The Best and Worst of 2015 – Genetic Genealogy Year in Review

Posted on January 1, 2016 by Roberta Estes

For the past three years I’ve written a year-in-review article. You can see just how much the landscape has changed in the 2012, 2013 and 2014 versions.

This year, I’ve added a few specific “award” categories for people or firms that I feel need to be specially recognized as outstanding in one direction or the other.

In past years, some news items, announcements and innovations turned out to be very important like the Genographic Project and GedMatch, and others, well, not so much. Who among us has tested their full genome today, for example, or even their exome? And would you do with that information if you did?

And then there are the deaths, like the Sorenson database and Ancestry’s own Y and mitochondrial data base. I still shudder to think how much we’ve lost at the corporate hands of Ancestry.

In past years, there have often been big new announcements facilitated by new technology. In many ways, the big fish have been caught in a technology sense. Those big fish are autosomal DNA and the Big Y types of tests. Both of these have created an avalanche of data and we, personally and as a community, are still trying to sort through what all of this means genealogically and how to best utilize the information. Now we need tools.

This is probably illustrated most aptly by the expansion of the Y tree.

The SNP Tsunami Growing Pains Continue

Going from 800+ SNPs in 2012 to more than 35,000 SNPs today has introduced its own set of problems. First, there are multiple trees in existence, completely or partially maintained by different organizations for different purposes. Needless to say, these trees are not in sync with each other. The criteria for adding a SNP to the tree is decided by the owner or steward of that tree, and there is no agreement as to the definition of a valid SNP or how many instances of that SNP need to be in existence to be added to the tree.

This angst has been taking place for the most part outside of the public view, but it exists just the same.

For example, 23andMe still uses the old haplogroup names like R1b which have not been used in years elsewhere. Family Tree DNA is catching up with updating their tree, working with haplogroup administrators to be sure only high quality, proven SNPs are added to branches. ISOGG maintains another tree (one branch shown above) that’s publicly available, utilizing volunteers per haplogroup and sometimes per subgroup. Other individuals and organizations maintain other trees, or branches of trees, some very accurate and some adding a new “branch” with as little as one result.

The good news is that this will shake itself out. Personally, I’m voting for the more conservative approach for public reference trees to avoid “pollution” and a lot of shifting and changing downstream when it’s discovered that the single instance of a SNP is either invalid or in a different branch location. However, you have to start with an experimental or speculative tree before you can prove that a SNP is where it belongs or needs to be moved, so each of the trees has its own purpose.

The full trees I utilize are the Family Tree DNA tree, available for customers, the ISOGG tree and Ray Banks’ tree which includes locations where the SNPs are found when the geographic location is localized. Within haplogroup projects, I tend to use a speculative tree assembled by the administrators, if one is available. The haplogroup admins generally know more about their haplogroup or branch than anyone else.

The bad news is that this situation hasn’t shaken itself out yet, and due to the magnitude of the elephant at hand, I don’t think it will anytime soon. As this shuffling and shaking occurs, we learn more about where the SNPs are found today in the world, where they aren’t found, which SNPs are “family” or “clan” SNPs and the timeframes in which they were born.

In other words, this is a learning process for all involved – albeit a slow and frustrating one. However, we are making progress and the tree becomes more robust and accurate every year.

We may be having growing pains, but growing pains aren’t necessarily a bad thing and are necessary for growth.

Thank you to the hundreds of volunteers who work on these trees, and in particular, to Alice Fairhurst who has spearheaded the ISOGG tree for the past nine years. Alice retired from that volunteer position this year and is shown below after receiving two much-deserved awards for her service at the Family Tree DNA Conference in November.

Best Innovative Use of Integrated Data

Dr. Maurice Gleeson receives an award this year for the best genealogical use of integrated types of data. He has utilized just about every tool he can find to wring as much information as possible out of Y DNA results. Not only that, but he has taken great pains to share that information with us in presentations in the US and overseas, and by creating a video, noted in the article below. Thanks so much Maurice.

Making Sense of Y Data

The advent of massive amounts of Y DNA data has been both wonderful and perplexing. We as genetic genealogists want to know as much about our family as possible, including what the combination of STR and SNP markers means to us. In other words, we don’t want two separate “test results” but a genealogical marriage of the two.

I took a look at this from the perspective of the Estes DNA project. Of course, everyone else will view those results through the lens of their own surname or haplogroup project.

Estes Big Y DNA Results
http://dna-explained.com/2015/03/26/estes-big-y-dna-results/

At the Family Tree DNA Conference in November, James Irvine and Maurice Gleeson both presented sessions on utilizing a combination of STR and SNP data and various tools in analyzing their individual projects.

Maurice’s presentation was titled “Combining SNPs, STRs and Genealogy to build a Surname Origins Tree.”
http://www.slideshare.net/FamilyTreeDNA/building-a-mutation-history-tree

Maurice created a wonderful video that includes a lot of information about working with Y DNA results. I would consider this one of the very best Y DNA presentations I’ve ever seen, and thanks to Maurice, it’s available as a video here:
https://www.youtube.com/watch?v=rvyHY4R6DwE&feature=youtu.be

You can view more of Maurice’s work at:
http://gleesondna.blogspot.com/2015/08/genetic-distance-genetic-families.html

James Irvine’s presentation was titled “Surname Projects – Some Fresh Ideas.” http://www.slideshare.net/FamilyTreeDNA/y-dna-surname-projects-some-fresh-ideas

Another excellent presentation discussing Y DNA results was “YDNA maps Scandinavian Family Trees from Medieval Times and the Viking Age” by Peter Sjolund.
http://www.slideshare.net/FamilyTreeDNA/ydna-maps-scandinavian-family-trees-from-medieval-times-and-the-viking-age

Peter’s session at the genealogy conference in Sweden this year was packed. This photo, compliments of Katherine Borges, shows the room and the level of interest in Y-DNA and the messages it holds for genetic genealogists.

This type of work is the wave of the future, although hopefully it won’t be so manually intensive. However, the process of discovery is by definition laborious. From this early work will one day emerge reproducible methodologies, the fruits of which we will all enjoy.

Haplogroup Definitions and Discoveries Continue

Often, haplogroup work flies under the radar today and gets dwarfed by some of the larger citizen science projects, but this work is fundamentally important. In 2015, we made discoveries about haplogroups A4 and C, for example.

Haplogroup A4 Unpeeled – European, Jewish, Asian and Native American
http://dna-explained.com/2015/03/05/haplogroup-a4-unpeeled-european-jewish-asian-and-native-american/

New Haplogroup C Native American Subgroups
http://dna-explained.com/2015/03/11/new-haplogroup-c-native-american-subgroups/

Native American Haplogroup C Update – Progress
http://dna-explained.com/2015/08/25/native-american-haplogroup-c-update-progress/

These aren’t the only discoveries, by any stretch of the imagination. For example, Mike Wadna, administrator for the Haplogroup R1b Project reports that there are now over 1500 SNPs on the R1b tree at Family Tree DNA – which is just about twice as many as were known in total for the entire Y tree in 2012 before the Genographic project was introduced.

The new Y DNA SNP Packs being introduced by Family Tree DNA which test more than 100 SNPs for about $100 will go a very long way in helping participants obtain haplogroup assignments further down the tree without doing the significantly more expensive Big Y test. For example, the R1b-DF49XM222 SNP Pack tests 157 SNPs for $109. Of course, if you want to discover your own private line of SNPs, you’ll have to take the Big Y. SNP Packs can only test what is already known and the Big Y is a test of discovery.

Best Blog

Jim Bartlett, hands down, receives this award for his new and wonderful blog, Segmentology.

Making Sense of Autosomal DNA

Our autosomal DNA results provide us with matches at each of the vendors and at GedMatch, but what do we DO with all those matches and how to we utilize the genetic match information? How to we translate those matches into ancestral information. And once we’ve assigned a common ancestor to a match with an individual, how does that match affect other matches on that same segment?

2015 has been the year of sorting through the pieces and defining terms like IBS (identical by state, which covers both identical by population and identical by chance) and IBD (identical by descent). There has been a lot written this year.

Jim Bartlett, a long-time autosomal researcher has introduced his new blog, Segmentology, to discuss his journey through mapping ancestors to his DNA segments. To the best of my knowledge, Jim has mapped more of his chromosomes than any other researcher, more than 80% to specific ancestors – and all of us can leverage Jim’s lessons learned.

Segmentology.org by Jim Bartlett
http://dna-explained.com/2015/05/12/segmentology-org-by-jim-bartlett/

When you visit Jim’s site, please take a look at all of his articles. He and I and others may differ slightly in the details our approach, but the basics are the same and his examples are wonderful.

Autosomal DNA Testing – What Now?
http://dna-explained.com/2015/08/07/autosomal-dna-testing-101-what-now/

Autosomal DNA Testing 101 – Tips and Tricks for Contact Success
http://dna-explained.com/2015/08/11/autosomal-dna-testing-101-tips-and-tricks-for-contact-success/

How Phasing Works and Determining IBS vs IBD Matches
http://dna-explained.com/2015/01/02/how-phasing-works-and-determining-ibd-versus-ibs-matches/

Just One Cousin
http://dna-explained.com/2015/01/11/just-one-cousin/

Demystifying Autosomal DNA Matching
http://dna-explained.com/2015/01/17/demystifying-autosomal-dna-matching/

A Study Using Small Segment Matching
http://dna-explained.com/2015/01/21/a-study-utilizing-small-segment-matching/

Finally, A How-To Class for Working with Autosomal Results
http://dna-explained.com/2015/02/10/finally-a-how-to-class-for-working-with-autosomal-dna-results/

Parent-Child Non-Matching Autosomal DNA Segments
http://dna-explained.com/2015/05/14/parent-child-non-matching-autosomal-dna-segments/

A Match List Does Not an Ancestor Make
http://dna-explained.com/2015/05/19/a-match-list-does-not-an-ancestor-make/

4 Generation Inheritance Study
http://dna-explained.com/2015/08/23/4-generation-inheritance-study/

Phasing Yourself
http://dna-explained.com/2015/08/27/phasing-yourself/

Autosomal DNA Matching Confidence Spectrum
http://dna-explained.com/2015/09/25/autosomal-dna-matching-confidence-spectrum/

Earlier in the year, there was a lot of discussion and dissention about the definition of and use of small segments. I utilize them, carefully, generally in conjunction with larger segments. Others don’t. Here’s my advice. Don’t get yourself hung up on this. You probably won’t need or use small segments until you get done with the larger segments, meaning low-hanging fruit, or unless you are doing a very specific research project. By the time you get to that point, you’ll understand this topic and you’ll realize that the various researchers agree about far more than they disagree, and you can make your own decision based on your individual circumstances. If you’re entirely endogamous, small segments may just make you crazy. However, if you’re chasing a colonial American ancestor, then you may need those small segments to identify or confirm that ancestor.

It is unfortunate, however, that all of the relevant articles are not represented in the ISOGG wiki, allowing people to fully educate themselves. Hopefully this can be updated shortly with the additional articles, listed above and from Jim Bartlett’s blog, published during this past year.

Recreating the Dead

James and Catherne Crumley segments above, compliments of Kitty Cooper’s tools

As we learn more about how to use autosomal DNA, we have begun to reconstruct our ancestors from the DNA of their descendants. Not as in cloning, but as in attributing DNA found in multiple descendants that originate from a common ancestor, or ancestral couple. The first foray into this arena was GedMatch with their Lazarus tool.

Lazarus – Putting Humpty Dumpty Back Together Again
http://dna-explained.com/2015/01/14/lazarus-putting-humpty-dumpty-back-together-again/

I have taken a bit of a different proof approach wherein I recreated an ancestor, James Crumley, born in 1712 from the matching DNA of roughly 30 of his descendants.
http://www.slideshare.net/FamilyTreeDNA/roberta-estes-crumley-y-dna

I did the same thing, on an experimental smaller scale about a year ago with my ancestor, Henry Bolton.
http://dna-explained.com/2014/11/10/henry-bolton-c1759-1846-kidnapped-revolutionary-war-veteran-52-ancestors-45/

This is the way of the future in genetic genealogy, and I’ll be writing more about the Crumley project and the reconstruction of James Crumley in 2016.

Lump Of Coal Award(s)

This category is a “special category” that is exactly what you think it is. Yep, this is the award no one wants. We have a tie for the Lump of Coal Award this year between Ancestry and 23andMe.

Ancestry Becomes the J.R. Ewing of the Genealogy World

Attribution : © Glenn Francis, http://www.PacificProDigital.com

Some of you may remember J.R. Ewing on the television show called Dallas that ran from 1978 through 1991. J.R. Ewing, a greedy and unethical oil tycoon was one of the main characters. The series was utterly mesmerizing, and literally everyone tuned in. We all, and I mean universally, hated J.R. Ewing for what he unfeelingly and selfishly did to his family and others. Finally, in a cliffhanger end of the season episode, someone shot J.R. Ewing. OMG!!! We didn’t know who. We didn’t know if J.R. lived or died. Speculation was rampant. “Who shot JR?” was the theme on t-shirts everyplace that summer. J.R. Ewing, over time, became the man all of America loved to hate.

Ancestry has become the J.R. Ewing of the genealogy world for the same reasons.

In essence, in the genetic genealogy world, Ancestry introduced a substandard DNA product, which remains substandard years later with no chromosome browser or comparison tools that we need….and they have the unmitigated audacity to try to convince us we really don’t need those tools anyway. Kind of like trying to convince someone with a car that they don’t need tires.

Worse, yet, they’ve introduced “better” tools (New Ancestor Discoveries), as in tools that were going to be better than a chromosome browser. New Ancestor Discoveries “gives us” ancestors that aren’t ours. Sadly, there are many genealogists being led down the wrong path with no compass available.

Ancestry’s history of corporate stewardship is abysmal and continues with the obsolescence of various products and services including the Sorenson DNA database, their own Y and mtDNA database, MyFamily and most recently, Family Tree Maker. While the Family Tree Maker announcement has been met with great gnashing of teeth and angst among their customers, there are other software programs available. Ancestry’s choices to obsolete the DNA data bases is irrecoverable and a huge loss to the genetic genealogy community. That information is lost forever and not available elsewhere – a priceless, irreplaceable international treasure intentionally trashed.

If Ancestry had not bought up nearly all of the competing resources, people would be cancelling their subscriptions in droves to use another company – any other company. But there really is no one else anymore. Ancestry knows this, so they have become the J.R. Ewing of the genealogy world – uncaring about the effects of their decisions on their customers or the community as a whole. It’s hard for me to believe they have knowingly created such wholesale animosity within their own customer base. I think having a job as a customer service rep at Ancestry would be an extremely undesirable job right now. Many customers are furious and Ancestry has managed to upset pretty much everyone one way or another in 2015.

