Which Groups Have the most Neanderthal and Denisovan DNA?  


Neanderthal and Denisovan contributions to different populations by chromosome (source)

Here are the numbers I’ve found so far for Neanderthal and Denisovan DNA in different populations:

 et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, 2016, report:

Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
Europeans: 1.06%

(I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.)

Prufer et al, [pdf] 2017, report somewhat higher values:

East Asians: 2.3–2.6%
Europeans: 1.8–2.4%

While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)

The Mixe and Karitiana people of Brazil have 0.2% Denisovan (source); other estimates for the amount of Denisovan DNA in Native populations are much lower–ie, 0.05%.

I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:

Population Individuals Neandertal ancestry (%)
Autosomes X
Europeans CEU–Euros from Utah 85 1.17±0.08 0.21±0.17
FIN–Finnish 93 1.20±0.07 0.19±0.14
GBR–British 89 1.15±0.08 0.20±0.15
IBS–Spain 14 1.07±0.06 0.23±0.18
TSI–Tuscan 98 1.11±0.07 0.25±0.20

East Asians CHB–Han Chinese Beijing 97 1.40±0.08 0.30±0.21
CHS–Han Chinese South 100 1.37±0.08 0.27±0.21
JPT–Japan, Tokyo 89 1.38±0.10 0.26±0.21

Americans CLM: Colombians from Medellin 60 1.14±0.12 0.22±0.16
MXL: Mexicans from LA 66 1.22±0.09 0.21±0.15
PUR: Puerto Ricans 55 1.05±0.12 0.20±0.15

Africans LWK: Luhya in Webuye, Kenya 97 0.08±0.02 0.04±0.07
ASW: African Americans South West US 61 0.34±0.22 0.07±0.11

Since the paper is older, all of its estimates are lower than current estimates, because we now have more Neanderthal DNA to compare against. However, you can still see the general trend.

The difference between “autosomes” and “X” highlighted here is that (IIRC) autosomes includes all chromosomes except the XY pair, and X is the X from that pair. They’re breaking them up this way because the X chromosome tends to have very little Neanderthal on it (and the Y even less), probably because Neanderthal DNA on these particular chromosomes was selected against.

Neanderthal DNA appears to have been selected for in areas that control hair and skin–people who had just left Africa were adapted to the African environment, and Neanderthal hair and skin traits helped them survive in colder, darker winters. We also see a lot of Neanderthal DNA influencing inflammation/immune response–these may have helped people fend off new diseases. But we see almost no Neanderthal (or Denisovan) DNA in areas of the genome that code for sperm, eggs, testes, ovaries, etc. These parts of people were probably already finely tuned to work together, didn’t need to change with the environment, and changing anything probably just made them less efficient–so Neanderthal (and Denisovan) DNA on the X and Y chromosomes has been purged from the Homo Sapiens gene pool.

North African Populations Carry Signature of Admixture with Neanderthals reports its data relative to the European average (which I believe is the CEU pop, 1.17%, so I’ll do the math for you to figure how much Neanderthal they have.)

Algeria 44.57% = 0.52% Neanderthal
Tunisia 100.16% = 1.172 N
Tunisia 138.13% = 1.6% N (This is an interesting population that has been highly endogamous and thus better reflects historical populations in the area.)
Egypt 58.45% = 0.68% N
Libya 56.36% = 0.66% N
Morroco North 69.17% = 0.81% N
Morocco South 17.90% = 0.21% N
Saharawi 50.90% = 0.6% N
Canary Island* 101.44% = 1.187% N
China Beijing 193.43% = 2.26 % N
China 195.41% = 2.29% N
Texas Indu Gupti 84.37% =0.987% N
Andalusia*118.66% = 1.39% N
Tuscan 94.90% = 1.11% N
Basque BASC 129.48% = 1.51% N
Galicia* GAL 115.86% = 1.36% N
Yoruba YRI  0.00% = 0% N
Luyha LWK  −14.89% = N

The authors note that they are not sure how the Luyha received a negative score–perhaps the presence of admixed DNA from yet another species is interfering with the results.

According to Wikipedia:

Denisovan DNA is most commonly found in Melanesians, Papulans, Aboriginal Australians and Aboriginal Filipinos, who all have similar amounts around 4-6%, indicating that they probably were all one group when their ancestors met the Denisovans. However, the similar-looking but historically quite isolated Onge people have no Denisovan–so they split off before the event.

In Papuans, Neanderthal DNA tends to be expressed in brain tissue, Denisovan in bones and other tissues.

Asians have a small amount of Denisovan DNA; Tibetans have a particular gene that lets them absorb oxygen effectively at high altitudes that they got from the Denisovans.

The Mende People of Sierra Leon may derive 13% of their DNA from an as-yet unknown hominin species (ancient DNA and bones do not preserve well in parts of Africa, so finding remains and identifying the species may be difficult.)

The Yoruba derive 8 or 9% of their DNA from the same hominin.

Masai have a small fraction of Neanderthal–since they are 30% non-African, probably about 0.35% of their genome–but you can read the paper yourself. 

