The Y Chromosome: Ancestry, Genetics, and the Making of a Man
Genes on the Y Chromosome
Every human has 23 pairs of chromosomes – organized packets of genetic information (DNA) which code for all the necessary amino acids to create a human being. The twenty-third set of chromosomes determine the gender of a person: two X chromosomes create a female, and an X paired with a Y creates a male.
The Y chromosome is much smaller than a typical X chromosome, and contains somewhere between 70-200 genes (the entire human genome comprises approximately 20,000-25,000 genes). Some important genes on the Y chromosome include:
SRY: The SRY (Sex
Determining Y Region) gene determines gender. This gene will bind to other DNA
in the cell, distorting it out of shape. This single gene creates the male
phenotype. In a very rare genetic event, the gene sometimes gets translocated onto an X chromosome. When this happens, the child carries a genome that should be female (46, XX), but develops as a male. Adult men with a 46, XX karyotype and a translocated SRY gene are often identified due to infertility or hypogonadism (underdeveloped testes).
SHOX: The SHOX gene (Short Stature Homeobox) is located on the X and the Y chromosome. This gene is responsible for skeletal growth. While many genes are located only on the X chromosome, this gene is present in both the X and the Y chromosome, so that each gender receives two functional copies of the gene.
USP9Y: This gene (ubiquitin specific peptidase 9, Y-linked) is found on the Y chromosome, and is only present in males. This gene is involved in the production of healthy sperm, and infertile males sometimes have a mutation in this gene.
Is the Y Chromosome Necessary to Make a Man?
The Y chromosome is not necessary for the male phenotype. The SRY gene is required, however, and it is almost always located on the Y chromosome. In a few rare cases, the SRY gene has been translocated (moved) to the X chromosome by accident. In these cases, the genotype is 46, XX – this would normally indicate a female genotype. In the rare case of translocation of the SRY gene, however, a man can be 46, XX: these men are often fully masculinized, but are infertile. This is sometimes called the “XX Male Syndrome.”
There are also reports of men who have a 46, XX genotype without the SRY gene. The causes of this rare occurrence have not been completely investigated. Like the men with the translocated SRY gene, these men are infertile.
Determining Gender With a Single Gene
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Ancestry Determined from the Y Chromosome
Paternal lineage DNA tests can trace a family’s origins through the Y chromosome. This test only works for males, as the DNA handed down on the Y chromosome is nearly identical to the man’s ancestor’s DNA. The DNA on the Y chromosome changes very little over time, so a man can trace his family ancestry through genetic testing of the Y chromosome.
The chromosome is tested for markers in specific locations on the Y chromosome. These markers are numbered 1-33, or 1-46, and a corresponding number is assigned to each marker. The number assigned to each marker is the number of “short tandem repeats” (STRs) at the genetic location: by comparing the number of STRs for each marker, men can find distant relatives who share the same DNA.
In addition, the Y chromosome bears a specific haplogroup which can determine ancient family origins. Some companies are able to give predictions about which haplogroup a man’s ancestors belonged to when humans migrated out of Africa over 100,000 years ago.
Y Chromosome Haplotype Distribution
Y Chromosome Haplogroups
About once every 7,000 years, a mutation known as a single nucleotide polymorphism (SNP) occurs on the Y chromosome. The known rate of mutation has allowed scientists to trace migration routes of early humans out of Africa. There are over 150 known haplogroups, with 31 STR markers creating subgroups for each haplogroup (the subgroups are known as haplotypes).
The Haplogroups are from the following geographical areas:
Haplogroup A: One of the oldest haplogroups. Found in Southern Africa and the Southern Nile region.
Haplogroup B: This haplogroup is only found in Africa, and is one of the oldest known haplogroups.
Haplogroup C: This group colonized Australia, New Guinea, and is also found in India and among some Native American tribes. The C group started in southern Asia and spread in many directions.
Haplogroup D: The first Japanese humans originated from this haplogroup, which began in Asia. The aboriginal Japanese still carry this haplogroup, along with inhabitants of the Tibetan plateau.
Haplogroup E: Haplogroup E is only found in Africa. Interestingly, this haplogroup is closely related to Haplogroup D, which is not found in Africa. This haplogroup arose in Northeast Africa or the Middle East.
Haplogroup F: This haplogroup is the "father" of most of the remaining haplogroups - haplogroup F is the originator of haplogroups G through R. Over 90% of the world's population comes from this haplogroup or one of its progeny. This haplogroup originated during the migration out of Africa: it is almost never found within sub-Saharan Africa.
Haplogroup G: Originating from Pakistan or India, this haplogroup is found in Europe, central Asia, and the Middle East.
Haplogroup H: This haplogroup is only found in Sri Lanka, India, and Pakistan.
Haplogroup I: Nearly one fifth of the European population carries this haplogroup. This haplogroup is not found outside of Europe, and probably arose when ice sheets covered most of Europe. Certain subtypes are specific to Scandinavians and those from Iceland. Viking invaders and Anglo-Saxons can be typed from the British population using specific markers from this haplogroup.
Haplogroup J: North Africa and the Middle East are the locations where haplotype J is found - it probably arose in this general geographic area.
