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paleoanthropology, genetics and evolution

Photo Credit: Pre-Clovis Gault Assemblage artifacts. Thomas Williams et al. (2018) CC-BY-NC

William. W. Howells (1980), writing on the way that new discoveries have affected the interpretation of Homo erectus:

The pattern of discovery to a degree continues that of the past. Java has gone on producing material at a familiar pace, while in Europe fossils have been sparse and fragmentary, with two spectacular exceptions (Petralona, Arago), India continues a blank; China has just begun to produce significant finds again. Africa has taken more of its rightful place. However, if one were to take Weidenreich or Boule as a standard, description has been rather slow, and even preparation, especially in the case of delicate specimens, has delayed up full appreciation of some finds.


Howells, W. W. (1980). Homo erectus—who, when and where: a survey. American Journal of Physical Anthropology, 23(S1), 1-23.

Funding must make room for exploration

Scientists often say that you already need to have a result in hand to have a chance at being funded for research. Applications where the results are truly unknown are almost never funded.

Instead, applications succeed when they include slick “pilot data” showing the likely outcome, frame the research in terms of well-known earlier results, and seem certain to lead to a positive result. Failure to reject a null hypothesis is not an option. Replication of other research is almost never funded.

This system is wonderful if the goal is to add one brick at a time to the foundation of what we already think we know. But in many areas of science, what we think we know is wrong. And as many others have noted, the bias against negative results and replication has led some fields to a crisis of false published results.

If we want to get at the nature of things, we need scientists who explore new ideas, even if they don’t come pre-packaged with pilot data.

Times Higher Education has a conversation with Nobel Prize-winning scientist Saul Perlmutter, who “Nobel laureate says scientific breakthrough ‘would not be possible’ today”.

“People forget that what you’re looking for is gigantic surprises and transformations that allow us to do things that we never thought were possible,” he said.
“The only thing we know of that seems to work is to create an environment where people are thoughtful, they’re hopeful and they’re trying many ideas.”
He said that this approach can even be seen among venture capitalists, who only expect a “small fraction” of their investments to be successful.
“You’re looking for those rare, special investments and you have to spread the resources in order to get them,” he said.
Saul Perlmutter. Photo: Wikimedia Commons

Over Twitter in the last few weeks, I’ve seen disappointment from several professional colleagues after the rejections of their latest grant applications. The most heartbreaking had reviewers who wrote that their labs “did not have the necessary expertise to carry out the research.” Of course, I know the people, and I know that in each of these cases, these researchers have already published previous work close to their new proposals. They not only have the expertise, I would consider them among the world’s experts.

Think about this kind of comment. I’ve gotten the same thing on my own applications for funding in the past. This is why researchers are driven to include pilot data in their applications, to show that they have already produced results. It’s why researchers apply for funding to do nearly-completed research, so that they can redirect a fraction of the funds to the next project.

Maybe in an environment where the probability of funding were higher, these kinds of comments would be ignored. But take that idea seriously for a moment. Doesn’t it mean that with less funding, we are being even more conservative in what we fund? Doesn’t that make us even less likely to learn something new?

I don’t want to look at the same questions, the same experimental models, again and again. I want to work on new ideas, with a great team of people who have a wide range of backgrounds. It’s what Perlmutter is saying, “create an environment where people are thoughtful, they’re hopeful, and they’re trying many ideas.”

Exploration may not always lead to discovery, but it’s the only thing that does.

Essential reading on the effects of sexual harassment and assault in field paleoanthropology: “In case this helps you: This happened to me while I was trying to become a paleoanthropologist.”

UPDATE (2017-05-28): This post was removed from the linked website by its author, so the link is dead.

Notable: O’Malley, R. C., Stanton, M. A., Gilby, I. C., Lonsdorf, E. V., Pusey, A., Markham, A. C., & Murray, C. M. (2016). Reproductive state and rank influence patterns of meat consumption in wild female chimpanzees (Pan troglodytes schweinfurthii). Journal of human evolution, 90, 16-28. doi:10.1016/j.jhevol.2015.09.009

Synopsis: Looking at long-term data on diet and reproductive status in wild chimpanzees at Gombe, Tanzania, O’Malley and colleagues found that pregnant females ate more meat than lactating or non-pregnant, non-lactating females. This effect was concentrated in low-ranking females, who have less access to meat than high-ranking females, so social rank and pregnancy both interact as factors influencing female meat consumption.

