CARTA: Ancient DNA and Human Evolution – Johannes Krause: Ancient European Population History

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So I would like to talk today about a more recent chapter in human history. So we
have heard a lot about the early chapters of human history today about the early
evolution of modern humans in Africa and also about the interaction between archaic
humans and early modern humans. But I would like to talk today and turn our
focus from the ice age, the Pleistocene, into the Holocene into the last 10,000
years of human history and I try to convince you that this is also an
extremely exciting time period where we even see a lot of changes even in human
evolution into human phenotype in several parts of the world. So as I mentioned,
we’re actually living today in this time period, the Holocene which is a time
period of relative climate stability, some people might even say that we have
actually changed our environment so much that we’re now living in a time period
which we call the Anthropocene which might have started in the last 2,000 years but
the main focus of this talk should really be the Holocene, so the last 10,000 years
of human history. Most of this time period actually we do not have historical
documents so we have no information that people wrote down about human history in
this last 10,000 years where we usually have to rely on archeological information
for example, or paleo-anthropological findings, so human skeletons for example
that might tell us something about things that changed in the past the same thing
for example like migration, genetic admixture or the genetic turnover of the
human population. But we and others have actually started in the last few years to
use genetic data to tell us something about changes that happened recently in
our evolution or in human history and I would like to focus my talk today about
one event that archeologists had already identified many years ago and that is
probably the biggest change in human history that happened in the last few
million years and it’s actually the change from the subsistence strategy of hunting
and gathering, to Neolithic farmers that relied on agriculture and started to
domesticate animals. And this revolution, this big change in human history is called
the Neolithic Revolution. So this Neolithic Revolution started in central
Europe about seven and half thousand years ago and in other parts of the world a few
thousand years earlier and a few thousand years later. But this big change is really
the cornerstone of our modern civilization because it provided people then with
resources that actually allow us to sustain millions and even billions of
people today and that basically came with this big change from this foraging
lifestyle to this early farming lifestyle. What archeologist have debated for more
than 100 years now is whether this change of subsistence strategy from foraging to
farming was actually related due to the spread of ideas and culture. So was it
just cultured ideas that were passed on from village or from region to region or
was it actually people that were bringing agriculture to different parts of the
world? For example, to central Europe about 7,000 years ago. So this big
question, was it pots or people that basically then spread agriculture into
Europe and other parts of the world. And this question is very hard to address just
based on archeological artifacts, for example, or anthropological findings
because it is very difficult to really see if biological identity of people changes
just based on archeological artifact. And this is actually a question which is much
easier to address if we look at genetic data. So if we look at the DNA, if we look
at the genetic makeup of the people because it makes very clear predictions
for this two different hypothesis, whether it was ideas that were spreading during
that time or whether it was actually people.
So if we assume that ideas and culture was, for example, spreading and
agriculture, we would expect that there would be direct genetic continuity
between, for example, the first people that lived in Europe, foragers 10,000
years ago, and then the first Neolithic people and then the people that live in
Europe today. So you would see genetic continuity if it was just the spread of
ideas. However if it was actually people spreading agriculture, for example, into
Europe we would expect the genetic discontinuity, something that’s called
“demic diffusion,” we would actually see that people would then, for example, come
to Europe and change the genetic structure so new genes would arrive, for example, in
Europe. And we and many others have tried to address this question based on
mitochondria but as you have seen in some of the previous talks, mitochondrial DNA
can be quite decisive. So therefore we have decided then in the last few years to
actually study whole genomes of early farmers as well as late hunter-gatherers,
so ancient foragers, to study this question whether there was actually
