Two Denisovan Admixture Events?

Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice

Asian genomes carry introgressed DNA from Denisovans and Neanderthals

East Asians show evidence of introgression from two distinct Denisovan populations

South Asians and Oceanians carry introgression from one Denisovan population

I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.) 

According to Wikipedia:

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed,[50][51] and that a second introgression event from Denisovans into humans occurred. A study of Han ChineseJapanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[52]  …

The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later. 

Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex. 

We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples. 

The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines. 

On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent: 

In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …

Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?

Timeline of ancient Indonesian and Filipino hominin findings, from John Hawks’s article

I recommend you read the whole thing.

What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:

The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin.[54] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[16] A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome.[55][56] In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.[57]

It is a great era in genetics. 

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Neanderthal DNA–hey!–what is it good for?

Quite a bit.

First, a bit of history:

neanderthalmap
map of Neanderthal DNA in humans

It appears that there were (at least) 3 main cross-breeding events with Neanderthals. The first event most likely happened when one small band of humans had left Africa and ventured into the Middle East, where Neanderthals were living. The DNA acquired from that partnership can be found in all modern non-Africans, since they are all descended from this same group. (Since there has also been back-migration from the Middle East into Africa sometime in the past 70,000 years, many African groups also have a small amount of this DNA.)

Soon after, the group that became the Melanesians, Papuans, and Aborigines split off from the rest and headed east, where they encountered–and interbred with–the mysterious Denisovans, a third human species that we know mostly from DNA. Various sources claim this happened before the second neanderthal inter-breeding event, but just looking at the amount of admixed neanderthal in Oceanans suggests this is wrong.

Meanwhile, the rest of the non-African humans, probably still living in the Middle East or Eurasian Steppe, encountered a second band of Neanderthals, resulting in a second admixture event, shared by all Asians and Europeans, but not Melanesians &c. Then the Asians and Europeans went their separate ways, and the Asians encountered yet a third group of Neanderthals, giving them the highest rates of Neanderthal ancestry.

nature-siberian-neanderthals-17.02.16-v2

During their wanderings, some of these Asians encountered Melanesians, resulting in a little Denisovan DNA in today’s south Asians (especially Tibetans, who appear to have acquired some useful adaptations to Tibet’s high altitude from ancient Denisovans.)

There were other interbreeding events, including a much older one that left homo sapiens DNA in Neanderthals, and one that produced Denny, a Neanderthal/Denisovan hybrid. There were also interbreeding events in Africa, involving as-yet unidentified hominins. (In the human family tree to the right/above, Melanesians are included within the greater Asian clade.)

Who married whom? So far, we’ve found no evidence of Neanderthal mitochondrial DNA–passed from mothers to their children–in modern humans, so the pairings most likely involved Neanderthal men and human women. But we have also found extremely little Neanderthal DNA on the Y chromosome–so it is likely that they only had female children, or any male children they had were infertile.

Anthropogenesis-DenisovaAlleleMapInterestingly, we find higher amounts of Neanderthal DNA in older skeletons, like the 40,000 year old Tianyuan Man, or this fellow from Romania with 10% Neanderthal DNA, than in modern humans. Two potential explanations for the decrease: later mixing with groups that didn’t have Neanderthal DNA resulted in dilution, or people with more Neanderthal DNA just got out-competed by people with less.

Given the dearth of DNA on the Y chromosome and the number of diseases linked to Neanderthal DNA, including Lupus, Crohn’s, cirrhosis, and Type-2 diabetes, the fact that morphological differences between Sapiens and Neanderthals are large enough that we classify them as different species, and the fact that Neanderthals had larger craniums than Sapiens but Sapiens women attempting to give birth to hybrid children still had regular old Sapiens pelvises, gradual selection against Neanderthal DNA in humans seems likely.

However, the Neanderthals probably contributed some useful DNA that has been sorted out of the general mix and come down the ages to us. For example, the trait that allows Tibetans to live at high altitudes likely came from a Denisovan ancestor:

Researchers discovered in 2010 that Tibetans have several genes that help them use smaller amounts of oxygen efficiently, allowing them to deliver enough of it to their limbs while exercising at high altitude. Most notable is a version of a gene called EPAS1, which regulates the body’s production of hemoglobin. They were surprised, however, by how rapidly the variant of EPAS1spread—initially, they thought it spread in 3000 years through 40% of high-altitude Tibetans, which is the fastest genetic sweep ever observed in humans—and they wondered where it came from.

