Heteroplasmies and Poly-Cytosine Stretches – An mtDNA Case Study

I don’t match my mother’s mtDNA test results.

How is that possible?

Last fall during the sales at Family Tree DNA, I ordered an mtDNA test for my mother. Now, usually there isn’t a need to test your mother’s mtDNA if you’ve tested your own, and vice versa. You should have the same mtDNA results, and in almost all cases you will.

However, I decided to test my mother because I have a mutation that puts me at an mtDNA genetic distance of 1 relative to matches that are likely related about 200 years ago in the Caymans where my mtDNA came from. That mutation always bugged me. Although it certainly isn’t unusual to have a GD=1 at 200 years, my maternal line is a work in progress so I want as much information as possible. So I decided to “walk back” the mtDNA line as far as I could. Although my mother was only one generation further back, it couldn’t hurt to have her mtDNA sequenced just in case it could shed light on this mutation (and, frankly, the sale was too good to pass up!). ... Click to read more!

Informed Consent Agreement and Beneficiary Agreement

Last year in the Facebook group Genetic Genealogy Tips & Techniques, we were discussing the need in the community for an informed consent agreement and a beneficiary designation form. Provided below are informed consent agreement and beneficiary designation form that I drafted with very helpful feedback from the GGT&T community early last summer. Feel free to use these agreements/forms pursuant to the disclaimers below, and pursuant to the CC license under which they are distributed!

Please note that this is NOT legal advice. I do NOT make any representation that these forms are legally binding or sufficient for their intended purpose. I highly recommend that you see an attorney if you have any questions or concerns.

Informed Consent Agreement ... Click to read more!

DNA Central! A New DNA Resource Launching April 2018!

DNA is hard. There’s no way around it. Sure, it’s easy to spit in a tube, but once you have all those percentages and centiMorgans and matches, how do you make sense of it? What does it all mean? And how can it help you understand where you came from and how to use it to explore your ancestry?

Announcing DNA Central, a new resource for everything DNA! This new subscription-based site will have blog posts about the latest and greatest, how-to content (including a  “What Next?” series), short videos (such as the “3-Minute DNA” series), webinars, and forums! We’ll also have monthly giveaways and much more! It’s everything you need to finally understand and apply the results of your DNA testing! ... Click to read more!

TGG’s Top Posts in 2017

I started The Genetic Genealogist on February 12, 2007 with my first post, “New estimates for the arrival of the earliest Native Americans.” There were few educational resources for genetic genealogy back then, and all testing was Y-DNA and mtDNA. Although 23andMe would launch the first large-scale atDNA test a few months later in November of 2007 (see “23andMe Launches Their Personal Genome Service” announcing the $1,000 test), it would be a couple of years until they used the results for cousin matching. Today, almost 11 years later, there are 617 posts with more than 310,000 words.

Here’s a screenshot from the blog in December 2007:

This year I posted about 30 times about a wide variety of topics. Here are the most popular posts in 2017: ... Click to read more!

A Small Segment Round-Up

If you aren’t already a member of the coolest Facebook group ever, Genetic Genealogy Tips & Techniques, you really should be! We have a friendly and engaging environment, and everyone learns something new every day!

This post is meant to answer a question or issue that is raised almost daily in the group, and that is the issue of small shared DNA segments. Although these small segments are alluring, they are the mythological sirens of the genealogical world!

Small Segments Executive Summary

Here’s a bite-sized summary of the content below:

  • Many to most small segments (at least 7 cM and smaller) are FALSE, meaning they are NOT actually shared by the two matches, and therefore do NOT indicate shared ancestry;
  • This is supported by a 2014 paper by 23andMe scientists showing that at least 33% of 5 cM phased DNA segments are false-positive (and it’s much worse for unphased segments or segments smaller than 5 cM);
  • This is further supported by evidence that anywhere from 20-35% of distant matches at a testing company are not shared with either tested parent;
  • This is further supported by evidence that phasing your DNA with two tested parents significantly reduces the number of matches below 10 cM (with proportionally more matches reduced as the segment size gets smaller);
  • There is currently no evidence that triangulating segments or finding a paper trail provides a mechanism for distinguishing between false segments and valid segments;
  • Since we can’t tell the difference between false small segments and valid small segments, we must avoid these small segments to avoid poisoning our genealogical conclusions with false data; and
  • Beware any research or conclusion that uses these small segments without specifically addressing the issues that are known – based on all the scientific research and evidence gathered to date – to surround small segments.

