that they were so excited about their discovery that they told everyone in the pub that they had discovered the secret of life, only to have everyone ignore them and just go back to their pint of ale.  It had to be an extremely anti-climactic day for them – but if any patron remembers the crazy men in the pub that day that announced the discovery of the recipe of life itself – they indeed were a witness to a momentous discovery.

Cavendish 7

Inside the pub, in a stairway to the loo (bathroom) we found this sign.

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The Pub actually holds more information about the discovery of DNA than the university location does.  I find this really unfortunate, as well as ironic, but maybe not as many people as I imagine might be interested in the history of DNA.

I would think they would at least mark the DNA “Double Helix Trail.”  It could end, or begin, in London at the Science Museum where the helix model resides today.

The pub itself is in a very historic area, literally in the middle of the “old town”.  Here’s a photo of the street itself, the pub, on the right.

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Cambridge is a place of thinkers, and obviously, of doers as well.  It turns out that DNA was not the only discovery in the Cavendish labs.

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I wonder what other discoveries were made in these hallowed halls.  Did you know that Mitochondrial DNA was first mapped at Cambridge in 1981, hence, the CRS or Cambridge Reference Sequence?  What is it with DNA here?  Rosalind Franklin, pioneer molecular biologist and a key contributor to the discovery of DNA studied at Newnham College at Cambridge, but when she made her x-ray diffraction images of DNA, utilized by Watson and Crick, she was at King’s College in London.

Cambridge is steeped in history never more than a few feet away.  In the photo of the pub, above, if you turn right when the street ends, you’ll be greeted with this scene, the King’s College Chapel with its rich history of starting and stopping construction through the reigns of 3 kings and the English Civil War.  This is the steeple you saw in the distance in the photo of the street where the Cavendish lab is located.

OLYMPUS DIGITAL CAMERA

The architecture of this building is utterly stunning.

Cavendish 12

The first part was built by Henry the 6th for the 70 professors at Cambridge at the time.  The second part to the rear was finished many years later by Henry the 8th, after the War of the Roses and was very opulent with carvings on all the walls, heraldry, etc.  The first part was very simple by comparison.  The picture below is of the second part.

Cavendish 13

One of the most impressive aspects of this chapel, aside from the stunning windows, is the ceiling made of carved stone flying buttresses itself.  Because of the ceiling construction and the amount of glass in the windows, it’s actually very light inside and I could take these photos without flash photography which was prohibited.

Cavendish 14

The church forms part of a 4 building complex that is connected in a square and inside is a courtyard.

Cavendish 15

I can’t even imagine going to school is this wonderfully nurturing environment.  No wonder DNA was discovered here. No one wanted to leave.  My university was constructed of concrete blocks, for the most part, and everyone left as soon as possible.

Bachelor degrees at Cambridge are 3 year degrees, not 4, and if you live in Europe, it’s about 9,000 pounds which would be about 14,000 US dollars without lodging and food which is about another 8,000 pounds.  If you’re from elsewhere, it’s 18,000 pounds plus lodging.  Nurturing and inspiring, yes, but not inexpensive.

Cambridge is a beautiful and inspirational medieval city sprouting seeds for the future. There is a beautiful, ethereal umbilical connection between its past, my present and mankind’s future. It is truly awe-inspiring.  As I pondered and reflected upon all of this, I was struck with the weight of responsibility that all of us who work with DNA carry.

DNA is a gift, indeed, a map, of the past, of the present and a cartographic key to the future.  We have the responsibility and obligation to work with this Divine gift, ethically, morally and with only the best and most honorable of intentions.  We now have the key to the genome, the Holy Grail of humanity.  What will we do with it?  What does the future in another 60 years, 2073, hold?  Everyday in this new field, as we work individually to create a better whole, we are weaving our genetic legacy.

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

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Neanderthal Genome Further Defined in Contemporary Eurasians

DNA X

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29th titled “When Populations Collide” provides some interesting insights about Neanderthal DNA in modern humans.  This study compared the full Neanderthal genome to that of 1004 living individuals.

In general, people in East Asia carry more Neanderthal than Europeans who carry 1-3%, and Africans carry none or very little.  It appears, according to David Reich, that Neanderthal DNA is not proportionately represented in contemporary humans, meaning that some areas of Neanderthal DNA are commonly found and others not at all.  Some Neanderthal genes are carried by more than 60% of Europeans or Asians, most often associated with skin and hair color, or keratin.  Reich’s thought is that people exiting Africa assimilated with Neanderthals and selected for these genes that gave them an adaptive and survival advantage in the cooler non-African climate.