AncestryDNA Has Now Thoroughly Lost Its Mind
https://digginupgraves.wordpress.com/2015/04/02/ancestrydna-has-now-thoroughly-lost-its-mind/

Kenny, Kenny, Kenny
https://digginupgraves.wordpress.com/2015/04/10/kenny-kenny-kenny/

Dear Kenny – Any Suggestions for our New Ancestor Discoveries?
https://digginupgraves.wordpress.com/2015/04/13/dear-kenny-any-suggestions-for-our-new-ancestor-discoveries/

RIP Sorenson – A Crushing Loss
http://dna-explained.com/2015/05/15/rip-sorenson-a-crushing-loss/

Of Babies and Bathwater
http://www.legalgenealogist.com/blog/2015/05/17/of-babies-and-bathwater/

Facts Matter
http://legalgenealogist.com/blog/2015/05/03/facts-matter/

Getting the Most Out of AncestryDNA
http://dna-explained.com/2015/02/02/getting-the-most-out-of-ancestrydna/

Ancestry Gave Me a New DNA Ancestor and It’s Wrong
http://dna-explained.com/2015/04/03/ancestry-gave-me-a-new-dna-ancestor-and-its-wrong/

Testing Ancestry’s Amazing New Ancestor DNA Claim
http://dna-explained.com/2015/04/07/testing-ancestrys-amazing-new-ancestor-dna-claim/

Dissecting AncestryDNA Circles and New Ancestors
http://dna-explained.com/2015/04/09/dissecting-ancestrydna-circles-and-new-ancestors/

Squaring the Circle
http://legalgenealogist.com/blog/2015/03/29/squaring-the-circle/

Still Waiting for the Holy Grail
http://legalgenealogist.com/blog/2015/04/05/still-waiting-for-the-holy-grail/

A Dozen Ancestors That Aren’t aka Bad NADs
http://dna-explained.com/2015/04/14/a-dozen-ancestors-that-arent-aka-bad-nads/

The Logic and Birth of a Bad NAD (New Ancestor Discovery)
http://dna-explained.com/2015/08/12/the-logic-and-birth-of-a-bad-nad-new-ancestor-discovery/

Circling the Shews
http://legalgenealogist.com/blog/2015/05/24/circling-the-shews/

Naughty Bad NADs Sneak Home Under Cover of Darkness
http://dna-explained.com/2015/08/24/naughty-bad-nads-sneak-home-under-cover-of-darkness/

Ancestry Shared Matches Combined with New Ancestor Discoveries
http://dna-explained.com/2015/08/28/ancestry-shared-matches-combined-with-new-ancestor-discoveries/

Ancestry Shakey Leaf Disappearing Matches: Now You See Them – Now You Don’t
http://dna-explained.com/2015/09/24/ancestry-shakey-leaf-disappearing-matches-now-you-see-them-now-you-dont/

Ancestry’s New Amount of Shared DNA – What Does It Really Mean?
http://dna-explained.com/2015/11/06/ancestrys-new-amount-of-shared-dna-what-does-it-really-mean/

The Winds of Change
http://legalgenealogist.com/blog/2015/11/08/the-winds-of-change/

Confusion – Family Tree Maker, Family Tree DNA and Ancestry.com
http://dna-explained.com/2015/12/13/confusion-family-tree-maker-family-tree-dna-and-ancestry-com/

DNA: good news, bad news
http://legalgenealogist.com/blog/2015/01/11/dna-good-news-bad-news/

Check out the Alternatives
http://legalgenealogist.com/blog/2015/12/09/check-out-the-alternatives/

GeneAwards 2015
http://www.tamurajones.net/GeneAwards2015.xhtml

23andMe Betrays Genealogists

In October, 23andMe announced that it has reached an agreement with the FDA about reporting some health information such as carrier status and traits to their clients. As a part of or perhaps as a result of that agreement, 23andMe is dramatically changing the user experience.

In some aspects, the process will be simplified for genealogists with a universal opt-in. However, other functions are being removed and the price has doubled. New advertising says little or nothing about genealogy and is entirely medically focused. That combined with the move of the trees offsite to MyHeritage seems to signal that 23andMe has lost any commitment they had to the genetic genealogy community, effectively abandoning the group entirely that pulled their collective bacon out of the fire. This is somehow greatly ironic in light of the fact that it was the genetic genealogy community through their testing recommendations that kept 23andMe in business for the two years, from November of 2013 through October of 2015 when the FDA had the health portion of their testing shut down. This is a mighty fine thank you.

As a result of the changes at 23andMe relative to genealogy, the genetic genealogy community has largely withdrawn their support and recommendations to test at 23andMe in favor of Ancestry and Family Tree DNA.

Kelly Wheaton, writing on the Facebook ISOGG group along with other places has very succinctly summed up the situation:
https://www.facebook.com/groups/isogg/permalink/10153873250057922/

You can also view Kelly’s related posts from earlier in December and their comments at:
https://www.facebook.com/groups/isogg/permalink/10153830929022922/
and…
https://www.facebook.com/groups/isogg/permalink/10153828722587922/

My account at 23andMe has not yet been converted to the new format, so I cannot personally comment on the format changes yet, but I will write about the experience in 2016 after my account is converted.

Furthermore, I will also be writing a new autosomal vendor testing comparison article after their new platform is released.

I Hate 23andMe
https://digginupgraves.wordpress.com/2015/06/14/i-hate-23andme/

23andMe to Get Makeover After Agreement With FDA
http://dna-explained.com/2015/10/21/23andme-to-get-a-makeover-after-agreement-with-fda/

23andMe Metamorphosis
http://throughthetreesblog.tumblr.com/post/131724191762/the-23andme-metamorphosis

The Changes at 23andMe
http://legalgenealogist.com/blog/2015/10/25/the-changes-at-23andme/

The 23and Me Transition – The First Step
http://dna-explained.com/2015/11/05/the-23andme-transition-first-step-november-11th/

The Winds of Change
http://legalgenealogist.com/blog/2015/11/08/the-winds-of-change/

Why Autosomal Response Rate Really Does Matter
http://dna-explained.com/2015/02/24/why-autosomal-response-rate-really-does-matter/

Heads Up About the 23andMe Meltdown
http://dna-explained.com/2015/12/04/heads-up-about-the-23andme-meltdown/

Now…and not now
http://legalgenealogist.com/blog/2015/12/06/now-and-not-now/

Cone of Shame Award

Another award this year is the Cone of Shame award which is also awarded to both Ancestry and 23andMe for their methodology of obtaining “consent” to sell their customers’, meaning our, DNA and associated information.

Genetic Genealogy Data Gets Sold

Unfortunately, 2015 has been the year that the goals of both 23andMe and Ancestry have become clear in terms of our DNA data. While 23andMe has always been at least somewhat focused on health, Ancestry never was previously, but has now hired a health officer and teamed with Calico for medical genetics research.

Now, both Ancestry and 23andMe have made research arrangements and state in their release and privacy verbiage that all customers must electronically sign (or click through) when purchasing their DNA tests that they can sell, at minimum, your anonymized DNA data, without any further consent. And there is no opt-out at that level.

They can also use our DNA and data internally, meaning that 23andMe’s dream of creating and patenting new drugs can come true based on your DNA that you submitted for genealogical purposes, even if they never sell it to anyone else.

In an interview in November, 23andMe CEO Anne Wojcicki said the following:

23andMe is now looking at expanding beyond the development of DNA testing and exploring the possibility of developing its own medications. In July, the company raised $79 million to partly fund that effort. Additionally, the funding will likely help the company continue with the development of its new therapeutics division. In March, 23andMe began to delve into the therapeutics market, to create a third pillar behind the company’s personal genetics tests and sales of genetic data to pharmaceutical companies.

Given that the future of genetic genealogy at these two companies seems to be tied to the sale of their customer’s genetic and other information, which, based on the above, is very clearly worth big bucks, I feel that the fact that these companies are selling and utilizing their customer’s information in this manner should be fully disclosed. Even more appropriate, the DNA information should not be sold or utilized for research without an informed consent that would traditionally be used for research subjects.

Within the past few days, I wrote an article, providing specifics and calling on both companies to do the following.

To minimally create transparent, understandable verbiage that informs their customers before the end of the purchase process that their DNA will be sold or utilized for unspecified research with the intention of financial gain and that there is no opt-out. However, a preferred plan of action would be a combination of 2 and 3, below.
Implement a plan where customer DNA can never be utilized for anything other than to deliver the services to the consumers that they purchased unless a separate, fully informed consent authorization is signed for each research project, without coercion, meaning that the client does not have to sign the consent to obtain any of the DNA testing or services.
To immediately stop utilizing the DNA information and results from customers who have already tested until they have signed an appropriate informed consent form for each research project in which their DNA or other information will be utilized.

And Now Ancestry Health
http://dna-explained.com/2015/06/06/and-now-ancestry-health/

Opting Out
http://legalgenealogist.com/blog/2015/07/26/opting-out/

Ancestry Terms of Use Updated
http://legalgenealogist.com/blog/2015/07/07/ancestry-terms-of-use-updated/

AncestryDNA Doings
http://legalgenealogist.com/blog/2015/07/05/ancestrydna-doings/

Heads Up About the 23andMe Meltdown
http://dna-explained.com/2015/12/04/heads-up-about-the-23andme-meltdown/

23andMe and Ancestry and Selling Your DNA Information
http://dna-explained.com/2015/12/30/23andme-ancestry-and-selling-your-dna-information/

Citizen Science Leadership Award

The Citizen Science Leadership Award this year goes to Blaine Bettinger for initiating the Shared cM Project, a crowdsourced project which benefits everyone.

Citizen Scientists Continue to Push the Edges of the Envelope with the Shared cM Project

Citizen scientists, in the words of Dr. Doron Behar, “are not amateurs.” In fact, citizen scientists have been contributing mightily and pushing the edge of the genetic genealogy frontier consistently now for 15 years. This trend continues, with new discoveries and new ways of viewing and utilizing information we already have.

For example, Blaine Bettinger’s Shared cM Project was begun in March and continues today. This important project has provided real life information as to the real matching amounts and ranges between people of different relationships, such as first cousins, for example, as compared to theoretical match amounts. This wonderful project produced results such as this:

I don’t think Blaine initially expected this project to continue, but it has and you can read about it, see the rest of the results, and contribute your own data here. Blaine has written several other articles on this topic as well, available at the same link.

Am I Weird or What?
http://dna-explained.com/2015/03/07/am-i-weird-or-what/

Jim Owston analyzed fourth cousins and other near distant relationships in his Owston one-name study:
https://owston.wordpress.com/2015/08/10/an-analysis-of-fourth-cousins-and-other-near-distant-relatives/

I provided distant cousin information in the Crumley surname study:
http://www.slideshare.net/FamilyTreeDNA/roberta-estes-crumley-y-dna

I hope more genetic genealogists will compile and contribute this type of real world data as we move forward. If you have compiled something like this, the Surname DNA Journal is peer reviewed and always looking for quality articles for publication.

Privacy, Law Enforcement and DNA

Unfortunately, in May, a situation by which Y DNA was utilized in a murder investigation was reported in a sensationalist “scare” type fashion. This action provided cause, ammunition or an excuse for Ancestry to remove the Sorenson data base from public view.

I find this exceedingly, exceedingly unfortunate. Given Ancestry’s history with obsoleting older data bases instead of updating them, I’m suspecting this was an opportune moment for Ancestry to be able to withdraw this database, removing a support or upgrade problem from their plate and blame the problem on either law enforcement or the associated reporting.

I haven’t said much about this situation, in part because I’m not a lawyer and in part because the topic is so controversial and there is no possible benefit since the damage has already been done. Unfortunately, nothing anyone can say or has said will bring back the Sorenson (or Ancestry) data bases and arguments would be for naught. We already beat this dead horse a year ago when Ancestry obsoleted their own data base. On this topic, be sure to read Judy Russell’s articles and her sources as well for the “rest of the story.”

Privacy, the Police and DNA
http://legalgenealogist.com/blog/2015/02/08/privacy-the-police-and-dna/

Big Easy DNA Not So Easy
http://legalgenealogist.com/blog/2015/03/15/big-easy-dna-not-so-easy/

Of Babies and Bathwater
http://www.legalgenealogist.com/blog/2015/05/17/of-babies-and-bathwater/

Facts Matter
http://legalgenealogist.com/blog/2015/05/03/facts-matter/

Genetic genealogy standards from within the community were already in the works prior to the Idaho case, referenced above, and were subsequently published as guidelines.

Announcing Genetic Genealogy Standards
http://thegeneticgenealogist.com/2015/01/10/announcing-genetic-genealogy-standards/

The standards themselves:
http://www.thegeneticgenealogist.com/wp-content/uploads/2015/01/Genetic-Genealogy-Standards.pdf

Ancient DNA Results Continue to Amass

“Moorleiche3-Schloss-Gottorf” by Commander-pirx at de.wikipedia – Own work. Licensed under CC BY-SA 3.0 via Commons

Ancient DNA is difficult to recover and even more difficult to sequence, reassembling tiny little blocks of broken apart DNA into an ancient human genome.

However, each year we see a few more samples and we are beginning to repaint the picture of human population movement, which is different than we thought it would be.

One of the best summaries of the ancient ancestry field was Michael Hammer’s presentation at the Family Tree DNA Conference in November titled “R1B and the Peopling of Europe: an Ancient DNA Update.” His slides are available here:
http://www.slideshare.net/FamilyTreeDNA/r1b-and-the-people-of-europe-an-ancient-dna-update

One of the best ongoing sources for this information is Dienekes’ Anthropology Blog. He covered most of the new articles and there have been several. That’s the good news and the bad news, all rolled into one. http://dienekes.blogspot.com/

I have covered several that were of particular interest to the evolution of Europeans and Native Americans.

Yamnaya, Light Skinned Brown Eyed….Ancestors?
http://dna-explained.com/2015/06/15/yamnaya-light-skinned-brown-eyed-ancestors/

Kennewick Man is Native American
http://dna-explained.com/2015/06/18/kennewick-man-is-native-american/

Botocudo – Ancient Remains from Brazil
http://dna-explained.com/2015/07/02/botocudo-ancient-remains-from-brazil/

Some Native had Oceanic Ancestors
http://dna-explained.com/2015/07/22/some-native-americans-had-oceanic-ancestors/

Homo Naledi – A New Species Discovered
http://dna-explained.com/2015/09/11/homo-naledi-a-new-species-discovered/

Massive Pre-Contact Grave in California Yields Disappointing Results
http://dna-explained.com/2015/10/20/mass-pre-contact-native-grave-in-california-yields-disappointing-results/

I know of several projects involving ancient DNA that are in process now, so 2016 promises to be a wonderful ancient DNA year!