genetic change of people when agriculture was introduced to Europe, or whether there
was direct genetic continuity. So we have sequenced genomes of about 12 early
hunter-gatherers some years ago and combined that with data sets that had been
provided by other people, for example, like the Iceman genome. This famous
Tyrolean mummy that was discovered a few years ago and was actually frozen for
about 5,000 years in the Alps. As well as a genome from a hunter-gatherer that was
found here in Spain some years ago. And we then compared those ancient human genomes
with the genome of about 2,000 people that come from various populations, about 200
populations in the world today with the data set that is called the “Human
Origins” data set that is based genome-wide data of now up to 5,000 people
from many different populations in the world. If you then take genomic data from
ancient and modern people and you want to compare that, you can imagine you have
heard those genomes are really big, there’s a lot of data and one way to break
down this data into two dimensions that you can actually look at is a so-called
principal component analysis, where you basically take this genetic information
from all those people and break it down into two most informative components,
principal component one and two. And if you do that for modern people, you get
those beautiful, colorful clouds that you see here. And actually if you look at the
right cloud here, this cloud is actually people that live today in Northern Africa,
in the near East as well as in the Caucasus. We actually see this climb that
stretches from Northern Africa into the Caucasus. Those populations here are
populations that live in Europe today. So people that live for example in Iberia,
France, Central Europe as well as Great Britain or Russia. What you actually see
here almost resembles geography. If you imagine this as kind of the Northern
African coast, this is in near East, here could be the Black Sea, this could be the
Mediterranean. So it could be an isolation by distance, people moved into those
places and then basically genetically slowly changed over time. However, if we
now look at our ancient individuals, our ancient foragers as well as the early
farmers from 7,000 years ago, we first see that our ancient foragers are genetically
actually quite distinct from the people that live in Europe today. Now there seems
to have been not a strong continuity between the ancient foragers and modern
Europeans. So basically no modern Europeans that live today that looked
genetically like ancient foragers. This is actually different for the ancient
farmers. So those 7,000 year old farmers from Central Europe they actually do
cluster with populations that live in Europe today. You could see this little
green cloud here. If you look at this cloud, this is actually people that live
in Sardinia today. And this was already discovered when the Iceman genome was
sequenced some years ago. The colleagues actually found that the Iceman looked
genetically very similar to people that live in Sardinia today, and that actually
made them also to hypothesize that maybe he was some sort of tourist from Sardinia
that had gotten lost in the Alps and just died there and froze to death. Today we
actually know that this was not quite the case because we now have genomic data from
many early farmers, from Scandinavia, from Iberia, from Central Europe, from Southern
Europe and they all cluster together with Sardinians. So it is not that they all
come from Sardinia, it is rather that modern Sardinians look genetically like
early farmers. But what you then also see is that people that live in Europe today
are not just a simple mixture between those ancient populations, so the foragers
and the farmers, we actually stretch all the way up here and if you can actually
see those little diamonds up there, that some more ancient genomes which are on
this plot that are actually populations which we call “Ancient North Eurasians”
which are best represented by people that lived about 10,000 20,000 years ago in
Siberia. For example, one child that was sequenced by the group in Copenhagen from
Lake Baykal which is called the Malta child. So you see that modern Europeans
seem to be a mixture between those three ancient genetic populations. But what is
also very clear is that if you look at that, neither the ancient farmer nor the
ancient forager seem to have this North Eurasian component. This North Eurasian
one is actually quite distinct and we wanted to find out when did this ancient
North Eurasian component arrive in Europe. To do that, we teamed up with David Rice’s
team as well as Svante Pääbo and collected also data from the team in Copenhagen and
now put together a data set of about 230 ancient human genomes that span 8,000
years of European history to see when the kind of different genetic components over
the last 8,000 years formed. So now we actually go forward in time starting about
8,000 years ago and look at the genetic structure of Europe.
