Crossovers: Frequency and Inheritance Statistics – Male Versus Female Matters

Recently, a reader asked if I had any crossover statistics.

They were asking about the number of crossovers, meaning divisions on each chromosome, of the parent’s DNA when a child is created. In other words, how many segments of your maternal and paternal grandparent’s DNA do you inherit from your mother and father – and are those numbers somehow different?

Why would someone ask that question, and how is it relevant for genealogists?

What is a Crossover and Why is it Important?

We know that every child receives half of their autosomal DNA from their father, and half from their mother. Conversely that means that each parent can only give their child half of their own DNA that they received from their parents. Therefore, each parent has to combine some of the DNA from their father’s chromosome and their mother’s chromosome into a new chromosome that they contribute to their child.

Crossovers are breakpoints that are created when the DNA of the person’s parents is divided into pieces before being recombined into a new chromosome and passed on to the person’s child.

I’m going to use the following real-life scenario to illustrate.

Crossover pedigree.png

The colors of the people above are reflected on the chromosome below where the DNA of the blue daughter, and her red and green parents are compared to the DNA of the tester. The tester is shown as the gray background chromosomes in the chromosome browser. The backgroud person is whose results we are looking at.

My granddaughter has tested her DNA, as have her parents and 3 of her 4 grandparents along with 2 great-grandparents, shown as red and green in the diagram above.

Here’s an example utilizing the FamilyTreeDNA chromosome browser.

Crossover example chr 1.png

On my granddaughter’s chromosome 1, on the chromosome brower above, we see two perfect examples of crossovers.

There’s no need to compare her DNA against that of her parent, the son in the chart above, because we already know she matches the full length of every chromosome with both of her parents.

However, when comparing my granddaughter’s DNA against the grandmother (blue) and her grandmother’s parents, the great-grandmother shown in red and great-grandfather shown in green, we can see that the granddaughter received her blue segments from the grandmother.

The grandmother had to receive that entire blue segment from either her mother, in red, or her father, in green. So, every blue segment must have an exactly matching red segment, green segment or combination of both.

The first red box at left shows that the blue segment was inherited partially from the grandmother’s red mother and green father. We know that because the tester matches the red great-grandmother on part of that blue segment and the green great-grandfather on a different part of the entire blue segment that the tester inherited from her blue grandmother.

The middle colored region, not boxed, shows the entire blue segment was inherited from the red great-grandmother and the blue grandmother passed that intact through her son to her granddaughter.

The third larger red boxed area encompassing the entire tested region to the right of the centromere was inherited by the granddaughter from her grandmother (blue segment) but it was originally from the blue grandmother’s red mother and green father.

The Crossover

The areas on this chromosome where the blue is divided between the red and green, meaning where the red and green butt up against each other is called a crossover. It’s literally where the DNA of the blue daughter crosses over between DNA contributed by her red mother and green father.

Crossover segments.png

In other words, the crossover where the DNA divided between the blue grandmother’s parents when the grandmother’s son was created is shown by the dark arrows above. The son gave his daughter that exact same segment from his mother and it’s only by comparing the tester’s DNA against her great-grandparents that we can see the crossover.

Crossover 4 generations.png

What we’re really seeing is that the segments inherited by the grandmother from her parents two different chromosomes were combined into one segment that the grandmother gave to her son. The son inherited the green piece and the red piece on his maternal chromosome, which he gave intact to his daughter, which is why the daughter matches her grandmother on that entire blue segment and matches her great-grandparents on the red and green pieces of their individual DNA.

Inferred Matching Segments

Crossover untested grandfather.png

The entirely uncolored regions are where the tester does not match her blue grandmother and where she would match her grandfather, who has not tested, instead of her blue grandmother.

The testers father only received his DNA from his mother and father, and if his daughter does not match his mother, then she must match his untested father on that segment.

Looking at the Big Inheritance Picture

The tester’s full autosomal match between the blue grandmother, red great-grandmother and green great-grandfather is shown below.

Crossover autosomes.png

In light of the discussion that follows, it’s worth noting that chromosomes 4 and 20 (orange arrows) were passed intact from the blue grandmother to the tester through two meiosis (inheritance) events. We know this because the tester matches the green great-grandfather’s DNA entirely on these two chromosomes that he passed to his blue daughter, her son and then the tester.

Let’s track this for chromosomes 4 and 20:

  • Meiosis 1 –The tester matches her blue grandmother, so we know that there was no crossover on that segment between the father and the tester.
  • Meiosis 2 – The tester matches her green great-grandfather along the entire chromosome, proving that it was passed intact from the grandmother to the tester’s father, her son.
  • What we don’t know is whether there were any crossovers between the green great-grandfather when he passed his parent or parents DNA to the blue grandmother, his daughter. In order to determine that, we would need at least one of the green great-grandfather’s parents, which we don’t have. We don’t know if the green great-grandfather passed on his maternal or paternal copy of his chromosome, or parts of each to the blue great-grandmother, his daughter.

Meiosis Events and the Tree

So let’s look at these meiosis or inheritance events in a different way, beginning at the bottom with the pink tester and counting backwards, or up the tree.

Crossover meiosis events.png

By inference, we know that chromosomes 11, 16 and 22 (purple arrows) were also passed intact, but not from the blue grandmother. The tester’s father passed his father’s chromosome intact to his daughter. That’s the untested grandfather again. We know this because the tester does not match her blue grandmother at all on either of these three chromosomes, so the tester must match her untested grandfather instead, because those are the only two sources of DNA for the tester’s father.

A Blip, or Not?

If you’ve noticed that chromosome 14 looks unusual, in that the tester matches her grandmother’s blue segment, but not either of her great-grandparents, which is impossible, give yourself extra points for your good eye.

In this case, the green great-grandfather’s kit was a transfer kit in which that portion of chromosome 14 was not included or did not read accurately. Given that the red great-grandmother’s kit DID read in that region and does not match the tester, we know that chromosome 14 would actually have a matching green segment exactly the size of the blue segment.

However, in another situation where we didn’t know of an issue with the transfer kit, it is also possible that the granddaughter matched a small segment of the blue grandmother’s DNA where they were identical by chance. In that case, chromosome 14 would actually have been passed to the tester intact from her father’s father, who is untested.

Every Segment has a Story

Looking at this matching pattern and our ability to determine the source of the DNA back several generations, originating from great-grandparents, I hope you’re beginning to get a sense of why understanding crossovers better is important to genealogists.

Every single segment has a story and that story is comprised of crossovers where the DNA of our ancestors is combined in their offspring. Today, we see the evidence of these historical genetic meiosis or division/recombination events in the start and end points of matches to our genetic cousins. Every start and end point represents a crossover sometime in the past.

What else can we tell about these events and how often they occur?

Of the 22 autosomes, not counting the X chromosome which has a unique inheritance pattern, 17 chromosomes experienced at least one crossover.

What does this mean to me as a genealogist and how can I interpret this type of information?

Philip Gammon

You may remember our statistician friend Philip Gammon. Philip and I have collaborated before authoring the following articles where Philip did the heavy lifting.

I discussed crossovers in the article Concepts – DNA Recombination and Crossovers, also in collaboration with Philip, and showed several examples in a Four Generation Inheritance Study.

If you haven’t read those articles, now might be a good time to do so, as they set the stage for understanding the rest of this article.

The frequency of chromosome segment divisions and their resulting crossovers are key to understanding how recombination occurs, which is key to understanding how far back in time a common ancestor between you and a match can expect to be found.

In other words, everything we think we know about relationships, especially more distant relationships, is predicated on the rate that crossovers occur.

The Concepts article references the Chowdhury paper and revealed that females average about 42 crossovers per child and males average about 27 but these quantities refer to the total number of crossovers on all 22 autosomes and reveal nothing about the distribution of the number of crossovers at the individual chromosome level.

Philip Gammon has been taking a closer look at this particular issue and has done some very interesting crossover simulations by chromosome, which are different sizes, as he reports beginning here.

Crossover Statistics by Philip Gammon

For chromosomes there is surprisingly little information available regarding the variation in the number of crossovers experienced during meiosis, the process of cell division that results in the production of ova and sperm cells. In the scientific literature I have been able to find only one reference that provides a table showing a frequency distribution for the number of crossovers by chromosome.

The paper Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans by Fledel-Alon et al in 2009 contains this information tucked away at the back of the “Supplementary methods, figures, and tables” section. It was likely not produced with genetic genealogists in mind but could be of great interest to some. The columns X0 to X8 refer to the number of crossovers on each chromosome that were measured in parental transmissions. Separate tables are shown for male and female transmissions because the rates between the two sexes differ significantly. Note that it’s the gender of the parent that matters, not the child. The sample size is quite small, containing only 288 occurrences for each gender.

A few years ago I stumbled across a paper titled Escape from crossover interference increases with maternal age by Campbell et al 2015. This study investigated the properties of crossover placement utilising family groups contained within the database of the direct-to-consumer genetic testing company 23andMe. In total more than 645,000 well-supported crossover events were able to be identified. Although this study didn’t directly report the observed frequency distribution of crossovers per chromosome, it did produce a table of parameters that accurately described the distribution of inter-crossover distances for each chromosome.

By introducing these parameters into a model that I had developed to implement the equations described by Housworth and Stahl in their 2003 paper Crossover Interference in Humans I was able to derive tables depicting the frequency of crossovers. The following results were produced for each chromosome by running 100,000 simulations in my crossover model:

Crossover transmissions from female to child.png

Transmissions from female parent to child, above.

Crossover transmissions male to child.png

Transmissions from male parent to child.

To be sure that we understand what these tables are revealing let’s look at the first row of the female table. The most frequent outcome for chromosome #1 is that there will be three crossovers and this occurs 27% of the time. There were instances when up to 10 crossovers were observed in a single meiosis but these were extremely rare. Cells that are blank recorded no observations in the 100,000 simulations. On average there are 3.36 crossovers observed on chromosome #1 in female to child transmissions i.e. the female chromosome #1 is 3.36 Morgans (336 centimorgans) in genetic length.

Blaine Bettinger has since examined crossover statistics using crowdsourced data in The Recombination Project: Analyzing Recombination Frequencies Using Crowdsourced Data, but only for females. His sample size was 250 maternal transmissions and Table 2 in the report presents the results in the same format as the tables above. There is a remarkable degree of conformity between Blaine’s measurements and the output from my simulation model and also to the earlier Fledel-Alon et al study.

The diagrams below are a typical representation of the chromosomes inherited by a child.

Crossovers inherited from mother.jpg

The red and orange (above) are the set of chromosomes inherited from the mother and the aqua and green (below) from the father. The locations where the colours change identify the crossover points.

It’s worth noting that all chromosomes have a chance of being passed from parent to child without recombination. These probabilities are found in the column for zero crossovers.

In the picture above the mother has passed on two red chromosomes (#14 and #20) without recombination from one of the maternal grandparents. No yellow chromosomes were passed intact.

Similarly, below, the father has passed on a total of five chromosomes that have no crossover points. Blue chromosomes #15, #18 and #21 were passed on intact from one paternal grandparent and green chromosomes #4 and #20 from the other.

Crossovers inherited from father.jpg

It’s quite a rare event for one of the larger chromosomes to be passed on without recombination (only a 1.4% probability for chromosome #1 in female transmissions) but occurs far more frequently in the smaller chromosomes. In fact, the male chromosome #21 is passed on intact more often (50.6% of the time) than containing DNA from both of the father’s parents.

However, there is nothing especially significant about chromosome #21.

The same could be said for any region of similar genetic length on any of the autosomes i.e. the first 52 cM of chromosome #1 or the middle 52 cM of chromosome #10 etc. From my simulations I have observed that on average 2.8 autosomes are passed down from a mother to child without a crossover and an average of 5.1 autosomes from a father to child.

In total (from both parents), 94% of offspring will inherit between 4 and 12 chromosomes containing DNA exclusively from a single grandparent. In the 100,000 simulations the child always inherited at least one chromosome without recombination.

Back to Roberta

If you have 3 generations who have tested, you can view the crossovers in the grandchild as compared to either one or two grandparents.

If the child doesn’t match one grandparent, even if their other grandparent through that parent hasn’t tested, you can certainly infer that any DNA where the grandchild doesn’t match the available grandparent comes from the non-tested “other” grandparent on that side.

Let’s Look at Real-Life Examples

Using the example of my 2 granddaughters, both of their parents and 3 of their 4 grandparents have tested, so I was able to measure the crossovers that my granddaughters experienced from all 4 of their grandparents.

Maternal Crossovers Granddaughter 1 Granddaughter 2 Average
Chromosome 1 6 2 3.36
Chromosome 2 4 2 3.17
Chromosome 3 3 2 2.71
Chromosome 4 2 2 2.59
Chromosome 5 2 1 2.49
Chromosome 6 4 2 2.36
Chromosome 7 3 1 2.23
Chromosome 8 2 2 2.11
Chromosome 9 3 1 1.95
Chromosome 10 4 2 2.08
Chromosome 11 3 0 1.93
Chromosome 12 3 3 2.00
Chromosome 13 1 1 1.52
Chromosome 14 3 1 1.38
Chromosome 15 4 1 1.44
Chromosome 16 2 2 1.58
Chromosome 17 2 2 1.53
Chromosome 18 2 0 1.40
Chromosome 19 2 1 1.18
Chromosome 20 0 1 1.19
Chromosome 21 0 1 0.74
Chromosome 22 1 0 0.78
Total 56 30 41.71

Looking at these results, it’s easy to see just how different inheritance between two full siblings can be. Granddaughter 1 has 56 crossovers through her mother, significantly more than the average of 41.71. Granddaughter 2 has 30, significantly less than average.

The average of the 2 girls is 43, very close to the total average of 41.71.

Note that one child received 2 chromosomes intact from her mother, and the other received 3.

Paternal Crossovers Granddaughter 1 Granddaughter 2 Average
Chromosome 1 2 2 1.98
Chromosome 2 3 2 1.85
Chromosome 3 2 2 1.64
Chromosome 4 0 1 1.46
Chromosome 5 1 2 1.46
Chromosome 6 2 1 1.41
Chromosome 7 1 2 1.36
Chromosome 8 1 1 1.23
Chromosome 9 1 3 1.26
Chromosome 10 3 2 1.30
Chromosome 11 0 1 1.20
Chromosome 12 1 1 1.32
Chromosome 13 2 1 1.02
Chromosome 14 1 0 0.97
Chromosome 15 1 2 1.01
Chromosome 16 0 1 1.02
Chromosome 17 0 0 1.06
Chromosome 18 1 1 0.98
Chromosome 19 1 1 1.00
Chromosome 20 0 0 0.99
Chromosome 21 0 0 0.52
Chromosome 22 0 0 0.63
Total 23 26 26.65

Granddaughter 2 had slightly more paternal crossovers than did granddaughter 1.

One child received 7 chromosomes intact from her father, and the other received 5.

Chromosome Granddaughter 1 Maternal Granddaughter 1 Paternal
Chromosome 1 6 2
Chromosome 2 4 3
Chromosome 3 3 2
Chromosome 4 2 0
Chromosome 5 2 1
Chromosome 6 4 2
Chromosome 7 3 1
Chromosome 8 2 1
Chromosome 9 3 1
Chromosome 10 4 3
Chromosome 11 3 0
Chromosome 12 3 1
Chromosome 13 1 2
Chromosome 14 3 1
Chromosome 15 4 1
Chromosome 16 2 0
Chromosome 17 2 0
Chromosome 18 2 1
Chromosome 19 2 1
Chromosome 20 0 0
Chromosome 21 0 0
Chromosome 22 1 0
Total 56 23

Comparing each child’s maternal and paternal crossovers side by side, we can see that Granddaughter 1 has more than double the number of maternal as compared to paternal crossovers, while Granddaughter 2 only had slightly more.

Chromosome Granddaughter 2 Maternal Granddaughter 2 Paternal
Chromosome 1 2 2
Chromosome 2 2 2
Chromosome 3 2 2
Chromosome 4 2 1
Chromosome 5 1 2
Chromosome 6 2 1
Chromosome 7 1 2
Chromosome 8 2 1
Chromosome 9 1 3
Chromosome 10 2 2
Chromosome 11 0 1
Chromosome 12 3 1
Chromosome 13 1 1
Chromosome 14 1 0
Chromosome 15 1 2
Chromosome 16 2 1
Chromosome 17 2 0
Chromosome 18 0 1
Chromosome 19 1 1
Chromosome 20 1 0
Chromosome 21 1 0
Chromosome 22 0 0
Total 30 26

Granddaughter 2 has closer to the same number of maternal and paternal of crossovers, but about 8% more maternal.

Comparing Maternal and Paternal Crossover Rates

Given that males clearly have a much, much lower crossover rate, according to the Philip’s chart as well as the evidence in just these two individual cases, over time, we would expect to see the DNA segments significantly LESS broken up in male to male transmissions, especially an entire line of male to male transmissions, as compared to female to female linear transmissions. This means we can expect to see larger intact shared segments in a male to male transmission line as compared to a female to female transmission line.

