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programs. ♪ [music] ♪ - [Narrator] We are the paradoxical ape;
bipedal, naked large-brained. Lone the master of fire, tools and language. But
still trying to understand ourselves. Aware that death is inevitable, yet filled
with optimism. We grow up slowly. We hand down knowledge. We empathize and deceive.
We shape the future from our shared understanding of the past. CARTA brings
together experts from diverse disciplines to exchange insights on who we are and how
we got here. An exploration made possible by the generosity of humans like you. ♪ [music] ♪ - [Brenna] Thank you so much for
having me. So, unlike most of your other speakers, I actually work with
contemporary humans and not fossils, but I will try to maintain your attention
anyway. I am mostly interested in human evolution. And as you've noticed from
these diagrams that people have put up regarding the phylogeny of Neanderthals
and Denisovans and modern humans, modern humans often get represented as sort of
just a single branch, or maybe a few genomes that come off this other branch.
And so what I want to do is really take a little bit of time and conceptualize what
it means to refer to the Homo sapiens as a single species. Did we have a single
origin. There's actually a lot of complexity in this question which isn't
necessarily addressed by one of these simple tri-part type phylogenies. So,
let's just break down kind of the known working model we have for human evolution
which is mostly based on contemporary DNA. So, if we start out in Africa roughly
about 100,000 years ago. I'm an advocate of a Southern African origin. I'm not
going to try to convince you of that today, but we actually don't know where in
Africa. There was a single origin of the Homo sapiens species if indeed it was a
single origin model, all right? And then from Southern Africa, putatively, there is
a migration and dispersal into the rest of the African continent. And certainly by
60, maybe even slightly earlier, 70,000 years, there were these individuals living
in Northeastern Africa at which time there was what we call a "founder event." So,
these populations moved out of Africa into the near East. Now, this event is actually
a major event in human evolution, or at least in the genomes of all non-Africans
living today. And that is because there was a strong reduction in genetic
diversity during this founder event. And that's indicated here by the fat arrow,
okay? So every time you see a fat arrow on this map, that indicates a reduction in
genetic diversity. Once humans left Africa, these individuals spread rapidly
across the Eurasian continent. There are some hypotheses of what they call the
South Indian or South Asian migration route which is along the coast of the
Indian subcontinent, and eventually into Southeast Asia and Oceania, certainly by
45,000 years ago. As well as additional migrations into Northern Asia and
eventually into the Americas where it was accompanied by yet another strong founder
event or population bottle neck which reduced the genetic diversity of those
populations. And we'll hear a little bit more about that today from Maria. So
that's our basic model of human evolution over the last 100,000 years. But you'll
notice that there's not a lot of detail in Africa, actually. There's just a few
arrows and some general little dates. Geneticists love to put arrows on maps and
I am no exception. So, I'd like to instead think about posing this question, "Where
in Africa did humans originate?" And there are different types of genetic evidence or
other types of evidence one might use to answer this question. And there's a sort
of presentation here. This is by Batini and Jobling where they suggest different
types of evidence one could look at. So you could look at for example, non-genetic
evidence, skulls that have been dug up from the ground by
paleo-anthropologists. You could look at evidence of what we call
"symbolic behaviors," such as the making of art,
so shell beads or these little crosshatch ocher pieces
that have been discovered. You might even look at language. So there's a really
fascinating paper from a few years ago that looked at phonemic diversity, not
genetic diversity, but looking at the number of phonemes in different languages
and can we learn anything about the origins of language by the amount of
diversity that's present in phonemes? And he argued, indeed, Africa has the highest
phonemic diversity. And in particular even Southern African has the highest phonemic
diversity. So I'm a geneticist. I focus on a different type of evidence and you can
break down genetic evidence also into these little patches. So one might be the
mitochondrial DNA. Mitochondrial DNA, as we've heard from other speakers, is
something that's inherited through the maternal lineage. So the mother passes it
on to her children and then it's passed on from the daughter to her children.