Biaka Pygmies and Bushmen (San): 2% from an unknown archaic.

With more testing, better and more comprehensive numbers are sure to turn up.


Greatest Hits: Native Americans and Neanderthal DNA.

Source: Ancient Beringians: A Discovery Changing Early Native American History

Over the years, a few of my posts have been surprisingly popular–Turkey: Not very Turkic, Why do Native Americans Have so much Neanderthal DNA?, Do Black Babies have Blue Eyes? and Can Ice packs help stop a seizure (in humans)?

It’s been a while since these posts aired, so I thought it was time to revisit the material and see if anything new has turned up.

Today, lets revisit Native Americans and Neanderthal DNA:

I’m sorry, but I no longer think Native Americans (aka American Indians) have higher than usual levels of Neanderthal DNA. Sorry. Their Neanderthal DNA levels are similar to (but slightly lower than) those of other members of the Greater Asian Clade. They also have a small amount of Denisovan DNA–at least some of them.

Why the confusion? Some Neanderthal-derived alleles are indeed more common in Native Americans than in other peoples. For example, the Neanderthal derived allele SLC16A11 occurs in 10% of sampled Chinese, 0% of Europeans, and 50% of sampled Native Americans. (Today, this gene makes people susceptible to Type 2 diabetes, but it must have been very useful to past people to be found in such a large percent of the population.)


And there was one anomalously high Neanderthal DNA measure in Natives living near the Great Slave Lake, Canada. (Look, I didn’t name the lake.)

But this doesn’t mean all Native Americans possess all Neanderthal alleles in greater quantities.

So how much Neanderthal do Native Americans have? Of course, we can’t quite be sure, especially since only a few Neanderthals have even had their DNA analyzed, and with each new Neanderthal sequenced, we have more DNA available to compare against human genomes. But here are some estimates:

Neanderthal and Denisovan contributions to different populations by chromosome (source)

 et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, report:

Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
Europeans: 1.06%

I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.

Prufer et al, [pdf] 2017, report somewhat higher values:

East Asians: 2.3–2.6%
Europeans: 1.8–2.4%

While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)

The Mixe and Karitiana people of Brazil have 0.2% Denisovan (source); other estimates for the amount of Denisovan DNA in Native populations are much lower–ie, 0.05%.

I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:

CLM–Colombians from Medellin: 1.14%
MXL–Mexicans in LA: 1.22%
PUR–Puerto Rico: 1.05%

Since this is an older paper, all of its estimates may be on the low side.

The absolute values of these numbers is probably less important than the overall ratios, since the numbers themselves are still changing as more Neanderthal DNA is uncovered. The ratios in different papers point to Native Americans having, overall, about the same amount of Neanderthal DNA as their relatives in East Asia.

Melanesians, though. There’s an interesting story lying in their DNA.

Denny: the Neanderthal-Denisovan Hybrid

Neanderthal Sites (source: Wikipedia)

Homo Sapiens–that is, us, modern humans, are about 200-300,000 years old. Our ancestor, Homo heidelbergensis, lived in Africa around 700,000-300,000 years ago.

Around 700,000 years ago, another group of humans split off from the main group. By 400,000 years ago, their descendants, Homo neanderthalensis–Neanderthals–had arrived in Europe, and another band of their descendants, the enigmatic Denisovans, arrived in Asia.

While we have found quite a few Neanderthal remains and archaeological sites with tools, hearths, and other artifacts, we’ve uncovered very few Denisovan remains–a couple of teeth, a finger bone, and part of an arm in Denisova Cave, Russia. (Perhaps a few other remains I am unaware of.)

Yet from these paltry remains scientists have extracted enough DNA to ascertain that no only were Denisovans a distinct species, but also that Melanesians, Papuans, and Aborigines derive about 3-6% of their DNA from a Denisovan ancestors. (All non-African populations also have a small amount of Neanderthal DNA, derived from a Neanderthal ancestors.)

If Neanderthals and Homo sapiens interbred, and Denisovans and Homo sapiens interbred, did Neanderthals and Denisovans ever mate?

The slightly more complicated family tree, not including Denny


The girl, affectionately nicknamed Denny, lived and died about 90,000 years ago in Siberia. The remains of an arm, found in Denisova Cave, reveal that her mother was a Neanderthal, her father a Denisovan.

We don’t yet know what Denisovans looked like, because we don’t have any complete skeletons of them, much less good skulls to examine, so we don’t know what a Neanderthal-Denisovan hybrid like Denny looked like.

But the fact that we can extract so much information from a single bone–or fragment of bone–preserved in a Siberian cave for 90,000 years–is amazing.

We are still far from truly understanding what sorts of people our evolutionary cousins were, but we are gaining new insights all the time.

When did language evolve?

The smartest non-human primates, like Kanzi the bonobo and Koko the gorilla, understand about 2,000 to 4,000 words. Koko can make about 1,000 signs in sign language and Kanzi can use about 450 lexigrams (pictures that stand for words.) Koko can also make some onomatopoetic words–that is, she can make and use imitative sounds in conversation.

