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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?

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    $\begingroup$ What is the hallmark of this DNA to make it a shocking discovery? These humans have this DNA -- well, humans do. Only if they could figure out it was alien would it be an issue. And given how old it was, it would probably just come across as human. $\endgroup$
    – Mary
    May 25 '20 at 0:52
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    $\begingroup$ "... and created a slave race called the Bassirid created from various species of hominin." So the Bassirid were entirely earthly DNA? No alien DNA at all? I think you answered your own question. $\endgroup$ May 25 '20 at 2:02
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    $\begingroup$ (Retro)Viruses. They deliberately released viral agent's which messed up the genetic markers. Maybe due to an accident or deliberately. Maybe an attempt of viral warfare gone wrong or deliberately an act of masking. $\endgroup$
    – pinegulf
    May 25 '20 at 11:17
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    $\begingroup$ If everyone of human descent had (any-kind-of) DNA why exactly would your scientists not see that as uni-ancestral DNA? Is it not true that today, at least most if not all geneticists believe all human are descended from a single "Black Eve" umpty-great-grand-mother? Either your groups can interbreed, or they can't. Which would you prefer? Indo-European I understand but where did you find "Afroasiatic"? Even "Afro-Asiatic" seems wholly alien to Earth history. $\endgroup$ May 25 '20 at 17:20
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    $\begingroup$ How did the Dosham avoid being buried under several hundred meters of ice during the Pleistocene? $\endgroup$ May 25 '20 at 21:32
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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.

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    $\begingroup$ And even if they did realize it was "interbreeding", almost certainly the other species would be considered an ordinary species. In the same way that we might have some neanderthal DNA going around in us. They might've come from space; we wouldn't be able to tell from their DNA. $\endgroup$
    – Erik
    May 25 '20 at 9:21
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    $\begingroup$ And DNA are not stamped with a label that says "This is Human DNA. This is Alien Race X-01 DNA". DNA analysis uses similarities. Your DNA is generally more similar to your parents than to your aunt. Can your DNA mutate in such a way that it is more similar to your aunt than your parents? Sure, but they'll have no way to really find out unless they breed people to test it out, but that is extremely unethical... $\endgroup$
    – Nelson
    May 26 '20 at 7:33
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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.

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  • $\begingroup$ This is unlikely to hold up given how easy it is these days to get your DNA analysed and how many students do it as a part of their courses. $\endgroup$
    – Erik
    May 25 '20 at 9:23
  • $\begingroup$ But all the DNA labs are owned and run by Duxiari and so are the companies which make the DNA analysis equipment which the student's use. Filtering the species differentiating genes out of result reports and replacing them with less revealing dummy values is a standard feature of that lab equipment used in all labs. It is only turned off in the doctoral level courses which non-Duxiari students never get to no matter how hard they try. $\endgroup$ May 25 '20 at 13:07
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    $\begingroup$ You might want to add some extra explanation about the sheer size and influence of this second caste; it sounds like one hell of a conspiracy you've got going on here, with probably hundreds of thousands to millions "in the know". $\endgroup$
    – Erik
    May 25 '20 at 13:17
  • $\begingroup$ Actually, since the winning species in any survival challenge is by definition larger than the loosing species, more than half of the planet's population are of Duxiari origin. The scale of the conspiracy overwhelms the limited imagination.of the Bassirid mind. ...but they are very good at what they do and have such a great advantage over us (in both numbers and intellectual capacity) that the few Bassirid who discover the truth are quickly convinced that keeping the secret is in everyone's best interest. Inevitably, there will someday be a species war and when it happens, we will loose. $\endgroup$ May 25 '20 at 13:26
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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.

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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.

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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.

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    $\begingroup$ MOST were sterile. But like horse/donkey hybrids, every once in a while one managed the feat. And, even more rarely, once in a while once of the offsprings-of-hybrids somehow survived to become - ZALGO!!!!! $\endgroup$ May 26 '20 at 21:31
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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.

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