The Family Tree Guide to DNA Testing and Genetic Genealogy

7

X-Chromosomal (X-DNA) Testing

What does it mean to share X-chromosomal DNA (X-DNA) with a match? One of the most powerful advantages of Y-chromosomal DNA (Y-DNA) and mitochondrial DNA (mtDNA) is that you always know exactly what ancestor in the family tree provided that piece of DNA. In contrast, with autosomal DNA (atDNA), any of your ancestors could have provided a segment of DNA. X-DNA falls between these two extremes; while there are many ancestors who could have contributed to your X-DNA, they make up only a small subset of your entire genealogical family tree. Thus, sharing X-DNA with a match means you only have to search that subset of your tree for the common ancestor. In this chapter, we’ll learn about X-DNA and how it can be utilized to explore common ancestry with your genetic matches.

The X Chromosome

The X chromosome (image A) is one of the twenty-three pairs of chromosomes found in the nucleus of the cell, and is one of the two sex chromosomes, the other being the Y chromosome (which, as you’ll recall, is found only in males). Unlike Y-DNA, both men and women have X-DNA. Women have two X chromosomes, one inherited unchanged from their father and one inherited from their mother. Men have just one X chromosome that they inherited from their mother.

The X chromosome, together with the Y chromosome, makes up the sex chromosomes, which can provide valuable information for genealogists. Note that only one copy of each of autosomal chromosome is shown above; in reality, each person has two copies of each of the twenty-two autosomes. Courtesy Darryl Leja, National Human Genome Research Institute.

The X chromosome is a relatively large chromosome of approximately 150 million base pairs, and contains about two thousand of the estimated twenty to twenty-five thousand genes found throughout the entire human genome.

The Unique Inheritance of X-DNA

Like both mtDNA and Y-DNA, X-DNA has a unique inheritance pattern that makes it valuable for genetic genealogy testing. A mother always passes down an X chromosome to all of her children, either male or female. In contrast, a father will only pass down his X chromosome to his female children. As a result, a father and son always break the transmission of X-DNA in a family tree.

A woman has two X chromosomes: one copy she received from her mother and one copy she received from her father. If a woman has children, she will pass down an X chromosome, although this inheritance can results in a few different scenarios based on random events during an egg cell’s creation. Sometimes a mother will pass down a full X chromosome to her child completely unchanged from the copy she received from either her mother or her father. In this scenario, the child will share X-DNA with only one maternal grandparent. Other times, the mother will jumble or recombine her two copies of the X chromosome, and the copy she passes down to her son or daughter will be a mixture of the two. In this scenario, the child will share at least some X-DNA with both maternal grandparents. These scenarios are equally possible.

A father, however, always passes down the X chromosome without recombination. Although the tips of the Y chromosome and the X chromosome will sometimes recombine, these regions of the Y chromosome are not utilized for genetic matching. Accordingly, the child will share X-DNA only with the paternal grandmother. A child will only share X-DNA with a paternal grandfather indirectly, through other lines of the family tree.

Image B shows the possible sources of X-DNA within a family tree for a woman. This tree traces back the possible path of a female X-DNA through seven generations, or to fifth great-grandparents. At that generation, an individual has 128 ancestors (or fewer, if there are recent cousin marriages). Of those 128 ancestors, a woman will have thirty-four potential contributors (thirteen males and twenty-one females) to her two X chromosomes. Since this is a chart for a woman who inherited X-DNA from her mother and father, there are possible sources of X-DNA on both sides of her family tree: The male possible sources of X-DNA are highlighted in blue, and the female possible sources of X-DNA are highlighted in pink.

Like mtDNA and Y-DNA, X-DNA has a unique inheritance pattern that can help test-takers identify from which ancestors they received genetic information. Women receive X-DNA from both their maternal and paternal lines. Possible X-DNA ancestors are in blue (for male ancestors) and pink (for female ancestors).

Note that although this chart shows the possible sources of X-DNA within a family tree for a woman, the actual sources of the woman’s X-DNA will be a small subset of the highlighted cells. For example, if the woman inherited her maternal grandfather’s X chromosome from her mother, none of her maternal grandmother’s family provided X-DNA.

Image C shows the possible sources of X-DNA within a family tree for a man. The male possible sources of X-DNA are highlighted in blue, and the female possible sources of X-DNA are highlighted in pink. Since this is a chart for a man who inherited his X chromosome entirely from his mother, only his mother’s ancestors could have provided X-DNA. For example, of the 128 ancestors at the seventh generation, only twenty-one of them (eight males and thirteen females) can potentially provide X-DNA to the man. As with the previous chart, the actual sources of the man’s X-DNA will be a small subset of the highlighted cells.

