(piano music) - [Narrator] We are the paradoxical ape. Bipedal, naked, large brained, long the master 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. - [Announcer] This program contains graphic images and discussion. Viewer discretion is advised. (cheerful music) - Okay, before I get started
I wanted to thank CARTA and I wanted to thank the
organizers for inviting me to what so far has been a
really interesting symposium. As Mark said, I'm gonna talk about the evolution of the human skull. It's gonna follow up a little bit on some of the materials
that were presented in the first two talks. When we look at the human skull, the skull of today's humans, we can see that it's
pretty different from that of the Neandertal that
you see on the slide. You can see that today's
human skull has a smaller face that's tucked underneath the brain case. Then we have a cranial
vault that is much shorter and taller than the elongated one that you see for the Neandertal. So there's these differences
that have been talked about in the first two talks, and if I put up another
member of our own genus, the genus Homo, other than a Neandertal you'd see that there are
also these differences. Some of them are the
same as the ones you see with the Neandertals and
some of them are different. There's some unique
features of the Neandertals, but in any case, the skull
of a present-day human is quite distinctive. It looks very different form what we see in earlier members of the genus Homo. So as you heard about
in the first two talks, we can use this distinctiveness as away to trace the
emergence of our own lineage and the migrations of
members of our lineage throughout the planet. By looking at the anatomy we can locate the emergence of our lineage to Africa. We can also couple this
with genetic evidence, which locates the origin
of our lineage in Africa. And then genetic evidence
couples with evidence from the anatomy can allow us to trace the movement of our
lineage outside of Africa and around the planet. This fossil from Herto in Ethiopia is a good example of this. We can use these features as
a marker to trace the origins, to trace the migrations of our lineage throughout the planet. This is of course very
fascinating, very interesting. We want to understand
how our lineage emerged and how it moved around the planet, but there are other
questions that we can ask looking at this anatomy. For example, we could ask questions like why don't our skulls look like those of other members of the genus Homo? Why do today's humans have such distinctive anatomy of the skull? We can ask questions about how rapidly did our distinctive anatomy appear? How rapidly did it appear and did it come in all at once or did it come in over
a longer period of time. These are the questions that I
would like to focus on today, focusing on these questions not so much using this anatomy as a marker for tracing the emergence of our lineage and the migrations of
us around the planet, but actually trying to understand
why we look the way we do and how rapidly this came about. In particular, my goal is to
try to dispel what I think are two misconceptions about the evolution of the human skull. This first one is that,
misconception number one, is that all differences between the skulls of today's humans and Neandertals, or all differences between
the skulls of today's humans and other members of the genus Homo, so not the Neandertals, are adaptive. Adaptive is a term that is used
by evolutionary biologists, but what I mean by this in this context is that there were some
functional differences between say our skull and
the skull of the Neandertals. So they functioned in a different way, and these differences
indicate something about differences in function between us and these other members of the genus Homo. So over the years there have been a number of adaptive explanations
for these features. On the one hand there's
adaptive explanations for the Neandertals, so one common one is thinking about Neandertal skull anatomy as somehow related to
the cold environments that they were living in and evolving in. Another explanation has
to do with the fact that there's evidence that maybe
they were using their jaws as a third hand, so there
was this mechanical loading that was associated with that, and it might have had some consequences on just the overall anatomy of the skull. On the other hand, there
are adaptive explanations for thinking about why do
we actually look different? So why does today's humans
look so distinctive? Probably the most fascinating and maybe interesting and exciting one is to think about it may have
something to do with speech. Because of course, speech and language are so important characteristics
about what makes us human, and so there could be
something about our skull that has to do with the
ability to produce the sounds that allow was to create languages. But there's an alternative. There's another possibility that I think we should seriously consider. There's this evolutionary process that we call genetic drift. Genetic drift is this
process where there are these chance changes that happen in populations just because any population
is finite in size. So if you think about different regions of the genome, so different genetic loci, and there's gonna be different alleles at those different loci, and those alleles are gonna
be in certain frequencies in any human population. But by this process of genetic
drift you can have shifts in the frequencies of those alleles, these chance changes, and just the fact that the population is finite in size, meaning just because of
