Ancient Sex Scandals: Did We Get It On With Neandertals?

Posted on: May 7, 2010 2:00 AM, by Christie Wilcox

This week, Science published two papers about the genetics of Neandertals from a team of scientists based
at the Max Planck Institute of Evolutionary Anthropology. The first (which is the only one anyone seems to
really care about) gives a draft version of the entire Neandertal genome - a whopping 4 billion base pairs of
DNA. They use this information to look for genomic regions that may have been affected by positive
selection in ancestral modern humans that led to their separation from Neandertals, and found some very
interesting ones that include genes involved in metabolism and in cognitive and skeletal development.

But, of course, that's not what everyone is saying about this paper. What everyone is talking about is that
this study 'proved' ancient people f*cked Neandertals. Not only were there romantic trysts between these
different hominid lineages, they led to human-Neandertal hybrids, the evidence of which is written in the
genomes of all people from Europe and Asia.

In the words of the media...

There's the blunt and simple: "Modern man had sex with Neanderthals"
Or the creative reversal: "Neanderthals 'had sex' with modern man"
Or, my personal favorite: "Neanderthal Genome Shows Most Humans Are Cavemen"

But what did the paper actually say, and is the authors' conclusion that modern humans and Neanderthals
screwed productively the only explanation?

The Neandertal Genome

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How did they get the Neandertal genome anyway? Well, they took small powder samples of otherwise
fairly useless bones from three female Neandertals, all of which were about 40,000 years old. Through
some complicated methods, they turned these bone fragments into libraries of DNA chunks, each less than
200 base pairs long. They then took these fragments and pieced them together, using human and chimp
genomes as road maps.

Now, the really tough part isn't getting and aligning sequences from Neandertal bones (though, that's not to
say that it's easy). It's making sure you're sequencing the bones and not something else. Over the years, the
bones have been handles by people, are coated in bacteria, and in general, are contaminated. When doing
genetics work with many, modern-day animals, such contamination isn't as much of an issue - for the most
part, primers are specific to one kind of organism or another, and the odds of samples being contaminated
by a similar enough organism to matter are low. In my lab, for example, the odds that the samples I make
from fish fin clips are contaminated with another fish's DNA are pretty low, so there's little worry that my
primers will amplify something other than the gene I want.

But these guys are trying to amplify DNA from a creature that is very, very much like us. Furthermore, they
don't know what to expect in terms of sequence, and have to use primers that are a little more universal to
all primate species. This means that if even one skin cell from one of the scientists falls into a PCR tube,
they'll be amplifying the wrong DNA to get their genome sequence. Such contamination has been a big
issue in the past studies on Neandertal genetics. In this study, the authors went to every extreme to prevent
contamination. Still, they estimate that human contamination in their samples may be as high as 0.5% for
the mitochondrial genome and 1.53% for the nuclear genome. I'll explain why that matters in a bit.

The Good Stuff: What They Found

So what did they find? Well, for one, the divergence between human and Neandertal genomes was just a
hair under 12.7%. Though you may have heard that you're 98% chimp, the actual sequence divergence
between humans and chimps is actually closer to 30%, and scientists have estimated that this represents
somewhere between 5.6 to 8.3 million years of separated evolution. Using that as a reference, Green and
colleagues estimated that humans and Neandertals diverged about 825,000 years ago. But that's not the
whole story, as any two people will have a certain amount of divergence between their genomes. The team
also looked at the divergence between native people from Africa, Asia and Europe, and found that the
overall sequence divergence between any two people was 8.2% to 10.3%. The Neandertal was significantly
more divergent from modern humans than lineages of modern humans are from each other, but the new
information changed the time line a little. In the end, they estimate that modern humans and Neandertals
became distinct between 270,000 and 440,000 years ago

What the scientists really wanted to know, though, was what was different. Were there clues to how human
intelligence, or any other traits, evolved, based on the information contained in our closest relatives? A
large part of the paper sought to find evidence of positive selection on the human lineage after the split
from Neandertals.

They did this two ways. First, they looked for genes that were the same in Neandertals and chimpanzees,
orangutans, and rhesus macaques, but were very different in us. There weren't as many differences as you
might think. Only 78 of our 20,000 or so protein genes have changed their amino acid sequence since the
split from Neanderthls. They also found 268 changes in sequences that don't code for proteins, but instead
function other ways, like as promoters, silencers, or microRNAs.

They also looked for stretches of genetic material that are symptomatic of natural selection. How does a set
of genes "look" like it's undergone selection? Well, when a single allele (variation of a gene) is strongly
favored due to selection, its proportion in the population rises. Sometimes, it becomes so common that the
rest of the alleles disappear, and this is what is called a "selective sweep." Scientists can find these sweeps
by looking at Single Nucleotide Polymorphisms (SNPs), or areas that differ by a single base pair. Most of
the areas that look this way between chimps and people are similar between people and Neandertals,

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because they occurred after hominids split from primates but before the human-Neandertal break. But,
some have occurred since. In all, they found 212 regions that showed evidence of this kind of selection.

Somewhere, in those 350-550 odd changes, is likely what makes us so different from anything else that has
every lived - where, though is still a mystery.

But wait - what about the sex?

Yeah, yeah, I'm getting to it. Geez! Y'all have a one-track mind.