  G1 Mat G2 Mat Mat Avg G1 Pat G2 Pat Pat Avg
Gen 1 56 30 41.71 23 26 26.65
Gen 2 112 60 83.42 46 52 53.30
Gen 3 168 90 125.13 69 78 79.95
Gen 4 224 120 166.84 92 104 106.60

Using the Transmission rates for Granddaughter 1, Granddaughter 2, and the average calculated by Philip, it’s easy to see the cumulative expected average number of crossovers vary dramatically in every generation.

By the 4th generation, the maternal crossovers seen in someone entirely maternally descended at the rate of Grandchild 1 would equal 224 crossovers meaning that the descendant’s DNA would be divided that many times, while the same number of paternal linear divisions at 4 generations would only equal 92.

Yet today, we would never look at 2 people’s DNA, one with 224 crossovers compared to one with 92 crossovers and even consider the possibility that they are both only three generations descended from an ancestor, counting the parents as generation 1.

What Does This Mean?

The number of males and females in a specific line clearly has a direct influence on the number of crossovers experienced, and what we can expect to see as a result in terms of average segment size of inherited segments in a specific number of generations.

Using Granddaughter 1’s maternal crossover rate as an example, in 4 generations, chromosome 1 would have incurred a total of 24 crossovers, so the DNA would be divided into in 25 pieces. At the paternal rate, only 8 crossovers so the DNA would be in 9 pieces.

Chromosome 1 is a total of 267 centimorgans in length, so dividing 267 cM by 25 would mean the average segment would only be 10.68 cM for the maternal transmission, while the average segment divided by 9 would be 29.67 cM in length for the paternal transmission.

Given that the longest matching segment is a portion of the estimated relationship calculation, the difference between a 10.68 cM maternal linear segment match and a 29.67 paternal linear cM segment match is significant.

While I used the highest and lowest maternal and paternal rates of the granddaughters, the average would be 19 and 29, respectively – still a significant difference.

Maternal and Paternal Crossover Average Segment Size

Each person has an autosomal total of 3374 cM on chromosomes 1-22, excluding the X chromosome, that is being compared to other testers. Applying these calculations to all 22 autosomes using the maternal and paternal averages for 4 generations, dividing into the 3374 total we find the following average segment centiMorgan matches:

Crossovers average segment size.png

Keep in mind, of course, that the chart above represents 3 generations in a row of either maternal or paternal crossovers, but even one generation is significant.

The average size segment of a grandparent’s DNA that a child receives from their mother is 80.89 cM where the average segment of a grandparent’s DNA inherited from their father is 1.57 times larger at 126.6 cM.

Keep the maternal versus paternal inheritance path in mind as you evaluate matches to cousins with identified common ancestors, especially if the path is entirely or mostly maternal or paternal which would skew the cumulative average. You can easily tell, for example, that matches who descend paternally from a common ancestor and carry the surname are likely to carry more DNA from that common male ancestor than someone who descends from a mixed or directly maternal line.

For unknown matches, just keep in mind that the average that vendors calculate and use to predict relationships, because they can’t and don’t have “inside knowledge” about the inheritance path, may or may not be either accurate or average. They do the best they can do with the information they have at hand.

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Native American & Minority Ancestors Identified Using DNAPainter Plus Ethnicity Segments

Ethnicity is always a ticklish subject. On one hand we say to be leery of ethnicity estimates, but on the other hand, we all want to know who our ancestors were and where they came from. Many people hope to prove or disprove specific theories or stories about distant ancestors.

Reasons to be cautious about ethnicity estimates include:

  • Within continents, like Europe, it’s very difficult to discern ethnicity at the “country” level because of thousands of years of migration across regions where borders exist today. Ethnicity estimates within Europe can be significantly different than known and proven genealogy.
  • “Countries,” in Europe, political constructs, are the same size as many states in the US – and differentiation between those populations is almost impossible to accurately discern. Think of trying to figure out the difference between the populations of Indiana and Illinois, for example. Yet we want to be able to tell the difference between ancestors that came from France and Germany, for example.

Ethnicity states over Europe

  • All small amounts of ethnicity, even at the continental level, under 2-5%, can be noise and might be incorrect. That’s particularly true of trace amounts, 1% or less. However, that’s not always the case – which is why companies provide those small percentages. When hunting ancestors in the distant past, that small amount of ethnicity may be the only clue we have as to where they reside at detectable levels in our genome.

Noise in this case is defined as:

  • A statistical anomaly
  • A chance combination of your DNA from both parents that matches a reference population
  • Issues with the reference population itself, specifically admixture
  • Perhaps combinations of the above

You can read about the challenges with ethnicity here and here.

On the Other Hand

Having restated the appropriate caveats, on the other hand, we can utilize legitimate segments of our DNA to identify where our ancestors came from – at the continental level.

I’m actually specifically referring to Native American admixture which is the example I’ll be using, but this process applies equally as well to other minority or continental level admixture as well. Minority, in this sense means minority ethnicity to you.

Native American ethnicity shows distinctly differently from African and European. Sometimes some segments of DNA that we inherit from Native American ancestors are reported as Asian, specifically Siberian, Northern or Eastern Asian.

Remember that the Native American people arrived as a small group via Beringia, a now flooded land bridge that once connected Siberia with Alaska.

beringia map

By Erika Tamm et al – Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, et al. (2007) Beringian Standstill and Spread of Native American Founders. PLoS ONE 2(9): e829. doi:10.1371/journal.pone.0000829. Also available from PubMed Central., CC BY 2.5, https://commons.wikimedia.org/w/index.php?curid=16975303

After that time, the Native American/First Nations peoples were isolated from Asia, for the most part, and entirely from Europe until European exploration resulted in the beginning of sustained European settlement, and admixture beginning in the late 1400s and 1500s in the Americas.

Family Inheritance

Testing multiple family members is extremely useful when working with your own personal minority heritage. This approach assumes that you’d like to identify your matches that share that genetic heritage because they share the same minority DNA that you do. Of course, that means you two share the same ancestor at some time in the past. Their genealogy, or your combined information, may hold the clue to identifying your ancestor.

In my family, my daughter has Native American segments that she inherited from me that I inherited from my mother.

Finding the same segment identified as Native American in several successive generations eliminates the possibility that the chance combination of DNA from your father and mother is “appearing” as Native, when it isn’t.

We can use segment information to our benefit, especially if we don’t know exactly who contributed that DNA – meaning which ancestor.

We need to find a way to utilize those Native or other minority segments genealogically.

23andMe

Today, the only DNA testing vendor that provides consumers with a segment identification of our ethnicity predictions is 23andMe.

If you have tested at 23andMe, sign in and click on Ancestry on the top tab, then select Ancestry Composition.

Minority ethnicity ancestry composition.png

Scroll down until you see your painted chromosomes.

Minority ethnicity chromosome painting.png

By clicking on the region at left that you want to see, the rest of the regions are greyed out and only that region is displayed on your chromosomes, at right.

Minority ethnicity Native.png

According to 23andMe, I have two Native segments, one each on chromosomes 1 and 2. They show these segments on opposite chromosomes, meaning one (the top for example) would be maternal or paternal, and the bottom one would be the opposite. But 23andMe apparently could not tell for sure because neither my mother nor father have tested there. This placement also turned out to be incorrect. The above image was my initial V3 test at 23andMe. My later V4 results were different.

Versions May Differ

Please note that your ethnicity predictions may be different based on which test you took which is dictated by when you took the test. The image above is my V3 test that was in use at 23andMe between 2010 and November 2013, and the image below is my V4 test in use between November 2013 and August 2017.

23andMe apparently does not correct original errors involving what is known as “strand swap” where the maternal and paternal segments are inverted during analysis. My V4 test results are shown below, where the strands are correctly portrayed.

Minority ethnicity Native V4.png

Note that both Native segments are now on the lower chromosome “side” of the pair and the position on the chromosome 1 segment has shifted visually.

Minority ethnicity sides.png

I have not tested at 23andMe on the current V5 GSA chip, in use since August 9, 2017, but perhaps I should. The results might be different yet, with the concept being that each version offers an improvement over earlier versions as science advances.

If your parents have tested, 23andMe makes adjustments to your ethnicity estimates accordingly.

Although my mother can’t test at 23andMe, I happen to already know that these Native segments descend from my mother based on genealogical and genetic analysis, combined. I’m going to walk you through the process.

I can utilize my genealogy to confirm or refute information shown by 23andMe. For example, if one of those segments comes from known ancestors who were living in Germany, it’s clearly not Native, and it’s noise of some type.

We’re going to utilize DNAPainter to determine which ancestors contributed your minority segments, but first you’ll need to download your ethnicity segments from 23andMe.

Downloading Ethnicity Segment Data

Downloading your ethnicity segments is NOT THE SAME as downloading your raw DNA results to transfer to another vendor. Those are two entirely different files and different procedures.

To download the locations of your ethnicity segments at 23andMe, scroll down below your painted ethnicity segments in your Ancestry Composition section to “View Scientific Details.”

MInority ethnicity scientific details.png

Click on View Scientific Details and scroll down to near the bottom and then click on “Download Raw Data.” I leave mine at the 50% confidence level.

Minority ethnicity download raw data.png

Save this spreadsheet to your computer in a known location.

In the spreadsheet, you’ll see columns that provide the name of the segment, the chromosome copy number (1 or 2) and the chromosome number with start and end locations.

Minority ethnicity download.png

You really don’t care about this information directly, but DNAPainter does and you’ll care a lot about what DNAPainter does for you.

DNAPainter

I wrote introductory articles about DNAPainter:

If you’re not familiar with DNAPainter, you might want to read these articles first and then come back to this point in this article.

Go ahead – I’ll wait!

Getting Started

If you don’t have a DNAPainter account, you’ll need to create one for free. Some features, such as having multiple profiles are subscription based, but the functionality you’ll need for one profile is free.

I’ve named this example profile “Ethnicity Demo.” You’ll see your name where mine says “Ethnicity Demo.”

Minority ethnicity DNAPainter.png

Click on “Import 23andme ancestry composition.”

You will copy and paste all the spreadsheet rows in the entire downloaded 23andMe ethnicity spreadsheet into the DNAPainter text box and make your selection, below. The great news is that if you discover that your assumption about copy 1 being maternal or paternal is incorrect, it’s easy to delete the ethnicity segments entirely and simply repaint later. Ditto if 23andMe changes your estimate over time, like they have mine.

Minority ethnicity DNAPainter sides.png

I happen to know that “copy 2” is maternal, so I’ve made that selection.

You can then see your ethnicity chromosome segments painted, and you can expand each one to see the detail. Click on “Save Segments.”

MInority ethnicity DNAPainter Native painting

Click to enlarge

In this example, you can see my Native segments, called by various names at different confidence levels at 23andMe, on chromosome 1.

Depending on the confidence level, these segments are called some mixture of:

  • East Asian & Native American
  • North Asian & Native American
  • Native American
  • Broadly East Asian & Native American

It’s exactly the same segment, so you don’t really care what it’s called. DNAPainter paints all of the different descriptions provided by 23andMe, at all confidence levels as you can see above.

The DNAPainter colors are different from 23andMe colors and are system-selected. You can’t assign the colors for ethnicity segments.

Now, I’m moving to my own profile that I paint with my ancestral segments. To date, I have 78% of my segments painted by identifying cousins with known common ancestors.

On chromosomes 1 and 2, copy 2, which I’ve determined to be my mother’s “side,” these segments track back to specific ancestors.

Minority ethnicity maternal side

Click to enlarge

Chromosome 1 segments, above, track back to the Lore family, descended from Antoine (Anthony) Lore (Lord) who married Rachel Hill. Antoine Lore was Acadian.

Minority ethnicity chromosome 1.png

Clicking on the green segment bar shows me the ancestors I assigned when I painted the match with my Lore family member whose name is blurred, but whose birth surname was Lore.

The Chromosome 2 segment, below, tracks back to the same family through a match to Fred.

Minority ethnicity chromosome 2.png

My common ancestors with Fred are Honore Lore and Marie Lafaille who are the parents of Antoine Lore.

Minority ethnicity common ancestor.png

There are additional matches on both chromosomes who also match on portions of the Native segments.

Now that I have a pointer in the ancestral direction that these Native American segments arrived from, what can traditional genealogy and other DNA information tell me?

Traditional Genealogy Research

The Acadian people were a mixture of English, French and Native American. The Acadians settled on the island of Nova Scotia in 1609 and lived there until being driven out by the English in 1755, roughly 6 or 7 generations later.

Minority ethnicity Acadian map.png

The Acadians intermarried with the Mi’kmaq people.

It had been reported by two very qualified genealogists that Philippe Mius, born in 1660, married two Native American women from the Mi’kmaq tribe given the name Marie.

The French were fond of giving the first name of Marie to Native women when they were baptized in the Catholic faith which was required before the French men were allowed to marry the Native women. There were many Native women named Marie who married European men.

Minority ethnicity Native mitochondrial tree

Click to enlarge

This Mius lineage is ancestral to Antoine Lore (Lord) as shown on my pedigree, above.

Mitochondrial DNA has revealed that descendants from one of Philippe Mius’s wives, Marie, carry haplogroup A2f1a.

However, mitochondrial tests of other descendants of “Marie,” his first wife, carry haplogroup X2a2, also Native American.

Confusion has historically existed over which Marie is the mother of my ancestor, Francoise.

Karen Theroit Reader, another professional genealogist, shows Francoise Mius as the last child born to the first Native wife before her death sometime after 1684 and before about 1687 when Philippe remarried.

However, relative to the source of Native American segments, whether Francoise descends from the first or second wife doesn’t matter in this instance because both are Native and are proven so by their mitochondrial DNA haplogroups.

Additionally, on Antoine’s mother’s side, we find a Doucet male, although there are two genetic male Doucet lines, one of European origin, haplogroup R-L21, and one, surprisingly, of Native origin, haplogroup C-P39. Both are proven by their respective haplogroups but confusion exists genealogically over who descends from which lineage.

On Antoine’s mother’s side, there are several unidentified lineages, any one or multiples of which could also be Native. As you can see, there are large gaps in my tree.

We do know that these Native segments arrived through Antoine Lore and his parents, Honore Lore and Marie LaFaille. We don’t know exactly who upstream contributed these segments – at least not yet. Painting additional matches attributable to specific ancestral couples will eventually narrow the candidates and allow me to walk these segments back in time to their rightful contributor.

Segments, Traditional Research and DNAPainter

These three tools together, when using continent-level segments in combination with painting the DNA segments of known cousins that match specific lineages create a triangulated ethnicity segment.

When that segment just happens to be genealogically important, this combination can point the researchers in the right direction knowing which lines to search for that minority ancestor.

If your cousins who match you on this segment have also tested with 23andMe, they should also be identified as Native on this same segment. This process does not apply to intracontinental segments, meaning within Europe, because the admixture is too great and the ethnicity predictions are much less reliable.

When identifying minority admixture at the continental level, adding Y and mitochondrial DNA testing to the mix in order to positively identify each individual ancestor’s Y and mitochondrial DNA is very important in both eliminating and confirming what autosomal DNA and genealogy records alone can’t do. The base haplogroup as assigned at 23andMe is a good start, but it’s not enough alone. Plus, we only carry one line of mitochondrial DNA and only males carry Y DNA, and only their direct paternal line.

We need Y and mitochondrial DNA matching at FamilyTreeDNA to verify the specific lineage. Additionally, we very well may need the Y and mitochondrial DNA information that we don’t directly carry – but other cousins do. You can read about Y and mitochondrial DNA testing, here.

I wrote about creating a personal DNA pedigree chart including your ancestors’ Y and mitochondrial DNA here. In order to find people descended from a specific ancestor who have DNA tested, I utilize:

  • WikiTree resources and trees
  • Geni trees
  • FamilySearch trees
  • FamilyTreeDNA autosomal matches with trees
  • AncestryDNA autosomal matches and their associated trees
  • Ancestry trees in general, meaning without knowing if they are related to a DNA match
  • MyHeritage autosomal matches and their trees
  • MyHeritage trees in general

At both MyHeritage and Ancestry, you can view the trees of your matches, but you can also search for ancestors in other people’s trees to see who might descend appropriately to provide a Y or mitochondrial DNA sample. You will probably need a subscription to maximize these efforts. My Heritage offers a free trial subscription here.

If you find people appropriately descended through WikiTree, Geni or FamilySearch, you’ll need to discuss DNA testing with them. They may have already tested someplace.

If you find people who have DNA tested through your DNA matches with trees at Ancestry and MyHeritage, you’ll need to offer a Y or mitochondrial DNA test to them if they haven’t already tested at FamilyTreeDNA.

