All chromosomes normally appear as an amorphous blob under the microscope and only take on a well-defined shape during mitosis.

It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.

[16] However, research published in 2008 analyzing the platypus genome[17] suggested that the XY sex-determination system would not have been present more than 166 million years ago, when monotremes split from other mammals.

[18] This re-estimation of the age of the therian XY system is based on the finding that sequences that are on the X chromosomes of marsupials and eutherian mammals are not present on the autosomes of platypus and birds.

[14][26] Comparative genomic analysis reveals that many mammalian species are experiencing a similar loss of function in their heterozygous sex chromosome.

Degeneration may simply be the fate of all non-recombining sex chromosomes, due to three common evolutionary forces: high mutation rate, inefficient selection, and genetic drift.

[28] Additionally, a scientific report in 2012 stated that only one gene had been lost since humans diverged from the rhesus macaque 25 million years ago.

[29] These facts provide direct evidence that the linear extrapolation model is flawed and suggest that the current human Y chromosome is either no longer shrinking or is shrinking at a much slower rate than the 4.6 genes per million years estimated by the linear extrapolation model.

[citation needed] The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed.

[14] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.

[30] The observation that the Y chromosome experiences little meiotic recombination and has an accelerated rate of mutation and degradative change compared to the rest of the genome suggests an evolutionary explanation for the adaptive function of meiosis with respect to the main body of genetic information.

[32] Without the ability to recombine during meiosis, the Y chromosome is unable to expose individual alleles to natural selection.

Due to this inability to sort through its gene content, the Y chromosome is particularly prone to the accumulation of "junk" DNA.

[14] The random insertion of DNA segments often disrupts encoded gene sequences and renders them nonfunctional.

[33] From the definition of entropy rate, the Y chromosome has a much lower information content relative to its overall length, and is more redundant.

Even if a well adapted Y chromosome manages to maintain genetic activity by avoiding mutation accumulation, there is no guarantee it will be passed down to the next generation.

In the case of the Y chromosomes, the palindromes are not noncoding DNA; these strings of nucleotides contain functioning genes important for male fertility.

The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other.

[37] These gene conversion events may reflect a basic function of meiosis, that of conserving the integrity of the genome.

Several species of rodent in the sister families Muridae and Cricetidae have reached a stage where the XY system has been modified,[38][39] in the following ways: Outside of the rodents, the black muntjac, Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and autosomes.

[56] The complete sequencing of a human Y chromosome was shown to contain 62,460,029 base pairs and 41 additional genes.

As a result, the NCBI RefSeq bacterial genome database mistakenly includes some Y chromosome data.

[80] Mosaic loss may be related to health outcomes, indicating that the Y chromosome plays important roles outside of sex determination.

[82] However, a 2022 study showed that mosaic loss of the Y chromosome causally contributes to fibrosis, heart risks, and mortality.

This usually results in defective testicular development, such that the infant may or may not have fully formed male genitalia internally or externally.

When the Y fragment is minimal and nonfunctional, the child is usually a girl with the features of Turner syndrome or mixed gonadal dysgenesis.

Mitochondrial DNA, maternally inherited to both sons and daughters, is used in an analogous way to trace the matrilineal line.

[95] In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal blood stream for as long as 27 years.

A total of 120 subjects (women who had never had sons) were investigated, and it was found that 21% of them had male DNA in their peripheral blood.

The subjects were categorised into four groups based on their case histories:[97] The study noted that 10% of the women had never been pregnant before, raising the question of where the Y chromosomes in their blood could have come from.