this sampling process that happens as parents
give rise to offspring and offspring give rise
to further offspring, you have this process
of genetic drift acting. If some of these alleles
at some of these loci underlie the anatomical differences that we see in the human skull, then you're also gonna get these changes that you see in the
skeletal anatomy as well. You can imagine a situation where you had some sort of an ancestral
population to Neandertals and an ancestral population
to Neandertals and us, but then they diverge from each other over a period of hundreds
of thousands of years, so there would have been lots of time for this process of genetic drift to act and produce at least
some of the difference that we see in today's skulls. My colleagues and I have been
trying to address this idea, the idea that maybe a
lot of these differences could actually be nonfunctional, they could actually be do to
this process of genetic drift. We try to address it over
a number of different ways and a number of different directions, but I want to present
today this new approach that we've taken and
some new results on this. In order to address this
we have to have some way of quantifying the anatomy, and you've seen this already
in the first two presentations. So we use these methods
of geometric morphometrics where we take these anatomical
locations or landmarks, or semi landmarks, and
use them to characterize the size and shape of the
skulls of today's humans but also Neandertals to really document the variation that we see. Then we take this data and we analyze it in a particular way. The approach we've taken is we use models from quantitative evolutionary theory to make predictions about
what we would expect if the divergence was entirely due to this process of genetic drift, and then we compare that
with the observed data and see if it looks like
it's consistent or not. So here is some of the results. You're looking at these
two dimensional plots, which are similar to what you've seen in the first two talks. What you're looking at is
actually a little bit different, but you have these same axes of variation, these principle component axes, and the black arrows are the
observed patterns of variation. This is for a comparison
between Neandertals and different populations
of today's humans, and also between more ancient humans we call upper paleolithic, individuals from the upper
paleolithic from Eurasia. That's what the black arrows are showing, but what the red ellipses are showing are the expectations if everything was entirely due to genetic drift. What you can see here
is that the black arrows are actually within the red ellipses, which suggests that that
these patterns of variation we see in the actual empirical data are consistent with this
process of genetic drift. This was an interesting result. It fits with some of the other analyses that my colleagues and I
have done over the years. But one thing you might be asking is, "Well, maybe it's consistent
with genetic drift, "but do we actually have
the ability or the power "to detect deviations from
this model of genetic drift?" Could the data look like it's consistent because we don't really have an ability to detect deviations from that? And so, one way we took to address this is we did another comparison. In this case we're comparing
us, Homo, Homo sapiens, to a number of different
species of great apes. We're comparing with common chimpanzees, we're comparing with bonobos, and we're comparing with gorillas. What you can see is in the same analysis, the same kind of analysis, you can see that the
situation is very different. In this case all the black
arrows are in most cases in the different
projections the black arrows are outside the red ellipsis, which suggests that it's inconsistent with a divergence by genetic drift. So, what this gives is confidence that we actually have an ability to detect deviations from this
process of genetic drift, and so the situation that we see in Homo, within our own genus, actually looks kind of different from the situation we see
when we compare Homo sapiens to other great apes. So the next misconception
that I wanted to talk about is that the modern human
skull appeared rapidly, about 200,000 years ago in Africa. The first presentation by Professor Ublat talked about this some,
and so I'm gonna cover some of the same ground. So when we actually look
at the fossil record what we see is we don't
see an abrupt appearance of this modern anatomy,
this anatomy that links these fossils with today's humans, we actually see as old as
maybe 300,000 years ago from Jebel Irhoud we see
faces that look similar to today's humans, but the brain cases don't look very similar to today's humans. Then more recently in time we see more of these features
like today's humans. It seems like it's this
gradual and lengthy process where you get this accumulation of these features through time. It doesn't seem to be a very abrupt or punctuated appearance
of modern human anatomy at 200,000 years ago. A lot of this what I'm talking about is a bigger sweep of human evolution. We're looking back many
hundreds of thousands of years and tracing this very longer period of the emergence of our lineage, but there's actually
some events that happened actually quite recently in time which I think were very important in determining what the skull anatomy of today's humans looks like. What I'm talking about is agriculture. In the last 10,000 years we have the emergence of agriculture. Step back a minute and think