Interesting because: Pregnancy and lactation have high energy costs and protein costs for females. Meat is a relatively high-energy and high-protein food source. A supply of meat in the diet of pregnant or lactating females would seem to be useful or adaptive, even though meat makes up a fairly small fraction of the chimpanzee diet and can easily be dominated by high-ranking females and males. These data show that female chimpanzees do compete effectively for meat despite low social rank, when they are pregnant.

Useful insight: Females did not significantly change insect consumption, even though it is another significant source of protein and energy, more reliable than meat. They seem to be eating insects at near a maximum, limited by the high time involved in foraging insects and insect defenses. Meat has a higher degree of variability.

Should we move to a system where every scientist gives grant money away?

Worth a read: “With this new system, scientists never have to write a grant application again”.

In Bollen’s system, scientists no longer have to apply; instead, they all receive an equal share of the funding budget annually—some €30,000 in the Netherlands, and $100,000 in the United States—but they have to donate a fixed percentage to other scientists whose work they respect and find important. “Our system is not based on committees’ judgments, but on the wisdom of the crowd,” Scheffer told the meeting.
Bollen and his colleagues have tested their idea in computer simulations. If scientists allocated 50% of their money to colleagues they cite in their papers, research funds would roughly be distributed the way funding agencies currently do, they showed in a paper last year—but at much lower overhead costs.

The incredible costs in time and money just to apply for grants and allocate grant funding are approaching insanity levels. With success rates spiraling down below 15%, researchers are spending more and more of their time writing grant applications and less and less doing research, teaching students, or sharing with the public. The average successful grant applicant sinks months of work into grant applications each year that could have been spent doing science, in a fairer system.

I’ve thought a lot about the kind of “self-organized fund allocation” described in the linked article. Allocating money on the condition that some must be given to other researchers would create several downstream benefits. Scientists who maximize the ability of other scientists to produce their own new and useful results would have a big advantage in this system. Jerks would be punished appropriately. Once they have a role in the system, scientists could make rational decisions about how to collaborate with other researchers to build a larger program, instead of trying to centralize into their own little kingdoms.

The article mentions that Bollen’s scheme includes a condition that you can’t just give money to coauthors. The supposed problem is that people will choose to allocate funding to their friends.

Personally, I think that kind of condition decreases the appeal. Maybe there should be a barrier to allocating within an individual’s institution, to prevent administrators from pressuring researchers to keep the money at home. But I think the ability to allocate money to friends will encourage the development of stable research collaborations across institutions (and internationally). Besides, giving other scientists the means to reward friendly behavior will create a lot more friendly environments for science in the future. I think people allocating money within “friend” networks is a feature of a system, not a bug.

But one thing that I think this model wouldn’t address is the risk-averseness of today’s scientists. Today’s funding model disincentivizes taking true intellectual risks. The funded applications are those for which outcomes can be predicted. As a result, some of the most talented researchers are aiming low, instead of trying to swing for the fences. But giving people money to allocate to others is not likely to address what I see as a big problem. To be sure, having a more stable funding, at a low level, will enable some people to try radical new ideas. But any system where a winner-take-all effects kick in is one where it’s hard to fund contrarian or risky research.

Of course, as applied to human evolution research, or even biological anthropology more broadly, this kind of system wouldn’t have quite the impact as biomedical science. If we divided all the NSF funding for Biological Anthropology among the bona fide researchers in this field working in the U.S., it would average less than $3000 per scientist. Still, I’m pretty sure that amount would generate a lot more research distributed across hundreds of working scientists instead of clumped into the overhead budgets of a few big winners.