Unlike women, men can only receive X-DNA from their maternal lines, as men inherit their single X chromosome from their mothers. Possible X-DNA ancestors are in blue (for male ancestors) and pink (for female ancestors).

As with any isolated autosomal chromosome, the fact that a woman can pass down the X chromosome with or without recombination means that X-DNA sharing with the previous generations can take many different forms. Image D demonstrates X-DNA inheritance through three generations of a family in which the X chromosome either did or did not recombine before it was passed down to the next generation.

Recombination (in addition to X-DNA inheritance patterns) can drastically affect which X-DNA is inherited through generations. Solid colors represent X-DNA that has not been recombined and so was passed down to the next generation unchanged. Note that males have only one X chromosome while females have two X’s.

Following the X-DNA through this chart to the four grandchildren raises several interesting observations regarding X-DNA inheritance:

1.     The paternal grandfather, David, has no daughters in this chart, and thus his X-DNA (indicated in blue) did not pass down to anyone else in this three-generation tree.

2.    The maternal grandfather, Nathan, has just a single copy of the X chromosome, and thus he passed down that single copy (indicated in red) completely unchanged to his daughter Susan.

3.    The paternal grandmother, Justine, passed down one copy of her X chromosomes without recombination (indicated in green). Benji, therefore, received a full chromosome from either his maternal grandfather or his maternal grandmother (i.e., from one of Justine’s parents).

4.    The maternal grandmother, Cara, recombined her two copies of the X chromosome when she passed a copy down to her daughter, Susan. Susan, therefore, has X-DNA from three of her four grandparents (Nathan’s mother and Cara’s two parents).

5.    Benji has just a single X chromosome, and thus he passed down that single copy completely unchanged to his two daughters, Ann and Donna.

6.    Siblings Philip and Ann each received an X chromosome from their mother without recombination, while siblings Rich and Donna each received a recombined X chromosome from their mother.

7.     Siblings Ann and Donna share a full X chromosome in common. This will always be the case for (full) sisters since they always receive the same X chromosome from their father.

8.    Philip shares X-DNA with Rich (the blue and purple in the “bottom half” of the chromosome) and Donna (the blue at the top), but none with Ann. It is not uncommon for siblings (who aren’t full sisters) to share no X-DNA in common.

How the Test Works

Currently, X-DNA is tested as part of an atDNA test, not as its own test. The test includes between approximately seventeen thousand to twenty thousand single nucleotide polymorphisms (SNPs) on the X chromosome, which will be included in the raw data.

The three main testing companies each treat X-DNA a little differently. Although AncestryDNA <dna.ancestry.com> tests the X chromosome, it does not use X-DNA when comparing individuals to the database. As a result, you will not have any matches at AncestryDNA that only share X-DNA.

At 23andMe <www.23andme.com>, the test-taker’s X-DNA is compared to that of other people in the database, meaning that some matches at 23andMe will only share X-DNA. Due to the fact that men have one X chromosome and women have two X chromosomes, the thresholds at 23andMe for comparing men and women will vary. The thresholds for X-DNA can be found in the following table.

View text version of this table

In the table, “Half-IBD,” or “half identical by descent,” for X-DNA comparisons means that two women share DNA on just one copy of their X chromosomes. Likewise, “Full-IBD,” or “full(y) identical by descent,” means that the two women share DNA at the same location on both copies of their X chromosomes. The matching threshold for Full-IBD is significantly lower than for Half-IBD. Since only females have two X chromosomes, only females can have half-IBD or full-IBD segments.

At Family Tree DNA, X-DNA matching is reported only if the matches also share atDNA above the matching threshold. Accordingly, you will not have matches at Family Tree DNA that only share X-DNA. As shown in the following table, the matching threshold for X-DNA is significantly lower than the matching threshold for atDNA.

View text version of this table

Both Family DNA and 23andMe will show X-DNA matching in their respective chromosome browsers. Image E is a screenshot of the Family Tree DNA chromosome browser that compares the X chromosome of a woman to those of three of her siblings: a sister (orange), a brother (blue), and another brother (green). As the viewer reports, the test-taker shares variable amounts of her X-DNA with each of her siblings.

Family Tree DNA has a chromosome browser tool that compares the test-taker’s X-DNA with that of other test-taker’s. In this case, the tool highlights the X-DNA that the test-takers shared with three other test-taker’s: her sister (orange), her brother (blue), and another brother (green).

Limitations of X-DNA Testing and Matching

Genetic genealogists have found that X-DNA matching is not perfect, and can be problematic for several reasons.

By its inheritance pattern, X-DNA can make it difficult to distinguish genetic relationships between two people or predict how much X-DNA two relatives will share. For example, as discussed earlier, the test-taker should share an entire X chromosome with her sister (indicated in orange) but, due to several limitations discussed later, doesn’t share certain pieces of X-DNA with her.

