Citizen Science

My husband, Jim, who is kind of a geeky guy in the best of ways and really is interested in genetic genealogy from a technologist’s perspective, asked me a question about the new mitochondrial comparative sequence, the RSRS (Reconstructed Sapiens Reference Sequence).  We’ve been talking about it on the blog and on the various DNA lists for days now.  So it stands to reason we’re talking about it at the dinner table too.

He asked, “Why now?  Why not before when the transition would have been easier?”  That’s a great question!  The answer isn’t nearly as short as the question.  I hate it when he does this to me!

The answer is Citizen Science – that means you and me – lots of us actually.  How is that possible?  Let’s take a look at some history.  It’s actually quite interesting!

In 1981 when the Cambridge Reference Sequence was published as a comparative model, the science of genetics was functionally brand new.  This anonymous person at Cambridge University was the first person to have all 16569 bases of their mitochondria sequenced, something anyone can have today for a couple of hundred dollars.  But back then in the not so distant past, it was groundbreaking.  The Y DNA hadn’t even been mapped yet, so this was the very beginning.  At that point in time, there was no concept of mitochondrial Eve or Y-line Adam.  So the CRS became the norm because we had no other basis for comparison.

In 1999, the CRS was resequenced, and surprisingly, 11 errors were found in the original sequence.  Today that is called the Revised Cambridge Reference Sequence, or rCRS, technically, and that is the sequence that is used for both academia and genetic genealogy.  Most people just refer to it as the Cambridge Reference Sequence because no one would use the older sequence today.

1999 was also the first year that any commercially available genetic genealogy tests were available to the public.  They were available from Oxford Ancestors and were prohibitively expensive, but that didn’t stop many of us from ordering one.  If you bought the book, “Seven Daughters of Eve” you could send in the form in the back of the book, with a hefty check, and you too could discover which of the 7 daughters you descended from.

What you received was one piece of paper in the mail, months later, with a gold attendance star (like from Sunday School when you were a kid) placed on your haplogroup name.  So for several hundred dollars, significantly more than a full sequence test today, I got a gold star on a J.  I still have that certificate and I was unbelievably excited to know I was a member of Jasmine’s clan.  Of course, in order to justify my DNA test, I had to test my husband’s too, so it cost me twice as much!

In the year 2000, Family Tree DNA opened their doors and began selling genetic genealogy testing kits. They also began surname projects.  I don’t know if that was a stroke of genius or a stroke of luck.  Soon thereafter, they added both haplogroup projects and geographic projects.  These various project types allowed people with specific interests to focus on those areas of genetic genealogy.  Little did we know that projects would eventually provide a huge pool of people who have been DNA tested for research areas, such as determining new haplogroups.  In the past all sequencing had been done at academic institutions and often did not use full sequences initially due to the prohibitive cost.  Many of the early academic papers were written with far fewer samples than today’s projects have members.  Full sequence commercial testing has fostered exponential change in this industry.

By 2006, Family Tree DNA was offering the full mitochondrial sequence for genealogists, something still not offered today by any of the other major commercial testing companies.  This not only enabled genealogists to determine who was actually a close match, but it also enabled the haplogroup projects to collect many samples of full sequence data.  The coding region (meaning not the HVR1, HVR2 and HVR3 regions) is not shown in the public projects because of the possibility that they may carry medical information, but they are available for project administrators to see, if the individual participant authorizes administrator view access.

Haplogroups aren’t just determined by the hypervariable (HVR) regions, but by mutations found in the entire mitochondrial sequence, including the coding region.  Never before had groupings of participants this size been available outside of academia, and often, not even within academia.

Many of the project administrators began discovering new haplogroups in a flurry of activity.  Two that come immediately to mind are both Jim Logan and Bill Hurst.  Bill began publishing about haplogroup K in the Fall 2007 JoGG issue, as did Ian Logan with a discussion of what the mitochondrial DNA of “mitochondrial Eve” might look like.  In Spring of 2008, Jim Logan published a groundbreaking paper for haplogroup J, still in use today.  Indeed, citizen science came into its own in the spring of 2005 when the Journal of Genetic Genealogy (JoGG) was launched to facilitate exactly this type of academic publishing effort.  The more traditional publications weren’t quite ready to deal with citizen scientists making discoveries.  Clearly, citizen scientists didn’t fit well into the academic publishing “box.”

Bill Hurst has been collaborating with Dr. Doron Behar for several years now and is recognized in his most recent paper.  They presented a joint session at the 5th International Conference on Genetic Genealogy for DNA Administrators in Houston, Texas in March of 2009.