Notable: Bocherens, Hervé, Martin Cotte, Ricardo A. Bonini, Pablo Straccia, Daniel Scian, Leopoldo Soibelzon, Francisco J. Prevosti. 2017. Isotopic insight on paleodiet of extinct Pleistocene megafaunal Xenarthrans from Argentina. Gondwana Research (in press). doi:10.1016/j.gr.2017.04.003

Synopsis: Bocherens and colleagues did stable isotopic sampling of bones and teeth from extinct sabertooths, horses, and various extinct xenarthrans including glyptodonts and giant ground sloths. The sabertooths obviously turned out like modern carnivores in their stable isotopes. The extinct megafaunal xenarthrans looked just like modern herbivores, with no sign of the in-between diet of some modern species that rely on insect-eating or occasional scavening, like armadillos.

Interesting because: Some paleoecologists had suggested that these weird-looking extinct species might, in addition to eating plants, have been part-time scavengers, or have relied on insect consumption. That is, they might have been a bit more like bears than elephants. That proves not to be the case in any significant way, at least for the South American extinct species sampled.

Best line: “Therefore Megatherium is not the cryptic flesh-eater suggested by some authors that could have accounted for the supposed imbalance of carnivores in the South American megafauna.”

Notable: van Leeuwen, Edwin J. C., Katherine A. Cronin, and Daniel B. M. Haun. 2017. Tool use for corpse cleaning in chimpanzees. Scientific Reports 7:44091. doi:10.1038/srep44091

Synopsis: van Leeuwen and colleagues watched as a female chimpanzee used a grass stem to clean the teeth of a male who had died, at a sanctuary for orphaned chimpanzees. Other group members all inspected or interacted with the body, but the female who cleaned the teeth was a close “adoptive” mother to this dead male.

Interesting because: It is the first recorded example of tool use upon a dead body of a conspecific by a non-human animal.

Best quote: “Like humans, chimpanzees may not treat deceased conspecifics carelessly, but instead handle corpses in a socially meaningful way – i.e. as social beings instead of inanimate objects”

A neat article in The Conversation by Justin Bradfield discusses new chemical approaches for identifying traces of poison in the archaeological record: “We’re closer to learning when humans first daubed arrows with poison”.

A recent archaeological discovery at Border Cave (on South Africa’s border with Swaziland), revealed trace amounts of a substance still adhering to a 24 000 year-old wooden poison applicator. This substance was identified as by-products of the poison ricin. Ricin is produced by the castor bean plant, from which castor oil originates. This discovery, though not without its detractors, sparked renewed interest in identifying poison ingredients on archaeological artefacts in various parts of the world.

It has been interesting to see these aspects of modern technical kits extending far back into the LSA. The development of a hunting tradition using poisons may have had enormous influence on the entire LSA tool repertoire. It may also have established a niche in which human body size and robusticity markedly declined. Yet the basis for the change was archaeologically invisible until very recently.

Agustín Fuentes has a short essay in New York magazine’s “Science of Us”: “Creative Collaboration Is What Humans Do Best.”

But in order to best deploy this capacity we need to remove the set of blinders most of us wear. Many humans have become convinced that we are individually powerless, and have forgotten what creativity is and how its spark resides in all of us.
Creativity is not a private endeavor vested in a single person or a select group of people. It is not solely about genius in the arts or sciences, or actions by prominent artists, celebrities, or politicians. It is not even limited to the work of particularly original thinkers. Creativity emerges from the interconnections of ideas, experiences, and imagination.

Fuentes’ new book is called The Creative Spark: How Imagination Made Humans Exceptional.

My University of Wisconsin–Madison colleague, Karen Strier, has studied the muriqui monkeys of Brazil for her entire career. Now, the in small patch of forest where she works, howler monkeys have become victims of the yellow fever epidemic spreading across the country.

The university has done an informative story on how the epidemic is affecting both the prospects for conservation of these wild primates and the scientific study of their behavior: “Yellow fever killing thousands of monkeys in Brazil”.

