Y chromosomes underlie sex determination in mammals, and have evolved differently in various groups, like monotremes and therians. These are the two major groups of mammals, monotremes being egg-laying mammals and therians the placental and marsupial mammals. Researchers have tried to study the evolution of the Y chromosome for decades, but it has been hard to do so because of its repeat-rich nature.



Figure 1. shows the structure of a Y chromosome in situ

They sequenced the Y chromosome from 10 species, and together with already available Y sequences, 15 species covering all major lineages of Mammalia could be investigated. The data was compared to an outgroup of birds, looking at when each Y gene evolved independently from their gametologue, their homologous gene on the other sex chromosome.

Differentiation of the Y chromosomes occurred because of recombination arrests, bringing gene decay and a smaller size compared to the X. The Y chromosome can be divided into very distinct regions called ‘strata’, which stopped recombining at different times, giving clues about the phylogenetic history of the Y chromosome. There was originally only a small non-recombining region, which started expanding at discrete intervals, which created the different stratas that can be identified by their differing genetic codes.

They found that the therian stratum 1 (S1) contains 4 genes, including a gene named SRY which is involved in the male sexual development. S1 originated shortly before the split between eutherians, the placental mammals, and marsupials around 180 million years ago.

After the split between eutherians and marsupials, the divergence rate for the Y chromosome stratas was significantly higher than their homologues on the X chromosome. This suggests that the rate of mutation was much higher in males, and heavily influenced the genomes of therians. Analysis of S3, S4, and S5 stratums revealed the evolution of several unique Y genes across species, which underscore the dynamic nature of Y chromosome evolution. Recent evolutionary progression in primates was also discovered; it was found that primate Y chromosomes have recently recruited additional genes through various transpositions and translocations from autosomes. The results for monotremes were quite different, as they could not find any significant differences between their Y and X gametologues.

In studying the functional evolution of the Y chromosome, researchers attempted to determine the reason why only small specific subsets have been preserved. Characteristic functions of these genes were searched for using various simulations; it was found that highly non-random gene sets with similar functions were maintained across different Y chromosomes. Analysis showed that current Y chromosomes are enriched for genes that are involved in transcription regulation, implying that current Y genes are preserved to maintain the ancestral gene dosage. They found that expression levels of therian Y genes have decreased during sex chromosome differentiation, highlighting partial regulatory decay of Y genes coupled with evolution towards new functions.

The result of this paper shows that there are very few remaining genes belonging to the first three strata, so there must have been great decay because of the lack of recombination. But there was also a drastic reduction in the decay once the small, essential range of genes was defined, preventing those genes from getting lost. The culmination of these findings present significant implications for the evolution of the Y chromosome, as this study was able to provide initial clues for the evolution of the Y chromosome.