FamilyTreeDNA is the only vendor who provides the Y DNA and mitochondrial DNA tests at the higher resolution level, beyond base haplogroups, required for matching and for a complete haplogroup designation.

If the person has taken the Family Finder autosomal test at FamilyTreeDNA, they may have already tested their Y DNA and mtDNA, or you can offer to upgrade their test.

Projects

Checking projects at FamilyTreeDNA can be particularly useful when trying to discover if anyone from a specific lineage has already tested. There are many, special interest projects such as the Acadian AmerIndian Ancestry project, the American Indian project, haplogroup projects, surname projects and more.

You can view projects alphabetically here or you can click here to scroll down to enter the surname or topic you are seeking.

Minority ethnicity project search.png

If the topic isn’t listed, check the alphabetic index under Geographical Projects.

23andMe Maternal and Paternal Sides

If possible, you’ll want to determine which “side” of your family your minority segments originate come from, unless they come from both. you’ll want to determine whether chromosome side one 1 or 2 is maternal, because the other one will be paternal.

23andMe doesn’t offer tree functionality in the same way as other vendors, so you won’t be able to identify people there descended from your ancestors without contacting each person or doing other sleuthing.

Recently, 23andMe added a link to FamilySearch that creates a list of your ancestors from their mega-shared tree for 7 generations, but there is no tree matching or search functionality. You can read about the FamilySearch connection functionality here.

So, how do you figure out which “side” is which?

Minority ethnicity minority segment.png

The chart above represents the portion of your chromosomes that contains your minority ancestry. Initially, you don’t know if the minority segment is your mother’s pink chromosome or your father’s blue chromosome. You have one chromosome from each parent with the exact same addresses or locations, so it’s impossible to tell which side is which without additional information. Either the pink or the blue segment is minority, but how can you tell?

In my case, the family oral history regarding Native American ancestry was from my father’s line, but the actual Native segments wound up being from my mother, not my father. Had I made an assumption, it would have been incorrect.

Fortunately, in our example, you have both a maternal and paternal aunt who have tested at 23andMe. You match both aunts on that exact same segment location – one from your father’s side, blue, and one from your mother’s side, pink.

You compare your match with your maternal aunt and verify that indeed, you do match her on that segment.

You’ll want to determine if 23andMe has flagged that segment as Native American for your maternal aunt too.

You can view your aunt’s Ancestry Composition by selecting your aunt from the “Your Connections” dropdown list above your own ethnicity chromosome painting.

Minority ethnicity relative connections.png

You can see on your aunt’s chromosomes that indeed, those locations on her chromosomes are Native as well.

Minority ethnicity relative minority segments.png

Now you’ve identified your minority segment as originating on your maternal side.

Minority ethnicity Native side.png

Let’s say you have another match, Match 1, on that same segment. You can easily tell which “side” Match 1 is from. Since you know that you match your maternal aunt on that minority segment, if Match 1 matches both you and your maternal aunt, then you know that’s the side the match is from – AND that person also shares that minority segment.

You can also view that person’s Ancestry Composition as well, but shared matching is more reliable,especially when dealing with small amounts of minority admixture.

Another person, Match 2, matches you on that same segment, but this time, the person matches you and your paternal aunt, so they don’t share your minority segment.

Minority ethnicity match side.png

Even if your paternal aunt had not tested, because Match 2 does not match you AND your maternal aunt, you know Match 2 doesn’t share your minority segment which you can confirm by checking their Ancestry Composition.

Download All of Your Matches

Rather than go through your matches one by one, it’s easiest to download your entire match list so you can see which people match you on those chromosome locations.

Minority ethnicity download aggregate data.png

You can click on “Download Aggregate Data” at 23andMe, at the bottom of your DNA Relatives match list to obtain all of your matches who are sharing with you. 23andMe limits your matches to 2000 or less, the actual number being your highest 2000 matches minus the people who aren’t sharing. I have 1465 matches showing and that number decreases regularly as new testers at 23andMe are focused on health and not genealogy, meaning lower matches get pushed off the list of 2000 match candidates.

You can quickly sort the spreadsheet to see who matches you on specific segments. Then, you can check each match in the system to see if that person matches you and another known relative on the minority segments or you can check their Ancestry Composition, or both.

If they share your minority segment, then you can check their tree link if they have one, included in the download, their Family Search information if included on their account, or reach out to them to see if you might share a known ancestor.

The key to making your ethnicity segment work for you is to identify ancestors and paint known matches.

Paint Those Matches

When searching for matches whose DNA you can attribute to specific ancestors, be sure to check at all 4 places that provide segment information that you can paint:

At GedMatch, you’ll find some people who have tested at the other various vendors, including Ancestry, but unfortunately not everyone uploads. Ancestry doesn’t provide segment information, so you won’t be able to paint those matches directly from Ancestry.

If your Ancestry matches transfer to GedMatch, FamilyTreeDNA or MyHeritage you can view your match and paint your common segments. At GedMatch, Ancestry kit numbers begin with an A. I use my Ancestry kit matches at GedMatch to attempt to figure out who that match is at Ancestry in order to attempt to figure out the common ancestor.

To Paint, You Must Test

Of course, in order to paint your matches that you find in various databases, you need to be in those data bases, meaning you either need to test there or transfer your DNA file.

Transfers

If you’d like to test your DNA at one vendor and download the file to transfer to another vendor, or GedMatch, that’s possible with both FamilyTreeDNA and MyHeritage who both accept uploads.

You can transfer kits from Ancestry and 23andMe to both FamilyTreeDNA and MyHeritage for free, although the chromosome browsers, advanced tools and ethnicity require an unlock fee (or alternatively a subscription at MyHeritage). Still, the free transfer and unlock for $19 at FamilyTreeDNA or $29 at MyHeritage is less than the cost of testing.

Here’s a quick cheat sheet.

DNA vendor transfer cheat sheet 2019

From time to time, as vendor file formats change, the ability to transfer is temporarily interrupted, but it costs nothing to try a transfer to either MyHeritage or FamilyTreeDNA, or better yet, both.

In each of these articles, I wrote about how to download your data from a specific vendor and how to upload from other vendors if they accept uploads.

Summary Steps

In order to use your minority ethnicity segments in your genealogy, you need to:

  1. Test at 23andMe
  2. Identify which parental side your minority ethnicity segments are from, if possible
  3. Download your ethnicity segments
  4. Establish a DNAPainter account
  5. Upload your ethnicity segments to DNAPainter
  6. Paint matches of people with whom you share known common ancestors utilizing segment information from 23andMe, FamilyTreeDNA, MyHeritage and AncestryDNA matches who have uploaded to GedMatch
  7. If you have not tested at either MyHeritage or FamilyTreeDNA, upload your 23andMe file to either vendor for matching, along with GedMatch
  8. Focus on those minority segments to determine which ancestral line they descend through in order to identify the ancestor(s) who provided your minority admixture.

Have fun!

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Disclosure

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Thank you so much.

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Mitochondrial DNA: Part 4 – Techniques for Doubling Your Useful Matches

This article is Part 4 of a series about mitochondrial DNA. I suggest you read these earlier articles in order before reading this one:

This article builds on the information presented in parts 1, 2 and 3.

Hellooooo – Is Anyone Home?

One of the most common complaints about ALL DNA matches is the lack of responses. When using Y DNA, which follows the paternal line directly, passed from father to son, hopefully along with the surname, you can often discern hints from your matches’ surnames.

Not so with mitochondrial DNA because the surname changes with each generation when the female marries. In fact, I often hear people say, “but I don’t recognize those names.” You won’t unless the match is from very recent generations and you know who the daughters married to the present generation.

Therefore, genealogists really depend on information from other genealogists when working with mitochondrial DNA.

Recently, I experimented at Family Tree DNA  to see what I could do to improve the information available. Family Tree DNA is the only vendor that provides full sequence testing combined with matching.

This exercise is focused on mitochondrial DNA matches, but you can use the same techniques for Y DNA as well. These are easy step-by-step instructions!

Let’s get started and see what you can do. You’ll be surprised. I was!

Your Personal Page at Family Tree DNA

mitochondrial personal page

On your personal page, under mtDNA, click on Matches.

Matches

You’ll be viewing your match list of the people who match you at some level.

You’ll see several fields on your match list that you’ll want to use. Many of the bullet points in this article refer to the fields boxed in red or red arrows.

mitochondrial matches

You can click this image to enlarge.

Let’s review why each piece of information is important.

  • Be sure you’re using viewing your matches for the HVR1, HVR2 and Coding region in the red box at the top. Those are your most relevant matches. That’s not to say that you shouldn’t also view your HVR1+HVR2 matches, and your HVR1 matches, because you literally never know what might be there. However, start with the HVR1+HVR2+Coding Region.
  • Focus on your Genetic Distance of 0 matches. Those are exact matches, meaning you have no mutations that don’t match each other. A genetic distance of 1 means that you have one mutation that doesn’t match each other. You can read about Genetic Distance here.
  • Be sure you’re looking at the match results for the entire data base or the project you want to be viewing. For example, if I’m a member of the Acadian AmerIndian project and have Acadian ancestry on my direct matrilineal line, knowing who I match within that project may be extremely beneficial, especially if I need to narrow my results to known Acadian families.
  • Look at the earliest known ancestor (EKA) information. Don’t just let your eyes gloss over it, really look at it. There may be secrets hidden here that are critical for solving your puzzle. The mother of Lydia Brown was discovered by a cousin recently after I had (embarrassingly) ignored an EKA in plain sight for years. You can read about that discovery here.
  • Click on the little blue pedigree icon on your match to view trees that go hand in hand with the earliest known ancestor (EKA) information. Some people provide more information in either the EKA or the tree, so be sure to look at both for hints.

mitochondrial tree

  • If your match’s pedigree icon is grey, they haven’t uploaded their tree. You can always drop them an email explaining how useful trees are and ask them if they will upload theirs.

Utilizing Other Resources

Many people don’t have both trees and an EKA at Family Tree DNA. Don’t hesitate to check Ancestry, MyHeritage or FamilySearch trees with the earliest known ancestor information your match provides if they don’t have a tree, or even if they do to expand their tree. We think nothing of building out trees for autosomal matches – do the same for your matches’ mitochondrial lines.

Finding additional information about someone’s ancestor is also a great ice-breaker for an email conversation. I mean, what genealogist doesn’t want information about their ancestors?

For example, if you match me and I’ve only listed my earliest known ancestor as Ellenore “Nora” Kirsch, you can go to Ancestry and search for her name where you will find several trees, including mine that includes several more generations. Most genealogists don’t limit themselves to one resource, testing company or tree repository.

mitochondrial ancestry tree

WikiTree includes a descendants link for each ancestor that provides a list of people who have DNA tested, including mtDNA. Here’s an example for my ancestor, Curtis B. Lore.

mitochondrial wiki tree

Unfortunately, no one from that line has tested their mitochondrial DNA, but looking at the descendants may provide me with some candidates that descend from his sisters through all females to the current generation, which can be male.

You can do that same type of thing at Geni if you have a tree by viewing that ancestor and clicking on “view a list of living people.”

mitochondrial Geni

While trees at FamilySearch, Ancestry and MyHeritage don’t tell you which lines could be tested for mitochondrial DNA, it’s not difficult to discern. Mitochondrial DNA is passed on by females to the current generation where males can test too – because they received their mitochondrial DNA from their mother.

Family Tree DNA Matches Profiles

Your matches’ profiles are a little used resource as many people don’t realize that additional information may be provided there. You can click on your match’s name to show their profile card.

mitochondrial profile

Be sure to check their “about me” section where I typed “test” as well as their email address which may give you a clue about where the match lives based on the extension. For example, .de is Germany and .se is Sweden.

You can also google their email address which may lead to old Rootsweb listings among other useful genealogical information.

Matches Map

mitochondrial matches map

Next, click on your Matches Map. Your match may have entered a geographical location for their earliest known ancestor. Beware of male names because sometimes people don’t realize the system isn’t literally asking for the earliest known ancestor of ANY line or the oldest ancestor on their mother’s side. The system is asking for the most distant known ancestor on the matrilineal line. A male name entered in this field invalidates the data, of course.

My Matches Map is incredibly interesting, especially since my EKA is from Germany in 1655.

mitochondrial Scandinavia

The white pin shows the location of my ancestor in Germany. The red pins are exact matches, orange are genetic distance of 1, yellow of 2 and so forth.

Note that the majority of my matches are in Scandinavia.

The first question you should be asking is if I’m positive of my genealogical research – and I am. I have proofs for every single generation. The question of paternity is not relevant to mitochondrial DNA, since the identity of the mother is readily apparent, especially in small villages of a few hundred people where babies are baptized by clergy who knows the families well.

Adoptions might be another matter of course, but adoptions as we know them have only taken place in the past hundred years or so. Generally, the child was still baptized with the parents’ names given before the 1900s. Who raised the child was another matter entirely.

Important Note: Your matches map location does NOT feed from your tree. You must go to the Matches Map page and enter that information at the bottom of that page. Otherwise your matches map location won’t show when viewed by your matches, and if they don’t do the same, theirs won’t show on your map.

mitochondrial ancestor location

Email

I KNOW nobody really wants to do this, but you may just have to email as a last resort. The little letter icon on your match’s profile sends an email, or you can find their email in their profile as well.

DON’T email an entire group of people at once as that’s perceived as spam and is unlikely to receive a response from anyone.

Compose a friendly email with a title something like “Mitochondrial DNA Match at Family Tree DNA to Susan Smith.” Many people manage several kits and if you provide identifying information in the title, you’re more likely to receive a response

I always provide my matches with some information too, instead of just asking for theirs.

Advanced Matching

mitochondrial advanced matches

Click on the advanced matching link at the bottom right of the mtDNA area on your personal page.

The Advanced Matches tool allows you to compare multiple types of tests. When looking at your match list, notice if your matches have also taken a Family Finder (FF) test. If so, then the advanced matching tool will show you who matches you on multiple types of tests, assuming you’ve taken the Family Finder test as well or transferred autosomal results to Family Tree DNA.

For example, Advanced Matches will show you who matches you on BOTH the mtDNA and the Family Finder tests. This is an important tool to help determine how closely you might be related to someone who matches you on a mitochondrial DNA test – although here is no guarantee that your autosomal match is through the same ancestor as your mitochondrial DNA match.

mitochondrial advanced matches filter

On the advanced matching page, select the tests you want to view, together, meaning you only want to see results for people who match you on BOTH TESTS. In this case, I’ve selected the full mitochondrial sequence (FMS) and the Family Finder, requested to show only people I match on both tests, and for the entire database. I could select a specific project that I’ve joined if I want to narrow the matches.

Note that if you don’t click the “yes” button you’ll see everyone you match on both tests INDIVIDUALLY, not together. So if you match 50 people on mtDNA and 1000 on Family Finder, you would show 1050 people, not the people who match you on BOTH tests, which is what you want. You might match a few or none on both tests.

Note that if you select “all mtDNA” that means you must match the person on the HVR1, HVR2 and coding region, all 3. That may not be at all what you want either. I select each one separately and run the report. So first, FMS and Family Finder, then HVR2 and Family Finder, etc.

When you’ve made your selection, click on the red button to run the report.

Family Finder Surnames

Another hint you might overlook is Family Finder surnames.

mitochondrial family finder surnames

Go to your Family Finder match list and enter the surname of your matches EKA in the search box to see if you match anyone with that same ancestor. Of course, if it’s Smith or Jones, I’m sorry.

mitochondrial family finder surname results

Entering Kirsch in my Family Finder match list resulting in discovering a match that has Kirsh from Germany in their surname list, but no tree. Using the ICW (in common with) tool, I can then look to see if they match known cousins from the Kirsch line in common with me.

Putting Information to Work

OK, now we’ve talked about what to do, so let’s apply this knowledge.

Your challenge is to go to your Full Sequence match page in the lower right hand corner and download your match list into a spreadsheet by clicking the CSV button.

mitochondrial csv

Column headings when downloaded will be:

  • Genetic Distance
  • Full Name
  • First Name
  • Middle Name
  • Last Name
  • Email
  • Earliest Known Ancestor
  • mtDNA Haplogroup
  • Match Date

I added the following columns:

  • Country
  • Location (meaning within the country)
  • Ancestral Surname
  • Year (meaning their ancestor’s birth/death year)
  • Map (meaning do they have an entry on the matches map)
  • Tree (do they have a tree)
  • Profile (did I check their profile and what did it say)
  • Comment (anything I can add)

This spreadsheet is now a useful tool.

Our goal is to expand this information in a meaningful way.

Data Mining Steps

Here are the steps in checklist format that you’ll complete for each match to fill in additional information on your spreadsheet.

  • EKA (earliest known ancestor)
  • Matches Map
  • Tree
  • Profile
  • Advanced matching
  • Family Finder surname list
  • Email, as a last resort
  • Ancestry, MyHeritage, FamilySearch, WikiTree, Geni to search for information about their EKA

Doubling My Match Information

I began with 32 full sequence matches. Of those, 13 had an entry on the Matches Map and another 6 had something in the EKA field, but not on the Matches Map.