When she first arrived at her study forest, known as RPPN Feliciano Miguel Abdala, there were just 50 muriquis. By September 2016, there were nearly 340, representing one-third of the species’ total known population. The animals reside in just 10 forests in southeastern Brazil and nowhere else in the world. Strier’s efforts and those of her colleagues have helped restore their numbers.
She is relieved that, so far, the muriquis appear to be less susceptible to yellow fever. “It was really tense – scary – to go into the forest, knowing the howlers were gone but not knowing how bad things might also be for the muriquis,” Strier recalls.

Here’s a nice article about two archaeologists, Gayle Fritz and David Freidel, and their efforts to better educate the public and their students about critical thinking. “Archaeological Fantasies and Hoaxes” presents a list of five big myths and why they are so pervasive in American culture.

The article touches on many valuable points. Here’s something I didn’t know:

“Incidentally, the opening scene shows Indiana Jones grabbing a golden idol off the altar,” Freidel says. “That’s actually a real jade artifact in the Dumbarton Oaks research library in Washington D.C., and it’s an image of the Aztec goddess Tlazolteotl. It’s a real piece of work, but it’s also an unprovenanced piece of work that was not found in good archaeological context. It was looted.”

When it comes to big public misconceptions, I’m not saying the biggest is aliens, but…

Ottoline Leyser, “chairwoman of the Royal Society Science Policy Advisory Group,” has published a brief essay on science assessment in the U.K.: “No researchers should be submitted to the REF”.

I wanted to share this paragraph from the essay, which was brought to my attention by Jennifer Rohn.

A high-quality research portfolio doesn’t consist only of groundbreaking discoveries. It contains work that cements initial findings, integrates existing work, develops tools and resources such as databases, engages diverse groups and nurtures the next generation of researchers.

I live by this principle in all my projects and scientific work.

South African San adopt code of research ethics

By Linda Nordling in Science: “San people of Africa draft code of ethics for researchers”:

The code, published here on 3 March, asks researchers to treat the San respectfully and refrain from publishing information that could be viewed as insulting. Because such sensitivities may not be clear to researchers, the code asks that scientists let communities read and comment on findings before they are published. It also asks that researchers keep their promises and give something back to the community in return for its cooperation.

The article points specifically to a 2010 study of San genome data by Stephan Schuster and colleagues, published in Nature, as one that posed many problems in the view of many San people.

Cover page of the new ethics statement

The research guidelines are available freely as an online booklet: “San Code of Research Ethics”. The preamble expresses the rationale for the code and some of the problems experienced with prior researchers.

We have encountered lack of respect in many instances in the past. In Genomics research, our leaders were avoided, and respect was not shown to them. Researchers took photographs of individuals in their homes, of breastfeeding mothers, or of underage children, whilst ignoring our social customs and norms. Bribes or other advantages were offered.
Failure by researchers to meet their promises to provide feedback is an example of disrespect which is encountered frequently.

This should be widely read and discussed by anthropologists and students.

It is noteworthy that the code singles out genomic research. Nordling’s article includes a quote from David Reich, who worries that complying with such a research code would prevent independent researchers from carrying out reanalysis or replication. The standard of data availability in human genetics as carried out in the U.S., Europe, China and Japan allows de-identified sequence data to be distributed freely online without restriction. If future samples are provided only under this code, it’s clear that such redistribution would not be permitted.

People have a right to decide they don’t want their genetic data freely available on the Internet, and to decide if want to participate in only one study and not any subsequent work. I do hesitate to accept that leaders of a group have “rights” to prevent group members from participating freely in research if they should choose to do so. At that level, I favor individual rights over any idea of cultural group rights. But cases where individuals are sought as research subjects precisely because they are members of some group are in my view on shaky ethical ground if they are pursuing aims that representatives of the group find damaging, unethical, or exploitative.

And there is no question that anthropological researchers have exploited San peoples. Many anthropologists who carried out research in the 1960s and 1970s have told me about the kind of practices that were acceptable in those days. It is not enough to say that times and standards have changed. Today’s anthropological and genomic researchers need to build trust and value into the relationships they have with their study communities.

