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The Y Chromosome: Ancestry, Genetics, and the Making of a Man

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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 determines 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 chromosomes, 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.

What is a Y chromosome?

What is a Y chromosome?

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.

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.

Distribution of Y chromosome haplotypes in Europe.

Distribution of Y chromosome haplotypes in Europe.

Y chromosome haplogroups within Europe. Click to enlarge.

Y chromosome haplogroups within Europe. Click to enlarge.

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 the 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.

This is a karyotype of an individual with Klinefelter Syndrome: the individual has two X chromosomes and a Y chromosome (47, XXY).

This is a karyotype of an individual with Klinefelter Syndrome: the individual has two X chromosomes and a Y chromosome (47, XXY).

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, and has a higher than average risk of developing osteoporosis, diabetes, and autoimmune disorders. Men with Klinefelter Syndrome may have a high-pitched voice and 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 pairs. 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 are 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 Y Chromosome is much smaller than it used to be.

The Y Chromosome is much smaller than it used to be.

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 backup 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

Question: 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?

Answer: 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.


Leah Lefler (author) from Western New York on October 25, 2018:

The Anglo-Saxon and Viking haplogroups are of Germanic origin and make up approximately half of all male lineages in England (including lower Scotland). These haplogroups include I1, R1a (L664;Z284), R1b-U106, I2a2a-Z161, and Q1a.

Nick Raspin on October 25, 2018:

You say for haplogroup I, that "Viking invaders and Anglo-Saxons can be typed from the British population using specific markers from this haplogroup".

Which markers are these, & do/can you recommend a particular company that can identify these - if applicable?

Leah Lefler (author) from Western New York on February 10, 2018:

Hello, Mohadeseh - send me a direct message and we can discuss publication in your magazine.

Mohadeseh Nazari on February 09, 2018:

It was fantastic and I learnt wonderful informations that I didn't know before. I was wondering if you let us to press a resume of your article with your name in our scientific magazine. It's a magazine that is prepared by the students in our university. New Plan (or Tarh_e No in my mother language) is the name of the magazine.

M.N from Tehran_Iran

Leah Lefler (author) from Western New York on September 24, 2017:

I find the study of genetics fascinating, Glenn. The Y chromosome plays a vital role despite it's diminutive size! The palindromic ability of the Y chromosome is a a good safeguard against its extinction!

Glenn Stok from Long Island, NY on September 24, 2017:

I found this article very informative with additional information not normally understood about the changes occurring over time with the human genome.

It's especially interesting how the Y chromosome is protecting itself from demise by creating a mirror image of its genes, known as the Y chromosome palindrome. The video you included was helpful, but you explained it more clearly.

Leah Lefler (author) from Western New York on August 07, 2015:

Hi Bug Bug,

Since all humans living in the Americas came from Africa, Europe, or Asia, they would have haplogroups derived from those areas. If you read the text of the article, haplogroups C and Q are found among Native Americans.

Those with Klinefelter Syndrome (XXY males) do not show an increased rate of homosexuality when compared with XY males.

Bug Bug on August 07, 2015:

Very interesting article. Following some discussions with close minded people about homosexuality, I've been wondering if the increase of it among men could be due to genetic mutation that have been passed on, for example, increase in Klinefelter Syndrome. Of course, it would not explain it all (personal choice vs genetic) but since many homosexual men tend to have more feminine features, could it be a possibility? Has any research been done about it? It would be very interesting to read more about the effects or conditions associated with the mutations of the Y chromosome or translocation of part of it. Is there additional readings you could recommend? Also, by curiosity, the haplogroups discussed in the article is mostly covering Africa, Asia and Europe (which is logical since they have an older history), however, what would be the most dominant haplogroups in America (South, Central and North)? Thanks!

Leah Lefler (author) from Western New York on July 31, 2013:

Parthenogenesis in humans never occurs naturally and will not produce a viable embryo - humans are diploid and require 2 sets of chromosomes for normal development. I have another article that delves into parthenogenesis here:

It is a fascinating subject, samowhamo!

samowhamo on July 30, 2013:

Very interesting article. Hey just out of curiosity (I am asking because this article reminds me of a similar subject) is it possible that parthenogenesis could be made possible in humans from what I have heard the answer is no because humans are just too complex and not designed for it.

