The Y chromosome has shed most of its original genes over its long history, and that is where the “disappearing Y” headlines come from. But the shrinking seems to have stalled long ago, and the genes that are left are tightly guarded. Even the worst case would not be the end of males, because some mammals already live without a Y and still produce sons.1Proceedings of the National Academy of Sciences. Novel sex-determination mechanism revealed in mammals For living men, the Y story that matters most is not evolution but what happens to the Y inside their own cells as they age.2PubMed. The effects of loss of Y chromosome on male health
How Much of the Y Chromosome Has Been Lost
Humans carry 23 pairs of chromosomes. Women have two X chromosomes, and men have an X and a Y. The X and Y evolved from a pair of ordinary chromosomes about 180 million years ago.3PubMed Central. Extinction of chromosomes due to specialization is a universal occurrence Since then the X has kept its genes in much the same content and order, while the Y has lost about 97% of its ancestral genes.4PubMed Central. Extinction of chromosomes due to specialization is a universal occurrence Fruit flies’ Y has followed the same path, losing most of its original genes.5PubMed Central. Y chromosome evolution: emerging insights into processes of Y chromosome degeneration
The X carries roughly 800 protein-coding genes, while the Y carries under a hundred, many of them repeated copies. The 97% describes loss across millions of years, not something happening in recent human history.
How do scientists know the Y was once an ordinary chromosome? The evidence is comparative. Many genes on the X have Y versions that look like worn-down cousins, which is what you would expect if both began as copies of the same chromosome. Comparing the X and Y across humans and other mammals also lets researchers date when different stretches stopped matching.
What remains is small but specialized. About 95% of the Y’s length is a male-only region that never pairs with the X.6PubMed. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes That region holds 78 protein-coding genes that make only 27 distinct proteins.7PubMed. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes Most of the Y’s surviving genes have male-specific jobs, especially making sperm.8PubMed Central. Y chromosome evolution: emerging insights into processes of Y chromosome degeneration
The Y was hard to read until recently. Much of it is long repeated stretches that older DNA-reading methods could not piece together, which is why it was often left out of genetic studies. The first complete end-to-end reading of a human Y, finished recently, added over 30 million DNA letters and 41 extra protein-coding genes missed before.9PubMed Central. The complete sequence of a human Y chromosome That does not overturn the basic story of heavy loss. Many of the added letters are repetitive stretches, not a hidden trove of new gene families.
Why the Y Chromosome Shrank
Most chromosome pairs swap matching pieces when eggs and sperm form. Swapping lets good versions of genes be separated from broken ones and passed on. The male-only part of the Y does not swap with the X. So when one bad mutation sits among useful genes, they are inherited as a single unit and natural selection weakens.10PubMed Central. The degeneration of Y chromosomes
If a man carries a harmful change on his Y, all his sons inherit it along with whatever useful genes sit beside it. Selection can only favor or reject the whole block. A block with one great gene and one damaging mutation may be rejected, or the mutation may survive because it rides with a useful gene. Over very long spans these small losses add up, and genes that did not matter much go first.
The X escaped this fate because in women the two X chromosomes still swap pieces with each other. That gives the X a cleaning mechanism the Y lacks, and it is why the X’s gene order has stayed so steady.
Meanwhile, junk DNA moves in as genes move out. On young Y chromosomes, short repeated DNA stretches expand first, while later stages bring accumulating mobile “jumping” DNA and shrinking.11PubMed Central. Expansion of Microsatellites on Evolutionary Young Y Chromosome In one plant with a huge Y, its size comes mostly from piled-up repeated and jumping DNA.12PubMed. Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres
“Degeneration” is easy to misread. Losing genes did not make the Y useless: it kept genes needed for male development and sperm, and many lost genes still have working copies on the X.
Has the Loss Stopped
Each section of the human Y went through rapid, accelerating gene loss and then switched to strict preservation.13PubMed Central. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes In the older sections, which make up most of the Y, gene loss stopped more than 25 million years ago.14PubMed Central. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes The rhesus monkey’s Y has lost none of those older genes in 25 million years either, despite a very different layout.15PubMed Central. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes The “extinction in a few million years” forecasts that assume steady loss do not match this record. Humans and rhesus monkeys split from a common ancestor about 25 million years ago, so finding the same old genes intact in both suggests the preservation is real, not a quirk of one species.