that so before 10,000 years ago every single human on the planet, all the foods that they were eating were coming from exclusively hunted or wild gathered resources. And then after 10,000 years
ago you have the emergence of agriculture in many
different parts of the world, and agriculture spreads very widely. Basically today almost everyone gets their food from agriculture, so from domesticated animals
and domesticated crops. There's this massive
transition in our diet, in our subsistence, that's happened just within the last 10,000 years. This is a very recent event, but it's a huge shift in our life ways. For a number of years
researchers have speculated and also collected data to suggest that this transition to agriculture actually had a pretty
profound effect on our skulls. The basic idea was as you
go from very hard foods to a much softer foods, and
because of these softer foods you have much lower mechanical
loading of your jaws, and because of the lower
mechanical loading of your jaws you have these changes in
the anatomy of the skull. This figure right here is a reconstruction where you go from the black outline of a hunter gatherer, to the blue outline of an agriculturalist. This basic idea is that
there's this big shift that happens with
agriculture that explains some of the distinctiveness of the skulls of people living today. This has been tested actually
on a number of samples, but mostly at a regional scale. A number of years ago a former
graduate student of mine and another colleague wanted to test this at a much larger scale, at a global scale. We collected samples of skull anatomy, documented skull anatomy
at a global scale. We wanted to really understand
the geographic distribution, but we collected our
samples in a particular way so within most geographic
regions we actually had a matched sample of hunter gatherer group and with an agriculturalist group. For example, in France we
have a Mesolithic sample, so Mesolithic hunter gatherers, matched with a neolithic sample, so neolithic agriculturalist. This really gave us a sample
that really allowed us to really think about
how these shifts in diet would have affected the
anatomy of the skull. We collected these anatomical landmarks that you've seen a lot earlier in my talk and also in the other talks. Actually, maybe a distinction to make is actually so far everything
that I've been talking about hasn't really technically been the skull, it's been technically about
what we call the cranium. Anatomically the skull is
composed of the cranium and the mandible, the
mandible being the lower jaw. I've mostly just been
talking about the cranium, but in this study we actually are talking about both the cranium and the mandible. This is important because the lower jaw is really implicated in these ideas about chewing and the
mechanical demands of chewing. Let me walk you through
a few results here. The analysis that we did really allowed us to figure out what are
the different factors that contribute to the variation
that we see in our samples, the variations in skull form that we see across different individuals. What you're looking at
on these graphs here, so the top is the cranium, the bottom is the mandible. What you're looking at
is this distribution, so how far out it is. The closer it is to the
400 end of the X axis or the closer in to the
50 end of the X axis, that's further in, so if it's further out and closer to 400 that means that it's a more important factor. If it's closer to the
50 side it means that it's a smaller factor. What it turns out actually is the most important source of variation is actually individual level
of variation within groups. This tells us any human
group or any human population is there's actually a lot
of individual variation. If you take a human group
from anywhere in the world and you look at their skull form, there's a lot of differences actually between different individuals
just from within that group. Everyone's an individual. Everyone looks different
from everyone else. This is an important thing
to point out is actually when you look at most features
of anatomy or morphology, most differences are actually
found within any human group. When you look at the genome you actually mostly see the same picture. Most of the variation in humans is actually found within groups. We found those too. But the next most important factor is what we call population history. This is populations that
are more closely related to each other, had a more shared history, are gonna look more similar
in their skull anatomy than populations who had
a more mandible shared or a shorter shared history and
a more distant relationship. But then finally there
is an effect of diet. This is hard versus soft diets. Diet, although it's the
least important factor, it is a significant effect. It does seem to have, at a global scale, have actually shaped the
anatomy of today's skulls. We can see these different factors that are overlaid on top of each other, and this combination is what allows us to understand the skull of today's humans. Just to now look at a little bit of some of the details a tiny bit, so for some of the factors
that we saw that were, some of the aspects of the
skull that were related to diet were in the mandible, this lower jaw, but there's also parts of
the cranium that we saw this. What you're looking at here
is points that are documenting the attachment site of one of the major muscles involved in chewing. What you can see is in yellow are the hard diet individuals, and in purple are the