Education

Many, many new people discover genetic genealogy every day and education continues to be an ongoing and increasing need. It’s a wonderful sign that all major conferences now include genetic genealogy, many with a specific track.

The European conferences have done a great deal to bring genetic genealogy testing to Europeans. European testing benefits those of us whose ancestors were European before immigrating to North America. This year, ISOGG volunteers staffed booths and gave presentations at genealogy conferences in Birmingham, England, Dublin, Ireland and in Nyköping, Sweden, shown below, photo compliments of Catherine Borges.

Several great new online educational opportunities arose this year, outside of conferences, for which I’m very grateful.

DNA Lectures YouTube Channel
http://dna-explained.com/2015/04/26/dna-lectures-youtube-channel/

Allen County Public Library Online Resources
http://dna-explained.com/2015/06/03/allen-county-public-library-online-resources/

DNA Data Organization Tools and Who’s on First
http://dna-explained.com/2015/09/08/dna-data-organization-tools-and-whos-on-first/

Genetic Genealogy Educational Resource List
http://dna-explained.com/2015/12/03/genetic-genealogy-educational-resource-list/

Genetic Genealogy Ireland Videos
https://www.youtube.com/channel/UCHnW2NAfPIA2KUipZ_PlUlw

DNA Lectures – Who Do You Think You Are
https://www.youtube.com/channel/UC7HQSiSkiy7ujlkgQER1FYw

Ongoing and Online Classes in how to utilize both Y and autosomal DNA
http://www.dnaadoption.com/index.php?page=online-classes

Education Award

Family Tree DNA receives the Education Award this year along with a huge vote of gratitude for their 11 years of genetic genealogy conferences. They are the only testing or genealogy company to hold a conference of this type and they do a fantastic job. Furthermore, they sponsor additional educational events by providing the “theater” for DNA presentations at international events such as the Who Do You Think You Are conference in England. Thank you Family Tree DNA.

Family Tree DNA Conference

The Family Tree DNA Conference, held in November, was a hit once again. I’m not a typical genealogy conference person. My focus is on genetic genealogy, so I want to attend a conference where I can learn something new, something leading edge about the science of genetic genealogy – and that conference is definitely the Family Tree DNA conference.

Furthermore, Family Tree DNA offers tours of their lab on the Monday following the conference for attendees, and actively solicits input on their products and features from conference attendees and project administrators.

Family Tree DNA 11^th International Conference – The Best Yet
http://dna-explained.com/2015/11/18/2015-family-tree-dna-11th-international-conference-the-best-yet/

All of the conference presentations that were provided by the presenters have been made available by Family Tree DNA at:
http://www.slideshare.net/FamilyTreeDNA?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email

2016 Genetic Genealogy Wish List

In 2014, I presented a wish list for 2015 and it didn’t do very well. Will my 2015 list for 2016 fare any better?

Ancestry restores Sorenson and their own Y and mtDNA data bases in some format or contributes to an independent organization like ISOGG.
Ancestry provides chromosome browser.
Ancestry removes or revamps Timber in order to restore legitimate matches removed by Timber algorithm.
Fully informed consent (per research project) implemented by 23andMe and Ancestry, and any other vendor who might aspire to sell consumer DNA or related information, without coercion, and not as a prerequisite for purchasing a DNA testing product. DNA and information will not be shared or utilized internally or externally without informed consent and current DNA information will cease being used in this fashion until informed consent is granted by customers who have already tested.
Improved ethnicity reporting at all vendors including ancient samples and additional reference samples for Native Americans.
Autosomal Triangulation tools at all vendors.
Big Y and STR integration and analysis enhancement at Family Tree DNA.
Ancestor Reconstruction
Mitochondrial and Y DNA search tools by ancestor and ancestral line at Family Tree DNA.
Improved tree at Family Tree DNA – along with new search capabilities.
23andMe restores lost capabilities, drops price, makes changes and adds features previously submitted as suggestions by community ambassadors.
More tools (This is equivalent to “bring me some surprises” on my Santa list as a kid.)

My own goals haven’t changed much over the years. I still just want to be able to confirm my genealogy, to learn as much as I can about each ancestor, and to break down brick walls and fill in gaps.

I’m very hopeful each year as more tools and methodologies emerge. More people test, each one providing a unique opportunity to match and to understand our past, individually and collectively. Every year genetic genealogy gets better! I can’t wait to see what 2016 has in store.

Here’s wishing you a very Happy and Ancestrally Prosperous New Year!

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Native American Haplogroup C Update – Progress!!

Posted on August 25, 2015 by Roberta Estes

Haplogroup C-P39 is the Native American branch of Y DNA paternal haplogroup C. It’s rare as chicken’s teeth. Most Native American males fall into haplogroup Q, making our haplogroup C-P39 project participants quite unusual and unique. So are the tools needed to identify branches on the Native American haplogroup C tree.

Last week, Family Tree DNA added a group of 9 SNPs found in haplogroup C to their product offering. This was done without an announcement and without any fanfare – but it’s really important. Without the ongoing support of Family Tree DNA, we wouldn’t have the Big Y test, nor the refining SNP tests that can be added to the Big Y in areas where the results are ambiguous. Individuals who don’t want to purchase the Big Y can purchase these haplogroup defining SNPs individually as well.

The Native defining SNP for haplogroup C is P39. People who test positive for C-P39 will then want to test Z30750 and Z30764.

Z30503
Z30601
FGC21495
Z30750
Z30764
PF3239
Z30729
FGC263
FGC31712

However, because haplogroup C-P39 is so rare – and to date – we have found several new SNPs in every man who has taken the Big Y test – and because those new, never before discovered SNPs are the bread crumbs that we need to follow to discover how our ancestors settled and dispersed across the Americas – we strong recommend the Big Y test at Family Tree DNA for all C-P39 men. The Big Y test doesn’t just look at known SNP locations, it scans the entire Y chromosome for mutations. Therefore, it’s both a genealogy and a research tool.

To that end, we very much want to fund this testing from the project coffers where necessary to advance our understanding. Just to whet your appetite, we have participants now across Canada and also in the American Southwest. We desperately want these men to take the Big Y test so we can get a much clearer picture of how they are related, and how many mutations they have individually – but don’t share – because that is how we estimate when they last shared a common ancestor. In other words, the mutations build the branches of the tree.

This week, we’ve ordered another new C-P39 Big Y test. If you are C-P39 – Native American haplogroup C – and have not yet taken the Big Y – please consider doing so.

If you are Native American and haplogroup C – please join the C-P39 and the American Indian projects. You can do so from your home page at Family Tree DNA by clicking on the “Projects” tab at the upper left of your personal page, then on “join projects.” You can search for the word “Indian” in the project list to find the American Indian project and scrolling down to the Y haplogroup projects and clicking on C will take you to the C-P39 link.

If you can contribute to funding these Big Y tests, please do – even small amounts help. The link to donate directly to the C-P39 project is: https://www.familytreedna.com/group-general-fund-contribution.aspx?g=Y-DNAC-P39

Each individual who takes the Big Y test is also encouraged to upgrade to 111 markers. We need as much information as we can get.

Marie Rundquist and I are co-administrators of the C-P39 project, and she wrote the following verbiage in honor of the 5 year anniversary of the first discovery of what is now C-P39 in the Native Community. We, as a community, have come a very long way in just 5 years!

It was in 2010, five years ago, when Keith Doucet first tested for the C P39 Y DNA (formerly C3b) Native American DNA type in the Amerindian Ancestry out of Acadia Family Tree DNA study — with numbers of Doucets (and Doucettes!) having the same, Native American, C P39 Y DNA result. It’s amazing when you think of our journey and how much this research has benefitted our knowledge of our history in North America!

Who can ever forget Keith Doucet’s discovery? http://www.familyheritageresearchcommunity.org/doucet_dna.html

Or Emile Broome’s Y DNA discovery, also from 2010? http://www.familyheritageresearchcommunity.org/broome_dna.html

…and the subsequent discoveries of related Doucets and Doucettes and other project members from all regions of the US and Canada who tested in our project and whose results showed the same Native American C P39 Y DNA haplogroup type?

There is great similarity among the DNA test results for our C P39 Y DNA candidates despite differences in geographic locations and surnames, with testers from across the United States, including the American Southwest, the North East, the South, and Canada compared. Initial Big Y DNA test results for project members have shown remarkable similarity as well. Additional Big Y test results for tests underway and the availability of 9 new SNPs for our project members help us discover whether this trend is amplified by the additional tests or if we (the C P39 Y DNA project) can distinguish downstream uniqueness among our participants. The C P39 Y DNA test has received the generous support of its members, Family Tree DNA leadership and scientists, product managers, and volunteer administrators in establishing our superior C P39 Y DNA baseline and we are grateful for your support.

Visit the C P39 Y DNA project site to learn more. https://www.familytreedna.com/public/ydna_C-P39/

Thank you to our project members for your continued participation! And thank you to Family Tree DNA for their ongoing dedication, research and support. Collectively, we discover more of our history every day!

______________________________________________________________

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Some Native Americans Had Oceanic Ancestors

Posted on July 22, 2015 by Roberta Estes

This week has seen a flurry of new scientific and news articles. What has been causing such a stir? It appears that Australian or more accurately, Australo-Melanese DNA has been found in South America’s Native American population. In addition, it has also been found in Aleutian Islanders off the coast of Alaska. In case you aren’t aware, that’s about 8,500 miles as the crow flies. That’s one tired crow. As the person paddles or walks along the shoreline, it’s even further, probably about 12,000 miles.

Whatever the story, it was quite a journey and it certainly wasn’t all over flat land.

This isn’t the first inkling we’ve had. Just a couple weeks ago, it was revealed that the Botocudo remains from Brazil were Polynesian and not admixed with either Native, European or African. This admixture was first discovered via mitochondrial DNA, but full genome sequencing confirmed their ancestry and added the twist that they were not admixed – an extremely unexpected finding. This is admittedly a bit confusing, because it implies that there were new Polynesian arrivals in the 1600s or 1700s.

Unlikely as it seems, it obviously happened, so we set that aside as relatively contemporary.

The findings in the papers just released are anything but contemporary.

The First Article

The first article in Science, “Genomic evidence for the Pleistocene and recent population history of Native Americans” by Raghaven et al published this week provides the following summary (bolding is mine):

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

This article in EurekAlert and a second one here discuss the Science paper.

Migration map from the Raghaven paper.

The paper included the gene flow and population migration map, above, along with dates.

The scientists sequenced the DNA of 31 living individuals from the Americas, Siberia and Oceana as follows:

Siberian:

Altai – 2
Buryat – 2
Ket – 2
Kiryak – 2
Sakha – 2
Siberian Yupik – 2

North American Native:

Tsimshian (number not stated, but by subtraction, it’s 1)

Southern North American, Central and South American Native:

Pima – 1
Huichol -1
Aymara – 1
Yakpa – 1

Oceana:

Papuan – 14

The researchers also state that they utilized 17 specimens from relict groups such as the Pericues from Mexico and Fuego-Patagonians from the southernmost tip of South America. They also sequenced two pre-Columbian mummies from the Sierra Tarahumara in northern Mexico. In total, 23 ancient samples from the Americas were utilized.

They then compared these results with a reference panel of 3053 individuals from 169 populations which included the ancient Saqqaq Greenland individual at 400 years of age as well as the Anzick child from Montana from about 12,500 years ago and the Mal’ta child from Siberia at 24,000 years of age.

Not surprisingly, all of the contemporary samples with the exception of the Tsimshian genome showed recent western Eurasian admixture.

As expected, the results confirm that the Yupik and Koryak are the closest Eurasian population to the Americas. They indicate that there is a “clean split” between the Native American population and the Koryak about 20,000 years ago.

They found that “Athabascans and Anzick-1, but not the Greenlandis Inuit and Saqqaq belong to the same initial migration wave that gave rise to present-day Amerindians from southern North America and Central and South America, and that this migration likely followed a coastal route, given our current understanding of the glacial geological and paleoenvironmental parameters of the Late Pleistocene.”

Evidence of gene flow between the two groups was also found, meaning between the Athabascans and the Inuit. Additionally, they found evidence of post-split gene flow between Siberians and Native Americans which seems to have stopped about 12,000 years ago, which meshes with the time that the Beringia land bridge was flooded by rising seas, cutting off land access between the two land masses.

They state that the results support all Native migration from Siberia, contradicting claims of an early migration from Europe.

The researchers then studied the Karitiana people of South America and determined that the two groups, Athabascans and Karitiana diverged about 13,000 years ago, probably not in current day Alaska, but in lower North America. This makes sense, because the Clovis Anzick child, found in Montana, most closely matches people in South America.

By the Clovis period of about 12,500 years ago, the Native American population had already split into two branches, the northern and southern, with the northern including Athabascan and other groups such as the Chippewa, Cree and Ojibwa. The Southern group included people from southern North America and Central and South America.

Interestingly, while admixture with the Inuit was found with the Athabascan, Inuit admixture was not found among the Cree, Ojibwa and Chippewa. The researchers suggest that this may be why the southern branch, such as the Karitiana are genetically closer to the northern Amerindians located further east than to northwest coast Amerindians and Athabascans.

Finally, we get to the Australian part. The researchers when trying to sort through the “who is closer to whom” puzzle found unexpected results. They found that some Native American populations including Aleutian Islanders, Surui (Brazil) and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as Ojibwa, Cree and Algonquian and South American Purepecha (Mexico), Arhuaco (Colombia) and Wayuu (Colombia, Venezuela). In fact, the Surui are one of the closest populations to East Asians and Australo-Melanese, the latter including Papuans, non-Papuan Melanesians, Solomon Islanders and hunter-gatherers such as Aeta. The researchers acknowledge these are weak trends, but they are nonetheless consistently present.

Dr. David Reich, from Harvard, a co-author of another paper, also published this past week, says that 2% of the DNA of Amazonians is from Oceana. If that is consistent, it speaks to a founder population in isolation, such that the 2% just keeps getting passed around in the isolated population, never being diluted by outside DNA. I would suggest that is not a weak signal.

The researchers suggest that the variance in the strength of this Oceanic signal suggests that the introduction of the Australo-Melanese occurred after the initial peopling of the Americas. The ancient samples cluster with the Native American groups and do not show the Oceanic markers and show no evidence of gene flow from Oceana.

The researchers also included cranial morphology analysis, which I am omitting since cranial morphology seems to have led researchers astray in the past, specifically in the case of Kennewick man.

One of the reasons cranial morphology is such a hotly debated topic is because of the very high degree of cranial variance found in early skeletal remains. One of the theories evolving from the cranial differences involving the populating of the Americans has been that the Australo-Melanese were part of a separate and earlier migration that gave rise to the earliest Americans who were then later replaced by the Asian ancestors of current day Native Americans. If this were the case, then the now-extinct Fuego-Patagonains samples from the location furthest south on the South American land mass should have included DNA from Oceana, but it didn’t.