Image F further demonstrates this particular limitation of X-DNA. The Family Tree DNA chromosome browser at the bottom compares the X chromosome of a great-grandmother, Alberta, to that of her two male great-grandchildren, Donald and Damian (orange and blue, respectively). Alberta passed down an X chromosome to her son, Bert, and he passed it down—unchanged—to his daughter, Catherine. Catherine then passed down an X chromosome to each of her sons, Donald and Damian. Due to the randomness of recombination, Donald and Damian could have received some, all, or none of Alberta’s X-DNA.

The chromosome browser displays the segments of Alberta’s X-DNA that are shared with the X-DNA of her two great-grandsons, Donald (orange) and Damian (blue).

The Family Tree DNA chromosome browser can shed some light on this, as it indicates both Donald and Damian received some of Alberta’s X-DNA, with one (in blue) receiving significantly more than the other (in orange). Note that because Donald and Damian could have only inherited X-DNA from the maternal grandfather (Bert) or the maternal grandmother (Catherine’s mother), the regions they don’t share in this chromosome browser view should match X-DNA from their maternal grandmother.

In addition, it is believed that the density of the SNPs tested on the X chromosome is much lower than on comparable chromosomes. The X chromosome is a relatively large chromosome of approximately 150 million base pairs, comparable to chromosome 7 (159 million base pairs). However, the number of chromosome-7 SNPs tested by the three testing companies is nearly double the number of SNPs tested on the X chromosome. As a result, a segment of X-DNA may have relatively few tested SNPs.

With a lower SNP density, there is a greater chance for a segment of DNA to appear like it is a shared segment when in fact it is not a true matching segment. For example, image G compares the two males’ X-DNA. If the highlighted SNPs were the only SNPs tested, the two strands of X-DNA would appear to match. However, if the SNP density were increased, results would immediately show that this is not a matching segment. Note this potential hazard is more likely to affect smaller segments of DNA samples, as larger segmented samples will have more SNPs tested.

In this example, all the SNPs that an X-DNA test sampled (highlighted in yellow) happened to match. As a result, the X-DNA test would report these two individuals’ strands of DNA as matches even though they contain several nonmatching SNPs.

As a result of the current limitations of X-DNA, test-takers should only analyze sufficiently long X-DNA segments. A commonly recommended threshold, for example, is 10 cMs, although some genetic genealogists set even higher thresholds at 15 or 20 cMs. While X-DNA matches absolutely share smaller segments, a genetic genealogist analyzing these small segments does not have enough information to decipher between a true match and a false positive match.

Another limitation of X-DNA matching is the low thresholds used to compare two people’s X-DNA. For example, both 23andMe and Family Tree DNA use X-DNA thresholds that are lower than the thresholds for atDNA. At 23andMe, for example, the threshold for comparing the X-DNA of two males is just 1 cM and two hundred SNPs. At Family Tree DNA, the threshold for comparing the X-DNA of any two individuals is just 1 cM and five hundred SNPs. Many genetic genealogists have found this low threshold leads to X-DNA matching that does not appear to be true matching.

Applying X-DNA Test Results in Genealogical Research

Despite its limitations, X-DNA matching can be very useful for genealogy, especially when combined with other types of DNA. For example, sharing both X-DNA and atDNA with a cousin suggests which lines of the genealogical family tree to look for a common ancestor.

However, sharing X-DNA and atDNA with a match suggests—but does not prove—that the atDNA common ancestor is also an X-DNA ancestor. This rule seems counterintuitive at first. After all, if we share both X-DNA and atDNA with a match, doesn’t that mean our common ancestor is on one of the X-DNA lines based on the charts we saw earlier in the chapter? Unfortunately, DNA is never that easy! Instead, even though we share atDNA and X-DNA with a genetic match, those segments of DNA could have come from different ancestors. Often, the matching atDNA and X-DNA will come from the same common ancestor. However, the genetic matches will share at least two different common ancestors on different lines just as often, with one line providing the matching atDNA and the other line providing the matching X-DNA (image H).

While genetic genealogists might assume they inherited their atDNA and X-DNA from the same ancestor, there are several scenarios (such as the one above) in which they have separate atDNA and X-DNA sources.

In addition to multiple ancestors, a genetic match might only share a very small segment of X-DNA that turns out to be a false segment. In this scenario, the genetic matches may spend a considerable amount of time looking for a common X-DNA ancestor who doesn’t exist. Deciphering between these possibilities will require an in-depth analysis of both test-taker’s family trees, and careful consideration of the size of the X-DNA segments involved.

