Hide and Seek at 23andMe, DNA Relatives Consent, Opt-In, Opt-Out and Close Relatives

Posted on October 25, 2014 by Roberta Estes

To say that the matching policies at 23andMe are confusing is an understatement. Of course, that would imply that we could figure out what those policies are, this week, exactly. What I have been able to discern is that there is widespread confusion about the entire topic. This is my attempt to figure out which end is up, and who can see whom, under what circumstances. I feel like this is a high-tech game of Hide and Seek, a game customers should not have to be playing.

On October 17, 2014, I received this e-mail for one of the 23andMe accounts that I manage. I did not receive it for any of the other accounts that I manage at 23andMe.

When I clicked on the “can’t miss it” red block in the e-mail, it did absolutely nothing. However, by clicking on the “view as a web page” link, clicking on the “Confirm your DNA Relatives participation” took me to the 23andMe signon screen.

I signed in, but was not taken to the account in question. When I switched to that account, this is what I saw – in essence, a second warning.

I was not allowed to proceed further until I clicked on yes or no.

Of course, this begs the question of why my other accounts weren’t asked the same question. With the exception of one, they are sharing in DNA Relatives too.

It also made me wonder about the sharing with Close Relatives option.

I decided to check the DNA Relatives Option information in the Privacy/Consent settings, but there was nothing further. You can visit your consent options by clicking on the down arrow by your name, shown on the upper right hand corner of the screen shot below, and selecting “account settings.”

So, what the heck happened to the close relatives option?

It seems that 23andMe discontinued the “close relatives” opt-in or opt-out, according to their June blog article, below.

At this point, if you had not ‘opted out’ then it was assumed that you had in effect ‘opted in’ and all of your matches including your close relatives would be shown.

But then the VOX article was published in September and the proverbial stuff hit the fan.

The day of the expected default opt-in change, based on the June announcement (above), 23and Me posted a retraction of the June article, on their community forum, below.

Dear Community,

We made a change from what we promised and I want to apologize. We promised that the roughly 350,000 customers that had not consented to see Close Relatives in our DNA Relatives feature would be automatically opted in at the end of a 30 day notification period. I understand that that was extremely exciting for many of you to have so much data potentially come your way. It was unfortunately a mistake that we promised that.

I do not think it was ever the right call to promise that we would automatically opt-in those customers. Core to our philosophy is customer choice and empowerment through data. The Close Relatives features can potentially give a customer life changing information, like the existence of an unknown sibling or the knowledge that a relative is not biologically related to them. Customers need to make their own deliberate and informed decision if they want this information. It is 23andMe’s responsibility to make sure our customers have a choice and that they understand the potential implications.

The timing of the change is unfortunate and I apologize the announcement came late on a Friday night at the end of the 30 day period. The article in Vox made me and others look into the language in the consent form and that is when I learned about the proposed changes coming to the DNA Relatives community. As 23andMe has moved from being a start up to a bigger and more mature company, I am not involved in every decision. This is a decision that should have come to my attention but it did not. We will learn from that. 23andMe is hiring a Chief Privacy Officer and that too will help us avoid these types of mistakes in the future. We are also already planning to evolve the consent process to make it simpler and more clear for customers.

Going forward, we will continue to prompt the customers that have not made a choice about Close Relatives to make a choice. We understand how important that is to you. We will do a mix of emails to these customers and pop-up prompts at login to get customers to make a choice.

I apologize again for the disappointment and for not having clearly communicated the reason for reversing course. 23andMe continues to grow and pioneer the way we think about consumers exploring their DNA. While we continue to innovate we may also err along the way. We can only promise that we will always listen to and do right by you, our customer, and will never fear having to redirect our course when it is the right thing to do.

Sincerely, Anne Wojcicki

So, now it appears that unless someone has specifically ‘opted in’ to DNA Relatives as a whole, they are automatically ‘opted out,’ a 180 degree reversal. Of course, if you were one of those 350,000 customers who received a notification about opting out, and did nothing, so that you could be opted in at the end of the 30 days referenced above, you would be thoroughly confused because you THINK you’re now opted in.

23andMe has a habit of posting information on their Forum which members must actively check, instead of sending e-mails to their customers or posting this kind of information on their blog that is sent by subscription. One of the forum followers was kind enough to point out this recent posting detailing changes that have occurred in October and the 23andMe policy moving forward.

It’s signed, Chistine on behalf of the 23andMe Product Team

I can find nothing on the current customer pages providing any information about these decisions or the match status of DNA Relatives/Close Relatives.

Furthermore, 23andMe is now asking some, but not everyone, who are opted in for DNA Relatives if they are sure. My account that was asked tested in 2010, so was not caught in the 2014 selection option confusion.

I feel that this methodology discourages many people from participation. It infers that there is something frightening that you ‘ought to be’ concerned about – especially if you are asked about the same topic several times.

In summary, here is, I think, what we know, as of October 16, 2014.

Everyone will have to make a specific choice to opt-in to DNA Relatives, one way or another, after testing. If you don’t specifically opt-in, you are opted out. Consent to test apparently doesn’t count as consent for DNA Relatives.
Clients prior to June 5, 2014 who were opted in to DNA Relatives but out of Close Relatives will be prompted to select an opt-in with close relatives included, or an opt-out entirely.
Clients prior to June 5, 2014, who did opt-in to participate in DNA Relatives, but did not have any selection to make about “Close Relatives” will be required to confirm that they want to continue in DNA Relatives before they can proceed to see their matches. This is apparently the e-mail that I received for one of my kits. It’s still a mystery why I never received it for the others who tested even earlier and clearly before the “Close Relatives” option existed.
Clients between June 5, 2014 and October 16, 2014 who were automatically opted in to DNA Relatives with close relatives included will also be prompted to confirm their participation in DNA Relatives and until they do confirm that option, they will not be visible nor able to view close relatives.
New customers will be prompted to opt-in or opt-out of DNA Relatives and opt-in will no longer be the default.
Participation in DNA Relatives will now include close relatives and that will not be a separate option.

I’m very glad to see that everyone who opts in to DNA Relatives includes close relatives. To do it any other way is not only confusing, it’s more than a little disingenuous, especially given that someone may not realize why their close matches aren’t showing. I had more than one client have a panic attack when their family member wasn’t showing as a match, especially when they were expecting to see a parent or sibling. In my opinion, having to enable the “close relatives” option caused huge problems and wholly unwarranted stress. If it’s truly gone, never to return, I’m very glad and applaud 23andMe for that decision.

The bad news is that many of the 350,000 people referred to in the September community forum posting are still anonymous, and they many not even realize it. Many probably presumed, quite logically, that because they were taking a DNA test that included matches, that they would receive matches without having to do anything further. Furthermore, they received the 30 day notification that they would be opted in if they did nothing, so they expected to be opted in. But they aren’t.

Currently, at 23andMe, you have to jump through more hoops to obtain your genealogy results than you did (when they were providing health information) to obtain your health results. I hope that the message provided to people who are making the “Opt In – Opt Out” decision can be worded a little more encouragingly and present both sides of the risk/reward coin. I would hate for their entire response to be fear based due to the tone of the selection message and the fact that they have to answer this question repeatedly – like the dreaded Alzheimer’s health question – back when 23andMe was providing health results.

Here, let me give you an example vignette:

Hi, 23andMe, I’d like to test for genealogy matches.

Great, send me $99 and you’re on the way.

Spit…mail….waiting…waiting…

Good news, your results are back. Do you want to opt into DNA Relatives? You know you could find out information about your family that is upsetting to you? It could change your family relations?

Really? Hmmm…I think I want to see. That’s why I tested.

Another e-mail: Are you sure, really positive that you want to remain in DNA Relatives? You know, you could find out really upsetting information. You can see other close relatives and they can see you.

Geeze, I don’t know….maybe not…I’ll wait till I sign on next time to deal with this.

Signing on next time….

Do you want to opt-in to DNA Relatives? You know, you could find out some really disturbing and upsetting things about your family? It could change your relationship with your family members.

