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paleoanthropology, genetics and evolution

Photo Credit: Hand remains of Homo naledi. John Hawks CC-BY 2.0

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.

References

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.

Hardy, K., Buckley, S., Collins, M. J., Estalrrich, A., Brothwell, D., Copeland, L., ... & Huguet, R. (2012). Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus. Naturwissenschaften, 99(8), 617-626.

Henry, A. G., Brooks, A. S., & Piperno, D. R. (2011). Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium). Proceedings of the National Academy of Sciences, 108(2), 486-491.

Naito, Y. I., Chikaraishi, Y., Drucker, D. G., Ohkouchi, N., Semal, P., Wißing, C., & Bocherens, H. (2016). Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen. Journal of human evolution, 93, 82-90. doi:10.1016/j.jhevol.2016.01.009

Radini, A., Buckley, S., Rosas, A., Estalrrich, A., de la Rasilla, M., & Hardy, K. (2016). Neanderthals, trees and dental calculus: new evidence from El Sidrón. Antiquity, 90(350), 290-301. doi:10.15184/aqy.2016.21

Weyrich, L. S., Duchene, S., Soubrier, J., Arriola, L., Llamas, B., Breen, J., ... & Farrell, M. (2017). Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. doi:10.1038/nature21674


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.


Ernst Mayr (1951):

It is very probable that additional finds will make the delimitation of sapiens against Neanderthal even more difficult. It seems best to follow Dobzhansky's suggestion and to consider the two forms, as well as the ancestral group that seems to combine their characters, as a single species.

Reference

Mayr, E. (1950). Taxonomic categories in fossil hominids. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 15, pp. 109-118). Cold Spring Harbor Laboratory Press.


The New York Times Magazine has just published a feature article by Jon Mooalem detailing his visit to the excavations at Gorham’s and Vanguard Caves in Gibraltar, and how they are informing new perspectives on Neandertal behavior: “Neanderthals Were People, Too”

There is a worldview, the opposite of Joachim Neander’s, that sees our planet as a product of only tumult and indifference. In such a world, it’s possible for an entire species to be ground into extinction by forces beyond its control and then, 40,000 years later, be dug up and made to endure an additional century and a half of bad luck and abuse.
That’s what happened to the Neanderthals. And it’s what we did to them. But recently, after we’d snickered over their skulls for so long, it stopped being clear who the boneheads were.

Mooalem combines some good description of the work at the archaeological sites with some perspective on the history of how scientists have looked at Neandertals. It covers many of the essentials (Boule, Solecki) without seeming stale. It would be a good article for introductory classes in anthropology.

And it features some of my favorite people!

Let’s make replicability a priority in human evolution research

Research on human evolution may have the worst history of data access for any field of science funded by the National Science Foundation. NSF has spent millions of dollars over the last twenty years on results that cannot be replicated. This is bad science.

I have been proud to have NSF select me to review a number of proposals over the years. But I am frustrated that my comments on proposals pointing to problems with data access plans have had no visible effects. Those of us who review proposals should use our reviews to turn around the trend of bad data access.

Before going further, I want to say that I recognize the hard work of NSF program officers and panels. Many of the field projects currently funded by NSF in biological anthropology and archaeology have established data access policies that allow independent scientists to see and replicate results. NSF has additionally directed funding toward databases, like MorphoSource, that allow researchers to archive data and share it with other researchers or the public. That’s good science.

With many scientists doing a good job, and every proposal now requiring a data access plan, it is frustrating to see some projects providing only lip service to data access.

Some research groups have resorted to chicanery. One project was funded to provide a database for all vertebrate specimens recovered at their field site, complete with scaled photographs. But hominin fossil material was accompanied only by tiny unscaled thumbnail images.

One project became notorious for publishing research in which standard measurements were noted as “present” or “absent” instead of providing the measurement values. All while acknowledging NSF funding.

Such examples are childish. Let’s stop funding projects that fail basic data reporting. We won’t be losing anything valuable. We’ll be gaining the opportunity to fund work that others can build upon.

