Decades of teasing apart Neanderthal DNA has produced an archive of ancient genes that spell out a history of love affairs between estranged branches of humanity's family tree.

Until now, the story has been rather lopsided. For whatever reason, the most well preserved material has come from female remains, leaving an entire male genetic history in the dark.

Finally, however, Neanderthal (aka Neandertal) men now get to tell their side, thanks to a newly conducting sequencing of their Y chromosome.

Researchers from around the globe collaborated to successfully identify male-specific DNA sequences from the remains of three Neanderthals recovered from sites in modern Russia, Spain, and Belgium.

All lived roughly 38,000 to 53,000 years ago, in what's essentially the twilight years of the now extinct humans.

These were compared with similar genes in their more eastern cousin, the Denisovan, represented by two sets of Siberian remains from individuals who lived around 70,000 and 120,000 years ago.

If we didn't know any better, we might guess these Neanderthal and Denisovan men would have fairly similar chromosomes. After all, they split from the same stock that divorced modern humans around 800,000 years ago, only their own separation was much more recent – about 400,000 years ago.

That wasn't what the researchers found at all. Rather, the Y chromosome in the Neanderthals was a closer match for ours than it was the Denisovans'.

"This was quite a surprise to us," says evolutionary geneticist Martin Petr from the Max Planck Institute for Evolutionary Anthropology, the study's lead author.

"We know from studying their autosomal DNA that Neandertals and Denisovans were closely related and that humans living today are their more distant evolutionary cousins. Before we first looked at the data, we expected that their Y chromosomes would show a similar picture."

This discrepancy implies a swap took place shortly after their separation, exchanging the Neanderthal's original Y chromosome for one more like ours.

Exactly why such an exchange took place isn't clear.

We know our ancestors couldn't keep their hands off one another (or pretty much any other human population), with frequent genetic mixing events leaving a legacy of DNA in our own genomes today.

But this isn't like leaving behind a small genetic recipe for coping with a disease or malnutrition. It's a whole recipe book that potentially affects a wide range of male sexual and non-sexual characteristics.

One possibility is that this version of the Y chromosome was simply doing a better job.

"We speculate that given the important role of the Y chromosome in reproduction and fertility, the lower evolutionary fitness of Neandertal Y chromosomes might have caused natural selection to favour the Y chromosomes from early modern humans, eventually leading to their replacement" says Petr.

Computer simulations showed that relatively small Neanderthal communities scattered across the continent could have easily amassed a bunch of problematic mutations through inbreeding.

A more robust version of a Y chromosome picked up from humans could have added a fertility boost, quickly gaining ground as it was passed from fathers to sons down the family line.

Whoever those chromosome donors were, they eventually petered out themselves. Though more closely related to our modern global community, their bloodlines were also a dead end.

Just getting this level of detail from ancient male bones was a task in itself. Jokes about fragile masculinity aside, the Y chromosome isn't exactly a solid piece of work.

In the study, the researchers put the early human Y chromosomes together by using modern Y sequences as a template for a special set of probes. Clinging to as much shared DNA as they could, the probes also dredged up enough unique sequences to build a complete picture.

It's technology we might be able to use to fill in even more of the missing chapters of the Neanderthal's past.

"If we can retrieve Y chromosome sequences from Neandertals that lived prior to this hypothesised early introgression event, such as the 430,000-year-old Neandertals from Sima de los Huesos in Spain, we predict that they would still have the original Neandertal Y chromosome and will therefore be more similar to Denisovans than to modern humans," says senior author Janet Kelso from the Max Planck Institute for Evolutionary Anthropology.

It's certainly possible, but given how studies like this tend to deliver more twists than any modern reality show, we're sure there'll be a surprise or two waiting in just about any set of male Neanderthal genes we find.

This research was published in Science.