After repeating this warning several times, it begins to appear like 23andMe is discouraging your participation, not informing you of risks and rewards. There is no upside mentioned, only repeated negatively framed warnings. Given that genealogy/ancestry is the only reason for the consumer to purchase this product right now, this approach seems a bit counter-intuitive and overkill. In the least, the warning should be given up front, during the purchase process, and then not constantly repeated.

However, given that 23andMe is still gathering your health information and utilizing it in their medical research, even if you opt-out or don’t opt-in to DNA Relatives, assuming you haven’t opted out of medical research as well, warning you up front would discourage a sale and would prevent them from collecting your genetic data. In essence, 23andMe doesn’t care one bit whether you opt-in or opt-out of DNA Relatives, but they care a whole lot about your money and your participation in medical research.

The constant changes and hoopla are confusing people and frightening some. Others are becoming too discouraged by a lack of positive genealogical results to continue.

23andMe was first in the game with consumer autosomal testing, but their ever-changing policies have become and remain confusing. They have done nothing to clarify publicly, leaving everyone uncertain and a little reluctant.

23andMe entered the genealogy marketspace, but they seem to be focused on protecting people from genealogy matches. This seems almost like a conflict of interest, or may be better stated, a Kobayashi Maru, or no-win situation. It seems that the health testing aspect is causing 23andMe to adopt such restrictive procedures that it’s making the genealogy aspect of their product increasingly restrictive and difficult. I’m sure this is reflective of their primary goal, which is medicine, and the fact that genealogists just happened to be interested in genetics as a tool was, for them, a happy accident that provided a source for test subjects. Genealogy is not something 23andMe is primarily interested in. I’m sure they aren’t making things difficult intentionally, but the net effect is far from encouraging.

I’m finding that their protections are barriers and the required steps are confusing for customers and self-defeating for genealogy, and they are, unfortunately, cumulative hurdles:

Having to specifically opt-in to DNA Relatives, even after consenting to test when purchasing the product which includes matching
Having to request to communicate with other participants
Having to request to “share DNA”
Having to confirm that yes, you really did want to ‘opt in’ to DNA Relatives
About a 10% communication request response rate
Most of the 10% of the people who do respond know little, if anything, about their genealogy, nor are they terribly interested
Having to utilize the 23andMe corporate message system instead of communicate with your matches via e-mail
Match limit at 1000 people unless you are communicating with more than that number. After 1000, matches fall off your list.
Their terrible trees. Yes, I realize they have recently partnered with My Heritage, but as Judy Russell says, we’ll see.
The misleading (health and ancestry) notation in a sharing request which frightens people as to why you want their health information, causing people to decline to share
Constant change about who you are/aren’t seeing as matches and why
Confusing and conflicting opt-in, opt-out information delivered on four different platforms; e-mail, on your personal page, their blog and their community forum. In essence, this means that almost everyone except the most dedicated 23andMe follower misses at least part of the information.

23andMe is approaching the point where the pain level of participation is at the threshold of no longer being worthwhile except for extraordinary cases like adoptions where the participant is desperate for any possible crumb.

I thought more about this situation, and I believe that the underlying problem is a fundamental disconnect in the focus of the two groups. 23andMe’s corporate focus is and always has been health related research, compilation and manipulation of genomic “big data.” Taking a look at their recent American Association of Human Genetics papers is a good yardstick of their corporate focus. Not one paper mentions the genealogical aspect of their business, and even the paper that does indirectly help genealogists by reducing false positive identical-by-descent segments is presented from a medical perspective. In essence, the genealogy community is a source for DNA for 23andMe. They aren’t focused on genealogy or interested in serving this community. That’s neither good nor bad…it’s just the way it is.

The genealogy community, on the other hand, is frustrated by the increasingly long list of confusing hurdles at 23andMe that people who test for genealogy must navigate before they can reap any of the potential benefits of matching for genealogical purposes. Each successive hurdle reduces the number of people who complete the course and those who make it to the end are either the died in the wool genealogists who have tested elsewhere anyway or people with little or no knowledge of their genealogy. Worst case, people who test at 23andMe for genealogy will leave with a bad taste in their mouth and never test again because, frankly, it’s neither easy nor fun.

We don’t know exactly how many people haven’t opted-in for DNA Relatives, but we can surmise some based on their publicly released information. In the September retraction, 23andMe said that there were 350,000 who had not opted in, or out. We don’t know how many have actively opted out. In their ASHG abstract, they mention that 550,000 have consented for research. That tells us that less than half of their clients are opted in for DNA Relatives, or about 200,000 (assuming no one opted out), or perhaps less now with the recent “are you sure” messages like I received. Given that only 10% of the people who DO actively opt-in for DNA Relatives respond to inquiries, that’s a whole lot of people not clearing the hurdles for one reason or another. Of their entire data base of 550,000, only about 20,000 people clear the hurdles and engage, or about 3.5%. That means that there are 530,000, or more if you include the unknown number of opt-outs, who don’t clear the hurdles.

I hope 23andMe gets their cumulative act together relative to genealogy customers. You’d think with genealogy customers being their only source of corporate revenue right now (except for government grants and venture capital), that they would be bending over backwards to make the genealogy related products and processes straightforward, accessible and easy to use. Now would be a great time for some positive changes!

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Peopling of Europe 2014 – Identifying the Ghost Population

Posted on October 21, 2014 by Roberta Estes

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

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

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

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

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

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

This graphic shows Europe during the last ice age.

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

2012 – Ancient Northern European (ANE) Hints

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

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

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

2013 – Mal’ta Child Stirs Excitement

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

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

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

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

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

2013 – Michael Hammer and Haplogroup R

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

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

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

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

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

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

2014 – Europe’s Three Ancient Tribes

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

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

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

The article summary states the following:

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

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

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

2014 – Michael Hammer on Europe’s Ancestral Population

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Haplogroup G represents the spread of farming into Europe.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

In Summary

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

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

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Stone Helix

Posted on October 16, 2014 by Roberta Estes

In the just for fun category, I was thrilled when I found these helix earthworks, made from stone by Thea Alvin, a stonemason, at www.myearthwork.com. They are just incredible with the stones held in place by gravity alone.

I don’t know about you, but I want one of these in my yard. Oh yeah!!!!

The three arch helix structure is on Thea’s property between Morrisville and Stowe, Vermont. She has transformed her yard into a sculpture park and it’s open 10-6 on weekends to the public, or by prior arrangement. You can also request a tour by dropping Thea an e-mail at thea@myearthwork.com. She has also opened an artistan gallery in her barn called Rock, Paper, Scissors.

From Stowe, take Route 100 south towards Morrisville; look for the looping, three-arch stone sculpture and My Earthwork sign. I have a trip planned to Vermont next year. Maybe I’ll visit.

Here’s an article in the local Stowe paper and here’s a video of Thea where she discusses wanting to create stoneworks that are timeless. I wonder if she realizes just how spiritual and timeless the helix, in particular the double helix is, reaching back through the entire timeline of humankind.

Maybe her next project will be to create a true double helix! What do you think, Thea? Are you game???

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DNA Day with Ancestry

Posted on October 8, 2014 by Roberta Estes

For quite some time now, the genetic genealogy community has been beating the living tar out of Ancestry.com for not listening, among other things. Well, I’m here to say, they are listening. Now, what I can’t say is how much they are hearing. The jury is out and we will see. However, we are hopeful.

Ancestry invited a few of the leaders in the genetic genealogy field to come and meet with them this week. They dedicated the resources of eighteen of their scientists and executives to this meeting and they spent the day with us, sharing information about the science underlying their upcoming product changes and having frank discussions with the group.

This was a very cordial, informative and I think, team-building, experience, but there was far from uniform agreement. There was a great deal of discussion which I think helps everyone understand the position and reasoning of the other parties involved. Like anything else, it’s not as simple as one might hope.

Another important aspect of these meeting is that they serve to put faces with names and humanize the other people involved.

I also found it encouraging that most of the people at Ancestry are genealogists and utilize their own tools.