After plowing through most of the paper, one arrives at a section titled "Neandertals are closer to non-
Africans than to Africans." In it, the scientists lay out their argument for inter-species sex. What they did to
determine this, in their own words was:

"To test whether Neandertals are more closely related to some present-day humans than to others, we
identified SNPs by comparing one randomly chosen sequence from each of two present-day humans and
asking if the Neandertals match the alleles of the two individuals equally often. If gene flow between
Neandertals and modern humans ceased before differentiation between present-day human populations
began, this is expected to be the case no matter which present-day humans are compared."
So they looked at how frequently the Neandertal genome matched each of the people from different
locations to see if one lineage of modern humans was more similar to the Neandertals than another.

They found that when they compared a European and an Asian to the Neandertals, there was no significant
difference. But when they compared an African and any non-African lineage, the Africans were less similar
to the Neandertals than other people. They estimate that 1-4% of non-Africans genome is Neandertal genes.

Now, the obvious first question is whether or not contamination explains this. After all, they said the
Neandertal nuclear sequences could have as high as 1.53% human contamination - which seeing as the
scientists themselves are of Eurasian decent, would certainly skew the Neandertal's genome that direction.
But they do give good explanations as to how it's not likely that this effect is due to contamination (which
involve some complex math and stats that I just can't see an easy way to break down).

The media stopped reading the paper right about there. Indeed, the authors strongly believe that their data
suggest that people and Neandertals interbred. But there are other explanations, even given by the authors,
that would cause the patterns they saw.

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 For example, it's possible that Neandertal's didn't split from all
people, but a subset that was on its way to becoming Eurasians. This is known as the "substructure within
Africa" hypothesis, where different groups of modern humans actually began splitting before leaving the
continent in search of the rest of the world. Carl Zimmer explains this idea rather nicely:

"Cast your mind back 500,000 years, before the populations of humans and Neanderthals had diverged.
Imagine that those ancestral Africans were not trading genes freely. Instead imagine that some kind of
barrier emerged to keep some gene variants in one part of Africa and other variants in another part.

Now imagine that the ancestors of Neanderthals leave Africa, and then much later the ancestors of
Europeans and Asians leave Africa. It's possible that both sets of immigrants came from the same part of
Africa. They might have both taken some gene variants with them did not exist in other parts of Africa.
Today, some living Africans still lack those variants. This scenario could lead to Europeans and Asians
with Neanderthal-like pieces of DNA without a single hybrid baby ever being born."

The substructure in Africa hypothesis is somewhat supported by other genetic and paleontological analyses.
Indeed, the authors note that they "cannot currently rule out a scenario in which the ancestral population of
present-day non-Africans was more closely related to Neandertals than the ancestral population of present-
day Africans due to ancient substructure within Africa"

There's another possible explanation, too, that the authors didn't bring up: selection.

Let's jump back those 500,000 years and take a look at our pre-split hominid population. Let's say, just for
argument's sake, that a given region had 10 variations in that group of individuals - we'll label them A, B,
C, D, E, F, G, H, I and J. Now, a group of them breaks northward. Due to founder effects, this small group
only has A, B, C, D and E to start with. As the rugged north takes its toll, certain variations prove more
useful - A and B, for example. Soon enough, genetic drift and selection leaves this population with only A,
B and D.

Meanwhile, the original population in Africa has been evolving. They have A. B. C. D. E. F. G. H, I, J and
how K, L, M, N and O. A small group from that population breaks off, too, and follows the path taken by
the first subgroup hundreds of thousands of years earlier. Again, due to founder effects, this new little
group has only a small amount of the variation that is in Africa - they take with them A, B, C, E, F, G, H, I,
M, N, and O. As they face the frigid winds and weakened sun, they are whittled down to only those that
give them the best advantage in the north - A, B, C, E, F, and O.

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Meanwhile, the African population is evolving, too. They find that some of their variations give them a
better chance in the African sun, like H through O. Over time, A, B and C just disappear.

So now you have one population with A, B and E, one with A, B, C, E, F and O, and one with E, F, G, H, I,
J, K, L, M, N and O. Although the two groups that stayed in Africa longer are more closely related, the
group that left first will be more similar to the second split off group because selection favored the same
variations in both that were present before the first split occurred. So you see, it's possible that selection
could explain some of the similarity between Eurasians and Neandertals, without a single person getting
hanky-panky with another hominid.

That's not to say that the hybridization hypothesis is without merit. Indeed, the authors did a damned good
job presenting their case, and their reasoning is sound. The point I'm making is that sex isn't the only
option. And if hybridization did occur to the extent they predict, we're likely to find more hints at its
existence. Analyzing the DNA of some of the suspected hybrid fossils, for example, might settle it once
and for all. Or we may never know if the gene variants that are similar between Eurasians and Neandertals
are due to sex, selection, or substructure. Time may have simply destroyed too much of the evidence for us
to be sure.

What is certain is that sex sells, which is why the only thing the media is talking about when it comes to
this paper is that ancient people may have shagged their evolutionary siblings. It's just so damned
frustrating because the sexual exploits of early humans is only the tiniest piece of this huge discovery. Oh,
the things we may learn from this genome about our own evolution, and our closest relatives! Whether we
had sex with Neandertals or not, the work this team has done will change forever our understanding of
hominid evolutionary history. The impact this genome will have on the science of human evolution is huge.
The breakthrough science, the future implications of this work - that's what the media should be talking
about - not ancient sex scandals.

http://scienceblogs.com/observations/2010/05/anceint_sex_scandals_did_we_ge.php

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Sex and the Single Neanderthal: Inter-Species Breeding in the Upper Palaeolithic?