softer diet individuals. You can see that this
aspect is being shifted by this shift in diet. Okay. So, in summary, why do the
skulls of today's humans look the way they do? I think that many of the
differences between today's humans and earlier Homo may be due to this process of genetic drift. So these chance changes
that happen in populations just because they're finite in size are probably explaining
a lot of variation we see across present day human
populations and their skulls, but also differences
between Neandertals and us, and us and other members
of the genus Homo. But it's also important to remember, and this came out I think
in the first presentation, that human skulls didn't stop
evolving 200,000 years ago. They continued to change by
this process of genetic drift, but also in response to local
environmental circumstances, local conditions, things
like the shifts in diet that we had with agriculture. You can see that there is a
bunch of different factors that are laid on top of each other that really allow us to understand why the skulls of today's humans look different from other
members of the genus Homo. With that I'd like to thank
all of you for listening and I would like to thank my collaborators and funding sources and curators who gave access to collections. Thank you very much. (audience clapping) - Stone technology is
actually an important component of our history. The data we have now is
that stone tool production, not just tool use, tool making, emerged at 3.3 million years and was replaced by metal
tools at about 4,000 years ago, although the process of
replacement was a long one. It took about 2,000 years for
people to abandon stone tools and turn into metallurgy. Now, the earliest sites
documenting stone tool making are in East Africa and spread
from 3.3 million years, such as site Lomekwi 3 in Kenya, to Olduvai, 1.8 in Tanzania. The earliest site is Lomekwi 3 in Kenya dated to 3.3 million years. It is a small assemblage,
about 149 artifacts, including also material from the surface. The inclusion of material from the surface is supported by the
refitting of a stone flake onto a core that comes
from the excavation. This is the refitted flake,
and this is the core. The main technique used is the so called block on block technique, which is rather similar by the technique used by chimpanzees to break open nuts. Cores are rather simple, but there are some flakes that show scars of previous removals. So the Lomekwian flakes appear to have been produced intentionally, but there are no
associated formal remains, and we do not know what
the flakes were used for. Generally, we can say that the
cores have very few removals. Now, in later sites the
production of sharp stone edges is clearly associated with butchering of medium to large animals. It is important to note that
chimpanzee hunt and kill pray, but that is typically
smaller than 20 kilos, and had never been observed to use tools to break open skulls or bones. There you can see chimpanzees
eating a vervet money or a bushpig, and they eat it directly without using tools to break the bones or to get access to the brain. We have to say a few things
about the knapping technique that is used throughout this
three million years of history. The most common technique
is direct percussion with a stone hammer, or sometimes later direct percussion was
done with a wood hammer, which would produce thinner
and more regular removals. Much, much later you would
have pressure flaking using a pointed bone, which would produce very regular, well shaped edges. Bipolar flaking, you
can see it on the slide, is said to have been used at Lomekwi. To tell you the truth,
I think that the photos that according to the excavator illustrate bipolar flaking are pretty bad. I haven't seen a single example that I would call bipolar flaking, but we can forget about it. (audience laughing) The next and very important site is a locality in the Ledi
Geraru area, Ethiopia, which is dated to 2.6 million years. There you have clearly flake production by direct percussion,
in particular you have a certain amount of core
and whole and broken flakes, and you can see that there
is systematic production of sharp edged tools. And we should be aware of the fact that this marks a fundamental shift in the dietary adaptions of early humans. At Gona, another of
these sites in Ethiopia, which is broadly contemporaneous
with Ledi Geraru. I'm not Ethiopian, I'm not
sure how it's pronounced. You can see that on one hand there is competent knapping
by direct percussion. You see clearly flakes that
have all the characteristics of flakes done by humans, and you have an SEM image of cutmarks done by a sharp edged
flake on a limb bone. This is quite important because the systematic flake production by direct percussion at Ledi Geraru and the use of cutting tool
edges on large animals at Gona about 2.6, 2.58, they are associated with an important behavioral
change by early humans. That is, to transport the
food to a central point for sharing probably with
other members of the group, thus creating a site
where artifacts are made and bones are discarded. These sites are the basis
of the archeological record and we are talking about
hundreds of thousands of flakes, of sites, which are
these clusters of bones and stone tools. The following long history
of stone tool making is punctuated by some
important innovations. The emergence of stable
patterns of flaking indicating planning and