What you see here in the background, those gray dots, are the modern populations and
those are the ancient individuals. So the first thing you observe if you look at the
ancient foragers, so the indigenous Europeans or Western Eurasians, you see
that they form this little cloud here and that there’s a gradient from the west to
the east. So this was the genetic structure of the hunter-gatherers that
lived in Europe about 8,000 years ago. If you look at the same time into the region
here which is Turkey today, Anatolia, you can see that the Anatolians at that time,
they already practiced agriculture, so they are Neolithic, so they’re early
farmers. They’re genetically, actually, quite distinct from those Europeans that
lived at the same time in Europe. If we then move ahead in the next thousand
years, agriculture comes to Europe and suddenly when you look at the people that
lived in Europe at the time, they look exactly like those Anatolian Neolithic
farmers. So it seems very clear now that those Neolithic patches actually spread
with those people because Europeans suddenly looked like that and not look
like that anymore. So there is very strong evidence, now, that there was this
discontinuity of the people, that genetically there was this large change of
people at that time period about seven and half thousand years ago in Central Europe.
If we now move in the next 2,000 years of human history in Europe, we can actually
see that the population structure doesn’t really change so much. Genetically, people
look again quite similar to those early farmers from Anatolia, but you could
actually see a little bit of this movement in this direction and this is indeed
something that we observe that there seems to be a bit of genetic admixture with the
hunter-gatherers that lived in Europe at the time, probably still in mountain
ranges and in regions where agriculture was not favorable. So there was a bit of
genetic admixture between those early farmers and the hunter-gatherers that were
living in Europe. However, again, this is modern Europeans. They’re not really
somewhere down here, so what’s happening? We should kind of look a bit more to the
East, and this is the same time period that we just looked at in Central Europe
now looking at Eastern Europe so looking at the populations which are found here,
this north of the Black Sea, or the Caspian Sea. We can actually see that this
population which is Neolithic or Bronze Age are steppe populations. So those are
also agriculturalists but they are not sedentary but pastoralists, so they’re
herding, for example, cows. And this population is very homogenous stretching
all kind of this region here and again they are kind of falling up here quite
distinct from the early farmers of Europe also quite distinct from the
hunter-gatherers. And you can actually see they are also pretty close to this
Eneolithic individuals here which are actually late hunter-gatherers from this
region. But they are a bit more stretched in this direction in fact and there seems
to be something hiding here and something I don’t really have the time to talk today
about, but that would be a different chapter in human history. But what’s now
going on with the modern Europeans that live today in Central Europe? When does
their genetic makeup actually form? And this is actually been happening about
4,800 years ago, 4,800 years ago and suddenly you have a major shift in the
genetic structure of Europe. So if we move now to this time period 4,800 years ago to
about 3,000 years ago, suddenly you have people in Central Europe that looked like
people that live in Central Europe today. So they are a genetic mixture of this
steppe component that we have in the Bronze Age here in the steppe, as well as
this early and middle Neolithic people that you had in Central Europe at that
time. So there seems to be a massive event of migration. Suddenly you see this
massive shift and you don’t only observe that in Central Europe and in Southern
Europe, but you even observe that in Central Asia as well as in the Altai,
there seems to be a very strong evidence now for a large migration. We can then
also quantify those genetic components in the different populations that live in
Europe today. So those three ancestral components the early foragers, the early
farmers, as well as this steppe pastoralists. You can actually see there
is a climb, so populations that live in Northern Europe today or Northeastern
Europe they have quite a high amount of steppe ancestry and quite a low amount of
early farmer ancestry. Whereas the people that live in Sardinia today have almost
exclusively early farmer ancestry as I’ve shown you before and very, very little
ancestry here from the steppe. And if we look at the ancient populations, you can
actually see that if you move from back in time towards today, you can see that early
on we have this really strong component of early farmer ancestry from Anatolia. Over
time you have a little bit of this forager indigenous European admixture that seems
to happen over the next few thousand years. But then 4,800 years ago we
suddenly have this green component coming in, the steppe component. In Central
Europe we actually see about a 70% replacement of the local agriculturalists
happening 4,800 years ago, an event that actually no archeologists or