There’s been some coverage of a recent announcement by Svante Pääbo of the Max Planck Institute, who
opines that Neanderthals and anatomically modern humans had sexual encounters as they co-habited in
Upper Palaeolithic Eurasia from around 42,000 bp to 24,500 bp. The main article is over at the London
Times, from which this is an excerpt:

Paabo recently told a conference at the Cold Spring Harbor Laboratory near New York that he was now
sure the two species had had sex — but a question remained about how “productive” it had been. “What
I’m really interested in is, did we have children back then and did those children contribute to our
variation today?” he said.

“I’m sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite
rigorously with the new [Neanderthal genome] sequence.” Such an answer might ease the controversy
over recent contradictory discoveries regarding Neanderthals. Some fossils seem to have both modern
human and Neanderthal features, suggesting that the two species interbred. Yet DNA scans have shown
that Neanderthal genes were very different from those of modern man.

Pääbo is reported to be at the point of publishing his analysis of the Neanderthal genome, and it seems clear
that he has gleaned something from the data that has prompted this latest assertion; previous research has
been interpreted as indicating that if the two species did interbreed it was at a very low level, apparently
evidenced by the almost complete lack of a Neanderthal presence in our own genome today.

Gene Expression comments thus:

The way Paabo is couching it, what he has found then seems likely to be evidence that humans who had
just expanded Out of Africa contributed to the genomes of Neandertals. In other words, modern human
introgression into Neandertals. Of course if the gene flow was from modern human to Neandertals
exclusively, then it would be an evolutionary dead end since that lineage went extinct.

In any case, for several decades some fossil-based paleoanthropologists have been claiming that there are
“intermediate” individuals in the record which indicate modern human-Neandertal hybridization. Most
prominently Erik Trinkaus. If Paabo’s finding becomes more solid, then it seems time to update the
probabilities on these sorts of claims based purely on morphology.

The story is taken up at Ad Hominin, where the following opinion is expressed:

Today, most researchers acknowledge that some sexual encounters could have occurred between
Neandertals and modern humans. The more interesting question is how common were these encounters
and did they leave their mark on the modern gene pool. Undoubtedly, modern humans and Neandertals
would have recognised each other as fellow humans but this does not mean that they would have acted
humanely to each another.

Countless social and psychological studies have shown humans to have a very strong “us versus them”
mentality, that no doubt also existed in our ancestors. It is unlikely that modern humans and Neandertals
had an easy relationship. Most sexual encounters that took place between the two were likely opportunistic
and probably involved enslavement and rape.

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Of course we have absolutely no evidence regarding the circumstances under which these liaisons may
have taken place, and I imagine the last sentence of the quote above is obliquely referring to the way in
which the indigenous Indian populations of the Americas were almost wiped from the face of the Earth by
the tide of white Europeans, who staged one of the most brutal and violent land-grabs in recorded history,
as they claimed other peoples’ territories for their own, killing thousands in the process.

However, Upper Palaeolithic Europe was a very different place to the Americas of a few centuries ago,
with no centralised governments, mobilised armies, or even slavery, as suggested above. I’m not even sure
what the duties of a putative slave in the UP would actually be, or how such a state of affairs could even be
enforced. The sheer numbers of humans involved in the theft of native peoples’ lands far eclipsed the
populations of Ice Age Europe, so although there might have been competition for land and resources, it
would have been on a far smaller scale than in modern times.

Moreover, the technological and cultural gap between Neanderthals and incoming moderns was
comparatively narrow, as opined by Professor Chris Stringer of the Natural History Museum in London:

“It’s possible that Neanderthals and humans were genetically incompatible, so they could have interbred
but their children would have been less fertile,” said Stringer. This phenomenon is seen in many other
species such as when lions breed with tigers and horses breed with zebras. “I used to believe
Neanderthals were primitive,” said Stringer, “but in the last 10,000-15,000 years before they died out,
around 30,000 years ago, Neanderthals were giving their dead complex burials and making tools and
jewellery, such as pierced beads, like modern humans.”

The popular notion of inter-species sex, as apparent in the previously quoted post, was that brutish
Neanderthal men had their wicked way with anatomically modern women by dragging them behind the
nearest bush, reinforcing the old stereotype of rapacious cavemen that has so blighted the way in which our
archaic ancestors have been viewed for nigh on 150 years.

Because the population of Europe in the Upper Palaeolithic was probably very low in both modern and
archaic communities, contact was likely to have been infrequent – indeed it seems quite possible that
members of both species lived entire lifetimes without encountering one another – as Neanderthal numbers
began to decline, any encounters would become increasingly rare.

And when moderns and Neanderthals did make primary contact, it could have been under any number of
circumstances, some of which may have resulted in violence and death, whilst others might have developed
into co-operation, friendship, up to and including, romance and kisses. Yet other encounters might have
ended in polite ‘nice-to-meet-you’ handshakes, after which the two species quietly got on with minding
their own business, without harbouring any particular feelings for or against their new acquaintances.

