The human genome is composed of 23 pairs of chromosomes. Each chromosome comes in a pair with one-half of the pair coming from your mother while the other comes from your father. 22 of these chromosome pairs are autosomal, while the 23rd is the sex chromosome - it is the one that determines a person's biological sex. For the sex chromosome, mothers pass down an X chromosome to both their sons and daughters, while fathers pass down an X chromosome to their daughters and a Y chromosome to their sons. This means that women have two X chromosomes while men have only one. While the X chromosome is included in our autosomal DNA test, Family Finder, it is inherited uniquely and can provide useful insights.
X-Chromosome Inheritance
In autosomal DNA, each chromosome passed down to a child is a combination of the two copies of each parent. Each parent, in turn, received one copy from each of their parents, which was a combination of their parents, and so on. These copies get recombined in a random way to form the copy they pass down to their child. In other words, one set of your chromosomes is a mixture of your maternal grandmother and grandfather, while the other set is a mixture of your paternal grandmother and grandfather.
These mixtures are random, so over the generations, you might end up with more DNA from one particular ancestor than another. For example, you may get more DNA from your maternal grandmother than your maternal grandfather. An analogy would be that a deck of cards is shuffled each time. Some cards survive many shuffles (generations) while others get shuffled out quickly.
The same thing happens with the X chromosome, but only in the maternal X chromosome. Men only have the one X chromosome that they received from their mother, so they pass this X down to their daughters as a complete, unmixed copy. Fathers do not pass down this X chromosome to their sons. Instead, they pass down the complete, unchanged Y chromosome they got from their father.
Mothers have two copies of her X chromosome, one from each parent, and those two get combined into the new X chromosome she passes down to each child
What this means for genealogy
This unique method of transfer means paternal and maternal X inheritance patterns are different, so let’s look at each side individually.
Maternal Side
The single X chromosome passed down to you from your father is the same single X chromosome passed down to him from his mother, your paternal grandmother. This X chromosome was, in turn, a combination of her mother's and father’s, your paternal great-grandmother's and great-grandfather’s. This means that with every successive generation, the field of possibilities is cut in half, as each male ancestor’s X line is cut in half. The following chart helps explain this concept. If you are female, an X match can connect you through any of the highlighted ancestral lines.
The same thing applies if your X match is female. This means you could connect to her on any of these lines on her tree.
Paternal side
For the paternal side, it is essentially the same chart, but with the paternal side entirely removed, because the father did not pass down an X chromosome at all.
If your match is male, the same holds true for his lines. He must connect to you on one of these lines in his tree.
X Matching
If a person is an X match to you, you can reference the chart above to see which ancestral line that person may connect to you. You can filter your matches to see only those that are X matches to you to help refine your match list and find clues.
Because the X chromosome is not recombined in the same way that the other chromosomes are, it is counted differently for matching. It undergoes fewer recombination events each generation, so a small block of centimorgans (cM) on one of the other chromosomes is counted as the same as a larger block of cM on the X chromosome. This can be a confusing concept, so let’s explain:
Think of it as a card shuffle: If you take a brand new deck of cards, every time you shuffle it it randomizes the cards more and more. A single shuffle will still leave you with a large number of consecutive cards, or a block. A second shuffle will make these blocks smaller, and so on.
The X chromosome passed from the father is not a combination of two X chromosomes like the mother. So this takes a shuffle out of the question. His X is a recombination of his mother's, but again, not his father's. This cuts down on another shuffle. In other words, only the ancestors highlighted in the charts above contribute to portions of the X chromosome, so bigger blocks from each ancestor as present.
Measuring X matches
Because X DNA is not inherited in the same way as other chromosomes, and we tend to see larger blocks from ancestors, the number of shared centimorgans is weighted differently. For example, a 16 cM block on the X chromosome represents the same probable number of recombination events (shuffles) as a 7 cM block on any other chromosome. This is because we know there are fewer shuffles involved in every generation on the X. For this reason, cM on the X chromosome do not contribute to overall shared cM. This can lead to confusing results where the number of cM on the X Match column is greater than the amount of Shared DNA.
In addition, unless a match meets the minimum number of shared cM (not counting X DNA), they will not appear on your match list.
X-DNA vs. mtDNA
X-DNA and mtDNA are often confused, so it is important to understand the distinction. They are similar in that they are both inherited by mothers, but their inheritance patterns and what they can tell you are very different. mtDNA, or mitochondrial DNA, is not in the nucleus like the rest of DNA, including X-DNA. Instead, it is found in tiny organelles in the cell called mitochondria. Mitochondria are found in human eggs, so only the mother’s mitochondria are passed on to the embryo.
Everyone has mitochondria, and therefore mtDNA, but both men and women only inherit it from their mothers. They inherit it from their mothers and so on. Because of this it represents an unbroken, exclusively maternal line, called a Direct maternal Line. X-DNA has limited ancestral paths that it can descend from, but mtDNA only has one. This can help trace deep ancestry of your mother's line.