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?

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.

_____________________________________________________________________

Standard Disclosure

This standard disclosure appears at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate.  If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase.  Clicking through the link does not affect the price you pay.  This affiliate relationship helps to keep this publication, with more than 900 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc.  In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received.  In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product.  I only recommend products that I use myself and bring value to the genetic genealogy community.  If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA, or one of the affiliate links below:

Affiliate links are limited to:

Concepts – DNA Recombination and Crossovers

What is a crossover anyway, and why do I, as a genetic genealogist, care?

A crossover on a chromosome is where the chromosome is cut and the DNA from two different ancestors is spliced together during meiosis as the DNA of the offspring is created when half of the DNA of the two parents combines.

Identifying crossover locations, and who the DNA that we received came from is the first step in identifying the ancestor further back in our tree that contributed that segment of DNA to us.

Crossovers are easier to see than conceptualize.

Viewing Crossovers

The crossover is the location on each chromosome where the orange and black DNA butt up against each other – like a splice or seam.

In this example, utilizing the Family Tree DNA chromosome browser, the DNA of a grandchild is compared to the DNA of a grandparent. The grandchild received exactly 50 percent of her father’s DNA, but only the average of 25% of the DNA of each of her 4 grandparents. Comparing this child’s DNA to one grandmother shows that she inherited about half of this grandmother’s DNA – the other half belonging to the spousal grandfather.

  • The orange segments above show the locations where the grandchild matches the grandmother.
  • The black sections (with the exception of the very tips of the chromosomes) show locations where the grandchild does not match the grandmother, so by definition, the grandchild must match the grandfather in those black locations (except chromosome tips).
  • The crossover location is the dividing line between the orange and black. Please note that the ends of chromosomes are notoriously difficult and inconsistent, so I tend to ignore what appear to be crossovers at the tips of chromosomes unless I can prove one way or the other. Of the 22 chromosomes, 16 have at least one black tip. In some cases, like chromosome 16, you can’t tell since the entire chromosome is black.
  • Ignore the grey areas – those regions are untested because they are SNP poor.

We know that the grandchild has her grandmother’s entire X chromosome, because the parent is a male who only inherited an X chromosome from his mother, so that’s all he had to give his daughter. The tips of the X chromosome are black, showing that the area is not matching the mother, so that region is unstable and not reported.

It’s also interesting to note that in 6 cases, other than the X chromosome, the entire chromosome is passed intact from grandparent to grandchild; chromosomes 4, 11, 16, 20, 21 and 22.

Twenty-six crossovers occurred between mother and son, at 5cM.  This was determined by comparing the DNA of mother to son in order to ascertain the actual beginning and end of the chromosome matching region, which tells me whether the black tips are or are not crossovers by comparing the grandchild’s DNA to the grandmother.

For more about this, you might want to read Concepts – Segment Survival – Three and Four Generation Phasing.

Before going on, let’s look at what a match between a parent and child looks like, and why.

Parent/Child Match

If you’re wondering why I showed a match between a grandchild and a grandparent, above, instead of showing a match between a child and a parent, the chromosome browser below provides the answer.

It’s a solid orange mass for each chromosome indicating that the child matches the parent at every location.

How can this be if the child only inherits half of the parent’s DNA?

Remember – the parent has two chromosomes that mix to give the child one chromosome.  When comparing the child to the parent, the child’s single chromosome inherited from the parent matches one of the parent’s two chromosomes at every address location – so it shows as a complete match to the parent even though the child is only matching one of the parent’s two of chromosome locations.  This isn’t a bug and it’s just how chromosome browsers work. In other words, the “other ” chromosome that your parents carry is the one you don’t match.

The diagram below shows the mother’s two copies of chromosome 1 she inherited from her father and mother and which section she gave to her child.

You can see that the mother’s father’s chromosome is blue in this illustration, and the mother’s mother’s chromosome is pink.  The crossover points in the child are between part B and C, and between part C and D.  You can clearly see that the child, when compared to the mother, does in fact match the mother in all locations, or parts, 3 blue and 1 pink, even though the source of the matching DNA is from two different parents.

This example shows the child compared to both parents, so you can see that the child does in fact match both parents on every single location.

This is exactly why two different matches may match us on the same location, but may not match each other because they are from different sides of our family – one from Mom’s side and one from Dad’s.

You can read more about this in the article, One Chromosome, Two Sides, No Zipper – ICW and the Matrix.

The only way to tell which “sides” or pieces of the parent’s DNA that the child inherited is to compare to other people who descend from the same line as one of the parents.  In essence, you can compare the child to the grandparents to identify the locations that the child received from each of the 4 grandparents – and by genetic subtraction, which segments were NOT inherited from each grandparent as well, if one grandparent happens to be missing.