The Second Article

A second article published this week, titled “’Ghost population’ hints at long lost migration to the Americas” by Ellen Callaway discusses similar findings, presented in a draft letter to Nature titled “Genetic evidence for two founding populations of the Americas” by Skoglund et al. This second group discovers the same artifact Australo-Melanesian DNA in Native American populations but suggests that it may be from the original migration and settlement event or that there may have been two distinct founding populations that settled at the same time or that there were two founding events.

EurekAlert discusses the article as well.

It’s good to have confirmation and agreement between the two labs who happened across these results independently that the Australo-Melanesian DNA is present in some Native populations today.

Their interpretations and theories about how this Oceanic DNA arrived in some of the Native populations vary a bit, but if you read the details, it’s really not quite as different as it first appears from the headlines. Neither group claims to know for sure, and both discuss possibilities.

Questions remain. For example, if the founding group was small, why, then, don’t all of the Native people and populations have at least some Oceanic markers? The Anzick Child from 12,500 years ago does not. He is most closely related to the tribes in South America, where the Oceanic markers appear with the highest frequencies.

In the Harvard study, the scientists fully genome sequenced 63 individuals without discernable evidence of European or African ancestors in 21 Native American populations, restricting their study to individuals from Central and South America that have the strongest evidence of being entirely derived from a homogenous First American ancestral population.

Their results show that the two Amazonian groups, Surui and Karitians are closest to the “Australasian populations, the Onge from the Andaman Island in the Bay of Bengal (a so-called ‘Negrito’ group), New Guineans, Papuans and indigenous Australians.” Within those groups, the Australasian populations are the only outliers – meaning no Africans, Europeans or East Asian DNA found in the Native American people.

When repeating these tests, utilizing blood instead of saliva, a third group was shown to also carry these Oceanic markers – the Xavante, a population from the Brazilian plateau that speaks a language of the Ge group that is different from the Tupi language group spoke by the Karitians and Surui.

The closest populations that these Native people matched in Oceana, shown above on the map from the draft Skoglund letter, were, in order, New Guineans, Papuans and Andamanese. The researchers further state that populations from west of the Andes or north of the Panama isthmus show no significant evidence of an affinity to the Onge from the Andaman Islands with the exception of the Cabecar (Costa Rica).

That’s a very surprising finding, given that one would expect more admixture on the west, which is the side of the continent where the migration occurred.

The researchers then compared the results with other individuals, such as Mal’ta child who is known to have contributed DNA to the Native people today, and found no correlation with Oceanic DNA. Therefore, they surmised that the Oceanic admixture cannot be explained by a previously known admixture event.

They propose that a mystery population they have labeled as “Population Y” (after Ypykuera which means ancestor in the Tupi language family) contributed the Australasian lineage to the First Americans and that is was already mixed into the lineage by the time it arrived in Brazil.

According to their work, Population Y may itself have been admixed, and the 2% of Oceanic DNA found in the Brazilian Natives may be an artifact of between 2 and 85% of the DNA of the Surui, Karitiana and Xavante that may have come from Population Y. They mention that this result is striking in that the majority of the craniums that are more Oceanic in Nature than Asiatic, as would be expected from people who migrated from Siberia, are found in Brazil.

They conclude that the variance in the presence or absence of DNA in Native people and remains, and the differing percentages argue for more than one migration event and that “the genetic ancestry of Native Americans from Central and South America cannot be due to a single pulse of migration south of the Late Pleistocene ice sheets from a homogenous source population, and instead must reflect at least two streams of migration or alternatively a long drawn out period of gene flow from a structured Beringian or Northeast Asian source.”

Perhaps even more interesting is the following statement:

“The arrival of population Y ancestry in the Americas must in any scenario have been ancient: while Population Y shows a distant genetic affinity to Andamanese, Australian and New Guinean populations, it is not particularly closely related to any of them, suggesting that the source of population Y in Eurasia no longer exists.”

They further state they find no admixture indication that would suggest that Population Y arrived in the last few thousand years.

So, it appears that perhaps the Neanderthals and Denisovans were not the only people who were our ancestors, but no longer exist as a separate people, only as an admixed part of us today. We are their legacy.

The Take Away

When I did the Anzick extractions, we had hints that something of this sort might have been occurring. For example, I found surprising instances of haplogroup M, which is neither European, African nor Native American, so far as we know today. This may have been a foreshadowing of this Oceanic admixture. It may also be a mitochondrial artifact. Time will tell. Perhaps haplogroup M will turn out to be Native by virtue of being Oceanic and admixed thousands of years ago. There is still a great deal to learn. Regardless of how these haplogroups and Oceanic DNA arrived in Brazil in South America and in the Aleutian Islands off of Alaska, one thing is for sure, it did.

We know that the Oceanic DNA found in the Brazilian people studied for these articles is not contemporary and is ancient. This means that it is not related to the Oceanic DNA found in the Botocudo people, who, by the way, also sport mitochondrial haplogroups that are within the range of Native people, meaning haplogroup B, but have not been found in other Native people. Specifically, haplogroups B4a1a1 and B4a1a1a. Additionally, there are other B4a1a, B4a1b and B4a1b1 results found in the Anzick extract which could also be Oceanic. You can see all of the potential and confirmed Native American mitochondrial DNA results in my article “Native American Mitochondrial Haplogroups” that I update regularly.

We don’t know how or when the Botocudo arrived, but the when has been narrowed to the 1600s or 1700s. We don’t know how or when the Oceanic DNA in the Brazilian people arrived either, but the when was ancient. This means that Oceanic DNA has arrived in South America at least twice and is found among the Native peoples both times.

We know that some Native groups have some Oceanic admixture, and others seem to have none, in particular the Northern split group that became the Cree, Ojibwa, Algonquian, and Chippewa.

We know that the Brazilian Native groups are most closely related to Oceanic groups, but that the first paper also found Oceanic admixture in the Aleutian Islands. The second paper focused on the Central and South American tribes.

We know that the eastern American tribes, specifically the Algonquian tribes are closely related to the South Americans, but they don’t share the Oceanic DNA and neither do the mid-continent tribes like the Cree, Ojibwa and Chippewa. The only Paleolithic skeleton that has been sequenced, Anzick, from 12,500 years ago in Montana also does not carry the Oceanic signature.

In my opinion, the disparity between who does and does not carry the Oceanic signature suggests that the source of the Oceanic DNA in the Native population could not have been a member of the first party to exit out of Beringia and settle in what is now the Americas. Given that this had to be a small party, all of the individuals would have been thoroughly admixed with each other’s ancestral DNA within just a couple of generations. It would have been impossible for one ancestor’s DNA to only be found in some people. To me, this argues for one of two scenarios.

First, a second immigration wave that joined the first wave but did not admix with some groups that might have already split off from the original group such as the Anzick/Montana group.

Second, multiple Oceanic immigration events. We still have to consider the possibility that there were multiple events that introduced Oceanic DNA into the Native population. In other words, perhaps the Aleutian Islands Oceanic DNA is not from the same migration event as the Brazilian DNA which we know is not from the same event as the Botocudo. I would very much like to see the Oceanic DNA appear in a migration path of people, not just in one place and then the other. We need to connect the dots.

What this new information does is to rule out the possibility that there truly was only one wave of migration – one group of people who settled the Americas at one time. More likely, at least until the land bridge submerged, is that there were multiple small groups that exited Beringia over the 8,000 or so years it was inhabitable. Maybe one of those groups included people from Oceana. Someplace, sometime, as unlikely as it seems, it happened.

The amazing thing is that it’s more than 10,000 miles from Australia to the Aleutian Islands, directly across the Pacific. Early adventurers would have likely followed a coastal route to be sustainable, which would have been significantly longer. The fact that they survived and sent their DNA on a long adventure from Australia to Alaska to South America – and it’s still present today is absolutely amazing.

We know we still have a lot to learn and this is the tip of a very exciting iceberg. As more contemporary and ancient Native people have their full genomes sequenced, we’ll learn more answers. The answer is in the DNA. We just have to sequence enough of it and learn how to understand the message being delivered.

______________________________________________________________

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DNA Testing Strategy for Adoptees and People with Uncertain Parentage

Posted on June 17, 2015 by Roberta Estes

Adoptees aren’t the only people who don’t know who their parents are. There are many people who don’t know the identity of one of their two parents…and it’s not always the father. Just this week, I had someone who needed to determine which of two sisters was her mother. Still, the “who’s your Daddy” crowd, aside from adoptees, is by far the largest.

The DNA testing strategy for both of these groups of people is the same, with slight modifications for male or female. Let’s take a look.

Males have three kinds of DNA that can be tested and then compared to other participants’ results. The tests for these three kinds of DNA provide different kinds of information which is useful in different ways. For example, Y DNA testing may give you a surname, if you’re a male, but the other two types of tests can’t do that, at least not directly.

Females only have two of those kinds of DNA that can be tested. Females don’t have a Y chromosome, which is what makes males male genetically.

If you look at this pedigree chart, you can see that the Y chromosome, in blue, is passed from the father to the son, but not to daughters. It’s passed intact, meaning there is no admixture from the mother, who doesn’t have a Y chromosome, because she is female. The Y chromosome is what makes males male.

The second type of DNA testing is mitochondrial, represented by the red circles. It is passed from the mother to all of her children, of both genders, intact – meaning her mitochondrial DNA is not admixed with the mtDNA of the father. Woman pass their mtDNA on to their children, men don’t.

Therefore when you test either the Y or the mtDNA, you get a direct line view right down that branch of the family tree – and only that direct line on that branch of the tree. Since there is no admixture from spouses in any generation, you will match someone exactly or closely (allowing for an occasional mutation or two) from generations ago. Now, that’s the good and the bad news – and where genealogical sleuthing comes into play.

On the chart above, the third kind of DNA testing, autosomal DNA, tests your DNA from all of your ancestors, meaning all of those boxes with no color, not just the blue and red ones, but it does include the blue and red ancestors too. However, autosomal DNA (unlike Y and mtDNA) is diluted by half in each generation, because you get half of your autosomal DNA from each parent, so only half of the parents DNA gets passed on to each child.

Let’s look at how these three kinds of DNA can help you identify your family members.

Y DNA

Since the Y DNA typically follows the paternal surname, it can be extremely helpful for males who are searching for their genetic surname. For example, if your biological father’s surname is Estes, assuming he is not himself adopted or the product of a nonpaternal event (NPE) which I like to refer to as undocumented adoptions, his DNA will match that of the Estes ancestral line. So, if you’re a male, an extremely important test will be the Y DNA test from Family Tree DNA, the only testing company to offer this test.

Let’s say that you have no idea who your bio-father is, but when your results come back you see a preponderance of Estes men whom you match, as well as your highest and closest matches being Estes.

By highest, I mean on the highest panel you tested – in this case 111 markers. And by closest, I mean with the smallest genetic distance, or number of mutations difference. On the chart below, this person matches only Estes males at 111 markers, and one with only 1 mutation difference (Genetic Distance.) Please noted that I’ve redacted first names.

Hint for Mr. Hilbert, below – there is a really good chance that you’re genetically Estes on the direct paternal side – that blue line.

The next step will be to see which Estes line you match the most closely and begin to work from there genealogically. In this case, that would be the first match with only one difference. Does your match have a tree online? In this case, they do – as noted by the pedigree chart icon. Contact this person. Where did their ancestors live? Where did their descendants move to? Where were you born? How do the dots connect?

The good news is, looking at their DNA results, you can see that your closest match has also tested autosomally, indicated by the FF icon, so you can check to see if you also match them on the Family Finder test utilizing the Advanced Matching Tool. That will help determine how close or distantly related you are to the tester themselves. This gives you an idea how far back in their tree you would have to look for a common ancestor.

Another benefit is that your haplogroup identifies your deep ancestral clan, for lack of a better word. In other words, you’ll know if your paternal ancestor was European, Asian, Native American or African – and that can be a hugely important piece of information. Contrary to what seems intuitive, the ethnicity of your paternal (or any) ancestor is not always what seems evident by looking in the mirror today.

Y DNA – What to order: From Family Tree DNA, the 111 marker Y DNA test. This is for males only. Family Tree DNA is the only testing company to provide this testing. Can you order fewer markers, like 37 or 67? Yes, but it won’t provide you with as much information or resolution as ordering 111 markers. You can upgrade later, but you’ll curse yourself for that second wait.

Mitochondrial DNA

Males and females both can test for mitochondrial DNA. Matches point to a common ancestor directly up the matrilineal side of your family – your mother, her mother, her mother – those red circles on the chart. These matches are more difficult to work with genealogically, because the surnames change in every generation. Occasionally, you’ll see a common “most distant ancestor” between mitochondrial DNA matches.

Your mitochondrial DNA is compared at three levels, but the most accurate and detailed is the full sequence level which tests all 16,569 locations on your mitochondria. The series of mutations that you have forms a genetic signature, which is then compared to others. The people you match the most closely at the full sequence level are the people with whom you are most likely to be genealogically related to a relevant timeframe.

You also receive your haplogroup designation with mitochondrial DNA testing which will place you within an ethnic group, and may also provide more assistance in terms of where your ancestors may have come from. For example, if your haplogroup is European and you match only people from Norway….that’s a really big hint.

Using the Advanced Matching Tool, you can also compare your results to mitochondrial matches who have taken the autosomal Family Finder test to see if you happen to match on both tests. Again, that’s not a guarantee you’re a close relative on the mitochondrial side, but it’s a darned good hint and a place to begin your research.

Mitochondrial DNA – What to Order: From Family Tree DNA, the mitochondrial full sequence test. This is for males and females both. Family Tree DNA is the only company that provides this testing.

Autosomal DNA

Y and mitochondrial DNA tests one line, and only one line – and shoots like a laser beam right down that line, telling you about the recent and deep history of that particular lineage. In other words, those tests are deep and not wide. They can tell you nothing about any of your other ancestors – the ones with no color on the pedigree chart diagram – because you don’t inherit either Y or mtDNA from those ancestors.

Autosomal DNA, on the other hand tends to be wide but not deep. By this I mean that autosomal DNA shows you matches to ancestors on all of your lines – but only detects relationships back a few generations. Since each child in each generation received half of their DNA from each parent – in essence, the DNA of each ancestor is cut in half (roughly) in each generation. Therefore, you carry 50% of the DNA of your parents, approximately 25% of each grandparent, 12.5% of the DNA of each great-grandparent, and so forth. By the time you’re back to the 4^th great-grandparents, you carry only about 1% of the DNA or each of your 64 direct ancestors in that generation.