A four year human knows about 4,000 words, similar to an exceptional gorilla. An adult knows about 20,000-35,000 words. (Another study puts the upper bound at 42,000.)

Somewhere along our journey from ape-like hominins to homo sapiens sapiens, our ancestors began talking, but exactly when remains a mystery. The origins of writing have been amusingly easy to discover, because early writers were fond of very durable surfaces, like clay, stone, and bone. Speech, by contrast, evaporates as soon as it is heard–leaving no trace for archaeologists to uncover.

But we can find the things necessary for speech and the things for which speech, in turn, is necessary.

The main reason why chimps and gorillas, even those taught human language, must rely on lexigrams or gestures to communicate is that their voiceboxes, lungs, and throats work differently than ours. Their semi-arborial lifestyle requires using the ribs as a rigid base for the arm and shoulder muscles while climbing, which in turn requires closing the lungs while climbing to provide support for the ribs.

Full bipedalism released our early ancestors from the constraints on airway design imposed by climbing, freeing us to make a wider variety of vocalizations.

Now is the perfect time to break out my file of relevant human evolution illustrations:

Source: Scientific American What Makes Humans Special

We humans split from our nearest living ape relatives about 7-8 million years ago, but true bipedalism may not have evolved for a few more million years. Since there are many different named hominins, here is a quick guide:

Source: Macroevolution in and Around the Hominin Clade

Australopithecines (light blue in the graph,) such as the famous Lucy, are believed to have been the first fully bipedal hominins, although, based on the shape of their toes, they may have still occasionally retreated into the trees. They lived between 4 and 2 million years ago.

Without delving into the myriad classification debates along the lines of “should we count this set of skulls as a separate species or are they all part of the natural variation within one species,” by the time the homo genus arises with H Habilis or H. Rudolfensis around 2.8 million years ag, humans were much worse at climbing trees.

Interestingly, one direction humans have continued evolving in is up.

Oldowan tool

The reliable production of stone tools represents an enormous leap forward in human cognition. The first known stone tools–Oldowan–are about 2.5-2.6 million years old and were probably made by homo Habilis. These simple tools are typically shaped only one one side.

By the Acheulean–1.75 million-100,000 years ago–tool making had become much more sophisticated. Not only did knappers shape both sides of both the tops and bottoms of stones, but they also made tools by first shaping a core stone and then flaking derivative pieces from it.

The first Acheulean tools were fashioned by h Erectus; by 100,000 years ago, h Sapiens had presumably taken over the technology.

Flint knapping is surprisingly difficult, as many an archaeology student has discovered.

These technological advances were accompanied by steadily increasing brain sizes.

I propose that the complexities of the Acheulean tool complex required some form of language to facilitate learning and teaching; this gives us a potential lower bound on language around 1.75 million years ago. Bipedalism gives us an upper bound around 4 million years ago, before which our voice boxes were likely more restricted in the sounds they could make.

A Different View

Even though “homo Sapiens” has been around for about 300,000 years (or so we have defined the point where we chose to differentiate between our species and the previous one,) “behavioral modernity” only emerged around 50,000 years ago (very awkward timing if you know anything about human dispersal.)

Everything about behavioral modernity is heavily contested (including when it began,) but no matter how and when you date it, compared to the million years or so it took humans to figure out how to knap the back side of a rock, human technologic advance has accelerated significantly over the past 100,000 and even moreso over the past 50,000 and even 10,000.

Fire was another of humanity’s early technologies:

Claims for the earliest definitive evidence of control of fire by a member of Homo range from 1.7 to 0.2 million years ago (Mya).[1] Evidence for the controlled use of fire by Homo erectus, beginning some 600,000 years ago, has wide scholarly support.[2][3] Flint blades burned in fires roughly 300,000 years ago were found near fossils of early but not entirely modern Homo sapiens in Morocco.[4] Evidence of widespread control of fire by anatomically modern humans dates to approximately 125,000 years ago.[5]

What prompted this sudden acceleration? Noam Chomsky suggests that it was triggered by the evolution of our ability to use and understand language:

Noam Chomsky, a prominent proponent of discontinuity theory, argues that a single chance mutation occurred in one individual in the order of 100,000 years ago, installing the language faculty (a component of the mind–brain) in “perfect” or “near-perfect” form.[6]

(Pumpkin Person has more on Chomsky.)

More specifically, we might say that this single chance mutation created the capacity for figurative or symbolic language, as clearly apes already have the capacity for very simple language. It was this ability to convey abstract ideas, then, that allowed humans to begin expressing themselves in other abstract ways, like cave painting.

I disagree with this view on the grounds that human groups were already pretty widely dispersed by 100,000 years ago. For example, Pygmies and Bushmen are descended from groups of humans who had already split off from the rest of us by then, but they still have symbolic language, art, and everything else contained in the behavioral modernity toolkit. Of course, if a trait is particularly useful or otherwise successful, it can spread extremely quickly (think lactose tolerance,) and neither Bushmen nor Pygmies were 100% genetically isolated for the past 250,000 years, but I simply think the math here doesn’t work out.