Tim Sullivan, CEO of Ancestry stopped by and talked with us for a few minutes. He asked us what we wanted, why and if we had any questions for him. He told us about his own genealogy experiences. And, we discovered, he does read our blogs. Tim is very actively engaged as is Ken Chahine, Senior Vice President and General Manager DNA, who is in many of the photographs because he was sitting at the end of the screen and was with us for the entire day.

I will be covering different aspects of the content of these meetings as time moves forward and as Ancestry’s new software version is implemented, but for now, I wanted to update you on the two burning questions in the genetic genealogy community.

These, as you might guess, were also the most contentious aspects of the entire meeting.

Will We Receive a Chromosome Brower?

I want to share with you readers that there is absolutely no question that Ancestry heard the message that we need a chromosome browser, loud, clear and uniformly from us. Ancestry is equally as adamant, it appears, as we are, that we don’t need one.

So, the short answer is no.

The longer answer is probably not.

Judy Russell, in comments to her article, “when less is more,” which I strongly encourage you to read, says about the chromosome browser:

“In my personal opinion, speaking only for myself and based solely on my own perceptions of the attitudes of some folks at AncestryDNA and not on any specific representations by anyone else, my judgment is that we may get a chromosome browser at AncestryDNA when hell freezes over.”

This was also followed by a comment about pigs flying…..plus, she took all the good phrases…not much left for me to say.

I think this pretty well sums it up.

I do want to discuss why Ancestry does not feel a chromosome browser is warranted. This topic was discussed directly and indirectly several times throughout the day. These concerns listed below are not necessarily in priority order based on discussions, because I couldn’t really discern a priority.

1. Given that Ancestry will hit the million kit DNA mark sometime in the first quarter of 2015, they feel that very few, a small percentage, of those people would ever utilize, or understand the results of a chromosome browser. Given that, they don’t feel it is a good investment of their engineering time to invest in something that few people, or a small percentage of the whole, will utilize.

2. Since Ancestry did not begin utilizing chromosome browsing in the beginning, they are concerned about privacy issues having to do with now introducing the feature to people who did not expect to have that to begin with.

3. Ancestry is concerned about unexpectedly and unintentionally revealing health information. For example, let’s say that today, a particular SNP is included in their information and is not known to be medically relevant. Next year, someone discovers that a particular SNP on chromosome 7 is connected to the genetic propensity for erectile dysfunction. Remember, a genetic propensity does NOT mean you have or will get the particular disease. In this case, of course, that would not apply to women.

Ancestry’s concern is that since they would have already been displaying that match on chromosome 7 between several people for months/years, the cow is proverbially out of the barn and closing the door at that point it a bit late, if possible at all.

Of course, as we pointed out to Ancestry, that’s the entire point of having testers sign a release, and both Family Tree DNA and 23andMe both deal with the same issue.

4. Ancestry feels that a chromosome browser would provide information to people that they should not be drawing conclusions from, and they are.

For example, as they showed us, there are areas in each person’s chromosome and their matches chromosomes that are what they call “pile up” areas. These are areas that we would call IBS, identical by state as opposed to IBD, identical by descent. Some of these pileup areas are so old that they could potentially be considered AIMs, or Ancestrally Informative Markers that harken back to continents like Africa, Asia or Europe.

This slide shows Cathy Ball, VP Genomics and Bioinformatics, showing me my own pileup areas. The two screens are a TV screen to the right where the colors resolved much better, and the larger screen where the display was larger.

What this shows you is that on the chart at left, I have one area that has a very large number of pileups, probably about 800 matches (out of my 12,500 total matches), two areas that have 400 each, two that have about 200. On the chart at right, the top of the chart is 25 match segments, so you can see that most of my matches fall below that. Ancestry feels that the higher matched segments are less relevant because they match to so many people, that they aren’t really indicative of shared ancestry in a genealogical timeframe.

And no, they did not tell me which chromosome these pileup segments are found on, and I’m DYING to know so that I can relate that to my ancestral chromosome mapping….but no cigar. It’s so frustrating that they know, they have the info, our info, but they won’t share it with us. I’m not referring here to the slide and my pileup, but the lack of segment information in general. I don’t know how that’s any worse that allowing customers to infer that a shakey leaf tree match is equivalent to a DNA match…..

Everyone has these pileup areas, which also means that they show up on your chromosome browser as matches. Ancestry is concerned that you will see three people, whether from a common genealogy line or not, who match on one segment and you will presume that they are genealogically related, when perhaps they aren’t, because their match is IBS from a pileup area.

Clearly, those of us who work in this field daily deal with IBS issues routinely, but Ancestry is concerned about the general consumer who doesn’t.

I suggested that the chromosome browser could be even more useful if they had a way to show but “grey out” those pileup areas, so we would be aware that their confidence is low, and to highlight the areas where the rarest alleles match, because those matches are most likely to indicate true genealogical matches. That suggestion met with polite silence.

Roberta’s Opinion

I do agree that many people won’t utilize the chromosome browser, but many people won’t utilize many of their services. That doesn’t prevent Ancestry from providing those services for those who want to utilize them. I’m fine with Ancestry making the Chromosome Browser part of a subscription kit so only subscribers have access, just like many of their data bases.

Unfortunately, without a chromosome browser, we are left with nothing concrete to base any matches on, nor the ability to utilize that information in conjunction with chromosome segment information from other companies to map our segments to various ancestors. The problem of incorrect ancestor attribution remains and will remain present in their matches.

They are changing their matching algorithm and in some ways, it will be improved, but in one way, I am gravely concerned that it will be worse. Ancestry will begin weighting various factors in calculating the match strength, and one of those factors will be the number of trees that list a particular ancestor. If you’ve just had a coronary…so did we. I thought one of the genetic genealogists was going to have the big one right there – they turned so red in the face.

A second confidence weighting factor will be the amount of source information for a particular tree which Ancestry feels helps judge the quality of the tree. In a sense, I agree, but attaching source information, perhaps incorrectly, to the wrong family, or having the wrong ancestor you’ve just attached source information to, is still the same large problem. Clearly, quality is not a matter of quantity, but just as clearly Ancestry cannot look at each tree individually and render an opinion, so they have to develop some automated methodology if they are going down this path.

Ancestry is trying to find ways to improve their matching and predictions of common ancestry. As time moves forward, I’ll be covering these developments. As someone in the meeting said, first steps first.

But back to the chromosome browser, my gut reaction to this is, and this is my opinion alone, that they don’t want to invest the development effort into something that will make the user experience more complex and may increase their customer support staff load to support and explain matching on a chromosome browser. I don’t think they believe the genealogy community has the ability to utilize and understand this type of tool. Ancestry is a genealogy marketing company. They want the user’s experience to be pleasant, easy and fulfilling…not difficult and certainly not upsetting.

Our message did not waiver, we need a chromosome browser and “trust me” simply won’t work.

The Y DNA and mtDNA Data Base

When Ancestry sent the invitation to this meeting, I had to wonder if they really thought through the fact that this meeting would occur less than a week after they decommissioned their Y and mtDNA data base.

Did they really want a group of people that were mad as wet hens arriving to meet with them? I fully expected to receive an “un-invitation” after my article and before the meeting, but I didn’t.

Without going into nitty-gritty detail, Ancestry indicates that the data base that held those results was literally on its last leg and they did not want to invest any money into something they was not bringing in any revenue and for a product they were no longer selling. I do believe that data base was indeed in its death throes because after the denial of service attack in June, it was no longer searchable.

In the ensuing discussion, the genetic genealogy community provided a number of alternative scenarios both within and outside of Ancestry as a way to salvage the information in that database. Ancestry has agreed to take the matter under consideration internally and discuss the various options. They made no promises, but I personally find it very encouraging that they are willing to discuss the matter and reconsider.

I told them I’d like nothing more than to write a retraction article that says that Ancestry did not, after all, burn the DNA courthouse.