As a brief aside, I can’t help but speculate that it might have been easier for Neanderthal women to give
birth to inter-species offspring than their AMH counterparts – bearing in mind that Neanderthal babies were
more robust, the shape and size of their skulls, even when hybridised, would have made it more difficult for
AMH mothers to give birth. A Neanderthal woman who had conceived a child fathered by an AMH male
would maybe have found it easier to give birth to the hybridised and possibly smaller baby she was
carrying – so should we expect to find that hybridised children conceived by Neanderthal women survived
in greater numbers than those conceived by AMH mothers? And how would we then consider the
evolutionary social factors that led to relationships between the two species that caused AMH men to bond
and breed with Neanderthal women? Such a question may be answered in part from this further quote from
Ad Hominin:

The recent announcement by Svante Pääbo that he is sure that Neandertals and modern humans had sex is
quite a bold pronouncement coming from a scientist. It raises the question of whether this ascertain is
based on some hard evidence they found while sequencing the Neandertal genome. It is possible that if
there was some Neandertal genes passed on to the first moderns in Europe, they could have got eliminated

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from the subsequent gene pool as population sizes fluctuated during the more severe climatic episodes. A
more likely scenario is that Pääbo’s team found evidence of modern introgression in the Neandertal
genome. In all likelihood the incoming modern humans were more numerous than the Neandertals, thereby
absorbing the endemic populations through genetic swamping.

This would seem to reinforce the point that any enforced sex is more likely to have been instigated by
incoming AMH males on the female Neanderthal population, if we are to take modern history of human
conquest and genocide into account and apply the same mind-set to life 30,000 to 40,000 years ago. But the
fact that the both modern and archaic populations may have co-existed in Europe for 10,000-15,000 years
at least hints that there was no large-scale or organised species cleansing undertaken by AMH, and it’s
quite possible that both they and the Neanderthals behaved a great deal better towards each other than has
often been the case in our own recorded histories.

It remains to be seen whether this latest research is able to resolve this question of interbreeding, or whether
instead tentative clues will emerge that raise more questions than answers.

See also: Video – Svante Pääbo discussing the Neanderthal Genome Project on YouTube.

http://anthropology.net/2009/10/27/sex-and-the-single-neanderthal-inter-species-breeding-in-the-upper-
palaeolithic/

NEANDERTALS LIVE!
I, for one, welcome my Neandertal ancestry.

It may not sound like a lot -- between 1 and 4 percent. But that's the equivalent of one
great-great-great grandparent's DNA contribution. In the case of the Neandertal
contribution, more than 1500 generations ago, it's an enduring legacy of an ancient group
of people, spread across many lines of the genealogies of living people. Beyond their
genealogical interest, Neandertal genes might have made a big difference to our
evolutionary potential.

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In case you wonder what the heck I'm talking about, here's the story: Two new papers in
Science describe the full draft sequence of the Neandertal genome, and perform
additional analyses to understand the pattern of adaptive evolution in the population
ancestral to living people.

Richard Green and colleagues report on the genome, demonstrating very convincingly
that present-day people have Neandertal ancestors. It is not entirely obvious when and
where the gene flow between Neandertals and other ancient populations happened --
whether it was associated with the dispersal of most of our ancestry from Africa, or
whether it may have been earlier. The gene flow was not limited to Europe, and evidence
for Neandertal ancestry occurs in East Asian and Australasian populations.

The paper is full of other good stuff, including some evidence about which gene regions
changed under selection in the ancestral human population.

Meanwhile, the second paper by Burbano and colleagues applies new microarray
techniques to assess how much of the human legacy of amino acid changes has arisen in
the latest, post-Neandertal period of our evolution.

So there's a lot about the pattern of evolution and gene flow leading to living people, and
a lot about adaptive and functional evolution. That makes a lot for me to cover -- and
while I have the papers a little early, time is short. Let's see how much I can help clarify
what's in this new research.

If you had to sum up in a few words, what does this mean for
paleoanthropology?

These scientists have given an immense gift to humanity.

I've been comparing it to the pictures of Earth that came back from Apollo 8. The
Neandertal genome gives us a picture of ourselves, from the outside looking in. We can
see, and now learn about, the essential genetic changes that make us human -- the things
that made our emergence as a global species possible.

And in doing so, they've taken a forgotten group of people -- whom even most
anthropologists had given up on -- and they've restored them to their rightful place in our
heritage.

Beyond that, they've taken all of their data and deposited it in a public database, so that
the rest of us can inspect them, replicate results, and learn new things from them. High
school kids can download this stuff and do science fair projects on Neandertal genomics.

This is what anthropology ought to be.

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What did they sequence?

The Max Planck group obtained most of their genomic sequence from three specimens
from Vindija -- Vi33.16, Vi33.25, and Vi33.26. These are all postcranial fragments with
minimal anatomical information. Green and colleagues were able to establish that the
three bones represent different women, and that Vi33.16 and Vi33.26 may represent
maternal relatives.

From these skeletons they got 5.3 billion bases of sequence. All this from an amount of
bone powder about equal in mass to an aspirin pill.

Amazing. I mean, I know the folks at Max Planck are reading this. It's inspiring to see
what they've been able to do. These are three pieces of barely diagnostic hominin bone,
and they've obtained literally hundreds of times more information than we have ever
gotten from the fossil record of Neandertals.

I'll describe the analyses of genetic similarity with humans in more detail below. As a
brief summary, of those positions where the human genome differs from chimpanzees,
Neandertals have the chimpanzee version around 12.7 percent of the time -- meaning that
across the genome, a Neandertal and a human will share a genetic ancestor an average of
around 800,000 years ago. This is a couple hundred thousand years higher than the same
number if we compare two humans to each other. The higher age of genetic common
ancestors reflects partial isolation between the Neandertal population and the African
populations that gave rise to most of our current genetic variation.

The team were able to identify 111 candidate duplications, almost all of which have some
evidence of copy number variation in humans or other primates. They tentatively show
that Neandertals have a bit more copy number variation than present-day humans, and
identify a few loci with substantially higher copy numbers in one group or the other.