Of course many anthropologists collect data within countries where government policy may restrict the open dissemination of original data. Some may say it would be unfair for NSF to discriminate against applicants who work in these circumstances.

But asking for basic reporting is not discrimination. NSF-funded researchers should facilitate reasonable access to their data. That doesn’t have to mean open access to the public. Good science demands the potential of replication, with data responsibly archived and clear instructions on how bona fide researchers can obtain permission to replicate results.

Recently I have heard that certain researchers permit other scholars to examine original fossil material, collected using NSF funds, only after they sit with casts before them and agree in advance upon the conclusions they will reach. If this practice is actually happening, it has to stop.

Fossils are national and world heritage objects, and access to these treasures is a privilege. Access to U.S. public funding is also a privilege, one that in today’s budget environment only a tiny minority of scholars will ever attain. I have been honored over the years to serve NSF in reviewing proposals, though I have never received funding myself. Like many, I volunteer sharing the hope that funding will be directed toward the best projects with the broadest impacts on the science. That cannot happen if data access is arbitrary, used to reward friends and punish enemies, only allowed when conclusions are preordained.

I call upon panelists and reviewers in this funding cycle to make data access a priority when you review research proposals. When you see a proposal with a strong data access plan and a record of demonstrable success, fund it. When you see a proposal from researchers with poor track records of data access, please just say no.

U.S. federal funding for human evolution research is precarious and could be taken away at any time. We can best sustain it by showing that we are serious about promoting the best, most replicable science.

I published this essay previously on Facebook.

New footprints from Laetoli and improving the science of fossil context

I’m jazzed this morning because eLife has published a paper by Fidelis Masao and colleagues describing new footprint trails from the famous site of Laetoli, Tanzania: “New footprints from Laetoli (Tanzania) provide evidence for marked body size variation in early hominins”.

The scientific theme of the paper is about body size and dimorphism. The species presumed to have made all the trackways is Australopithecus afarensis, the only species that has so far been reported from fossil remains at Laetoli, although the tracks at 3.66 million years old are a bit more ancient than any of the fossils. This is the same species as the Lucy skeleton, which was found at Hadar, Ethiopia, and the “First Family” series of fossils from Hadar in the locality known as A.L. 333. In 2010, Yohannes Haile-Selassie and colleagues reported a partial skeleton from Woranso-Mille, Ethiopia, some 3.6 million years old, which also seems to represent a large male individual, that stood just under 160 cm tall. Based on a regression of foot size to stature, the new footprint trail in test pit L8 represents an individual that probably stood around 165 cm, with 10 cm or so error either way.

Here’s a neat graphic showing stature estimates for early hominins up through early H. erectus:

Stature estimates for early hominins from Masao et al. 2016
Figure 12 from Masao et al. 2016. Original caption: "Estimates of predicted stature of fossil hominin individuals by species over time for the interval 4–1 Ma. Solid symbols (or crosses in bold) refer to stature estimates based on actual femur length; open symbols refer to stature estimates based on estimated femur length, in turn based on femur head diameter. For Laetoli and Ileret, stature estimates are based on footprint length (see Materials and methods). For Laetoli, Ileret and Woranso-Mille, the average value and range of predicted stature are shown. Colours are associated to the geographical location of each fossil/ footprint site on the map."

That’s a bit complicated but the point is pretty clear. A. afarensis overlaps with H. erectus substantially in stature. If we consider only the tiny Lucy skeleton (the lowest “x” in the figure at less than 110 cm), we get a misleading view of body size in this early hominin species. But at the same time, Lucy and some other specimens of A. afarensis really are quite a lot smaller than any H. erectus specimens. The conclusion made by Masao and colleagues, applying some statistics, is that A. afarensis was more variable and sexually dimorphic than humans and H. erectus.