In the same vein, I asked if they had any plans to decommission the Sorenson data base at www.smgf.org and they indicated that they do not have any plans at this point to do that. Obviously, nothing is forever, and they could reconsider in the future but at least it appears that resource is safe for now and adding the Y and mtDNA records from Ancestry into that data base was one option discussed.

In Conclusion

I do feel this was a productive meeting. The scientific aspects of having a large data base to draw from are quite interesting and I’ll be sharing some those in upcoming articles. Some of the best conversations took place beside the proverbial “water cooler.” I am hopeful that we made progress, or at least thawed the ice a little on the issues so critical for the genetic genealogy community, but time will tell. In a way, I felt like this was a United Nations type of meeting where everyone leaves with a better understanding.

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More Ancient DNA Samples For Comparison

Posted on October 4, 2014 by Roberta Estes

Felix Chandrakumar has prepared and added three additional ancient DNA kits to GedMatch. Thanks Felix! This is a wonderful service you’re performing for the genetic genealogy community!

The Linearbandkeramik (LBK) sample, also referenced as “Stuttgart,” reflecting where it was discovered in Germany. This individual was an early farmer dating from about 7,500 years ago and was one of the samples analyzed for the paper, Ancient genomes suggest three ancestral populations for present-day Europeans. Kit F999916
The La Brana-Arintero sample from Leon, Spain, about 7000 years old, represents a pre-agricultural European human genome – in other words, before the agriculturists from the Near East arrived. In an article at Science Daily, they have reconstructed his face. Original academic article available here. Kit F999915
The Mal’ta sample, from Siberia, about 24,000 years of age. The results were discussed in article, Native American Gene Flow – Europe?, Asia and the Americas, and the original article is available here. Kit F999914

These kits, along with the ones listed earlier, give us the opportunity to compare our own DNA with that of ancient people in specific populations. It’s like taking a step back in time and seeing if we carry any of the same small segments as these people did – suggesting of course that we descend from the same population.

This Ancient European DNA map by Richard Stevens shows the European locations where ancient DNA has been retrieved.

Recent discussion has focused on determining what matches to these specimens actually mean to genetic genealogists today. We obviously don’t have that answer at this point. We know that, due to their age, these samples are not close relatives in terms of genealogy generations, but in some cases, we find that we have matches far larger than one would expect to be found utilizing the 50% washout per generation math.

Endogamy, especially in a closed population such as Native Americans is certainly one explanation. That doesn’t explain the European matches however – either to Anzick, the Native American specimen, nor Europeans to the European samples. The higher no-call rate in the autosomal files can contribute as well, but wouldn’t account for all matches. In some cases, maybe everyone carries the same DNA because the population carries that DNA in very high rates – but the population carries the DNA in very high rates because the ancient ancestors did as well…so this is a bit of circular logic. All that said, we’re still left wondering what is real and what is Memorex, so to speak?

Ancient DNA is changing our understanding of the human past, and that of our ancestors. It allows us a connection to the ancient people that is tangible, parts of them found in us today, as unbelievable as it seems.

When Svante Paabo discovered that modern Europeans all carry pieces of Neanderthal DNA, he too was struck by what I’ll call “the disbelief factor,” thinking, of course, that it can’t possibly be true. He discussed this at length in his book, Neanderthal Man, In Search of Lost Genomes, and the steps taken by his team to prove that the matches weren’t in error or due to some problem with the ancient genome reconstruction process. Indeed, all Europeans and Asians carry both Neanderthal and Denisovan DNA, and by the same process of the DNA being carried by the entire population at one point, which must be the avenue for contemporary humans to carry other ancient DNA as well. As we find individual matches to small pieces of DNA with these matches, how much of that is “real” versus convergence or a result of no-calls in the ancient files?

In that vein, I find this article from Dienekes Anthropology Blog quite interesting, found in the ASHG Titles of Interest from the upcoming Conference in October in San Diego, CA.

Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis. E. Y. Durand, N. Eriksson, C. Y. McLean.

“Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases. A large number of methods to detect IBD segments have been developed recently. However, IBD detection accuracy in non-simulated data is largely unknown. In principle, it can be evaluated using known pedigrees, as IBD segments are by definition inherited without recombination down a family tree. We extracted 25,432 genotyped European individuals containing 2,952 father-mother-child trios from the 23andMe, Inc. dataset. We then used GERMLINE, a widely used IBD detection method, to detect IBD segments within this cohort. Exploiting known familial relationships, we identified a false positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. We show that nearly all false positives arise due to allowing switch errors between haplotypes when detecting IBD, a necessity for retrieving long (> 6 cM) segments in the presence of imperfect phasing. We introduce HaploScore, a novel, computationally efficient metric that enables detection and filtering of false positive IBD segments on population-scale datasets. HaploScore scores IBD segments proportional to the number of switch errors they contain. Thus, it enables filtering of spurious segments reported due to GERMLINE being overly permissive to imperfect phasing. We replicate the false IBD findings and demonstrate the generalizability of HaploScore to alternative genotyping arrays using an independent cohort of 555 European individuals from the 1000 Genomes project. HaploScore can be readily adapted to improve the accuracy of segments reported by any IBD detection method, provided that estimates of the genotyping error rate and switch error rate are available.”

I’m pleased to see that they are addressing smaller segments, in the 2cM-4cM range, because those are the ranges some are finding in matches to these ancient genomes. A few matches are even larger.

Of course, all of this ancient matching has caused an upsurge in interest in the cultures and populations of these ancient people whose DNA we carry.

I find this graphic very interesting from the paper, Toward a new history and geography of human genes informed by ancient DNA, just published this month, by Joseph Pickrell and David Reich. This map, which shows the population movement into and out of geographic regions of the world in the past, is especially interesting in that several back migrations are shown into Africa. I’ve never seen the “history of the world in population migration” summed up quite so succinctly before, but it helps us understand why certain DNA is found in specific locations.

As we find and fully sequence additional ancient DNA specimens, we’ll be able to better understand how the ancient populations were related to each other, and then, how we descend from each of them.

This is a fascinating age of personal discovery!

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Ancestry Destroys Irreplaceable DNA Database

Posted on October 2, 2014 by Roberta Estes

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In spite of petitions and letters and pleas, from their customers, from the genealogy community and from the leaders in genetic genealogy, Ancestry did exactly what they said they would do – they deleted the Y and mtDNA data bases and in effect, destroyed the contents – tens of thousands of irreplaceable records, gone, forever.

In other words, they burned the courthouse of the County DNA.

Worse yet, several years ago, in 2007, Ancestry had acquired the DNA results of the customers of Relative Genetics and incorporated them into their Y and mtDNA database. So the results of testing at two companies from the earliest days of genetic genealogy are gone – poof – up in smoke – not available for comparison or searching – the lynchpin of genetic genealogy.

It’s simply beyond me how a company that makes their living from rare historic records, like the census, for example, could be the one lighting the torch on something so valuable as a searchable database containing irreplaceable genetic data. Many of the early testers are deceased now but through their DNA tests that identified their lineage, their legacy could live on and benefit all genealogists. Some of those people were the end of their line.

I still can’t believe Ancestry did this. It’s unfathomable. Unthinkable. Unbelievable.

But they did.

I won’t even begin on the topics of responsibility, stewardship and ethics. It’s pointless.

Ancestry announced their intention to do so in early June, giving people in essence three months to retrieve their data or search the data base. A few days later, Ancestry suffered a denial of service attack which broke the search function of the data base. They never repaired that function, so, in essence, other than retrieving your own results, the data base had been non-functional since mid-June. They extended the deadline to the end of September, but that mattered little since the data base wasn’t operational.

Today, October 1, I checked to see if the data base was in fact, gone, and it is. We had held out hope to the very end that Ancestry could be persuaded to reconsider, or sell, or combine their results with the Sorenson data base they also maintain (as a function of their Sorenson purchase contract) – something – anything to salvage the resource – but no dice.

Ancestry did do one thing however. If you tested your Y or mtDNA or hand entered results previously, you can still download or print your own data. Any matching or other capabilities are gone and in their place, an ad, of course, for their autosomal DNA test….

