Exciting announcement, we just released a puzzle!
For our first-ever puzzle, we’re celebrating carcinization with a reconstruction of
what’s thought to be the oldest false crab: Platykotta
It’s available now at DFTBA.com!
And while you’re here, don’t forget:
Our 2023 calendar featuring some of our favorite “main characters
of paleontology” from classic Eons episodes is available now at ComplexlyCalendars.com!
In 2020, scientists studying the genomes of our closest extinct relatives,
the Neanderthals, found something…weird.
See, we’d already sequenced all of their other chromosomes, but we’d never been able to get
a good look at the Y-chromosome – one of the two chromosomes that determines sex…
Because the best-preserved remains just happened to be female.
So the researchers developed a new method to fish Y chromosome fragments out of the
less-well preserved remains of three male Neanderthals.
And when they finally managed that, what they found was totally unexpected.
The Neanderthal Y chromosomes were much more similar to ours,
Homo sapiens, than they’d anticipated.
In fact, it looked like these Y chromosomes were from ancient Homo
sapiens, but they were somehow hanging out in the genomes of male Neanderthals.
So how and why did this Y chromosome end up replacing the Neanderthal version?
Maybe it’s a bit self-centered that we can be pretty focused on the DNA that we
got from Neanderthals – but we shouldn’t forget that gene flow goes both ways.
And the missing Neanderthal Y chromosome points to a time that we changed their gene pool forever.
Scientists today generally agree that a group of Homo
sapiens from Africa migrated into Eurasia around 80,000 years ago.
There, they met and interbred with the other hominins that already
lived there -- our ancient cousins the Neanderthals and Denisovans.
And all living people of non-African descent come from those migrants,
so bits of Neanderthal and Denisovan DNA can still be found in our gene pool today.
We talked about this in our episode ‘When We Met Other Human Species’ – but now we want
to flip the script: what happened when these ancient cousins met us?
From the Neanderthal side, only a small percentage
of their total DNA can be traced back to interbreeding with us.
Overall, they were much more similar to Denisovans,
because they were each others’ closest evolutionary relatives.
So the fact that the Neanderthal Y-chromosome was
more like ours than like the Denisovans’ was a surprise…
One that suggests that the whole thing was completely
replaced in what seems to be all male Neanderthals!
But when did this Y chromosome replacement happen–and why?
The interbreeding events that took place around
80,000 years ago and after can’t explain where Neanderthals got a human-like Y chromosome.
We’d have to look much further back in time.
Scientists have known that there were multiple human dispersals out of Africa,
some of which didn’t leave modern descendants.
And we still don’t fully understand these ancient
interactions between different hominins and the implications of those meetings.
But the Y chromosome replacement points to one of them.
The researchers calculated that the human-like Y chromosome entered the
Neanderthal gene pool well before the migration out of Africa around
80,0000 years ago – probably as much as tens or hundreds of thousands of years before it.
Which means that many of the Neanderthals that
those migrants encountered must have already had human-like Y chromosomes!
Now, this was a really strange pattern,
unlike what we see in any of the other Neanderthal chromosomes.
But it wasn't entirely unique. See, the researchers realized
that a weird pattern had recently been found in their mitochondrial DNA, too.
Mitochondrial DNA is a small, separate second genome that is passed down only
from the mother. And, in Neanderthals, it also shows a puzzling link with ancient Homo sapiens.
The oldest Neanderthal mitochondrial genomes we have come from fossils
found in Spain dating to around 430,000 years ago.
And their mitochondrial DNA looks very Denisovan-like, rather than human-like.
This is what we’d expect, based on their evolutionary relationship.
But in later Neanderthals, this all changes.
The original Denisovan-like mitochondrial DNA is missing from all the younger Neanderthals
that we’ve sequenced. It’s been replaced with DNA that’s much more human-like.
And in 2017, it was proposed that the best way to explain this change is a previously unknown
period of very early gene flow between ancient Homo sapiens and Neanderthals.
