Key Concepts

Remembering high school biology, women have two x chromosomes, one inherited from the father and one from the mother. Men have an x chromosome inherited from the mother and a y chromosome inherited from the father. This difference comes about because each sperm contains either an x chromosome or a y chromosome, while each egg always contains an x chromosome. An xy combination makes a person male, while an xx combination makes a person female.

In simple terms, each man receives his y chromosome from his father, unchanged except for any mutations. So, a man’s yDNA will match his father and brothers exactly. His sisters will not have a y chromosome and cannot pass it on to their children.

yDNA Molecule

AGCT

The y chromosome is a DNA molecule consisting of 78 genes. One of those genes is SRY, which causes an embryo to develop as a male. The y chromosome is composed of 58 million smaller units, called base pairs. Each base pair is composed of two nucleotides. There are only four possible nucleotides — adenine (A), thymine (T), cytosine (C) and guanine (G).

Each nucleotide has a complementary nucleotide. So, along the strand of DNA, adenine is always paired with thymine, and cytosine is always paired with guanine. Because each nucleotide can only appear with its complement, it is not necessary to report both sides of the chain. So, the DNA chain can be expressed as a chain of nucleotides, for example, GATCACAGGT…

DNA tests look the non-coding region (“junk DNA”). This means the DNA in this part of the y chromosome doesn’t do anything. It doesn’t affect physical appearance or health. Because junk DNA is no longer used by the human body, mutations can accumulate without damage.

yDNA Mutations

Mutations on the y chromosome can take four forms:

  • Substitutions – the base pair at a particular location can change.
  • Deletions – the base pair at a particular location can be deleted.
  • Insertions – a new base pair can be inserted between existing locations.
  • Repeats – the number of repetitions of a pattern of base pairs at a particular location can increase or decrease.

The two most common yDNA tests are SNP tests and STR tests. Each type of test looks for different types of mutations. They give different information and are reported differently.

SNP Tests

A SNP test looks for the presence (or absence) of a particular substitution, insertion or deletion. (SNP stands for single-nucleotide polymorphism. It is pronounced snip.) 

Men with the same SNP mutation belong to the same haplogroup. Geneticists correlated information about SNP mutations to create the human family tree. 

The shorthand for SNP mutations uses a letter and number combination. The letter identifies the lab that discovered the mutation. The number is the order in which it was discovered. So, P303 is shorthand for a mutation discovered at Lab P (University of Arizona). It is number 303 in order of discovery. A man who tests positive has the mutation. He would be identified by the shorthand P303+. A man who doesn’t have the mutation would be P303-.

STR Tests 

Y Chromosome Diagram

Y Chromosome Diagram

An STR test looks at certain locations on the y chromosome to find the number of times a particular string of base pairs repeats at that location. The repeats are called Short Tandem Repeats (STRs), or allelles, or just repeats

Different male lineages have different numbers of repeats at different locations. The unique combination of different numbers of repeats at different locations is called a haplotype.

The shorthand for reporting STR tests uses a location number on the y chromosome plus the number of repetitions at that location. Locations have DYS numbers. (DYS stands for DNA Y-chromosome Segment.) So, for example, the test results might show a value of 7 at DYS 393. This result means that the place on the y chromosome that has been designated DYS 393 has 7 repeats of whatever pattern is present at that location. (The particular pattern doesn’t matter and isn’t usually mentioned.)

Comparing the Tests

Genetic tests for genealogy typically focus on STR tests, supplemented by SNP tests. Both types of mutations accumulate slowly, but SNP tests usually reveal a common ancestor thousands or even tens of thousands of years ago. On the other hand, STR tests can show a common ancestor within a thousand years, or even a few hundred years.

SNP mutations are rare, so we can be sure all men whose y chromosome contains a particular SNP are male-line descendants of a single ancestor who originally had that mutation. But, because they are rare the common ancestor might have lived some time in the very distant past.

STR mutations are less rare. To maximize results, geneticists test locations on the y chromosome that have a high mutation rate. When comparing two men, a single difference probably indicates their common ancestor lived about 25 to 40 generations ago. Two men with the same surname and same haplotype are almost certainly both descended from a man who adopted that surname.

However, because mutations are random, they can happen any time. Even two brothers might have a difference. A family group of grandfather, father, uncles, brothers and cousins might all have 7 repeats at DYS-393, but one brother might have 8 — he has had a mutation that increases the number of repeats. His descendants will all have 8 repeats at DYS-393.

In genealogy, the testing objective is often to find out whether two men who share a common surname are likely to have a common ancestor within the past thousand years. Therefore, STR tests are usually more valuable for genealogists, while SNP tests are more valuable for anthropologists. However, when STR tests are ambiguous because of convergence an SNP test can be helpful.

Convergence

Two men with the same STR haplotype might be related, but the result might be chance. The number of men who share the same haplotype is much smaller than the number of men with the same SNP haplogroup.  If the men have the same surname, they are almost certainly relative. But, if they have different surnames, the match might be the result of convergence — unrelated lineages can develop the same combination of STR markers independently. In these cases, more testing will show the problem. Testing more STR locations might show that the two men do not actually have the same haplotype, or an SNP test might show that they actually belong to different haplogroups.

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