A substantial part of the paper is dedicated to finding evidence of positive selection on

the human lineage after the emergence of Neandertals. The idea is to look for fixed
selective sweeps -- regions where humans are likely to have SNPs absent in Neandertals
and a relatively shallow gene tree. They identify 212 regions like this -- as I discuss
below, a surprisingly low number.

The second paper, by Hernán Burbano and colleagues, describes the application of a
targeted microarray to probe Neandertal genetic samples for protein-coding variants that
separate humans from chimpanzees. They identify 88 amino acid substitutions that seem
fixed in the known sample of living humans, but not present in the Neandertal sequence.
Those 88 are not necessarily all functionally important, although this list will include a
number of "structural" genetic changes that make a difference to proteins expressed
worldwide today. There is much to come in analyzing the categories and genes
represented in both lists, which may tell us very interesting things about our Late
Pleistocene evolution.

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What is the evidence for interbreeding?

From their initial work sequencing the nuclear genome in Neandertals, the Max Planck
group has followed a clever strategy: Don't look at the Neandertal sequence to see what
humans share, look at human variation to see which version the Neandertal sequence has.

The strategy is smart because it helps to obviate some major problems with ancient DNA
-- you don't have all the parts, and the parts you do have probably contain a lot of
sequencing errors of various kinds. By looking first at sites that vary within humans (or,
in some comparisons, between humans and chimpanzees), we can focus on a very simple
question -- did the Neandertal have one version, or the other?

Applied to human variation today, there are several ways we might use a Neandertal
genome test the hypothesis of no interbreeding. Green and colleagues focus on two
complementary approaches.

1. If Neandertals contributed no genes to living populations, then they should be equally

related to all living people, no matter where in the world those people live.

Green and colleagues show that the Neandertal genome is closer to some humans than
others. People whose ancestry lies outside Africa are significantly more like Neandertals
than are people who live in Africa today. In this study, the authors include whole
genomes from people in France, China and Papua New Guinea outside Africa, and
Yoruba and San inside Africa. The Africans are not as close to the Neandertal as any of
the non-Africans.

That doesn't mean that non-Africans derive most of their genes from Neandertals -- in
fact, as I describe below, the proportion is quite small. Living people are more like each
other -- even non-Africans and Africans -- than any of them are like Neandertals.

The point is that despite this great similarity of living people, we have genetic variants
that we share with the Neandertal genome, and that proportion is a lot higher outside
Africa than inside it. The natural conclusion is the Neandertals contributed more genes to
non-Africans than to Africans.

One thing is for sure: You can't explain this observation under the hypothesis that a
small, African population expanded out of Africa without interbreeding with Neandertals
along the way.

2. Look at the genes most likely to represent ancient population structure, the ones with
deep roots outside Africa.

This is an idea that we came up with to look for genes in living humans that might have
come in from Neandertals or other ancient populations (for example, we described it in
our 2008 review). Look for the parts of the genome with the deepest genealogical roots
outside of Africa. Those are candidates for Neandertal gene flow -- a high chance that

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one of the two sides of that deep root was present outside of Africa for hundreds of
thousands of years.

Green and colleagues took this idea to the next level. They found parts of the genome
where non-Africans have a deep root and Africans don't. Then they looked at the
Neandertal sequence. Out of the 12 regions they identified with deep roots outside Africa,
they found that the Neandertals had the deep, non-African specific version in 10 of those.

I mean, there's really not any other way you can explain this. We got those genes from
Neandertals. Every one of those loci is a region where some people have a Neandertal-
derived allele, and others don't. Those particular 10 loci are a small fraction of the overall
Neandertal-derived element of our heritage -- because they used Perlegen SNPs to find
them, they ended up with regions that are fairly long (100 kb or more in length). Those
are probably all really interesting, but there will be more of them when we can reliably
identify smaller segments with deep genealogies.

Could the results have been caused by contamination?

Green and colleagues are utterly convincing about the level of contamination in their
sequence. They have employed several independent checks, all of which arrive at the
same conclusion: The modern human contamination in almost all their comparisons is
limited to significantly less than one percent -- and for autosomal sequence they can give
a tight estimate of 0.7 percent contaminating sequence.

The methods that Green and colleagues used to test for a Neandertal contribution to non-
African populations are not likely to be strongly influenced by contamination. The probe
for deep roots in particular is extremely unlikely to be influenced by contamination in the
Neandertal sequence.

The very low contamination rate, and methods that should be robust to some
contamination, means that we can be very confident in their result.

How much Neandertal ancestry do we have?

The Neandertal contribution does not make up a major proportion of any population,
even outside of Africa. Green and colleagues apply a population model that involves
isolation between ancestral Neandertal and African populations, a dispersal from Africa
into Eurasia, and subsequent mixture with the Neandertals. Under this model, the
estimated fraction of Neandertal ancestry for non-African populations today is between 1
and 4 percent.

Now, let's put on our skeptics' hats. Is this the right model?

If Neandertal and African populations had not been isolated, then the amount of mixture
after an out-of-Africa dispersal would be lower. On the other hand, the dispersing African
population would already be part Neandertal, because of genetic mixture. The proportion

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of ancestry from ancestral Neandertals would be around the same amount, it would just
be distributed across a longer time.

They did not examine the question of how much of the genome came in from Neandertals
because of selection. The estimate they have, between 1 and 4 percent, is so high that this
is not just a few genes introgressing in from Neandertals -- it is a big fraction of the
neutral, non-coding part of the genome. So selection doesn't explain the similarity, nor
can parallelism -- the similarity is genome-wide, not just coding or functional changes,
and not as far as we know clustered into regions that might have hitchhiked with adaptive
alleles.