32 matches Map Additional EKA Nothing Useful
Begin 13 on Matches Map 6 but not mapped 13
End 29 remapped on Google 5 improved info 3

When I finished this exercise, only 3 people had no usable information (white rows), 29 could be mapped, and of the original 13 (red rows), 5 had improved information (yellow cells.)

mitochondrial spreadsheet

Please note that I have removed the names of my matches for privacy reasons, but they appear as a column on my original spreadsheet instead of the Person number.

Google Maps

I remapped my matches from the spreadsheet using free Google Maps.

mitochondrial Google maps

Purple is my ancestor. Red are the original Matches Map ancestors of my matches. Green are the new people that I can map as a result of the information gleaned.

The Scandinavian clustering is even more mystifying and stronger than ever.

Add History

Of course, there’s a story here to be told, but what is that story? My family records are found in Germany in 1655, and before that, there are no records, at least not where my ancestors were living.

Clearly, from this map and also from comparing the mutations of my matches that answered my emails, it’s evident that the migration path was from Scandinavia to Germany and not vice-versa.

How did my ancestor get from Scandinavia to Germany?

When and why?

Looking at German history, there’s a huge hint – the Thirty Years’ War which occurred from 1618-1648. During that war, much of Germany was entirely depopulated, especially the Palatinate.

Looking at where my ancestor was found in 1655 (purple pin), and looking at the Swedish troop movements, we see what may be a correlation.

mitochondrial Swedish troop movements

In the first few generations of church records, there were several illegitimate births and the mother was referred to as a servant woman.

It’s possible that my Scandinavian ancestor came along with the Swedish army and she was somehow left behind or captured.

The Challenge!

Now, it’s your turn. Using this article as a guideline, what can you find? Let me know in a comment. If you utilize additional resources I haven’t found, please mention those too!

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Disclosure

I receive a small contribution when you click on the link to one of the 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

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Full or Half Siblings?

Many people are receiving unexpected sibling matches. Everyday on social media, “surprises” are being reported so often that they are no longer surprising – unless of course you’re the people directly involved and then it’s very personal, life-altering and you’re in shock. Staring at a computer screen in stunned disbelief.

Conversely, sometimes that surprise involves people we already know, love and believe to be full siblings – but autosomal DNA testing casts doubt.

If your sibling doesn’t match at all, download your DNA files and upload to another company to verify. This step can be done quickly.

Often people will retest, from scratch, with another company just for the peace of mind of confirming that a sample didn’t get swapped. If a sample was swapped, then another unknown person will match you at the sibling level, because they would be the one with your sibling’s kit. It’s extremely rare, but it has happened.

If the two siblings aren’t biologically related at all, we need to consider that one or both might have been adopted, but if the siblings do match but are predicted as half siblings, the cold fingers of panic wrap themselves around your heart because the ramifications are immediately obvious.

Your full sibling might not be your full sibling. But how can you tell? For sure? Especially when minutes seem like an eternity and your thoughts are riveted on finding the answer.

This article focuses on two tools to resolve the question of half versus full siblingship, plus a third safeguard.

Half Siblings Versus Step-Siblings

For purposes of clarification, a half sibling is a sibling you share only one parent with, while a step-sibling is your step-parent’s child from a relationship with someone other than your parent. Your step-parent marries your parent but is not your parent. You are not genetically related to your step-siblings unless your parent is related to your step-parent.

Parental Testing

Ideally two people who would like to know if they are full or half siblings would have both parents, or both “assumed” parents to compare their results with. However, life is seldom ideal and parents aren’t always available. Not to mention that parents in a situation where there was some doubt might be reluctant to test.

Furthermore, you may elect NOT to have your parents test if your test with your sibling casts doubt on the biological connections within your family. Think long and hard before exposing family secrets that may devastate people and potentially destroy existing relationships. However, this article is about the science of confirming full versus half siblings, not the ethics of what to do with that information. Let your conscience be your guide, because there is no “undo” button.

Ranges Aren’t Perfect

The good news is that autosomal DNA testing gives us the ability to tell full from half-siblings by comparing the siblings to each other, without any parent’s involvement.

Before we have this discussion, let me be very clear that we are NOT talking about using these tools to attempt to discern a relationship between two more distant unknown people. This is only for people who know, or think they know or suspect themselves to be either full or half siblings.

Why?

Because the ranges of the amount of DNA found in people sharing close family relationships varies and can overlap. In other words, different degrees of relationships can be expected to share the same amounts of DNA. Furthermore, except for parents with whom you share exactly 50% of your autosomal DNA (except males don’t share their father’s X chromosome), there is no hard and fast amount of DNA that you share with any relative. It varies and sometimes rather dramatically.

The first few lines of this Relationship Chart, from the 2016 article Concepts – Relationship Predictions, shows both first and second degree relationships (far right column).

Sibling shared cM chart 2016.png

You can see that first degree relations can be parent/child, or full siblings. Second degree relationships can be half siblings, grandparents, aunt/uncle or niece/nephew.

Today’s article is not about how to discern an unknown relation with someone, but how to determine ONLY if two people are half or full siblings to each other. In other words, we’re only trying to discern between rows two and three, above.

As more data was submitted to Blaine Bettinger’s Shared cM Project, the ranges changed as we continued to learn. Blaine’s 2017 results were combined into a useful visual tool at DNAPainter, showing various relationships.

Sibling shared cM DNAPainter.png

Note that in the 2017 version of the Shared cM Project, the high end of the half sibling range of 2312 overlaps with the low end of the full sibling range of 2209 – and that’s before we consider that the people involved might actually be statistical outliers. Outliers, by their very definition are rare, but they do occur. I have seen them, but not often. Blaine wrote about outliers here and here.

Full or Half Siblings?

So, how to we tell the difference, genetically, between full and half siblings?

There are two parts to this equation, plus an optional third safeguard:

  1. Total number of shared cM (centiMorgans)
  2. Fully Identical Regions (FIR) versus Half Identical Regions (HIR)

You can generally get a good idea just from the first part of the equation, but if there is any question, I prefer to download the results to GedMatch so I can confirm using the second part of the equation too.

The answer to this question is NOT something you want to be wrong about.

Total Number of Shared cM

Each child inherits half of each parent’s DNA, but not the same half. Therefore, full siblings will share approximately 50% of the same DNA, and half siblings will share approximately 25% when compared to each other.

You can see the differences on these charts where percentages are converted into cM (centiMorgans) and on the 2017 combined chart here.

I’ve summarized full and half siblings’ shared cMs of DNA from the 2017 chart, below.

Relationship Average Shared cM Range of Shared cM
Half Siblings 1,783 1,317 – 2,312
Full Siblings 2,629 2,209 – 3,394

Fully Identical and Half Identical Regions

Part of the DNA that full siblings inherit will be the exact same DNA from Mom and Dad, meaning that the siblings will match at the same location on their DNA on both Mom’s strand of DNA and Dad’s strand of DNA. These sections are called Fully Identical Regions, or FIR.

Half siblings won’t fully match, except for very small slivers where the nucleotides just happen to be the same (identical by chance) and that will only be for very short segments.

Half siblings will match each other, but only one parent’s side, called Half Identical Regions or HIR.

Roughly, we expect to see about 25% of the DNA of full siblings be fully identical, which means roughly half of their shared DNA is inherited identically from both parents.

Understanding the Concept of Half Identical Versus Fully Identical

To help understand this concept, every person has two strands of DNA, one from each parent. Think of two sides of a street but with the same addresses on both sides. A segment can “live” from 100-150 Main Street, er, I mean chromosome 1 – but you can’t tell just from the address if it’s on Mom’s side of the street or Dad’s.

However, when you match other people, you’ll be able to differentiate which side is which based on family members from that line and who you match in common with your sibling. This an example of why it’s so important to have close family members test.

Any one segment on either strand being compared between between full siblings can:

  • Not match at all, meaning the siblings inherited different DNA from both parents at this location
  • Match on one strand but not the other, meaning the siblings inherited the same DNA from one parent, but different DNA from the other. (Half identical.)
  • Match identically on both, meaning the siblings inherited exactly the same DNA in that location from both parents. (Fully identical.)

I created this chart to show this concept visually, reflecting the random “heads and tails” combination of DNA segments by comparing 4 sets of full siblings with one another.

Sibling full vs half 8 siblings arrows

This chart illustrates the concept of matching where siblings share:

  • No DNA on this segment (red arrow for child 1 and 2, for example)
  • Half identical regions (HIR) where siblings share the DNA from one parent OR the other (green arrow for child 1 and 2, for example, where the siblings share brown from mother)
  • Fully identical regions (FIR) where they share the same segment from BOTH parents so their DNA matches exactly on both strands (black boxed regions)

If a region isn’t either half or fully identical, it means the siblings don’t match on that piece of DNA at all. That’s to be expected in roughly 50% of the time for full siblings, and 75% of the time for half siblings. That’s no problem, unless the siblings don’t match at all, and that’s entirely different, of course.

Let’s look at how the various vendors address half versus full siblings and what tools we have to determine which is which.

Ancestry

Ancestry predicts a relationship range and provides the amount of shared DNA, but offers no tools for customers to differentiate between half versus full siblings. Ancestry has no chromosome browser to facilitate viewing DNA matches but shared matches can sometimes be useful, especially if other close family members have tested.

Sibling Ancestry.png

Update 4-4-2019 – I was contacted by a colleague who works for an Ancestry company, who provided this information: Ancestry is using “Close Family” to designate avuncular, grandparent/grandchild and half-sibling relationships. If you see “Immediate Family “the relationship is a full sibling.

Customers are not able to view the results for ourselves, but according to my colleague, Ancestry is using FIRs and HIRs behind the scenes to make this designation. The Ancestry Matching White Paper is here, dating from 2016.

If Ancestry changes their current labeling in the future, this may not longer be exactly accurate. Hopefully new labeling would provide more clarity. The good news is that you can verify for yourself at GedMatch.

A big thank you to my colleague!

MyHeritage

MyHeritage provides estimated relationships, a chromosome browser and the amount of shared DNA along with triangulation but no specific tool to determine whether another tester is a full or half sibling. One clue can be if one of the siblings has a proven second cousin or closer match that is absent for the other sibling, meaning the siblings and the second cousin (or closer) do not all match with each other.

Sibling MyHeritage.png

Family Tree DNA

At Family Tree DNA, you can see the amount of shared DNA. They also they predict a relationship range, include a chromosome browser, in common matching and family phasing, also called bucketing which sorts your matches into maternal and paternal sides. They offer additional Y DNA testing which can be extremely useful for males.

Sibling FamilyTreeDNA.png

If the two siblings in question are male, a Y DNA test will shed light on the question of whether or not they share the same father (unless the two fathers are half brothers or otherwise closely related on the direct paternal line).

Sibling advanced matches.png

FamilyTreeDNA provides Advanced Matching tools that facilitate combined matching between Y and autosomal DNA.

Sibling bucketing both.png

FamilyTreeDNA’s Family Finder maternal/paternal bucketing tool is helpful because full siblings should be assigned to “both” parents, shown in purple, not just one parent, assuming any third cousins or closer have tested on both sides, or at least on the side in question.

As you can see, on the test above, the tester matches her sister at a level that could be either a high half sibling match, or a low full sibling match. In this case, it’s a full sibling, not only because both parents tested and she matched, but because even before her parents tested, she was already bucketed to both sides based on cousins who had tested on both the maternal and paternal sides of the family.

GedMatch

GedMatch, an upload site, shows the amount of shared DNA as well. Select the One-to-One matching and the “Graph and Position” option, letting the rest of the settings default.

Sibling GedMatch menu.png

GedMatch doesn’t provide predicted relationship ranges as such, but instead estimates the number of generations to the most recent common ancestor – in this case, the parents.

Sibling GedMatch total.png

However, GedMatch does offer an important feature through their chromosome browser that shows fully identical regions.

To illustrate, first, I’m showing two kits below that are known to be full siblings.

The green areas are FIR or Fully Identical Regions which are easy to spot because of the bright green coloring. Yellow indicate half identical matching regions and red means there is no match.

Sibling GedMatch legend.png

Please note that this legend varies slightly between the legacy GedMatch and GedMatch Genesis, but yellow, green, purple and red thankfully remain the same. The blue base indicates an entire region that matches, while the grey indicates an entire region not considered a match..

Sibling GedMatch FIR.png

Fully identical green regions (FIR) above are easy to differentiate when compared with half siblings who share only half identical regions (HIR).

The second example, below, shows two half-siblings that share one parent.

Sibling GedMatch HIR.png

As you can see, there are slivers of green where the nucleotides that both parents contributed to the respective children just happen to be the same for a very short distance on each chromosome. Compared to the full sibling chart, the green looks very different.

The half-sibling small green segments are fully identical by chance or by population, but not identical by descent which would mean the segments are identical because the individuals share both parents. These two people don’t share both parents.

The fully identical regions for full siblings are much more pronounced, in addition to full siblings generally sharing more total DNA.

GedMatch is the easiest and most useful site to work with for determining half versus full siblings by comparing HIR/FIR. I wrote instructions for downloading your DNA from each of the testing vendors at the links below:

Twins

Fraternal twins are the same as regular siblings. They share the same space for 9 months but are genetically siblings. Identical twins, on the other hand, are nearly impossible to tell apart genetically, and for all intents and purposes cannot be distinguished in this type of testing.

Sibling GedMatch identical twin.png

Here’s the same chart for identical twins.

23andMe

23andMe also provides relationship estimates, along with the amount of shared DNA, a chromosome browser that includes triangulation (although they don’t call it that) and a tool to identify full versus half identical regions. 23andMe does not support trees, a critical tool for genealogists.

Unfortunately, 23andMe has become the “last” company that people use for genealogy. Most of their testers seem to be seeking health information today.

If you just happen to have already tested at 23andMe with your siblings, great, because you can use these tools. If you have not tested at 23andMe, simply upload your results from any vendor to GedMatch.

At 23andMe, under the Ancestry, then DNA Relatives tabs, click on your sibling’s match to view genetic information, assuming you both have opted into matching. If you don’t match your sibling, PLEASE be sure you BOTH have completely opted in for matching. I can’t tell you how many panic stricken siblings I’ve coached who weren’t both opted in to matching. If you’re experiencing difficulty, don’t panic. Simply download both people’s files to GedMatch for an easier comparison. You can find 23andMe download instructions here.

Sibling 23andMe HIR.png

Scrolling down, you can see the options for both half and completely identical segments on your chromosomes as compared to your match. Above,  my child matches me completely on half identical regions. This makes perfect sense, of course, because my father and my child’s father are not the same person and are not related.

Conversely, this next match is my identical twin whom I match completely identically on all segments.

Sibling 23andMe FIR.png

Confession – I don’t have an identical twin. This is actually my V3 test compared with my V4 test, but these two tests are in essence identical twin tests.

Unusual Circumstances

The combination of these two tools, DNA matching and half versus fully identical regions generally provides a relatively conclusive answer as to whether two individuals are half or full siblings. Note the words generally and relatively.

There are circumstances that aren’t as clear cut, such as when the father of the second child is a brother or other close relative of the first child’s father – assuming that both children share the same mother. These people are sometimes called three quarters siblings or niblings.

In other situations, the parents are related, sometimes closely, complicating the genetics.

These cases tend to be quite messy and should be unraveled with the help of a professional. I recommend www.dnaadoption.com (free unknown parent search specialists) or Legacy Tree Genealogists (professional genealogists.)

The Final SafeGuard – Just in Case

A third check, should any doubt remain about full versus half siblings, would be to find a relative that is a second cousin or closer on the presumed mother’s side and one on the presumed father’s side, and compare autosomal results of both relatives to both siblings.

There has never been a documented case of second cousins or closer NOT matching each other. I’m unclear about second cousins once removed, or half second cousins, but about 10% of third cousins don’t match. To date, second cousins (or closer) who didn’t match, didn’t match because they weren’t really biological second cousins.

If the two children are full siblings meaning the biological children of both the presumed parents, both siblings will match the 2nd cousin or closer on the mother’s side AND the 2nd cousin or closer on the father’s side as well. If they are not full siblings, one will match only on the second cousin on the common parent’s side.

You can see in the example below that Child 1 and Child 2, full siblings, match both Hezekiah (green), a second cousin from the father’s side, as well as Susan (pink), a second cousin from the mother’s side.

Sibling both sides matching.png

If one of the two children only matches one cousin, and not the other, then the person who doesn’t match the cousin from the father’s side, for example, is not related to the father – although depending on the distance of the relationship, I would seek an additional cousin to test through a different child – just in case.