Alternatively, you could look at the Y-chromosome which has a different pattern
of inheritance from father to son, and so on and so on, for many generations. And
then last are what we call the autosomes, which are the remainder of the chromosomes
1 through 22 that compose the rest of your genome. So when this was done, and this
slide is a little bit dated, but from mitochondrial DNA and Y-chromosome DNA, it
was a little bit hard to pin-point precisely where the deepest divergence was
within Africa, I'm going to address that again later, but at least from the
autosomal information. Both if you look at SNPs or a single-nucleotide polymorphism,
just your vanilla mutation. They actually have the highest genetic diversity, or
heterozygosity, in Southern African populations and even other types of
polymorphism like microsatellites also look like they had the highest diversity
in Southern African populations. And so we're getting a lot of conflicting pieces
of information maybe from non-genetic evidence, from genetic evidence. So how
can we sort of conceptualize synthesizing all this information? So I'm actually an
anthropologist by training, despite the fact that I do genetics, and so I like to
sort of begin with the paleo-anthropology and that's what we're going to do right
now. So there's a fantastic amount of information that's been excavated from the
fossil record. And some of this information comes in the form of bones,
right? Like we've seen earlier on the talk. And on the right here, you have a
fossil cranium from Hurso, Ethiopia that was dug up. And it looks
like...morphologically, it's very similar to modern humans. So the front part of the
skull is actually tucked in underneath the brow ridge. The skull is actually pretty
short from front to back. The brain size is of course equivalent to what you would
see in contemporary human populations today. And if we put flesh on this
individual, they would probably look relatively similar to other human sapiens
around the world. However, so we know that there was morphologically individuals that
were probably similar to Homo sapiens walking around Africa at least 150,000
years ago. But in fact there's a lot of additional information that can be gleamed
from stone tools. So, there is a phrase that's called the "middle stone age." And
the middle stone age refers, at least roughly to 250,000 years ago to 50,000
years ago. And on this other map, what you see are sites in Africa where middle stone
age artifacts have been recovered. So we know that hominin populations were living
in these areas of Africa during this time period. And what you'll notice, right, is that
there is maybe not that many examples of this beautifully reconstructed skull from
all over Africa, but there are many, many geographic locations on this map that
actually date back to the middle stone age. And so what does that mean? So that
means of course that there were lots of hominins walking around the face of Africa
during this time period. And in fact there is also good evidence from North Africa as
well, even though it's cut off in this particular map. And so let's just kind of
make a little schematic and start to think about this. So if I look back into Africa
150,000 years ago, 200,000 years ago, I know that there are Homo sapien-like
populations, broadly speaking, that exist in different parts of the landscape. And
so we can ask a relatively simple question, "Were these populations
structured?" That means, are they different from one another? So perhaps we
have populations in North Africa, East Africa and Southern Africa. There is less
information from Central Africa for various reasons. And these environments
may have been very different from one another. So you might have had a cool,
Mediterranean climate up in North Africa and then a very hot desert-like climate,
let's say, in Southern Africa. And the question then is, are these populations
really separate from one another? Or are individuals moving in between them? So
population geneticists like to refer to this concept as population structure. So
let me just explain what that is briefly. In this little schematic, we have a SNP,
or a single nucleotide polymorphism up on the top that either comes in red or
yellow. And we have two populations on either side of this river and we can see
that they are very different from one another. So individuals on one side of the
river carry only the red allele, and individuals on the other side of the river
only carry the yellow allele. And this is structured populations, or populations
where there are strong differences in allele frequency. And this is in contrast,
down to the bottom, of populations which are carrying both the purple and the
orange alleles because there is migration between these two populations or gene
flow, if you refer to your little glossary on the handout, and this is because I've
given them a nice little bridge so people can walk across and migrate. So, we
can just sort of take that example and apply it to the rest of Africa as well.
So, were these populations structured at 200,000 and 150,000 years ago? Or was
there actually what we call "panmixia" or lots of migration among the different
sup-populations? And I think we have an actual answer to this particular question,
but it's somewhat complicated to infer in fact. And one thing to point out is that
in either of these scenarios, if you're thinking back to what the landscape would
have looked like 200,000 years ago, means that if I went and sampled individuals
from across the African landscape, their common ancestor, in terms of their
genetics, would have been very old. It would actually pre-date 150,000 years ago
or 200,000 years ago. In order to understand why that is, you have to again
take a little mini-class in population genetics here and think about the
difference between populations and genes. So this is what we call a "gene genealogy"
which is represented by these little lineages right here. And these lineages
exist within these two different populations, okay? So we can sort of trace
back the common ancestry of a given genetic segment to where that individual
shares a common ancestor. And these common ancestors exist in some ancestral
population which I'm going to then let evolve through time. So now, we have this
common ancestral population and there's been some sort of divergence and is
diverging to the blue and orange populations. And you can see that these
gene genealogies, these genetic lineages are sort of splitting nicely into the blue
and orange population. And then finally, at the present day, or down here. You
know, I might go and sample individuals from the orange population, and the blue
population and then ask when their common ancestor was, okay? And that common
ancestor is indicated up here just like in a normal phylogeny. The key thing to
remember actually when you're looking at that is that the common ancestor pre-dates
the population divergence, okay? And this is the case for most of the low side that
we would look at in the human genome. So, the common ancestor must be older than the
population divergence. So then, we can ask, "How old are the common genetic
lineages within human population?" So I'm going to do this for a relatively simple
locus, the Y-chromosome, right? So the Y-chromosome again is just passed on
between father and son. And one of the nice things about the Y-chromosome is that
it's relatively small, so it's easy to go in and sequence it from many individuals.