foresight at Lokalalei dated to 3.4 in Kenya. The emergence of tools with diversified morphology at Olduvai. Later, the adoption of
the Levallois technology for the production of
regular and thin edged flakes about 400 to 300,000 years ago. The Levallois technology is used till the very end of the Mousterian. The use of hafting, for which
we have the best evidence about 200,00 years ago, and then the development
of microlithic weapons. I am not going to be able to cover all these different kinds
of important innovations, but I want to point
out to you first of all the site of Lokalalei,
dated to 2.34 million years. Relatively small excavation that yielded more than 2,000 lithic artifacts. You can see from the
refitting of the flakes on the core that there is a production of many flakes done very
well or very good flakes in a clear pattern. We are dealing now really
with skilled knappers. We have to leave this million years and we have to move to a
more recent innovations, which I consider actually
the most important advance in the technological evolution of paleolithic humans: The
hafting of stone tools. Joining a handle to a knife or scraper and attaching a sharp
point to a wooden shaft made stone tools more
efficient and easier to use. Now, how do we find in
archeology evidence of hafting? Well, the first and
direct evidence would be to find intact hafted tools. This is extremely rare. The few examples are very late in time, and what you can see here for example is a part of a spear that
was thrown by a spear thrower from the Yukon in Canada melting
ice and dated to 4,000 BP. In other words, archeologists have to rely on indirect evidence of hafting. One is the presence of impact scars on stone tools that
were used as spear tips and also on the bases
of these stone tools, indicating strong impact
on bone and by rebound also removal flakes from the base of the tool which is inserted in the socket. You have examples of two points, two stillbay points from Blombos dated between 77 and 73,000 years ago where you have both the removal of a large flake from the tip, which is impact damage, and equally at the base. Again, it's a kind of impact damage. In reality the best evidence
that archeologists can get is the finding of residue
on the stone tools indicating the presence
of adhesive material, which can be chemically
analyzed and identified. The oldest stone tools that have adhesive, that is birch bark pitch, identified by gas chromatography
and mass spectrometry, comes from the site of
Compitello in Tuscany, Italy. The flakes were found in
association with remains of an elephas antiquus. The site is dated to 200,000 years BP by rodent biostratigraphy. Now, what you see here is an imprint that probably is imprint
of the wooden handle. Not all countries were
using birch bark pitch. They adapted to the environment they had. For example, in Syria
at the site Um el Tlel dated to 70,000 years ago the flakes were made in two points and they
were hafted with bitumen. The presence of a Levallois point embedded in the cervical
vertebra of a wild ass is a clear indication
that we are talking about spears either thrown or thrusting that have impacted the
vertebra of this animal and left a fragment. In other countries, like in Italy instead, after the use of the birch
bark pitch in Compitello we find use of resin from conifers. In particular there are 10
artifacts that we studies from two caves in Italy dating between 55 and 40,000 years ago. They were hafted with resin and the identified by
the chemical analysis, gas chromatography and mass spectrometry, and you can see the white
arrows indicate the residue that was chemically analyzed. Then there are other, R, which indicates other kinds of residues. You can see that these
were not spear points, these were just tools, for example, what was hafted down is a scraper and upper you see a flake
which is unretouched, and yet it was flake, it was hafted. And now I better talk about
the end of the stone age, because again, it leaves with
Italy, so it's my country. (audience chucking) Makes sense. Okay (chuckles) so a lot of people know Otzi, the mummified corpse
that was found in 1991 up in the Alps at 3,200 meters elevation on the border between Italy and Austria. The site is by few meters
in Italian territory. (audience laughing) That was enough for the material
to be taken from Austria and put in a museum in Bolzano. You can go and visit the
museum where there is the mummy and all these tools, because the fundamental interest of Otzi is the tools that were found with him. They were found either
around him or under him. By the way, Otzi was 45 years old, was killed by an arrow which
is still in the left shoulder, left shoulder blade, and it is estimated by various doctors that this arrow impacted a major artery which is near the clavicle, and so the guy died of blood loss. It's also estimated that his
body emerged from melting ice three days before discovery by two hikers. Otzi's tools are very interesting. There is one arrow with a flint head. It's only a portion of the
shaft that you are seeing and you can see that it is glued, the staff is glued with probably pitch. Then you have a dagger or
a flint knife if you want together with its sheath. Down there you see what is
called the pressure flaker, which has an antler tip. A very small point which was
used for pressure flaking, as you can see the gesture
for doing pressure flaking. Now, the analysis of these stone tools by expert technologists told them, one, that the flint were coming from at least two different
regions south of the Alps. Two, that Otzi was not a