But there's clearly a lot more to do, characterizing the functional implications of some
regions, testing for selection, and finding Neandertal variants that might have reached
very high frequencies in later populations. To the extent that selection has influenced the
pattern, it will also throw off the simple population model. But it doesn't throw off the
fraction of Neandertal ancestry -- if it's three percent, it doesn't matter whether it was
selected or neutral, it's still three percent.

So the bottom line is, the fraction is going to be about right, regardless of the mechanism
by which the genetic mixture happened.

Can we please take off our skeptics' hats? It's getting in the way of my
Neandertal victory dance.

No. All the cool paleoanthropologists wear hats.

What about population structure within Africa? Could that explain the
apparent Neandertal contribution?

We've known about the occasional deep-rooted genealogies outside Africa for a long time
(and Jeff Wall's work, as an example among others, has explained that pattern as archaic
human mixture into non-Africans). They've been talking about something like five
percent of the human genome coming from admixture with ancient groups outside of
Africa. So this shouldn't come as a shock.

Until now, though, it has been possible for some people to wave these results away. We
didn't really know that any of those deep roots were in archaic humans, and after all,
who's to say that they aren't variants that originated in Africa and have since been lost
there, or that we haven't found them yet? African variation is great, and if you imagine
that some variation might have once existed in northeastern Africa and was subsequently
lost within African populations, that might look like admixture with archaic humans
outside of Africa.

This line of argument is now special pleading. Why would we posit a cryptic mystery
population in Africa, which happens to look genetically identical to Neandertals, but has
subsequently disappeared? A big fraction of deep genealogies outside Africa really are in

13
Neandertals. By far the simplest explanation is that today's non-Africans got them from
ancient non-Africans. This is no surprise -- that's where the data have been pointing now
for five years.

Yet Africans are a lot more diverse than other populations, and this diversity itself does
reflect the dynamics of the ancient African population. The Neandertals aren't so different
from that pattern that now still exists within Africa -- they're extending the notion that
"modern" is something that's been evolving for a long time. I expect we'll be able to come
to a better understanding of ancient population interactions within Africa, by
understanding the parts of the genome that have come from Neandertals outside of
Africa.

Could the gene flow be due to ancient interactions between West Asia
and Africa?

Green and colleagues suggest that at most few genes from modern humans ended up in
Neandertals.

That is, although they find lots of evidence of old-looking genes in us that are shared with
the Neandertal genome, they find few cases of new-looking genes in us that are shared
with that genome.

That might suggest several things about interactions between Africa and West Asia and
Europe during the Middle to Late Pleistocene. For example, if there had been high gene
flow from Africa into West Asia after the first appearance of a distinct Neandertal
population, maybe 200,000 to 400,000 years ago, we might expect to find some new-
looking genes in humans that Neandertals also got.

On the other hand, the data are from European Neandertals, who are at the end of a fairly
long chain of populations from Northeast Africa. If gene flow had been ongoing into the
Levant or further into West Asia during the last 200,000 years, it's not obvious how many
of these genes would have made it into Europe. The rapid mitochondrial DNA
coalescence of Neandertals does suggest substantial mobility in the population across
Central Asia to Western Europe. But maybe that apparent dynamism had a boost from
mtDNA selection.

So just on the data, I don't think we know yet whether this is gene flow in the Levant
200,000 or 100,000 years ago, or whether it's genes coming from West Asian Neandertals
into dispersing Africans after 100,000 years ago. I expect all are likely. I have some ideas
how to test some of these things, and we will get started immediately.

The lack of apparent mixture of "modern" genes into Neandertals --

what does it mean?

It means that a model of one-way gene flow from Neandertals into us can explain the
pattern of genetic similarity.

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The authors explain this as a function of population expansion. The expanding population
(us) picks up some Neandertal genes that expand in numbers, while the contracting
population (Neandertals) doesn't have a chance to pick up as many genes because it is
declining in numbers. That model seems plausible, particularly in comparison with
historical cases of population contact.

On the other hand, the three Neandertals from which most of the genome sequence was
derived all date to before 40,000 years ago. There weren't any modern humans around for
them to have interacted with around Vindija at that time. So should we be surprised that
they don't have genes of modern humans?

A more interesting question was posed to me by a very sharp journalist: What would we
expect the result to have been if they had sequenced a Near Eastern Neandertal, like
Amud, for example?

The answer seems obvious -- the admixture fraction should have been higher. That
population, which is the most likely to have been the source of mixture, must have been
somewhat genetically different from the European Neandertals. Any extent of genetic
differentiation between them would make the European Neandertals look less like non-
Africans today than the Near Eastern ones.

I'll have more to say about these Near Eastern Neandertals in the next few days.

But wait a minute. I thought the mitochondrial DNA proved that

Neandertals are extinct!

Selection. Selection. Selection.

I've been saying it for years. I've published it. Will you learn to listen to me, already?

The mtDNA of Neandertals is gone because it conferred some disadvantage. There are
many reasons to suspect this -- the Neandertal variation is itself apparently recently
derived; the human variation is clearly in disequilibrium, especially outside Africa; the
mtDNA genes affect functions that differ greatly in Neandertal and recent populations,
including energetics, longevity, and brain; there are clear signs of mtDNA selection in
many recent human populations.

Mitochondrial DNA is useful for a lot of reasons, but nobody should ever have relied on
it alone as evidence of Neandertal population dynamics.

Is it really true that there is no variation in Neandertal ancestry outside

Africa?