What this means is that the DNA testing can locate common segments between you and your genetic cousins that are the same, and if you share the same ancestors, you can prove that this DNA in fact comes from a specific ancestor. The more closely you are related, the more DNA you will share.

Another benefit that autosomal testing provides is an ethnicity prediction. Are these predictions 100% accurate? Absolutely not! Are they generally good in terms of identifying the four major ethnic groups; African, European, Asian and Native American? Yes, so long at the DNA amounts you carry of those groups aren’t tiny. So you’ll learn your major ethnicity groups. You never know, there may be a surprise waiting for you.

The three vendors who provide autosomal DNA testing and matching all provide ethnicity estimates as well, and they aren’t going to agree 100%. That’s the good news and often makes things even more interesting. The screen shot below is the same person at Ancestry as the person above at Family Tree DNA.

If you’re very lucky, you’ll test and find an immediate close match – maybe even a parent, sibling or half-sibling. It does happen, but don’t count on it. I don’t want you to be disappointed when it doesn’t happen. Just remember, after you test, your DNA is fishing for you 24X7, every single hour of every single day.

If you’re lucky, you may find a close relative, like an uncle or first cousin. You share a common grandparent with a first cousin, and that’s pretty easy to narrow down. Here’s an example of matching from Family Tree DNA.

If you’re less lucky, you’ll match distantly with many people, but by using their trees, you’ll be able to find common ancestors and then work your way forward, based on how closely you match these individuals, to the current.

Is that a sometimes long process? Yes. Can it be done? Absolutely.

If you are one of the “lottery winner” lucky ones, you’ll have a close match and you won’t need to do the in-depth genealogy sleuthing. If you are aren’t quite as lucky, there are people and resources to help you, along with educational resources. www.dnaadoption.com provides tools and education to teach you how to utilize autosomal DNA tools and results.

Of course, you won’t know how lucky or unlucky you are unless you test. Your answer, or pieces of your answer, may be waiting for you.

Unlike Y and mtDNA testing, Family Tree DNA is not the only company to provide autosomal of testing, although they do provide autosomal DNA testing through their Family Finder test.

There are two additional companies that provide this type of testing as well, 23andMe and Ancestry.com. You should absolutely test with all three companies, or make sure your results are in all three data bases. That way you are fishing in all of the available ponds directly.

If you have to choose between testing companies and only utilize one, it would be a very difficult choice. All three have pros and cons. I wrote about that here. The only thing I would add to what I had to say in the comparison article is that Family Tree DNA is the only one of the three that is not trying to obtain your consent to sell your DNA out the back door to other entities. They don’t sell your DNA, period. You don’t have to grant that consent to either Ancestry or 23andMe, but be careful not to click on anything you don’t fully understand.

Family Tree DNA accepts transfers of autosomal data into their data base from Ancestry. They also accept transfers from 23andMe if you tested before December of 2013 when 23andMe reduced the number of locations they test on their V4 chip

Autosomal DNA: What to Order

Ancestry.com’s DNA product at http://www.ancestry.com – they only have one and it’s an autosomal DNA test

23andMe’s DNA product at http://www.23andMe.com – they only have one and it’s an autosomal DNA test

Family Tree DNA – either transfer your data from Ancestry or 23andMe (if you tested before December 2013), or order the Family Finder test. My personal preference is to simply test at Family Tree DNA to eliminate any possibility of a file transfer issue.

Third Party Autosomal Tools

The last part of your testing strategy will be to utilize various third party tools to help you find matches, evaluate and analyze results.

GedMatch

At GedMatch, the first thing you’ll need to do is to download your raw autosomal data file from either Ancestry or Family Tree DNA and upload the file to www.gedmatch.com. You can also download your results from 23andMe, but I prefer to utilize the files from either of the other two vendors, given a choice, because they cover about 200,000 additional DNA locations that 23andMe does not.

Ancestry.com provides you with no tools to do comparisons between your DNA and your matches. In other words, no chromosome browser or even information like how much DNA you share. I wrote about that extensively in this article, and I don’t want to belabor the point here, other than to say that GedMatch levels the playing field and allows you to eliminate any of the artificial barriers put in place by the vendors. Jim Bartlett just wrote a great article about the various reasons why you’d want to upload your data to Gedmatch.

GedMatch provides you with many tools to show to whom you are related, and how. Used in conjunction with pedigree charts, it is an invaluable tool. Now, if we could just convince everyone to upload their files. Obviously, not everyone does, so you’ll still need to work with your matches individually at each of the vendors and at GedMatch.

GedMatch is funded by donations or an inexpensive monthly subscription for the more advanced tools.

DNAGEDCOM.com

Another donation based site is http://www.dnagedcom.com which offers you a wide range of analytical tools to assist with making sense of your matches and their trees. DNAGEDCOM works closely with the adoption community and focuses on the types of solutions they need to solve their unique types of genealogy puzzles. While everyone else is starting in the present and working their way back, adoptees are starting with the older generations and piecing them together to come forward to present. Their tools aren’t just for adoptees though. Tools such as the Autosomal DNA Segment Analyzer are great for anyone. Visit the site and take a look.

Third Party Y and Mitochondrial Tools – YSearch and MitoSearch

Both www.ysearch.org and www.mitosearch.org are free data bases maintained separately from Family Tree DNA, but as a courtesy by Family Tree DNA. Ysearch shows only a maximum of 100 markers for Y DNA and Mitosearch doesn’t show the coding region of the mitochondrial DNA, but they do allow users to provide their actual marker values for direct comparison, in addition to other tools.

Furthermore, some people who tested at other firms, when other companies were doing Y and mtDNA testing, have entered their results here, so you may match with people who aren’t matches at Family Tree DNA. Those other data bases no longer exist, so Ysearch or Mitosearch is the only place you have a prayer of matching anyone who tested elsewhere.

You can also adjust the match threshold so that you can see more distant matches than at Family Tree DNA. You can download your results to Ysearch and Mitosearch from the bottom of your Family Tree DNA matches page.

Answer the questions at Mito or Ysearch, and then click “Save Information.” When you receive the “500” message that an error has occurred at the end of the process, simply close the window. Your data has been added to the data base and you can obtain your ID number by simply going back to your match page at Family Tree DNA and clicking on the “Upload to Ysearch” or Mitosearch link again on the bottom of your matches page. At that point, your Y or mitosearch ID will be displayed. Just click on “Search for Genetic Matches” to continue matching.

Get Going!

Now that you have a plan, place your orders and in another 6 to 8 weeks, you’ll either solve the quandry or at least begin to answer your questions. Twenty years ago you couldn’t have begun to unravel your parentage using DNA. Now, it’s commonplace. Your adventure starts today.

Oh, and congratulations, you’ve just become a DNA detective!

I wish you success on your journey – answers, cousins, siblings and most importantly, your genetic family. Hopefully, one day it will be you writing to me telling me how wonderful it was to meet your genetic family for the first time, and what an amazing experience it was to look across the dinner table and see someone who looks like you.

______________________________________________________________

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Yamnaya, Light Skinned, Brown Eyed….Ancestors???

Posted on June 15, 2015 by Roberta Estes

Late last fall, I reported that scientists had discovered a European ghost population. This group of people then referred to as the ANE, Ancient Northern Europeans, was a previously unknown population from the north that had mixed into the known European populations, the Hunter-Gatherers and the farmers from the Middle East, the Neolithic.

That discovery came as a result of the full genome sequencing of a few ancient specimens, including one from the Altai.

Recently, several papers have been published as a result of ongoing sequencing efforts of another 200 or so ancient specimens. As a result, scientists now believe that this ghost population has been identified as the Yamnaya and that they began a mass migration in different directions, including Europe, about 5,000 years ago. Along with their light skin and brown eyes, they brought along with them their gene(s) for lactose tolerance. So, if you have European heritage and are lactose tolerant, then maybe you can thank your Yamnaya ancestors.

1.Haak et al. http://doi.org/z9d (2015) from Feb. 18, 2015 “Steppe migration rekindles debate on language origin” by Ellen Callaway

For those of us who avidly follow these types of discoveries, this is not only amazing, it’s wonderful news. It helps to continue to explain how and why some haplogroups are found in the Native American population and in the Northern European population as well. For example, haplogroup Q is found in both places – not exact duplicates, but certainly close enough for us to know they were at one time related. It also explains how people from Germany, for example, are showing small percentages of Native American ancestry. Their common ancestors were indeed from central Asia, thousands of years ago, and we can still see vestiges of that population today in both groups of people.

So, if the Yamnaya people are the ghost people, the ANE, who are they?

The Yamna culture was primarily nomadic and was found in Russia in the Ural Region, the Pontic Steppe, dating to the 36^th-23^rd century BC. It is also known as the Pit Grave Culture, the Ochre Grave Culture and feeds into the Corded Ware Culture.

“Corded Ware culture” by User:Dbachmann – Own work based based on Image:Europe 34 62 -12 54 blank map.png. Licensed under CC BY-SA 3.0 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:Corded_Ware_culture.png#/media/File:Corded_Ware_culture.png

Characteristics for the culture are burials in kurgans (tumuli) in pit graves with the dead body placed in a supine position with bent knees. The bodies were covered in ochre. Multiple graves have been found in these kurgans, often as later insertions. The first known cart burial is also found in a kurgan grave. A kurgan often appears as a hill, example shown below, and have been found in locations throughout eastern and northern Europe..

Hallstatt-era tumulus in the Sulm valley necropolis in Austria, photo by Hermann A. M. Mucke.

Additionally, some scientists believe that the Yamna culture was responsible for the introduction of PIE, Proto-Indo-European-Language, the now defunct mother-tongue of European languages. Others think it’s way too soon to tell, and that suggestion is jumping the gun a bit.

Why might these recent discoveries be important to many genetic genealogists? Primarily, because Y haplogroup R has been identified in ancient Russian remains dating from 2700-3400 BCE. Haplogroup R and subgroups had not been found in the ancient European remains sequenced as of last fall. In addition, subgroups of mitochondrial haplogroups U, W, H, T and W have been identified as well.

Keep in mind that we are still dealing with less than 300 skeletal remains that have been fully sequenced. This trend may hold, or a new discovery may well cause the thought pattern to be “reconfigured” slightly or significantly. Regardless, it’s exciting to be part of the learning and discovery process.

Oh yes, and before I forget to mention it…it seems that your Neanderthal ancestors may not be as far back in your tree as you thought. They have now found 40,000 year old skeletal remains that suggest that person’s great-great-grandfather was in fact, full Neanderthal. That’s significantly later than previously thought, by 10,000 or 20,000 years, and in Europe, not the Near East…and who knows what is just waiting to be found. The new field of ancient DNA is literally bursting open as we watch.

I’ve accumulated several recent articles and some abstracts so that you can read about these interesting developments, in summary, and not have to do a lot of searching. Enjoy!

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Modern Europe was formed by milk-drinking Russians: Mass migration brought new genetic makeup to continent 5,000 years ago
http://www.dailymail.co.uk/news/article-3119310/How-white-Europeans-arrived-5-000-years-ago-Mass-migration-southern-Russia-brought-new-technology-dairy-farming-continent.html

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DNA Deciphers Roots of Modern Europeans
http://www.nytimes.com/2015/06/16/science/dna-deciphers-roots-of-modern-europeans.html?smid=fb-nytimes&smtyp=cur&_r=1

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Science – Nomadic Herders Left a Strong Genetic Mark on Europeans and Asians
http://news.sciencemag.org/archaeology/2015/06/nomadic-herders-left-strong-genetic-mark-europeans-and-asians

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Nature – DNA Data Explosion Light Up the Bronze Age
http://www.nature.com/news/dna-data-explosion-lights-up-the-bronze-age-1.17723

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From the European Nucleotide Archive. http://www.ebi.ac.uk/ena/data/view/PRJEB9021

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native American

Description

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

Abstract

The findings echo those of a team that sequenced 69 ancient Europeans ³. Both groups speculate that the Yamnaya migration was at least partly responsible for the spread of the Indo-European languages into Western Europe.

The report on the 69 ancient remains sequenced is below.

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Steppe migration rekindles debate on language origin
http://www.nature.com/news/steppe-migration-rekindles-debate-on-language-origin-1.16935

The Harvard team collected DNA from 69 human remains dating back 8,000 years and cataloged the genetic variations at almost 400,000 different points. The Copenhagen team collected DNA from 101 skeletons dating back about 3,400 years and sequenced the entire genomes.

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Population genetics of Bronze Age Eurasia
http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2014/06/ancient-dna-from-bronze-age-altai.html

Forensic Science International: Genetics Received 2 January 2014; received in revised form 21 May 2014; accepted 25 May 2014. published online 04 June 2014.

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages.

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2013/06/mtdna-from-late-bronze-age-west-siberia.html

Includes mitochondrial haplogroups C, U2e, T, U5a, T1, A10.

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Population Genetics copper and Bronze Age populations of Eastern Steppe, thesis by Sandra Wilde
http://ubm.opus.hbz-nrw.de/volltexte/2015/3975/ (in German)

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Eurogenes blog discusses
http://eurogenes.blogspot.com/2015/03/population-genetics-of-copper-and.html

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Polish Genes Blog
http://polishgenes.blogspot.com/2015/05/r1a1a-from-early-bronze-age-warrior.html

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Early European May Have Had Neanderthal Great-Great-Greandparent
http://www.nature.com/news/early-european-may-have-had-neanderthal-great-great-grandparent-1.17534

40,000 year old Romanian skeleton with 5 – 11% Neanderthal, including large parts of some chromosomes – as close as a great-grandparent. Previously thought that interbreeding was in the Middle East and 10,000 or 20,000 years earlier.

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How is this all happening?

The Scientist Magazine has a great overview in the June 1, 2015 edition, in “What’s Old is New Again.”
http://www.the-scientist.com/?articles.view/articleNo/43069/title/What-s-Old-Is-New-Again/

______________________________________________________________

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Are You Native? – Native American Haplogroup Origins and Ancestral Origins

Posted on May 21, 2015 by Roberta Estes

At Family Tree DNA, having Haplogroup Origins and Ancestral Origins indicating Native American ancestry does not necessarily mean you are Native American or have Native American heritage.

This is a very pervasive myth that needs to be dispelled – although it’s easy to see how people draw that erroneous conclusion. Let’s look at why – and how to draw a correct conclusion.

The good news is that more and more people are DNA testing. The bad news is that errors in the system are tending to become more problematic, or said another way, GIGO – Garbage in, Garbage Out.

I want to address this problem in particular having to do with Native American ancestry – or the perception thereof.

At Family Tree DNA, everyone who tests their Y DNA or their mitochondrial DNA have both Haplogroup Origins and Ancestral Origins tabs as two of your 7 information tabs detailing your results.