very good flint knapper. In fact,
(audience laughing) you can see them, you can see that they're pretty
ugly to tell you the truth. Both the arrowhead and the flint knife, according to technologists
did not do these tools, he just bought them or
bartered them or exchanged them and they were already made. These are mostly (mumbles) done. They are smaller now through use and continuous retouching by him. He was good at retouching
by pressure flaking, but making that, no. One thing that is particularly interesting about this collection of
tools is the copper axe. This is the beginning of metallurgy. We are here at 3,300 BC. Now, the copper axe is
made of yew wood and is fixed into the haft with birch tar and bound with leather strap. Isotopic analysis indicate that the source of the metal is southern Tuscany, an area rich in copper deposits. The blade was made by smelting
and casting in a mold. Clearly a form of technology that has nothing to do
with stone technology. It was almost certainly acquired by the iceman through trade. The incorporation of metallurgy
into prehistoric society was a rather complex process. Stone tools continued to be
made in Europe for at last 2,000 years after the iceman. Flint imitations of copper daggers were made in Western Europe
between 3,000 and 2,500 BC. You can see this is
flint and this is copper. The archeologists don't
know if the artisan were imitating copper blades or whether the copper blades were
imitating the flint daggers. At any rate, in the near east stone tools continued to be used for
butchering until 1,200 BC. That is more or less the
very end of the stone age. And there is for final
and last interesting thing to be said about the
beginning of metallurgy and the end of the stone age is that when you mine copper or
other metals from ores you end up creating extensive
dumps of mining debris. Also, lead and copper
contaminate the soil. The beginning of metallurgy
really marks the beginning of a modern feature, pollution. (audience chuckling) (audience clapping) - Thank you for this opportunity to present some of my work. I'm going to talk about
archaic introgression and what we've learned about introgression from these archaic hominins
in the history of non-Africans and more recent work that talks about archaic introgression
in African populations. Analyses of genetic data
have shown the broad outlines of the evolution of modern humans. We know that modern
humans evolved in Africa and that there was this
out of Africa exodus. What has happened in the last 10 years is this revolution in ancient DNA has given us access to genome sequences from two archaic hominins, Neanderthals and their
sister species, Denisovans. By comparing these genome
sequences to modern human genomes we're learning about
the interactions between archaic and modern human populations. For example, we now know
that all non-Africans today trace a small proportion
of their genetic ancestry to the Neanderthals. On the other hand, Oceanian populations, in addition to their Neanderthal ancestry, also trace some ancestry
to the Denisovans. Now, because these introgression events introduced a large number of mutations within a short span of time
into the humane gene pool, there has been the hypothesis that these introgression events could have had a major impact on human biology. This has motivated a number of efforts to better understand and connect these introgression events
to impact on specific traits. Here's an example of an early
effort that I was involved in where we were looking for
genetic variants that predispose Mexican-Americans to type two diabetes. This analyses unveiled
a novel genetic variant, and what we found was this variant had a unique geographic distribution where the risk variant was
essentially absent in Africa. It was present in low
frequencies outside of Africa, but it was particularly
present at higher frequencies in most of the Americas. When we compared the
mutations that were present on this genetic variant
to the Neanderthal genome we found that this was
likely to have introgressed into the modern human gene pool from the Neanderthal introgression event. There have been several
such other notable examples of specific introgressed variants that have affected biology. For example, there's been an introgression that has been documented
in the STAT2 gene, which is particularly important
in immune related function. Another extremely exciting
discovery was the EPAS1 gene. This is a gene where specific
mutations that have been found in Tibetans have been
shown to be important in adapting to higher altitude living. A recent analysis showed
that this mutation that contributes to
higher altitude adaptation is introgressed from the
Denisovan population. To better understand the
contribution of introgressed DNA to specific biological phenotypes we'd like to go from
understanding which genes might be introgressed to a
more genome wide assessment. This has motivated efforts to build maps of introgressed DNA. What does that mean? If you look at a population
that is descended from introgression between a
modern human and an archaic, the genome of this population
has a mosaic structure, where there are parts of the genome that are inherited from
the archaic population and others that are inherited from the modern human population. Because of the way the
combination chops up the holotypes that are passed on from on generation to the other, if you look at these genome sequences the length of these introgressed segments are characteristic of the time before which the introgression occurred. How do we go about building