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New Native Mitochondrial DNA Haplogroups Extrapolated from Anzick Match Results

Posted on September 24, 2014 by Roberta Estes

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I’ve been working with the ancient DNA results these past few days, as discussed in two previous articles, Utilizing Ancient DNA at GedMatch and Analyzing the Native American Clovis Anzick Ancient Results.

As I worked with the Anzick matches at GedMatch at all of the various threshold levels between 1cM and 7cM, each of which produced 1500 matches, except for the 7cM, which produced 1466 matches. The matches were not always the same, because obviously the sort order was different depending on how matches actually occurred before and after the 1500 cutoff threshold.

Given that, and given the autosomal ethnicity analysis of several individuals, and given that mitochondrial haplogroups A, B, C, and D are not known to be routinely found in the European population, I decided to extract all of the associated mitochondrial DNA haplogroups. Furthermore, parts of haplogroup X are known to be Native, and haplogroup M, which is quite rare, has long been suspected, but unproven.

In some cases, looking at the Anzick matches, we know that because of the very high level of Native heritage, the individual is either not admixed or only very slightly admixed. In other words, it makes perfect sense that their mitochondrial DNA is indeed Native as well as their Y haplogroup. At nearly 100% Native, both of those lines would have to be Native.

We found some surprises.

We found repeated instances of many mitochondrial haplogroups not previously identified as Native. In fact, with the exception of a couple subgroups of the M and X haplogroups, all of the Native haplogroups were found repeatedly in these samples.

Many of the participants tested at 23andMe, so even if we were to ask them for actual results, they don’t have any to give. However, even the haplogroup alone is useful, for just this reason – it can be identified as Native.

I maintain an exhaustive list of all Native American mitochondrial haplogroups that have been documented and attributed to Native Americans, along with the source. To date, there are 62. I compared the list extracted from the Anzick matches with the known list of proven haplogroups, and found quite a surprise.

There are a total of 85 new haplogroups extracted from this group. Now granted, there may be a few that will not stand up to scrutiny, in particular, perhaps haplogroup X2b which has long been debated as to whether it is Native as well as European. Additionally, some of the very basic haplogroups, such as A, B, C, etc. might be broken down further with full sequence testing if that hasn’t already been done. However, the majority of these haplogroups are found repeatedly and in individuals with little or no admixture. In addition, a paper was released in 2013 that reported that 85-90% of Mexican women’s DNA was indeed Native American.

I view this list of haplogroups as an incredible gift from the analysis of that Anzick child’s remains. If we can discover this much from the full genomic sequencing of one Native American, imagine what we could do with more. This new list of 85 provisional Native haplogroups is more, in one fell swoop, than the 62 we have to date from more than 15 years of research. We’ve increased the list by 138% to a total of 147.

Provisional Native American Haplogroups Extrapolated from Anzick Match Results

A
A2ab
A2c
A2c-C64T
A2d
A2d1a
A2e
A2f
A2f1a
A2g
A2g1
A2h
A2h1
A2i
A2j
A2k
A2k1
A2p
A2q
A2u
A2v
A2z
B
B1
B2
B2a1a
B2a1a1
B2b2
B2c
B2c2b
B2d
B2f
B2g
B2g1
B4
B4’5
B4a1a
B4a1b1
B4f1
B5b2a
B5b3
C1b1
C1b11
C1b2
C1b2a
C1b3
C1b4
C1b7
C1ba
C1c1
C1c1b
C1c2
C1c5
C1c6
C2b
C4a1
C4c1
D
D1d
D4g1
D4h1a
D4h1a2
D4h1a1
D4h3a
D5a2a
D5b1
M
M1a
M1b1
M23
M3
M30c
M51
M5b3e
M7b1’2
M9a3a
X
X2
X2a1a
X2a1b1a
X2b-T226C
X2c2
X2d
X2e1
X2e2

I’ll be confirming these as far as possible and preparing a new comprehensive Native haplogroup list shortly.

Analyzing the Native American Clovis Anzick Ancient Results

Posted on September 23, 2014 by Roberta Estes

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This ancient DNA truly is the gift that keeps on giving.

Today, Felix Chandrakamur e-mailed me and told me that the Anzick results were not yet fully processed at Gedmatch when I performed a “compare to all.” He knows this because he knows when he uploaded the results, and after they were finished, he ran the same compare and obtained vastly different results. I am updating my original article to point to this one, so the data will be accurately reflected.

In fact, the results are utterly fascinating, take your breath away kind of fascinating. Felix wrote an article about his findings, Clovis-Anzick-1 ancient DNA have matches with living people!

While finding what appear to be contemporary matches for the Anzick child may sound ho-hum, it’s not, and when you look at the results and the message they hold for us, it’s absolutely astounding.

Felix ran his comparison with default values of 7cM. This is the threshold that is typically utilized as the line in the sand between “real” and IBS, matches – real meaning the results are and could be, if you could find your common ancestor, genealogically relevant. In this case, that clearly isn’t true.

The exception to this rule is heavily admixed groups, such as Ashkenazi Jewish people who are related to every other Askhenazi Jewish person autosomally. It seems, looking at these results, that this is the same situation we find with the 12,500 year old Anzick child and currently living people. This population had to be painfully small for a very long time and the DNA had to exist in every person within that population group for it to be passed in segments this large to people living today.

After receiving Felix’s e-mail, of course, I had to go back and run the compares again. In particular, I wanted to run the one to many, as he had.

I began at the 1cM level and noticed that I received exactly 1500 results, which seemed to me like a cutoff – not an actual number of matches. So, I upped that threshold to 2, then 3, then 4, then 5, then 6, then finally to the default of 7. It was only at 7, the IBS/IBD default, that the results were under the 1500 threshold, at 1466.

1466 current matches?????

This is absolutely amazing. The Anzick child lived about 12,500 years ago in Montana. How are 1466 matches to currently living people possible?

Many of these matches are to people from the southwest and Mexico today. They are not, for the most part, from eastern Canada.

Let’s take a look at what we found.

In the 1466 results, as Felix mentioned, the closest matches match at current “cousin” levels to Anzick. The highest 7 matches that show haplogroups are haplogroup Q1a3a. Unfortunately, with the constant renaming of the haplogroups recently, it’s difficult to interpret the haplogroup exactly, which is why we’ve gone to SNP names. Looking at some of the names and e-mails, several appear to carry Spanish surnames or be from Mexico or South America.

Of the 1466 results:

2 were Y haplogroup C
79 were Y haplogroup Q
520 carried a mitochondrial DNA haplogroup of A, B, C, D, M or X
Of the 79 haplogroup Q carriers, 52 also carried a Native mitochondrial haplogroup.
A total 549 individuals out of 1466 carried at least one Native American haplogroup, or about 37.5%. That’s amazingly high.

Of these closest matches who are Y haplogroup Q, they also all carry variant Native American mitochondrial DNA haplogroups as well, so these people may not be heavily admixed. In other words, they may be almost “pure” Native American.

In order to test this theory, I entered the number of the kit that rated the highest in terms of total cM at 160.1 with the largest segment at 14.8. You can click on the images to enlarge.

As you can see, this individual is very nearly 100% Native American.

The second individual on the list, who may be from Guatemala, also carries almost no admixture.

Of the highest 21 matches that listed any haplogroup information, all have either or both Native Y or mitochondrial DNA haplogroups.

Out of curiosity, I ran the first person on the list who had neither a Native American Y or mitochondrial haplogroup – both being European.

As you can see, below, they are still clearly heavily Native American, but clearly admixed.

I moved to the last person of the 1466 on this list whose DNA matched at a total of 7cM, who did not carry a Native haplogroup. This individual, below, is more heavily admixed.

Lastly, I ran the same admixture tool on the last person, who had a total of 7cM matching that did have a Native American mitochondrial haplogroup.

Not surprisingly, the individual with almost no non-Native admixture is much more likely to carry the ancient segments in higher percentages than the individuals who are admixed. This again strongly suggests that at one point, these segments were present in an entire group of Native people and may still be present in very high numbers in people who carry no admixture.

