[ Music ] When we think about what has
changed in the last 5 years of understanding human
evolution, there is no story that is bigger than the
story of the Denisovans. This is a population
that we know today only through their genomes,
and it's a population that archaeologists had not
suspected they would find to exist. It's a really crazy
story, and it's one that so illustrates the
importance of ancient DNA and reshaping our view of
the dynamics and interactions of ancient humans in the past. We have, through ancient DNA
technology, recovered evidence of a population that
is among the ancestors of living humans today, and
that's tremendously exciting, but it also shows us just
how much the fossil record and the archaeological
record leave out as we're considering the
dynamics of ancient populations and how they came
to be modern humans. Denisova Cave is a cave in the
Altai Mountains of Siberia. It's a region that is today
in the nation of Russia, and the Altai Mountains
are themselves a very interesting area. There's archaeological evidence
of very early modern humans, of Neandertals and now
of this third population, the Denisovans. All of which were existing in what is a relatively small
area near the borders of Russia, Kazakhstan, Mongolia, China. It's a tremendously
interesting area, an area that is really the
crossroads of Central Asia, and it's an area that has
been investigated intensively by Russian archaeologists
for now, at Denisova Cave
more than 30 years. The Denisova excavation has
produced really interesting evidence of the behaviors
of ancient people, and until recently,
everyone assumed that these ancient people that were being documented
there were likely Neandertals. I will say that at Denisova
Cave itself, there are bones that do represent Neandertals, because we have ancient
DNA evidence from some of them that's very similar
to Neandertal specimens that are found elsewhere in
Europe and in Central Asia. But the evidence from one of
these bones was very different from Neandertals and
even more different from most living people. That evidence came from
one bone which is the tip of a fifth finger, or a pinky,
and represents an older juvenile or a young adolescent female. We know it's female from the
two X chromosomes in the genome. That bone produced better, more well-preserved
ancient DNA evidence than any other bone had
before this one was sequenced. Denisova is truly an
extraordinary situation, in terms of ancient
DNA preservation. The reason why is that the
Denisova Cave is a cold cave year-round. It's a cave where the
average temperature around the year is
zero degrees Celsius. So, essentially freezing. That low temperature maintained
over tens of thousands of years has effectively
preserved DNA from multiple specimens. So the really, really interesting genome
came from a pinky bone. It's something that as a
paleoanthropologist I have to say is shocking. This is the kind of bone that
if you're really a specialist, you will know that there was a
pinky bone from Denisova Cave, but otherwise you're not going
to pay a lot of attention to it. The pinky doesn't tell us a lot about the behaviors
of ancient hominins. You can probably do your
dissertation on every pinky that was found anywhere
in the world, but it wouldn't be a very
interesting dissertation. Osteologically, this
is not great evidence about this ancient group, but the genetics give us the 3
billion base pairs copied twice that existed in this
ancient person's genome. They're telling us
today far more about this ancient population than we could ever have
discovered from bones alone. So it's hugely important. How do we know the Denisova
individual represents a different population? When we look at the sequence
of this genome compared to human sequences, compared
to Neandertal sequences, it is very different
from both of them. Now, across the genome
as a whole, it's slightly more similar
to Neandertals than it is to living people around
the world and especially to living people in Africa now. So there is some
relationship between this genome and Neandertals, but that
genome is very slight compared to the relationships
among modern humans now, and it's very slight compared to the relationships among
different Neandertal sequences that we have. So this genome appears
to represent a group that was quite distinct
from Neandertals and quite distinct
from recent humans. It was a different population. We know something about the
dynamics of that population. For one thing, this genome
shares some functional genes with Neandertals that
lived in Central Asia. Those functional genes are
genes related to immunity, and so there was interbreeding
between this population and the nearby Neandertal
populations, interbreeding that was sufficient to
spread at least some genes that had adaptive value. We also know from this
genome that it has parts that are very divergent
from Neandertals and from recent people. Most of the genome is sort
of somewhat divergent, but some parts of the
genome are very divergent, and that includes the
mitochondrial DNA. The mitochondrial DNA of the Denisova genome
is very different from Neandertal mitochondrial
DNA and very different from the DNA of living people. Living humans for their
mitochondrial DNA share an ancestor around 200,000
years ago. We share an ancestor with