maps of archaic DNA? We use statistical models, which compare the genome
sequence we're interested in to an archaic genome as well
as to the modern human genome. By comparing the genetic
variation that is shared between the test genome,
the archaic genome and the modern human genome we can essentially build
these maps that tell us what regions of this test genome trace their ancestry to
the archaic population. Using these maps we
can begin to understand at a very fine scale how archaic ancestry is distributed both across populations and across the genome. For example, we looked
at a very diverse set of modern human individual today and we built maps of Neanderthal
DNA in these populations. What we show is we
recover the signal where there's an enrichment of Neanderthal DNA in populations residing outside of Africa. There is interesting variation
within these populations and I think Josh Achey's
talk will touch upon the factors behind this variation. We can also build maps for Denisovan DNA and we see an enrichment
of Denisovan introgression in Oceanian populations,
but we also see populations in East Asia, which have small amounts of Denisovan introgressed material. Beyond looking genome
wide across populations we can ask how does introgressed
DNA vary along the genomes. What we can see is that
there is a wide variation in how much in introgressed material a person carries as we move
along their chromosomes. For example, there are
places in the genome where there is an enrichment
of introgression DNA. In other words, where a
lot of people present today carry introgressed DNA variants. For example, EPAS1 was the
example that we started off with, has a high proportion
of introgressed variance when we look at Tibetan populations. These are variants introgressed
from the Denisovan lineage. Here's another example. This is a gene that's
a particular outlier. It lies in this locus called
the basal nucleon gene, a gene that is known to be involved in skin related function, and at this gene present in Europeans, about half of them carry
the Neanderthal variant, compared to about 50,000 years ago when only about 2% of them
carried the Neanderthal sequence. We can try to figure out
what might have resulted in an increase in the Neanderthal
frequency at this gene, likely because this had
some adaptive benefit. However, it's not the case that all introgressed Neanderthal variants
are necessarily adaptive. Indeed, we think that genome wide most introgressed Neanderthal or
Denisovan DNA is deleterious. For example, there are
large regions of the genome which we call deserts of archaic ancestry where no present day human carries either Neanderthal or Denisovan DNA. These are particularly interesting because these are places in the genome that seem to be resistant to introgression and potentially they harbor mutations that are responsible for
the modern human phenotype. Here is one particularly interesting example of a desert. This is a desert which
is resistant to both Neanderthal and Denisovan introgression, and it overlaps a gene called FOXP2. FOXP2 is this famous gene
that has shown to be involved and important in speech and language. Now, moving beyond non-Africans, we'd like to switch our attention to introgression in Africa. The reason why our
understanding of introgression outside of Africa has been so advanced is because of the availability
of whole genome sequences from archaic populations, like the Neanderthals and Denisovans. But once we turn our attention to Africa the situation becomes a lot less clear. The reason is we don't have ancient DNA from archaic hominin groups. It would be wonderful to have them but the technology hasn't
yet been successful in extracting material. What we decided to do
was to look for signals of introgression in Africa
without needing access to ancient archaic hominin genomes. To do this we adapted two
complementary approaches. One is an approach that
looks at genome wide data and it counts up the
different classes of mutations that a person carries along their genome. It turns out that these
classes of mutations are indicative of characteristics of the history of archaic introgression. The second line of evidence
involves building these maps but doing so without recourse to an archaic reference genome. Let's talk about the
first line of evidence. The statistical summary of the data we're going to be looking
at is something called the site frequency spectrum. In a brief way, a way to think of the
site frequency spectrum is we are looking at positions
along the person's genome and you are counting up
what kinds of mutations occur at a given position. Here we have genomes from Africa, we have the Neanderthal genome, and we have the genome from a chimpanzee. You're going to focus on those positions where there's a difference in the state carried by the Neanderthal
and the chimpanzee, and at those positions we are going to see what count of African
genomes carry a state that matches the Neanderthal. For example, at this position the Neanderthal does not
match the chimpanzee, and when you look at the Africans they have two copies of the mutation that matches the Neanderthal. When you look at this
position the Neanderthal again does not match the chimpanzee, and the Africans carry
three copies of the mutation that matches the Neanderthal. So we go along this genome and tabulate this statistical summary, which we call the conditional site frequency spectrum. Now, why do we do this? It turns out that there is