During this time, Family Tree DNA implemented an authorization system for people to make their full sequence DNA results, if they wanted, available to Dr. Behar for research.

Dr. Behar’s paper (along with several other authors), “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root” was published earlier this year, defining the RSRS (Reconstructed Sapiens Reference Sequence) revealing the genetic fingerprint of Mitochondrial Eve, the original mother of us all.  He was able to do this, in part, as a result of the many full sequence test results made available by Family Tree DNA customers, you and me, and by the hard work of haplogroup administrators like Bill Hurst and Jim Logan.  Of course, there are many other hard-working administrators too, and I don’t mean to slight anyone.

So, this is a long-winded way to answer Jim’s question, which, in case you’ve forgotten, was “why now for the RSRS and why not before?”  The answer is quite simply, Citizen Scientists were needed.  People like you and me.  Until the stars aligned where haplogroup projects existed, full sequence mitochondrial data became affordable and widely available, and there was a way for genealogists to contribute their results for scientific research, it couldn’t have been done – at least not yet.  It’s been a long way from the gold star on haplogroup J to the beautifully elegant RSRS, the mitochondrial map of Eve, the common ancestor of everyone living today – the entire trip made in just a dozen years.  Congratulations and thank you to everyone involved.  Indeed, it’s really quite a remarkable story!

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

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The mtDNA Community

When you look at your mitochondrial DNA results on your personal page at Family Tree DNA, the third tab, after rCRS and RSRS is the mtDNA Community. You will only see this tab if you have taken the full sequence test.

The mtDNA Community software was developed to facilitate easy donation of your full sequence mitochondrial DNA sequences for scientific research purposes.  You can read about it here:  http://www.mtdnacommunity.org/default.aspx and here: http://www.mtdnacommunity.org/about.aspx

You too can be a part of science research by uploading your mitochondrial DNA sequence so that it can be included in the sequences studied by scientists.

Many of the leaps and bounds in genetic genealogy, the discovery of new haplogroups and learning how the people who carried them lived and where they settled has been through the volunteer efforts of genetic genealogists, just like yourself.

Let’s talk a minute though about what this means.  First, we don’t yet have a FAQ about the mtDNA Community from Family Tree DNA.  Much of what is known now is through working with the products personally, Rebekah Canada and Bill Hurst, both of whom have been rather intimately involved in the research and rollout process and Max Blankfeld, the President of Family Tree DNA – all of whom made themselves available over the weekend to sort through this.

There are really two levels of research here, but one leads to the other.  If you authorize your full sequence results to be uploaded to mtDNA Community you are authorizing your results to be included in scientific research.  In the mtDNA Community, you are not anonymous.  This means that your sequence can be tracked back to you.  This is neither a bad thing or a good thing, it’s just the way it works. Of course, there are benefits to you, other than being altruistic, for uploading your information.  We’ll discuss those in a minute.

The second part of the research quotient is that when papers are written using mitochondrial DNA sequences, most of the time those sequences are uploaded, anonymously, to GenBank.  At GenBank, the contact information is the submitting researcher and paper that the sequence is associated with.  This is done, at least in part, so that this research can be corroborated by others.  So if you upload your results to mtDNA Community, you are in essence granting permission for your results to be uploaded anonymously at some point in the future to GenBank.

What is GenBank?

The GenBank sequence database is an open access collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration (INSDC). The National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. In more than 20 years since its establishment, GenBank has become the most important and most influential database for research in almost all biological fields, whose data were accessed and cited by millions of researchers around the world.

You can read more about GenBank here:  http://en.wikipedia.org/wiki/GenBank and here:  http://www.ncbi.nlm.nih.gov/genbank/

Why is this important?

The science of genetic genealogy has grown by leaps and bounds in the past few years as a result, at least in part, of vast amounts of data becoming readily available through the genetic genealogy community and citizen scientists.  Without these sequences to study, scientific advances like the RSRS model wouldn’t have happened, at least not yet.

Is providing your mitochondrial DNA sequence for research the right choice for you?

For me, it was.  I provided my sequence to GenBank some time ago.  For everyone, it might not be.  It’s a personal decision.  But once it’s uploaded and in the scientific “stream” so to speak, there is no recalling it.  Even if the mtDNA community administrators would remove your sequence, and the same for GenBank, that doesn’t mean that someone hasn’t already downloaded it for study.