Out of curiosity, and assuming that these first two individuals are not known to be related to each other, I ran them against each other in a one to one comparison.

There were no matches at the default values, but by dropping them just a little, to 5cM and 500 SNPs, they match on 6 segments.

It looks like they should match on chromosome 17 at the 700 SNP/7 cM default threshold.

At 200 SNPs and 2cM, there were 67 segments. These are clearly ancient in nature and size, but matching just the same. By lowering the threshold to 100 SNPs and 1cM, they share a whopping 990 segments.

Indeed, these two men very clearly share a lot of population specific DNA from the ancient people of the New World, including that of Anzick male child who lived in Montana 12,500 years ago.

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DNA Buys the Truth

Posted on September 17, 2014 by Roberta Estes

Recently, George Doe, clearly a pseudonym, a man with a PhD in Cell and Molecular Biology, a professional stem cell and reproductive biologist, related his story to Julia Belluz. Vox published the resulting article titled, “With Genetic Testing I Gave My Parents the Gift of a Divorce.” The original rather unflattering and somewhat derisory article by Julia is here, titled Genetic Testing Brings Families Together and Sometimes Tears Them Apart.

In these articles, Dr. Doe tells us that last year, in a class he was teaching, he used the 23andMe test to demonstrate how to collect a spit sample.

In fact, he was so excited that he bought kits for his parents as well:

“I had spent many years looking at the genes of other animals — particularly mice — but I never looked at my own. Because I was so excited about it, I got two 23andMe kits for my mom and dad as gifts. It’s a lot more fun when you can incorporate your family because you can trace not just the chromosomes but individual alleles on the chromosome so you don’t just see them, but where they came from. Also, I felt I had a good handle on my family’s medical history so I was very interested in confirming any susceptibility to cancers that I heard had run in my family, like colon cancer. I wanted to know if I had a genetic risk.”

But Dr. Doe found more than he anticipated. He found a half brother, an adoptee, sired by his father.

“When I saw that I share about 22 percent of my genome with a person, I thought, “That’s huge.” It took a bit of time to realize Thomas and I actually share the same genome with my father. This is how it happened: when you share around 25 percent genetic similarity with someone, that means that either it’s your grandfather, uncle, or half-sibling. 23andMe listed Thomas as a grandfather, which was confusing to me. I called my dad. All I had was his name, Thomas, and the fact that he’s male. I just asked my dad, “Does this name sound familiar?” He said no. He logged into his account, and Thomas wasn’t showing up at all. I was so confused. We figured out that at the very bottom of your profile, there’s a little box that says “check this box if you want to see close family members in this search program.”

Dad checked it, and Thomas’ name appeared in his list. 23andMe said dad was 50 percent related with Thomas and that he was a predicted son.”

Given Dr. Doe’s next comments, one can surmise that this child was not conceived before Dr. Does’ parents married, nor was Dr. Doe’s father a sperm donor.

“Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We’re not anywhere close to being healed yet and I don’t know how long it will take to put the pieces back together.”

Correction Note: CeCe Moore provides information that Doe’s half-brother was conceived prior to the marriage, as reported by Belluz. However, we don’t know that the conception was outside of the time span of the relationship of the parents. CeCe also states that “both Neil Schwartzman and I were misquoted/misrepresented in the article. Neil says that he never told her it was a negative experience for him. (Some of my quotes have been changed – with no correction noted interestingly, but there is still some misrepresentation of our conversation.) So, this does make me wonder if Ms. Belluz got Doe’s story exactly right as well. Ms. Belluz clearly had an agenda and twisted the “truth” to support it.”

At this point, I felt really bad for the Doe family, and I still do. But Dr. Doe’s next paragraph bothered me when I first read it and it bothers me now.

Instead of laying the blame for this problem where it clearly resides, at the feet of his father, he is unhappy instead with the testing company, in this case, 23andMe.

“After this discovery was made, I went back to 23andMe and talked to them. I said, “I’m not sure all your customers realize that when they participate in your family finder program, they’re participating in what are essentially really advanced paternity tests.” People find out that their parents aren’t who they think they are. They have nearly a million people in the database. If there happens to be anyone in there you’re related to, they’ll find your match. This is a solid science.”

Dr. Doe goes onto say;

“I don’t want to say if I knew that I wouldn’t have participated. But I’m really devastated at the outcome. I wrestle with these emotions. I love my family. This is nothing I ever would have wished. My dream would be to introduce Thomas to dad, to incorporate a new family tradition, to merge families. We all get to broaden our horizons and live happily ever after. At least right now, that’s not what happened. I still hold out hope that in time we can resolve things. But I also worry that as these transitions happen there may have been some permanent emotional damage that may not be able to be undone.”

Dr. Doe goes on to say that 23andMe isn’t doing enough to protect the public from themselves, in essence. 23andMe did and does have a special box to click to indicate that you DO want to see close relatives. Most people have no idea that this box even exists, let alone that they need to click it. In fact, the mere fact that you have to click the box, and it’s not front and center, makes your results unreliable because you believe that you’re seeing all of your results, when you aren’t. He even describes how this option confused his father and his father could not see his children. His father isn’t the only one. This option has caused more panic among families that “should” match until someone explains this hidden “Opt In” option and where they have to click.

Now, I’ve been quiet all week, mulling this situation over. While I was mulling, 23andMe, who had previously announced that they were going to make seeing close relatives an “opt out” instead of an “opt in,” announced they had changed their mind. Coincidence? Doubtful. In fact, Vox, who published the original two articles also published 23andMe’s announcement and stated that the announcement was a result of their original articles.

I find this stance personally abhorrent. I believe that the people who test have the right to the truth – all of it – and not just if they happen to discover that all of their results are not being displayed. They are adults. They choose to take, or not take the test. If you take the test, you have every right to expect you’re seeing all of your results.

Dr. Doe, of all people, has absolutely no right to complain. He, of all people, a PhD in this field, knew exactly what he could discover. The problem is that the truth is sometimes inconvenient and ugly, especially if you don’t expect to discover that your father cheated on your mother, or vice versa.

Dr. Doe – the problem is not that 23andMe did not protect you from yourself. You, admittedly, clicked right through the options, believing of course, that it “couldn’t be me.” The problem is your family’s choices, perhaps then, and certainly now.

23andMe’s reversal on their policy will do nothing, absolutely nothing, to protect people like Dr. Doe from himself. The only policy that will do that is the French policy of making DNA testing illegal to “protect the family unit.” God forbid that we ever become that paranoid.

What 23andMe’s policy does it to continue to obscure the truth from unsuspecting testers. Unfortunately, even if they put a big red box dead center in the screen today that says “If you don’t click here, you won’t see close relatives including sons, daughters……,” many people will never see it, because many people never sign on again after receiving their initial results. In other words, many of their clients’ data would remain dark. The only way to solve that problem is to do what 23andMe announced they would do and were preparing to do, to shift the option from “Opt In” to “Opt Out,” until Dr. Doe created a publicity nightmare because he couldn’t handle the results of his own test, AFTER, he intentionally and with full knowledge, clicked the “Opt In” option.

Furthermore, Dr. Doe could have discovered the same thing if he had found his father’s old journals, for example. He could have discovered an old letter from a sweetheart. He could have found the letter telling his father that the child would be put up for adoption. What would he have done then? Who would he complain to that no one protected him from himself? The company that created the paper and the ink??? The post office because they might deliver a letter with disturbing information inside?

I don’t mean to be insensitive here, but it’s vastly unfair to make hundreds of thousands of people pay the price for Dr. Doe’s family issues. The timing of this article with the much anticipated 23andMe change has created the perfect media storm. Dr. Doe whined, loudly, and publicly, and 23andMe doesn’t want to create even more negative publicity.