Most of today’s researchers are very ethical. But in genomics it is unfortunately common for samples to be taken and examined by bioinformaticians who were not involved in sample collection and do not know any members of the study community. Research teams need to do a better job of educating people at all levels of their project about the histories of research and the current needs of study communities. A research ethics statement like this one helps to clarify the expectations, but it is up to the scientific community to demand better and to follow through.

A postscript: It is very unfortunate that the story begins with the line,

The San people of Southern Africa are among the closest living relatives of our hunting and gathering ancestors.

This is not true. All living humans everywhere in the world share a common heritage in hunting and gathering populations living before 200,000 years ago. We are all equally descendants of these ancestors, although the fractions of different groups of people living at that time, including some sub-Saharan African populations and Neandertals and Denisovans, vary among living peoples.

The various groups that are today known as San peoples, including the ‡Khomani San, Ju|’hoansi, !Kung, and others, comprise a lineage that emerged early within the differentiation of modern humans within Africa. They have their own long legacy, marked by many genetic variations that are rare or missing from other populations in the world. It is this contribution to human diversity that makes San peoples of great research interest for human geneticists, not the mistaken idea that they are closer to our common ancestors.

Mushroom-munching poplar-popping Neandertals

Neandertals ate mushrooms. That’s the conclusion of new work examining the DNA remnants in ancient dental calculus. Can we believe it?

Laura Weyrich and colleagues (2017) describe their work on dental calculus samples from five Neandertal individuals. The specimens include two from El Sidrón, Spain, two from Spy, Belgium, and one from Grotta Breuil, Italy (which did not in the end produce results). They also examined a larger number of ancient modern human specimens, including two Neolithic skeletons from Sudan, a number of South African Late Stone Age and Pastoralist Period skeletons, and a fairly large sample (n=75) of nineteenth-century Germans.

The last few years have seen an enormous increase in our knowledge of Neandertal dietary breadth. As recently as 10 years ago, while there was growing evidence that some Neandertals were using small game, shellfish, and other coastal resources, the going belief was that the Neandertal diet might have been composed almost entirely of meat—as much as 95% meat by some estimates.

This is understandable in light of the near-invisibility of plant foods in the archaeological record. It wasn’t only that plants don’t have bones. Neandertals and earlier people never made vessels or specialized artifacts that some later human populations used to collect and prepare plant foods. If Neandertals relied upon cooked grains, for example, you might expect them to have used grindstones once in a while.

Today, with new technology and some clever archaeological detective work, plants are no longer so invisible. Some Neandertals did cook and eat grains. Others relied on the starchy underground storage organs of plants like water lilies. They toasted pine nuts and lentils and ate dates. Some of this revolution in understanding Neandertal diet has come from microscopic remains of plant starches and phytoliths within layers of calcified plaque on their teeth, called calculus. Some has come from microscopic or biochemical examination of sediments within archaeological sites.

Now, ancient DNA from dental calculus is joining the party. I’ve heard some experts are skeptical of these new results. So what do they say and what are the weaknesses that we should know about?

Neandertal oral microbiome

Probably the main aim of the study was to characterize the bacterial oral microbiome of the Neandertals. Calculus includes genetic material from the bacteria that live in the mouth, and setting aside contamination, this bacterial signal makes up the vast majority of the DNA reads from the ancient specimens. Weyrich and colleagues found that the bacterial communities in the mouths of Neandertals were most similar to the African hunter-gatherers that they sampled. The single wild chimpanzee that they sampled also had a similar oral microbiome by this assessment. All these “wild” food eaters show a very different bacterial composition than the humans in the sample, both ancient and modern, who eat agricultural diets.

The paper includes the whole-genome sequencing of a species of archaea within the calculus of the sample from El Sidrón 1. As this specimen lived around 48,000 years ago, they call it the “oldest microbial draft genome” yet assembled.

Date estimates using a strict molecular clock place the divergence between the M. oralis strains of Neanderthals and modern humans between 112–143 ka (95% highest posterior density interval; mean date of 126 ka) (Fig. 3b; see Supplementary Information). As this is long after the genomic divergence of Neanderthals and modern humans (450–750 ka), it appears that commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East.