Specifically, sometime between 470,000 and 220,000 years ago, a wave of ancient Homo
sapiens from Africa - or a group closely related to them - migrated into Eurasia.
While this wave eventually died out without leaving any direct descendants
in modern-day populations, they did leave a genetic legacy behind in Neanderthals.
At least one female individual from that group reproduced with a male Neanderthal,
and their hybrid offspring inherited her mitochondrial DNA.
Those hybrids must have been absorbed into Neanderthal populations and went
on to reproduce with other Neanderthals.
This allowed female hybrids to spread their mother’s human-like
mitochondrial DNA through the Neanderthal gene pool.
Eventually, over tens to hundreds of thousands of years, this mitochondrial
DNA seems to have completely replaced the original Denisovan-like mitochondrial DNA in Neanderthals.
So when the researchers later found human-like Y chromosomes
had also taken over the Neanderthal gene pool, they realized it must be
another piece of evidence for very early periods of interbreeding.
The only real difference is that, in this case,
at least one human male had sons with a female Neanderthal, introducing his
Y chromosome into the Neanderthal gene pool via those male hybrid offspring.
Now, for us to actually confirm that early gene flow is behind the Y chromosome situation,
we’d need to find the same evidence that we have for the mitochondrial DNA.
Namely, we’d need to sequence some really old male Neanderthals that
predate any gene flow with ancient Homo sapiens.
If and when we manage it, we’d expect that their Y chromosomes would be like
the original version – the one that looks more like the Denisovan version than ours.
Right now we only have the replacement Y chromosome, not the one that was replaced.
Ok, but why did the human mitochondrial DNA and Y
chromosome end up totally pushing out the ancestral Neanderthal versions?
After all, it’s not like we see this happen in just a few Neanderthal lineages in a couple
of locations. As far as we can tell, all Neanderthals eventually ended up with them.
Well, for such dramatic parallel replacements to have occurred,
they must have provided some kind of fitness advantages over the Neanderthal versions.
Now, we don’t know exactly what those advantages were, but we do have a good idea about why ancient
Homo sapiens DNA might’ve had an edge - and it all comes down to population size.
See, in small populations, natural selection is way worse at weeding out harmful mutations,
so they build up at a faster rate than in bigger populations, all else being equal.
And it’s been argued for a while based on both fossil and genetic evidence
that Neanderthal population sizes were pretty small, probably for a long time.
Which means that their Y chromosomes and mitochondrial genomes probably
had a higher build-up of harmful mutations.
So, as soon as ancient human versions were introduced, they were immediately
favored by natural selection and rapidly spread through the Neanderthal gene pool.
As for why we don’t see similar replacements in the Denisovan gene pool, well, it probably
just came down to distance. They lived much further away than the Neanderthals,
and were concentrated in Asia and Oceania as far as we can tell.
So there would have been less gene flow between ancient Homo sapiens
and Denisovans during those early waves of migration – certainly
much less than with Neanderthals, who lived in the Middle East and Europe.
Together, the Neanderthal Y chromosome and mitochondrial DNA are two new lines
of evidence that point to a much more complex and ancient relationship between
us and our closest cousins than we otherwise would have known.
They hint that ‘the’ out of Africa migration was only one of several
waves of ancient human dispersals into Eurasia.
And when that successful migration happened around
80,000 years ago, it was only the latest in a series of encounters between humans
and Neanderthals stretching back tens to hundreds of thousands of years.
Those Neanderthals had already been changed forever by the introduction
of human DNA into their gene pool long ago.
Thanks to our fellow humans, this month’s Eontologists!
Jacksy Weiss, Colton, Melanie Lam Carnevale, Chase Archambault,
Annie & Eric Higgins, John Davison Ng, Jake Hart By becoming an Eonite at patreon.com/eons you can
get fun perks - like submitting a joke for us to read. Like this one from The Burgins
What do you get when you cross a submerged land-bridge with a woolly mammoth? Wet!
[laughs]
Yeah sometimes simplicity is just funny
And as always thanks for joining me in the Adam Lowe studio. Subscribe at
youtube.com/eons for more evolutionary escapades.