This idea of higher dimorphism in early hominins has been the subject of pointed debate over the past fifteen years, a debate that has been driven by insufficient fossil data. One group of authors has, through the use of increasingly complicated statistical games, tried to show that a tiny sample of fossils are not really as variable as they look to the eye.

These new data don’t revolutionize the question, they just move the ball downfield slightly. Adding a few more data points, even very large individuals, doesn’t vastly narrow the confidence limits on second- and higher moments of a size distribution. But what these footprints should remind us is that discovering new fossils is a lot more valuable than statistical games. With that in mind, I think we should also be skeptical about whether these footprints were really produced by A. afarensis. That species already has problems at Hadar and at Woranso-Mille, where some researchers now recognize multiple species are present. At Laetoli, we should probably apply a level of skepticism to the idea that only one fossil species could be present.

As I was reading this new paper, what struck me was that the authors had some difficulty being certain that the new footprints represent the same “Footprint Tuff” in which the older track G hominin footprints were found back in the 1970s. They found that the original scientists involved in describing the footprints, including Tim White, Mary Leakey, and Richard Hay, had been very thorough in describing the footprints themselves and some aspects of the geological setting. But those original descriptions just did not present sufficient detail about some geological aspects essential to recognizing the geological layers in the field setting. There were no published photographs of the stratigraphic sequence, for example, and no description of the color or “eye-scale characteristics” of the tuffs. Without such details, it is difficult to do replicable work on new aspects of the geology. That is, the level of detail sufficient to publish fossils in the 1980s does not meet the basic needs of scientists today. We need better descriptions of the context of fossils, and we need to know when those fossils are really in situ like these footprints.

We have come a long way in understanding aspects of microstratigraphy and taphonomy, and we have come to demand greater contextual detail in addition to the basic description of fossils. You can see that shift manifested in this paper by Masao and colleagues, which includes clear field descriptions of all the geological units they encountered.

Figure 3 from Masao and colleagues 2016
Figure 3 from Masao and colleagues (2016), illustrating footprint trail L8 with an elevation map applied.

What we demand in descriptions today is also much more detailed than forty years ago. Then, it was sufficient to publish line drawings of footprints, with a few topographic views. But even then, researchers recognized that publications didn’t provide all the detail that was necessary to really evaluate the science. So they made casts available to allow other researchers to compare the evidence. Of course we all know that some scientists have stopped exercising such care, but for the rest of us, we place higher demands on the evidence we’re willing to accept.

Today, we can make three-dimensional models available instantly. So in addition to the different modes of visualization used in the research paper, Masao and colleagues have placed research-grade models of the footprint trails on Morphosource for anyone to download. That’s the same mechanism we used to distribute 3D surface models of the Homo naledi discovery, and it is great to see more and more scientists taking advantage of the opportunity to increase the replicability and quality of their science in this way.

It’s just really exciting to see researchers around the world engaging with new discoveries like this, getting them out to the public in open access journals, and building the global support for our science.

References

Masao F, Ichumbaki EB, Cherin M, Barili A, Boschian G, Iurino DA, Menconero S, Moggi-Cecchi J, Manzi G. 2016. New footprints from Laetoli (Tanzania) provide evidence for marked body size variation in early hominins. eLife 2016;5:e19568. doi:10.7554/eLife.19568

Jungers WL. 2016. Paleontology: These feet were made for walking. eLife 2016;5:e22886. doi:10.7554/eLife.22886

Haile-Selassie, Y., Latimer, B. M., Alene, M., Deino, A. L., Gibert, L., Melillo, S. M., ... & Lovejoy, C. O. (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. Proceedings of the National Academy of Sciences, 107(27), 12121-12126.

Link: A deep dive into Cahokia

Annalee Newitz has a detailed and fascinating story in Ars Technica about the Cahokia site, on the Illinois side of the Mississippi River from St. Louis: “Finding North America’s lost medieval city”.