If you think that I’m speaking from an ivory tower, or a vacuum, so to speak, I’m not. Let me explain about infidelity and betrayal. After my former husband’s massive stroke, when I was in my late 30s and he was in his late 40s, I found pictures of him with another female, with the sailboat that I bought him. Yep, he was on vacation, with another woman, while I was staying home and working. I felt terribly, horribly betrayed…not to mention gullible, stupid and naïve…oh yes, and angry.

I found those pictures a month or two after his stroke, when he was so terribly incapacitated that he couldn’t even speak, sit up, or eat, let alone answer any questions. Really, there was nothing he could have said anyway – the pictures, multiple pictures, over multiple summers….were all the evidence I needed. But I wanted them, I so wanted them to not be true. But they were. Staring back at me in living color.

The truth was ugly and painful and devastating. But it was also freeing. It freed me from the pain of loss of something I never had – a loving and loyal husband. I only thought I did. At the time it was horrifically painful. Today, I’m incredibly grateful that I didn’t spend my entire married life with a cheating, lying scoundrel.

I also know about infidelity within a family when we discovered that my half-brother through my father was not my father’s child. I lived through the pain of that too, and I can tell you that my brother, Dave, who wasn’t my biological brother, and I were far closer than many biological family members.

DNA does not tear families apart, people do. Infidelity does. Poor choices do.

My grandfather, about 1910, recently married to my grandmother, was present in his mother-in-law’s kitchen the day that a young man knocked on the back door. His mother-in-law, Nora Kirsch Lore had recently been widowed after being married to Curtis Benjamin “CB” Lore for more than 20 years. The young man asked for CB, by name. Nora asked him to come inside and figured he was one of the young men who had worked for CB in his construction and racehorse business. That’s not at all why the young man was looking for CB Lore. CB Lore, according to the young man’s mother, was his father. Let’s just say that it was a very awkward day in that kitchen as Nora asked the young man what year he was born.

In 1910, there was no way to prove, or disprove, this allegation. Today, there is – DNA. Nora too was devastated by her husband’s indiscretion, to put is softly, or outright betrayal to call it what it was. But she was not without a hint – he had always been somewhat of a playboy. Had she known specifically about this woman? No, but it didn’t entirely surprise her either. It only confirmed, or at least potentially confirmed, what she suspected happened when he traveled. It certainly was not this young man’s fault for showing up to find his father. Just like it isn’t DNA’s fault today.

Dr. Doe is not responsible for “outing” his father. His father obviously made his own choices. So did his mother.

Dr. Doe did not buy his parents a divorce, his parents did. Pure and simple. Their choice. Sounds like that divorce was, perhaps, years overdue.

What Dr. Doe gave his mother was possibly the gift of truth and freedom. Mrs. Doe obviously had the option of discussing things with her husband. She didn’t. Dr. Doe himself said it brought up repressed memories, and they obviously were not pleasant. This was only a festering scab and he, unfortunately, was the one who bumped up against it and knocked it off.

I’m glad Dr. Doe is getting help. I hope the entire family is getting help.

As I tell people, if you can’t stand the heat, get out of the kitchen. If you don’t want the truth, don’t DNA test. Period.

The culprit in this story is not Dr. Doe, is not 23andMe, but is very clearly Dr. Doe’s father’s original behavior combined with current family dynamics.

Sadly, the people that are ultimately paying the price for Dr. Does’ family turmoil are the hundreds of thousands of people that now continue to have their results obscured because of 23andMe’s abrupt change of policy.

That’s not right either.

23andMe lives and dies not on genetic genealogy or on the revenue from the tests themselves, but on their customers allowing them to use their results to compile for medical studies and to sell. If you want to make your feelings known, you can personally opt out of allowing 23andMe to utilize your results for those types of endeavors. In other words, 23andMe will no longer be able to make money from your DNA.

Perhaps 23andMe will hear and understand that message. Companies understand dollars.

To remove your consent for 23andMe to utilize your DNA, or to at least review the consent form, sign on and click on the down arrow beside your name.

Then click on “Privacy and Consent.”

Scroll down to the bottom of the page to “Basic Research Consent.” If you have given consent, this is what you will see.

Click in the green box on “view/change consent.” You will then see the consent document.

Scroll down again. You will see that the “give consent” box, in green, has been clicked already.

Underneath that box, click on the blue “click here to change your consent.” You will then see a green and a red box with your consent options.

You can see that I’ve selected “I am this person and I don’t give consent,” in the red box. Then click on the green “Save” button.

The change takes place imediately for any future projects or initiatives, but does not affect any studies or data sales that have previously taken place.

Furthermore, e-mail 23andMe’s Human Projects Administrator at hpa@23andMe.com and tell them why.

You have a voice in this matter. Use it.

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Jack the Ripper???

Posted on September 8, 2014 by Roberta Estes

The DNA community had some exciting news this past week about the identity of Jack the Ripper, notorious serial killer of prostitutes in the Whitechapel area of London in 1888. In total, there were 11 murders potentially linked to Jack the Ripper, with 5 being considered the most likely to be positively his victims. He slit the throats of his victims, in some cases disemboweled them and mutilated their faces.

While there were many suspects and much speculation, the identity of the murderer was never established. Among the suspects was one 23 year old Polish immigrant, Aaron Kosminski. Aaron worked and lived in Whitechapel and was reportedly seen with one of the victims, but incriminating evidence was not given by the witness and he was released. In 1891 he was committed to an insane asylum, probably a paranoid schizophrenic, where he eventually died. He heard “solitary voices” and indulged in “unmentionable vices” which typically means activity of a sexual nature.

Last week, the British tabloid newspaper, the Daily Mail, ran a “world exclusive” article that Jack the Ripper has actually been identified as Aaron Kosminski utilizing DNA evidence found at the scene of one of the murders, that of Catherine Eddowes.

This was followed almost immediately by articles much more skeptical in nature, one in the Oregon Live and one by our own Judy Russell.

The reader’s digest version of the DNA part of the story is that a shawl was found with Catherine when she was murdered, although there is no evidence that the shawl was hers. It’s believed that the killer left the shawl for some unknown reason.

The first problem with this story is that there is no proof that this shawl was indeed found with the body. Catherine was so poor she reportedly hawked her shoes the night before, and the shawl in question was worth more than the shoes. She has also just been released from jail for drunkenness before she was found murdered, and no shawl was mentioned by anyone. Just the same, that doesn’t mean the shawl didn’t exist, and there is powerful DNA evidence, if it’s accurate, suggesting that this shawl was found exactly as stated, with Catherine’s body.

Russell Edwards purchased the blood-soaked shawl at auction, the shawl purportedly being found by a policeman the night of the murder and taken home to his wife, a dressmaker, who put it away unwashed. Edwards hoped to somehow use the shawl to prove it was not only authentic, but to identify Jack the Ripper.

Edwards contacted Dr Jari Louhelainen, a leading expert in genetic evidence from historical crime scenes who combines his day job as senior lecturer in molecular biology at Liverpool John Moores University with working on cold cases for Interpol and other projects. He agreed to conduct tests on the shawl in his spare time.

Catherine’s DNA

He was able to extract DNA from some of the blood on the shawl and eventually managed to obtain mitochondrial DNA results.

Edwards managed to track down an individual, Karen Miller, who descends from the same matrilineal line as Catherine Eddowes, her three times great-granddaughter, and the mitochondrial DNA matched. This is interpreted as confirming the identity of the blood on the shawl as that of Catherine.

Herein lies the second problem.

The article states that they “managed to get six complete DNA profiles from the shawl” and that they were “a perfect match.”

I’m assuming, here, and I passionately hate to assume, because we all know what assume does…but I’m assuming that they are referring to mitochondrial full sequences here, all 16,569 locations on the mitochondria. It would have been very helpful had they stated exactly what they tested.

They also don’t tell us what haplogroup they are working with. If this is haplogroup H, it’s possible to have hundreds of “exact matches” because haplogroup H, itself, comprises almost 50% of Europeans today. Of course, if they managed to sequence the entire mitochondria, the results would likely fall into a subclade, and some subclades are very rare, even within haplogroup H.