Modern humans have Neanderthal DNA variants for keratin (a protein found in skin, nails, hair, etc.,) and UV-light adaptations that likely helped us deal with the lower light levels found outside Africa. There’s circumstantial evidence that microcephalin D could have Neanderthal origins (it appeared about 37,000 years ago and is located primarily outside of Africa,) but no one has found microcephalin D in a Neanderthal, so this has not been proven. (And, indeed, another study has found that Neanderthal DNA tends not to be expressed in the brain.)

Yet on the other hand, Neanderthal admixture affected sapiens’ skull shapes:

Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology. First, as a validation of our approach, we demonstrate that a greater load of Neanderthal-derived genetic variants (higher “NeanderScore”) is associated with skull shapes resembling those of known Neanderthal cranial remains, particularly in occipital and parietal bones. Next, we demonstrate convergent NeanderScore-related findings in the brain (measured by gray- and white-matter volume, sulcal depth, and gyrification index) that localize to the visual cortex and intraparietal sulcus. This work provides insights into ancestral human neurobiology and suggests that Neanderthal-derived genetic variation is neurologically functional in the contemporary population.

(Not too surprising, given Neanderthals’ enormous craniums.)

Homo sapiens also received Neanderthal genes affecting the immune system, which were probably quite useful when encountering new pathogens outside of Africa, and genes for the “lipid catabolic process,”[19] which probably means they were eating new, fattier diets that Neanderthals were better adapted to digest.

Even Neanderthal-derived traits that today we cast as problems, like Type II Diabetes and depression, might have been beneficial to our ancestors:

“Depression risk in modern human populations is influenced by sunlight exposure, which differs between high and low latitudes, and we found enrichment of circadian clock genes near the Neanderthal alleles that contribute most to this association.”

Why would we find an association between Neanderthal DNA and circadian clock genes? Neanderthals had thousands of years more exposure to Europe’s long nights and cold winters than homo Sapiens’; it is unlikely that they developed these adaptations in order to become less well-adapted to their environment. It is more likely that Neanderthals downregulated their activity levels during the winter–to put it colloquially, they hibernated.

No problem for furry hunter-gatherers who lived in caves–much more problematic for information age workers who are expected to show up at the office at 9 am every day.

Type II diabetes affects digestion by decreasing the production of insulin, necessary for transporting converting carbs (glucose) into cells so it can be transformed into energy. However, your body can make up for a total lack of carbs via ketosis–essentially converting fats into energy.

Our hunter-gatherer ancestors–whether Neanderthal or Sapiens–didn’t eat a lot of plants during the European and Siberian winters because no a lot of plants grow during the winter. If they were lucky enough to eat at all, they ate meat and fat, like the modern Inuit and Eskimo.

And if your diet is meat and fat, then you don’t need insulin–you need ketosis and maybe some superior lipid digestion. (Incidentally, the data on ketogenic diets and type II diabetes looks pretty good.)

In sum, Neanderthal and Denisovan DNA, while not always useful, seems to have helped Homo sapiens adapt to colder winters, high altitudes, new pathogens, new foods, and maybe changed how we think and perceive the world.

 

 

Which Groups Have the most Neanderthal and Denisovan DNA?  

 

beautifulneanderthalDenisovan
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.

Native-American-populations
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.)

neanderthalmap

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:

beautifulneanderthalDenisovan
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.

YES Two Out of Africa Events! (Also, Aborigines)

I’ve long suspected (given the archaeological evidence, like 80,000 year old human remains in China,) that there were two Out of Africa (OOA) events–an early one that headed east, toward Australia, and a later one that headed everywhere (including Australia)–and now it looks like this has been genetically confirmed:

Graphic created by the Estonian genetics team cited in the NY Times article. Their full article: Genomic analyses inform on migration events during the peopling of Eurasia
Graphic created by the Estonian genetics team cited in the NY Times article. Their full article: Genomic analyses inform on migration events during the peopling of Eurasia

Isn’t this a great graphic? My hat’s off to the Estonians. Beautiful work.

Graphic created by the Estonian genetics team cited in the NY Times article. Their full article: Genomic analyses inform on migration events during the peopling of Eurasia

Here’s another one they made (sadly small) with less color and more detail on the Eurasian lines. (IIRC, Chinese have more Neanderthal ancestry than Europeans, so technically the schematic ought to be a wee bit more complicated than this, but it’s already complicated enough and this is a solid general overview.)

It might just be the sleep dep + lots of coffee talking, but I am so excited about this.

Some quotes from the NY Times article:

In Israel, for example, researchers found a few distinctively modern human skeletons that are between 120,000 and 90,000 years old. In Saudi Arabia and India, sophisticated tools date back as far as 100,000 years.