At the city's apex in 1100, the population exploded to as many as 30 thousand people. It was the largest pre-Columbian city in North America, bigger than London or Paris at the time. Its colorful wooden homes and monuments rose along the eastern side of the Mississippi, eventually spreading across the river to St. Louis. One particularly magnificent structure, known today as Monk’s Mound, marked the center of downtown. It towered 30 meters over an enormous central plaza and had three dramatic ascending levels, each covered in ceremonial buildings. Standing on the highest level, a person speaking loudly could be heard all the way across the Grand Plaza below. Flanking Monk’s Mound to the west was a circle of tall wooden poles, dubbed Woodhenge, that marked the solstices.
Despite its greatness, the city’s name has been lost to time. Its culture is known simply as Mississippian. When Europeans explored Illinois in the 17th century, the city had been abandoned for hundreds of years. At that time, the region was inhabited by the Cahokia, a tribe from the Illinois Confederation. Europeans decided to name the ancient city after them, despite the fact that the Cahokia themselves claimed no connection to it.

She reports from the scene where she participated in some archaeological work, including some of my favorite bits: digging in the houses and structures used by ordinary people, on the outskirts of the monumental area.

Link: A consideration of religion and Neandertals

Barbara King asks, “Were Neanderthals religious?”

Given their intelligence, it seems to me likely that the Neanderthals contemplated, in some way, the mysteries of life. Wouldn't they have wondered not only about unexpected and surprising weather events and sky events but also what happens when our lives comes to an end? If they thought about these questions, did they do so with awe, dread or reverence?

I provided a quote for the piece, which discusses what kinds of evidence archaeologists consider. I have come to recognize that the recognition of mortality and cultural practices associated with death may be among the deepest behavioral aspects of human evolutionary history.

Third molar agenesis: a puzzling case of recent human evolution

One of the most obvious cases of recent human evolution is the increasing frequency with which individuals don’t develop third molars, what is called “M3 agenesis”. This condition is when the third molars, or wisdom teeth, don’t form at all – the individual never developed them.

I could be wrong, and I’m sure that a reader will remind me if I am, but I cannot think of an instance of M3 agenesis in hominins outside of modern humans. It was entirely typical for most hominins throughout our evolutionary history to develop and erupt third molars into normal occlusion.

Agenesis of the third molars is different from cases where the M3 fails to erupt normally or remains impacted within the jaw. It is also different from the dental or surgical removal of third molars, which is now carried out on a very high proportion of people in the United States and many other countries. The number of students in my courses at the University of Wisconsin that still have their third molars is pretty small, generally less than 20 percent and often less than 10 percent. The majority of third molar removal is for orthodontic purposes. When third molars erupt, they exert forces on the rest of the teeth that can cause crowding and malocclusion, and more rarely, severe pain. One of the easiest ways to maintain straight teeth is to pull the ones in the back.

The problems with crowding of the anterior teeth points to the reason that anthropologists have traditionally given for the change toward a higher incidence of agenesis. Our Pleistocene ancestors very rarely had malocclusions due to dental crowding. The development of our jaws and teeth evolved within a context where people lived hunter-gatherer lifestyles and ate fairly tough foods, even as young children. By contrast, crowding of the dentition and resulting malocclusion have been very common in many Holocene populations, mostly those with agricultural subsistence. Agriculturalists don’t eat as many tough foods; they eat a large fraction of cooked grains and easy-to-chew cooked plants, milk, and meats. The idea is that the development of the jaw is plastic, and a reduction of the forces exerted on the dentition during early childhood can alter the developmental trajectory of the mandible and maxilla. If the jaws don’t develop as to as large an adult size, the teeth will tend to be crowded, and the last teeth to initiate development, the third molars, may not form at all.

This is an elegant story in some ways, but in fact we don’t know whether it’s true.

We do know that the teeth develop from an embryonic tissue sheet, which is divided into segments by genes during early development. Those segments expand and wrinkle into the form of tooth germs in a characteristic pattern, which is retained across most mammal orders, although many of the orders have come to have different numbers of teeth, which result from evolution of this early developmental pattern. Within a species, if an individual ends up with a segment that is too small or doesn’t develop quite right, that tooth will not form. The most common change is to the extreme tooth, which is the third molar. Less commonly, individual teeth within the other types may fail to develop – P4 agenesis is fairly frequent, sometimes I2 agenesis. Some of these kinds of agenesis are syndromic, meaning that other biological traits covary strongly with them.