The comparisons in the paper are highly convincing because of the sheer amount of
sequence taken from the sampled individuals. A single gene locus from an individual
may be unrepresentative of the person's population, but averaged across the whole

15
genome, the difference between two people from distant populations is very, very close
to the difference between the two populations.

But they sampled very few individuals. So we are left with a question -- do we really
know we've sampled variation outside Africa enough to make regional estimates of
Neandertal gene flow?

I think we could do better with more genomes. For example, when it comes to finding
deep genealogies, we need to be able to find shorter regions than the ones used by Green
and colleagues. That will expand the sample of candidate loci, and will catch some
Neandertal-derived genes that we're missing now. Moreover, if gene flow was really
around 1-4 percent, many SNPs that came in from Neandertals will be rare enough to be
missing from the big SNP genotyping samples. We may find some variants with whole-
genome sequencing on larger samples that will be worth examining.

But most important, we'll be able to develop strategies based on this success to find
ancient population structure involving groups where we don't yet have the DNA -- like
populations of South and East Asia. Some of those may give us the chance to test those
methods soon, as for the Denisova individual.

Is this multiregional evolution, or just out-of-Africa with some leakage

of earlier Eurasian genes?

Out-of-Africa movement was a major mechanism of recent human evolution. The genetic
ancestry of living people is multiregional.

I see no contradiction between those statements. From now on, we are all
multiregionalists trying to explain the out-of-Africa pattern.

There was clearly a dispersal of African genes into the rest of the world during the Late
Pleistocene, sometime between 50,000 and 100,000 years ago. Living people everywhere
on Earth derive more than 90 percent of their genes from African populations who lived
100,000 years ago. That much is plain.

(Why did I not write "more than 96 percent?" See below.)

These genetic observations require some kind of out-of-Africa event. This event was not
limited to a few genes, and selection of a few genes even with substantial hitchhiking of
surrounding genome cannot account for the pattern. There must have been some kind of
demographic expansion including African-derived populations and preferentially
excluding the genes of Eurasian populations like the Neandertals. Selection on a gene
network might have mediated the expansion, as suggested by Eswaran (2002). Or the
expansion might have been culturally or technologically mediated, as many other people
have suggested.

16
Those are hypotheses about mechanisms. How did it come to be that living people trace
the overwhelming majority of their ancestry to Africa within the last 100,000 years?
These explanations may answer that question.

The present study shows that Neandertals were at a minimum partially isolated from their
contemporaries in Africa, and that the genetic divergence between those populations was
larger than the genetic differences between European, Asian, and African populations
today.

Yet those Neandertals are among our ancestors. Late Pleistocene humans had
multiregional origins, and the evolution of the Neandertals was itself a case of relatively
recent population dispersal from Africa or West Asia. Human and Neandertal genes
mostly derive from common genetic ancestors between 400,000 and a million years ago
-- much, much later than the initial habitation of Eurasia 1.8 million years ago.

But 1-4 percent is so minor, can it be an important part of our

evolution?

There are three things you have to ask about the fraction of Neandertal ancestry.

1. How much gene flow would it take to guarantee that anything adaptive in the
Neandertal population survived into later people?

The answer to that question is simple -- it takes a few dozen matings to get most adaptive
genes into our population. If there was a lot of interference with the genetic background,
it might take more -- just to make sure that the advantageous alleles had a chance to be
de-linked from the genetic background.

If Neandertals are one percent of the ancestry of non-Africans, we can be very sure that
any gene in a Neandertal that had adaptive value in the later population is here now. That
means they were important in an evolutionary sense.

2. What fraction of the human population 50,000 years ago were Neandertals?

This is very important -- when it comes to neutral genetic loci, the essential question is
how much the Neandertals may be underrepresented today relative to their numbers in
the past. Is three percent too low? It seems very unlikely that the fraction of Neandertals
compared to the rest of humans was as high as 10 percent -- we know that Africa already
had a large population 50,000 years ago, and everything we know about Neandertals
suggests a very low population density, an effective size much smaller than 10,000
individuals. Were five percent of the people on Earth 50,000 years ago Neandertals?

We don't really know the answers, but now we have a chance to test hypotheses about
ancient population size and expansion in Neandertals. My point at the moment is only
this: If today Neandertal genes make up only one percent of the gene pool of the 5 billion
people outside Africa, that's the genetic equivalent of 50 million Neandertals.

17
In relative terms, their contribution to our population may be a reduction from their
fraction of the Late Pleistocene population. Not that great a reduction, not a massive
crash to zero. A reduction in the wake of the out-of-Africa movement, possibly from five
percent to three.

<b<3. how="" many="" neandertals="" are="" there="" with="" us="" now?=""></b<3.>

You might think the answer to this is obviously zero. But in genetic terms, we can ask,
how many times has the average Neandertal-derived gene been replicated in our present
gene pool? Those aren't Neandertal individuals -- that is, a forensic anthropologist
wouldn't classify them as Neandertals. They're the genetic equivalent.

The answer to this is also simple: In absolute terms, the Neandertals are here around
us, yawping from the rooftops.

There are more than five billion people living outside of Africa today. If they are one
percent Neandertal, that's the genetic equivalent of fifty million Neandertals walking the
Earth around us.

Does that sound minor? If I told you that your average gene would be replicated into fifty
million copies in the future, would you be satisfied? Maybe your ambition is greater, but
I think the Neandertals have done very well for themselves.

Does this mean that Neandertals belong in our species, Homo sapiens?

Yes.