Strict preservation does not mean a freeze in DNA letters. Genes that survived the early loss are those where losing them would hurt a male’s fitness, so selection removes men carrying broken copies. Small harmless changes still occur, but the genes keep working. What stopped falling is the count of working genes.
The kept genes are not just for sperm. About a dozen work in tissues throughout the body, helping cells read and use the rest of the genome.16Whitehead Institute of MIT. From liability to viability: Genes on the Y chromosome prove essential for male survival That broad role likely helps explain why selection guards them so tightly.
The Y also repairs itself using backup copies. Much of it is built from mirror-image stretches holding sperm-making genes.17PubMed. The hows and Ys of genome integrity Each arm can use the other as a template to fix mutations, removing harmful changes and keeping good ones.18PubMed. Y chromosome palindromes and gene conversion The same mirror structure can occasionally break wrongly and cause infertility, sex reversal or Turner syndrome.19PubMed. The hows and Ys of genome integrity
Experts still disagree about the long term. One leading view holds that Y chromosomes degrade relentlessly, and points to rodents that have already lost theirs.20PubMed. Is the Y chromosome disappearing?–both sides of the argument The opposing view notes the Y has survived for hundreds of millions of years and most of its genes show active protection.21PubMed. Is the Y chromosome disappearing?–both sides of the argument Even the pessimistic estimates run to millions of years, far longer than our species has existed.
Animals That Have Already Lost Their Y
In most mammals a Y gene called SRY flips the switch that makes an embryo male. Yet two Japanese spiny rat species have lost the Y completely, keeping a few Y genes that moved onto the X.22PubMed Central. Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There? Their males and females have chromosome sets that look the same, and they lack SRY.23PubMed. Sex determination without the Y chromosome in two Japanese rodents Tokudaia osimensis osimensis and Tokudaia osimensis spp. A third related species still has a Y, fused with another chromosome.24PubMed Central. Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?
Because SRY is the trigger in nearly all mammals, its loss in these rats was surprising. Yet the males still develop testes and make sperm, so the Y’s male-switch job was taken over rather than abandoned.
A new switch evolved. Males of the Amami spiny rat carry an extra copy of a DNA stretch near a gene called Sox9 on chromosome 3.25Proceedings of the National Academy of Sciences. Novel sex-determination mechanism revealed in mammals That extra copy turns Sox9 up without SRY, steering the embryo toward testes.26Proceedings of the National Academy of Sciences. Novel sex-determination mechanism revealed in mammals Sox9 is the key because SRY’s main job is to switch it on, and Sox9 then drives testis development. Any route that turns Sox9 on can stand in for the Y.
When the stretch was added to female mouse embryos, they began switching on testis-forming genes.27Proceedings of the National Academy of Sciences. Novel sex-determination mechanism revealed in mammals This shows the stretch can act as a switch, though it does not mean the mice became fully male. The result: the male-determining job moved to an ordinary chromosome, the first known case in mammals.28Proceedings of the National Academy of Sciences. Novel sex-determination mechanism revealed in mammals The rats show the Y is not necessary for making males in every mammal; they do not show the human system is likely to change soon.
Sex Chromosomes in Other Animals
Not every Y is gene-poor. The bull’s male-only Y region holds 1,274 genes, the densest in its genome, while primate Y regions have only 31 to 78 genes.29PubMed Central. Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development A shrunken Y is not inevitable in every mammal. Part of the bull’s count comes from many copies of certain genes, and copies are not all different genes, so the count can look bigger than the number of distinct jobs. Still, the contrast shows that Y chromosomes of different mammals have followed different histories, not one fixed path.
Other systems are stranger. The platypus has five X and five Y chromosomes linked in a chain.30PubMed Central. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes The chain links up during sperm formation, so the chromosomes are passed on as a group. Males carry five X and five Y; females carry ten X. Its X chromosomes resemble the bird Z sex chromosome more than the human X,31PubMed Central. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes which suggests they arose by a different route from the one in other mammals.
