Y-DNA Testing for Genetic Genealogy

//Y-DNA Testing for Genetic Genealogy
Y-DNA Testing for Genetic Genealogy 2018-02-18T10:45:06+00:00

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Vocabulary

Allele

⋅ Base pair

Binary Polymorphism

⋅ Convergence

⋅ Deletion

Haplogroup

Haplotype

⋅ Ancestral haplotype

⋅ Modal haplotype

Insertion

⋅ Locus

⋅ Micro-allele

⋅ Mutation

⋅ Mutation rate

⋅ NexGen sequencing

Non-paternity event

⋅ Pedigree collapse

⋅ RecLOH

Short tandem repeat (STR)

⋅ Single-nucleotide polymorphism (SNP)

⋅ Clade & Subclade

⋅ Triangulation

Unique-event polymorphism (UEP)

Y-chromosome

Y Chromosome Consortium

Y-DNA testing (Y-chromosome DNA testing) is used for paternal genealogy. Y-DNA is passed from a father to his sons. Thus, it traces a direct paternal line. Only men have Y-DNA. Thus, only men can take Y-DNA tests. Perfect matches are evidence that two people share a common paternal ancestor. Close matches are evidence of a potential relationship.

There are three reasons to take a Y-DNA test. The first is for genealogy evidence. The second is for ethnic origins. The third is for random match discovery. That is, genealogy match fishing. Y-DNA testing does well for the first two.

Its utility for the third use depends on three factors. They are the type of Y-DNA test used, database size, and ethnic background.

What gets tested

Y-DNA has two types of genetic markers that can be tested. They are Y-chromosome STRs, Y-STRs, and Y-chromosome SNPs, Y-SNPs. Y-STRs are what people in the past have tested first. However, Y-SNPs are emerging as definitive evidence for genealogy.

It is now usual to test both types of Y-DNA for genealogy.

Y-DNA STR testing

Y-STR testing for genealogy uses set panels of STR markers on the Y-chromosome. The results of the panels are compared to others for matching. This type of testing is good for finding if you match someone else with the same surname.

Y-DNA SNP testing

There are several ways Y-DNA SNP variants can be tested to help with your genealogy.

The first is direct Y-DNA testing using Next Generation sequencing. This method sequences a large part of the Y-chromosome. Results include variants that exist there. It's the best method for finding new variants. With direct testing, one can best understand matches. The second is targeted Y-DNA testing. It tests a set of known variants. These are picked from variant databases and from known haplogroups.

Family Tree DNA (FTDNA) and Full Genomes Corporation (FGC) both do direct testing. This is FTDNA's Big Y test and FGC's Y Elite 2.1 test.

An older method of direct Y-DNA testing is Sanger sequencing. This method tests specific SNP variants and part of the DNA to either side of the variant. Thus, it can find some new variants. However, it cannot do it on the same scale as Next Generation sequencing. FTDNA's former Walk Through the Y (WTtY) test used this method. It may also be used for individual SNP variant tests.

The other approach to SNP variant testing is targeted testing. This uses set panels of known variants. The panels can either be small or large. Targeted testing is used to answer ethnic origins questions. Small panels of 50 to 160 variants may be used someone who already done some Y-DNA testing. Family Tree DNA and YSeq offer this type of test.

Microarray chips may be used for targeted testing. In this case, thousands of Y-DNA SNP variants are tested. Companies that use microarray chips like 23andMe, the Genographic Project, and Living DNA use targeted testing.

For genealogy, direct testing of SNP variants is best. At times, targeted testing may be OK to prove a hypothesis wrong.

Understanding Y-DNA testing results

The Y-chromosome

Human Y-chromosome - Wikipedia

Human Y-chromosome – Wikipedia

The human Y-chromosome is the human male sex chromosome. It is located in the nucleolus of every cell in males.

The Y-chromosome is passed from father to son each generation. With each transfer, there is a chance for small changes to occur. The inheritance pattern means that the Y-chromosome is useful for male line genealogy research. This includes surname research. The rare minor changes make it possible to distinguish between different genetic branches of a male ancestor's descendants.

