Some interesting things

Here’s a post a friend linked me to detailing the writer’s experience of discovering that the true background of two famous photos of the Vietnam War was very different from the background they had been taught:

As I read the article about the photos, I felt a sense of disbelief. I wasn’t quite sure what I was reading was correct. Surely, if this information about both photos were true, I’d have heard about it before this. After all, thirty years had passed.

I spent the next few hours searching the subject online and found quite a bit more information, but no serious or credible refutation of the stories I’d just learned. …

Then the strangest feeling came over me. I don’t even have a word for it, although I usually can come up with words for emotions.

This was a new feeling. The best description I can come up with is that it was a regret so intense it morphed seamlessly into guilt, as though I were responsible for something terrible, though I didn’t know exactly what. Regret and guilt, and also a rage that I’d been so stupid, that I’d let myself be duped or misled or kept ignorant about something so important, and that I’d remained ignorant all these years.

I sat in front of my computer and put my face down on the keyboard. I stayed in that position for a few minutes, energyless and drained. When I lifted my head I was surprised to find a few tears on my cheeks.

This is the emotion more blasely referred to as “red pilling;” the moment you realize that many of the things you had been taught to believe are, in fact, a lie.

It’s a very interesting article and I encourage you to read it.

Denisovan Jawbone in Tibet?

But now, an international team of scientists has announced the identification of another Denisovan fossil, from a site 1,500 miles away. It’s the right half of a jawbone, found some 10,700 feet above sea level in a cave in China’s Xiahe County, on the eastern edge of the Tibetan plateau. The Xiahe mandible, as it is now known, is not only the first Denisovan fossil to be found outside Denisova Cave, but also the very first Denisovan fossil to be found at all. It just took four decades for anyone to realize that.

So there may be a lot of old bits of bone or pieces of skulls lying unidentified in various old collections, especially in Asia, that we’ll be able to identify and piece together into various homo species as we fill in more of the information about our human family tree

To be honest, I am a little annoyed about how every article about the Denisovans expresses a form of supposed confusion at how a group whose only fossils (until now) were found in a cave in Siberia could have DNA in Tibetans and Melanesians. Obviously we just haven’t figured out the full ancestral ranges of these groups, and they used to overlap. If Tibetans have high-altitude adaptations that look like they came from Denisovans, then obviously Denisovans lived in Tibet, and old Tibetan bones are a great place to look for Denisovans.

Indeed, the Xiahe mandible, which is 160,000 years old, is by far the earliest hominin fossil from the Tibetan plateau. Researchers used to think that Homo sapiens was unique in adapting to the Himalayas, but the Denisovans were successfully living on the roof of the world at least 120,000 years earlier. They must also have adapted to extremely thin air—after all, the mandible was found in a cave that’s some 8,000 feet higher above sea level than Denisova itself. “Their presence that high up is truly astonishing,” Douka says.

Fascinating article about the genetics of circadian rhythms and their relationship to health matters:

Perhaps the most ubiquitous and persistent environmental factor present throughout the evolution of modern species is the revolution of the earth about its own axis, creating a 24 h solar day. The consequent recurrent pattern of light and darkness endows a sense of time to organisms that live on this planet. The importance of this sense of time is accentuated by an internal clock that functions on a 24 h scale, inherent in the genetic framework of living organisms ranging from cyanobacteria (Johnson et al., 1996) to human mammals (Herzog and Tosini, 2001). An internal, molecular program drives circadian oscillations within the organism that manifest at the molecular, biochemical, physiological and behavioral levels (Mazzoccoli et al., 2012). Importantly, these oscillations allow anticipatory responses to changes in the environment and promote survival.

The term “circadian” comes from the Latin “circa,” meaning “around” and “diem,” meaning “day.” Circadian events recur during the subjective day or the lighted portion of the 24 h period and the subjective night or the dark part of the 24 h period allowing physiological synchrony with the light/dark environment (Reddy and O’Neill, 2010). The circadian clock has been demonstrated in almost all living organisms (Johnson et al., 1996Herzog and Tosini, 2001Mazzoccoli et al., 2012). The two defining characteristics of the circadian timing system are perseverance of oscillation under constant environmental conditions, which define these rhythms as self-sustained and endogenously generated, and the ability to adapt to environmental change, particularly to changes in the environmental light/dark cycle (Tischkau and Gillette, 2005).

