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Y-DNA Tutorial

What is Y-DNA?

Y-DNA is the DNA of the Y chromosome. Humans have 23 pairs of chromosomes. 22 pairs are autosomal chromosomes and the 23rd pair are the sex chromosomes, which determine a person’s gender. Males have one Y chromosome and one X chromosome (XY), while females have two X chromosomes (XX) and no Y chromosome.

How does Y-DNA hold ancestral information?

These are the unique characteristics of Y-DNA which make it ideal for paternal ancestry analyses:

1. Strict paternal inheritance from father to son

2. Low recombination rate, so it remains “unmixed”

3. Fast mutating STR markers enable the tracing of recent paternal lineages

4. Slow mutating SNP markers determine an individual’s ancient ancestry

Paternal inheritance pattern of Y-DNA

Y-DNA is passed down directly from father to son. This means that all males who descend from the same paternal lineage have exactly the same or very similar Y-DNA profiles.

Low recombination rate of the Y-DNA

We inherit one copy of each autosomal chromosome from each parent. At each generation, these autosomal chromosome pairs can mix together, and parts of each chromosome can be swapped in a process known as recombination. However, a male only inherits a single copy of the Y chromosome (from their father). This means that there is effectively no chromosome “partner” to mix with, so very little recombination occurs.

Y-DNA has two marker types that provide ancestral information

The Y-DNA has two very different types of markers which are useful for tracing paternal ancestry: STR markers and SNP markers.

1. Y-STR Markers

STR stands for “short tandem repeat.” These are short sequences of DNA (2-13 base pairs) which are repeated over and over again. The number of repeated sequences for each STR marker varies between individuals. This variation is known as an individual’s Y-DNA haplotype or Y-DNA profile.

STR markers have a very fast mutation rate (approximately one mutation every 20 generations). The rapid mutation rate of Y-STR markers makes this marker type useful for examining recent ancestry, i.e. ancestral events within the past few hundred years.

2. Y-SNP Markers

SNP stands for “single nucleotide polymorphism.” This is when a single nucleotide (DNA building block) varies between individuals.

SNP markers have an extremely slow mutation rate (approximately one mutation every few thousand years). SNP markers are used for investigating ancient ancestry from tens of thousands of years ago, and can determine an individual’s Y-DNA haplogroup.

What is the difference between a Y-DNA haplotype and Y-DNA haplogroup?

A Y-DNA haplotype is an individual’s Y-STR profile and includes the number of repeats at specific Y-STR markers. Y-DNA haplotypes are useful for tracing recent paternal lineages and connections.

An individual’s Y-DNA haplogroup represents his “deep ancestry” or ancient family group. Y-DNA studies have shown that all males living today are descendants of a single root paternal ancestor who lived in Africa approximately 150,000 years ago. Over time, our ancestors migrated out of Africa in waves and populated the world. All males can be traced to one of the main Y-DNA haplogroups. Haplogroups are useful for scientists who are studying human migration patterns and have archaeological value. Y-DNA haplogroups are determined by testing Y-SNPs.

Y-STR marker testing to determine Y-DNA haplotype

During Y-STR marker testing, the number of repeats are determined for several different STR markers. The resulting set of repeat numbers is known as the individual’s Y-DNA haplotype (or Y-DNA profile).

The number of repeats for each Y-STR marker does not contain ancestral information by itself. However, it becomes useful when it is compared against other individuals or specific population groups. All males who descend from the same paternal lineage have the same or very similar Y-STR marker profiles. Comparing your Y-STR marker profile against another male in question, or against a database of populations, allows you to search for relatives along your paternal line and also allows you to find out which population groups are the closest match to your paternal lineage.

The next four sections discuss the most common types of Y-STR markers that are used for paternal ancestry testing.

Single-copy Y-STR markers

Single-copy Y-STR markers are STR markers that occur only once in the human genome. A single repeat number (allele value) will show for each single-copy marker in a paternal ancestry report.

Multi-copy Y-STR markers

Multi-copy Y-STR markers are markers that occur more than once in the human genome. More than one allele value will show for each of these markers in a paternal ancestry report.

For example, the DYS385, DYS459 and YCAII are typically present at two different locations on the Y chromosome; therefore, they are also termed “duplicated markers.”

Special multi-copy markers:

  • DYS389: Unlike other multi-copy Y-STR markers, only one location of DYS389 is amplified. The forward primer for DYS389 binds at a specific location on the Y chromosome, whereas the reverse primer binds at two different locations. This yields two PCR products: the shorter DYS389I fragment and the longer DYS389II fragment, so two allele values are always reported for this marker.
  • DYS464: This is a special Y-STR marker that is known to have 4 to 7 alleles. Previously, the “genotype” was reported. When the genotype was reported, identical repeats were reported multiple times. However, recent policies implemented by the American Association of Blood Banks mandate that all accredited DNA testing laboratories must report the “phenotype” instead of “genotype” for multi-copy markers, especially if the marker has more than 2 alleles. This means that if an individual has duplicate repeat values, they will only be reported once using the “phenotype” reporting procedure.

Using your Y-DNA haplotype to search for, or verify, family linkages

Your Y-DNA haplotype is the same or very similar to that of all males who descend from the same forefather as yourself. This means that your father, grandfather and great-grandfather along your paternal lineage all carry the same Y-DNA haplotype as you.

Once you have tested your Y-STR markers, you can use your haplotype to search the DNA Reunion database for people who are linked to you on your paternal line.

*Only males can take a Y-DNA Test*

Since only males have Y-DNA, only males can take a Y-DNA test to trace their paternal ancestry. Females wishing to trace their paternal ancestry must test the Y-DNA of a male family member such as a brother, father, uncle, or male cousin along their direct paternal lineage.