some population genetic theory that tells us what we should expect to see in this statistical summary of the data. For example, if Africans
and Neanderthals split and never interbred then
this summary of the data is uniformly distributed
across all mutational classes. Now, what do we see in the data? When we look at the west
African population the Yoruba, the conditional site frequency spectrum, which here is the blue
dots, are far from uniform. They have this U shaped pattern. We looked at other west
African populations and we find the same
characteristic U shaped pattern. In other words, at least a simple model where Africans and Neanderthals
split and went their own way does not fit the data. We then asked could this be explained by other models of human history? For example, we have a
fairly good understanding of the relationship between Africans and archaic populations. Could this potentially explain it? We find that, again, current
models of human history do not offer a good enough fit
to the data that we observed. Then we explored additional models that are more complicated, which in involve different
levels of introgression into the African population. For example, we asked whether there was structure within Africa, this is quite possible
given all the evidence about deep structure within
different African populations. Is it possible that
there was introgression from a Neanderthal related
population into the Africans? Or is it possible that there
is a super archaic population that introgressed into Africa? For each of these models
we tried to figure out which of them best explains our signal. The model that does explain the signal of the conditional site frequency spectrum is one where there was introgression into the African population
from a super archaic population that split off prior to the split between Neanderthals and modern humans. This is neither Neanderthal or Denisovan, so we term this a ghost
archaic population. The key thing to remember here is this is actually quite deeply diverged, farther more than the Neanderthals and the Denisovans
compared to modern humans. Now we can be more quantitative
about this analysis and we can try to figure out when did this population split off, when did it come back and interbreed, and what proportion of archaic ancestry is present in Africans today. We did further analyses
and these are estimates with quite wide uncertainties, but what we estimate is a
date of about 600,000 years for the split time, and
an interbreeding time of around 43,000 years. This is still fairly
recent interbreeding event in the history of the African population. Further, we estimate a fairly
substantial contribution of this archaic ghost
lineage of about 11%. So compared to the
Neanderthal and the Denisovan introgression event,
which are of the order of a couple of percent. So we try to have a
complementary line of evidence to convince ourselves
that this was plausible. And to do this we went back
and tried to extract segments of DNA in the African population that could potentially arise
from this ghost archaic. To do this we had to
have a statistical model which does not require
an archaic population because we don't have
this reference genome. So we validated this model,
we showed that it works under different settings, and then we applied it to
the west African Yoruba. We got these segments of archaic DNA, which we went back and asked, "Is this closely related
to one of the genomes "that we have sequenced data from?" We compared the introgressed
DNA segments in Africa to hunter gatherer genomes,
genomes form pygmy populations. These are populations which
have been shown to have complex interactions with the west African populations
that we've analyzed. And finally to known archaic genomes like Neanderthals and Denisovans. What we are showing here is
the measure of divergence. On the left you are closely related, on the right you are farther related. What we find are that
these archaic segments compared to other non-archaic segments are not particularly closely related to any of these populations
that we have genomes from. So what is this population? We don't know. This is one of the questions that we'd like to be able to
answer going forward. Just to summarize, there is clear evidence that there is archaic introgression within and outside Africa. We have an increasing
complexity in the picture of interactions between
modern humans and archaics. John Hocks also talked
about these pre-print that came out last week
from Alan Rodger's group, which showed that there are additional archaic introgression
event in human history. A big question for us is
to have a holistic picture, which puts together these
different introgression events, asks whether some of these are coming from the same population or are these distinct archaic groups. This is a challenging task and to be able to do
this we need to analyze diverse modern and ancient
genomes from Africa. We don't have ancient archaic genomes but we do have ancient genomes from other modern human populations. We need to do this in the context of these more realistic models of history which take into account
deep introgressions. And finally, the statistical
models that we've talked about are making certain assumptions which are fairy simplistic and those need to be extended
to handle this complexity. With that I'd like to
acknowledge my student, Arun, who's done a lot of this work on ghost archaic introgression, funding, and I'd be be
happy to take questions. (audience clapping) (cheerful music)