However, that doesn’t mean Chomsky isn’t on to something. For example, Johanna Nichols (another linguist,) used statistical models of language differentiation to argue that modern languages split around 100,000 years ago.[31] This coincides neatly with the upper bound on the Out of Africa theory, suggesting that Nichols may actually have found the point when language began differentiating because humans left Africa, or perhaps she found the origin of the linguistic skills necessary to accomplish humanity’s cross-continental trek.

Philip Lieberman and Robert McCarthy looked at the shape of Neanderthal, homo Erectus, early h Sapiens and modern h Sapiens’ vocal tracts:

In normal adults these two portions of the SVT form a right angle to one another and are approximately equal in length—in a 1:1 proportion. Movements of the tongue within this space, at its midpoint, are capable of producing tenfold changes in the diameter of the SVT. These tongue maneuvers produce the abrupt diameter changes needed to produce the formant frequencies of the vowels found most frequently among the world’s languages—the “quantal” vowels [i], [u], and [a] of the words “see,” “do,” and “ma.” In contrast, the vocal tracts of other living primates are physiologically incapable of producing such vowels.

(Since juvenile humans are shaped differently than adults, they pronounce sounds slightly differently until their voiceboxes fully develop.)

Their results:

…Neanderthal necks were too short and their faces too long to have accommodated equally proportioned SVTs. Although we could not reconstruct the shape of the SVT in the Homo erectus fossil because it does not preserve any cervical vertebrae, it is clear that its face (and underlying horizontal SVT) would have been too long for a 1:1 SVT to fit into its head and neck. Likewise, in order to fit a 1:1 SVT into the reconstructed Neanderthal anatomy, the larynx would have had to be positioned in the Neanderthal’s thorax, behind the sternum and clavicles, much too low for effective swallowing. …

Surprisingly, our reconstruction of the 100,000-year-old specimen from Israel, which is anatomically modern in most respects, also would not have been able to accommodate a SVT with a 1:1 ratio, albeit for a different reason. … Again, like its Neanderthal relatives, this early modern human probably had an SVT with a horizontal dimension longer than its vertical one, translating into an inability to reproduce the full range of today’s human speech.

It was only in our reconstruction of the most recent fossil specimens—the modern humans postdating 50,000 years— that we identified an anatomy that could have accommodated a fully modern, equally proportioned vocal tract.

Just as small children who can’t yet pronounce the letter “r” can nevertheless make and understand language, I don’t think early humans needed to have all of the same sounds as we have in order to communicate with each other. They would have just used fewer sounds.

The change in our voiceboxes may not have triggered the evolution of language, but been triggered by language itself. As humans began transmitting more knowledge via language, humans who could make more sounds could utter a greater range of words perhaps had an edge over their peers–maybe they were seen as particularly clever, or perhaps they had an easier time organizing bands of hunters and warriors.

One of the interesting things about human language is that it is clearly simultaneously cultural–which language you speak is entirely determined by culture–and genetic–only humans can produce language in the way we do. Even the smartest chimps and dolphins cannot match our vocabularies, nor imitate our sounds. Human infants–unless they have some form of brain damage–learn language instinctually, without conscious teaching. (Insert reference to Steven Pinker.)

Some kind of genetic changes were obviously necessary to get from apes to human language use, but exactly what remains unclear.

A variety of genes are associated with language use, eg FOXP2. H Sapiens and chimps have different versions of the FOXP2 gene, (and Neanderthals have a third, but more similar to the H Sapiens version than the chimp,) but to my knowledge we have yet to discover exactly when the necessary mutations arose.

Despite their impressive skulls and survival in a harsh, novel climate, Neanderthals seem not to have engaged in much symbolic activity, (though to be fair, they were wiped out right about the time Sapiens really got going with its symbolic activity.) Homo Sapiens and Homo Nanderthalis split around 800-400,000 years ago–perhaps the difference in our language genes ultimately gave Sapiens the upper hand.

Just as farming appears to have emerged relatively independently in several different locations around the world at about the same time, so behavioral modernity seems to have taken off in several different groups around the same time. Of course we can’t rule out the possibility that these groups had some form of contact with each other–peaceful or otherwise–but it seems more likely to me that similar behaviors emerged in disparate groups around the same time because the cognitive precursors necessary for those behaviors had already begun before they split.

Based on genetics, the shape of their larynges, and their cultural toolkits, Neanderthals probably did not have modern speech, but they may have had something similar to it. This suggests that at the time of the Sapiens-Neanderthal split, our common ancestor possessed some primitive speech capacity.

By the time Sapiens and Neanderthals encountered each other again, nearly half a million years later, Sapiens’ language ability had advanced, possibly due to further modification of FOXP2 and other genes like it, plus our newly modified voiceboxes, while Neanderthals’ had lagged. Sapiens achieved behavioral modernity and took over the planet, while Neanderthals disappeared.


Open Thread: Hot Cocoa, Neanderthal Boats, Sadists and Incompetents

imagesIt’s been a slow week for comments, probably because everyone is still passed out/out of town/tired/sick/busy from all of the holiday revelry. Some of you are still celebrating. Still, I invite you all to come in, take a seat by the fire, pick up a warm mug of cocoa, and enjoy yourselves with some relaxing chat and mingle.