The fascinating thing about sleep is that it exists; you would think that, given how vulnerable we are during sleep, animals that sleep would have long ago been eaten by animals that don’t, and the entire kingdom would have evolved to be constantly awake. And yet it hasn’t, suggesting that whatever sleep does, it is vitally important.

Modern Shamans: Financial Managers, Political Pundits, and others who help tame life’s uncertainties:

Like all magical specialists, [shamans] rely on spells and occult gizmos, but what makes shamans special is that they use trance. …

But these advantages are offset by the ordeals involved. In many societies, a wannabe initiate lacks credibility until he (and it’s usually a he) undergoes a near-death experience or a long bout of asceticism.

One aboriginal Australian shaman told ethnographers that, as a novice, he was killed by an older shaman who then replaced his organs with a new, magical set. …

Manifesting as mediums, channelers, witch doctors and the prophets of religious movements, shamans have appeared in most human societies, including nearly all documented hunter-gatherers. They characterized the religious lives of ancestral humans and are often said to be the “first profession.” …

… Like people everywhere, contemporary Westerners look to experts to achieve the impossible – to heal incurable illnesses, to forecast unknowable futures – and the experts, in turn, compete among themselves, performing to convince people of their special abilities.

So who are these modern shamans?

According to the cognitive scientist Samuel Johnson, financial money managers are likely candidates. Money managers fail to outperform the market – in fact, they even fail to systematically outperform each other – yet customers continue to pay them to divine future stock prices. …

Very interesting insight. It might explain why we stuck with doctors for so many centuries even when they were totally useless (or even negatively useful,) and why we trusted psychiatry throughout most of the 20th century, despite it being obvious bullshit.

There are a lot of unknowns out there, and we feel more comfortable trusting someone than just leaving it unknown–which introduces a lot of room for people to take advantage of us.

Finally, on a similar note, Is Dogma Eugenic? 

As he explains, belief in the supernatural can be attributed to the above heuristics. If belief in the supernatural became a problem, we would have to evolve to loose those heuristics.

Heuristics can be good. But, insofar as heuristics have us create harmful dogmas that can perpetuate themselves socially, we will have to replace them with pure logic, or at least lessen their impact. 

So, insofar as humans have the capacity to believe harmful dogmas, we will lose heuristics and become more logical. Heuristics can be “gamed;” logic cannot. In this manner, humans evolve to act less on instinct. The logical part of our brain becomes more pronounced.

You might have to RTWT to really get the argument, but it’s fun.

Cracks in the Out of Africa Theory?

The most exciting finding of the past two decades in biological anthropology has been, without a doubt, evidence for interbreeding between Homo sapiens, Neanderthals, Denisovans, etc. and the sheer multiplicity of new hominin species being uncovered.

Exactly where the lines between species lie is a bit of a matter of semantic debate–where exactly did our ancestors end and Homo sapiens begin? Should we classify Neanderthals and Sapiens as one species if we interbred? etc–but if we accept the current classifications as decent approximations, we have:

Capture
Source: Wikipedia

Sorry, I realized it would be much more efficient if I just grabbed the family tree off Wikipedia instead of copying it over bit by bit. The top part of the tree got cut off, so I’ll note that Homini (6.3 million years ago) includes us + chimps, while Hominina (5.7 million years ago) has no chimps, but includes australopithecines. Gorillas are way back in Homininae, with an e. Homo, our genus, includes all of the “human” species, but usually doesn’t include australopithecines.

There is further debate on exactly who descended from whom. We’re finding new fossils all the time, which is quite exciting, but our current record is not nearly as complete as we’d like it to be. So sometimes branches get moved around or re-categorized as more data comes to light.

The most recent notable additions to our genus are the Denisovans, Homo floresiensis, Homo luzonensis, Homo Naledi, Homo doesn’t have a name yet, and more Denisovans.