In frogs, sex chromosomes come from different ancestral chromosomes even within one family, and sex can reverse easily.32PubMed Central. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles Reptiles’ sex chromosomes stay much more alike across related species.33PubMed Central. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles
Men Losing the Y in Their Own Cells
Losing the Y from some cells after birth, called mosaic loss of Y or LOY, is the most common acquired genetic change in men.34PubMed. The effects of loss of Y chromosome on male health It was long thought to be a harmless part of aging.35PubMed Central. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men’s Health It is now linked to heart disease, brain degeneration and many cancers.36PubMed Central. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men’s Health This is different from the evolutionary story: it happens in one man’s cells over decades, and children do not inherit it.
A man with this change has a mix of cells, some with a Y and some without. It is mostly found in blood cells, and the share of affected cells tends to rise with age. He would not feel or see it; it is detected only by laboratory tests on a blood sample.
There is evidence it causes harm. Mice given bone marrow lacking the Y developed scarred hearts, weaker heart function and died earlier.37PubMed Central. Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality In men followed over time, losing the Y in blood was tied to higher risk of heart disease and death from heart failure.38PubMed Central. Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality It seems to change how the immune system works, with likely causal roles in heart scarring, bladder cancer and Alzheimer’s.39PubMed. The effects of loss of Y chromosome on male health
The proposed reason is that blood cells without a Y may behave differently because Y genes help control other genes in the cell. Immune cells travel through the whole body, so a change in them can affect organs such as the heart. This mechanism is supported by mouse and human data but is not yet proven in every detail.
Cancer adds a twist. Bladder tumours that lost the Y grew more aggressively by wearing out the immune cells that attack them.40PubMed Central. Y chromosome loss in cancer drives growth by evasion of adaptive immunity But that same exhaustion made them more responsive to a type of immunotherapy, PD-1 blockers.41PubMed Central. Y chromosome loss in cancer drives growth by evasion of adaptive immunity
For a man, there is no routine test for this in standard check-ups. Older age and smoking are widely reported links, so not smoking is a reasonable step. The heart and cancer screening already recommended for your age matters more than knowing your status.
Missing Pieces of the Y and Male Fertility
Among infertile men with very low or no sperm in one large group, about 1 in 7 had a missing piece of the Y, called a Y microdeletion.42PubMed Central. An analysis of Y-chromosome microdeletion in infertile Korean men with severe oligozoospermia or azoospermia Three regions, AZFa, AZFb and AZFc, contain genes needed for making sperm, and which one is missing affects how much sperm production is lost. That is why a test result names the region.
The most common missing region, AZFc, accounts for about 80% of deletions.43PubMed Central. Y-microdeletions: a review of the genetic basis for this common cause of male infertility Men with AZFc loss may have some sperm in semen, very little, or none. Those with no sperm in semen have about a 50% chance of sperm being found surgically,44PubMed Central. Y-microdeletions: a review of the genetic basis for this common cause of male infertility so surgery can be a reasonable try, though the figure is a probability, not a guarantee for any one man. Losing the whole AZFa region means no sperm, and surgical retrieval is generally not recommended.45PubMed Central. Y-microdeletions: a review of the genetic basis for this common cause of male infertility Complete AZFb loss is rare, 1 to 5% of deletions, with similar results.46PubMed Central. Y-microdeletions: a review of the genetic basis for this common cause of male infertility
For a couple, men with very low or no sperm are commonly offered a blood test for these deletions. Genetic counselling before sperm-injection IVF explains that sons would carry the same deletion.
Before sperm-injection IVF (ICSI), men with these deletions rarely fathered children, so the deletions were seldom passed on.47PubMed. Does intracytoplasmic sperm injection lead to a rise in the frequency of microdeletions in the AZFc region of the Y chromosome in future generations? Sons conceived this way can inherit the deletion and the same fertility problem.48PubMed. Genetic risks of intracytoplasmic sperm injection in the treatment of male infertility: recommendations for genetic counseling and screening Even so, one model estimates the share of men with AZFc deletions would at most double, plateauing after about five generations.49PubMed. Does intracytoplasmic sperm injection lead to a rise in the frequency of microdeletions in the AZFc region of the Y chromosome in future generations? Fertility treatment is not on track to erase the Y.