Haplogroup K: Haplogroup K is found in Iran and the southern region of Central Asia. It is estimated that this haplogroup arose 40,000 years ago.
Haplogroup L: Sri Lankans, people from India, and others from the Middle East may carry haplogroup L.
Haplogroup M: A whopping 33%-66% of the Papua, New Guinea population carries haplogroup M.
Haplogroup N: While this haplogroup probably arose in China or Mongolia, it is currently found in Northeast Europe and Siberia. This is the most common haplogroup among Finns and native Siberians.
Haplogroup O: The vast majority (80%) of East Asians are haplogroup O. It evolved about 35,000 years ago and is found exclusively in East Asia.
Haplogroup P: This is a fairly rare haplogroup, found in India, Pakistan, and central Asia.
Haplogroup Q: Native Americans and Northern Asians carry haplotype Q: this is the population that migrated out of Asia and into North America. Native Americans carry the specific haplotype Q3, which is restricted to the population of humans who migrated across the Bering Strait.
Haplogroup R: One strain of this haplogroup is found among people who live near the Caspian Sea in Eastern Europe: the culture of the people in this area domesticated the first horses. Another haplotype from the R group is found in Europe and is found in high concentrations in Western Ireland.
Haplogroup S: The highlands of Papua, New Guinea carry this haplogroup, along with some people living in nearby Indonesia and Melanesia.
Haplogroup T: This haplogroup is found in Southern Europe, Southwest Asia, and throughout Africa.
The Y Chromosome
Disorders of the Y Chromosome
Klinefelter Syndrome: This syndrome is caused by the inheritance of more than one X chromosome alongside the Y chromosome. A man with Klinefelter Syndrome will have a genotype that is XXY, XXXY, or a mosaic of XY and XXY. This syndrome often causes sterility, have a higher than average risk of developing osteoporosis, diabetes, and autoimmune disorders. Men with Klinefelter Syndrome may have a high pitched voice and have much less body hair than a man with an XY karyotype. Some of the symptoms of Klinefelter Syndrome can be alleviated with a prescription of testosterone at puberty.
XYY Syndrome: Instead of having too many X chromosomes, men with XYY syndrome have an extra Y chromosome. Adults with this syndrome are taller than average (generally over six feet tall), but are otherwise typical in appearance. Adolescents with the syndrome are likely to be very lean, prone to severe acne, and may have difficulty with coordination. Individuals with XYY Syndrome have a higher level of testosterone than typical – the syndrome is likely under-diagnosed, as there are few symptoms to trigger testing.
Turner Syndrome: When There is No X or Y Chromosome
In some individuals, the 23rd set of chromosomes is missing one of the pair. Instead of being XY or XX, the karyotype reads as XO, because there is no second chromosome present. This is known as Turner Syndrome – people with Turner Syndrome are female, because genes located on the Y chromosome is necessary for male development. Girls with Turner Syndrome are shorter than average, and are infertile. Estrogen therapy is often given to girls with Turner Syndrome around the time of puberty.
The Disappearing Y Chromosome
All chromosomes are a matched set, save one: the Y chromosome has no identical partner. This is a negative when it comes to mutations – the other chromosomes have a back-up when an error (mutation) occurs. The identical, “back-up” chromosome gives the cell the needed information when one has an error. The Y chromosome does not have this protective mechanism, so when an error occurs, the gene essentially disappears. Over time, the errors have added up and more and more of the genes on the Y chromosome have been eliminated. Scientists theorize that the Y chromosome used to have as many genes as the X chromosome (approximately 1,000 genes), but it has dwindled down to an estimated 80 genes.
The Y chromosome is not doomed, however, as it has developed protective mechanisms to ensure its survival. This is quite good news, as the survival of the human species depends on its existence. Scientists recently discovered that the Y chromosome has been making mirror-image copies of its most important genes – a mechanism known as the Y chromosome palindrome. A palindrome is a word which is read the same forward and backward: “level” is a good example. The Y chromosome palindromes contain genetic information reading forward in the first half, and then the same information is repeated in reverse. Essentially, this means the most important genes on the Y chromosome do occur in tandem: instead of appearing on two separate chromosomes, however, the information is coded within a palindrome on the same chromosome.
Y chromosome palindromes mean that the Y chromosome is well-protected from demise, and will probably not shrink far beyond its current state.
A Glossary of Basic Terms
Chromosome: An organized unit of DNA within a cell.
Gene: A unit of heredity. Each gene is comprised of a differing number of DNA base pairs, coding for amino acids that create proteins.
Haplogroup: A group of similar haplotypes that share a common ancestor.
Haplotype: A set of alleles closely linked on a chromosome, that are often inherited together.
Karyotype: A complete set of human chromosomes. Karyotypes are often reviewed when a chromosomal disorder is suspected in an individual. Chromosomes are photographed when they reach the metaphase stage of mitosis.
Questions & Answers
When a parent is told that the newborn baby is missing one chromosome after testing from having a seizure at one day old, what does that mean? Can they find out what is missing?
I would ask your physician for the medical report to get all of the details from the genetic testing they performed. If a child is missing an entire chromosome, they will be able to tell you which chromosome is missing and a genetic counselor will be able to help the family understand the medical and developmental implications.Helpful 1