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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 bottleneck 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's 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 bottleneck during this time period, 200,000 to
100,000 years ago. And maybe that bottleneck 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
bottleneck 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 absorbed 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] ♪