The goals of these two pages are to provide the testers with locations around the world where their haplogroup is found, and locations where their matches’ ancestors are found – according to their matches.

Did a little neon danger sign start flashing? It should have.

Haplogroup Origins

Haplogroup Origins provides testers with information about the origins of other individuals who match your haplogroup both exactly and nearly. This data base uses the location information from both the Family Tree DNA participant data base and other academic or private databases.

Ancestral Origins

Ancestral Origins is comprised primarily of the results of the “most distant ancestor” country of your matches at Family Tree DNA. This tab is designed to provide you a view into the locations where your closest matches are found at each of the testing levels. After all, that’s where your ancestors are most likely to be from, as well.

Most of the time this works really well, providing valuable information to testers, assuming two things:

1. Participants who are entering the information for their “most distant ancestor” understand that in the case of the Y line DNA – this is the most distant direct MALE ancestor who carries that paternal surname. Not his wife or someone else in that line.

Sometimes, people enter the name of the person in that line, in general, who lived to be the oldest – but that’s not what this field is requesting – the most distant – meaning further back in that direct line.

For mitochondrial DNA, this is the most distant FEMALE in your mother’s mother’s mother’s mother’s direct line – directly on up that maternal tree until you run out of mothers who have been identified. I can’t tell you how many male names I see listed as the “most distant ancestor” when I do DNA reports for people – and I know immediately that information is incorrect – along with their associated geographic locations.

In this mitochondrial example, the third match shows a male Indian Chief. The first problem is that this is a mitochondrial DNA test, so the mitochondrial DNA could not have descended from a male. If you don’t understand how Y and mitochondrial DNA descends from ancestors, click here.

Secondly, there is no known genealogical descent from this chief – but that really doesn’t matter because the mtDNA cannot descend from a male and the batter is out with the first problem, before you ever get to the second issue. However, if you are someone who is “looking for” Native American ancestry, this information is very welcome and even seems to be confirming – but it isn’t. It’s a red herring.

Unfortunately, this may now have perpetuated itself in some fashion, because look at the first and last lines of this next entry – again – another male chief. The second entry with a name is another male too, Domenico. Hmmm….maybe information entered by other participants isn’t always reliable and shouldn’t be taken at face value….

2. This approach works well if people enter only known, verified, proven information, not speculation. Herein lies the problem with Native American heritage. Let’s say that the family oral history says that my mother’s mother’s line is Native American. I decide to DNA test, so for the “Most Distant Ancestor” location I select “United States – Native American.”

The DNA test comes back and shows heritage other than Native, but that previous information that I entered is never changed in the system. Now, we have a non-Native haplogroup showing as a Native American result.

Unfortunately, I see this on an increasingly frequent basis – Native American “location” associated with non-Native haplogroups.

This scenario has been occurring for some time now. Family Tree DNA at one point attempted to help this situation by implementing a system in which you can select “United States” meaning you are brick walled here, and “United States Native American” which means your most distant ancestor in that line is Native American.

Native American Haplogroups

There are a very limited number of major haplogroups that include Native American results. For mitochondrial DNA, they are A, B, C, D, X and possibly M. I maintain a research list of the subgroups which are Native. Each of these base haplogroups also have subgroups which are European and/or Asian. The same holds true for Native American Y haplogroups Q and C.

In the Haplogroup Origins and Ancestral Origins, there are many examples where Non-Native haplogroups are assigned as Native American, such as haplogroup H1a below. Haplogroup H is European..

A big hint as to an incorrect “Native” designation is when most or many of the other exact haplogroups, especially full sequence haplogroups, are not Native. As Bennett Greenspan says, haplogroups and ethnicity are “guilt by genetic association.” You aren’t going to find the same subhaplogroup in Czechoslovakia, Serbia or England and as a Native American too.

Haplogroup J is European.

Haplogroup K is European, and so is U2e1, below.

Unfortunately, what is happening is that someone tests and see that out of several matches, one is Native American. People don’t even notice the rest of their matches, they only see the Native match, like the example above. They then decide that they too must be Native, because they have a Native match, so they change their own “most distant ancestor” location to reflect Native heritage. This happens most often when someone is brick walled in the US.

Another issue is that people see haplogroup X and realize that haplogroup X is one of the 5 mitochondrial haplogroups, A, B, C, D and X. that define Native American DNA. However, those haplogroups have many subgroups and only a few of those subgroups are Native American. Many are Asian or European. Regardless, participants see the main haplogroup designation of X and assume that means their ancestor was Native. They then enter Native American.

In the example above, haplogroup X1c has never been found in a Native American individual or population, although we are still actively looking. Haplogroup X2a is a Native American subgroup.

In some cases, we are finding new subgroups of known Native haplogroups that are Native. I recently wrote about this for haplogroup A4 where different subgroups are Asian, Jewish, Native and European. This is, however, within an already known base haplogroup that includes a Native American subgroup – haplogroup A4.

When testers see these “Native American” results under Haplogroup and Ancestral Origins, they become very encouraged and excited. Unfortunately, there is no way to verify which of your matches entered “Native American,” nor why, unless you have only a few matches and you can contact all of them.

When someone has tested at the full sequence level, remember that their results will show on these pages in the HVR1 section, the HVR2 section and the full sequence section. So while it may look like there are three Native American results, there is only one, listed once in all three locations where it “counts.” In the example below, there are two V3a1 full sequence matches that claim Native American. Those were the chiefs shown above. There are those two, plus one more HVR1+HVR2 individuals who has entered Native American as well. However, if the match total was one for the HVR1, HVR2 and coding regions, that would mean there is one person who tested and matched in all 3 categories, not that 3 people tested. In other words, you don’t add the match totals together.

What Does A Native Match Look Like?

Of course, not all matches that indicate Native heritage are incorrect. It’s a matter of looking at all of the available evidence and finding that guilt by genetic association.

In this first confirmed Native example, we see that the haplogroup is a known Native haplogroup, and all of the matches from outside the US are from areas known to have a preponderance of Native Americans in their population. For example, about 80% of the people from Mexico carry Native American mitochondrial DNA.

In this second example, we see Native American indicated, plus Mexico and Canada, which it typical. In addition we see Spain. Just like some people assume Native American, some people from Mexico, Central and South America presume that their ancestors are from Spain, so I always take these with a grain of salt. Japan is a legitimate location for haplogroup B as well, especially given that this result is listed at the HVR1 level. If this individual tested at the HVR2 or full sequence level, they might be assigned to a different subgroup, and therefore would no longer be considered a match.

It’s not just what is present that’s important, but what is absent as well. There is no long list of full sequence matches to people whose ancestors come from European countries like the U2 example above. Spain is understandable, given the history of the settlement of the Americas, and that can be overlooked or considered and set aside. Japan makes sense too. But a European haplogroup combined with a long list of primarily European high level matches with only one or two “Native” matches is impossible to justify away.

What Does Native American Mean?

This discussion begs the question of what Native American means.

It’s certainly possible for someone with a European or African haplogroup to descend from someone who was a proven member of the a tribe. How is that possible? Adoption, slavery and kidnapping. All three were very prevalent practices in the Native culture.

For example, Mary Jemison is a very well-known frontierswoman adopted by the Seneca with many descendants today. Was she Native? Yes, she was adopted by the tribe. Is her DNA Native? No. Were her ancestors Native? No, they were European. So, are her descendants Native, through her? She married a Native man, so her descendants are clearly Native through him. Whether you consider her descendants Native through her depends on how you define Native. I think the answer would be both yes and no, and both should be a part of the history of Mary Jemison and her descendants.

If a European or African women was kidnapped, enslaved or adopted into the tribe, and bore children, her children were full tribal members. Of course, today her descendants might have be unaware of her European or African roots, prior to her tribal membership. Her mtDNA would, of course, come back as European or African, not Native.

This is a case where the culture of the tribe involved may overshadow the DNA in terms of definition of “Indian.” However, genetically, that ancestor’s roots are still in either Europe or African, not in the Americas.

How Do We Know Which Haplogroups Are Native?

One of the problems we have today is that because there are so many people who carry the oral history of grandmother being “Cherokee,” it has become common to “self-assign” oneself as Native. That’s all fine and good, until one begins to “self-assign” those haplogroups as Native as well – by virtue of that “Native” assignment in the Family Tree DNA data base. That’s a horse of a different color.

Because having a Native American ancestor has become so popular, there are now entities who collect “self-assigned” Native descendants and ancestors and, if you match one of those “self-assigned” Native descendants and their haplogroups, voila, you too are magically Native.

I can tell you, being an administrator for the American Indian, Cherokee, Tuscarora, Lumbee and other Native American DNA projects – that list of “self-assigned” Native haplogroups would include every European and African haplogroup in existence – so we would one and all be Native – using that yardstick for comparison. How about that!

Bottom line – no matter how unhappy it makes people – that’s just not true.

A great deal of research has been undertaken over the past two decades into Native American genetic heritage – and continues today. The reason I started my Native American Mitochondrial DNA Haplogroup list is because it’s difficult to track and keep track of legitimate developments. Any time someone tells me they have “heard” that haplogroup H, for example, is Native, I ask them for a credible source. I’ve yet to see one.

How do we determine whether a haplogroup is Native, or not?

The litmus paper test is whether or not the haplogroup has been found in pre-contact burials. If yes, then it can be considered that the ancestor was living on this continent prior to European contact. Native people arrived from Asia, across Beringia into what is now Alaska, and then scattered over thousands of years across all of North and South America. We see subgroups of these same haplogroups across this entire space.

In some locations, the Native people are much less admixed than, for example, the tribes that came into the earliest and closest contact Europeans. These tribes were decimated and many are now extinct. I wrote about this in my paper titled, “Where Have All the Indians Gone.”

The tribes that are less admixed are probably the best barometers of Native heritage today.

We are hoping for new discoveries every day, but for today, we must rely on the information we have that is known and proven.

Interpreting Results Today

Native American haplogroup results today are subsets of Y DNA haplogroups Q and C. If you find a haplogroup O result that might potentially be Native, PLEASE let me know. This is also a possibility, but as yet unproven.

Mitochondrial Native American haplogroups include subgroups of A, B, C, D, X and possibly M.

If anyone tells you otherwise, personally or indirectly via Haplogroup or Ancestral Origins – keep in mind that extraordinary claims require extraordinary proof and data is only as good as its source. Look at all of the information – what is present, what is absent, the testing level and what kind of documentation your matches have to share.

Finding your haplogroup listed as Native American in the Haplogroup or Ancestral Origins doesn’t make you Native American any more than it would make you an elephant if someone else listed “purple elephant.”

The only things that make you Native American are either a confirmed Native haplogroup subgroup, preferably with proven Native matches, or a confirmed genealogical paper trail. Best of all scenarios is a combination of a Native haplogroup, matches that suggest or confirm your tribe and a proven paper trail. That combination removes all doubt.

Evidence

Of the various kinds of evidence, some can stand alone, and some cannot.

Evidence Type	Evidence Results	Comments
DNA Y or mitochondrial	Confirmed Native American subgroup – can stand alone sometimes	With deep level testing, this can be enough to prove Native ancestry. For Y this generally means advanced SNP testing or matching to other proven Native participants. For mitochondrial DNA, it means full sequence testing.
Proven paper trail	Proven Native tribal membership, but does not prove ancestral origins	Needs DNA evidence to prove whether the tribal member was admixed.
Matches to Haplogroup or Ancestral Origins	If Native is indicated, need to evaluate the rest of the information.	Level of testing, haplogroup, locations of most distant ancestors of other matches need to be evaluated, plus any paper trail evidence.
Autosomal DNA matches	To people with Native ancestry	Unless you can prove a common ancestor through triangulation, those individuals with Native ancestry could be related to you through any ancestor. Matches to several people with Native ancestry does not indicate or suggest that you have Native ancestry.
Native DNA ethnicity through autosomal testing	Native American results	You can generally rely on these results, especially if they are over 5%. Unless you have reason to believe that other regions could be providing some interfering results, this is probably a legitimate indication of Native heritage. Locations that sometimes give Native results are Asia and eastern European countries that absorbed Asian invaders, such as the Slavic countries and Germany. I wrote about this here.

If you don’t test, you can’t play. If you think you have Native American ancestry, you can take the Y DNA test (at least to 37 markers) if you are a male, the full sequence test if you are testing mitochondrial DNA, or Family Finder to match family members from all ancestral lines and discover if you show any Native American in your ethnicity estimate provided in myOrigins. Men can take all 3 tests and women can take the mitochondrial DNA and Family Finder tests. Family Tree DNA is the only testing company providing this comprehensive level of testing.

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Haplogroup A4 Unpeeled – European, Jewish, Asian and Native American

Posted on March 5, 2015 by Roberta Estes

Mitochondrial DNA provides us with a unique periscope back in time to view our most distant ancestors, and the path that they took through time and place to become us, here, today. Because mitochondrial DNA is passed from generation to generation through an all-female line, un-admixed with the DNA from the father, the mitochondrial DNA we carry today is essentially the same as that carried by our ancestors hundreds or even thousands of years ago, with the exception of an occasional mutation.

You can see in the pedigree chart above that the red mitochondrial DNA is passed directly down the matrilineal line. Women contribute their mitochondrial DNA to all of their children, of both genders, but only the females pass it on.

Because this DNA is preserved in descendants, relatively unchanged, for thousands of years, we can equate haplogroups, or clans, to specific regions of the world where that particular haplogroup was born by virtue of a specific mutation. All descendants carry that mutation from that time forward, so they are members of that new haplogroup.

For example, here we see the migration path of haplogroup A, after being born in the Middle East, spreading across Eurasia into the Americas, courtesy of Family Tree DNA.

This pie chart indicates the frequency level at which haplogroup A is found in the Americas as compared to haplogroups B, C, D and X.

However, not all of haplogroup A arrived in the Americas. Some subgroups are found along the path in Asia, and some made their way into Europe. There are currently 48 sub-haplogroups of haplogroup A defined, with most of them being found in Asia. Every new haplogroup and sub-haplogroup is defined by a new mutation that occurs in that line. I wrote about how this works recently in the article, Haplogroups and The Three Brothers.

In the Americas, Native American mitochondrial haplogroups are identified by being subgroups of haplogroup A, B, C, D and X, as shown in the chart below.

In the paper, Beringian Standstill and Spread of Native American Founders, by Tamm et al (2007), haplogroup A2 was the only haplogroup A subgroup identified as being Native American.

As of that time, no other sub-haplogroups of A had been found in either confirmed Native American people or burials.

In June, 2013, I realized that a subgroup of mitochondrial haplogroup A4 might, indeed, be Native American.

The haplogroup A4 project was formed as a research project with Marie Rundquist as a co-administrator and we proceeded to recruit people to join who either were haplogroup A4 or a derivative at Family Tree DNA, or had tested at Ancestry.com and appeared to be haplogroup A4 based on a specific mutation at location 16249 in the HVR1 region. As it turns out, location 16249 is a haplogroup defining marker for haplogroup A4a1.