In our Parental Chromosome pink and blue diagram illustration above, the child did NOT inherit the pink parts A, B and D, and did not inherit the blue part C – but did inherit something from the parent at every single location. They also didn’t inherit an equal amount of their grandparents pink and blue DNA. If they inherited the pink part, then they didn’t inherit the blue part, and vice versa for that particular location.

The parent to child chromosome browser view also shows us that the very tip ends of the chromosomes are not included in the matching reports – because we know that the child MUST match the parent on one of their two chromosomes, end to end. The download or chart view provides us with the exact locations.

This brings us to the question of whether crossovers occur equally between males and female children.  We already know that the X chromosome has a distinctive inheritance pattern – meaning that males only inherit an X from their mothers.  A father and son will NEVER match on the X chromosome.  You can read more about X chromosome inheritance patterns in the article, X Marks the Spot.

Crossovers Differ Between Males and Females

In the paper Genetic Analysis of Variation in Human Meiotic Recombination by Chowdhury, et al, we learn that males and females experience a different average number of crossovers.

The authors say the following:

The number of recombination events per meiosis varies extensively among individuals. This recombination phenotype differs between female and male, and also among individuals of each gender.

Notably, we found different sequence variants associated with female and male recombination phenotypes, suggesting that they are regulated by different genes.

Meiotic recombination is essential for the formation of human gametes and is a key process that generates genetic diversity. Given its importance, we would expect the number and location of exchanges to be tightly regulated. However, studies show significant gender and inter-individual variation in genome-wide recombination rates. The genetic basis for this variation is poorly understood.

The Chowdhury paper provides the following graphs. These graphs show the average number of recombinations, or crossovers, per meiosis for each of two different studies, the AGRE and the FHS study, discussed in the paper.

The bottom line of this paper, for genetic genealogists, is that males average about 27 crossovers per child and females average about 42, with the AGRE study families reporting 41.1 and the FHS study families reporting 42.8.

I have been collaborating with statistician, Philip Gammon, and he points out the following:

Male, 22 chromosomes plus the average of 27 crossovers = an average of 49 segments of his parent’s DNA that he will pass on to his children. Roughly half will be from each of his parents. Not exactly half. If there are an odd number of crossovers on a chromosome it will contain an even number of segments and half will be from each parent. But if there are an even number of crossovers (0, 2, 4, 6 etc.) there will be an odd number of segments on the chromosome, one more from one parent than the other.

The average size of segments will be approximately:

  • Males, 22 + 27 = 49 segments at an average size of 3400 / 49 = 69 cM
  • Females, 22 + 42 = 64 segments at an average size of 3400 / 64 = 53 cM

This means that cumulatively, over time, in a line of entirely females, versus a line of entirely males, you’re going to see bigger chunks of DNA preserved (and lost) in males versus females, because the DNA divides fewer times. Bigger chunks of DNA mean better matching more generations back in time. When males do have a match, it would be likely to be on a larger segment.

The article, First Cousin Match Simulations speaks to this as well.

Practically Speaking

What does this mean, practically speaking, to genetic genealogists?

Few lines actually descend from all males or all females. Most of our connections to distant ancestors are through mixtures of male and female ancestors, so this variation in crossover rates really doesn’t affect us much – at least not on the average.

It’s difficult to discern why we match some cousins and we don’t match others. In some cases, rather than random recombination being a factor, the actual crossover rate may be at play. However, since we only know who we do match, and not who tested and we don’t match, it’s difficult to even speculate as to how recombination affected or affects our matches. And truthfully, for the application of genetic genealogy, we really don’t care – we (generally) only care who we do match – unless we don’t match anyone (or a second cousin or closer) in a particular line, especially a relatively close line – and that’s a horse of an entirely different color.

To me, the burning question to be answered, which still has not been unraveled, is why a difference in recombination rates exists between males and females. What processes are in play here that we don’t understand? What else might this not-yet-understood phenomenon affect?

Until we figure those things out, I note whether or not my match occurred through primarily men or women, and simply add that information into the other data that I use to determine match quality and possible distance.  In other words, information that informs me as to how close and reasonable a match is likely to be includes the following information:

  • Total amount of shared DNA
  • Largest segment size
  • Number of matching segments
  • Number of SNPs in matching segment
  • Shared matches
  • X chromosome
  • mtDNA or Y DNA match
  • Trees – presence, absence, accuracy, depth and completeness
  • Primarily male or female individuals in path to common ancestor
  • Who else they match, particularly known close relatives
  • Does triangulation occur

It would be very interesting to see how the instances of matches to a certain specific cousin level – say 3rd cousins (for example), fare differently in terms of the average amount of shared DNA, the largest segment size and the number of segments in people descended from entirely female and entirely male lines. Blaine Bettinger, are you listening? This would be a wonderful study for the Shared cM Project which measures actual data.

Isn’t the science of genetics absolutely fascinating???!!!

______________________________________________________________________

Standard Disclosure

This standard disclosure will now appear at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 850 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA.