endocast

A whisper to a scream

/ zcofran

Endocasts are the faint whispers of ancient minds. These fossilized phantoms are just about all we have to tell us about the evolutionary history of brains. We are (we are, we are) rather helpless—how can we turn a whisper to a scream?

A human brain (left) and its endocast (center), and a colormap showing distance between endocast and brain (right). Produced using data published by Balzeau and colleagues (2026) and the R package “Morpho” by Stefan Schlager .

Antoine Balzeau and colleagues have recently published an incredible resource for studying brain endocasts, which they aptly call the ‘Rosetta Stone for paleoneurology.’ This is the latest paper from their project PaleoBRAIN, which draws on advanced techniques for studying endocasts and reconstructing the brains of extinct hominins. A few years ago the group published an article led by Nicole Labra asking “What do brain endocasts tell us?”, where they demonstrated the extent to which experts in brain anatomy can nevertheless misidentify actual brain impressions on endocasts. This is a big deal since the identification of brain features, namely sulci separating specific parts of the cortex, is essential for understanding how the human brain has evolved over the past several millions of years. When looking at an endocast, are we really seeing the brain structures that we think we’re seeing?

Balzeau and colleagues make another major contribution to address this problem for paleoneurology. The researchers used advanced MRI brain scanning methods to directly compare the brains and bony endocasts of 75 living humans. They used software that automatically identifies brain sulci from MRI scans and then examined the extent to which each individual’s sulci (left image, above) were expressed on their endocast (center image, above). The study expands greatly on similar work by Jean Dumoncel and colleagues using a slightly different approach. As in the previous research, Balzeau and co found that the endocast can serve as a decent proxy for the underlying brain anatomy, but with some pretty big limitations.

One of the major differences the authors identified between brain and endocast is that whereas brain sulci are often like long valleys (for instance, the long, straight lateral sulcus separating the temporal and frontal/parietal lobes), the corresponding sulci on endocasts are usually much shorter: that is, less of the sulcus makes an impression. Worse, sulci are often broken up into separate segments on the endocast. This is important because if a sulcus isn’t fully preserved we may not know its true course or the spatial relationship between certain brain structures. Plus, if a sulcus is broken up on an endocast, we risk misidentifying the different segments as other, incorrect sulci.

Perhaps the most shocking and sobering observation is that endocasts may bear imprints that are completely unrelated to any actual brain sulci, which they term “MNAS” (marks not associated with sulci). What causes these impish impressions is unclear at this point, but it raises the harrowing possibility that we might identify and interpret fossilized impressions that didn’t actually exist in the brains of ancient animals. Fortunately, Balzeau and team found that MNASes tend to be located closer to the top of an endocast where the brain is not impressing as strongly, whereas true cerebral impressions are strongest in the lower regions of the endocast.

Along these lines, one cool result of the study is that the orbitofrontal sulci, from the part of the brain sitting directly above the eye sockets, were “the most visible impressions” and were observed in all 75 of the endocasts they studied. The orbitofrontal cortex is involved in regulating emotions and impulse control (reviewed in Rudebeck & Rich, 2018), so this part of the brain may have been very important for the evolution of human social behavior. The findings of Balzeau and colleagues suggests we may be able to study this region reliably in the human fossil record. A fossil called MLD 6, for example, is best known for being a beautiful Australopithecus face (well, the right part of it). Yet the fossil is also another overlooked endocast from Makapansgat, South Africa. Specifically, MLD 6 shows pronounced impressions of several of the orbitofrontal sulci, though it is admittedly only well preserved toward the middle.

The partial face and brain endocast of the fossil MLD 6. Views: Front view of the face (top left), face rendered transparent to show the mirror-imaged endocast (top right), right lateral view of the transparent face and endocast (bottom left), and inferior view of the mirror-imaged endocast (bottom right). The “H-shaped” impressions on either side are the medial and lateral orbital sulci connected by the transverse orbital sulcus.

The other major contribution of this paper by Balzeau and colleagues is that all of the data are publicly available (here), meaning that other researchers can validate and expand on this research. This is huge. Historically, most paleoneurologists would have to assess a fossil endocast by consulting an atlas of brain anatomy, which overlooks normal variability. If one were lucky, they could use publications documenting brains of more than one individual, such as the annotated chimpanzee brain images published by Dean Falk and colleagues. The normal variability in both brain morphology and endocranial preservations that Balzeau and co present in this study are great resources on their own. Making all the original data available, though, is a huge step toward putting all paleoneurologists on the same page.

References

Balzeau, A., Bardinet, É., Bardo, A., Bernat, A., Derrey, T., Didier, M., Filippo, A., Hui, J., Kubicka, A. M., Labra, N., Leprince, Y., Mangin, J., Mounier, A., Prima, S., Rivière, D., Santin, M. D., & Giolland, V. (2026). The ‘Rosetta Stone’ of palaeoneurology: A detailed study of the link between the brain and the endocast on 75 volunteers. Journal of Anatomy, joa.70101. https://doi.org/10.1111/joa.70101

Cofran, Z., Hurst, S., Beaudet, A., & Zipfel, B. (2023). An overlooked Australopithecus brain endocast from Makapansgat, South Africa. Journal of Human Evolution, 178, 103346. https://doi.org/10.1016/j.jhevol.2023.103346

Dart, R. A. (1949). The cranio‐facial fragment of Australopithecus prometheus. American Journal of Physical Anthropology, 7(2), 187–214. https://doi.org/10.1002/ajpa.1330070204

Dumoncel, J., Subsol, G., Durrleman, S., Bertrand, A., De Jager, E., Oettlé, A. C., Lockhat, Z., Suleman, F. E., & Beaudet, A. (2021). Are endocasts reliable proxies for brains? A 3D quantitative comparison of the extant human brain and endocast. Journal of Anatomy, 238(2), 480–488. https://doi.org/10.1111/joa.13318

Falk, D., Zollikofer, C. P. E., Ponce de León, M., Semendeferi, K., Alatorre Warren, J. L., & Hopkins, W. D. (2018). Identification of in vivo sulci on the external surface of eight adult chimpanzee brains: Implications for interpreting early hominin endocasts. Brain, Behavior and Evolution, 91(1), 45–58. https://doi.org/10.1159/000487248

Labra, N., Mounier, A., Leprince, Y., Rivière, D., Didier, M., Bardinet, E., Santin, M. D., Mangin, J. F., Filippo, A., Albessard‐Ball, L., Beaudet, A., Broadfield, D., Bruner, E., Carlson, K. J., Cofran, Z., Falk, D., Gilissen, E., Gómez‐Robles, A., Neubauer, S., … Balzeau, A. (2024). What do brain endocasts tell us? A comparative analysis of the accuracy of sulcal identification by experts and perspectives in palaeoanthropology. Journal of Anatomy, 244(2), 274–296. https://doi.org/10.1111/joa.13966

Rudebeck, P. H., & Rich, E. L. (2018). Orbitofrontal cortex. Current Biology, 28(18), R1083–R1088. https://doi.org/10.1016/j.cub.2018.07.018

Shilton, D., Breski, M., Dor, D., & Jablonka, E. (2020). Human social evolution: Self-domestication or self-control? Frontiers in Psychology, 11. https://doi.org/10.3389/fpsyg.2020.00134

The snail in your ear telling you about evolution

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The bony labyrinth combines two of my favorite things: skull cavities that tell us about living and extinct animals, and Jim Henson dark fantasy films. This ludicrous structure is nestled within each of the two temporal bones of the skull, filled with fluid surrounding the organs of balance and hearing.

Modified movie poster from the 1986 film Labyrinth. The word "Labyrinth" is scrawled fantastically across the top. Beneath, David Bowie playing Jareth the Goblin King holds out a crystal ball containing 5 bony labyrinths.
Bony labyrinths in roughly frontal view, semicircular canals branching toward the top, cochlea coiled beneath.

As former senator Ted Stevens once famously described the internet, the labyrinth is kind of like a series of tubes: namely the cochlear duct and three semicircular ducts, each housed within its own bony canal. These ducts (and canals) meet one another in the bony vestibule, where they’re interconnected with two “otolithic” organs called the utricle and saccule. Movement of fluid within these ducts (and otolithic structures) gets translated into signals that are then sent to the brain. The vestibular system including semicircular ducts and otolithic organs helps you detect your head and body’s movement through space (or as the world falls down), while the cochlear system translates waves of pressure hitting the ear into sound.