You have probably heard of the “hobbit,” Homo floresiensis. The remains we have uncovered of this diminutive hominin are remarkably good, including a skull in great condition (despite some damage caused after excavation.) They lived on the island of Flores from about 200,000 to 50,000 years ago (though their arrival may get pushed back considerably because there are stone tools on Flores that are much older–700,000 years old–we just don’t know yet who used them.)

The hobbits are remarkable in multiple ways. First, they lived in an area that was not connected to the mainland by any landbridges–that is, they had to swim, boat, or otherwise be carried to their island. I am skeptical of the idea of anyone surviving a tsunami as a means of populating an island, but they arrived in an era when, as far as we know, humans had yet to build boats. So perhaps their ancestors were among the first humans to build boats, and we just haven’t found the remains of their crafts (wood being a material that degenerates very quickly.)

Second, the Hobbits are most likely descended from Homo erectus, who lived nearby on mainland Indonesia (at the time, connected to the rest of Asia via a landbridge), but are morphologically very different. They are tiny–shorter than pygmies, Homo erectus, or even australopithecines.

There is much debate about whether they are descended directly from erectus, or part of a sister-clade to erectus that descended from a common ancestor. It was previously believed that erectus was the first hominin to leave Africa, but if Floresiensis is not descended from erectus, Flores could be the first.

Now a similarly diminutive hominin has turned up in the Philippines, also past a significant water barrier that would require some effort to cross. It has been dubbed Homo luzonensis. Not much is known, yet, about luzonensis, (we haven’t found as many of its bones), but what we do know is tantalizing:

It was soon apparent to Détroit that the remains featured a puzzling mosaic of traits both modern and ancient. “Each of the features [of Homo luzonensis] corresponds to some hominin or another,” he says. “But the combination makes for something really unique. There’s no known species with this same suite of features.”

They’re small, possibly even smaller than the Hobbits. Their feet resemble australopithecines, but australopithecines supposedly died out a couple million years before Luzonensis arrived on the scene. And their teeth were “remarkably uniform,” which probably sounds boring to anyone who isn’t a dentist, but provides strong evidence of them being a different species.

Two island dwelling species in the same area supports the idea that their ancestors either developed boats or were remarkably skilled at surviving tsunamis, and that southeast Asia was a remarkable hotspot of hominin diversity.

And then there are the Denisovans!

Denisovans are mysterious because we have so few of their bones–a chunk of skull was recently uncovered, but we have no jaws, no faces, no ribs, etc–so we don’t have a good idea of what they looked like. What we do have are Denisovan DNA (extracted from those fragments of skeletons) and traces of Denisovan DNA in modern humans.

Oddly, those Denisovan bones turned up in Siberia (a good place for preserving old bones, but not such a great place for humans adapted to warm climates) while the humans with Denisovan DNA live in modern Papua New Guinea and nearby areas.

The obvious answer to this puzzle is that both the Denisovans had a much broader range than one cave in Siberia and the ancestors of modern folks from PNG used to live in different areas than they do now.

A more detailed analysis of PNG DNA was recently released, which reveals three separate, significant groups of Denisovans who interbred with sapiens:

… modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated [from each other] over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

The Wallace line is a place that’s too deep for a landbridge, and thus the area to the east was an island even during the Ice Age. In other words, it looks like Denisovans could use boats. (Or survive tsunamis, pfft.)

Next, we sought to retrieve dates of divergence between D1, D2, and the Altai Denisovan genome … to encompass two deeply divergent Denisovan-related components, our best fitting model indicates that D1 and D2 split from the Altai Denisovan approximately 283 kya … respectively (Figure 4B). While clearly branching off the Denisovan line, D2 diverged so closely to the Neanderthal-Denisovan split that it is perhaps better considered as a third sister group… For context, even the youngest of these divergence times is similar to the evolutionary age of anatomically modern humans … Our model implies substantial reproductive separation of multiple Denisovan-like populations over a period of hundreds of thousands of years. … 

The genetic diversity within the Denisovan clade is consistent with their deep divergence and separation into at least three geographically disparate branches, with one contributing an introgression signal in Oceania and to a lesser extent across Asia (D2), another apparently restricted to New Guinea and nearby islands (D1), and a third in East Asia and Siberia (D0). This suggests that Denisovans were capable of crossing major geographical barriers, including the persistent sea lanes that separated Asia from Wallacea and New Guinea. They therefore spanned an incredible diversity of environments, from temperate continental steppes to tropical equatorial islands.