How jaw forces might influence the pattern of tooth development is not well understood. Nor is it well understood how heritable M3 agenesis may be – to the extent it seems to run in families, this might reflect similar environments or similar genetics.

We do know quite a bit about the incidence of M3 agenesis in different human populations. The trait is nearly universal – it occurs everywhere in large enough samples of people, even in hunter-gatherer peoples who have recently continued eating “wild” food diets. But it differs greatly in frequencies.

Carter and Worthington (2015) did a meta-analysis of studies that have estimated M3 agenesis frequencies in particular human populations. By looking at 92 studies in different regions of the world, they give a global picture of where humans are more or less likely to have agenesis of the third molars. They limited their analysis to include studies of living human populations with radiographic evidence, so the agenesis was clearly documented.

Here’s the picture summarizing the frequencies in different regions:

Studies showing M3 agenesis frequencies
Figure 3 from Carter and Worthington (2015). Original caption: "Bean plot of the proportion of individuals with agenesis of at least 1 third molar, partitioned by geographic provenience (92 studies, 100 effect sizes). Solid diamonds and error bars denote the means (inverse variance weighted) and 95% confidence intervals (CIs) of proportions for each region. Dark gray circles are individual studies, while light gray polygons are kernel density estimates of the distribution of proportions within each region. Analysis was performed on logit-transformed proportions, but means and 95% CIs are back-transformed for easier interpretation. LRT, likelihood ratio test."

The incidence of M3 agenesis is lowest in African populations today. This chart represents only two studies in Africans, but the observation of a very low frequency of M3 agenesis is in accord with studies of skeletal samples in my experience. Other populations have a higher frequency, although the study does not include any populations indigenous to Australia, New Guinea or the nearby areas of Melanesia, which in my experience also have low frequencies of M3 agenesis. Some of the highest population frequencies are observed in Asia; these are sampled broadly, including one sample from South India, several studies of Japanese, Turkish, Israeli and Iraqi. So it’s not specifically East Asian, but more broadly some population samples across the continent.

The most common M3 agenesis is a single missing third molar, and that is what is illustrated in the chart. It is less common to be missing two molars, and very uncommon to be missing three or all four of them. Women are slightly more likely to be missing an M3 than men (Carter and Worthington found a 14 percent greater likelihood in women).

I know that many anthropologists lecture about M3 agenesis as a recent evolutionary change, but it is a complicated one. Few look deeply into the pattern, which is strongly parallel across many human populations, not regionalized. In a broad sense, the frequencies of M3 agenesis across populations covary with molar sizes, and it may simply be that the evolution of smaller tooth size has M3 agenesis as a frequent side effect. The greater incidence of agenesis in women also might be expected as a correlate of smaller molar sizes.

There is no evidence that M3 agenesis is itself an adaptation that has been favored by natural or sexual selection. The possibility of sexual selection presents itself in this context because of the possible effects of a crowded dentition on mating preferences in past populations. But if M3 agenesis owes its recent high frequency to selection, it is likely as a side effect of selection for smaller teeth. However, even that is hardly so simple, as the pattern of size reduction in teeth was not uniform in Holocene populations, and the frequencies of M3 agenesis fluctuate substantially among studies.

And we do not know how much of M3 agenesis may be explained by plasticity of development within current environments. Some studies show a difference within a geographic sample between people who have originated from different immigrant populations (for example, in Singapore between people of Chinese, Malay, and Indian ethnicity), but none have really evaluated the frequencies in second-generation and third-generation immigrants. The genetics of the trait, even heritability, is basically an open question. Of course, if it were entirely explained by environment, M3 agenesis would not be an example of evolutionary change at all.

