The gene that most likely determines the sex of the platypus and echidna has been identified by Australian and Swiss researchers.
The study also shows that the Y chromosome, contrary to previous assumptions, carries genes that are important to the basic viability of male mammals, says geneticist Dr Paul Waters from the University of New South Wales.
Although the Y chromosome is known to be important in sex determination, little is known about the function and evolution of its genes, says Waters.
He says this is because it has so many repetitive and palindromic sequences, which make it hard to reconstruct the true sequences of its genes from fragments of sequenced DNA.
Monotremes (the platypus and the echidna), whose males have 5 X chromosomes and 5 Y chromosomes, are especially challenging.
"No one had really characterised any Y chromosomes in platypus before because they've got quite a complex sex chromosome system," says Waters.
Waters and colleagues from the University of Adelaide and the University of Lausanne now report on their new analysis of male and female DNA from 15 representative mammals, including human, elephants, marsupials and monotremes.
The study, reported recently in the journal Nature, is the largest of its kind, and relied on a rapid new sequencing technique.
For each species, the researchers identified Y chromosome genes by looking for those DNA sequences that were specific to males.
By using a molecular clock, which combines fossil evidence and rates of change in DNA sequences, the researchers were also able to work out when specific genes evolved.
Waters says the process uncovered for the first time a gene, called AMH [for Anti-Müllerian hormone], on the oldest of the platypus Y chromosomes that appears to determine if an animal becomes male.
"If an animal has that gene it will act as a master switch to turn on testis development," he says.
"That was quite a big finding because we had no idea what might be causing male platypus to develop as males."
Waters says short of knocking out the gene in platypus and finding out how it affects their sex, this is the "best evidence to date" on what determines if an animal becomes male.
Unlike monotremes, male marsupials, like kangaroos, and placental mammals, like humans, have only one X and one Y chromosome, and a different sex-determining gene, called SRY.
Waters and colleagues worked out that both this Y chromosome system and the monotreme system evolved around 180 million years ago, but arose independently of other.
"It's a case of convergent evolution," he says.
The researchers are not sure what determined sex prior to the evolution of these genes.
"It could have been an environmental cue such as temperature or could have been a different genetic sex determining system that doesn't exist today," says Waters.
Waters says Y chromosomes started their existence as non-sex chromosomes but over time lost a number of genes.
"As the Y chromosome evolved, it withered away, losing most of the 1000 genes that are found on today's X chromosome."
He says because females don't have a Y chromosome it was believed that over all genes on the Y chromosome could not be too important.
"It was hypothesised that the Y chromosome can't hold anything that's critical to life."
But it turns out this is not the case.
The new study has found that while some of the genes preserved on the Y chromosome evolved for male-specific functions, such as testis development or sperm production, in most species, most Y-specific genes are actually important for the male's basic viability.
They include genes involved in regulation of protein production, which require two copies to be functional. In males, this means having one copy on the X chromosome and one on the Y.