Is there a downside?

I can’t tell you that there is not.  What I can say is that I don’t know of any.  The mtDNA Community is new software released in conjunction with Dr. Behar’s paper in order to facilitate the study of mitochondrial DNA.  Before, submitting your results to GenBank was not straightforward and took quite a bit of effort on your part.  Now it’s as easy as clicking….and there are some benefits to you too.  So whether you do or not, follow along as I upload my results to the mtDNA Community.

Uploading your Results

Uploading your results is easy.  Just click on the mtDNA Community tab, shown above, on your personal page.  Fill in the blanks and click on the orange Upload button which you will see to the right of the blanks (not shown here).

You will then see the screen, above.  Click on the words “mtDNA Community” which will take you to the website to create your account.

Once you’re on the mtDNA Community website, you’ll need to do some setup.  It’s minimal, but do complete the profile questions, because that process leads you to the good stuff.  And yes, there is a bug in the year selection for your oldest ancestor, but I’m sure that will be fixed shortly.

The important part of this is the information in the Results box, shown at the bottom, above, and shown enlarged below.  You will notice that these are not all of your mutations.  The mutations you carry that are part of the haplogroup designation are not shown here. 

This information displays your new, extended haplogroup under the RSRS model, but even more important, it shows you any “private mutations.” These are important, because they are your family mutations, meaning those not found in the haplogroup as a whole.  These have developed in your family line, and everyone you are related to in a genealogically relevant timeframe will carry these as well.  These are your personal filters that differentiate your family from everyone else in the larger haplogroup, or your extended clan.

There are also other matching features, but it’s unclear how this would differ, at least today, from your matches at Family Tree DNA.  Maybe eventually this data base will hold more sequences other than those donated from Family Tree DNA.  If so, this would provide us with new avenues to find matches.

We will know more when the FAQ is released and as we use this tool a bit more.

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Disclosure

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

Thank you so much.

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The CRS and the RSRS

Before we talk about the new Reconstructed Sapiens Reference Sequence, RSRS, let’s talk for a minute about the current comparison model, the Cambridge Reference Sequence, also known as the CRS or rCRS.

When analyzing mitochondrial DNA, your results are compared to the results of an anonymous individual whose DNA was sequenced in 1981 at Cambridge University.  This set of results which has become the standard is called the Cambridge Reference Sequence, or CRS.  Everyone else’s DNA is compared against theirs, and the differences (mutations) duly noted.

What this means is that for comparison purposes, the current state of their mitochondrial DNA in 1980 is considered “normal” and any differences are then considered “mutations.”

All DNA testing companies as well as academia use this model, but this is changing.  Enter, the RSRS.  What is the RSRS?

The Reconstructed Sapiens Reference Sequence or RSRS

In April, 2012, a groundbreaking, watershed, paper was published by Dr. Doron Behar and 8 other authors titled “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root.”

You can read the paper and download the supplementary data at this link:  http://www.cell.com/AJHG/abstract/S0002-9297(12)00146-2

Previous to this new paper, mitochondrial DNA results have always been reported by comparing your mtDNA to the Cambridge Reference Sequence.  This has been problematic for a number of reasons, but let’s just look at one example.

Mutation 16519C is present in just about everyone.  In fact, in more than half of the people.  So what this really means is that it’s not really a mutation in the people who carry 16519C, it really was a mutation in the anonymous person who is the Cambridge Reference Sequence.  But since they did not carry 16519C, it’s reported as a mutation in the rest of us.  However, it’s really the “normal” state of the DNA, or what we call the ancestral state.  And it’s relatively useless when comparing your results to others because nearly everyone has it.

What Dr. Behar has spent years doing is going back in time, genetically, and reconstructing what we believe the original “mitochondrial Eve” looked like, at least in terms of her mitochondrial DNA.  He could do that because he took the time to sort through each haplogroup, taking him back in time to the ancestral state of all of the mutations, in other words, before they happened.

The result is something called the Reconstructed Sapiens Reference Sequence, or RSRS.

Why does this matter to you?

Today, when people at other companies are still using the older CRS, it doesn’t matter much, but it will in time as other companies adopt the new model too. It means that your reported mutations change. The RSRS is much more accurate and allows for a uniform naming of the various haplogroups from an ancestral base.  Your haplogroup name may and probably will change between the two.  Today, they are still the same on your personal page at Family Tree DNA, but in the future, they won’t be.

