Why haven’t scientists found evidence of humans interbreeding with aliens?

Question

In my alternative universe, Atlantis was a real city that existed, although it wasn’t called Atlantis or founded by humans. Atlantis or rather, Dosham was a city on an isolated landmass in the northeast Atlantic Ocean, which would later become the Rockall Plateau belonging to a dying race of aliens called the Duxiaris. The Duxiaris colonised Earth in 40,972 BCE and created a slave race called the Bassirid created from various species of hominin.

At some point, the Bassirid would overthrow their masters and commit genocide against them, becoming the dominant species on Earth. But the Bassirid’s reign didn’t last long because they fought a dramatic civil war that reduced their numbers and would almost go extinct in 14,000 BCE after trying to summon a planet-killing abomination, which led to Dosham sinking. Yet several thousand Bassirid fled the sunk city and found refugee in prehistoric Eurasia without their technology.

These surviving Bassirid would then adopt a nomadic hunter-gatherer lifestyle, wandering across the Eurasian landmass and diverge into two subcultures at an undetermined point. One made their way towards the Pontic-Caspian Steppes and the other migrated into the Levant. As these groups ventured further into the unknown, they interbred with humans to maintain genetic diversity at the cost of becoming more and more humanoid.

Soon both subcultures would become assimilated into the Yamna and Natufian cultures, ending the Bassirid’s species. Yet, their legacies would live on through complex distorted oral traditions, which would influence Indo-European and Afroasiatic cultures. This phenomenon explains shared motifs like pantheons ruled by all-powerful sky gods that battle chaos serpents and cosmogenesis via sexual unity or corpse mutilation.

The only problem is that going extinct, both the Bassirid and Duxiaris did extensive interbreeding. After these species vanished, archaeologists, anthropologists or geneticists would have found that every one of Indo-European and Afroasiatic descent has Duxiaris DNA in them after their ancestors mingled with Bassirid.

Why hasn’t such a shocking discovery occurred?

Answer 1

There is nothing intrinsically alien about alien DNA. If you took a random string of alien DNA and compared it human DNA you would not be able to tell the difference. Therefore, since the alien DNA is so old, people just assume it is human DNA. Sure, there is a large shift, but there have been large genetic shifts throughout history, and if it really is so large that it must be noticed, then the two species would probably not be genetically compatible, so no interbreeding specimen would be viable.

Professor: Ah yes, that bit of genetic code that only occurs in indo-European and Afroasiatic peoples. My theory is that 16 millennia ago a great warrior was able to conquer the world similar to Genghis Khan, with similar genetic results. Because this was pre-history no records exist, but the DNA tells the story.

Student: But professor, I think it was alien interbreeding.

Professor: But that is impossible, there were no cows to probe or crops to make circles in.

The class laughs as the student sits down in shame.

Answer 2

The Duxiaris modifications were made deliberately, with careful analysis of each genetic change's consequences weighed against the progress it would make towards a specific, now unknown goal.

The Bassirid modifications were made in desperation, in pursuit of survival. The changes which they introduced to the humanoid gene line were more random and although still elevating the base humanoid to a higher potential, were no rival to the elevation provided to the humanoids under Duxiari care.

Now, with all of the original humanoids extinct after forty millenia of competition with two distinct breeds of alien enhanced humanoids, the world belongs entirely to the hybrids. And that world is divided into two distinct castes of people. Those who know they are of the Duxiari, who hold all the key power positions and scientific roles; and us, the others, who do not know of our alien ancestry, nor that we are dominated by a cousin species which far exceed our intellectual potential.

Answer 3

Human/Alien hybrids were not viable without sufficiently advanced technology

It is very much impossible for aliens and humans to interbreed naturally. They developed in completely separate ecosystems. Aliens might not even have DNA in the same way life on Earth has. It would be an amazing coincidence of convergent evolution if they would, and even more so if they happen to be compatible with humans. It's more likely for humans and jellyfish to interbreed.

So how did the aliens make it work?

Technology! Using their godlike biological knowledge, they found a way to create human/alien hybrids. But the alien technology is required to keep it working. It is not possible for the hybrids to procreate without it.

When Dosham was abandoned, the survivors managed to save these gadgets and drugs in sufficient quantities.

They then kept carrying that stuff with them. Over the generations they forgot how it actually worked or how to reproduce it. But it became part of their hunter-gatherer culture in form of culturally significant holy artifacts used in "fertility rites". But eventually the technology would malfunction or run out. Or they lost the knowledge how to perform these "fertility rites" correctly and most of the time they didn't work. The hybrids became infertile. Now that procreation of the alien genes was no longer possible, the hybrids died out and their genes were removed from the pool.

Answer 4

No point of reference. Plus genetic swapping takes place in nature it's called "Horizontal gene transfer" The point is... there's no way to determine an alien contribution to the human genome without an alien whose genetics we can analyze. If you're a biologist and you wanna name a new species you need a type specimen to analyze. Science demands proof and replicable experiments.

Answer 5

Answer: Mules.

The offspring of the alien/human were sterile and unable to reproduce further. With such a small pool of specimens, none of them have become preserved like Otzi the Iceman and are not available for study in the modern age.

Only the pure-bred Bassirid were capable of producing viable descendants. As the generations wore on, interbreeding became more common and fewer pure-bred Bassirid were born, leaving an ever-decreasing pool.

Whether the cause of the sterility is obvious or not might depend on the needs of your plot. If it needs to be invisible, then perhaps the males simply have lower sperm count, or the females lower egg production. Maybe males have excess testosterone and are more combative, tending to die in youth or combat before reproducing. Or if it helps to be obvious, perhaps the males are born with no testes.

Answer 6

The genes were destroyed by a gene-coded bioweapon

It was created either by the Duraxians as a means of controlling the Bassirids or by the Bassirids themselves during the civil war. But what it was is a pathogen which looks for alien DNA and destroys it. Fortunately it was never deployed successfully. But centuries later it eventually did get activated due to some unlikely coincidence and spread across the globe. Purebred humans weren't affected by the disease, but carried it. Any pure-bred aliens who got it died very quickly. People with just a bit of alien DNA got sick and had a chance to survive, but the disease would purge all alien DNA from their genome, so their offsprings would be pure humans.

If you are looking for a real historic event which might represent that genetic cleansing, then the Bubonic Plague might be a viable candidate. Although it might require some handwaving, because the Yersinia Pestis bacterium that caused it still exists, is still lethal to humans and is too well-researched for this story to be plausible to anyone who knows a bit about microbiology.