There weren’t many of these Ancestry people – maybe 20 in total at that time. Ancestry has since discontinued their mitochondrial and Y DNA testing and has destroyed the data base, so it’s a good thing I checked when I did. That resource is gone today.

Family Tree DNA has always been extremely supportive of scientific studies, whether through traditional academic channels or via citizen science, and they were kind enough to subsidize our testing efforts by offering reduced prices for mitochondrial testing to project members. I want to thank them for their support.

Other haplogroup administrators have also been supportive. I contacted the haplogroup A administrator and she was kind enough to send e-mails to her project members who were qualified to join the A4 project. Supportive collaboration is critically important.

I wrote an article about the possibility that A4 might be Native, and through that article, raised money to enable people to test at Family Tree DNA or upgrade to the full sequence test. Full sequence testing is critical to obtaining a full haplogroup designation. Many of these people were only, at that time, defined by HVR1 or HVR1+HVR2 testing as haplogroup A. Haplogroup A is, indeed, a Native American haplogroup, but it’s also an Asian haplogroup and we see it in Europe from time to time as well. The only way to tell the difference between these groups is through full sequence testing. Haplogroup A was born in Asia, about 30,000 years ago and has many subgroups.

What Do We Know About Haplogroup A4?

Haplogroup A4 has been identified as a subgroup of the parent haplogroup A and is the parent haplogroup of A2. In essence, haplogroup A gave birth (through a mutation) to subgroup A4 who gave birth through a mutation to subgroup A2.

To date, before this research, all confirmed Native American haplogroups were subgroups of haplogroup A2.

In the Kumar et al 2011 paper, Schematic representation of mtDNA phylogenetic tree of Native American haplogroups A2 and B2 and immediate Siberian-Asian sister clades (A2a, A2b, A4a, A4b and A4c), no A4 was reported in the Americas, although A4 is clearly shown as the parent haplogroup of A2, which is found in the Americas.

On the graph below, from the paper, you can see the color coded “tabs” to the right of the haplogroup A designations that indicate where this haplogroup is found. As you can see, A4 and subgroups is found only in Siberia and Asia, not in the Americas, which is indicated by yellow.

Schematic representation of mtDNA phylogenetic tree of Native American haplogroups A2 and B2 and immediate Siberian-Asian sister clades (A2a, A2b, A4a, A4b and A4c). Coalescent age calculated in thousand years (ky) as per the slow mutation rate of Mishmar et al. [58] and as per calibrated mutation rate of Soares et al. [59] are indicated in blue and red color respectively. The founder age wherever calculated are italicized. The geographical locations of the samples are identified with colors. For more details see complete phylogenetic reconstruction in additional file 2 (panels A-B) and additional file 3. Kumar et al. BMC Evolutionary Biology 2011 11:293 doi:10.1186/1471-2148-11-293

I then checked both GenBank and www.mtdnacommunity.org for haplogroup A4 submissions. Ian Logan’s checker program makes it easy to check submissions by haplogroup.

MtDNACommunity reflected one A4 submission from Mexico and from the United States, which does not necessarily mean that the United States submission is indigenous – simply that is where the submission originated. The balance of the submissions are from either academic papers or from Asia.

During this process, I utilized PhyloTree, Build 15, shown below, as my reference tree. Build 16 was introduced as of February 2014. It renames the A4 haplogroups. In order to avoid confusion, I am utilizing the Build 15 nomenclature. These are the haplogroup names currently in use by the vendors and utilized in academic papers.

I am also utilizing the CRS version, not the RSRS version of mutations. Again, these are the mutations referenced by academic papers and the version generally used among genealogists.

Family Tree DNA provides an easy reference chart of which mutations are haplogroup defining. For haplogroup A4, we find the following progression.

A4	T16362C
A4a	G1442A
A4a1	G9713A, T16249C
A4a1a	T4928C

This means that everyone who falls in haplogroup A4 carries this specific mutation at location 16362. The original value at that location was a T and in haplogroup A, that T has mutated to a C. This defines haplogroup A4. So, if you don’t have this mutation, you definitely aren’t in haplogroup A4. Everyone in haplogroup A4 carries this mutation (unless you’ve had a back mutation, a very rare occurrence.)

This is actually a wonderful turn of events, because it means that the defining mutation for A4 is in the HVR1 region, which further means that regardless of how the haplogroup A individual is classified, I can tell with a quick glance if they are A4 or not.

In addition, subgroups are defined by other mutations as well, shown above. For example, haplogroup A4a carries the A4 mutation of T16362C plus the additional mutation of G1442A that defines subclade A4a.

Full sequence testing showed that there was actually quite a variety of subhaplogroups in the project participants.

What Did We Find?

In the haplogroup A4 project, we now have 55 participants who fell into 11 different haplogroups when full sequence tested.

I have removed all haplogroup A2 individuals from further discussion, as we already know A2 is Native. We have established a haplogroup A2 project for them, as well.

A4b

We found two haplogroup A4b individuals. The most distant known ancestor of one is found in Tennessee, but the most distant ancestor of the other is found in England. These two individuals have 19 HVR1 matches, of which many are to other A4b individuals. There is no evidence of Native American ancestry in this group.

A4-A200G

This unusual haplogroup name indicates that this is a subgroup of haplogroup A4, defined by a mutation at location 200 that has changed from A to G. The new subgroup is waiting to be named. So eventually A4-A200G will be replaced with something like A4z, just as an example.

This individual is from Asia, so this haplogroup is not Native.

A10

One individual, upon full sequence testing, was found to carry haplogroup A10, which is not a subgroup of A4. This is quite interesting, because the most distant ancestor is Catherine Pillard, originally believe to be one of the “Kings Daughters,” meaning French. This article explains the situation and the question at hand.

All five of her full sequence matches are either to other descendants of Catherine Pillard, or designated as French Canadian.

One of this woman’s ten HVR2 matches shows her ancestor, Annenghton Annenghto, as born at the Ossosane Mission, Huronia, La Rochelle, Ontario, Canada and died in 1657 in Canada. If this is correct and can be confirmed, haplogroup A10 could be Native, not French. Her daughter, Marie Catherine Platt has a baptismal record dated March 30, 1651, was also born at the mission, and is believe to be Huron.

This article more fully explains the research and documents relevant to Catherine Pillard’s ancestry.

Based on these several articles, it seems that an assumption had originally been made that because the individual fell into haplogroup A, and haplogroup A was Asian and Native, that this individual would be Native as well.

This determination was made in 2007, based on only the HVR1 and HVR2 regions of the mitochondrial DNA, and on the fact that the DNA results fell within haplogroup A, as documented here. The HVR1 and HVR2 regions do not include the haplogroup defining mutations for haplogroup A10, so until full sequence testing became available, this sequence could not be defined as A10. The conclusion that haplogroup A equated to Native American was not a scientific certainty, only one of multiple possibilities, and may have been premature.

I contacted several French-Canadian scholars regarding the documents for Catherine Pillard and there is no consensus as to whether she was Native or European, based on the available documentation. In fact, there are two very distinct and very different opinions. There is also a possibility that there are two women whose records are confused or intermixed.

So it seems that both Catherine Pillard’s DNA and supporting documents are ambiguous at this point in time.

One of the ways we determine mitochondrial ethnicity in situations like this is “guilt by genetic association,” to quote Bennett Greenspan. In other words, if you have exactly the same DNA and mutations as several other people, and they and their ancestors are proven to live in Scotland, or Paris, or Greece, you’re not Native American. This works the other way too, as we’ll see in Kit 11 of the haplogroup A4 outliers group.

Looking at other resources, MtDNA Community shows two references to A10, one submitted from Family Tree DNA and one from the below referenced article.

Haplogroup A10 has one reference in Mitogenomic Diversity in Tatars from the Volga-Ural Region of Russia by Malyarchuk et al, (201 Molecular Biological Evolution) but has since been reassigned as haplogroup A8, as follows:

However, some of the singular haplotypes appear to be informative for further development of mtDNA classification. Sample 23_Tm could be assigned to A10 according to nomenclature suggested by van Oven and Kayser (2009). However, phylogenetic analysis of complete mtDNAs (fig. 1) reveals that this sample belongs to haplogroup A8, which is defined now by transition at np 64 and consists of two related groups of lineages—A8a, with control region motif 146-16242 (previously defined as A8 by Derenko et al. [2007]), and A8b, with motif 16227C-16230 (supplementary table S3, Supplementary Material online). Analysis of HVS I and II sequences in populations indicates that transition at np 64 appears to be a reliable marker of haplogroup A8 (supplementary table S3, Supplementary Material online). The only exception, the probable back mutations at nps 64 and 146, has been described in Koryak haplotype EU482363 by Volodko et al. (2008). Therefore, parallel transitions at np 64 define not only Native American clusters of haplogroup A2, that is, its node A2c’d’e’f’g’h’i’j’k’n’p (Achilli et al. 2008; van Oven and Kayser 2009), but also northern Eurasian haplogroup A8. Both A8 and subhaplogroups are spread at relatively low frequencies in populations of central and western Siberia and in the Volga-Ural region. A8a is present even in Transylvania at frequency of 1.1% among Romanians, thus indicating that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from Siberia and the Volga-Ural region to Central Europe (Malyarchuk et al. 2006; Malyarchuk, Derenko, et al. 2008).

On Phylotree build 15, A10 is defined as T5393C, C7468T, C9948A, C10094T A16227c, T16311C! and the submissions are noted as the Malyarchuk 2010b paper noting it as “A8b”and a Family Tree DNA submission.

At this point, haplogroup A10 is indeterminate and could be either Native or European. We won’t know until we have confirmed test results combined with confirmed genealogy or location for another A10 individual.

Haplogroup A4 itself is not the haplogroup I originally suspected was Native. When this project first began, we had few A4s, and I suspected that they would become A4a1 when full sequence tested. I expected A4a1 would be Native American.

Subsequent testing has shown that haplogroup A4 very clearly falls into major subgroups, as defined by different mutations.

A4 European

The European A4 group is comprised of three participants. Of those three, two are matches to each other and the third is quite distant with no matches. I suspect that we are dealing with two different European sub-haplogroups of A4.

Two project participants, one from Romania and one from Poland match each other and both match one additional individual from Hungary who is not a project member. This group is eastern European.

The Romanian and Polish kits that match each other both carry mutations at locations 16182C, 16183C, 16189C, 150T, 204C, 3213G, 3801C and 14025C. The third person that they match, who is not a project member, from Hungary, matches one of those kits exactly, so that gives us three kits carrying this same series of mutations. These mutations do not match any other individuals carrying haplogroup A4. This group appears to be Jewish, as all three of the participants are of the Jewish faith.

This leaves the third project participant from Poland who does not have any matches today, within or outside of the project. This participant is clearly a different subclade of A4. They match none of the defining markers of the group above. They do have unique mutations at locations not found in other A4 participants within the project.

This provides us with the following European haplogroup A4 results:

Eastern European –Jewish – 2 participants plus one exact full sequence match outside of project
Eastern European – does not match group above, has no matches today, five unique mutations including 4 in the coding region.

A4 Chinese

This A4 participant is from China.

This sequence is actually very interesting because of its relative age. This individual has 109 matches at the HVR1 level. This means, of course, that they are exact matches. They match many people in varying locations such as people with Spanish surnames, participants from Michigan, Mexico and Asia which include people with extended haplogroups of A, A4 and A4-A200G haplogroup designations.

At first this appears confusing, until you realize two things. First, the participant doesn’t continue those matches at the HVR2 level and second, this means that all of those people still carry the Haplogroup “A4 signature” HVR1 mitochondrial DNA, exactly.

This means that those matches stretch back in time thousands of years, until before the divergence of Native Americans and Asians, so at least 12,000 years, if not longer. People who have incurred mutations in the HVR1 region don’t match, but those who have not, and today, there are only 109 in the Family Tree DNA data base, still match each other – reaching back to their common Asian ancestor many millennia ago.

This individual has developed two mutations in the HVR2 region at locations 156G and 159G. The participant also does not carry the haplogroup A defining mutation at location 263G which means either that 263G actually defines a subgroup, or this participant has had a back mutation to the original state at this location. This individual did not test at the full sequence level.

A4 Americas

This leaves a total of 14 haplogroup A4 individuals within the project.

In order to show a comparison, I have removed all private mutations where none of this group matches each other. I have also removed the haplogroup defining mutations as well as 16519C and all insertions and deletions since those areas are considered to be unstable. In other words, what I’m looking for are groups of mutations where this group matches each other and no one else. These are very likely sub-haplogroup defining mutations.

In addition to all private mutations, deleted columns include: 16223, 16332, 16290, 16319, 16362, 16519, 73, 152, 235, 263, 309.1, 309.2, 315.1, 522, 523, 663, 750, 1438, 1736, 2706, 4248, 4769, 4824, 7028, 8794, 8860, 11719, 12705, 14766, 15326.

I then rearranged the remaining columns and color coded groups. You can click on the chart to enlarge.

Note: na means not available, indicating that the participant did not test at that level. An x in the cell indicates that the mutation indicated in that column was present.

The purple and apricot groupings show different clusters of matches. The light purple is the largest group, and within that group, we find both a dark purple group and an apricot group. However, not everyone fits within the groups.

A4 – Virginia

The first thing that is immediately evident is that the first kit, Kit 1, is not a member of this purple grouping. This person has three full sequence matches outside of the project, one whose ancestor was born in Texas. This individual has three unique full sequence mutations. This grouping may be Native, but lacks proof.

Additional genealogical research might establish a confirmed Native American connection. If Kit 1 is Native, this line diverged from this larger A4 group long ago, before any of these purple or apricot mutations developed.

This participant’s ancestor traces to Virginia. Regardless of whether this haplotype is Native or not, it is most likely a sub-haplogroup of A4.

A4 – Colombia

The next least likely match is Kit 2. This individual shares two of the common HVR2 markers, 146 and 153, but did not test at the full sequence level. Given what I’m seeing here, I suspect that 146 might be a sub-haplogroup defining mutation for this light purple group. In addition, 8027 and 12007 might be as well. That includes everyone (who has tested at the relevant levels) except for Kit 1 and Kit 11.

Haplogroup A4 from Colombia is most likely Native. Few people are in the public data bases are from Colombia. One would expect several mutations to have occurred as groups migrated. At the HVR1 level, this individual has 18 matches, most of which have Spanish surnames. This participant has no HVR2 matches.

A4 – California Group

The next group is the apricot group which I’ve nicknamed the California group. Both of these participants, Kit 3 and Kit 4, find their ancestors in either southern California or Baja California, into Mexico. Finding these haplogroups among the Mexican, Central and South American populations is an indicator of Native heritage, as between 85% and 90% of Mexicans carry Native American matrilineal lineage.