So, a few years ago, we captured about 10 megabases of the Y-chromosome from a
variety of individuals across human populations and we actually had a strong
focus here on sampling African populations because that's what I'm obsessed with, is
African populations. And what you'll see is all the African individuals are sort of
on the bottom half of this segment and you're just looking at a normal gene
genealogy or phylogeny that's been flipped on it's side. So the common ancestor is
right here and then each one of these lineages represents a single individual's
Y-chromosome that was sampled from a man. Now the first thing obviously to notice is
that individuals from outside of Africa have very little genetic diversity on
their Y-chromosomes compared to individuals from Africa. And you can
easily see that by their relatively short branch lengths up here. So these are all
the out of African individuals, okay? So people from Cambodia, people from the
Americas, people from Europe and so on. And instead if I look within Africa, I see
individuals that carry really, really long branches, okay? So for example,
individuals from West Africa and North Africa diverge around here. And
individuals that are from these African hunter-gatherer populations, which are
particularly special, carry extraordinarily long branches all the way
back to the common ancestor. So that graph can be a little bit hard to read for some
people who are not geneticists so I've tried to make a schematic. If we look at
the time to the common ancestor and we try to date in years how long ago that might
have been, we can kind of put an upper bound on the population divergence among
all human populations. And so when we do this with the Y-chromosome, what you
actually see is that the upper bound on population divergence would have been
around 150,000 years ago plus or minus a couple of tens of thousands of years,
okay? So we're actually seeing relatively shallow divergence among contemporary
human populations. And with a little bit of additional modeling we can actually
say, "Well, which population diverged first from all other human populations and
when was that?" And at least looking at the Y-chromosome sequence it's most likely
to have been these Khoisan populations from Southern Africa and we date it to
approximately around 90,000 years ago. Now, you could say, "Well that's just the
Y-chromosome. It's just a single locus and has this bizarre pattern of inheritance
from father to son." So independently, there was additional papers published by
Renaut [SP] and also Veeramah approximately about a year before we
published our Y-chromosome work, and they actually independently came up with a very
similar estimate on this time of population divergence between these
Southern African hunter-gatherer groups and the other humans within Africa. And
that time of population divergence is approximately 100,000 to 120,000 years
ago. So again, what you're seeing is that the gene genealogies certainly go back in
time, but the actual time depth of this population divergence is quite shallow,
okay? And if we try to map that on to these sort of schematics of Africa, what
would that mean? It means that neither of those two maps that I showed you before
could really represent the actual true ancestors to the human population. So
something must have happened to reduce the genetic diversity between 200,000 years
ago and 100,000 years ago. And so let's just think for a moment what that might
have been or what that could have looked like. So one hypothesis could be that
there was a strong population bottle-neck during this time period, 200,000 to
100,000 years ago. And maybe that bottle-neck was associated for example
with climate. So populations actually could have moved from one region to
another because of climatic fluctuation. And in this case, I've had all the
individuals that are living in Eastern Africa and Northern Africa just sort of
trickle down and move into Southern Africa where things were nicer during that time
period. That doesn't have to necessarily be the only location, it's just one
example. This movement into a refugium would likely have been accompanied by a
population bottle-neck as you can imagine. If things are stressful in a given
environment then usually what we see is a reduction in population size. Conversely,
you could also think about it in a slightly different way, maybe there was
some stressful climatic experience and that these other populations simply went
extinct, okay? So you have local extinction events for example here in
Eastern Africa, or Northern Africa, and only a population persists in one
geographic region again indicated here by these little Xs in Southern Africa. Then
what would have happened, right? So then at a 100,000 years ago, we know humans
began expanding again. So if they did sort of localize to one specific place on the
African continent, what would that then look like? They would have expanded into these
other regions again but maybe they absorb individuals that persisted there. So maybe
there wasn't complete extinction events in these other geographic regions, or indeed
maybe all these individuals that were living in Eastern and Northern Africa did
completely go extinct and we don't see their signatures in the human genome. So
this I want to sort of end by emphasizing that this is a single origin model for the
modern human species, but it fits the data actually quite nicely because of this
shallow divergence we see in the genetic lineages. And I will emphasize that there