Interbreeding with fertile offspring in nature. That's the biological species concept.

Now, some paleontologists might still disagree -- maintaining that species are units that
can be distinguished morphologically, or by one or more derived features, or any number
of other definitions. That's fine with me, as long as they're clear. But understand: It does
define all non-Africans today as an interspecific hybrid population.

So maybe they want to rethink that one?

If Eurasians got less than 4 percent from Neandertals, doesn't that

mean that they got more than 96 percent from Africa?

I look at the 1-4 percent estimate as a minimum, for several reasons. As I'll note below,
this estimate mainly refers to the excess Neandertal ancestry outside Africa, which means
there may be some additional amount that both recent African and non-African
populations share.

But more important, Neandertals weren't the only people living in Eurasia 100,000 years
ago. China didn't have Neandertals, nor did Southeast Asia and Java. India was full of

18
hominins, which might or might not have shared substantial genetic similarity with
Neandertals. They're close enough to the known Neandertal range to speculate that they
may have been close, but the only available fossil, the Middle Pleistocene Narmada skull,
is not very informative. Any of these populations might have been genetically different
from Neandertals, and might have also contributed genes to present-day human
populations -- genes that wouldn't show up by scanning the Neandertal genome.

The recent genetic sequencing of the Denisova pinky (a.k.a. the X-woman) from the Altai
Mountains reminds us that these populations outside of Africa may have been quite a bit
closer to us, genetically, than we might have expected from the 1.8-million-year record of
humans outside Africa. These populations were dynamic in ways that many
paleoanthropologists haven't yet appreciated.

Do living Africans have Neandertal ancestry, too?

I think that the present study doesn't have the power to answer this question, at least with
the design that the authors used. The fact that living Africans are less genetically similar
to the Neandertals is extremely important evidence of the Neandertals' genetic
contribution to populations outside Africa. But it doesn't bear on how much back-
migration into Africa may have happened.

We know that the answer is nonzero, because Africa has received immigrants from other
parts of the world during historic times. The same genetic patterns that reflect population
contacts up and down the East African coast, and across the Sahara into West Africa,
show the possible conduits for the flow of Neandertal-derived genes into African
populations.

But how much genetic dispersal into Africa happened in LSA or late MSA times?
Mitochondrial and Y chromosome distributions in Northeast Africa suggest there was
been some. Nevertheless, Africa would have been a very difficult place to return, for
humans who had begun adapting to different ecological and disease environment.

I think that some Neandertal genes might have made it back into Africa, even in ancient
times, but I wouldn't be surprised if that number was small.

The big shoe left to drop is the extent of population differentiation within Africa during
MSA times. So far we've seen hints that these populations might have been nearly as
differentiated from each other as they were from Neandertals, with substantial gene flow
homogenizing them in the last 30,000 years. This paper includes an additional Bushman
genome, after the four published earlier this year. Comparing that new genome to the
Neandertals, its modal difference from the human reference (Hg18) genome is between
the other humans and the Neandertal. Not quite halfway between, but nearly so. There's a
lot of genomic variation within Africa, and exploring the population history that explains
that variation may turn up some surprises.

19
What about recent selection?

One of the really exciting aspects of this work is that both Green and colleagues and
Burbano and colleagues look for things that all humans today share but Neandertals lack.

You might call these "the genes that make us modern," although functionally we have
little idea what any of them do.

Both papers show one thing that is extremely interesting: There aren't very many such
genetic changes.

Burbano and colleagues put together a microarray including all the amino acid changes
inferred to have happened on the human lineage. They used this to genotype the
Neandertal DNA, and show that out of more than 10,000 amino acid changes that
happened in human evolution, only 88 of them are shared by humans today but not
present in the Neandertals.

That's amazingly few.

Green and colleagues did a similar exercise, except they went looking for "selective
sweeps" in the ancestors of today's' humans. These are regions of the genome that have
an unusually low amount of incomplete lineage sorting with Neandertals, and therefore
represent shallow genealogies for all living people. They identify 212 regions that seem
to be new selected genes present in humans and not in Neandertals. This number is
probably fairly close to the real number of selected changes in the ancestry of modern
humans, because it includes non-coding changes that might have been selected.

Again, that's really a small number. We have roughly 200,000-300,000 years for these to
have occurred on the human lineage -- after the inferred population divergence with
Neandertals, but early enough that one of these selected genes could reach fixation in the
expanding and dispersing human population. That makes roughly one selected
substitution per 1000 years.

Which is more or less the rate that we infer by comparing humans and chimpanzees.
What this means is simple: The origin of modern humans was nothing special, in
adaptive terms. To the extent that we can see adaptive genetic changes, they happened at
the basic long-term rate that they happened during the rest of our evolution.

Now from my perspective, this means something even more interesting. In our earlier
work, we inferred a recent acceleration of human evolution from living human
populations. That is a measure of the number of new selected mutations that have arisen
very recently, within the last 40,000 years. And most of those happened within the past
10,000 years.

In that short time period, more than a couple thousand selected changes arose in the
different human populations we surveyed. We demonstrated that this was a genuine

20
acceleration, because it is much higher than the rate that could have occurred across
human evolution, from the human-chimpanzee ancestor.

What we now know is that this is a genuine acceleration compared to the evolution of
modern humans, within the last couple hundred thousand years.

Our recent evolution, after the dispersal of human populations across the world, was
much faster than the evolution of Late Pleistocene populations. In adaptive terms, it is
really true -- we're more different from early "modern" humans today, than they were
from Neandertals. Possibly many times more different.

21