To do this type of testing, it is necessary to test males from the right lineage. This means that genealogists often have to do extensive research to seek out the right men to test.

Y-STR results

Y-STRs are repeating sequences of DNA values. For example, the Y-STR DYS393 is made up of repeats of the AGAT sequence. It is the number of repeats that varies between men, so that is what is measured. If a man has twelve copies of AGAT for DYS393, he has DYS393 = 12.

Most Y-STR markers are named with the DYS prefix and a sequential number. Note that these numbers are not related to the actual position of the Y-STR on the Y-chromosome. Rather, they reflect the order in which the Y-STRs were named.

Below is an example of how a panel of 12 Y-STRs, Y12, would be reported.

DYS393
DYS390
DYS19
DYS391
DYS385
DYS426
DYS388
DYS439
DYS389i
DYS392
DYS389ii
13
23
14
10
14-14
11
14
11
12
11
28

Y-SNP results

Y-SNPs are single value changes in the DNA. They are often called variants. The relative mutation rate for a Y-SNP is extremely low. However, the entire Y-chromosome is large enough that one can expect a new Y-SNP in a male lineage every 1 to 4 generations on average. Together, the slow rate of change and the large amount of the Y-chromosome tested means that modern Y-SNPs work for both recent genealogy and for building the deeper paternal tree of humanity.

Y-SNPs are named with a letter code and a number. The letter indicates the lab or research team that discovered the SNP. The number indicates the order in which it was discovered. For example, M173 is the 173rd SNP documented by the Human Population Genetics Laboratory at Stanford University, which uses the letter M.

While the details of ones results for M173 might be an A or a C value, Y-SNP variants are usually described in terms of being positive for the change or negative for it. Thus, when someone has the original value A, they are said to be negative. When they have the new value C, they are said to be positive.

Below is an example of how someone's results might be reported.

M161-, M170+, M21-, M223-, M227-, M253+, M258+, M26-, M307+, M72-, P109+, P19+, P259-, P30+, P37-, P38+

Understanding Matches

Y-DNA testing – Inheritance and research strategy

Y-DNA Testing Inheritance

Y-DNA Inheritance Path

Y-DNA is passed by a father to his sons. Thus, only men can test for their father's Y-DNA profile.

Who you test depends on your goals. To know your ancestry on your direct maternal line, you may test yourself or a male relative if you are female. To know if two men descend from the same man, both people must test.

Hypothesis testing

Genealogists use Y-DNA for hypothesis testing. One first forms a hypothesis. Second, one finds cousins from the right branches to test. Third, one tests the cousins. Finally, one analysis test results.

Ethnic Origins

The second use is for ethnic background testing.

Y-DNA follows a direct line. Ancient ancestry for these lines covers both recent and distant parts of the human journey.

Y-DNA is good for determining ethnic origins and ancient history. However, for a full picture of your ancestry, you need to test as many of your Y-DNA lines as possible.

The chart on the left shows the paternal lines for a five generation pedigree. Those who do this type of testing often contact many cousins.

Database matching

FTDNA offers Y-DNA matching to others in their database. Results can then be used for match fishing. That is, finding recent cousins through random testing. Matching is available for both Y-STR tests and Big Y tests.

Y-STR matching

Y-DNA exact matches may be 10 or more generations in the past. This is often before genealogy records. Therefore, match fishing is not the best use of Y-DNA results.

Big Y matching

Big Y close and exact matches are well within the last 3 to 7 generations. Thus, Big Y matching will eventually be a good way to discover recent relatives. It will work even when two men do not share a recent surname. However, the FTDNA Big Y database is still small. It is less than 100,000 people as of February, 2018. You should not expect a random match then from Big Y testing yet.

Y-DNA testing – Sources & Resources

Websites

YDNA Testing Basics – Family Tree DNA

Frequently Asked Questions

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