Neandertal mitochondrial DNA around about 500 to
700,000 years ago. We share a common ancestor with the Denisova
mitochondrial DNA well more than a million years ago. Coupled with evidence
from other genes that also show this pattern,
the Denisova genome looks like it represents an
interaction with a population that was yet more different from
us than the Neandertals were. The Denisova genome may have
interbred with something like a Homo erectus population or a significantly divergent
archaic human population that we haven't yet discovered. That is so interesting, because
it's showing us the dynamics of populations that we can't
witness with bones alone. We also know something
about the population in which the Denisova
genome existed. That population was smaller than
the population that gave rise to living people, because the
Denisova genome is more inbred than living people are. So Denisovans were a
pretty tight-knit group, a group that was relatively
small and persisted for a long time relatively quite
separate from other populations but with some interbreeding
with quite distant populations. The other thing that we
know about the dynamics of the Denisova population
is that they interbred with the ancestors of
some living humans. We know that because when we
compare the Denisova genome to the genomes of people living
today in aboriginal Australians, Highland New Guinea, to
some extent Melanesia -- which includes New
Caledonia, New Britain and nearby islands -- and in
the very easternmost parts of Indonesia and across
the Pacific in Polynesia, when we compare the
genomes of those people, we discover that they
have similarities with the Denisova
genome that no one else in the world today shares. So the Denisovans were partial
ancestors of the genetics of these populations that live
at the southeastern most extreme of the old world
human existence. That is super interesting
because what it tells us is that the Denisovan
population was extensive enough that the emerging
population of modern humans, carrying with them a very high
fraction of African ancestry, interacted with and interbred
with this Denisovan population, giving rise to the colonization
of Australia, of Melanesia, and of other points
in the Pacific, and that later there
was a movement of people that did not carry the Denisovan
signature of intermixture that spread across Asia
and covered up the evidence of this earlier mixture. Present-day Asians have
a very, very small degree of Denisovan admixture. In aboriginal Australians
and Highland New Guinea, we see 5% of the
genetic heritage of those people is a
population that was like the Denisova genome. On the mainland of Asia
it's well under 1%. Maybe as low as .2%. So we're looking at a
very complex dynamic in which human populations
emerged. They mixed. They separated to some degree. Further populations emerged and
mixed and colonized new areas. Later populations emerged
and spread and covered up the evidence of some
of the earlier mixture. Human populations in their
genetic history are what archaeologists would
call a palimpsest. A palimpsest is a
manuscript that was written on and then rubbed out
and written on again. In medieval times monks that were copying manuscripts
sometimes reused the same pages. Modern human genetic
ancestry is like that. Our ancestry comes from multiple
layers of ancient movements that emerged from Africa,
became somewhat differentiated from each other, mixed with
each other and then remixed as later people left Africa. It is a really complicated
and interesting scenario, and the Denisova genome
demonstrates it more than anything else. But the Denisova
genome is not alone. We're increasingly learning, as
we'll see later in the course, that when we look at ancient
DNA within regions of the world, we discover that the ancient
DNA comes from populations that no longer are strong
representatives of the ancestors of living people in
the same regions. Ancient Europeans that
lived before the time that agriculture spread into Europe represent
only a small fraction of the ancestry of
living Europeans. Ancient Indonesians that were
there as Australians originated from that area are no
longer representative of present-day Indonesians
that lived in the same area, and the Denisovans show
that that goes back into deeper time periods. So that modern humans are
coming from a complex process, where ancient variations
are being established and then remixing and then
partially being rubbed out by the movements of new
people that are expanding with some mixture and successive
layers of this process. The Denisova genome is telling
us about these ancient dynamics. They're dynamics that go well
back into the Pleistocene and that involve archaic
humans that lived in Africa and that lived across Eurasia. It's a tremendously
interesting discovery, and there are other
aspects to it that involve the
functions of these genes. I'll talk about the importance
of gene functions and the way that we're learning about the
biology of these ancient people when I talk about
Neandertal genetics, because in those cases we're
able to discover something about the biology of an ancient
population beyond its bones. The Denisova genome is giving
rise to similar insights about a population
where the bones that we have are very, very few.