This is fascinating if true. The claim is that an African-derived oral commensal species colonized the mouths of Neandertals in the Near East sometime after 126,000 years ago, then was carried to the furthest reaches of western Europe through sparse Neandertal populations, ending up in a Spanish Neandertal some 48,000 years ago.

Earlier studies have pointed to evidence of possible exchanges of human pathogens or parasites among archaic human populations or species. Maybe the most notable is the evidence of louse transfer. Last year it was suggested that human papillomavirus had been exchanged from Neandertals into modern human populations (“Today’s genital warts came from trysts between Neanderthals and Homo sapiens). Weyrich and colleagues are the first to document a possible exchange of a microbial species using ancient DNA evidence.

Still, before accepting this conclusion, we need to have greater confidence in the divergence time of these microbial strains as estimated from their DNA. Assembly of more microbial genomes from the Neandertals might yield a lot more information about such interactions.

These are examples of the cool stuff in the paper. A metagenomic library has many dimensions of variation to explore, and the paper can only summarize many of them.

Neandertal food DNA

The one part that got a lot of news coverage was the idea of “vegetarian” Neandertals.

This part of the study reflects a very small fraction of the DNA recovered from the calculus, the reads that map to some eukaryotic (as opposed to bacterial or archaean) genome. To get an idea how small a dataset this is, the shotgun sequencing of the Spy 2 individual yielded more than 17 million sequence reads, after filtering out more than 80% as probable contaminants. Only 532 of these reads mapped to possible eukaryotic dietary sources.

But of those 532 reads, 62% mapped to sheep and 34% to rhinoceros. That’s a pretty suggestive result, particularly when combined with the archaeology of the site, which includes sheep and woolly rhinoceros bones.

Of course, the presence of these other bones in the site itself prompts a question. Could the evidence of DNA from these species actually reflect ancient environmental contamination from within the sediment of the site? That’s a very hard hypothesis to test, since the site was excavated more than a hundred years ago. Although Weyrich and colleagues took precautions against including DNA from the surface of the calculus samples, the study cannot rule out the possibility of DNA uptake from ancient sources.

The Spy 2 calculus sample also contained DNA that maps to the genome of the grey shag mushroom, an edible species.

Grey shag mushrooms. Andreas Geminder CC-BY-NC-SA 3.0.

Weyrich and colleagues found that the calculus of the Spy 1 Neandertal was dominated by contaminating modern DNA sequence, so conclusions about diet from eukaryotic sequence reads are really not warranted.

Calculus samples from both the El Sidrón individuals contained DNA that maps to pine trees. The El Sidrón 1 calculus sample had a greater diversity of eukaryotic DNA, including sequences mapping to the split gill mushroom, poplar tree, and a species of moss.

The presence of such species, plus the lack of non-human mammalian DNA in the El Sidrón samples, gave rise to the “vegetarian Neandertal” idea in the press. That’s a vast overstatement of the data, since any one of these individuals would have had a diet including scores of eukaryotic species, even though only a tiny number were recovered from their calculus. Calculus data cannot document dietary breadth or the average diet, it can only document a few of the species that were eaten or were otherwise processed in the mouth. We already know from previous microscopic analysis of Spy and El Sidrón calculus samples (Henry et al. 2011, Hardy et al. 2013) that both sets of Neandertals had consumed starchy plant foods, as evidenced by abundant starch granules. These starchy plants are not present in the DNA data. So the ancient DNA in calculus is providing additional data that does not necessarily duplicate what is visibly present as microfossils.

The moss is interesting. Laura Buck and Chris Stringer (2014) suggested that one way Neandertals might have gotten plant foods into their diet is by eating the stomach contents of their prey animals. This is a practice in some recent hunter-gatherer groups living in Arctic or extreme northern environments. Poplar bark might also have gotten into the diet in this way.