is a lot of additional sequencing that needs to be done particularly in African
populations were we probably have the fewest samples of full human genomes that
have been sequenced. And we really need to actually think explicitly about testing
these models in a context that connects the genetic data with the
paleo-anthropological information. And I will stop right there. Thank you very
much. ♪ [music] ♪ - [Johannes ] So thanks for the
invitation. 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 stared 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 and into
Europe 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 make up 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 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 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 make up 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 Baltic 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] ♪ - [Maria] I was very ambitious
when I decided this title. And it's not going to be covered all of it in 20
minutes for sure. But I'll try to cover as much as possible and give you an idea of
what we know about the genetic history of the Americas, mostly informed by ancient
DNA studies. So the last continent to be...the Americas was the last continent
to be settled by humans and many questions have been debated as to where did the
first people to enter the Americas came from, when did they come to the
Americas, through what route, and if there was one major or two major or three major
migrations into the Americas. So there has been a lot of debate and attempts to
answer these questions. And many fields have contributed to the discussion and
genetics has been very important but it has received contributions as well from
linguistics, archeology, paleo-anthropology, paleo-climate and
other disciplines. And it is now kind of agreed that the first people to enter the
continent did so from Siberia, Northeast Asia, through Beringia around 15,000 years
ago. And we set that date because the oldest human occupation site in the
Americas is Monte Verde which is here in Chile. And this human occupation site is
dated to 14,000 to 14,500 years old. So the people who first entered the continent
had to do so before then and like allowing of time for people to get here. So ancient
DNA has contributed a lot to understanding exactly how this happened, how people
moved through the continent and where did they come from. And we don't have
thousands or hundreds of ancient genomes, we have only a handful from the Americas.
So I will try to give you some of the insights that we've gained from studying
ancient Native American genomes. So the first one is this genome from the Anzick
boy where some remains found here in Montana and where they dated to around
12,600 years old. And they were found in association with these fluted stone spear
points which were part of the Clovis culture. And as far as I know, these are
the only remains that have been found in association to these tools. So this
allowed the opportunity to investigate like the genetic affinities of a Clovis
culture by studying the genome. When the genome was sequenced and compared to human
populations around the globe, like contemporary populations around the globe,
this heat map, flash map was generated which basically shows in warmer colors the
population, each circle is a population. So in warmer colors, you have the
populations that have the highest genetic history sharing. So, the first thing that
was observed by sequencing this 12,000 year old individual was that most Native
Americans, basically all Native Americans are more similar to this individual than
any other population in the world. And most interestingly, it was found that even
though it was found like in the northern part of the Americas, it was more closely
related or have more genetic affinity to Central and South American contemporary
individuals, Native Americans actually. And this already gave us an idea about
kind of the structure that was occurring in the Americas back then. And together
with these observations and other statistical analyses, the authors of these
study which I should mention Morten Rasmussen who did this between Copenhagen
and Stanford. Well, they came up with this model in which there was a divergence
predating the 12,000 years old of this ancient genome. A divergence between the
Northern Native Americans and the Southern Native Americans. And that Anzick would be
sitting here. So, this genome was very
insightful in that it gave us an idea of some
early population structure in the Americas predating the age of this genome. And it
also gave us the idea that most Native Americans today are descendant of a
population related to this Clovis-associated genome. A second genome
that was sequenced just recently and published recently and the source of a lot
of debate was that of the Kennewick Man. The remains of this individual were found
in the Kennewick area in Washington state. And they were dated to 8,500 years. And
there was... Again, this is a study by Morten Rasmussen. This was a source of a
lot of controversy because the first analysis on the skeletal remains and
particularly on the morphology of the skull. So the scientists who did this
first analysis they said that the morphology of the skull was more similar
to contemporary individuals of Southeast Asia and Polynesians. So, what that led
to was the owners of the land, which was actually the US Army, not giving the
remains to the Native American tribes who were claiming these remains for reburial.
