Y-DNA Testing for Genealogy
The basic science: 
Because males carry the yDNA of their surname ancestors, we can test them as representatives of their ancestors. Each man gets his yDNA from his father, who got it from his father…all the way back.
The yDNA test is used for testing males only, but females can make use of this test if they can convince a male relative to participate.
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This test is only useful in testing the male participant's father's father's ... father's line.
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As this line is associated with Surnames in western societies, it is pretty easy to visualize - and to track through genealogy. All men who share the same "common ancestor" will carry essentially the same yDNA and receive tests results that are also essentially the same.
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These Y chromosomes are passed from father to son virtually unchanged (If there were no changes, each man would have exactly the same yDNA as "Adam" and with each other.) .
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Over time, there may be slight changes, or “mutations”, which occur during replication of cell DNA, but the majority of Y-chromosome DNA remains the same.
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When a mutation does occur, all male descendants of the man carrying the changed Y-chromosome DNA will have that mutation.
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When a second mutation occurs, all of that man’s descendants will carry that mutation as well as the first one, and will be a distinct sub-group of the group with the first mutation.
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Essentially, these represent "branches" on the human Y-chromosome DNA tree.
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The laboratory examines the DNA sample and uses standardized protocols to count the number of repeats of genetic patterns at standardized locations on the DNA helix. A yDNA result is the number of times a specific pattern repeats (alleles) at particular addresses (markers).
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A single Y-DNA test is not that useful, but by comparing the numbers at the markers against other men’s test results, we can determine if a man shares a common ancestor with a second sample.
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Generally, there is a higher reliability at a higher number of markers, and the closer the match in numbers, the closer the relationship. The more markers in common, the more likelihood of a common ancestor.
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By itself, a DNA test cannot confirm that a specific individual is the ancestor of the test participant. However, DNA testing can confirm that two test participants share a common ancestor.
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DNA testing can also be conclusive in proving that a male from an earlier generation is NOT an ancestor and that two males do not share a common ancestor.
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The most useful comparisons are between men who have closely matching yDNA patterns and who have also established paper trails (genealogies).
Y-DNA Haplogroups
Fortunately, there are random and subtle changes that allow us to see differences in different "genetic families".
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Using these differences, scientists have been able to group all men into major branches called "Haplogroups".
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These can be arranged into a "family tree of man" that shows the different branches that have separated over 1000s and 10,000s of years.
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Each man today can be assigned to a Haplogroup, which tells him the "deep ancestry".
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Many men's haplogroup can be estimated by looking at their results, while others have to have a test done called the "SNP test" (pronounced "snip")
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More about yDNA haplogroups
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List of the Y-Haplogroup Projects and their websites
Mutations
yDNA is passed from father to son "essentially unchanged". However, on a
random, but predictable basis for a large group, minor changes occur that we call "mutations".
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These mutations occur at intervals that are especially useful for genealogy and are the focus of yDNA testing in surname genealogy.
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We cannot predict when these mutations will occur in an individual family, but we do know that a mutation that occurs in one man will be passed on to his sons - and that they will pass it on to their sons, and so on ....
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These mutations have occurred through the centuries, giving us the Haplogroups mentioned above,
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These mutations occur with a frequency that makes them particularly useful in genealogy. (Our genealogical paper trails usually extend a few hundred years, with a fortunate minority having paper trails reaching back 400 years or so. And, there a very few who have paper trails reaching back as much as 1000 years or more.)
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As surnames emerged into general usage around 1100 to 1200 A.D. (and later), we are able to correlate the yDNA results to Surnames in many cases.
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By examining the closeness of the results, we can draw conclusions on which men share a common ancestor and estimate (but with a disappointingly wide range) when this common ancestor would have lived.
Results
The results are generated by examining the genetic material at specific "addresses" which scientists know how to find.
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A count is made of repeating patterns at each address. yDNA results are reported as a string of numbers, with each number representing the count at a specific address.
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By comparing the closeness of the string of numbers, we can determine an approximate time back to the two men's common ancestor.
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As an example: one man may have an 11 at specific address, while another man who shares the same common ancestor may have a 12 at the same address.
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This means that somewhere in the line of one of these men - and after their most recent common ancestor - a mutation occurred to change the count at that address for one of the men's family, but not the other.
Test Options
You can be tested at different "resolution" levels (12, 25, 37, 67, or 111 markers).
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FTDNA strongly encourages group testing - often called testing through your "Surname Project".
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Other examples of a group project are the Clan, Family, Geographic, Regional and Ethnic projects.
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Ordering your yDNA test through a project gives you a lower test price and automatically makes you a member of the project.
Choosing the right yDNA test: Learn more about choosing a yDNA test.
Finding a Project: Search for your Surname Project.