Anyone making New Years’ Resolutions?

Mine involve being more social in real life.

Some interesting links:

Role of Parenting in the Prediction of Criminal Involvement


“Sadists” more likely to take “courageous” action against “injustice” on the internet:


Could Neanderthals Build Boats?

But the stone tools on Naxos appeared to be hewn by Paleolithic people — much more ancient humans, perhaps not members of our species at all.

Since 2013, Carter has co-directed a new round of investigations on Naxos. He and a handful of others working in the region have begun to furnish evidence that humans reached the islands of the Aegean Sea 250,000 years ago and maybe earlier. If those dates are confirmed, it means the first people there were Neanderthals, their probable ancestors, Homo heidelbergensis or maybe even Homo erectus. …

Other researchers insist that much better evidence needs to be discovered to attribute such complex behaviours to Neanderthals and other hominins …

Then, in 1988, archeologists began excavating a collapsed rock shelter on the southern shore of Cyprus. They found about 1,000 bladelets and small tools typically associated with pre-Neolithic people.

“There was a lot of skepticism at first,” said Alan Simmons, an anthropologist at the University of Nevada Las Vegas who was involved in the work. “But once we had all the radiocarbon dates, it came to be accepted.”

The site pushed the peopling of Cyprus back to 12,000 years ago — only a few millennia, but enough to break the Neolithic barrier and establish the presence of hunter-gatherers. Today, the distance to mainland Turkey is about 75 kilometres. Sea levels have fluctuated and the crossing was once shorter, but Cyprus has always been an island.

The discoveries on Cyprus overturned the idea that hunter-gatherers were incapable or unwilling to travel by sea. But the debate was still confined to the activities of our species, Homo sapiens.

In 2008, a Greek-American team of archeologists began searching on the southwest coast of Crete for pre-Neolithic artifacts. They found many from roughly the same era as those on Cyprus. But they also found rough quartz hand axes and cleavers that appeared to be much more ancient.

The team discovered artifacts eroding out of a layer of soil that dated to at least 130,000 years ago, and the tools themselves looked like those archeologists associate with archaic hominin sites on the mainland — ones that are at least 250,000 years old. …

c0y7hezxeaa6akkFinally, a memorial fund for the wife and family of Polish truck driver Lukasz Urban, murdered in Germany 19th December 2016. Poor man, poor family.

On a related note, here’s an interesting quote about the importance of transparency to prevent government incompetence from Julian Assange of Wikileaks fame.

“Incompetence” murdered Kukasz Urban. Among many other things.


On to our Comments of the Week!

Unknown123 has contributed a couple of good comments to our discussion of race and crime:

“only about one-quarter of one percent (0.25 percent) of all whites will be violently victimized by a black person this year”

This would mean that its 2,5% every 10 years. A typical american white lives 80 years this would mean their lifelong chance of getting attacked by a black is 20%(!!!) exactly the same number they argue the chance of a women is to be raped in life. The same Tim Wise made a big deal of how high that is. Of course he takes anual number for other crime and lifelong numbers for rape.

And Race Realist contributed a fine post on correlations between weight and IQ:

Kanazawa (2014), reviewed the data on the research between obesity and IQ. What he found was that those studies that concluded that obesity causes lowered intelligence only observed cross-sectional studies. Longitudinal studies that looked into the link between obesity and intelligence found that those who had low IQs since childhood then became obese later in life and that obesity does not lead to low IQ. … He states that those with IQs below 74 gained 5.19 BMI points, whereas those with IQs over above 126 gained 3.73 BMI points in 22 years, which is a statistically significant difference. Also noted, was that those at age 7 who had IQs above 125 had a 13.5 percent chance of being obese at age 51, whereas those with IQs below 74 at age 7 had a 31.9 percent chance of being obese.

Thanks everyone, and keep up the good work/great comments!

Updated Tentative map of Neanderthal DNA

Picture 1

Based on my previous tentative map of archaic DNA, plus recent findings, eg Cousins of Neanderthals left DNA in Africa, Scientists Report. As usual, let me emphasize that this is VERY TENTATIVE.

Basically: Everyone outside of Africa has some Neanderthal DNA. It looks like the ancestors of the Melanesians interbred once with Neanderthals; the ancestors of Europeans interbred twice; the ancestors of Asians interbred three times.

Small amounts of Neanderthal DNA also show up in Africa, probably due to back-migration of people from Eurasia.

Denisovan DNA shows up mainly in Melanesians, but I think there is also a very small amount that shows up in south east Asia, some (or something similar) in Tibetans, and possibly a small amount in the Brazilian rainforest.

Now some kind of other archaic DNA has been detected in the Hazda, Sandawe, and Pygmies of Africa.

Native Americans and Neanderthal DNA

Since “Do Native Americans have Neanderthal DNA?” (or something similar) is the most popular search that leads people to my blog, I have begun to suspect that a clarification is in order.

Native Americans (Indians) are not Neanderthals. They are not half or quarter or otherwise significantly Neanderthal. If they were, they would have very noticeable fertility problems in mixed-race relationships.

