Human DNA is packaged into thread-like structures called chromosomes. And each individual receives DNA, packaged in 23 chromosomes, from his or her mother and also receives DNA, packaged in 23 chromosomes, from his or her father.
So humans have 46 chromosomes (23 received from mother and 23 received from father). One of the 23 chromosomes is called the sex chromosome because it determines a person's sex - 2 Xs for female and 1 X and 1 Y for male.
So Y-DNA refers to the DNA in the Y Chromosome, the sex chromosome carried by males.
A male has 1 Y and 1 X Chromosome and he passes his Y Chromosome unchanged to his sons and his X Chromosome unchanged to his daughters.
So the DNA of a male's Y chromosome (Y-DNA) should be exactly the same as his father's, paternal grandfather's and the other males in this line for thousands of years – because a man passes a copy of his Y chromosome unchanged to all of his sons.
So the Y-DNA test is used to trace the male ancestry in a family.
If a son receives his father's Y-DNA with a small mutation or change then that son will pass on the mutated or changed Y-DNA to his sons who will pass on that mutated or changed Y-DNA to their sons.
For example assume that a man had 5 sons and 1 son received a Y-DNA mutation and the other 4 sons did not receive any Y-DNA mutations. Then the son with the Y-DNA mutation would pass that mutation on to his male descendants. However, the other 4 sons would pass on the Y-DNA without any mutations to their male descendants.
So genealogists can use these mutations or changes in the Y-DNA to determine the relationships among individuals and create a DNA family tree because each mutation or change is like a branch on a tree that is slightly different from its parent.
Scientists know which sections of Y-DNA have changed or mutated most often over the years and so these sections of DNA are used as the markers for the Y-DNA testing.
Today most Y-DNA testing companies offer their Y-DNA Tests for 3 different levels - 37, 67 or 111 markers.
The Y-DNA test evaluates the nitrogenous bases and determines the presence of the nitrogen base (A, T, G or C) at each of the DNA locations selected for the test. The results can then be compared to the results of other individuals and reference groups.
The 4 nitrogenous bases are adenine (A), thymine (T), guanine (G) and cytosine (C). For more information about these nitrogenous bases see our discussion Use DNA Testing to Determine Your Ancestry.
An individual's Y-DNA test results for the DNA markers will be compared to the test results of other individuals in the testing company's database. Based on the number of matches the testing company can estimate how 2 people are related.
For example, if one male and another male matched on 37 of 37 markers the testing company might say that there is a 95% chance that the most recent common ancestor (MRCA) for these 2 males was within the past 7 generations. Different MRCA generations estimates might also be given for different matches - like 35 of 37, 67 of 67 or 111 of 111.
Most Y-DNA testing companies also query their databases and provide a list of people who share a common direct paternal (your father, father’s father, father’s father’s father, etc.) ancestor within the past 25 generations.
The companies also provide a deep ancestral migratory route estimate and determine a person's haplogroup.