And that was just based on the scientist who drew these conclusions on the
morphology of the skull alone. So of course, there was a lot of scientific
debate. And because the first attempts to extract DNA were unsuccessful, there was a
lot of controversy and litigation for many years, at least nine years. But finally
this group in Copenhagen, they're very good at this, were given the opportunity
to try again to do some genetic analysis. And they were able to sequence an entire
genome of the Kennewick Man. So the very first observation is that it actually
falls within Native American variation, just like that. And so this is a BCA plot
similar to what Johannes just showed. And these are contemporary Native Americans,
these are populations from the rest of the world, this is Europe. So, that was the
first result, this individual is Native American. And when looking at the genetic
affinities within America, it was shown something similar to what was shown for
the Anzick individual. It shares more genetic history with Central, North and
South Americans than with other Native Americans from the North, even though it
was found here. But it was also interesting to find that tribes for the
same area where the Kennewick Man was found, also shared a high level of genetic
ancestry with the Kennewick Man. So this was like another piece of evidence about
the past genetic structure in the Americas. So again, with this observation
and more sophisticated statistical methods, what this study proposed was
that, so this was the original branching between Northern Native Americans and
Southern Native Americans. The Anzick sits here as an ancestor to modern South and
Central Native Americans. But there was another branching here, and Kennewick is
here, that gave rise to Pacific Northwest Native Americans. But there was a follow
by some gene flow from East Asia that probably obscures a little bit the genetic
affinity of the Kennewick to the Pacific Northwest Native Americans. So this was a
very important contribution and not only gave us insights about the past genetic
structure of the Americas, but it also helped resolve this controversy about
whether Kennewick Man was Native American or not. And now, just an additional report
supporting this was published three days ago probably. So we could hopefully put an end
to this litigation and these remains...well, we don't know because many
tribes are claiming the remains so maybe there will be yet another debate. But
anyway, this is what we learned from the scientific standpoint. And the third
genome I will tell you about is this from the Saqqaq Paleo-Eskimo, which is very
interesting because it was sequenced from a tuft of hair and this hair was preserved
for around 4,000 years in the present permafrost in Southwest Greenland. And
this is an artistic reconstruction of the individual based on genotype, like
phenotypic information that was taken from the genome that was sequenced. So this was
actually the first ancient human genome to be sequenced and again, this was done in
Copenhagen by Morten Rasmussen and colleagues. So what we learned about this
genome was also very interesting. So the Saqqaq individual was found here but the
genetic affinity surprisingly, or not to some, are not to modern contemporary
Greenlanders. So this individual is genetically more similar to individuals
from Siberia like Chukchi and Koryaks here. So what this indicated is that there
was probably a past migration like predating 4,000 years ago, probably 5,000
to 6,000 years, a migration from Northeast Asia to the Americas that was later
replaced by a population that gave rise to modern day Inuits. So these are like three
single genome studies, but thanks to the development in next generation sequencing
we have been able to generate now multi- or... Well, yes, complete or semi-complete
genomes from different individuals more than just one at a time. So we generated
some genomic data from multiple individuals to test one particular
hypothesis. This was part of a larger study but my contribution was testing
this Paleo-American relics hypothesis. So, again, based on this morphology of the
skull, it was suggested that the very first people to enter the Americas and for
which we have remains like for example, Lucia from the Lagoa Santa and
the Penan] woman which are really, really old, that the morphology of this
skull is more similar to present day people from Melanesia. Some scientists
suggest that there was a first migration of people with this Paleo-American skull
that was later replaced completely by Siberia, like the first migration I
mentioned. And that there was a complete wipeout and replacement. But that there
were some relic populations because based on the morphology of the skull of some
individuals who are in isolated parts of the continent like the Pericos in the tip
of Baja, California and the Fuego-Patagonians here, these had a
particular skull morphology that resembles also Austra-Melanesians. So this was a
theory and we wanted to test it. So we sequenced partial genomes from 17
individuals from these supposedly a relict populations. And what we found, we
were actually expecting this already, was that they all fall within Native American
variations, so there was no evidence of any connection to Austra-Melanesia
whatsoever. But more interestingly is that we observe a genetic continuity with
modern populations in the same geographic area. For example, the people from
Fuego-Patagonia in PCA space, they fall in proximity to present day Fuego-Patagonians
from Chile, so they [inaudible 00:52:26] from Chile. And similar in Mexico. The
Pericos from Mexico not only fell within the native variation in Mexico, but they
did so with Northern population from Mexico. So we were able to pin down that
they were very closely similar to Tarahumara and Purépecha which are
Northern Native groups in Mexico. Well, first we just disprove this idea of relict
Paleo-Americans. And secondly we demonstrated that there is this genetic
continuity. And actually we observed this in many samples now, in many genomes that
have been sequenced. And we observed so, as I showed a little bit with the
Kennewick Man that had genetic affinity to populations from the same geographic area.
