One of the big discoveries of human evolution is that our species can't keep it in our pants. As modern humans migrated out of Africa we mated with at least two other species of human (that we know of).
However, it turns this sort of inter-species promiscuity isn't a uniquely human trait. Researchers have found that our earlier ancestors actually mated with other apes.
Around 7 million years ago several species of ape were living side by side. This includes the ones that would eventually evolve into us. True to form, these apes mated with their neighbours. This spread genes between us that we still have today.
Meet the family
To really understand inbreeding you obviously first need to know who you're related too. So let me first quickly introduce the human family tree. Or at least, what it looked like 6 - 7 million years ago.
This is an important part of our history as it's when the human lineage began splitting from the chimp lineage. All those on the human side are called "hominins", if you want to get technical, and would eventually give rise to us. Those on the chimp side haven't given themselves a cool name, so we just call them "panins". After the chimp species name, Pan troglodytes.
Ok, let's stop with the technical terms. Even I struggle to remember many of them, which isn't helped when scientists keep giving groups dumb names. Like Gorilla gorilla gorilla. Yes, that's a real species, look it up.
So let's pretend we're just a regular family.
We are Jane Hominin. Our brother is Jessy Panin. Despite our different appearances, we have the same mother. She also had a sibling, who would be our aunt. They're now the gorillas. Our grandmother (the mother of our mother and the gorillas' mother) also had a sister. The orangutans. They're our most distant living relatives in the ape family.
Although if you wanted to get really technical since our aunt and great aunt have kept evolving then gorillas and orangutans would be their descendants. Not our actual great aunt and aunt. Thus, gorillas and orangutans would actually be our first and second cousins respectively.
So now you know the gist of the ape family tree, let's look at how our ancestors violated it.
NUMTy
Normally when scientists find evidence of interbreeding, it's because they found some ancient genome of a different species. When they discover key similarities between our genome and theirs it's a sure sign we were getting very friendly.
However, when looking at interbreeding amongst our great-grandparents, DNA just doesn't survive that long. Instead, they had to turn to a quirk of genetics called a NUMT, or "nuclear pseudogenes of mitochondrial DNA". Essentially, these are bits of our mtDNA that have gotten mixed up in the main nuclear genome. There they do nothing, except exist as a "fossil" of the mtDNA.
Enter a NUMT called pc5. It's found in us, chimps, and gorillas. This indicates it made the leap to NUMT status sometime in our grandparent's life. If it did so in our great-grandparents' lives, orangutans would also have it.
What's more, we can actually pinpoint when this happened. After a NUMT enters the DNA it doesn't evolve much since it no longer does anything. Thus, only random mutations influence them; which occur at a fairly well-defined rate. This rate indicates ps5 entered our DNA around 6 million years ago.
These apes mated
So, to summarise, ps5 became entered our DNA from our mtDNA 6 million years ago. There it became the NUMT we all know and love.
Now, here's where things get interesting. See, ps5 doesn't look like mtDNA 6 million years old. It actually looks dramatically older. In fact, it seems to have gone through an extra 4.5 million years of evolution.
The only way to explain this extra evolution is if it came from a different species of ape. That ape must have been independently evolving for some time, producing distinct mtDNA. Then our ape ancestors mated with this different species. Our grandparent inherited some mtDNA, including Ps5. It then made the jump to NUMT status, where it still exists in us to this day.
The implications of this are fairly huge. Of course, the big take home is our ape grandparents were interbreeding with other apes. But it also means there were an unknown ape species living with them. Maybe we've already found fossils of it, or maybe it's a completely new discovery!
The other interesting finding is that this inbreeding and the subsequent NUMT-ification of ps5 happened after our gorilla-like grandparents were supposed to have lived. Remember, the NUMT developed 6 million years ago? However, our grandparents were supposed to have produced our parents 8 million years ago.
This disconnect means that our parents still shared genes with their gorilla siblings, even after they had begun to diverge. Ps5 is one of these we still have.
Scarily, it means we're the result of our parent's incest. That makes us King Joffrey.
*shudder*
tl;dr
Some time ago a human, chimp, or gorilla ancestor mated with another species of ape. This introduced ps5 into their lineage. Interbreeding between those aforementioned apes spread ps5 around, so now we all have it.
References
Popadin, K., Gunbin, K., Peshkin, L., Annis, S., Kraytsberg, G., Markuzon, N., Ackermann, R.R. and Khrapko, K., 2017. Mitochondrial pseudogenes suggest repeated inter-species hybridization in hominid evolution. bioRxiv, p.134502.