(We will probably reclassify some of the older fossils from Asia as Denisovans once we figure out what they looked like.)

Then we have Homo naledi, from South Africa. Naledi lived around 250,000 years ago, about the same time as Homo sapiens were differentiating from their ancestors. We have a wonderful array of Homo naledi fossils, preserved in the bottom of a cave pit. If they were placed here intentionally, this was pretty advanced behavior, though I wonder if perhaps they just got lost in the cave from time to time and then died in the pit.

At about 5 ft tall, (male height) naledi was short, but not nearly as short as Floresiensis, and taller than some groups of sapiens. Its skull was significantly smaller than a modern skull, however, and I find it odd that, out of the thousands of bones and fragments discovered, we have not yet recovered much of the front of their faces. Perhaps their faces were shattered when they fell into the cave?

Naledi, like Floresiensis and Luzonensis, shares some more modern traits with other members of the homo genus, and some traits with the older australopithecines. Unlike them, we have yet to uncover evidence that Naledi used tools.

The we have a couple of unnamed hominins

These so-called “ghost populations” are known entirely from their presence in the DNA of modern humans. We don’t have any fossils from them, either because they lived in areas where the weather didn’t favor preservation, or the modern political climate makes searching for fossils difficult.

The pygmies and Bushmen derive about 2% of their DNA from an archaic population or two that we estimate split off from the rest of us about 700,000 years ago. They met and mated with these other hominins around 35,000 years ago.

More interesting is another ghost population that shows up in the genomes of west African groups like the Mende. Now, the average non-African has about 1-4% Neanderthal DNA, and Melanesians have about 4-6% Denisovan, but some tribes in west Africa, such as the Yoruba, Mende, Gambians, and Esan, may derive about 10% of their DNA from an otherwise unknown ghost population that split off before the Neanderthals! (Razib’s very nice article summarizing the paper.)

 

Oh, jeeze, it’s three am, let me finish this in the next post…

 

 

Links Post: Evolution and More

road-to-bigger-brains
From State of the Science: Finding Human Ancestors in New Places

The Puerto Rican rainforest is beautiful and temporarily low on bugs. (Bugs, I suspect, evolve quickly and so can bounce back from these sorts of collapses–but they are collapses.)

More evidence for an extra Neanderthal or Denisovan interbreeding event in East Asians and Melanesian genomes:

 In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage.

(Congratulations to the authors, Mondal, Bertranpetit, and Lao.)

Really interesting study on gene-culture co-evolution in Northeast Asia:

Here we report an analysis comparing cultural and genetic data from 13 populations from in and around Northeast Asia spanning 10 different language families/isolates. We construct distance matrices for language (grammar, phonology, lexicon), music (song structure, performance style), and genomes (genome-wide SNPs) and test for correlations among them. … robust correlations emerge between genetic and grammatical distances. Our results suggest that grammatical structure might be one of the strongest cultural indicators of human population history, while also demonstrating differences among cultural and genetic relationships that highlight the complex nature of human cultural and genetic evolution.

I feel like there’s a joke about grammar Nazis in here.

Why do we sleep? No one knows.

While humans average seven hours, other primates range from just under nine hours (blue-eyed black lemurs) to 17 (owl monkeys). Chimps, our closest living evolutionary relatives, average about nine and a half hours. And although humans doze for less time, a greater proportion is rapid eye movement sleep (REM), the deepest phase, when vivid dreams unfold.

Sleep is pretty much universal in the animal kingdom, but different species vary greatly in their habits. Elephants sleep about two hours out of 24; sloths more than 15. Individual humans vary in their sleep needs, but interestingly, different cultures vary greatly in the timing of their sleep, eg, the Spanish siesta. Our modern notion that people “should” sleep in a solid, 7-9 hour chunk (going so far as to “train” children to do it,) is more a result of electricity and industrial work schedules than anything inherent or healthy about human sleep. So if you find yourself stressed out because you keep taking a nap in the afternoon instead of sleeping through the night, take heart: you may be completely normal. (Unless you’re tired because of some illness, of course.)