These participants also match a third individual who is not a project member whose ancestor is also found in Baja California. This group’s defining mutations are likely 16209C, 5054T, 7604A, 7861C and 12513G. Fortunately, these will be relatively easy to discern due to the HVR1 mutation at 16209.

A4 – Puerto Rico Group

The dark purple group, Kits 5-9, is the Puerto Rican group even though it includes one kit from Mexico and one from Cuba. The Mexican kit, Kit 5, in teal, is only a partial match. Kits 6-9 match each other plus several additional people not in the project whose most distant ancestors are found in Puerto Rico as well. This group has several defining markers including 16083T, 16256T, 214G, 2836T, 6632C and possibly 16126C, although Kit 5 carries 16126C while Kit 9 does not.

The Puerto Rico DNA project has another 18 individuals classified as haplogroup A or A4 and they all carry 16083T, 16256T and those who have taken the HVR2 test (10) carry 214G as well. Only one carries 16126C, so that would not be a defining mutation for this major group, but could be for a subgroup of the Puerto Rico group.

Given the history of Puerto Rico, this is probably a signature of the Taino or Carib people.

In 2003, 27 Taino DNA sequences were obtained from pre-Columbian remains and reported in this paper by Laluezo-Fox et al. This was very early in DNA processing, especially of remains, and they were found to carry only haplogroups C and D. These remains were not from the islands, but were from the La Caleta site in the Dominican Republic.

The Taino today are considered to be culturally extinct due to disease, enslavement and harsh treatment by the Spanish, but they maintained their presence into the 20^th century and were a significant factor in the population of the West Indies, including Puerto Rico. Their descendants would be expected to be found within the population today. The Taino were the primary tribe found on Puerto Rico and were an Arawak indigenous people who arrived from South America. The Taino were in conflict with the Caribs from the southern Lesser Antilles.

Carib women were sometimes taken as captives by the Taino. The Caribs originated in South American near the Orinoco River and settled on the islands around 1200AD, after the Taino were already settled in the region.

It’s therefore possible that haplogroup A4 is a Carib signature. In 2001, Martinez-Cruzaco et al published a paper titled Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico in which they found that haplogroup A was absent in the Taino by testing the Yanomama whose territory was close to the Taino. If this is the case, then haplogroup A must have arisen and admixed from another native culture, or, conversely, the Yanomama tested were an incomplete sampling or simply not adequately representative as a proxy for the Taino. However, if haplogroup A4 is not found in the Taino, the most likely candidate would be the Caribs, assuming that the Martinez-Cruzaco paper conclusions are accurate, or the even older Ortoiroid, Saladoid culture or Arawak tribe who are believed to have assimilated with or were actually another name for the Taino.

A4 – Mexican/Puerto Rican Mutation 16126 Group

This group, Kits 5-8, is defined by mutation 16126C. It’s quite interesting, because it includes Kit 5 that does not match the rest of the Puerto Rican markers. Only some Puerto Rican samples carry 16126C. Kits 5-8 in this the A4 project do carry this mutation, but 18 of the haplogroup A kits in the Puerto Rican project which do carry the dark purple signature mutations do not carry this mutation. This mutation may be a later mutation in some of the people who settled on Puerto Rico and some of which remained on the mainland. The most distant ancestor of Kit 5 is from Tangancícuaro de Arista, Michoacan de Ocampo, shown below.

Kit 5 has five full sequence matches, all of which carry Spanish surnames.

A4 Outliers

This leaves only kits 10-14. These kits don’t match each other but do fall, at least on some markers, within the light purple group.

Kit 12 is from Costa Rica and has no matches at the HVR1 level because of a mutation at location 16086C, but has not tested at the HVR2 or full sequence levels. They might fit into a group easily with additional testing.

Kit 13 is from Mexico and has only two HVR1 matches who have not tested at a higher level. This kit, like Kit 5, does not carry mutation 16111T which could indicate an early split from the main group or a back mutation.

Kit 10 is from Mexico, has 17 HVR1 matches, some of which indicate that their ancestors are from Texas and Mexico. Kit 10 has no HVR2 or full sequence matches.

Kit 11 is from Honduras and interestingly, has 158 HVR1 matches to a wide variety of people including those from Costa Rica, Mexico, South Carolina, Oklahoma, a descendant of a Crow Tribal member, North Dakota, Guatemaula, the Cree/Chippewa, a descendant of an Arikawa and one person who indicated their oldest ancestor is from Aragon, in Spain. This means that all of these people carry the light purple group defining 16111T mutation.

Kit 14 is from Honduras and has only two matches at the HVR1 level, one which is from El Salvador. Both of the matches have only tested to the HVR1 level. Kit 14 does carry the 16111T mutation as well as most of the other light purple mutations, but is missing mutation 164C which is present in the entire rest of the light purple group. This could signify a back mutation. In addition, Kit 14 matches on marker 16189T with kit 6 from Puerto Rico and on 16311C with Kit 1 from Virginia, but with no other participants on these markers.

These people and their matches and mutations could well represent additional subgroups of haplogroup A4

A4a1

This leaves us with the A4a1 subgroup, which is where I started 18 months ago.

The haplogroup A4a1 group is very interesting, albeit not for the reasons I initially anticipated. Again, the same columns were deleted as noted in A4, above, leaving only columns (mutations) unique to this group. As with the other subgroups, these are likely sub-haplogroup defining mutations.

Note: na means not available, indicating that the participant did not test at that level

A4a1 Mexico

Kit 15, the pink individual did not take the HVR2 or full sequence test, but does not match any other participants at the HVR1 level. This person’s maternal line is from Mexico. Kit 15 could be Native and with additional testing could be a different subclade.

A4a1 European Group

The three yellow rows are positively confirmed from Europe. Kits 1 and 2 do not match each other nor any other participants.

Kit 3 however, matches Kits 4-14.

Kits 3-14, all match each other at the HVR1 level. One individual has not taken the HVR2 test and one has not taken the full sequence test, but otherwise, they also all match at the HVR2 and full sequence level. Note that Kit 3 is also in the confirmed European group based on two sets of census documentation.

Within the group of participants comprising kits 3-14, several have oral history and some have circumstantial evidence suggesting Native ancestry, but not one has any documented proof, either in terms of their own ancestors being proven Native, their ancestor’s family members being proven Native, or the people they match being proven as Native.

Kit 3 states that their ancestor was born in England in 1838. I verified that the 1880 census for New York City confirms that birth location of their ancestor. The daughter’s mother’s birthplace is also noted to be England in the 1900 census.

Therefore, based on the fact that Kit 3 is proven to be English, according to the census, and this kit matches the rest of the group, Kits 4-14, at the HVR1, HVR2 and full sequence levels, it is very unlikely that this group is Native.

Kit 15, who does not match this group, but who has not tested above the HVR1 level, is the only likely exception and may be Native. Full sequence testing would likely suggest a different or expanded subgroup of haplogroup A4a1.

Further documentation could add substantially to this information, but at this point, none has been forthcoming.

In Summary – The Layers of Haplogroup A4

Full sequence testing was absolutely essential in sorting through the various participant results. As demonstrated, the full sequence results were not always what was expected.

When full sequence tested, one participant was determined to be Haplogroup A10, which is not a subgroup of A4. Haplogroup A10 is indeterminate and could be Native but could also be European. Additional A10 results will hopefully be forthcoming in the future which will resolve this question.

None of the haplogroup A4a1 participants provide any direct evidence of Native ancestry, with the possible exception of one A4a1 kit whose matrilineal ancestors are from Mexico and who has not tested at a higher level. Three A4a1 participants have confirmed European ancestry and one of those participants matches most of the others. A4a1, with possibly one exception, appears to be European. The A4a1 participant whose ancestors are from Mexico does not match any of the other participants and could eventually be classified as a subhaplogroup.

Haplogroup A4 itself appears to be divided into multiple subgroups, several of which may eventually form new sub-haplogroups based on their clusters of mutations.

There is clearly a European and a Chinese A4 grouping. The European group is broken into two subgroups, one of which is Jewish.

In the Americas, there are several A4 subgroups, including:

Virginia – indeterminate whether Native
Colombia – likely Native
California – likely Native
Puerto Rico (2 groups) – very likely Native

There are also 5 outliers who don’t match others within the group, hailing from:

Costa Rica – likely Native
Mexico (2) – likely Native
Honduras – matching several confirmed Native people in multiple tribes at the HVR1 level
Honduras – likely Native

Note: Undet, short for undetermined, means that the results could be Native or European but available evidence has not been able to differentiate between those alternatives today.

*A4 needs to be further divided into additional haplogroup subgroups.

Dedication

Obviously, a study of this complexity couldn’t be done without the many resources I’ve mentioned and probably some that I’ve forgotten. I thank everyone who contributed and continues to contribute. I also want to thank the people who contributed to the funding for participant testing. We could not have done this without your contributions in combination with the discounts offered by Family Tree DNA.

However, the most important resource is the participants and their willingness to share – their DNA, their research and their family stories. During this project, two of our participants have passed away. I would like to take this opportunity to dedicate this research to them, and I hope they know that their DNA keeps on giving. This is their legacy.

Acknowledgements

I would like to thank Ian Logan for his assistance with haplogroup designation, Family Tree DNA for testing support and discounts, my project co-administrator, Marie Rundquist, Bennett Greenspan, Dr. Michelle Fiedler and Dr. David Pike for paper review.

______________________________________________________________

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Haplogroups and The Three Brothers

Posted on February 26, 2015 by Roberta Estes

Do you remember when you first started working with genealogy and you encountered your first “three brothers” story?

For those of you who don’t have one, it goes like this:

There were three brothers who came to <fill in the location.> They had an argument about <a woman, religion, where to settle, other> and they all three went in different directions, never to see each other or speak again.

Well, of course, that might have happened and it probably did from time to time, but not nearly as often as the story would have you believe.

In my case, I had several “three brother” stories and even a “seven brother” story. Even as a novice genealogist, I began to get suspicious when I heard the third or fourth story and they all seemed eerily similar. Too similar. Too convenient.

Enter the age of DNA testing. Many of the three brothers stories seem to stem from three men with the same surname found in different or sometimes not-so-distant locations whose ancestries could not be tied nearly together, so surely someone said, “well they must have been three brothers who went different ways” and from that the “three brothers “ myth was born, to take on an entire life of its own.

But then, there are the stories that are real. In some cases, the DNA testing does prove that those men descended from a common ancestor. Of course, we can’t ever prove that they were brothers by their descendants DNA testing today. We can only prove that they weren’t, if their Y DNA doesn’t match.

Recently, someone asked me a very basic DNA question, and the answer that came to mind was, “well, there were three brothers, you see…..”

The question was: “How can one haplogroup have descendants on different continents?”

For example, how can a specific haplogroup include people who are Asian, European and Native American.

Let’s take a look at how that works. It’s a lot like a pedigree chart. In fact, it’s exactly the same.

There isn’t a haplogroup Z Y-DNA haplogroup, so let’s use that as a hypothetical example. This example is equally applicable to mitochondrial DNA as well.

In our example, haplogroup Z was born a very long time ago, let’s say 30,000 or 40,000 years ago in Eurasia – we don’t know where and it doesn’t matter.

Haplogroup Z had two sons, and each one had a mutation different from the father, haplogroup Z, so the sons were named haplogroups Z1 and Z2. One liked the hill to the west and one liked the river to the east, so they settled in opposite directions from their father.

Over time, the families and descendants of these two sons expanded until they had to move to new ground in order to have enough game to hunt.

Haplogroup Z1’s descendants had had two mutations as well. One group, Z1a, went to Siberia and one group, Z1b went to China – or what is today China.

On the other hand, haplogroup Z2’s descendants also had two mutations that set their lines apart from each other. One of these, Z2c went to what is now Europe and one, Z2d, went north to Scandinavia.

You can see as you look on out to the fourth generation that haplogroup Z1a, in Siberia had two sons with mutations. Z1a1 went to Russia and Z1a2 crossed into Beringia, following game, and eventually would settle in North America.

Z1a2 then had two sons as well, both with mutations. One of those, Z1a2a, traveled across the north and today his descendants are found primarily in eastern Canada and the US.

Now here’s the important part. Z1a2a is known ONLY as Native American, because that mutation happened here, in the New World, and is not found in either Europe or Asia. Z1a2b is also only Native American, found primarily in South America because that son followed the western coastline instead of traveling east cross country.

On the other hand, haplogroup Z1a2 might be found in BOTH Asia and the New World if it was born in Siberia but then migrated to the New World. Some carriers might be found in both places, so if found in the New World, it likely indicates Native American, and yet it is also found in Siberia. It is not found in other parts of the world though.

You can see that while the base haplogroup Z is today found worldwide, as defined by its subgroups, the subgroups themselves tend to be localized to specific regions. You can also begin to see why determining locations of the birth of haplogroups is so difficult. Europe is one big melting pot, and so is the UK, the US, Canada, Australia and New Zealand.

We, as the genetic genealogy community, are still trying to sort through this, which is why you see new haplogroup subgroup designations on nearly a daily basis. The Y tree changes almost hourly (thanks to advanced tests like the Big Y at Family Tree DNA) and the mitochondrial tree has had many additions in the past months and years, with more yet to come shortly as a result of ongoing research.

In the mitochondrial DNA world, haplogroups are still named in the pedigree type fashion. For example, I’m J1c2f. However, in the Y tree, the names became so unwieldy, some up to about 20 characters long, that the pedigree type name has been replaced by the defining mutation (SNP) for that haplogroup. So, R1b1a2, the most common male haplogroup in Europe, is now referred to as R-M269. Not as easy to tell the pedigree by looking, but much more meaningful, especially as branches are added and rearranged. The SNP name assigned to the branch will never change, no matter where the branch is moved on the tree as more discoveries are made.

If a DNA participant only tests to the most basic of levels, they are only going to receive a rather basic haplogroup designation. Let’s say, in our example, Z or Z1 or Z2. Clearly, additional testing would be in order to figure out whether that individual is Native American or from Scandinavia. And yes, we have exactly this situation in many of the Native American haplogroups – because all the Native American base haplogroups for Y DNA: C and Q, and for mitochondrial DNA: A, B, C, D, X and possibly M, were founded and born in Asia, thousands of years ago.

And yes, it seems they all had three siblings…..

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

Posted on December 30, 2014 by Roberta Estes

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.

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 great 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/

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.

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

Compare this with today’s tree, below.

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/

10^th 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 10^th annual. And yes, it was my 10^th 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.

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.

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

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

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/

I 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.

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.

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.

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

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

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.

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, 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.

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.

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

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.

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?