One particularly big Neanderthal genetic desert is the X chromosome, a phenomenon called hybrid sterility.  Reich suggests that this means that when Neanderthals and humans exiting from Africa interbred, they were on the cusp of being unable to reproduce successfully.  Reich explains that “when two populations are distantly related, genes related to fertility inherited on the X chromosome can interact poorly with genes elsewhere in the genome and that interference can render males, who carry only one X, sterile.”

Given the recent discussions about the X chromosome and the possibility that it may be inherited in an all-or-nothing manner more often than the other chromosomes, I had to wonder how they determined that this was hybrid sterility and not an case of absence of recombination.

Reich’s team apparently had the same question, so they evaluated the genes related to the function of the testes, confirming they too had a particularly low inheritance frequency of Neanderthal DNA.  These, combined, would eventually cause the X to be present in very small quantities in the genome of descendants since the Neanderthal X could only be inherited from women and then would cause the resulting males to be sterile.  So in essence, only females could pass the X on and only their daughters would pass it further.  Males carrying that X not only wouldn’t pass the X, they wouldn’t pass anything at all due to sterility.

If, in addition to this, the X has unusual recombination features, that could exacerbate the situation.  Conversely, if the X is inherited intact more often than not at all, it could increase the likelihood of the X being brought forward in the population.

Reich says his team is now focused on looking at Neanderthal DNA and human disease genes.  He says that his new study revealed that lupus, diabetes and Crohn’s Disease likely originate from Neanderthals.

Another study, published the same day in Science titled “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” reaches the same conclusions about the Neanderthal inherited traits related to skin color.  This study compared the full genomes of 379 East Asians and 286 Europeans to Neanderthal genomes and discovered that they could map about 20% of the Neanderthal DNA in those individuals today.  This, conversely, means that 80% of the Neanderthal genome is missing, so either truly missing or simply missing in the people whose DNA they sequenced.  It will be interesting to see what is found as more contemporary genetic sequences are compared against Neanderthal, and as more Neanderthal DNA is found and sequenced.

Fortunately, recent advances in dealing with contaminated ancient DNA hold a great deal of promise in terms of increasing our ability to sequence DNA that was previously thought to be useless.  This report is described in the article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neanderthal” and was used in the sequencing and analysis of the Neanderthal toe bone found in Siberia.

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

“This experiment of nature has been done,” says Dr. Reich, “and we can study it.”

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That Unruly X….Chromosome That Is

Iceberg

Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

The $1000 Genome? – Not Exactly

HiSeqXTen

You may have seen the headlines and the announcement this week by Illumina, manufacturer of gene sequencing equipment, that the $1000 genome is finally here.  Hallelujah –  jump for joy – right?  Sign me up – where can I order???

Well, not so fast.

It’s a great headline – and depending on how you figure the math – it’s not entirely untrue, but it’s a real struggle to get there.  Some marketing maven did some real spreadsheet magic!  What is that old saying, “lies, damned lies and statistics”?  Maybe that’s a little harsh, but it’s not too far off.

So, is the $1000 genome here or not?  Well, kindof.  It depends on how you count, and who you are.  You see, it’s a math thing.

It’s kind of like a mortgage.  How much did your house cost?  Let’s say $100,000 – that was the price on the “for sale” sign.  But by the time you get the mortgage paid off, 30 years later, the cost of that house is way more than $100,000, probably more than $250,000 and if you add in the cost of taxes, closing costs and maintenance, even more.  This will only depress you, so don’t think about, especially when you sell your house for $150,000 and declare that you “made” $50,000.  But I digress…

So, let’s translate this to the $1000 genome.

Dr. David Mittleman, Chief Scientific Officer for Gene by Gene, Ltd., parent company of Family Tree DNA, was at the conference this week where the Illumina announcement was made. I asked him several questions about this new technology and if it was ready for prime time yet.

His first comment shed some light on costs.

“The HiSeqX Ten system is actually a ten-pack of new HiSeq instruments, each costing 1 million dollars. So you have to spend $10 million on equipment before you can even get started.”

Ouch.  I guess I won’t be buying one anytime soon!