They may have slightly higher than average Neanderthal admixture than other groups, but that is extremely speculative I don’t know of any scientists who have said so. We’re talking here about quite small amounts, like 0.5%, most of which appears to code for things like immune response and possibly some adaptations for handling long, cold winters. None of this appears to code for physical traits like skull shape, which have been under different selective pressures over the past 40,000 years.

As much as I would love to discover a group with significant Neanderthal DNA, that’s just not something we’ve found in anyone alive today.

Sorry, guys.

Tentative map of Neanderthal (and Denisovan) DNA in humans

I couldn’t find one, so I made one:

This is really tentative! And I am not a geneticist, so at this point, I’m just crossing my fingers and hoping I didn’t read any graphs backwards.


This map shows Neanderthal DNA admixture in modern human groups (solid color) and Denisovan DNA (polka dots.) The Denisovan estimates are less exact than the Neanderthal estimates. (Also, the guys with Denisovan DNA also have Neanderthal DNA; I just don’t know how much.)

The biggest problem I ran up against was a total lack of numbers. Seriously, everyone likes quoting that “1-4% of non-African DNA is Neanderthal” stat, but no one likes breaking it down by individual country or group.

Some of the sources contradict each other–first we have papers claiming that Europeans have more Neanderthal DNA than Asians, then papers claiming that Asians have more. I went with the Asians have more estimates, since they were more recent. Also, we now think that many African groups also have some Neanderthal DNA, due to more recent back-migration of Eurasians into Africa.

Most of this map is still completely blank, even though I’m sure the data is out there somewhere. I would really appreciate if any of my readers can point me toward a good old list of Neanderthal (or Denisovan) DNA %s by country or group.

Alternatively, if you’ve had your DNA analyzed and know your Neanderthal and/or Denisovan %s, feel free to share in the comments.

When I have more data, I’ll update the map.

Sources read:

Dienekes: Neandertal admixture in modern humans

John Hawks: Neandertal ancestry iced, Neandertal introgression 1,000 genomes style

The Atlantic: The Other Neanderthal

1000 Genomes: about

Wang et al, Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations







Please, please let me know if you find some better lists of the %s of Neanderthal and Denisovan DNA in different populations.

So Why do Native Americans have so much Neanderthal DNA?

Warning: highly speculative post ahead.

As I mentioned the other day:

Worldwide distribution of B006, (from Yotova et al. “An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations,” Mol. Biol. Evol. 28 (7), 2011).
Worldwide distribution of B006, (from Yotova et al. “An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations,” Mol. Biol. Evol. 28 (7), 2011).
SNP PCA from Skoglund & Jakobsson’s “Archaic Human Ancestry in East Asia” (2011)
SNP PCA from Skoglund & Jakobsson’s “Archaic Human Ancestry in East Asia” (2011)

(Please note that Africans do not have chimpanzee admixture, despite the labeling on the graph–no human group has chimp admixture, because chimps and humans have different #s of chromosomes, so even if you could get a successful cross, the resulting child would be infertile, like a mule. I assume the point of the chimp node is just to represent that which has neither Neanderthal nor Denisovan admixture, though of course there is the possibility of some other form of archaic hominin admixture in Africans.)


So, Native Americans appear to have a ton of Neanderthal DNA. (Relatively speaking.)


  1. It’s all measurement error/convergent evolution/something else other than archaic admixture.

As much as I hate to say it, I still consider this very likely. There is just a ton of stuff that we don’t about the Americas–like how and when people first got here. I’m sticking here with what I think are the most scientifically-supported theories, but a lot of this is still quite disputed. In particular, all of this genetic admixture business is still kind of speculative, and when people start talking about finding admixture in the admixture, either life is totally awesome, or we’re trying too hard.

2. Survival at the Fringes theory

A lot of people seem to look at this data and respond with something like, “But Neanderthals are from Europe, not America!” But this is not a big issue; the Indians are descended from people who passed through Neanderthal-inhabited regions (the Middle East), just like everyone else with Neanderthal DNA. The migration to the Americas took place long after they acquired Neanderthal admixture.

But this doesn’t explain why they have so much of it.

My “concentration on the edge” theory states that when one population is displaced by another population, you end up with a “fringe” of the original population’s traits. Sometimes this fringe results in isolated groups, as the invading population completely surrounds or cuts off a remnant population from their former range.

The Ainu, for example, resemble certain other Oceanin groups, but not their neighbors, the Japanese. I’m speculating here, so don’t take my word for it.

But I have a much better case with the distribution of red hair: Frequency-of-red-hair-in-Europe

(So far I have found nothing explaining that dot over in Russia.)

Red hair is highly associated with the so-called Celtic fringe. It looks like it’s highly concentrated in Wales, Scotland, and parts of Ireland, but since I know a little history, and I know these aren’t areas of concentration, but just the areas that managed to escape being displaced by Anglo-Saxon invaders, just by virtue of being further away from the south-east coast of Britain.

One can imagine that the isolated dot in the middle of Russia might, at one time, have been connected with the other red-haired regions before other peoples invaded the lands between them and cut them off.