There may be a time during the transition where you’ll need to know if you’re using CRS or RSRS numbers.  Fortunately, for Family Tree DNA clients, you’re being provided with both, so you’ll be able to use either one or switch back and forth, as needed.

Haplogroup Name Changes

Whether or not the new reference sequence becomes widely accepted or not, this project by Dr. Behar has very successfully found many new subgroups of haplogroups.  In some cases, the haplogroups got shuffled a bit as to where their branch lives on the tree, based on new discoveries.  In my case, I have a new letter appended to my former haplogroup name, J1c2 to J1c2f, but for others, the change is significant.  Today, on the Family Tree DNA pages, the haplogroup names remain the same, but the updated names will be added in the future.

mtDNA Community

If you can’t wait (I couldn’t) to find about your haplogroup name changes, you can follow the instructions on the mtDNA Community tab.  We will talk about the mtDNA Community in a future blog.

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Disclosure

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

Thank you so much.

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What Happened to My Mitochondrial DNA???

Did you notice?  If you tested at Family Tree DNA, something happened to your mitochondrial DNA while you were sleeping.  Go ahead….quick….go and take a look.  There is something new….very new.

Family Tree DNA rolled out the very new RSRS sequencing and has positioned it right beside your Cambridge Reference Sequence (CRS) values.  These are the mutations you’ve always seen, are familiar with, know and love.  Your CRS results are on the first tab shown, so still there and very much visible.  See below.

So you have the old and you have the new, side by side, but what is the RSRS and what does it mean to you?  Why are they so different?  Tune in tomorrow where we’ll talk about the brand new, watershed RSRS, the Reconstructed Sapiens Reference Sequence, what it is and why it’s important to you.  This is cutting edge science, and you get to be a part of it!!!

And congratulations to Family Tree DNA for being the first company to bring us this new science, up close and personal.

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Disclosure

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

Thank you so much.

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I’ve Never Met a DNA Test I Wouldn’t Take….

Ok, so maybe that is a bit of an exaggeration, but not much.

Someone commented recently that they were surprised that I had taken tests with other companies since I am affiliated with Family Tree DNA.  I’d like to talk about that.

First, I am affiliated with Family Tree DNA.  I provide the Personalized DNA Reports that they sell.  We teamed up several years ago to offer these.  I am not an employee, but a contractor to them.  Having said that, I was a customer long before that.  I’ve established several projects there, and for many reasons, I believe they are the best in this industry.

However, that has never kept me from testing at other companies, for several reasons.

First, I feel an obligation to my clients to be well versed in what the industry has to offer, and how can you be well versed if you don’t take the tests?  At least, that’s what I tell my husband when he asks why all those DNA testing bills:) So that’s my story and I’m sticking to it!

Secondly, I believe in fishing in different ponds.  Your DNA is fishing for you 24x7x365.

Third, there are lots of people in lots of places conducting research today.  I’m involved with a number of those projects as well, as a volunteer.

Fourth, if one company has a better tool for DNA analysis, I’m all for it, and for them.  For example, 23andMe was the first to offer the full spectrum autosomal tests, and I tested there and so did many of my family members.  I have also benefitted from the health information.

Fifth, I like to compare similar information between companies.  You can see an example of this and how I used it in my genealogy in the paper I wrote (published in JoGG), Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis.

So, I’m by no means a DNA snob or in an exclusive relationship with Family Tree DNA relative to testing.  In fact, I recently ordered Ancesty.com’s autosomal DNA test.  I want to see what they say, find cousins in that data base who may help to break down genealogical brick walls, and how my percentages of ethnicity are calculated there.  I’ll let you know as the results come in and how they stack up with similar tests at Family Tree DNA and 23andMe.

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Disclosure

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

Thank you so much.

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Sorenson (SMGF) Update

Update: Ancstry discontinued the Sorenson database.

Many of you know about using the DNA records at www.smgf.org.  The good news is that those  of you who don’t will still get the opportunity to make discoveries by searching their data bases, at least for awhile.  They have provided, for some number of years, free data base searches to their records for both Y-line and mitochondrial DNA.

Sorenson’s assets were recently acquired by Ancestry.com, a move which has caused a non-trivial amount of consternation among genetic genealogists.  In particular, people, me included, contributed their DNA and their pedigree charts and they want to know what is going to happen to that information.  The testing was performed for free.  People never received individual results, but as their tests were processed, their results were added to a publicly searchable data base, so you could find and identify yourself with a little effort.  Equally as important, it’s a resource that many genealogists use for finding additional matches outside of the commercial testing companies.