Weyrich and colleagues speculate that the poplar bark may instead be further evidence of the use of medicinal plants by Neandertals:

Our findings support previous suggestions that El Sidrón 1 may have been self-medicating a dental abscess. This was the only individual whose calculus included sequences corresponding to poplar, which contains the natural pain-killer salicylic acid (the active ingredient in aspirin), and also notably contained sequences of the natural antibiotic producing Penicillium from the moulded herbaceous material. The sample from this individual also included sequences matching the intracellular eukaryotic pathogen microsporidia (Enterocytozoon bieneusi), which causes acute diarrhoea in humans, indicating another health issue that potentially required self-medication.

Another possibility is that the Neandertals were making artifacts or picking their teeth with poplar wood. The authors attribute the presence of pine DNA to consumption of pine nuts; charred pine nuts have been found at other archaeological sites. It’s also conceivable that the Neandertals were orally processing artifacts that involved pine wood or tar. Radini and colleagues (2016) last year reported finding fibers and compounds within the calculus of El Sidrón Neandertals compatible with conifer wood, and suggested this was non-dietary processing of wood for utilitarian purposes. The DNA traces may be tracking the same activity.

Teeth were tools, too. Photo: Stanley Zimny CC-BY-NC 2.0

Reasons for caution

I’ve seen some skepticism expressed about this study in my social networks. It is important to consider the limitations of this kind of work.

The eukaryotic data represent only a very small fraction of the sequence reads within the filtered datasets. This raises the possibility that a small fraction of contaminating sequence might generate such results. These are not singular reads. There are 23 reads mapping to split gill mushroom within the El Sidrón 1 calculus sample, for example. But it will take some careful comparisons to see whether they might be explained by other sources than dietary mushrooms.

There are two particular issues that should lend caution to the dietary interpretations. One issue is represented well by the sequence hits for DNA from a tick species (Ixodes scapularis) in the living human calculus sample that was newly examined in this study. Weyrich and colleagues aver that this individual was probably not eating ticks. Instead, this tick species’ draft genome likely incorporates contaminating human DNA reads which have been wrongly assembled together with the tick’s own DNA. It’s also possible that the tick genome draft mistakenly includes microbial DNA from the tick’s own microbiome. Such incorporation of contaminating DNA into genome drafts is a surprisingly common problem in genomes that are available in databases today; there has been a lot of sloppy genome assembly, particularly for arthropod genomes. The authors filtered their data against known human sequence contaminants within such genomes, but they did not rule out all such effects (as evidenced by the tick).

The second issue that concerns me is that nobody has yet sequenced the genomes of many potential food species of Neanderthals (and recent human hunter-gatherers). A short read that maps to split-gill mushrooms may indeed be from that species, but it is possible that relatives of this species, even quite distantly related, might actually be the source of the DNA. They just haven’t been included in databases yet.

It’s not likely that DNA from a bison will map to a mushroom. But many unmapped reads within the calculus data may represent species that haven’t yet been studied at the whole-genome level. As more and more potential food species are added to genome datasets, they may yield more (or better) hits from these same sequence reads.

Setting aside these issues of sequence data quality, for me the biggest reason for caution is our lack of actualistic data on calculus uptake of dietary DNA. The study provides no indication of how DNA trapped in the calculus of living people reflects their diets. We don’t know whether some kinds of foods are more likely to be taken up than others, whether foods are representative of certain times (when calculus is more likely to calcify, for instance) or whether some food sources are more durable in their DNA preservation within calculus (for example, woody tissues). We do know that trace microfossils that are present in some calculus samples represent species with no DNA evidenced in other calculus samples from the same individuals. So there’s a lot of information loss here.

What I’d like to see is a lot more work on living people with varied diets. Track what they eat, and see what species show up in their calculus. Of course, that’s tricky within populations that tend to remove calculus from their teeth by dentistry. Every biological comparison between living people and ancient people has to face the many differences in lifestyles that have emerged over the years, and calculus formation has a lot of variation among populations.

