The Y chromosome is one of the two sex chromosomes found in certain mammals, including humans. Every person has one pair of sex chromosomes in the DNA of every cell. The Y chromosome appears in males, who have one Y and one X chromosome. Meanwhile, females have two X chromosomes.
The presence of the Y chromosome determines the sex of an embryo, but research suggests that it has degenerated and shrunk over time. (Today, it has about 45 genes compared to the X chromosomes estimated 1,000.) Therefore, the question has arisen: Is the Y chromosome dying out?
What is Happening to the Y Chromosome?
“Our sex chromosomes weren’t always X and Y,” said Melissa Wilson, an evolutionary biologist at Arizona State University. “What determined maleness or femaleness was not specifically linked to them.” She explains that the first mammals didn’t have any sex chromosomes when they had evolved 100 or 200 million years ago. Instead, the X and Y structures were identical to any other set of chromosomes.
Keep in mind, some animals don’t need sex chromosomes, even today. Jennifer Graves, a geneticist at La Trobe University in Melbourne, Australia, points out that all chromosomes have a mix of genes, and not all are sex-related. In the Y chromosome, only the SRY gene stands out for causing male development instead of the default female. But for turtles and alligators, there is no switch; the embryos’ sex depends on the temperature of their environment. Graves theorized that a similar setup existed until the SRY suddenly evolved and continued. 
The degeneration of the Y has a simple explanation. Throughout time, genes develop harmful mutations but they have a system to avoid passing them on. When the body produces sperm and eggs, chromosomes mix and recombine with each other to increase the chances that only functioning copies will get passed on during reproduction. The paternal and maternal chromosomes can mix and match with each other, except for the Y, which doesn’t have an equal to recombine with.
“If a bad mutation occurs, usually you’d be able to swap with your partner. But the Y can’t do that,” Wilson said. Therefore, Y chromosomes had no choice but to keep the mutations, which made the Y smaller over time.
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“The whole Y will disappear in 4.5 million years”
Research conducted by Graves indicates that the Y may have had 1,669 genes 166 million years ago. “Same as the X chromosome,” she said. “So it doesn’t take a great brain to realize that if the rate of loss is uniform — 10 genes per million years — and we’ve only got 45 left, the whole Y will disappear in 4.5 million years.”
However, recent research has found the Y has slowed its degeneration, possibly to a standstill. For instance, a Danish study examined the Y from 62 men and found that it can conduct structural rearrangements to allow gene amplification, which helps sperm function and reduce gene loss. The study also found that the Y has created a unique palindrome structure to protect itself. Essentially, the palindromic sequences have a process that copies genes to take the place of damaged ones. 
The disappearance of the Y has already happened in other species, Graves added. Two species of rodents called mole voles have lost the Y, in addition to three endangered species of spiny rats in Japan. Moreover, these species still exist, proving that the loss of the Y doesn’t mean extinction. In fact, mole voles and spiny rats still have distinct females and males. “People think that sex is sort of a very determined thing,” said Rasmus Nielsen, a geneticist at the University of California, Berkeley, “That if you have a Y chromosome, then you’re a man, or you don’t have [a] Y chromosome, then you’re female. But it doesn’t work like that.”
The Future of the Y Chromosome
Although the Y chromosome receives all the acclaim for determining sex, 95% of genes that differentiate between females and males don’t come from the Y and X chromosomes. For example, the gene that encodes estrogen receptors — vital for female growth and development — comes from chromosome 6.
“Losing the Y chromosome doesn’t mean losing the male,” Nielsen concluded. Plus, Graves stated that it’s likely another gene would compensate for the Y if it ever loses its function to determine the sex of an embryo. Meanwhile, some scientists argue that the Y chromosome can’t cease existing because of inbuilt mechanisms, like the palindrome structure, that will protect it from losing its genetic material. Whether it happens or not, it’s not a pressing concern since the estimated expiry date is over 4 million years. 
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- “Y chromosome.” Medline Plus.
- “Is the Y chromosome dying out?” Live Science. Isobel Whitcomb. August 29, 2020
- “The Y chromosome is disappearing – so what will happen to men?” The Conversation. Darren Griffin and Peter Ellis. January 7, 2018
- “Are men going extinct?” The University of Melbourne. September 13, 2020