You can see in the example below that Child 2 matches both Hezekiah (green) and Susan (pink), but Child 1 only matches Susan (pink), from the mother’s side, meaning that Child 1 does not descend from John, so isn’t the child of the Presumed Father (green).
Sibling both sides not matching.png

If neither child matches Hezekiah, that’s a different story. You need to consider the possibility of one of the following:

  • Neither child is the child of the Presumed Father, and could potentially be fathered by different men
  • A break occurred in the genetic line someplace between John and Hezekiah or between John and the Presumed Father.

In other words, the only way this safeguard works as a final check is if at least ONE of the children matches both presumed parents’ lines with a second cousin or closer.

And yes, these types of “biological lineage disruptions” do occur and much more frequently that first believed.

In the End

You may not need this safeguard check when the first and second methodologies, separately or together, are relatively conclusive. Sometimes these decisions about half versus full siblings incorporate non-genetic situational information, but be careful about tainting your scientific information with confirmation bias – meaning unintentionally skewing the information to produce the result that you might desperately want.

When I’m working with a question as emotionally loaded as trying to determine whether people are half or full siblings, I want every extra check and safeguard available – and you will too. I utilize every tool at my disposal so that I don’t inadvertently draw the wrong conclusion.

I want to make sure I’ve looked under every possible rock for evidence. I try to disprove as much as I try to prove. The question of full versus half siblingship is one of the most common topics of the Quick Consults that I offer. Even when people think they know the answer, it’s not uncommon to ask an expert to take a look to confirm. It’s a very emotional topic and sometimes we are just too close to the subject to be rational and objective.

Regardless of the genetic outcome, I hope that you’ll remember that your siblings are your siblings, your parents are your parents (genetic or otherwise) and love is love – regardless of biology. Please don’t lose the compassionate, human aspect of genealogy in the fervor of the hunt.

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Disclosure

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

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

 

The Big Y Test Increases Again to Big Y-700

In Japan, at the Tanabata or Star Festival, attendees write their wishes on tanzaku, or small ribbon-like colorful pieces of paper and hang them on the tanzaku bamboo tree. For a very long time, Y DNA project administrators pestered Bennett Greenspan at Family Tree DNA to add more STR markers, useful in determining relationships between and within family lines.

We’ve been getting our wishes granted at breakneck speed in this past year, with the addition of the Big Y-500 (that’s 500 free STR markers) in April 2018. Now, our wishes have been granted again as Family Tree DNA expands the Big Y to 700 included STR markers.

Big Y-700 Tanzaku tree.png

Family Tree DNA just announced the Big Y-700 which replaces the Big Y-500.

The Big Y test itself provides a scan of the majority of the Y chromosome, providing results to testers including:

  • All SNPs found, both ancestral (original value) and derived (mutated state)
  • New mutations never discovered before known as Private Variants. It’s exciting to be a part of scientific discovery AND these are useful genealogically as well. I wrote about using the Estes Big Y results here.
  • Reports for named SNPs and private variants, both
  • Matching for SNPs
  • SNP tree placement
  • The new Block Tree
  • First 500, now 700 STR values included for free. You can read about how these markers work, here.
  • Matching to other testers for both SNPs and STRs above 111 (STRs below 111 are handled separately). I wrote about how the new matching above 111 markers works here. You can read about the difference between STRs and SNPs here.

According to this announcement, testers whose Big Y-500 results are now pending will automatically receive the new Big Y-700 instead of the Big Y-500 that they ordered. Family Tree DNA added another 200 STR markers. No need to do anything on your part.

This is great news for everyone who ordered on or after November 1, 2018 or anyone who has not yet received Big Y results. For the first time in history, no one will bemoan delayed results!

Family Tree DNA provided the following schedule of when Big Y-700 results can be expected – some very soon!

Order Placed Results Expected By
Before November 1, 2018 February 8, 2019
November 2018 February 20, 2019
December 1, 2018 to present March 6, 2019

It looks like another benefit of the new genetic testing technology will be quicker delivery dates now and into the future. Family Tree DNA hopes to reduce their delivery time on the Big Y-700 after the current backlog is released to 2-4 weeks.

How Did They Squeeze Another 200 Markers Out?

New chemistry used in processing the Big Y-700 test results in more uniform coverage of the Y chromosome and includes a much broader target region. This combination does three things:

  • Allows quality reads of regions previously unavailable
  • Provides more consistent results
  • Provides better coverage, meaning fewer no-reads
  • Allows for more STRs to be accessed and reliably read, hence the Big Y-500 is replaced by the Big Y-700

Price

The Big Y-700 prices, according to the Family Tree DNA e-mail to group administrators:

Big Y-700 pricing.png

Upgrades

Since the new Big Y-700 test provides an additional 200 markers above and beyond the Big Y-500, many people will want to know if upgrades are available. The answer is yes, they will be but not just yet and the upgrade price has not been announced. Expect an e-mail with this information around mid-March if you have already taken a Big Y or Big Y-500 test.

Because the new chemistry is needed to obtain the Big Y-700 results, this isn’t just reprocessing the existing data. Therefore, a new test actually has to be run in the lab on the sample to facilitate the Big Y-700 upgrade from the Big Y-500.

Obviously, if not enough of the original sample remains, this could be a problematic situation. I would suggest thinking conservatively about upgrading a Big Y-500 test where the tester can’t provide a new sample for testing. Every situation will be different.

Will My Big Y-500 Markers Change?

If you upgrade to the Big Y-700, your STR markers values above 111 may change due to the improved quality of the technology involved.

This means three things:

  • You may not match people you did before, or vice versa, on some markers
  • You may have results for markers you did not have results for before
  • Your matches to people who have also taken the Big Y-700 test will likely be more accurate than to people who took a Big Y-500 test. Apples to apples, so to speak.

What If My Results Change and I Want to Keep the Old Results?

You won’t be able to mix and match at will between the results of the Big Y-500 and Big Y-700 tests. No merging or combining results of the two tests allowed!

I asked about the situation where a tester has results for a specific marker in the Big Y-500, but that location is a no-call using the new Big Y-700 technology. Family Tree DNA replied that they did not anticipate this being an issue. I hope they are right.

I also asked about the situation where a marker value changes to NOT match men who have taken the Big Y-500 of the same surname. Would the person who took the Big Y-700 be able to “revert” to the older value (in other words, merge values for the two tests) for that conflicting marker? The answer is no, that the Big Y-700 technology is superior and more accurate. Remember that matching, meaning who is on your match list, is actually determined by the first 111 STR markers, not the additional STR markers provided by the Big Y-500 or Big Y-700, so markers above 111 will not affect who you do and don’t see on your match list.

The long-term answer is of course to upgrade the other men to Big Y-700 as well. In cases where that isn’t possible, project administrators and family members comparing these results for ancestral line marker mutations will simply have to make a note of any discrepancy.

If you do upgrade once the Big Y-700 upgrade becomes available, I would recommend printing or otherwise storing a copy of your Big Y-500 results for reference.

New Match Comparison Tools Planned

While the Big Y-500 (and soon 700) results are compared on an individual tester’s results page, there is currently no tool to allow administrators to compare groups of men, which is often how surname project grouping is achieved. This also means that results above 111 markers aren’t available on the pubic project pages.

While you may not have noticed if you’re just looking at your own results, project administrators need grouping tools in order to discern line marker mutations for specific lineages. The usefulness of Y DNA testing is, after all, in the comparison of the results to other men and forming clusters of men who match into genetic families. Every family group who is participating in Y DNA testing wants to discover markers that delineate between various male lines descending from a specific progenitor.

Let me give you a quick example. In my Campbell line, we’re still trying to discover the identity of the father of Charles Campbell, born about 1750. We know that he’s from the Campbell Clan line (Duke of Argyll) of Scotland based on his descendants’ Y DNA tests, but we can’t figure out which Campbell male he descends from (probably in Virginia) before he moved to Hawkins County, Tennessee about 1780. Hopefully, these new Y DNA STR markers may provide enough granularity, if a sufficient number of men upgrade, to help us track our line back in time. We need markers that are found only in Charles’s descendants and his father’s other descendants, whoever they might be, to connect us with the correct lineage. Hey, I’m a desperate genealogist – I’ll take every hint I can find! Fingers crossed.

Family Tree DNA indicates that new grouping tools for project administrators, and I presume that means project displays as well, are coming soon. I realize that scrolling to the right forever to see beyond 111 markers would be a pain, but I can’t think of a better way to facilitate comparisons of many men. If you have an idea, give me a shout. If you’d like to see a surname project example, here’s a link to the Estes project.

I look forward to the new FREE and included Big Y markers and upcoming tools. Thanks again Family Tree DNA!

______________________________________________________________

Disclosure

I receive a small contribution when you click on some (but not all) 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

Big Y-500 STR Matching

Family Tree DNA recently introduced Big Y-500 STR matching for men who have taken  the Big Y-500 test. This is in addition to the SNP results and matching. If you’d like an introduction or definition of the terms STR and SNP, you can read about SNPs and STRs here.

Beginning in April 2018, Family Tree DNA included an additional 379+ STR markers for free for Big Y testers as a bonus, meaning for free, including all earlier testers.

While the Big Y-500 STR marker values have been included in customers’ results for several months, unless you contacted your matches directly, you didn’t know how many of those additional markers above 111 you matched on – until now.

If you haven’t taken the Big Y test, the article Why the Big Y Test? will explain why you might want to. In addition to the Big Y results, which refine your haplogroup and scan the entire gold standard region of the Y chromosome looking for SNPs, you’ll also receive at least 389 Y STR markers above the 111 STR panel for total of at least 500, for free – which is why the name of the Big Y test was changed to the Big Y-500. If you haven’t tested at the 111 marker level, don’t worry about that because the cost of the upgrade is bundled in the price of the Big Y-500 test. Click here to sign in to your account and then click on the blue upgrade button to view pricing.

Big Y-500 STR Matching

To view your matches and values above the traditional 111 makers, sign on to your account and click on Y DNA matches.

You’ll see the following display.

Y500 matches

The column “Big Y-500 STR Differences” is new. If you have not taken the Big Y-500 test, you won’t see this column.

If you have taken the Big Y-500, you’ll see results for any other man that you match who has taken the Big Y-500 test. In this example, 5 of this person’s matches have also taken the Big Y-500 test.

What Are Big Y-500 STR Differences?

The “Big Y-500 STR Differences” column values are expressed in the format “4 of 441” or something similar.

The first number represents the number of non-matching locations you have above 111 markers – in this case, 4. In the csv download file, this value is displayed in the “Big Y-500 Differences” column.

The second number represents the total number of markers above 111 that have a value for both of you – in this case, 441. In other words, you and the other man are being compared on 441 marker locations. In the csv download file, this value is displayed in the “Big Y-500 Compared” column.

Because the markers above 111 are processed using NGS (next generation sequencing) scan technology, virtually every kit will have some marker locations that have no-calls, meaning the test doesn’t read reliably at that location in spite of being scanned several times.

It’s more difficult to read STRs accurately using NGS scan technology, as compared to SNPs. SNPs are only one position in length, so only one position needs to be read correctly. STRs are repeated of a sequence of nucleotides. A 20 repeat sequence could consist of 20 copies of a series of 4 nucleotides, so a total of 80 positions in a row would need to be successfully read several times.

Let’s take a look at how matching works.

How Does Big Y-500 STR Matching Work?

If you have a total of 441 markers that read reliably, but your match has a total of 439 that produced results, the maximum number of markers possible to share would be 439. If you both have no calls on different marker locations, you would match on fewer than 439 locations. Here’s an example just using 9 fictitious markers.

Y500 match example

Based on the example above, we can see that the red cells can’t match because they experienced no-calls, and the yellow cells do have results, but don’t match.

Y500 summary

New Filter

There’s also a new filter option so you can view only matches that have taken the Big Y-500 test.

Y500 filter

Let’s look at some of the questions people have been asking.

Frequently Asked Questions

Question 1: Are the markers above 111 taken into account in the Genetic Distance column?

Answer: No, the values calculated in the genetic distance column are the number of mismatches for the marker level you are viewing using a combination of the step-wise and infinite alleles mutation models. (Stay with me here.)

In our example, we’re viewing the 111 marker level, so the genetic distance tells you the number of mismatches at 111 markers. If we were viewing the 67 marker level, then the genetic distance would be for 67 markers.

The number of mismatches above 111 markers shows separately in the “Big Y-500 STR Differences” column and is calculated using the infinite alleles model, meaning every mutation is counted as one difference. You can read more about genetic distance in the article, Concepts – Genetic Distance.

The good news is that you don’t need to calculate anything, but you may want to understand how the markers are scored and how the genetic distance is calculated. If so, go ahead and read question 2. If not, skip to question 3.

Question 2: What’s the difference between the step-wise model and the infinite alleles model?

Answer: The step-wise model assumes that a mutated value on a particular marker of multiple steps, meaning a difference between a 28 for one man and a 30 for another is a result of two separate mutation events that happened at different times, so counted as 2 mutations, 2 steps, so a genetic distance of 2.

However, this doesn’t work well with palindromic markers, explained here, where multi-copy markers, such as DYS464, often mutate more than one step at a time.

Counting multiple mathematical differences as only one mutation event is called the infinite alleles model. For example, a dual copy marker that has a value of 15-16 could mutate to 15-18 in one step and would be counted as one mutation event, and one difference and a genetic distance of one using the infinite alleles model. The same event would count as 2 mutation events (steps) and a genetic distance of 2 using the step-wise mutation model. In this article, I explain which markers are calculated using which methodology.

Another good infinite alleles example is when a location loses it’s DNA at a marker entirely. If the marker value for most men being compared is 10 and is being compared to a  person with no DNA at that location, resulting in a null value of 0 (which is not the same as a no-call which means the location couldn’t be read successfully), the mutation event happened in one step, and the difference should be counted as one event, one step and a genetic distance of one, not 10 events, 10 steps and a genetic distance of 10.

To recap, the values of markers 1-111 are calculated by a combination of the step-wise model and the infinite alleles model, depending on the marker number and situation. The differences in markers above 111 are calculated using the infinite alleles model where every mutation or difference equals a distance of one unless a zero (null) is encountered. In that case, the mutation event is considered a one. However, above 111 markers, using NGS technology, most instances where no DNA is encountered results in a no-read, not a null value.

Question 3: Has the TIP calculator been updated?

Answer: No, the TIP calculator does not take into account the new markers above 111. The TIP calculator relies upon the combined statistical mutation frequency for each marker and includes haplogroup differences. Therefore, it would be difficult to compensate for different numbers of markers, with various markers missing for each individual above 111 markers. The TIP calculator only utilizes markers 1-111.

Question 4: Do projects display more than 111 markers?

Answer: No, projects don’t display the additional markers, at least not yet. The 111 marker results require scrolling to the right significantly, and 500 markers would require 5 times as much scrolling to compare values. Anyone with an idea how to better accomplish a public project display/comparison should submit their idea to Family Tree DNA.

Question 5: Which markers above 111 are fast versus slow mutating?

Answer: Results for these markers are new and statistical compilations aren’t yet available. However, initial results for surname projects in which several men who share a surname and match have tested indicate that there’s not as much variation in these additional markers as we’ve seen in the previous 111 markers, meaning Family Tree DNA already selected the most informative genealogical markers initially. This suggests that the additional markers may provide additional mutations but probably not five times as many as the initial 111 markers.

Question 6: Why do I have more mutations in the first 111 markers than I do in the 389+ markers above the 111 panel?

Answer: That’s a really good question. You’ve probably noticed in our example that the men have dis-proportionally more mutations in the first 111 markers than in the markers above 111.

Y500 genetic distance

The trend is clearly for the first 111 markers to mutate more frequently than the 379+ markers above 111. This means that the first 111 markers are generally going to be more genealogically informative than the balance of the 379+ markers. However, and this is a big however, if the line marker mutation that you need to sort out your group of men occurs in the markers above 111, the number of mutations and the percentages don’t mean anything at all. The information that matters is how you can utilize these markers to differentiate men within the line you are working with, and what story those markers tell.

Of course, the markers above 111 are free as part of the Big Y-500 test which is designed to extract as much SNP information as possible. In essence, these STR markers are icing on the cake – a treat we never expected.

Bottom Line

Here’s the bottom line about the Big-Y 500 STR markers. You don’t know what you don’t know and these 379+ STR markers come along with the Big Y test as a bonus. If you’re looking for line-marker STR mutations in groups of men, the Big Y-500 is a logical next step after 111 marker testing.

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Disclosure

I receive a small contribution when you click on some (but not all) 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

AutoClustering by Genetic Affairs

The company Genetic Affairs launched a few weeks ago with an offer to regularly visit your vendor accounts at Family Tree DNA, Ancestry and 23andMe, and compile a spreadsheet of your matches, download it, and send it to you in an e-mail. They then update your match list at regular intervals of your choosing.