paleo-anthropologists had predicted so far. So there seems to have really a mass
migration at the end of the Neolithic. So in summary, what we can say is that
agriculture likely spread from the near East through Anatolia into Central Europe,
starting about 7,000 to 8,000 years ago. So it was actually people coming to Europe
introducing agriculture. What we also have then, when the agriculturalists are
spreading in different parts of Europe or into Scandinavia in the next 2,000 years,
Great Britain as well as to Iberia, there seem to have a bit of genetic admixture
with the local hunter-gatherers that are still present in Europe that time. And
then in the late Neolithic, about four and a half to 5,000 years ago, we have this
what seems to be massive migration coming from this region here from a culture which
is called the Yamnaya, which is genetically extremely close with people
that have a culture which is called the Corded Ware that stretches all the way up
to the Baltics as well into Switzerland here and into Western Europe. So there was
this massive migration which expanded into the West here, into Central Europe as well
as into the other direction, into the Altai Mountains. One of the big questions
we currently have is how was that possible? We can easily explain why there
was this first migration of agriculture to Europe because you could imagine that
agriculture can sustain a much bigger population so the first people that
brought agriculture to Europe probably had a much bigger population size. But then
how was it possible that 5,000 years ago, those early farmers were replaced by other
farmers? So what did those farmers have when they came here that kind of made them
able to replace the people that lived in Central Europe? And we don’t really have a
good explanation currently but our colleagues from Copenhagen recently
published a study where they could actually find that in those people that
came to Europe, they actually found Yersinia pestis, the causative agent of
plague, which is actually quite incredible but it seems that during this time about
four and half thousand years ago, plague was for the first time introduced to
Europe, potentially causing a pandemic and you could imagine if we have a pandemic,
like for example during the Black Death where 50% of the people in Europe died. If
something like that happened five and half thousand years ago, it could open an
ecological niche so people could actually move in and then replace the local
farmers. Just briefly what we could also do is we could actually also look at the
genetic and phenotypic change through time. We could actually look at different
phenotypes, how they change over the last 8,000 years, to look at evolution
basically and see, too. What we saw was actually quite surprising that the first
Europeans or the Europeans that lived about 8,000 years ago, the
hunter-gatherers, they actually had a very distinct phenotype from people that live
in Europe today. They actually have dark skin and blue eyes, all of them. You can
actually see that 100% frequency of those foragers had blue eyes and dark skin. So
that actually goes down blue eyes frequency then was the early
agriculturalists and then spreads again in the last few thousand years. And actually
light skin that we have so typically in Europe today is in low frequency even in
the early farmers but only starts to spread in the Bronze Age. So this
phenotype which is so typical for Europeans, this light skin, seems to be
only about 4,000 years old, so actually quite a recent chapter in our evolution.
What we could also show which was quite interesting is the ability to digest milk
during adulthood, so lactase-resistance. That’s a phenotype that a lot of people
attributed to the early agriculturalists, that basically those people that had cows
were for sure then also able to drink a lot of milk. But actually the frequency in
those people of this gene is actually zero. So they didn’t have it. And it only
appears then during the Bronze Age and it really spreads only in the last 3,000
years. And we’re not even sure when it happened during antiquity, during the
Medieval time or maybe in the last few hundred years. I’d like to end and
summarize that the Neolithic revolution is really a diffusion of people, it was
people coming to Europe. Those people brought genes, potentially new phenotype,
but they also brought new diseases and that’s actually quite exciting, quite
interesting the first evidence we have of that. What we also can say now is it was
not just one migration, it was not just those people from the near East that
brought agriculture, but there was a second large migration about 5,000 years
ago. Again, we’re not really sure why it was triggered but the introduction of
diseases is one possibility. So with that, I’d like to thank a lot of collaboration
partners for the first paper that I mentioned, mostly of course David Rice and
his team, but also Svante Paabo and his group in Leipzig. The second study I
presented, it was coordinated actually with Copenhagen and Adelaide at the time,
now with us and Yena [SP] and also David Rice’s group. And the third paper talked
about which was again coordinated by David Rice and Ian Matterson in Harvard. I’d
like to thank my group, a lot of funding bodies. Thank you for your attention,
thank you. ♪ [music] ♪