Last October, Chinese scientists reported finding teeth belonging to Homo sapiens that are at least 80,000 years old and perhaps as old as 120,000 years. …

Examining their data separately, all three groups came to the same conclusion: People everywhere descend from a single migration of early humans from Africa. The estimates from the studies point to an exodus somewhere between 80,000 and 50,000 years. …

n Papua New Guinea, Dr. Metspalu and his colleagues found, 98 percent of each person’s DNA can be traced to that single migration from Africa. But the other 2 percent seemed to be much older.

Dr. Metspalu concluded that all people in Papua New Guinea carry a trace of DNA from an earlier wave of Africans who left the continent as long as 140,000 years ago, and then vanished.

Obviously, in science, replication and caution are key. Don’t get too excited. These results might turn out to be wrong–sometimes samples get contaminated or data coded incorrectly and we get results that turn out to be completely wrong. And, okay, this isn’t really “huge” in the grand scheme of things–we’re only talking about 2% of Papuans’ ancestors, not, like, 40% of them. But it does explain all of those anomalously old findings.

Now someone needs to explain the Red Deer Cave People:

The Red Deer Cave People were the most recently known prehistoric Hominin population that did not look like modern humans. Fossils dated to between 14,500 and 11,500 years old were found in Red Deer Cave and Longlin Cave in China. Having a mix of archaic and modern features, they are (tentatively) thought to be a separate species of humans that persisted until recent times and became extinct without contributing to the gene pool of modern humans.[1]

On a related note, we have some awesome news about Aborigine DNA/language trees: A genomic history of Australia and Why Australia is home to one of the Largest Language Families in the World. (Well duh it’s because Aborigines spent thousands of years as tiny bands of hunter gatherers, in which each isolated band started developing its own language.) These articles have an oddly inverted structure, (burying the lead, I guess,) so let’s rearrange the abstract for coherency:

We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. … Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages.

(kya = thousand years ago). So about 10-32 thousand years ago, one group of Australians conquered all of the other groups of Australians.

The science article notes:

To the researchers’ amazement, the genetic pattern mirrored the linguistic one. “It’s incredible that those two trees match. None of us expected that,” says paleoanthropologist Michael Westaway of Griffith University, Nathan, in Australia, a co-author on the Willerslev paper. “But it’s confusing: The [genetic splits] date to 30,000 years ago or more but the linguistic divisions are only maybe 6000 years old.”

Willerslev says he first thought the languages must be much older than thought. “But the linguists told me, ‘no way.'”

Both types of data also show that the population expanded from the northeast to the southwest. This migration occurred within the last 10,000 years and likely came in successive waves, Bowern says, in which existing languages were overlaid by new ones. This expansion also seems to correspond with a stone tool innovation called a backed edge blade. But the accompanying gene flow was just a trickle, suggesting that only a few people had an outsize cultural impact, Willerslev says. “It’s like you had two men entering a village, convincing everyone to speak a new language and adopt new tools, having a little sexual interaction, then disappearing,” he says. Then the new languages continued to develop, following the older patterns of population separation. “It’s really strange but it’s the best way we can interpret the data at this stage.”

Three things going on here. 1. The group from the north conquered the group from the south, raped their women, and imposed their language. They were able to do this because they had better weapons (“backed edge blades.”) But the group from the north was not very big, and so did not leave a very big genetic signature.

2. They conquered an existing population structure, at which point their language got absorbed into that structure, probably picking up some linguistic substrate from the groups’ previous languages along the way. Since most people learn language from their parents, it’s not too surprising to find cases where language and genetics line up. (Note that people do not always learn languages from their parents.)

3. Intellectuals are kind of naive.

The other really interesting thing here is that the linguistics team came to their conclusions by feeding a big database of Aboriginal words into a computer and having it run similar algorithms to the ones geneticists use for examining human ancestry (see the lovely graphics above.) I’ve been wondering for a long time why they don’t just do this, and am excited that they finally are.

Now please someone put all of the languages + reconstructed proto-langauges into the computer and find the most likely trees.

(Sorry, Nick. The regularly scheduled Anthropology Friday is going to have to wait a week. There just aren’t enough days.)

Tentative map of Neanderthal (and Denisovan) DNA in humans

I couldn’t find one, so I made one:
neandermap

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.

Notes:

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.

The neighbors don’t use trash pickup: the cellular automata of ethnic competition

I’ve noticed that the neighbors don’t put out their trash can on trash day. At first I thought nothing of it; perhaps they just hadn’t put their can out yet, or had accidentally slept through trash pickup. I don’t normally devote too much thought to the neighbors’ trash habits, but somehow, their cans never seemed to be out.