Compare to the map of blond hair:


Blond hair looks like it has been spreading steadily outward from a central source.

So what does this have to do with Neanderthal admixture in Native Americans?

It means that I think the Native Americans may have closer to original levels of Neanderthal admixture, while people in Europe and Asia have lower admixture because they mixed with later waves of people who came from Africa and had no Neanderthal admixture.

3. The Bering Strait selected for Neanderthal admixture

Alternatively, the harsh conditions of life in the Bering Strait–where some scientists think the ancestors of today’s Indians hung out (or “paused”) for thousands of years before the ice sheets opened up to let them through–may have selected for winter adaptations that came from ice-age Neanderthals. I have speculated previously that Type-2 Diabetes may actually be a winter adaptation picked up from Neanderthal DNA; now scientists think this DNA may be responsible for high rates of Type-2 Diabetes in Native Americans.

4. Western diseases selected for Western immune responses

One of the interesting things about the Neanderthal DNA hanging around in people is that it appears to code for certain immune responses. West Hunter recently had a great post (TLRs, PAMPs, and Alley Oop) detailing how they work, but for our purposes, “provide immunity” is sufficient. Austin Whittall suggests that back when smallpox, influenza, measles, and all of the other Western diseases tore through the Native Americans, killing about 90% of them, the guys who had more Neanderthal DNA were more likely to survive because they were more likely to be immune to the same stuff as Europeans. By contrast, those Indians with less Neanderthal DNA may have had less immunity to the European diseases, and so been more likely to die, leaving behind a population of high-Neanderthal DNA people.

5. One thing we can say for sure: if the data’s correct, the peopling of the Americas was more complex than previously thought.

There are four areas of particular interest:

A. The highly Neanderthal area in the Pacific Northwest

B. The highly Denisovan area in Brazil

C. The low-Neanderthal area on the South American coast

D. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.

I’ve got nothing on A and C; supply your own theories.

6. Speculations on the origins of high-Denisovan people in Brazil:

A couple of papers in Science and Nature recently proposed that Melanesian-related people somehow made it to the rain forest long after the other Indians got to the area. West Hunter helpfully summarizes them.

West Hunter suggests that the Melanesian-related people with their high-Denisovan DNA got to the Americas first, and were then replaced throughout the continents by later invaders, the ancestors of current Indians. The one place the Melanesian-related people managed to survive was in the depths of the rainforest, a very difficult place to conquer. Even today, there are “uncontacted tribes” living in the Amazon rainforest; if anywhere were a good spot for a group of humans to avoid getting conquered, the depths of the rainforest is a good one.

7. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.

So what’s up with that? As far as I know, the only people who don’t have any Neanderthal or Denisovan are Africans. (And even there, there’s a little, just due to back-migration from the rest of the world.)

Are these people descended from a totally different group that came directly from Africa?

There’s a tiny ethnic group in the area, called the Seri:

Dona Ramona of the Seri Indians of Sonora, Mexico
Dona Ramona of the Seri Indians of Sonora, Mexico

According to the Wikipedia, the Seri speak a language isolate–that is, their language, like Basque, doesn’t appear to be related to any other language on Earth–and they are not culturally connected with any of their neighbors. They’ve also held out significantly against Spanish and Mexican assimilation. In other words, they might very well be a totally isolated population that is not related at all to any of their neighbors.

Some more information on the Seris.

Then I found this interesting map:

map showing global distribution of the HLA-B*73:01 allele
maps showing global distribution of the HLA-B*73:01 allele

I found these maps over on Austin Whittall’s post on Denisovans and America.

Looks like the same spot, doesn’t it?

The two different “real” maps how different things because they come from different scientists who came up with different data, but the overall picture is similar–if you look closely, both maps show a hotspot in Israel, for example. The second map looks less detailed, (hence their miss of several Middle Eastern hotspots,) but has a wider global range, which is obviously useful for our purposes. They also help show the importance of not putting too much stock in any single study about the distribution of a particular gene or allele or whathaveyou; different scientists come up with different numbers.

At any rate, while this could be just a totally random coincidence, if it isn’t, it’s awfully interesting, isn’t it? I know the Egyptians circumnavigated Africa; the Carthaginians and Phoenicians were also noted sea-farers. Or perhaps some other group I know nothing about from the region, before folks started keeping good records. Who knows?

8. Other people’s theories: Neanderthals, Denisovans, and H erectus made it to America before we did, and H Sapiens intermixed with them after they arrived; humans evolved in American, and then migrated to the rest of the world from there.

Review: Decoding Neanderthals on PBS (Nova)

Available on Netflix, maybe elsewhere.

Overall: Recommended if you like Neanderthals or human ancestry. Probably not useful if you are already an expert in the field.

Pros: interesting discussion of flint-knapping, gluey pitch production, and Neanderthal burials.