Although today’s update from Sorenson doesn’t answer all of the questions about what will happen, or when, they do tell us that the data base will be available for some time to come.  I hope that Ancestry continues to maintain this free service, as it is certainly in line with the expectations of the people who donated their DNA/pedigree charts and also the vision of James Sorenson who founded SMGF several years before his death.  It does call into question, however, what is going to happen to these records.  Are they going to be absorbed into the Ancestry.com databases without notifying the participants?  As a participant myself, that certainly wasn’t what I expected or signed up for.

As of this morning, the new records have been added to the data base for this last and final update, but early reports also indicate that some records previously included are now missing.

Here’s what Sorenson had to say today:

Dear Friends of SMGF,

SMGF is happy to announce the addition of new haplotypes and genealogical records to the Sorenson mtDNA and Y-chromosome databases. We invite you to search these updated databases to find new family connections at http://www.smgf.org.

From the time it was founded in 1999 by molecular genealogy pioneer, James Levoy Sorenson, the mission of SMGF has been to support an important public purpose, namely the advancement of DNA-based genealogy research. Thanks to the continued philanthropic support of Mr. Sorenson and his family and the generosity of enthusiastic SMGF participants, SMGF has built the most comprehensive database of linked DNA and pedigree information in the world. Additionally, SMGF has contributed greatly to the emerging field of genetic genealogy in other ways, such as providing online DNA databases to the public and publishing numerous scientific articles detailing new discoveries.

In order to remain a leader in this rapidly growing and dynamic field, SMGF’s resources and capabilities would have to be substantially increased. Therefore, SMGF has decided that AncestryDNA is better positioned to provide the benefit to the public that is central to SMGF’s mission. For this reason, SMGF’s DNA-related assets were acquired by AncestryDNA in March 2012. SMGF is very excited to join AncestryDNA, and we are confident that the pioneering work begun at SMGF will continue to grow and have an even greater impact on the future scientific understanding and public outreach of genetic genealogy.

As we redirect our efforts to the integration with AncestryDNA it will be necessary to discontinue updates to the smgf.org website. Therefore, this will be the last update made to the Sorenson online databases. This update includes all of the Y-chromosome and mtDNA haplotypes that were generated by SMGF over the course of its operations.

The smgf.org site will continue to operate for the foreseeable future as a freely accessible tool for the genetic genealogy community, so we invite users to continue searching for family connections on smgf.org. We express our sincerest thanks to all those who participated in the SMGF project.

Sincerely,

The SMGF Team

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Disclosure

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

Thank you so much.

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Did You Test at GeneTree???

If you ever tested at GeneTree, then this message affects you.  I received the following information from GeneTree about the DNA records of their clients.  They recently sold their assets to Ancestry.com.  So if you tested there, you may want to download your records while you still can.

Dear GeneTree Customer,

You may have recently heard the exciting news that GeneTree has been acquired by AncestryDNA™ ( http://corporate.ancestry.com/press/press-releases/2012/05/ancestry.com-dna-launches/ ). As we redirect our efforts to the integration with AncestryDNA it will be necessary to discontinue the GeneTree.com website. However, as a valued GeneTree customer, you will be able to access GeneTree.com through the rest of this year, until January 1, 2013. Following this date, access to your account will no longer be available through the GeneTree site, so we recommend that you download your DNA results and pedigree data while the site is still available.

If you’d like to learn more about how to download and continue using your information and family tree outside of GeneTree, see click here To help answer some frequently asked questions, please visit our FAQs. We greatly appreciate you being a part of GeneTree and hope that you continue with your genetic genealogy and family history research.

Sincerely, The GeneTree Team

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Disclosure

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

Thank you so much.

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Welcome to the World of Genetic Genealogy

For several years now, I’ve been writing Personalized DNA Reports, publishing articles in newsletters about genetic genealogy and blogging about the Native Heritage Project.

I’ve often felt the need to be able to talk to and with people who have questions.  I learned long ago that if one person has a question about something, many others probably have that same question.  Blogging is an interactive, personal way to communicate.

Genetic genealogy is a world full of promise, but it changes rapidly and can be confusing.  People need to understand how to use the numerous tools available to us to unravel our ancestral history.

People also love to share stories.  We become inspired by the successes of others, and ideas are often forthcoming that we would not have otherwise thought of.

So, I invite you to follow along with this blog as I share things I learn, answer people’s questions and generally, have fun with genetic genealogy!!!

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research