I didn’t take advantage of this, mostly because Ancestry doesn’t provide me with segment information and while 23andMe and Family Tree DNA both do, I maintain a master spreadsheet that the new matches wouldn’t integrate with. Granted, I could sort by match date and add only the new ones to my master spreadsheet, but it was never a priority. That was yesterday.

AutoClustering

That changed this week. Genetic Affairs introduced a new AutoClustering tool that provides users with clustered matches. I’m salivating and couldn’t get signed up quickly enough.

Please note that I’ve cropped the names for this article – the Genetic Affairs display shows you the entire name.

In short, each tiny square node represents a three-way match, between you and both of the people in the intersection of the grid. This does NOT mean they are triangulated, but it does mean there’s a really good chance they would triangulate. Think of this as the Family Tree DNA matrix on steroids and automated.

This tool allows me by using my mother’s test as well to actually triangulate my matches. If they are on my mother’s side of the tree, match me and mother both, and are in the match matrix, they must triangulate on my mother’s side of my tree if they both match me on the same segment.

With this information, I can check the chromosome browser, comparing my chromosomes to those other two individuals in the matrix to see if we share a common segment – or I can simply sort the spreadsheet provided with the AutoCluster results. Suddenly that delivery service is extremely convenient!

No, this service is not free, but it’s quite reasonable. I’m going to step through the process. Note that at times, the website seemed to be unresponsive especially when moving from one step to another. Refreshing the page remedied the problem.

Account Setup

Go to www.geneticaffairs.com. Click on Register to set up your account, which is very easy.

After registering, move to step 2, “Add website.”

Add websites where you have accounts. All of your own profiles plus the other people’s that you manage at both Ancestry and 23andMe are included when you register that site in your profile.

You’ll need your signon information and password for each site.

At Family Tree DNA, you’ll need to add a new website for each account since every account has its own kit number and password.

I added my own account and my mother’s account since mother’s DNA is every bit as relevant to my genealogy as my own, AND, I only received half of her DNA which means she will have many matches that I don’t.

When you’re finished adding accounts, click on “Websites and Profiles” at the top to open the website tab of your choosing and click on the blue circular arrows AutoCluster link. You are telling the system to go out and gather your matches from the vendor and then cluster your matches together, generating an AutoCluster graphic file.

There are several more advanced options, but I’m going to run initially with Approach A, the default level. This will exclude my closest matches. Your closest matches will fall into multiple cluster groups, and the software is not set up to accommodate that – so they will wind up as a grey nonclustered square. That’s not all bad, but you’ll want to experiment to see which parameters are best for you.

If you have half-siblings, you may want to work with alternate settings because that half-sibling is important in terms of phasing your matches to maternal or paternal sides.

Asking me if “I’m sure” always causes me to really sit back and think about what I’ve done. Like, do I want to delete my account. In this case, it’s “overworry” because the system is just asking if you want to spend 25 credits, which is less than a dollar and probably less than a quarter. Right now, you’re using your free initial credits anyway.

The first time you set up an account, Genetic Affairs signs in to your account to assure that your login information is accurate.

I selected my profile and my mother’s profile at Family Tree DNA, plus one profile each at 23andMe and Ancestry. I have two profiles at both 23andMe (V3 and V4) and Ancestry (V1 and V2).

When making my selections, I wasn’t clear about the meaning of “minimum DNA match” initially, but it means fourth cousin and closer, NOT fourth and more distant.

My recommendation until you get the hang of things is to use the first default option, at least initially, then experiment.

Welcome

While I was busy ordering AutoClusters, Genetic Affairs was sending me a welcome e-mail.

Hello Roberta Estes,

Thank you for joining Genetic Affairs! We hope you will enjoy our services.

We have a manual available as well as a frequently asked questions section that both provide background information how to use our website.

You currently have 200 credits which can be supplemented using single payments and/or monthly subscriptions. Check out our prices page for more information concerning our rates.

Please let us know if anything is unclear, we can be reached using the contact form.

The great news is that everyone begins with 200 free credits which may last you for quite some time.  Or not. Consider them introductory crack from your new pusher.

Options

Genetic affairs will sign on your account at either Ancestry, 23andMe or Family Tree DNA, or all 3, periodically and provide you with match information about your new matches at each website. You select the interval when you configure your account. After each update, you can order a new AutoCluster if you wish.

Each update, and each AutoCluster request has a cost in points, sold as credits, associated with the service.

To purchase credits after you use your initial 200, you will need to enter your credit card information in the Settings Page, which is found in the dropdown (down arrow) right beside your profile photo.

You can select from and enroll in several plans.

Prices which varies by how often you want updates to be performed and for how many accounts. To see the various service offerings and cost, click here.

Here’s an example calculation for weekly updates:

This is exactly what I need, so it looks like this service will cost me $2.16 per month, plus any Autoclustering which is 25 credits each time I AutoCluster. Therefore, I’ll add another 100 credits for a total of $3.16 per month.

It looks like the $5 per month package will do for me. But don’t worry about that right now, because you’re enjoying your free crack, um, er, credits.

Ok, the e-mail with my results has just arrived after the longest 10 minutes on earth, so let’s take a look!

The Results E-mail

In a few minutes (or longer) after you order, an e-mail with the autoclustering results will arrive. Check your spam filter. Some of my e-mails were there, and some reports simply had to be reordered. One report never arrived after being ordered 3 times.

The e-mail when it arrives states the following:

Hello Roberta Estes,

For profile Roberta Estes: An AutoCluster analysis has been performed (access it through the attached HTML file).

As requested, cM thresholds of 250 cM and 50 cM were used. A total number of 176 matches were identified that were used for a AutoCluster analysis. There should be two CSV files attached to this email and if enough matches can be clustered, an additional HTML file. The first CSV file contains all matches that were identified. The second CSV file contains a spreadsheet version of the AutoCluster analysis. The HTML file will contain a visual representation of the AutoCluster analysis if enough matches were present for the clustering analysis. Please note that some files might be displayed incorrectly when directly opened from this email. Instead, save them to your local drive and open the files from there.

Attached I found 3 files:

  • Matches list
  • Autocluster grid csv file
  • Autocluster html file that shows the cluster itself

The Match Spreadsheet

The first thing that will arrive in your e-mail is a spreadsheet of your matches for the account you configured and ordered an AutoCluster for.

In the e-mail, your top 20 matches are listed, which initially confused me, because I wondered if that means they are not in the spreadsheet. They are.

At 23andMe, I initially selected 5th cousins and closer, which was the most distant match option provided. I had a total of 1233 matches.

23andMe caps your account at 2000 (unless you have communicated with people who are further than 2000 away, in which case they remain on your list), but you can’t modify the Genetic Affairs profile to include any people more distant than 5th cousins

Note that the 23andMe download shows you information about your match, but NOT the actual matching segment information☹

At Ancestry, I selected 4th cousin and closer and I received a total of 2698 matches. I could select “distant cousin” which would result in additional matches being downloaded and a different autoclustering diagram. I may experiment with this with my V2 account and compare them side by side.

This Ancestry information provides an important clue for me, because the matches I work with are generally only my Shared Ancestor Hints matches. If the Viewed field equals false, this tells  me immediately that I didn’t have a shared ancestor hint – but now because of the clustering, I know where they might fit.

At Family Tree DNA, I selected 4th cousin, but I could have selected 5th cousins. I have a total of 1500 matches.

This report does include the segment information (Yay!) and my only wish here would be to merge the two downloads available at Family Tree DNA, meaning the segment information and the match information. I’d like to know which of these are assigned to maternal or paternal buckets, or both.

AutoClustering

The Autocluster csv file is interesting in that it shows who matches whom. It’s the raw data used to construct the colored grid.

My matches are numbered in their column. For example, person M.B. is person 1. Every person that matches person 1 is noted at left with a 1 in that column.  Look at the second person under the Name column, C. W., who matches person 1 (M.B.), 2 (C.W.), 3 (T.F.), 4 (purple) and 5 (A.D.).

All of these people are in the same cluster, number 3, which you’ll see below.

The AutoCluster Graph

Finally, we get to the meat of the matter, the cluster graph.

Caveat – I experienced a significant amount of difficulty with both my account and my graph. If your graph does not display correctly, save the file to your system and click to open the file from your hard drive. Try Edge or Internet explorer if Chrome doesn’t work correctly. If it still doesn’t display accurately, notify GeneticAffairs at info@geneticaffairs.com. Consider this software release late alpha or early beta. Personally, I’m just grateful for the tool.

When you first open the html file, you’ll be able to see your matches “fly” into place. That’s pretty cool. Actually, that’s a metaphor for what I want all of my genealogy to do.

This grid shows the people who match me and each other as well, so a trio – although this does NOT mean the three of us match on the same segment.

The first person is Debbie, a known cousin on my father’s side. She and all of the other 12 people match me and each other as well and are shown in the orange cluster at the top left.

I know that my common ancestor couple with Debbie is Lazarus Estes and Elizabeth Vannoy, so it’s very likely that all of these same people share the same ancestral line, although perhaps not the same ancestral couple. For example, they could descend from anyone upstream of Lazarus and Elizabeth. Some may have known ancestors on either the Estes or Vannoy side, which will help determine who the actual oldest common ancestors are.

You’ll notice people in grey squares that aren’t in the cluster, but match me and Debbie both. This means that they would fall into two different clusters and the software can’t accommodate that. You may find your closest relatives in this grey never-never-land. Don’t ignore the grey squares because they are important too.

The second green cluster is also on my father’s side and represents the Vannoy line. My common ancestor with several matches is Joel Vannoy and Phoebe Crumley.

Working my way through each cluster, I can discern which common ancestor I match by recognizing my cousins or people who I’ve already shared genealogy with.

The third red cluster is on my mother’s side and I know that it’s my Jacob Lentz and Fredericka Ruhle line. I can verify this by looking at my mother’s AutoCluster file to see if the same people appear in her cluster.

You can also view this grid by name, # of shared matches and the # of shared cMs with the tester. Those displays are nice but not nearly as informative at the AutoClusters.

Scroll for More Match Information

Be sure to scroll down below the grid (yes, there is something below the grid!) and read the text where you’re provided a list of people who qualify to be included in the clusters, but don’t match anyone else at the criteria selection level you chose – so they aren’t included in the grid. This too is informative.  For example, my cousin Christine is there which tells me that our mutual line may not be represented by a cluster. This isn’t surprising, since our common ancestor immigrated in the 1850s – so not a lot of descendants today.

You’re also provided with AutoCluster match information, including whether or not your match has a tree. I do have notes on my matches at Family Tree DNA for several of these people, but unfortunately, the file download did not pick those notes up.

However, the fact that these matches are displayed “by cluster” is invaluable.

You can bet your socks that I’m clicking on the “tree” hotlink and signing on to FTDNA right now to see if any of these people have recognizable ancestors (or surnames) of either Elizabeth Vannoy or Lazarus Estes, or upstream. Some DO! Glory be!

Better yet, their DNA may descend from one of my dead-ends in this line, so I’ll be carefully recording any genealogical information that I can obtain to either confirm the known ancestors or break through those stubborn walls.

Dead ends would become evident by multiple people in the cluster sharing a different ancestor than one you’re already familiar with. Look carefully for patterns. Could this be the key to solving the mystery of who the mother of Nancy Ann Moore is? Or several other brick walls that I’d love to fall, just in time for Christmas. Who doesn’t have brick walls?

By signing on to Family Tree DNA and looking carefully at the trees and surnames of the people in each group, I was able to quickly identify the common line and assign an ancestor to most of the matching groups.

This also means I’ll now be able to make notes on these matches at Family Tree DNA paint these in DNAPainter! (I’ve written several articles about using DNAPainter which you can read by entering DNAPainter into the search box on this blog.)

Mom’s Acadian Cluster

Endogamy is always tough and this tool isn’t any different. Lots of grey squares which mean people would fit into multiple clusters. That’s the hallmark of endogamy.

My Mom’s largest clustered group is Acadian, which is endogamous, and her orange cluster has a very interesting subgroup structure.

If you look, the larger loosely connected orange group extends quite some way down the page, but within that group, there seems to be a large, almost solid orange group in the lower right. I’m betting that almost solid group to the right lower part of the orange region represents a particular ancestral line within the endogamous Acadian grouping.

Also of interest, my Mom’s green cluster is the same as my red Jacob Lentz/Frederica Ruhle cluster group, with many of the same individuals. This confirms that these people match me and that other person on Mom’s side, so whoever in this group matches me and any other person on the same segment is triangulated to my Mom’s side of my genealogy.

You can also use this information in conjunction with your parental bucketing at Family Tree DNA.

In Summary

I’m still learning about this tool, it’s limitations and possibilities. The software is new and not bug-free, but the developer is working to get things straightened out. I don’t think he expected such a deluge of desperate genealogists right away and we’ve probably swamped his servers and his inbox.

I haven’t yet experimented with changing the parameters to see who is included and who isn’t in various runs. I’ll be doing that over the next several days, and I’ll be applying the confirmed ancestral segments I discover in DNAPainter!

This is going to be a lot of fun. I may not surface again until 2019😊

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Disclosure

I receive a small contribution when you click on some (but not all) 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

MyHeritage LIVE Conference Day 2 – The Science Behind DNA Matching    

The MyHeritage LIVE Oslo conference is but a fond memory now, and I would count it as a resounding success.

Perhaps one of the reasons I enjoyed it so much is the scientific aspect and because the content is very focused on a topic I enjoy without being the size and complexity of Rootstech. The smaller, more intimate venue also provides access to the “right” people as well as the ability to meet other attendees and not be overwhelmed by the sheer size.

Here are some stats:

  • 401 registered guests
  • 28 countries represented including distant places like Australia and South America
  • More than 20 speakers plus the hands-on workshops where specialist teams worked with students
  • 38 sessions and workshops, plus the party
  • 60,000 livestream participants, in spite of the time differences around the world

I was blown away by the number of livestream attendees.

I don’t know what criteria Gilad Japhet will be using to determine “success” but I can’t imagine this conference being judged as anything but.

Let’s take a look at the second day. I spent part of the time talking to people and drifting in and out of the rear of several sessions for a few minutes. I meant to visit some of the workshops, but there was just too much good, distracting content elsewhere.

I began Sunday in Mike Mansfield’s presentation about SuperSearch. Yes, I really did attend a few sessions not about DNA, but my favorite was the session on Improved DNA Matching.

Improved DNA Matching

I’m sure it won’t surprise any of my readers that my favorite presentations were about the actual science of genetic genealogy.

Consumers don’t really need to understand the science behind autosomal results to reap the benefits, but the underlying science is part of what I love – and it’s important for me to understand the underpinnings to be able to unravel the fine points of what the resulting matches are and are not revealing. Misinterpretation of DNA results leading to faulty conclusions is a real issue in genetic genealogy today. Consequently, I feel that anyone working with other people’s results and providing advice really needs to understand how the science and technology together works.

Dr. Daphna Weissglas-Volkov, a population geneticist by training, although she clearly functions far beyond that scope today, gave a very interesting presentation about how MyHeritage handles (their greatly improved) DNA Matching. I’m hitting the high points here, but I would strongly encourage you to watch the video of this session when they are made available online.

In addition to Dr. Weissglas-Volkov’s slides, I’ve added some additional explanations and examples in various places. You can easily tell that the slides are hers and the graphics that aren’t MyHeritage slides are mine.

Dr. Weissglas-Volkov began the session by introducing the MyHeritage science team and then explaining terminology to set the stage.

A match is when two people match each other on a fairly long piece of DNA. Of course, “fairly long” is defined differently by each vendor.

Your genetic map (of your chromosomes) is comprised of the DNA you inherit from different ancestors by the process of recombination when DNA is transferred from the parents to the child. A centiMorgan is the relatively likelihood that a recombination will occur in a single generation. On average, 36 recombinations occur in each generation, meaning that the DNA is divided on any chromosome. However, women, for reasons unknown have about 1.5 times as many recombinations as men.

You can’t see that when looking at an example of a person compared to their parents, of course, because each individual is a full match to each parent, but you can see this visually when comparing a grandchild to their maternal grandmother and their paternal grandmother on a chromosome browser.

The above illustration is the same female grandchild compared to her maternal grandmother, at left, and her paternal grandmother at right. Therefore the number of crossovers at left is through a female child (her mother), and the number at right is through a male child (her father.)

# of Crossovers
Through female child – left 57
Through male child – right 22

There are more segments at left, through the mother, and the segments are generally shorter, because they have been divided into more pieces.

At right, fewer and larger segments through the father.

Keep in mind that because you have a strand of DNA from each parent, with exactly the same “street addresses,” that what is produced by DNA sequencing are two columns of data – but your Mom’s and Dad’s DNA is intermixed.

The information in the two columns can’t be identified as Mom’s or Dad’s DNA or strand at this point.

That interspersed raw data is called a genotype. A haplotype is when Mom’s and Dad’s DNA can be reassembled into “sides” so you can attribute the two letters at each address to either Mom or Dad.

Here’s a quick example.