To begin with, without the cost of the kits or processing or staff or software or installation or financing or support contracts or profit, a company would have to sell 10,000 kits at $1000 to even bring the cost of the equipment to $1000 per kit.

So, how did Illumina figure the cost of the $1000 genome?  The $1000 is broken down as $800 on reagents, $135 on equipment depreciation over 4 years, and $65 on staff/overheads.

This means that to obtain that $1000 per genome price, you have to run the equipment at full capacity, 24X7, 18,000 kits per year, for 4 full years.  And that still doesn’t include everything.  You also need service contracts, installation, additional labor, etc.  You can read more about the math and cost of ownership here.

And sure enough, when I asked David about who has purchased one so far, there are two buyers and both are institutions.  This is an extremely high end product, not something for the DTC consumer marketspace.

Now this isn’t to say this announcement is a bad thing – it’s not – it’s just not exactly what the headlines suggest.  It’s the $1000 genome for those with deep pockets who can purchase a $10,000,000 piece of gear and then run 18,000 samples, for 4 years, plus expenses.  But yes, it does technically break down to $1000 per test as long as you hit all of those milestones and ignore the rest of the expenses.  If you can afford $10 million and have the staff to run it, you probably don’t care about the cost of installation, labor and support contracts.  They are just necessary incidentals – like gas for my lawn mower!

In spite of the fancy math, it’s truly amazing how far we’ve come when you consider that a single full genome sequence still cost about 3 million in 2007, and in November 2012 Gene by Gene was the first to offer full sequencing commercially and offered it to their customers for an introductory price of $5495.  Of course, with no analysis tools and few testers, I can’t imagine what one would do with those results.  This has changed somewhat today.  The full genome with some analysis is available today to consumers for $7595, but the question of what is available that is genealogically useful to do with these results still remains, and will, until many more people test and meaningful comparisons are available.

The Illumina announcement also raises the issue of software investment to do something useful with the massive amount of data this new equipment will generate…also nontrivial, and that software does not exist yet today.

There are other issues to be addressed as well, like open access libraries.  Will they exist?  If so, where?  Who cares for them?  How are they funded?  Who will have access?  Will this data be made available in open access libraries, assuming they exist?

Illumina has reported that entire countries have approached them asking for their population to be sequenced, which also begs questions of privacy, security and how exactly to anonymize the samples without them becoming useless to research.  This high tech watershed announcement may spur as many questions as answers, but these issues need to be resolved in the academic environment before they trickle down to the consumer marketspace.

This is not to minimize the science and technology that has propelled us to this breakthrough.  It is a wonderful scientific and technological advancement because it will allow governments or large institutes to do huge population-wide studies.  This is something we desperately need.  Think for a minute if our Population Finder ethnicity results were based on tens of thousands of samples instead of selected hundreds.

For genetic genealogists, we are poised to benefit in the future, probably the more distant than the near future.  The $1000 genome for consumers not only isn’t here, it’s not even within sniffing distance.  So put your checkbooks away or better yet, buy a Big Y or a Family Finder test for a cousin, something that will benefit you in the short term.

This next step in the world of genetic discovery is exciting for research institutes, but it’s not yet ready for consumer prime time.  We will be the beneficiaries, but not the direct consumers….yet…unless you want to move to one of those countries who wants their entire population sequenced.  Our turn will come.  Maybe the next time we see an announcement for the $1000 genome it will be calculated in normal home-owning-human terms.

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

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2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

Last year I wrote a column at the end of the year titled  “2012 Top 10 Genetic Genealogy Happenings.”  It’s amazing the changes in this industry in just one year.  It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen.  I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal.  Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention.  To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy!  I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order.  We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007.  This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested.  However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled.  The resolution to this tree shuffling hasn’t yet come out in the wash.  Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined.  That publication has been discussed and anticipated for some time now, but it has yet to materialize.  In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree.  While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company.  Kind of like Jekyll and Hyde.  See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg.  The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs.  This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