Because haplogroup H is so large, there is a great deal of diversity within H, and many of the subclades are small. Furthermore, some people have no “unusual markers,” and those people tend to have many more matches than people who do have “unusual markers.” Unusual markers are those mutations that have probably occurred in a family line and are not generally found in the majority of those of that particular subclade.

By way of example, here are the results from someone who is a member of haplogroup V, from eastern Europe. They do not fall into a subclade of V and they have several extra mutations and one missing mutation compared to what is typically found in haplogroup V participants.

This individual has 3 full sequence matches, two of which are exact matches, but neither of those lead to the same ancestor. This is a rather typical situation, not out of the ordinary.

The Ripper’s DNA

Another discovery on the shawl was that of semen, possible evidence of the Ripper himself. They enlisted the help of Dr. David Miller who found surviving epithelium cells, a type of tissue that coats organs, in this case, thought to have come from the urethra during ejaculation.

Here a quote from Dr. Louhelainen about the DNA findings from these cells.

“Then I used a new process called whole genome amplification to copy the DNA 500 million-fold and allow it to be profiled.

Once I had the profile, I could compare it to that of the female descendant of Kosminski’s sister, who had given us a sample of her DNA swabbed from inside her mouth.

The first strand of DNA showed a 99.2 per cent match, as the analysis instrument could not determine the sequence of the missing 0.8 per cent fragment of DNA. On testing the second strand, we achieved a perfect 100 per cent match.

Because of the genome amplification technique, I was also able to ascertain the ethnic and geographical background of the DNA I extracted. It was of a type known as the haplogroup T1a1, common in people of Russian Jewish ethnicity. I was even able to establish that he had dark hair.”

Here is the third problem.

This description seems to combine two types of sequencing. Now, that’s not a bad thing, it’s simply confusing. Based on the haplogroup of T1a1, we know that they sequenced mitochondrial DNA and that they did in fact manage to sequence it to the full sequence level. How do we know this? Because each mitochondrial haplogroup is designated by certain specific mutations. In this case, the final 1 of T1a1 is indicated by location 9899 in the coding region of the mitochondria – so in order to designate this individual as a member of haplogroup T1a1, they had to sequence the coding region. Again, we presume (the cousin of assume – with the same consequences) that they were able to successfully sequence the entire mitochondria.

Now for the fly in the ointment, I have not found this haplogroup in Russian Jewish people. In fact, the clients who I have done DNA Reports for who fall into this haplogroup are not Jewish – none of them, nor do they have Jewish matches. Neither does Dr. Behar identify this as a Jewish haplogroup in his founding mother’s paper. Nor is this identified elsewhere as a Jewish haplogroup. Of course, this Daily Mail article has no sources, so we can’t independently verify what was said, but it looks like this assertion of T1a1 typical of Jewish people may be in error.

However, from his discussion, we can also tell that additional sequencing has been done on the DNA retrieved, because you can’t determine traits like hair color without autosomal sequencing. Therefore, if the descendant is truly related to Jack the Ripper, then at least part of their autosomal DNA should match as well, and that was not addressed. If the autosomal DNA does not match, at least in part, then it calls into question the conclusions drawn by the mitochondrial DNA match.

We know that Kosminski was born about 1865 if he was 23 in 1888 when the crimes were committed. The DNA matches a descendant of his sister. Let’s assume, for purposes of argument that his sister was born about the same time. And let’s use the standard genealogy generation of 30 years. This means that the sister’s child was born in 1895, her child in 1925, her child in 1955 and maybe yet another child in 1985. That’s a total of 6 DNA transmission events to a common ancestor, being the parents of the Kosminski siblings. Therefore, Kosminski is the great-great-uncle to the child born in 1955. Therefore, the individual born in 1955 should share about 6.25 of their autosomal DNA with Kosminski. If they don’t, then there’s a problem.

If they do, then why didn’t the article tell us that. This information would, in essence, seal the deal – well, assuming all of the other presuming is remedied.

Is It True???

First, let me state that in science, I’m always very, very skeptical of publication via newspaper or internet, especially publication via tabloid. This has been fraught with problems. Debbie Kennett has covered this repeatedly on her blog. Another example is the announcement of Pict DNA being identified – published and never proven. I know of other cases in which DNA evidence is intentionally twisted, inaccurately, to fit the intentions of the publishing entity. So, yes, I’m a rabid skeptic without provable evidence.

I want to see this assertion go through the verification process with a second, reputable, lab. By reputable, I mean one not associated with any of these other questionable assertions. Then, I’d like to see the results published in an industry accepted journal. Yes, that takes time, and yes, there are questions to answer, but the resulting paper carries with it credibility that is impossible to obtain otherwise. Unfortunately, publishing results in a tabloid paper immediately causes me to question why they would have made that choice if they had solid proof.

Ok, now that I’ve said that, I want to address the question at hand. Is it true? Might it be true?

I’d like to make two points. First, while I used random examples of mitochondrial matching, this isn’t a random situation. This is a known individual in both cases, with known and I’m assuming, provable, genealogy to both Catherine Eddowes and to Aaron Kosminski. We’re not looking at random matches here and we’re not looking for a common ancestor. We know who the common ancestor is in both of these situations and we’re looking for matches to confirm that identity. This, by the way, is exactly how our armed forces identify remains of soldiers and repatriate them to the family. This uses the exact same premise – that we’re not looking for random matches, but for a match with a known family member of known provenance – with possibly, hopefully, family line mutations.

Now, let’s use a bit of math, which is sometimes, but not always, my friend.

I’m going to use two examples, haplogroup T1a1 and haplogroup J1c2f because it’s mine and I have easy access to those results. We know that the mitochondrial DNA attributed to Kosminski is T1a1 and we’ll just let mine stand in for Catherine Eddowes.

In the Family Tree DNA data base, haplogroup T represents 8.06% of the participants and haplogroup J, 7.77%. As of September 8, they have a total of 43,329 full sequence mitochondrial DNA results in their data base. I calculated the number of members of each haplogroup based on that percentage and then I checked the corresponding DNA project at Family Tree DNA. Then I checked to see how many occurrences of the subgroups of J1c2f and T1a1 were found and calculated the percentage of haplogroup J and T they represent. The total subgroup percentage is the percentage of J1c2f and T1a1 of the entire FTDNA full sequence population.

	% FTDNA	# Members	Hap Project #	#J1c2f/ T1a1	% of Hap Proj	Total % subgroup
J1c2f	7.77	3336	2165	6	.2	.01
T1a1	8.06	3492	673	52	.73	.12

London’s population was estimated to be 1 million in 1800 and 6.7 million in 1900, so let’s use the figure of 6 million for 1888 as an estimate.

Of 6 million people, you would expect to find 600 people carrying haplogroup J1c2f and 7200 people carrying T1a1. Therefore to find two of those individuals whose DNA is found on the same scarf, who have a forensic tie, or a suspicion of a tie, is astronomically small.

If math is my friend today, we would multiple values of each haplogroup in the population together to find the odds of finding both in one place.

That would be .0001 times .0012, which equals 1.2e-7 which means, 0.00000012, in other words, about one in 1.2 billion. The population of the world in 1875 was calculated to be about 1.3 billion

So, assuming their work is accurate, and assuming that this isn’t a huge elaborate hoax, it’s very likely accurate, and Jack the Ripper is very probably Aaron Kosminski.

Where’s the Beef???

Remember the old Wendy’s refrain, “Where’s the Beef?’’

Well, I want to believe this story, especially since it’s such a feel good fairy tale story involving a Jack the Ripper hobbyist and DNA, of course. But I’m really left waiting for some kind of corroboration. Was it Carl Sagan that said “extraordinary claims require extraordinary evidence?” Well, they do and I really hope the authors will subject their findings to peer review and authenticate their claims. If this isn’t true, it’s a hugely elaborate and well-planned hoax perpetrated probably to sell a resulting book or movie which should, if that is true, be named “Jack the Ripoff.”

I want this to be true, and I want the authors to make a believer out of me. I want no presumes or assumes left standing. So….where’s the beef???

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