So M3 agenesis is a fascinating example of recent biological change in human populations, and we know very little about how and why it has changed.

Reference

Carter, K., & Worthington, S. (2015). Morphologic and Demographic Predictors of Third Molar Agenesis A Systematic Review and Meta-analysis. Journal of dental research, 94(7), 886-894. doi:10.1177/0022034515581644


Just a note that ducks provide many great examples of hybridization dynamics, particularly invasive ducks. This recent paper on geese by Jente Ottenburghs and colleagues (“Hybridization in geese: a review”) shows that they are much the same. Lots of geese species, lots of hybridization, including cross-generic hybridization.

Most hybrid geese are fertile; only in crosses between distantly related species do female hybrids become sterile. This fertility pattern, which is in line with Haldane’s Rule, may facilitate interspecific gene flow between closely related species. The knowledge on hybrid geese should be used, in combination with the information available on hybridization in ducks, to study the process of avian speciation.

Travis Pickering and colleagues have a paper presenting new teeth from Swartkrans, which they attribute to Paranthropus robustus: “New early Pleistocene hominin teeth from the Swartkrans Formation, South Africa”. I’m pointing to the paper because it has a long and clear review of the complex history of site formation in this ancient cave.

Neandertal anti-defamation files, 22

This, from ScienceAlert:

We caught modern genital warts because our ancestors were banging Neanderthals

Nothing like this story as been such a race to the bottom for headlines for a long time.

I will note that Annalee Newitz has a much better version of the story with this winning quote:

[A]lways practice safer sex, even if you're getting down with a Denisovan.

There is, by the way, the interesting question of whether Neandertal immune variants might influence susceptibility to the strain in question, which has made little inroad into sub-Saharan Africa.

Race and the medical student

Ike Swetlitz in Stat has an article about the ways that some medical educators are trying to build a more anthropological knowledge of race and health in their students: “Teaching medical students to challenge ‘unscientific’ racial categories”. Unfortunately both the headline and article get a bit snarled in their use of language. Maybe that’s inevitable.

“You see ‘African American,’ automatically just circle ‘sickle cell,’” said Nermine Abdelwahab, a first-year student at the University of Minnesota Medical School, recounting tips she’s heard from older classmates describing the “sad reality” of the tests.
Medical school curricula traditionally leave little room for nuanced discussions about the impact of race and racism on health, physicians and sociologists say. Instead, students learn to see race as a diagnostic shortcut, as lectures, textbooks, and scientific journal articles divide patients by racial categories, reinforcing the idea that race is biological. That mind-set can lead to misdiagnoses, such as treating sickle cell anemia as a largely “black” disease.

In an episode of M*A*S*H from the early 1980s, Corporal Klinger starts suffering from a rare side effect of the anti-malarial drug primaquine. The doctors know that the drug has the potential of negative side effects in blacks, but issue it to everyone else. Hawkeye and the other doctors assume Klinger is just goldbricking. But another soldier, Private Goldman, starts to exhibit the same symptoms. The doctors determine that both Klinger and Goldman are suffering anemia, and take them off the primaquine. At the end of the program, it is revealed that people of Levantine origin (like Klinger) and Ashkenazi Jews (like Goldman) also may have the same susceptibility to primaquine side effects owing to their ancestry.

The side effect in question is a breakdown of blood cells and consequent anemia in people with G6PD deficiency, which is indeed very common in sub-Saharan and North Africans, and less common but still notable in people of broader Mediterranean descent.

I like the program quite a lot, and I remember it from the first time it was broadcast. It is a well-scripted way illustration of how a physician can make erroneous assumptions about ancestry and genetics that lead to bad treatment. But it also goes to show that there’s very little new in today’s attempts to improve medical school training with respect to race and medicine. These are all ideas that were well-known more than forty years ago and have been staples of anthropology.