Flint knapping is one of my occasional interests. It is surprisingly difficult to just pick up a rock and produce a useful tool. Without a good teacher, you quickly degenerate to banging the rock on the ground as hard as you can like a retarded monkey. If Kanzi the bonobo saw me trying to make stone tools, he’d probably bring me some fruit out of pity. “Poor hairless idiot ape,” Kanzi would think. “Can’t even make tools. If I don’t feed it, it’ll starve.”

Amusing digression time: Once I was walking through the city, in a semi-developed/semi-overgrown lot, and saw a bit of shiny rocks lying around on the ground. Unusual for the area, because the local geographic history hasn’t led to a lot of rocks on the surface, and most of those are of the duller sedimentary sorts (or, obviously, landscaping materials.) So I picked up this bit of flint, then another bit of flint, and then a larger one with obvious convex areas from being struck with another piece. And a few feet away, here was a piece that fit comfortably into my hand, perfect for knocking chips off the other chunk. Some of the pieces I even managed to fit back together, reassembling the rock that once was.

I came back with a small box and picked up all the bits of flint before development began on the lot. One piece does look like an arrowhead, but given that I found it alongside a bunch of chips that are more or less flint-knapping trash, the arrowhead’s creator probably thought there was something wrong with it.

Sure, the whole little box may be filled with little more than ancient trash, there is something I love about picking up these rocks and being able to see in their shapes the actions of some other humans, the angle they held that rock at, the way they smacked it with another rock to produce these flakes. To feel this connection between myself and some other human who walked here before me, and the traces of their life that no one else walking through that place had noticed.

Anyway, turns out the Neanderthals had a pretty interesting/unique way of making flint tools, that involved first shaping a large block of flint into a specific shape by flaking bits off the sides, and then, with one good hit, knocking off one large slice. This is a more complicated process than merely picking up a rock and whacking bits off of it it until you get an edge.

The gluey pitch seems to have been derived (distilled?) from birch bark. Some scientists demonstrated the process by burning a roll of birch bark in a pit, but they obviously did not use enough bark, and only got a smudge of goo. It’s a bit frustrating watching someone do something obviously wrong–since you’re filming this for TV, why not use a great big bunch of birch bark so you can get enough pitch to actually show us?

Anyway, looks like Neanderthals distilled this gluey stuff and then used it to help secure the flint tips to their spears, before thrusting them into the sides of enormous shaggy elephants, which are quite formidable animals. So the pitch (and bindings) had to be pretty darn good.

Neanderthals also seem to have buried their dead, though the show notes that their potential grave-goods pale in comparison to similar human burials.

The parts about Neanderthal DNA will be of interest to you if you don’t know about the Neanderthal/human DNA admixture business already, or you’ve heard about it but are still a little unclear on the details. The scientists interviewed claimed that it looks like there were a lot of interbreeding incidents rather than just a few, but “a lot” in this case does not necessarily mean “thousands”.


Cons: For a program that goes into depth on how inaccurate depictions of Neanderthals happened (ages ago, someone found a skeleton with arthritis and concluded that all Neanderthals were stooped,) their depiction of the homo Sapiens who first encountered the Neanderthals was also inaccurate.

The first encounters between humans and Neanderthals probably happened in the Middle East, shortly after h Sapiens left Africa, but before they had split into Asian and European branches. In other words, not to put too fine a point on it, whites did not yet exist. We’re not sure exactly when white skin evolved, but it probably wasn’t before h Sapiens got to Europe.

(Of course, it could be the other way around, and it’s the Bushmen who’ve changed since they split off.)

Either way, it’s pretty easy to assume things that are probably wrong, and the h Sapiens who first encountered h Neanderthals were probably more similar in appearance to modern Africans or Middle Easterners than Europeans.

A second issue occurred during a dramatization of the Neanderthal and h Sapiens DNA. Neanderthal DNA was depicted as red, and h Sapiens as blue. (Erm, I think. Unless I’ve got it backwards.) They then showed a “combined” DNA strand with blue and red pieces.

While this is a fine way to visualize what’s going on, I would just like to clarify that DNA isn’t actually blue or red, nor are there folks running around with mosaic red/blue variants.

You may be laughing (I burst out laughing at the sight of it,) but I know people who would very sincerely and devoutly insist that “Humans have different colored DNA from Neanderthals. I saw this program on PBS all about it, and I know PBS is accurate. You should watch the program!”

You can imagine how talking to these people makes me feel.

Finally, my last complaint is that there was no discussion of Neanderthal DNA in Native Americans!

Worldwide distribution of B006, (from Yotova et al. “An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations,” Mol. Biol. Evol. 28 (7), 2011).
Worldwide distribution of B006, (from Yotova et al. “An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations,” Mol. Biol. Evol. 28 (7), 2011).
SNP PCA from Skoglund & Jakobsson’s “Archaic Human Ancestry in East Asia” (2011)
SNP PCA from Skoglund & Jakobsson’s “Archaic Human Ancestry in East Asia” (2011)

Right, so what’s up with Native Americans? You may have noticed that during the discussion with the map, no jellybeans were placed on the Americas at all. What a pity, when there’s still so much about the peopling of the Americas that we don’t know.

In the future, I’m hoping for similar documentaries about the Denisovans and their DNA admixture in modern humans.