http://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

http://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera.  A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA.  One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed.  And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches.  We, as a community, suddenly woke up and started ordering these tests in droves.  A few months later, Family Tree DNA also began offering this type of testing as well.  The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy.  To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base.  For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease.  That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole.  Judy Russell, the Legal Genealogist, discussed this here.  It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent.  Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment.  But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013.  This made me decidedly uncomfortable.  Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal.  I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be.  And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it.  They did not say they won’t sell it.  This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using?  So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22nd cease and desist order) for several years.  The FDA wants assurances that what 23andMe is telling consumers is accurate.  Based on the letter issued to 23andMe on November 22nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc.  They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time.  However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company.  Period.  No excuses.  Something that critically important should be on the agenda of every executive management meeting.   Why?  In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them.  There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation.  The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them.  I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing.  However, in reality, the FDA was only meting out the consequences that 23andMe asked for.  My teenage kids knew this would happen.  If you do what you’re not supposed to….X, Y and Z will, or won’t, happen.  It’s called accountability.  Just ask my son about his prom….he remembers vividly.  Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me.  It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information.  I don’t think so, at least not in this case.  Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone.  The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information.  The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy.  The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be.  The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else.  But 23andMe didn’t, they decided to fight the fight, and we all supported their decision.  But they let us all down.  The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence.  This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA.  Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records.  In other cases, segments that previously matched are disappearing.  One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not.  They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year.  The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

http://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

http://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

http://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

http://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

http://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented.  Myriad Genetics held patents on two BRCA genes that predisposed people to cancer.  The cost for the tests through Myriad was about $3000.  Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995.  Other firms followed suit, and all were subsequently sued by Myriad for patent infringement.  I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything.  Making it stick is yet another matter.  Many firms settle to avoid long and very expensive legal battles.  Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive.  It potentially won’t be settled for a long time.

http://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

http://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results.  This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

http://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year.  More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests.  That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records.  Of course, the operative word here is “was” but that may revive when the FDA issue is resolved.  One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate.  They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies.  This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example.  Unfortunately, not enough people know about GedMatch, or are willing to download their files.  Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward.  For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect.  Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung.  In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

http://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

http://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

http://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

http://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

http://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

http://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

http://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible.  Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time.  This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately.  Multiple steps?  Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob.  Please remember that Rob’s site is free, meaning it’s donation based.  So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available.  GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools.  They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done.  When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release.  All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree.  The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other.  Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent.  And there wasn’t just one, not two, but three instances of this.  What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other.  In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection.  They have found a genealogical cousin, and it MIGHT be the genetic connection.  But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base.  No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions.  The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic.  See the Ethnicity Makeovers section for more on this.  The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising.  Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching.  I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now.  Ancestry has the funds to do development.  They are not a small company.  This is obviously not a priority because they don’t need to develop this feature.  Why is this?  Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed.  I’m reminded of an old joke.  The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet.  They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools.  One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

http://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

http://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable.  We have learned a great deal, and there are many more skeletal remains just begging to be sequenced.  One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA.  Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G.  It will be very interesting as the data bases of fully sequenced skeletons are built and compared.  The history of our ancestors is held in those precious bones.

http://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

http://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

http://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

http://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

http://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

http://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

http://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

http://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

http://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both.  Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this.  Sensationalist reporting, while irritating, can be dealt with if the science is sound.  However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

http://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years.  By this, I mean when citizen scientists work as part of a team on a significant discovery or paper.  Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model.  As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research.  JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication.  Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research.  This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

http://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

http://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

http://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

http://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

http://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other.  But I have to hand it to them, their marketing is amazing.  When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.”  Yea, a new me, based on Ancestry’s erroneous interpretation.  And by reversed, I’m serious.  I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different.  Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time.  My results at 23andMe are relatively accurate.  I saw very little change, but others saw more.  Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results.  In some cases, they are flat out wrong, as with Ancestry, and can be proven.  This does not engender a great deal of confidence.  I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.”  That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

http://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well.  Recently Family Tree DNA has also sponsored a series of free Webinars.  I know that at least one book is in process and very near publication, hopefully right after the first of the year.  We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014.  Genetic genealogy is going mainstream!!!  Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

http://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

http://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference.  All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators.  In addition, everyone who answers questions on a list or board or on Facebook is a volunteer.  Many donate their time to coordinate events, groups, or moderate online facilities.  Many speak at events or for groups.  Many more write articles for publications from blogs to family newsletters.  Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki.  Without our volunteer army, there would be no genetic genealogy community.  Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises.  And if there is one thing this industry is well known for….it’s surprises.  I can’t wait to see what 2014 has in store for us!!!  All I can say is hold on tight….

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