Last week, I witnessed them piling a mountain of trashbags into a truck. This week, again, no trash can.

It is technically legal, and cheaper, to not pay for trash pickup and instead pay a small fee to deposit your trash directly at the dump. So the neighbors are storing up a month or two’s worth of trash in their garage and then hauling it to the dump.

This is (or was) a nice neighborhood. Low crime, good schools, modern infrastructure, nice houses.

Now one of the other neighbors has been complaining to me that he’s concerned about rats coming from that house to his house.

I’ve heard a lot of complaints about this household, generally from other neighbors. Noisy, late-night parties. Guests who pee in other people’s bushes. Litter. Parking disputes (thankfully, not with me.) Mundanities that you have to put up with if you’re living around other humans. But this is a bit much.

So what to do? Call up the HOA and demand that they pass a resolution mandating that people pay for trash pickup? (Can the HOA even do that?) I don’t actually like the idea of getting the HOA to regulate the minutia of other people’s behavior, but then, I’ve never had a neighbor opt to keep giant piles of trash in their house instead of pay for trash pickup.

If all of this sounds familiar, it’s because I happened to highlight trash-related behaviors back in “Increasing Diversity => Fascism.” I’d call this a coincidence, but I suspect that disputes over proper trash disposal are actually very common.

I’m just glad we’re renting, so it’s not my money going down the drain–no, my money did that elsewhere. We cut our losses and got out shortly after the home invasions started and I found used drug needles on the playground. So we decided to pay extra, this time, for a nicer neighborhood, somewhere clean and safe.

So much for clean.

Why would anyone who can’t afford trash pickup live in this neighborhood? There are cheaper-but-still-nice neighborhoods nearby.

The answer is probably the obvious one. People who live on million-dollar estates on islands accessible only by ferry, who happily talk about how the cost of the ferry ride “keeps out the riff-raff,” vote for policies that move people from ghettos to middle-class neighborhoods.

****

This all gets back to competition, the Prisoner’s Dilemma, and ethnicity.

You and I are in competition.

If it’s any consolation, we’re also in competition with pretty much everyone on Earth. Each of us, whether consciously or not, is attempting to secure resources for ourselves and our progeny.

The easiest person to conquer is your neighbor.

You are unlikely to care terribly much about the behavior of someone living across the country, or even across the state. If some guy a thousand miles away from you is storing up a pile of trash, well, that’s weird, but it doesn’t affect you. If your neighbor is storing up a pile of trash, suddenly it starts looking like your business.

Most violence is committed against people known to the attacker, or members of their own community. Most wars are waged against a country’s immediate neighbors. And if I can’t conquer my neighbors, perhaps I can ally with someone from far away–someone not an immediate threat to me–to conquer them.

The easiest way to get people to stop fighting with their neighbors and band together for the common good is to confront them with an even bigger, credible threat from further away. England and France finally managed to ally when confronted with Germany; if space aliens invaded tomorrow, I bet most countries on earth would forget their nationalistic squabbles pretty darn quickly.

But as long as there isn’t a bigger, credible threat, then stealing my neighbor’s resources can lead to my own success. And pretty soon, we’re back to squabbling.

In other words, getting people to cooperate instead of defect is pretty tough.

Indeed, a great percent of ethnic conflicts are phrased along the lines of, “My people are great and virtuous cooperators who bend over backwards for other groups of people, but your people are dastardly defectors who are taking advantage of our naive goodwill!” And for good reason–if you can consistently defect against someone who consistently cooperates, you’ll do really well for yourself.

Society can only function if people cooperate, but short-term interests are benefitted by defection. Why put in all of the effort to engage in trade when you can let other people do trade and then mug them? Society therefore has a strong incentive to punish defection–if society can actually identify it.

We’ve gotten into the habit of attempting to prove that we are great cooperators by accusing others of defecting–ironically, defecting against them in the process.

Most whites are in direct competition–for jobs, popularity, and mates–with other whites. Lower class (and some middle class) whites are also in competition with blacks and Hispanic immigrants. High class whites are not.

When low class whites complain about black behavior, it sounds to high class whites like defection–or as we more commonly put it, racism. When high class whites say so, this sounds like defection to the low class whites–especially when they believe the blacks defected on them first. (And the blacks, of course, will inform you that the whites defected on them first.)

When whites move out of neighborhoods as blacks move in, it looks an awful lot to elites like defection. When elites make sanctimonious noises about the evils of “white flight,” this sounds like defection to the whites whose property values were destroyed as crime and trash–in the literal sense–invaded their neighborhoods. And when whites attempt to keep prospective black buyers out of neighborhoods (or drive them out after they’ve moved in,) this looks like defection, too.