Interestingly:

Within any culture, people also prefer to rest and rise at different times: In most populations, individuals range from night owls to morning larks in a near bell curve distribution. Where someone falls along this continuum often depends on sex (women tend to rise earlier) and age (young adults tend to be night owls, while children and older adults typically go to bed before the wee hours).

Genes matter, too. Recent studies have identified about a dozen genetic variations that predict sleep habits, some of which are located in genes known to influence circadian rhythms.

While this variation can cause conflict today … it may be the vestige of a crucial adaptation. According to the sentinel hypothesis, staggered sleep evolved to ensure that there was always some portion of a group awake and able to detect threats.

So they gave sleep trackers to some Hadza, who must by now think Westerners are very strange, and found that at any particular period of the night, about 40% of people were awake; over 20 nights, there were “only 18 one-minute periods” when everyone was asleep. That doesn’t prove anything, but it does suggest that it’s perfectly normal for some people to be up in the middle of the night–and maybe even useful.

Important dates in the evolution of human brain genes found:

In May, a pair of papers published by separate teams in the journal Cell focused on the NOTCH family of genes, found in all animals and critical to an embryo’s development: They produce the proteins that tell stem cells what to turn into, such as neurons in the brain. The researchers looked at relatives of the NOTCH2 gene that are present today only in humans.

In a distant ancestor 8 million to 14 million years ago, they found, a copying error resulted in an “extra hunk of DNA,” says David Haussler of the University of California, Santa Cruz, a senior author of one of the new studies.

This non-functioning extra piece of NOTCH2 code is still present in chimps and gorillas, but not in orangutans, which went off on their own evolutionary path 14 million years ago.

About 3 million to 4 million years ago, a few million years after our own lineage split from other apes, a second mutation activated the once non-functional code. This human-specific gene, called NOTCH2NL, began producing proteins involved in turning neural stem cells into cortical neurons. NOTCH2NL pumped up the number of neurons in the neocortex, the seat of advanced cognitive function. Over time, this led to bigger, more powerful brains. …

The researchers also found NOTCH2NL in the ancient genomes of our closest evolutionary kin: the Denisovans and the Neanderthals, who had brain volumes similar to our own.

And finally, Differences in Genes’ Geographic Origins Influence Mitochondrial Function:

“Genomes that evolve in different geographic locations without intermixing can end up being different from each other,” said Kateryna Makova, Pentz Professor of Biology at Penn State and an author of the paper. “… This variation has a lot of advantages; for example, increased variation in immune genes can provide enhanced protection from diseases. However, variation in geographic origin within the genome could also potentially lead to communication issues between genes, for example between mitochondrial and nuclear genes that work together to regulate mitochondrial function.”

Researchers looked at recently (by evolutionary standards) mixed populations like Puerto Ricans and African Americans, comparing the parts of their DNA that interact with mitochondria to the parts that don’t. Since mitochondria hail from your mother, and these populations have different ethnic DNA contributions along maternal and paternal lines. If all of the DNA were equally compatible with their mitochondria, then we’d expect to see equal contributions to the specifically mitochondria-interacting genes. If some ethnic origins interact better with the mitochondria, then we expect to see more of this DNA in these specific places.

The latter is, in fact, what we find. Puerto Ricans hail more from the Taino Indians along their mtDNA, and have relatively more Taino DNA in the genes that affect their mitochondria–indicating that over the years, individuals with more balanced contributions were selected against in Puerto Rico. (“Selection” is such a sanitized way of saying they died/had fewer children.)

This indicates that a recently admixed population may have more health issues than its parents, but the issues will work themselves out over time.

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. 

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.

Denny: the Neanderthal-Denisovan Hybrid

Carte_Neandertaliens
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?

nature-siberian-neanderthals-17.02.16-v2
The slightly more complicated family tree, not including Denny

Yes.

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.