Leah Lefler (author) from Western New York on June 01, 2012:

This article is about the Y chromosome, which doesn't apply to mitochondrial DNA lineage - mitochondrial DNA is maternally inherited, so not really relevant to the Y chromosome. It is fascinating, though - the mitochondrial genome is handed down from mother to child, allowing generations to be traced through the mother. Thanks for your comment, Stella!

StellaSee from California on June 01, 2012:

Leah, this hub explains one of the exact areas of genetics I would love to research on! It's especially interesting to me when genetics is applied to the study of whether a population's genetic variation corresponds to the archaeological/historical evidence of a particular place. I just realized you didn't talk about mitochondrial DNA..not that you really needed to for such a thorough hub :)

Leah Lefler (author) from Western New York on January 01, 2012:

Thanks, Lovely 7 - it is interesting to see how we can trace ancestry and human migration through the Y chromosome!

Lovely 7 on January 01, 2012:

Very Informative hub

Thanks for sharing

Leah Lefler (author) from Western New York on June 27, 2011:

No worries - the Y chromosome isn't going to disappear any time soon!

Akhil Anil on June 27, 2011:

You really scared me off by the end! ;) Great hub!!

Leah Lefler (author) from Western New York on April 17, 2011:

I was definitely more interested in the biochemistry/molecular biology aspect of my degree. I was much relieved when I was finished with physics, calculus, and chemistry!

Baileybear on April 13, 2011:

yes, physchem was my weakest area, as I'm not much good at calculus. Any quantum stuff got rather too abstract. I really enjoyed the bio subjects that blended with chem

Nell Rose from England on April 11, 2011:

Hi, this is absolutely fascinating, what a great hub! cheers nell

Nan Mynatt on April 11, 2011:

A lot of detailed research was done to do your hub. It takes a lot of reading and documentation to come up with the results.

Marie McKeown from Ireland on April 11, 2011:

Really loved the section about ancestry in Europe - so interesting!

Leah Lefler (author) from Western New York on April 04, 2011:

I had to study some chemistry, but I only did general chem and organic chemistry. I stayed away from P-chem and Q-chem (though my husband studied quantum chemistry - that seemed beyond me)!

Baileybear on April 04, 2011:

I did my degree in the early 90s when they were only just starting the human genome project. I enjoyed the bio subjects I studied: genetics, biochemistry, microbiology.

mackdaye on April 03, 2011:


Leah Lefler (author) from Western New York on April 03, 2011:

I took genetics and advanced human genetics in the late 1990's (part of my bio degree), but the knowledge has increased exponentially since then! It is almost impossible to keep up with the advancements!

Baileybear on April 03, 2011:

well researched and very interesting. I studied genetics until second year at university as part of my chemistry degree. It's amazing how much more is known since then

Leah Lefler (author) from Western New York on April 01, 2011:

Thank you! I am fascinated by genetics, and the use of the Y chromosome to track humanity's progress out of Africa is interesting (mitochondrial DNA is used to track the maternal line: it is handed down in an unchanged manner from mother to daughter). I focused on the Y chromosome for this article, since many people are using at-home DNA tests to trace their ancestry via the Y chromosome.

Simone Haruko Smith from San Francisco on April 01, 2011:

Goodness gracious, this is fascinating. I'm going to need to come back and read this again when I have time to really sit and think about all this! GREAT Hub!

Leah Lefler (author) from Western New York on April 01, 2011:

I thought the ancestry information was really interesting. My dad actually did the Y chromosome test - our family lore was that everyone had immigrated from Germany to the USA. As it turns out, the paternal line is Irish - with a very close (identical) match still living in Ireland. It was fascinating!

medor from Michigan, USA on April 01, 2011:

Excellent... thanks for bringing me up to date on this interesting topic...