Of course today we can know from anyone’s genotype data whether they have a susceptibility to some adverse drug reactions, and that includes many that do not have much higher frequencies in one population or another. Whatever there is to be said for genotyping, it beats census categories if you are looking to diagnose most common traits influenced by Mendelian genes. If we are training medical students for the world of five or ten years from now, allowing them to make effective use of this information should be the priority.

Will virtual reality compete with museums or help them?

Linking to a provocative piece that “VR Will Break Museums”.

The article discusses many issues with museums both large and small. The best museums add context to the objects that they display, putting them into a story that builds knowledge in the museum-goer. But some concepts are incredibly difficult to communicate in that fashion, and others rely so much on place that removing objects to a museum does not convey their context accurately.

And the crowds suck. Nothing is better than a huge museum on a very empty day, and those don’t happen very often.

The problem is, museums don’t scale well. The British Museum sees almost 7 million visitors a year. What would it take to accommodate double that number? Ten times that number? It simply cannot be done, not for any reasonable amount of money.
The Internet, on the other hand, is built for scale. The marginal cost of an extra YouTube viewer or app download is practically zero. That’s how a video about the history of Japan can be made for free, distributed for free, and enjoyed for free by more people in a single month than who walk through the doors of the Louvre in an entire year.

Museums are a very important part of human evolution research, both by serving as repositories for the objects we study and for helping the public to understand the importance of our science. I’ve consulted with many museums over the years and have visited a large fraction of the major museums of natural history in the world.

Human genetics is more and more important to how we understand human evolution. Yet this is one of the most difficult parts of science to illustrate in a museum setting. Museums excel at visual material and unique objects. While it is possible to do video or virtual content for genetics, whenever I encounter videos at a museum, I groan. They’re always a chore and rarely hit the mark as well as simple text accompanying an object.

Honestly, I think that museums face much the same problem as movies. Studios invest tremendous sums of money in movies that have bad scripts. There are many reasons for this – sometimes the director has too much power and keeps shifting the script, sometimes the original idea relied upon visuals that cannot be realized, sometimes studio executives ruin a cohesive script by committee. Whatever is the case, the ultimate reason why this situation happens so often is the same: Audience demand for certain kinds of movies is just not very responsive to script quality.

Likewise, public visitation to certain museums doesn’t respond much to the quality of stories they can effectively tell. A museum exhibition with bad videos is regrettable, but most people skip the videos anyway. Especially if the first few seconds of the first one doesn’t connect.

The great thing about the idea of virtual experiences is that they may be laboratories for real innovation in storytelling. The stories that work should be translated into the museums that audiences already value. As someone who has done a lot of museum consulting, I can really imagine having a lot of fun helping make virtual experiences that educate and convey exciting science.

Incidental capuchin flake manufacture

This is a nice article by Ed Yong about Michael Haslam’s research documenting how capuchin monkeys incidentally make stone flakes as a side effect of their nut smashing: “Rock-Smashing Monkeys Unintentionally Make Sharp Stone Tools”.

The interesting thing is that many of the flakes are indistinguishable on technical grounds from Oldowan flakes. That raises the possibility that intermittent, possibly local traditions of nut-cracking among some forms of primates might create the appearance of localized flake assemblages.

He also thinks that archaeologists should spend more time looking for the works of ancient monkeys and apes. “[We should] consider what other non-human primates in Africa and elsewhere may have been up to for the past tens of millions of years,” he says. “There is no reason why stone flakes may not be littered throughout primate history, at unknown places and times.”

Actually, I think there is nothing materially different about what these capuchins are doing and what early hominins were doing when they made flakes. One may say that the hominins made flakes “intentionally”, or with a goal in mind to use the flake. But the difference here is not cognitive, it that the capuchins have not learned socially to use flakes for anything.

Primatologists already observe capuchin monkeys learning socially to lift rocks nearly half their body weight, thrust them down onto a platform with a fruit, and repeat this until yummy bits of nutmeat scatter everywhere. It would not take any great cognitive advance for them to learn how to use flakes, if there were something useful for them to do. The ability to generalize is simply the ability to emulate others.