Do Chilblains Affect Blacks More than Whites?

toes afflicted with chilblains
toes afflicted with chilblains

While tromping through a blizzard, seeking insight into circum-polar peoples, I discovered a condition called chilblains. The relevant Wikipedia page is rather short:

Chilblains … is a medical condition that occurs when a predisposed individual is exposed to cold and humidity, causing tissue damage. It is often confused with frostbite and trench foot. Damage to capillary beds in the skin causes redness, itching, inflammation, and sometimes blisters. Chilblains can be reduced by keeping the feet and hands warm in cold weather, and avoiding extreme temperature changes. Chilblains can be idiopathic (spontaneous and unrelated to another disease), but may also be a manifestation of another serious medical condition that needs to be investigated.

The part they don’t mention is that it can really hurt.

The first HBD-related question I became interested in–after visiting a black friend’s house and observing that she was comfortable without the AC on, even though it was summer–is whether people from different latitudes prefer different temperatures. It seems pretty obvious: surely people from Yakutsk prefer different temperatures than people from Pakistan. It also seems easy to test: just put people in a room and give them complete control over the thermostat. And yet, I’d never heard anyone discuss the idea.

Anyway, the perfunctory Wikipedia page on chilblains mentioned nothing about racial or ethnic predisposition to the condition–even though surely the Eskimo (Inuit) who have genetic admixture from both ice-age Neanderthals and Denisovans:

“Using this method, they found two regions with a strong signal of selection: (i) one region contains the cluster of FADS genes, involved in the metabolism of unsaturated fatty acids; (ii) the other region contains WARS2 and TBX15, located on chromosome 1.” …

“TBX15 plays a role in the differentiation of brown and brite adipocytes. Brown and brite adipocytes produce heat via lipid oxidation when stimulated by cold temperatures, making TBX15 a strong candidate gene for adaptation to life in the Arctic.” …

“The Inuit DNA sequence in this region matches very well with the Denisovan genome, and it is highly differentiated from other present-day human sequences, though we can’t discard the possibility that the variant was introduced from another archaic group whose genomes we haven’t sampled yet,” Dr. Racimo said.

The scientists found that the variant is present at low-to-intermediate frequencies throughout Eurasia, and at especially high frequencies in the Inuits and Native American populations, but almost absent in Africa.

Sub-Saharan Africans have their own archaic admixture, but they have very little to no ice-age hominin–which is probably good for them, except for those who’ve moved further north.

Imagine my surprised upon searching and discovering very little research on whether chilblains disproportionately affects people of different races or ethnicities. If you were a dermatologist–or a genetically prone person–wouldn’t you want to know?

So here’s what I did find:

The National Athletic Trainers Association Position Statement on Cold Injuries notes:

Black individuals have been shown to be 2 to 4 times more likely than individuals from other racial groups to sustain cold injuries. These differences may be due to cold weather experience, but are likely due to anthropometric and body composition differences, including less-pronounced CIVD, increased sympathetic response to cold exposure, and thinner, longer digits.3,6

I think CIVD=Cold-Induced Vasodilation

The Military Surgeon: Journal of the Association of Military Surgeons of the United States, Volumes 36-37, states:

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c2ijvyvveaaehdz c2ijw49vqaajuou

The text continues with descriptions of amputating rotting feet.

A PDF from the UK, titled “Cold Injury,” notes:

c2ilp17uaaaonao

Notice that the incidence of chilblains is actually less in extremely cold places than moderately cold places–attributed here to people in these places being well-equipped for the cold.

c2ilp4evqaet4lu

Finally I found a PDF of a study performed, I believe, by the US Military, Epidemiology of US Army Cold Weather Injuries, 1980-1999:

picture-2

While I would really prefer to have more ethnic groups included in the study, two will have to suffice. It looks like trench foot may be an equal-opportunity offender, but chilblains, frostbite, and other cold-related injuries attack black men (at least in the army) at about 4x the rate of white men, and black women 2x as often as white women (but women in the army may not endure the same conditions as men in the army.)

On a related note, while researching this post, I came across this historic reference to infectious scurvy and diabetes, in the Journal of Tropical Medicine and Hygiene, Volumes 4-5 (published in 1902):

c2iou5uviae83si

Note: this is why it is important to discard bad theories after they’ve been disproven. Otherwise, you kill your scurvy victims by quarantining them instead of giving them oranges.

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.