As noted by Christopher Smith (the scientist who studies the labyrinth, not the filmmaker who has directed the TV show Labyrinth), this elegant sensory system is present in all vertebrates, inherited from our common ancestor that lived over 500 million years ago. The structure is so important to individual survival that it seems to be fully formed before birth [1], surrounded by the densest bone in the body [2]. This snail in your ear therefore has a lot to say about life on Earth.

The labyrinth has been studied to trace the evolutionary origins of endothermy (warm-bloodedness) in mammals [3]. Because the size of semicircular ducts/canals correlates with sensitivity to head movements, it has been used to reconstruct how extinct primates moved around[4], including the earliest human ancestors to walk on two feet [5]. Because cochlea length and coiling correlates with hearing capacities [6], scientists can use the labyrinth to reconstruct what kinds of sounds extinct organisms could have heard [7]. Some studies have found the labyrinth to be sexually dimorphic in humans [8,9] (though this varies across different populations [10,11]), meaning that it could be used to estimate sex from archaeological or fossil remains, including of non-adults.

As David Bowie sang in the movie Labyrinth, “Down in the underground you’ll find someone true.” He could well have been singing about the bony labyrinth, a gift to paleontologists: a small, strange time capsule brimming with biological information.

References

1. Jeffery, N., & Spoor, F. (2004). Prenatal growth and development of the modern human labyrinth. Journal of Anatomy, 204(2), 71–92. https://doi.org/10.1111/j.1469-7580.2004.00250.x

2. Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., Anders, A., Pietrusewsky, M., Rollefson, G., Jovanovic, M., Trinhhoang, H., Bar-Oz, G., Oxenham, M., Matsumura, H., & Hofreiter, M. (2015). Optimal ancient dna yields from the inner ear part of the human petrous bone. PLOS ONE, 10(6), e0129102. https://doi.org/10.1371/journal.pone.0129102

3. Araújo, R., David, R., Benoit, J., Lungmus, J. K., Stoessel, A., Barrett, P. M., Maisano, J. A., Ekdale, E., Orliac, M., Luo, Z.-X., Martinelli, A. G., Hoffman, E. A., Sidor, C. A., Martins, R. M. S., Spoor, F., & Angielczyk, K. D. (2022). Inner ear biomechanics reveals a Late Triassic origin for mammalian endothermy. Nature, 607(7920), 726–731. https://doi.org/10.1038/s41586-022-04963-z

4. Ryan, T. M., Silcox, M. T., Walker, A., Mao, X., Begun, D. R., Benefit, B. R., Gingerich, P. D., Köhler, M., Kordos, L., McCrossin, M. L., Moyà-Solà, S., Sanders, W. J., Seiffert, E. R., Simons, E., Zalmout, I. S., & Spoor, F. (2012). Evolution of locomotion in Anthropoidea: The semicircular canal evidence. Proceedings of the Royal Society B: Biological Sciences, 279(1742), 3467–3475. https://doi.org/10.1098/rspb.2012.0939

5. Spoor, F., Wood, B., & Zonneveld, F. (1994). Implications of early hominid labyrinthine morphology for evolution of human bipedal locomotion. Nature, 369(6482), 645–648. https://doi.org/10.1038/369645a0

6. Manoussaki, D., Chadwick, R. S., Ketten, D. R., Arruda, J., Dimitriadis, E. K., & O’Malley, J. T. (2008). The influence of cochlear shape on low-frequency hearing. Proceedings of the National Academy of Sciences, 105(16), 6162–6166. https://doi.org/10.1073/pnas.0710037105

7. Coleman, M. N., & Boyer, D. M. (2012). Inner ear evolution in primates through the cenozoic: Implications for the evolution of hearing. The Anatomical Record, 295(4), 615–631. https://doi.org/10.1002/ar.22422

8. Osipov, B., Harvati, K., Nathena, D., Spanakis, K., Karantanas, A., & Kranioti, E. F. (2013). Sexual dimorphism of the bony labyrinth: A new age‐independent method. American Journal of Physical Anthropology, 151(2), 290–301. https://doi.org/10.1002/ajpa.22279

9. Braga, J., Samir, C., Risser, L., Dumoncel, J., Descouens, D., Thackeray, J. F., Balaresque, P., Oettlé, A., Loubes, J.-M., & Fradi, A. (2019). Cochlear shape reveals that the human organ of hearing is sex-typed from birth. Scientific Reports, 9(1), 10889. https://doi.org/10.1038/s41598-019-47433-9

10. Uhl, A., Karakostis, F. A., Wahl, J., & Harvati, K. (2020). A cross-population study of sexual dimorphism in the bony labyrinth. Archaeological and Anthropological Sciences, 12(7), 132. https://doi.org/10.1007/s12520-020-01046-w

11. Ward, D. L., Pomeroy, E., Schroeder, L., Viola, T. B., Silcox, M. T., & Stock, J. T. (2020). Can bony labyrinth dimensions predict biological sex in archaeological samples? Journal of Archaeological Science: Reports, 31, 102354. https://doi.org/10.1016/j.jasrep.2020.102354

New course: “Is the Human Brain Special?”

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For the first time in many years, I’m offering a new advanced undergrad seminar here at Vassar. When I arrived here 8 years ago, I was mainly thinking about Homo naledi and ontogeny, so those were the foci of my seminars. But my research has begun looking more at brain evolution and especially the evidence from fossil endocasts, and there is a lot of literature I need to catch up on.

So I’ve invited students along for this brainstorm, using the question “Is the human brain special?” as a starting point to learn about how the beautifully congealed soup sloshing around inside our skull makes us such quirky animals. In the first half of the semester we’ll read up on brain anatomy and structure, and students will use some of the fossil endocast data I’ve accrued over the years to learn more about a given brain region and extinct hominin. In the second half of the semester we’ll read about the brains, behavior, and endocast fossils of very distant relatives — invertebrates, birds, whales, and dogs — that have been celebrated for their own ‘advanced intelligence.’ We’ll also read about how the evolution of our brains may have predisposed us to certain conditions like addiction and Alzheimer’s, and how brain science has been exploited toward racist and sexist ends (increasingly relevant in America today, sadly).

It will be a lot of work (I’m a very slow, distractible reader) but I’m excited to delve into this literature and see what insights our super sharp students here at Vassar come up with in discussions and projects. The course syllabus (ANTH 323) is available on my Teaching page — I’d be keen to hear suggestions for readings and assignments from folks who know more about brains than I do!

Krapina endocast update (open data & code)

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In the Summer of 2019 I worked with some great Vassar undergrads to make virtual endocasts and generate new brain size estimates for the Neandertals from the site of Krapina, which we then published in 2021 (discussed in this blog post). The virtual approach to endocast reconstruction uses 3D landmark-based geometric morphometrics methods, and so in the spirit of open science we also published all the landmark data used for the study (as well as a bunch of other fossil human brain size estimates) in the Zenodo repository (here).

Neandertal fossil specimens Krapina 3 (purple/green) and Krapina 6 (yellow/red) with preserved landmarks and virtually reconstructed endocasts.

Something major and global happened around that time — who can even remember what? — and so I never got around to posting R code to accompany the study. So, I’ve finally gotten around to adding some very basic code to the Zenodo entry (better late than never). The code simply reads in the landmarks, estimates missing data for fossils, and does some very basic shape analysis and visualization. It’s doesn’t get into all the nuts and bolts of our study, but it should be enough to help folks check our data or get started with shape analysis in R.

R code includes ways to visualize the landmark data. Left: Principal components analysis graph of endocast shape for humans (red) and Neandertals (blue). Right: Triangle meshes of the average human and Neandertal endocast shapes, viewed from the right, bottom, and back.

Original article
Cofran Z, Boone M, Petticord M. 2021. Virtually estimated endocranial volumes of the Krapina Neandertals. American Journal of Physical Anthropology 174: 117–128. (link)

What do brain endocasts tell us?

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What makes the human brain special, and how did it change throughout our evolutionary history? One way to answer this question is by comparing actual brains or MRI scans of living animals. But only fossils can show what changed and when over the past several million years, and sadly brains are basically an elaborately congealed soup that doesn’t stay fresh upon death, so they never fossilize (well, almost never). Happily, though, bones can preserve for millions of years, and they are literally molded by their soft and squishy surroundings. As the brain grows, it pushes outward against the inner surface of the skull, which can save the scars of the submerged cerebrum: nerds like me call these impressions an “endocast.”

Endocasts of Homo naledi (pink) and Homo erectus (yellow). Fossils are viewed from the left side and are variably preserved.

Nicole Labra and Antoine Balzeau have led a cool study, hot off the press, examining what such endocasts can tell us about the underlying brain anatomy. Importantly, they show how difficult it is to clearly and consistently identify many brainy boundaries. This is very salient in “paleoneurology,” the study of brain evolution especially based off endocasts: the problem probably best illustrated by the nearly century-long debate about the natural endcoast of the “Taung child” fossil (Australopithecus africanus).

Labra & colleagues used a clever approach to address this paleontological and epistemological problem. They first generated an endocast directly associated with its brain from an MRI scan of a living human, allowing them see precisely where specific brain grooves (“sulci”) lay relative to the endocast surface. They then asked a bunch of researchers—myself included—to try to identify sulci on the endocast, and then looked at how our responses compared to both one another’s and to the actual, known sulcus positions.

Figure 1 from Labra et al. (in press) showing how the brain and endocast were obtained and analyzed.

Their analysis showed that we varied quite a bit in our identifications on the endocast. As Emiliano Bruner (who also participated) discusses in his blog post, we tended to identify the stronger impressions toward the bottom and sides of the endocast better and more consistently. Some of this variability and uncertainty among researchers is due to the faintness and incompleteness of many brain impressions, and some due to biased expectations about where a given sulcus “should” be based on our previous experiences and published references.

When Antoine Balzeau first contacted me about this project, I was just beginning to dabble in paleoneurology, learning some brain anatomy for the first time for a description of an old Australopithecus endocast called “MLD 3.” I initially thought MLD 3 would be a quick and simple study—boy was I spectacularly disappointed!

Figure 3 from Cofran et al. 2023, comparing two different chimpanzee brains, and two corresponding interpretations of the MLD 3 endocast.

Probably reflecting observer bias and desire for definitive results, we initially interpreted the endocast impressions on MLD 3 as representing a ‘human-like’ anatomy that is super rare in living chimpanzees (namely the “LS” depicted in the right half of the figure above). The researchers who peer-reviewed the first draft of our paper, though, suggested we be more cautious in our interpretations; one reviewer outright disagreed with us in support of a more ‘ape-like’ interpretation (left half of the figure above). The review process alone underscored the subjectivity and uncertainty in analyzing endocasts. In the end we presented both interpretations, and I honestly don’t know which (if either) is most likely to be correct. So the study by Labra and colleagues provides a nice empirical illustration of this cranial conundrum.

Fortunately, researchers are developing methods to help identify brain structures on endocasts. Amélie Beaudet, Jean Dumoncel, and Edwin de Jager among others have done some really impressive work looking at variability in both brains (for instance here) and endocasts (for instance here). By using computer-based 3D data and methods, these researchers have shown where many brain sulci tend to be located (see here). By developing a better understanding of variation in where sulci sit on an endocast, we can have a better idea of which sulci might be represented on fossil endocasts, which in turn can tell us about the brains of our extinct relatives. Edwin and Amélie presented a very cool new analysis of Australopithecus/Paranthropus boisei endocasts, building off this digital approach, at the recent ESHE conference. And as noted in our MLD 3 paper, I think machine learning and other ‘artificial intelligence’ approaches could also help us identify ambiguous features from frustrating fossil fragments.

Brain size & scaling – virtual lab activity

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Each year in my intro bio-anthro class, we start the course by asking how our brains contribute to making us humans such quirky animals. Our first lab assignment in the class uses 3D models of brain endocasts, to ask whether modern human and fossil hominin brains are merely primate brains scaled up to a larger size. In the Before Times, students downloaded 3D meshes that I had made, and study and measure them with the open-source software Meshlab. But since the pandemic has forced everyone onto their own personal computers, I made the activity all online, to minimize issues arising from unequal access to computing resources. And since it’s all online, I may as well make it available to everyone in case it’s useful for other people’s teaching.

The lab involves taking measurements on 3D models on Sketchfab using their handy measurement tool, and entering the data into a Google Sheets table, which then automatically creates graphs, examines the scaling relationship between brain size (endocranial volume, ECV) and endocast measurements, and makes predictions about humans and fossil hominins based off the primate scaling relationship. Here’s the quick walk-through:

Go to the “Data sources” tab in the Google Sheet, follow the link to the Sketchfab Measurement Tool, and copy the link to the endocast you want to study (3D models can only be accessed with the specific links).

Following the endocast Sketchfab link (column D) will bring you to a page with the 3D endocast, as well as some information about how the endocast was created and includes its overall brain size (ECV in cubic cm). Pasting the link when prompted in the Measurement Tool page will allow you to load, view, and take linear measurements on the endocast.

Hylobates lar endocast, measuring cerebral hemisphere length between the green and red dots.

Sketchfab makes it quite easy to take simple linear measurements, by simply clicking where you want to place the start and end points. The 3D models of the endocasts are all properly scaled, and so all measurements that appear in the window are in millimeters.

The assignment specifies three simple measurements for students to take on each endocast (length, width, and height). In addition, students get to propose a measurement for the size of the prefrontal cortex, since our accompanying reading (Schoenemann, 2006) explains that it is debated whether the human prefrontal is disproportionately enlarged. All measurements are then entered into the Google Sheet — I wanted students to manually enter the ECV for each endocast, to help them appreciate the overall brain size differences in this virtual dataset (size and scale are often lost when you have to look at everything on the same-sized 2D screen).

Feel free to use or adapt this assignment for your own classes. The assignment instructions can be found here, and the data recording sheet (with links to endocast 3D models) can be found here — these are Google documents that are visible, but you can save and edit them by either downloading them or making a copy to open in Docs or Sheets.

Ah, teaching in the pandemic 🙃

Latest from the lab: Brain size at Krapina

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In the latest paper out of the lab (here), my students and I reconstructed the brain endocasts of the Krapina Neandertals. The Krapina rock shelter in Croatia is a remarkable site. Dating to around 130,000 years ago (if not older), the Krapina fossils are early members of the Neandertal lineage. In addition, the fossils represent dozens of Neandertals, from infants to adults. Part of what drew me to the site were the juvenile skulls, since they can tell us about growth and development in these early humans. But, the fossils are quite fragmentary, and needed to be reconstructed to estimate important characteristics like brain size.

Figure 1 from our paper, showing the five Krapina crania (A & B are the same individual) with the endocranial surface highlighted.

Vassar College has a great program called URSI, where students team up with faculty to get hand on experience conducting research over the summer. So, two summers ago my students and I worked on virtually putting these Humpties Dumpty back together again. Using 3D surface scans of the original fossils and CT scans of modern humans, we used virtual methods to digitally reconstruct the endocasts, which are a good proxy for brain size and shape. Here’s the basic workflow:

Figure 2 from the paper, depicting the workflow for virtually reconstructing fossil endocasts, represented by the famous Krapina 3 or “C” cranium.

The human endocasts were produced from recent humans from the Terry Anatomical Collection, generously made available here by Dr. Lynn Copes. We have posted the 3D landmark data for the humans, the preserved landmarks from the Neandertals, and a big list of estimated brain sizes for Neandertals, in the open access repository Zenodo (here). So, hopefully anyone can repeat our results, or use these data in their own research.

With virtual methods, we could generate multiple reconstructions of each Neandertal fairly easily, giving an idea of how certain or uncertain our brain size estimates were. In the end, we showed that i) the Krapina juveniles, who were probably around 6-7 years old, had brain sizes within the adult range (it’s same with modern humans); ii) average brain size at Krapina was a little lower than previously estimated; and iii) although later Neandertals from other sites had larger brains on average, the difference is not necessarily greater than could be expected by chance.

I’ve participated in Vassar’s URSI program for the past few years and it has been a lot of fun. Last (virtual) summer, my students and I compared hip growth in humans and Australopithecus africanus, and this coming summer we will examine the brains of the greatest animals of all time — gibbons!