Bottom line

Of course, all kinds of calculus research, including previous studies that have shown plant consumption and cooking in Neandertals (e.g., Henry et al. 2011), face the limitation that calculus does not sample dietary breadth. What remains in a single calculus sample is only a tiny subset of the dietary behavior of any species. A sample may demonstrate some of the dietary lifeways of past peoples, but it is helpful to have other sources of evidence as well.

When it comes to total diet composition, the best evidence we have right now is for the Spy Neandertals. Last year, Naito and colleagues (2016) looked at isotopic evidence for diet in the Spy Neandertals, using an approach that considers the stable isotope contribution of individual amino acids within proteins. This finer-scale consideration of the sources of dietary protein was consistent with up to 20% of the protein composition of these individuals’ diet coming from plants. As Naito and coauthors point out, plants are much lower in protein composition than meat, so the total dietary fraction made up by plant sources would likely have been higher. That puts the Spy individuals into the range of modern human hunter-gatherer peoples at lower latitudes.

Different Neandertal groups had different dietary compositions, as reflected by microwear evidence from the teeth (El Zaatari et al. 2011). That means that the El Sidrón Neandertals really may have had a higher intake of plants than the Spy Neandertals, although isotopic results that would point in that direction are not yet available. I wouldn’t expect that any of them were vegetarians. The El Sidrón skeletal remains are thought themselves to be the result of cannibalism, and recent work on the El Sidrón microwear suggests a mixed diet (Estalrrich et al. 2017).

But what’s clear is that the overall plant use by Neandertals is much greater than anthropologists believed 10 years ago.


Buck, L. T., & Stringer, C. B. (2014). Having the stomach for it: a contribution to Neanderthal diets?. Quaternary Science Reviews, 96, 161-167.

El Zaatari, S., Grine, F. E., Ungar, P. S., & Hublin, J. J. (2011). Ecogeographic variation in Neandertal dietary habits: evidence from occlusal molar microwear texture analysis. Journal of Human Evolution, 61(4), 411-424.

Estalrrich, A., El Zaatari, S., & Rosas, A. (2017). Dietary reconstruction of the El Sidrón Neandertal familial group (Spain) in the context of other Neandertal and modern hunter-gatherer groups. A molar microwear texture analysis. Journal of Human Evolution, 104, 13-22.

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Charles Darwin, in Descent of Man (1871) pp. 51–52:

It has often been said that no animal uses any tool; but the chimpanzee in a state of nature cracks a native fruit, somewhat like a walnut, with a stone. Rengger easily taught an American monkey thus to break open hard palm-nuts, and afterwards of its own accord it used stones to open other kinds of nuts, as well as boxes. It thus also removed the soft rind of fruit that had a disagreeable flavour. Another monkey was taught to open the lid of a large box with a stick, and afterwards it used the stick as a lever to move heavy bodies; and I have myself seen a young orang put a stick into a crevice, slip his hand to the other end, and use it in the proper manner as a lever. In the cases just mentioned stones and sticks were employed as implements; but they are likewise used as weapons. Brehm states, on the authority of the well-known traveller Schimper, that in Abyssinia when the baboons belonging to one species (C. gelada) descend in troops from the mountains to plunder the fields, they sometimes encounter troops of another species (C. hamadryas), and then a fight ensues.The Geladas roll down great stones, which the Hamadryas try to avoid, and then both species, making a great uproar, rush furiously against each other. Brehm, when accompanying the Duke of Coburg-Gotha, aided in an attack with fire-arms on a troop of baboons in the pass of Mensa in Abyssinia. The baboons in return rolled so many stones down the mountain, some as large as a man's head, that the attackers had to beat a hasty retreat; and the pass was actually for a time closed against the caravan. It deserves notice that these baboons thus acted in concert. Mr. Wallace on three occasions saw female orangs, accompanied by their young, "breaking off branches and the great spiny fruit of the Durian tree, with every appearance of rage; causing such a shower of missiles as effectually kept us from approaching too near the tree."

This is a really well-known passage. I’m sure that I’ve missed a great deal of commentary on it, but I took a look through 1960s and 1970s literature on tool use in chimpanzees and didn’t see any references to Darwin’s views on the matter.