The goal, of course, is to figure out how to reassemble your DNA into Mom’s side and Dad’s side so that we know that someone matching you is actually matching on all As (Mom) or all Gs (Dad,) in this example, and not a false match that zigzags back and forth between Mom and Dad.

The best way to accomplish that goal of course is trio phasing, when the child and both parents are available, so by comparing the child’s DNA with the parents you can assign the two strands of the child’s DNA.

Unfortunately, few people have both or even one parent available in order to actual divide their DNA into “sides,” so the next best avenue is statistical phasing. I’ve called this academic phasing in the past, as compared to parental phasing which MyHeritage refers to as trio phasing.

There’s a huge amount of confusion about phasing, with few people understanding there are two distinct types.

Statistical phasing is a type of machine learning where a large number of reference populations are studied. Since we know that DNA travels together in blocks when inherited, statistical phasing learns which DNA travels with which buddy DNA – and creates probabilities. Your DNA is then compared to these models and your DNA is reshuffled in order to assemble your DNA into two groups – one representing your Mom’s DNA and one representing your Dad’s DNA, according to statistical probability.

Looking at your genotype, if we know that As group together at those 6 addresses in my example 95% of the time, then we know that the most likely scenario to create a haplotype is that all of the As came from one parent and all of the Gs from the other parent – although without additional information, there is no way to yet assign the maternal and paternal identifier. At this point, we only know parent 1 and parent 2.

In order to train the computers (machine learning) to properly statistically phase testers’ results, MyHeritage uses known relationships of people to teach the machines. In other words, their reference panels of proven haplotypes grows all of the time as parent/child trios test.

Dr. Weissglas-Volkev then moved on to imputation.

When sequencing DNA, not every location reads accurately, so the missing values can be imputed, or “put back” using imputation.

Initially imputation was a hot mess. Not just for MyHeritage, but for all vendors, imputation having been forced upon them (and therefore us) by Illumina’s change to the GSA chip.

However, machine learning means that imputation models improve constantly, and matching using imputation is greatly improved at MyHeritage today.

Imputation can do more than just fill in blanks left by sequencing read errors.

The benefit of imputation to the genetic genealogy community is that vendors using disparate chips has forced vendors that want to allow uploads to utilize imputation to create a global template that incorporates all of the locations from each vendor, then impute the values they don’t actually test for themselves to complete the full template for each person.

In the example below, you can see that no vendor tests all available locations, but when imputation extends the sequences of all testers to the full 1-500 locations, the results can easily be compared to every other tester because every tester now has values in locations 1-500, regardless of which vendor/chip was utilized in their actual testing.

Therefore, using imputation, MyHeritage is able to match between quite disparate chips, such as the traditional Illumina chips (OmniExpress), the custom Ancestry chip and the new GSA chip utilized by 23andMe and LivingDNA.

So, how are matches determined?

Matching

First your DNA and that of another person are scanned for nearly identical seed sequences.

A minimum segment length of 6cM must be identified for further match processing to occur. Anything below 6cM is discarded at this point.

The match is then further evaluated to see if the seed match is of a high enough quality that it should be perfected and should count as a match. Other segments continue to be evaluated as well. If the total matching segment(s) is 8 total cM or greater, it’s considered a valid match. MyHeritage has taken the position that they would rather give you a few accidental false matches than to miss good matches. I appreciate that position.

Window cleaning is how they refer to the process of removing pileup regions known to occur in the human genome. This is NOT the same as Ancestry’s routine that removes areas they determine to be “too matchy” for you individually.

The difference is that in humans, for example, there is a segment of chromosome 6 where, for some reason, almost all humans match. Matching across that segment is not informative for genetic genealogy, so that region along with several others similar in nature are removed. At Ancestry, those genome-wide pileup segments are removed, along with other regions where Ancestry decides that you personally have too many matches. The problem is that for me, these “too matchy” segments are many of my Acadian matches. Acadians are endogamous, so lots of them match each other because as a small intermarried population, they share a great deal of the same DNA. However, to me, because I have one great-grandfather that’s Acadian, that “too matchy” information IS valuable although I understand that it wouldn’t be for someone that is 100% Acadian or Jewish.

In situations such as Ashkenazi Jewish matching, which is highly endogamous, MyHeritage uses a higher matching threshold. Otherwise every Ashkenazi person would match every other Ashkenazi person because they all descend from a small founder population, and for genealogy, that’s not useful.

The last step in processing matches is to establish the confidence level that the match is accurately predicted at the correct level – meaning the relationship range based on the amount of matching DNA and other criteria.

For example, does this match cluster with other proven matches of the same known relationship level?

From several confidence ascertainment steps, a confidence score is assigned to the predicted relationship.

Of course, you as a customer see none of this background processing, just the fact that you do match, the size of the match and the confidence score. That’s what genealogists need!

Matching Versus Triangulation Thresholds

Confusion exists about matching thresholds versus triangulation thresholds.

While any single segment must be over 6 cM in length for the matching process to begin, the actual match threshold at MyHeritage is a total of 8 cM.

I took a look at my lowest match at MyHeritage.

I have two segments, one 6.1 cM segment, and one 6 cM segment that match. It would appear that if I only had one 6 cM segment, it would not show as a match because I didn’t have the minimum 8 cM total.

Triangulation Threshold

However, after you pass that matching criteria and move on to triangulation with a matching individual, you have the option of selecting the triangulation threshold, which is not the same thing as the match threshold. The match threshold does not change, but you can change the triangulation threshold from 2 cM to 8 cM and selections in-between.

In the example below, I’m comparing myself against two known relatives.

You won’t be shown any matches below the 6 cM individual segment threshold, BUT you can view triangulated segments of different sizes. This is because matching segments often don’t line up exactly and the triangulated overlap between several individuals may be very small, but may still be useful information.

Flying your mouse over the location in the bubble, which is the triangulated segment, tells you the size of the triangulated portion. If you selected the 2 cM triangulation, you would see smaller triangulated portions of matches.

Closing Session

The conference was closed by Aaron Godfrey, a super-nice MyHeritage employee from the UK. The closing session is worth watching on the recorded livestream when it becomes available, in part because there are feel good moments.

However, the piece of information I was looking for was whether there will be a MyHeritage LIVE conference in 2019, and if so, where.

I asked Gilad afterwards and he said that they will be evaluating the feedback from attendees and others when making that decision.

So, if you attended or joined the livestream sessions and found value, please let MyHeritage know so that they can factor your feedback onto their decision. If there are topics you’d like to see as sessions, I’m sure they’d love to hear about that too. Me, I’m always voting for more DNA😊

I hope to hear about MyHeritage LIVE 2019, and I’m voting for any of the following locations:

  • Australia
  • New Zealand
  • Israel
  • Germany
  • Switzerland

What do you think?

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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

DNA Painter – Touring the Chromosome Garden

This is the third article in a series about DNA Painter. To know DNA Painter is to love DNA Painter! Trust me!

The first two articles are:

The Chromosome Sudoku article introduces you to DNA Painter, it’s purpose and how to use the tool. The Mining Vendor Data article illustrates exactly how to find the segments you can paint from each of the main autosomal testing vendors and GedMatch.

This article is a leisurely tour through my colorful chromosome garden so that, together, we can see examples of how to utilize the information that chromosome painting unveils.

Chromosome painting can do amazing things: walk you back generations, show visual phasing…and reveal that there’s a mistake someplace, too.

If you’re not willing to be wrong and reconsider, this might not be the field for you😊

Automatic Triangulation

Chromosome painting automatically mathematically triangulates your DNA and in a much easier way than the old spreadsheet method. In fact, triangulation just happens, effortlessly IF you can determine which side is maternal and which side is paternal. Of course, you’ll always want to check to be sure that your matches also match each other. if not, then that’s an indication that maybe one or both are identical by chance.

The definition of triangulation in this context means:

  • To find a common segment
  • Of reasonable size (generally 7cM or over)
  • That is confirmed to a common ancestor with at least two other individuals
  • Who are not close family

Close family generally means parents, siblings, sometimes grandparents, although parents and grandparents can certainly be used to verify that the match is valid. The best triangulation situation is when you match those two other people through a second child, meaning siblings of your ancestor.

Different matches, depending on the circumstances, have a different level of value to you as a genealogist. In other words, some are more solid than others.

The X chromosome has special matching and triangulation rules, so we’ll talk about that when we get to that section.

Don’t think of chromosome painting as “doing” triangulation, because triangulation is a bonus of chromosome painting, and it just happens, automatically, so long as you can confirm that the segment is from either your maternal or paternal line.

What does triangulation look like in DNA Painter?

Here’s what my painted chromosome 15 looks like.

Here, I’ve drawn boxes around the areas that are triangulated. Actually, I made a small mistake and omitted one grey bar that’s also part of a second triangulation group. Can you spot it? Hint – look at the grey bars at far right in the overlapping triangulation group boxes where the red arrow is pointing. The box below should extend upwards to incorporate part of that top grey bar too.

Triangulation are those several segments piled up on top of each other. It means they match you at the same address on either the maternal or paternal chromosome. That’s good, but it’s not the same as an official “pileup area.”

Ok, so what’s a pileup area?

Pileup Areas

Certain locations in the human genome have been designated as pileup regions based on the fact that many people will match on these segments, not necessarily because they share a common relatively recent ancestor, but instead because a particular segment has a very high frequency in the general human population, or in the population of a specific region. Translated, this means that the segment might not be relevant to genealogy.

But before going too far with this discussion, it doesn’t mean that matches in pileup regions aren’t relevant to genealogy – just consider it a caution sign.

Aside from chromosome 6, which includes the HLA region, I’ve always been rather suspicious of pileup regions, because they don’t seem to hold true for me. You can view a chart that I assembled of the known pileup regions here.

DNA Painter generously includes pileup region warnings, in essence, along a chromosome bar at the top indicating “shared” or “both.”

Please note that you can click to enlarge any image.

Pileups regions are indicated by the grey hashed region at right. In my case, on chromosome 1, the pileup region isn’t piled up at all, on either the paternal (blue) chromosome or the maternal (pink) chromosome.

As you can see, I have exactly one match on the maternal side (green) and one (gold) on the paternal side (with a smidgen of a second grey match) as well, with both extending significantly beyond the pileup region. There is no reason to suspect that these gold and green matches aren’t valid.

If I saw many more matches in a pileup region than elsewhere, or many small matches, or DNA that was supposed to be from multiple ancestors not in the same line, then I’d have to question whether a pileup region was responsible.

Stacked Segments

DNA Painter provides you with the opportunity to see which of your ancestors’ segments stack. Stacking is a very important concept of DNA painting.

Before we talk about stacking, notice that the legend for which segments are color coded to specific ancestors is located at right. You can also click on the little grey box beside “Shared or Both,” at left, to show the match names beside the segments.  This is very useful when trying to analyze the accuracy of the match.

I wish DNA Painter offered an option to paint the ancestor’s names beside the segments. Maybe in V2. It’s really difficult to complain about anything because this tool is both free and awesome.

I’m using Powerpoint to label this group of stacked matches for this example.

This is a situation where I know my pedigree chart really well, so I know immediately upon looking at this stacked segment group who this piece of DNA descends from.

Here’s my pedigree chart that corresponds to the stacked segment.

We attribute each DNA segment to a couple initially based on who we match. In this case, that’s William George Estes and Ollie Bolton, my grandparents. The DNA remains attributed to them until we have evidence of which individual person in the couple received that DNA from their ancestors and passed it on to their descendant.

Therefore, the pink people are the half of the couple who we now know (thanks to DNA Painter) did NOT contribute that DNA segment, because we can track the DNA directly through the yellow line until we’re once again to another genetic brick wall couple.

My father is listed at left, and the DNA path runs back to William Crumley the second and his unknown wife who is haplogroup H2a1, the yellow couple at far right. How cool is this? One of those ancestors (or a combined segment from both) has been passed intact to me today. This is not a trivial segment either at 23.3 cM. I would not expect a segment passed to 5th cousins to be that large, but it is!

Also, note that the grey segment of DNA from Lazarus Estes (1848-1918) and Elizabeth Vannoy (1847-1918) is sitting slightly to the left of the dark blue segment from William Crumley III, so part or all of the grey or blue segment may originate with a different ancestor. Perhaps we’ll know more when additional people test and match on this same segment.

Double Related

I have one person who is related to me through two different lines. I need a way to determine which line (or both) our common DNA segment descends from.

I painted the segment for both of our common ancestor couples. The pink is George Dodson (1702-1770) & Margaret Dagord. The bright blue segment is William Crumley III (1788-1859) & Lydia Brown.

Those two lines don’t converge, at least not that we know of.

Now, as I map additional people, I’ll watch this segment for a tie breaker match between the two ancestors. The gold is not a tie breaker because that’s my grandparents who are downstream of both the pink and blue ancestors.

Painted Ethnicity

23andMe does us the favor of painting our ethnicity segments and allowing us to download a file with those segments. Conversely, DNA Painter does us the favor of allowing us to paint that entire file at once.

I already know my two Native segments on chromosome 1 and 2 descend through my mother, because her DNA is Native in exactly the same location. In other words, in this case, my ethnicity segment does in fact phase to my mother, although that’s not always the case with ethnicity.

Multiple Acadian ancestors are also proven to be Native by both genealogical records and maternal and/or paternal haplogroups.

Therefore, I’ve painted my Native segments on my mother’s side in order to determine exactly from which ancestor(s) those Native segment descend.

Confirming Questionable Ancestors

One very long-standing mystery that seemed almost unsolvable was the identity of the parents of Elijah Vannoy (1784->1850). We know he was the son of one of 4 Vannoy brothers living in Wilkes County, NC. Two were eliminated by existing Bibles and other records, but the other two remained candidates in spite of sifting through every available record and resource. We were out of luck unless DNA came to the rescue. Y DNA confirmed that Elijah was descended from one of the Vannoy males, but didn’t shed light on which one.

I decided that the wives would be the key, since we knew the identity of all four wives, thankfully. Of course, that means we’d be using autosomal DNA to attempt to gather more information.

I entered one candidate couple at Ancestry as Elijah’s parents – the one I felt most likely based on tax records and other criteria – Daniel Vannoy and Sarah Hickerson.  I also entered Sarah’s parents, Charles Hickerson (c 1725-<1793) and Mary Lytle.

I began getting matches to people who descend from Charles Hickerson and Mary Lytle through children other than Sarah.

The grey segment is from a descendant of Lazarus Estes & Elizabeth Vannoy. The salmon segments are from descendants of Charles Hickerson and Mary Lytle.

These segments aren’t small, 12.8 and 16.1 cM, so I’m fairly confident that these multiple segments in combination with the Elizabeth Vannoy segment do indeed descend from Charles Hickerson and Mary Lytle.

At Ancestry, I have 5 matches to Charles Hickerson and Mary Lytle through three of their children. However, only two of the individuals has transferred their results to either Family Tree DNA, MyHeritage or GedMatch where segment information is available to customers.

Finally, the thirty year old mystery is solved!

Shifting, Sliding, Offset or Staggered Segment Groups

Occasionally, you can prove an entire large segment by groups of shifting or sliding segments, sometimes referred as offset or staggered segments.

The entire bright pink region is inherited from Jacob Lentz (1783-1870) and Fredericka Reuhl (1788-1863.) However, it’s not proven by one individual but by a combination of 6 people whose segments don’t all overlap with each other.  The top two do match very closely with me and each other, then the third spans the two groups. The bottom 3 and part of the middle segment match very closely as well.

I can conclude that the entire dark pink region from left to right descends from Jacob and Fredericka.

Two Matches – 7 Generations

Two matches is all it took to identify this segment back to George Dodson and Margaret Dagord.

The mustard match is to my grandparents (22cM), and the pink match is to George Dodson (1702-1770) and his wife (22cM) – 7 generations. These people also match each other.

Additional matches would make this evidence stronger, although a 22cM triangulated match is very significant alone. Future might also suggest ancestors further back in time.

First Chromosome Fully Mapped

I actually have chromosome 5 entirely mapped to confirmed ancestors. I’m so excited.

Uh Oh – Something’s Wrong

I found a stack that clearly indicates something is wrong.  The question is, what?

The mustard represents my paternal grandparents, so these segments could have come through either of them, although on the pedigree chart below, we can see that this came through my grandfathers line..

There is only a small overlap with the magenta (Nicholas Speak 1782-1852 and Sarah Faires 1786-1865) and green (James Crumley 1711-1764 and Catherine c1712-c1790,) which could be by chance given that the Nicholas segment is 7.5 cM, so I’m leaving the magenta out of the analysis.

However, the rest of these segments overlap each other significantly, even though they are stepped or staggered.

As you can see from the colors on the pedigree chat, it’s impossible for the green segment to descend from the same ancestor as the purple segment. The purple and orange confirm that branch of the tree, but the red cannot be from the same ancestor or the same line as the green ancestor.