Society needs a better way to determine who is and isn’t defecting.

 

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.

Hey, DNA: What is it good for?

So why do we still have bits of Neanderthal DNA hanging around after so many years? Of course it could just be random junk, but it’s more fun to think that it might be useful.

And the obvious useful thing for it to do is climate adaptation, since Neanderthals had been living in dark, cold, ice-age Europe for much longer than the newly-arrived h. Sapiens, and so might have had some adaptations to help deal with it.

Okay, so here is something related I was reading the other day, that I consider pretty interesting. So it looks like the people who live up on the Tibetan Plateau (like the Tibetans,) are really well-adapted to the altitude. No mean feat, considering that other populations who live at similar altitudes don’t seem to be as well-adjusted, despite living up there for similar lengths of time.

Well, now it appears that the Tibetans have actually been living in Tibet for waaaay longer than expected, because the original h. Sapiens who moved into Tibet intermarried with archaic hominids who had already lived there for hundreds of thousands of years, and so probably picked up their altitude adaptations from those guys.

BTW, “species” is a social construct and you probably shouldn’t bother with it here.

So what kind of useful stuff might we have picked up from Neanderthals?

First I’d like to interject that I still find declarations of “aha, we got this gene from Neanderthals and it does this!” to be speculative and prone to changing. All of the articles I’ve read tend to report the same list of stuff in a similar fashion, so I suspect they’re all workign off one or two sources, which makes everything doubly sketchy. So we’re going in here with a big “if” this is true…

Some of the results are fairly boring, like Neanderthal DNA affecting hair and skin. We already speculate that skin tone helps us deal with sunlight levels, so that’s sensible.

More interesting is the claim that Neanderthal DNA may predispose people to Type-2 Diabetes and depression.

Now why the hell would it do that? It’s probably not *just* random–after all, large stretches of DNA have little to no Neanderthal admixture at all, suggesting that genes in those spots just weren’t useful, so why would we have retained such apparently negative traits?

Maybe, like sickle cell anemia, these things actually have a positive function–at least in the right environments.

I read a fascinating theory a few years ago that Type 2 Diabetes and Seasonal Affective Disorder are actually just part of our bodies’ natural mechanisms for dealing with winter. Basically, you’re supposed to eat plants and get fat all summer long, while plants are available, and then by winter, your ability to absorb more glucose shuts down (there’s no point since the plants are all dead) and you switch over to burning ketones instead and eating an all-mammoth diet.

(Some groups, like the Inuit and Masai, historically [and may today still] survived on diets that included virtually no plants and so ran all of their cellular energy needs through the ketogenic instead of the glucose system.)

During this winter time, humans, like other animals, slowed down and semi-hibernated to save energy and because why the fuck not, it’s dark and no one has invented lightbulbs, yet.

By spring, you’ve lost a lot of weight, the plants come back, and so does your ability to use glucose.

This theory is laid out in the book Lights Out by T. S. Wiley, if you’re curious. I thought it was a really interesting book, but you might just think it’s all crank, I dunno.

Anyway, a big hole in Wiley’s plot is how we actually got this adaptation in the first place, since it’s a pretty complicated one and h. Sapiens hasn’t actually been living in places with winter for all that long. Wiley just claims that it’s a deep internal mechanism that animals have, which always struck me as kinda bunk because why would a species that evolved in Africa, from other animals in Africa, etc., probably going back for million upon millions of years, have some sort of complicated system like this still functional in its genome? A trait that is not undergoing positive selective pressure is probably going to become non-functional pretty quickly. But the theory was cool enough otherwise to ignore this bit, so I’ve kept it around.

Right, so here’s the (potential) answer: h. Sapiens didn’t have this adaptation hiding deep inside of them, Neanderthals had it. Neanderthals had been living in cold places for way, way longer than h. Sapiens, and by inter-breeding with them, we got to take advantage of a bunch of cold-weather adaptations they’d developed over that time frame–thus getting a jump-start on evolving to cope with the weather.

At any rate, if Wiley is correct, and SAD and Type-2 Diabetes are actually part of a dealing with winter complex that benefited our cold-weather ancestors, then that wold explain why these genes would have persisted over the years instead of being bred out.

An easy way to test this would be to compare rates of Type-2 Diabetes and SAD among African immigrants to Europe/other wintery latitudes, African Americans (who have a small amount of Euro admixture,) and Europeans. (Watching out, of course, for Vit D issues.) If the Euros have more SAD and Type-2 Diabetes than Africans living at the same latitude, then those would appear to be adaptations to the latitude. If the Africans have more, then my theory fails.