But we've observed through almost 8,000 years so we have different genomes from
different ages here. And what we've observed continuously is that there seems
to be this genetic continuity in the Americas, and that is in contrast with
what Johannes just showed of these massive demographic shifts. So the Americas, at
least Central and South America, the Northern part seems to be a bit more
complex, but at least Central and South have been kind of very stable for many
thousands of years, so that's interesting. A question that hasn't been resolved quite
yet is if there were three or two migration waves into the Americas.
Different groups with different data sets from modern populations support one or the
other. So there is one model that...there was one major migration that gave rise to
most Native Americans followed by a second and a third that were mostly just Northern
Native Americans. And there is another model that instead of suggesting a second
migration, suggests that there was divergence within America of a Northern
and a Southern branch and that this occurred within America approximately
13,000 years ago. And something that has been a bit puzzling for us who study
genetic diversity in the Americas is the observation by two independent studies of
something that looks like gene flow from Austra-Melanesians or Papua New Guinians,
or population related to contemporary Papua New Guinians and Melanesians, into
populations in the Amazonian, like the Xavante, Suruí and Karitiana. And two
independent studies have identified this signal, although yet we don't have a good
explanation of how or when this happened. So it's very puzzling actually. And just
for the last part, I want to make the point that so far I just talked about the
peopling of the Americas but there's actually much more genetic history in the
recent 15,000 years of course. So I think we can use ancient DNA to investigate, or
a combination of ancient and modern DNA, to investigate other regional aspects of
the history of the Americas. An example here, for example is the peopling of the
Caribbean. By it's location you can argue it could have been people from Florida,
from the Yucatan peninsula or from South America. And now combining data from
modern population, modern Caribbean population and studying the Native
American fraction of this population and comparing to reference panel of Native
Americans, it has been suggested that it was people, actually, by South America
here, facilitated by the Orinoco River. And we have been able to kind of prove this with
ancient genomes from Taino genomes. And I'm just showing here an example of one
sample from Cuba, from Chorro de Maita, Cuba which also falls in the genetic
variation of Arawakan speakers, like Wahiro, Piapoco and Ticuna. So this is
another way we're complimenting information from modern and ancient
population to resolve a question about the particular event in history. And I'm also
doing something on the same lines. I don't have the time to tell you more about it
but we're doing something similar in the peopling of the Patagonia, like the very
last part that was people in the Americas. And lastly, I want to make the point that
we can also use ancient DNA even in historical times, but for events in
history where the historical record is sparse. So, I'll just show you an example
where we used ancient DNA to learn about the past history of people brought to the
Americas as a result of the Trans-Atlantic Slave Trade. You can argue that there is
historical records about this, but this exact origins of people in Africa that
were brought to the Americas that was basically not recorded, it's kind of
absent in the historical record. So we can also use ancient DNA to reconstruct some
of this history. So in this, very quickly, it was a pilot study where we had three
individuals from the Caribbean and we wanted to know where in Africa were they
from. They were found in the same burial site. And by comparing to a reference
panel in Africa, we sequenced fractions of their genomes, we were able to find that
one of them was more closely related to Bantu-speaking populations. And two of
them were more closely related to non-Bantu-speaking populations and we had
evidence to argue that this three people were put in the same embarkation and
brought to the Americas together. But we are really missing information about how
culturally diverse were the people who were brought from Africa to the Americas.
So, just to summarize, most Native Americans...because I went through
something very general like the peopling of the Americas to something super
specific about an episode in history. But I want you to take this messages home. So
most Native Americans trace their ancestry to a single migration from East
Asia to Beringia between 15,000 and 20,000 years ago. If there was one, two or three
subsequent migration is still under debate. There is evidence of ancient gene
flow from population related to Austra-Melanesians into some Amazonian
populations, although we don't know exactly how that happened. The sequencing
of ancient genomes from the Americas has complimented the knowledge generated from
studying genome-wide data from modern populations. But we still have very few
compared to Europe, for example. And this last point, it's also something very
important for me, ancient DNA research can also be useful for investigating other
aspects apart from the initial peopling of the continent. I think we put too much
attention into that that we've forgotten about the more recent history or
pre-history, like the source populations in Africa of the people who were brought
during the Trans-Atlantic Slave Trade. And with that I'll complete. And thank
you. ♪ [music] ♪