I suspect that the purple and orange line is correct, because there are 4 segments from different people with the same ancestral line.

This means that we have one of the following situations with the red and green segments:

  • The smaller segments are incorrect, false positives, meaning matching by chance. The green segment is 14 cM, so quite large to match by chance. The red segment is 10 cM. Possible, but not probable.
  • The segments are population-based matches, so appear in all 3 lines. Possible, technically, but also not probable due to the segment size.
  • The segments are genuine matches, and one of the lines is also found in one of the other lines, upstream. This is possible, but this would have to be the case with both the red and green lines. To continue to weigh this possibility, I’ll be watching for similar situations with these same ancestors.
  • Some combination of the above.

I need more matches on this segment for further clarity.

Visual Phasing – Crossovers

A crossover point is where the DNA on one side of a demarcation line is descended from one ancestor and the DNA on the other side is descended from another ancestor, represented by the pink and blue halves of the segment, below.

Crossovers occur when the DNA is combined from two different ancestors when it is passed to the child. In other words, a chunk of mom’s ancestors’ DNA is contributed by mom and a chunk of dad’s ancestors’ DNA is contributed as well. The seam between different ancestor’s DNA pieces is called a crossover.

In this example, the brown lines confirmed by several testers to be from Henry Bolton (c1759-1846) and Nancy Mann (c1780-1841) is shown with a very specific left starting point, all in a vertical line. It looks for all the world like this is a crossover point. The DNA to the left would have been contributed by another, as yet unidentified, ancestor.

The gold lines above are matches from more recent generations.

Naming Those Unnamed Acadians

My Acadian ancestry is hopelessly intertwined, but chromosome painting may in fact provide me with some prayer of unraveling this ball of twine. Eventually.

When I know that someone is Acadian, but I can’t tell which of many lines I connect through, I add them as “Acadian Undetermined.”

There’s a lot of Acadian DNA, because it’s an endogamous population and they just keep passing the same segments around and around in a very limited population.

On my maternal chromosome, all of the olive green is “Acadian Undetermined.”  However, that blue segment in the stack is Rene de Forest (1670-1751) and Francoise Dugas (1678->1751).

In essence, this one match identified all of the DNA of the other people who are now simply a row in the Acadian Undetermined stack. Now I need to go back and peruse the trees of these individuals to determine if they descend form this line, or a common ancestor of this line, or if (some of) these matches are a matter of endogamy.

Endogamous matches can be population based, meaning that you do match each other, but it’s because you share so much of the same DNA because you have small pieces of many common ancestors – not because a particular segment comes from one specific ancestor. You can also share part of your DNA from Mom’s side and part from Dad’s side, because both of your parents descend from a common population and not because the entire segment comes from any particular ancestor.

On some long cold winter weekend, I’ll go through and map all of the trees of my Acadian matches to see what I can unravel. I just love matches with trees. You just can’t do something like this otherwise.

Of course, those Acadians (and other endogamous populations) can be tricky, no matter what, one click up from a needle in a haystack.

Acadian Endogamy Haystack on Steroids

At first, our haystack looks like we’ve solved the mystery of the identity of the stack.  However, we soon discover that maybe things aren’t as neat and tidy as we think.

Of course, the olive green is Acadian Undetermined, but the three other colored segments are:

  • Pink – Guillaume Blanchard (1650-1715/17) & Huguette Goujon (c1647-1717)
  • Brown/Pink – Francois Broussard (c1653-1716) & Catherine Richard (c1663-1748)
  • Coffee – Daniel Garceau (1707-1772) & Anne Doucet (1713-1791)

Looking at the pedigree chart, we find two of these couples in the same lineage, so all is good, until we find the third, pink, couple, at the bottom.

Clearly, this segment can’t be in two different lines at once, so we have a problem.  Or do we?

Working the pink troublesome lines on back, we make a discovery.

We find a Blanchard line consisting of Guilluame Blanchard born circa 1590 and Huguette Poirier also born circa 1690.

Interesting. Let’s compare the Guillaume Blanchard and Huguette Goujon line. Is this the same couple, but with a different surname for her?

No, as it turns out, Guillaume Blanchard that married Huguette Goujon was the grandson of Guilluame Blanchard and Huguette Poirier. That haystack segment of DNA was passed down through two different lines, it appears, to converge in three descendants – me, the descendant of the pink segment couple and the descendant of the brown/burgundy segment couple. This segment reaches back in time to the birth of either Guilluame Blanchard or Huguette Poirier in 1590, someplace in France, rode over on the ship to Port Royal in the very early 1600s, probably before Jamestown was settled, and has been kicking around in my ancestors and their descendants ever since.

This 18 or so cM ancestral segment is buried someplace at Port Royal, Nova Scotia, but lives on in me and several other people through at least two divergent lines.

The X Chromsome

Several vendors don’t report the X chromosome segments. I do use X segments from those who do, but I utilize a different threshold because the SNP density is about half of that on the other chromosomes. In essence, you need a match twice as large to be equivalent to a match on another chromosome..

Generally, I don’t rely on segments below 10 for anyone, and I generally only use segments over 14cM and no less than 500 SNPs.

Having just said that, I have painted a few smaller segments, because I know that if they are inaccurate, they are very easy to delete. They can remain in speculative mode. The default for DNAPainter and that’s what I use.

The great thing about the X chromosome is that because of it’s special inheritance path, you can sometimes push these segments another 2 generations back in time.

Let’s use an X chromosome match in conjunction with my X fan chart printed through Charting Companion.

On the paternal X, I inherited the gold segment from the couple, William George Estes (1873-1971) & Ollie Bolton (1874-1955.) However, since my father didn’t inherit an X from William George Estes (because my father inherited the Y from his father,) that X segment has to be from Ollie Bolton, and therefore from her parents Joseph Bolton (1853-1920) and Margaret Claxton (1851-1920.)

The segment from Lazarus Estes (1848-1918) and Elizabeth Vannoy (1847-1918) that’s 14 cM is false. It can’t descend from that couple. Same for the 7.5 cM from Jotham Brown (c1740-c1799) & Phoebe unk (c1747-c1803.) That segment’s false too. The green 48 cM segment from Samuel Claxton (1827-1876) and Elizabeth Speak (1832-1907)?  That segment’s good to go!

On my mother’s side, there’s a 7.8 cM Acadian Undetermined, which must be false, because Curtis Benjamin Lore (1856-1909) did not inherit an X chromosome from his Acadian father, Antoine Lore (1805-1862/67.)  Therefore, my X chromosome has no Acadian at all. I never realized that before, and it makes my X chromosome MUCH easier.

How about that light green 33cM segment from Antoine Lore (1805-1862/67) & Rachel Hill (1814/15-1870/80)? That segment must come from Rachel Hill, so it’s pushed back another generation to Joseph Hill (1790-1871) and Nabby Hall (1792-1874.)

I love the X chromosome because when you find a male in the line, you automatically get bumped two more generations back to his mother’s parents. It’s like the X prize for genetic genealogy, pardon the pun!

Adoptees

Some adoptees are lucky and receive close matches immediately. Others, not so much and the search is a long process.

If you’re an adoptee trying to figure out how your matches connect together, use in-common-match groupings to cluster matches together, then paint them in groups.  Utilize the overlapping segments in order to view their trees, looking for common surnames. Always start with the groups with the longest segments and the most matches. The larger the match, the more likely you are to be able to find a connection in a more recent generation. The more matches, the more likely you are to be able to spot a common surname (or two.)

Painting can speed this process significantly.

Much More Than Painting

I hope this tour through my colorful chromosomes has illustrated how much fun analysis can be. You’ll have so much fun that you won’t even realize you’re triangulating, phasing and all of those other difficult words.

If you have something you absolutely have to do, set an alarm – or you’ll forget all about it. Voice of experience here!

So, go and find some segments to paint so all of these exciting things can happen to you too!

How far back will you be able to identity a segment to a specific ancestor?  How about a triangulated segment? An X segment?

Have fun!!! Don’t forget to eat!

PS – If you’d like to learn more about Phasing, Triangulation or hear my keynote speech, consider signing up for the Virtual DNA Conference June 21-24. I’ll be presenting on both of those topics. You can sign in anytime for the next year to listen to the sessions, not just during the conference days. The keynote will be recorded and available afterwards as well.

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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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Family Tree DNA Names 100,000 New Y DNA SNPs

Recently, Family Tree DNA named 100,000 new SNPs on the Y DNA haplotree, bringing their total to over 153,000. Given that Family Tree DNA does the majority of the Y DNA NGS “full sequence” testing in the industry with their Big Y product, it’s not at all surprising that they have discovered these new SNPs, currently labeled as “Unnamed Variants” on customers’ Big Y Results pages.

The surprising part was twofold:

Family Tree DNA single-handedly propelled science forward with the introduction of the Big Y test. They likely have performed more NGS Y chromosome tests than the entire rest of the world combined. Assuredly, they have commercially.

Originally, in the early 2000s, a new SNP wasn’t named until there were three independent instances of discovery. That pre-NGS “rule” didn’t take into account three men from the same family line because very few men had been tested at that point in time, let alone multiple men from the same family. This type of testing was originally only done in an academic environment. A caveat was put into place by Family Tree DNA when they started discovering SNPs that the 3 individuals had to be from separate family lines and the SNP in question had to be verified by Sanger sequencing before being considered for name assignment and tree placement. At that time, they were pushing the scientific envelope.

In recent years, that criteria changed to two individuals. With this new development, the SNP is being named with one reliable occurrence, BUT, the SNP still is not being placed on the tree without two high quality occurrences.

Naming the SNPs early while awaiting that second occurrence allows discussion about the validity of that particular finding. Family Tree DNA was not the first to move to this practice.

Some time ago, two other firms began analyzing the BAM files produced by Family Tree DNA for an additional analysis fee. Those firms began naming SNPs before three occurrences had been documented, a practice which has been well-accepted by the genetic genealogy community. Everyone seems to be anxious to see their SNP(s) named and placed on the tree, although there is little consensus or standardization about the criteria to place a SNP on the tree or the line between high, medium and low quality SNP read results.

The definition of a new haplogroup, meaning a high quality named SNP, is a new branch in the Y tree. Every new SNP mutation has the potential to be carried for many generations – or to go extinct in one or two.

As the industry has matured, SNP naming procedures have evolved too.

How SNP Names Are Assigned

The lab or entity that discovers a SNP gets to name the SNP. That means that their abbreviation is appended to the beginning of the SNP number, thereby in essence crediting that entity for the discovery. Clearly more conservative namers can’t append their initials to nearly as many SNPs as aggressive namers.

Here’s a list of the naming entities, maintained by ISOGG.

In 2006, the first year that ISOGG compiled a SNP tree, the number of Y DNA haplogroups was 460, including singletons, not tens of thousands. No one would ever have believed this SNP tsunami would happen, let alone in such a short time.

Naming SNPs

Family Tree DNA waiting to name SNPs until 3 were discovered in unrelated family lines, and requiring confirmation by Sanger sequencing allowed the analysis entities to “discover” and name the SNP with their own preceding prefix by implementing less stringent naming criteria. It also increased the possibility of dual naming, a phenomenon that occurs when multiple entities name the same SNP about the same time.

Some people who maintain trees list all of these equivalent SNPs that were named for the exact same mutation, at the same time. Family Tree DNA does not. If the same SNP is named more than once, Family Tree DNA selects one to name the tree branch – in the example below, ZP58. Checking YBrowse, this SNP was also named FGC11161 and ZP56.2.

However, you can see, that SNP ZP58 has several other SNPs keeping it company on the same branch, at least for now.

The FGC SNPs above are only assigned as branch equivalents of ZP58 until a discovery is made that will further divide this branch into two or more branches. That’s how the tree is built.

Sometimes defining a unique SNP is not as straightforward as one would think, especially not utilizing scan technology.

While YFull doesn’t do testing, Full Genomes Corporation does. All of the YFull named SNPs are a result of interpreting BAM files of individuals who have tested elsewhere and naming SNPs that the testing labs didn’t name.

Today, YBrowse, also maintained by ISOGG in conjunction with Thomas Krahn shows the following three organizations with the highest named SNP totals:

  • Family Tree DNA – BY and L prefixes, (L from before the Big Y test) – 153,902
  • YFull – Y prefix – 133,571 (plus 6447 YP SNPs submitted by citizen scientists for verification)
  • Full Genomes Corporation – FGC prefix – 81,363

Just because a SNP is named doesn’t mean that it has been placed on the haplotree. Today, Family Tree DNA has just over 14,100 branches on their tree, with a total of 102,104 SNPs (from all naming sources) placed on their tree. That number increases daily as the following placement criteria is met:

  • Read quality confirmed by the lab
  • Two or more instances of the SNP

SNPs Applied to Family History

All SNPs discovered through the Big Y process and named by Family Tree DNA begin with BY, so my Estes lineage is BY490. This mutation (SNP) occurred since Robert Eastye born in 1555, because one of his son’s descendants carries only BY482 and the descendants of another son carry BY490.

In the pedigree above, kit 166011, to the far right is BY482 and the rest are all BY490, which is one mutation below BY482 on the haplotree.

This means of course that the mutation BY490, occurred someplace between the common ancestor of all of these men, Robert Eastye born in 1555, and Abraham Estes born in 1647. All of Abraham’s descendants carry BY490 along with BY482, but kit 166011 does not. Therefore, we know within two generations of when BY490 occurred. Furthermore, if someone descended from one of Abraham’s brothers (Robert, Silvester, Thomas, Richard, Nicholas or John,) represented on this chart by Richard, we could tell from that result if the mutation occurred between Robert and Silvester, or between Silvester and Abraham.

Unnamed Variants Versus Named SNPs

As it turns out, reserving a location for the Unnamed Variants in the SNP tree is much like making a dinner reservation. It’s yours to claim, assuming everyone shows up.

In the case of Unnamed Variants, Family Tree DNA reserved the SNP name and the SNP will be placed on the tree as soon as a second occurrence is discovered and the SNP is entirely vetted for quality and accuracy. Palindromic and high repeat regions were excluded unless manually verified.

While this article isn’t going to delve into how to determine read quality, every SNP placed on the tree at Family Tree DNA is individually evaluated to assure that they are not being placed erroneously or that a “mutation” isn’t really a misalignment or read issue.

Currently, Family Tree DNA is working their way through the entire haplotree, placing SNPs in the correct location. As you can see, they have more than 100,000 to go and more SNPs are discovered every day.

In the case of the Estes men, you can see their branch placement in the much larger tree.

As we learn more, sometimes branch placements move.

Is Your Unnamed Variant on the List?

ISOGG maintains an index of BY SNPs. BY of course equates to Big Y.

Before using the index, you first need to sign on to your Family Tree DNA account and look at your Unnamed Variants on your Big Y personal page.

If you don’t have any Unnamed Variants, that means all of your Unnamed Variants have already been named. Congratulations!

If you do have Unnamed Variants, click on the position number to take a look on the browser.

This unnamed variant result is clearly a valid read, with almost every forward and reverse read showing the same mutation, all high-quality reads and no “messy” areas nearby that might suggest an alignment issue. You can read more about how to work with your Big Y results in the article, Working With the New Big Y Results (hg38).

Next, go to the ISOGG BY Index page and enter the position number of the variant in the search box – in this case, 13311600.

In this case, 13311600 is not included in the BY Index because YFull already beat Family Tree DNA to the punch and named this SNP.

How do I know that? Because after seeing that there was no result for 13311600 on the ISOGG page, I checked YBrowse.

You can utilize YBrowse to see if an Unnamed Variant has previously been named. You can see the SNP name, Y93760, directly above the left side of the red bar below. The “Y” of course tells you that YFull was the naming entity. (Note that you can click on any image to enlarge.)

YBrowse is more fussy and complex to use than doing the simple ISOGG search. You only need to utilize YBrowse if your Unnamed Variant isn’t listed in the BY ISOGG search tool.

To use YBrowse successfully, you must enter the search in the format of “chrY:13311600..1311600” without the quotation marks and where the number is the variant location, and then click search.

The next Unnamed Variant, 14070341, is included in the ISOGG search list, so no need to utilize YBrowse for this one.

To see the new name that this SNP will be awarded when/if it’s placed on the tree, click on the link “BY SNPs 100K.” You’ll see the page, below.

Then, scroll down or use your browser search to find the variant location.

There we go – this variant will be named BY105782 as soon as Family Tree DNA places it on the tree! I’ll be watching!

Where will it be located on the tree, and will it be the new Estes terminal SNP, meaning the SNP that defines our haplogroup? I can’t wait to find out! It’s so much fun to be a part of scientific discovery.

If you’re a male and haven’t taken the Big Y test, now’s a great timeClick here to order. You can play a role in scientific discovery too. Does your Y DNA carry undiscovered SNPs?

A big thank you to Family Tree DNA for making resources available to answer questions about their new SNPs and naming processes.

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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