In addition to the fact that an X-DNA match does not guarantee an atDNA match, genealogists should bear in mind that a lack of X-DNA sharing is almost never informative about a particular relationship. Failing to share X-DNA with another person is almost never evidence of the existence or non-existence of a relationship. There are only a few rare exceptions when two people must share X-DNA: a mother and her children (both male and female), a father and his daughters (who will be full matches with the paternal grandmother), and “full” sisters who have the same father.

Other than these relationships, it is possible that two people who are either closely or distantly related may or may not share X-DNA. For example, while sisters who have the same father will always share a full chromosome, siblings who don’t share a father may not share X-DNA. Similarly, brothers and sisters may or may not share X-DNA with their mother. Of course, not sharing X-DNA does not mean that siblings are not related like they thought they were. Instead, they may have received entirely different X-DNA from their mother.

Keeping in mind the limitations and rules outlined in this section, genealogists can analyze an X-DNA match to find the common ancestor or ancestors. X-DNA testing (and analyzing X-DNA and atDNA results with X-DNA inheritance rules in mind) can help shed light on who two individuals’ common ancestor might be.

Let’s walk through an example in action. In image I, two people share a segment of DNA on the X chromosome (indicated in orange) of approximately 25.28 cMs. Based on the results of an atDNA test (image J), the two individuals also share several segments of atDNA, including segments on chromosome 10 (10 cMs), chromosome 12 (36.94 cMs), and chromosome 16 (16.26 cMs). Family Tree DNA predicts these two, Julia and April, to be second to fourth cousins. And when Julia and April compare family trees, they discover a potential ancestor in common (a man named Hiram Alden) who would make them fourth cousins. Hiram Alden is an ancestor of Julia’s paternal grandfather and an ancestor of April’s maternal grandmother.

The results from an X-DNA test, such as these for Julia and April, can (and should) be used in conjunction with other pieces of genealogical information.

Combine atDNA results, such as these for Julia and April, with traditional family trees and the results of an X-DNA test to draw conclusions about the test-takers’ relationships to each other and to a common ancestor. (Note: Gray indicates areas not covered by the test.)

So is Hiram Alden the common ancestor? X-DNA inheritance patterns tell us no. As shown in the X-DNA inheritance charts earlier in this chapter, Julia could not inherit any X-DNA from her paternal grandfather. Accordingly, while Julia and April may have inherited some segments from Hiram, he cannot be the source of that shared X-DNA. Julia and April must share another ancestor somewhere along their X-DNA lines.

In the next example, shown in image K, Darcy was adopted, and her descendants have no clues about her biological heritage. Darcy and her children are deceased, but two of her grandchildren—Carol and Jason—are living and have both taken an atDNA test that includes X-DNA. When they compare their test results, they see that they share three large segments on the X chromosome (21.65 cMs, 26.83 cMs, and 18.57 cMs). Carol and Jason are curious about where this X-DNA came from and how they can use it to learn about their grandmother’s ancestry.

Carol and Jason share the X-DNA highlighted in orange on the chromosome browser. Based on the large amounts of shared X-DNA, they can safely assume they both inherited their X-DNA from their grandmother, Darcy. Carol and Jason can find more of Darcy’s relatives and work backwards to find her ancestors by finding individuals with similar X-DNA to theirs.

While X-DNA can’t provide any definitive answers in this case, it can give Carol and Jason some new avenues of research. The large amounts of shared DNA (indicated in orange) suggest the two share a recent common X-DNA ancestor, and based on this info and their family tree, Carol and Jason likely obtained their shared X-DNA from their grandmother. Carol and Jason could now look for other people who share these segments of X-DNA to find Darcy’s other relatives.

CORE CONCEPTS: X-CHROMOSOMAL (X-DNA) TESTING

The X chromosome is one of the two sex chromosomes, of which men have one copy (from their mother) and women have two copies (one from their mother and one from their father).

X-DNA is inherited from a small subset of ancestors, meaning that the possible pool of ancestors with whom a test-taker shares an X-DNA cousin is smaller than the pool for the other chromosomes.

X-DNA testing is typically done by SNP testing and only as part of an atDNA test (rather than as a standalone test).

The results of an X-DNA test can be used to fish for genetic cousins.

Due to the low SNP density of current X-DNA tests, as well as the low thresholds utilized by the companies, X-DNA matches must be very carefully scrutinized, and only large X-DNA matching should be pursued.

Sharing X-DNA and atDNA with a match suggests that the atDNA common ancestor is an X-DNA ancestor, but it is also possible that the atDNA and the X-DNA came from different ancestors.

Lack of shared X-DNA is rarely informative about a particular relationship, since there are only a few relationships in which relatives must share X-DNA.