If you’re interested in learning more, keep reading!

Small Segments In Detail

One of the most common questions in the group has to do with small segments. There’s no exact definition of “small” when it comes to small segments, but many of us define them as being a single segment of DNA of 7 cM or smaller. Others use 5 cM or smaller, while others use 10 cM or smaller. Personally, I consider segments of 7 cM or less to be “small,” although when I’m being very conservative I use a definition of 10 cM or smaller. ... Click to read more!

An X-DNA Case Study

This summer, I finally asked my maternal great-aunt (we’ll call her “Victoria”) if she was interested in testing her DNA for me. She agreed, and we sent off a sample of her DNA to Family Tree DNA for mtDNA and atDNA analysis. A few weeks later, the results were back and ready for digging in!

I found a close match that shared 201 cM (including 47 cM on the X chromosome). This close match had a tree, and I immediately found the most likely common ancestor. The shared X-DNA interested me the most, and I decided to review that a little closer.

Mom and My Great-Aunt Victoria

My mother is the daughter of Victoria’s brother. Now, that means that my mother has an exact copy of her father’s X chromosome (daughters receive a copy of their father’s single X chromosome). Any X-DNA that my mother and her aunt Victoria share, is the same X-DNA that her father and Victoria shared. ... Click to read more!

How Many Segments Do You Share?

I have told people in the past that we share a single segment of meaning IBD DNA with the vast majority of our genetic matches (where IBD means Identity-by-Descent, or a valid matching segment of DNA from a recent genealogical relationship). I usually say that we share a single segment of DNA with 99% of our matches, but that’s been an off-the-cuff estimate. I wanted to have better data to cite, so I took a closer look at this issue.

At FTDNA, you can download a list of all of your matches:

I downloaded my list and removed all of my targeted test-takers (anyone that I tested or I asked to test). These close test-takers would skew the data.

After removing them from my match list, I have a total of 2,491 matches at Family Tree DNA.

Family Tree DNA also allows you to download a list of all the segments you share with your matches: ... Click to read more!

Using Shared Matches – A Quick Example

I logged into my results at AncestryDNA today, and I had new fourth cousin match: Vivian Reese Wescott (ALL names in these screenshots are changed to protect privacy unless noted otherwise). This is a significant match to me, my 22nd closest match (not counting family members that I’ve tested). The relationship is estimated to be fourth cousin.

When I open up Vivian’s profile, I can see that she’s a new member, and likely hasn’t seen her results yet (I check frequently, but she hasn’t logged in since September 23rd). I also see that she doesn’t have a tree associated with her profile:

The first thing I would normally do is review her tree for clues as to our relationship.

Since I can’t do that, I’ll skip that step and now I’ll look to see how much DNA we share in common: ... Click to read more!

Inheritance of DNA Segments

DNA is randomly inherited. As a result, a match that shares 100 cM DNA with a parent will likely NOT share exactly 50 cM with the parent’s child; rather, there are a range of possibilities (100 cM, 50 cM, 0 cM, and everything in between, for example). On average it will be about 50%, but there is lots of room for variation.

Prompted by a great question in the Genetic Genealogy Tips & Techniques Facebook group, I used the “People who match one or both of 2 kits” tool at GEDmatch to look at the random inheritance pattern of DNA between my father and myself with regard to matches sharing about 35 cM (the examples here worked out great, but you can pick any size).

We can see the randomness of inheritance in this table. And we see a surprise (that I just discovered today with this exercise!) that reminds of the fact that matching DNA can come from BOTH parents! ... Click to read more!

Sharing Large Segments With a Match Does Not Validate Small Segments Shared With That Match

OK, that could be one of the worst blog titles I’ve written, but it’s intentional. When people share this post, I want the title to clearly convey the lesson.

Small Segments are Poison

We know that many small segments are false, and thus that many distant matches are false positives. I have written about small segments and distant matches many times. For a few background articles, see the following:

The (most current as of September 2017) definitive article on the nature of false versus true small segments is “Reducing Pervasive False-Positive Identical-by-Descent Segments Detected by Large-Scale Pedigree Analysis.” The paper is available online for free (http://mbe.oxfordjournals.org/content/31/8/2212). In the paper, the researchers found that more than 67% of all reported segments shorter than 4 cM are false-positive segments. At least 60% of 4cM segments were false-positive, and at least 33% of 5 cM segments were false-positive. The number of false-positives decreased fairly rapidly above 5 cM. See my analysis of this paper here. ... Click to read more!