hominin

Mind the gaps, mend the gaps

/ zcofran

A very long time ago I asked whether Neandertals’ brains grew like ours do today, a question raised by conflicting results coming from two research teams. Both teams reconstructed the brain endocasts of modern humans and fossil Neandertals, and compared how endocast shapes changed during growth and development. As I mused in that post, the different results seem to result largely from differences in how a critical fossil specimen (the Neandertal newborn from Mezmaiskaya, Russia) was reconstructed.

Physical reconstruction of a Homo erectus cranium (A and turquoise in C) compared to its “virtual” reconstruction (B and gray in C), by Karen Baab (2025).

This is a perennial problem for paleoanthropology. Our knowledge of the human past hinges on a few thousands of individuals whose bones and teeth managed to survive and be discovered after several thousands or millions of years. Most of these precious remains are fragmentary and cannot speak for themselves. So, researchers must rely on their own anatomical expertise and a bit of artistic license to reconstruct what many key fossils would have looked like in their original condition.

Over thirty years ago Christophe Zollikofer and colleagues (1995: 283) reported that, “Fossil specimens can be restored, measured and replicated without physical contact using … computer assisted reconstruction.” The development of these “virtual anthropology” methods has made fossil reconstruction much more accessible. Most importantly, virtual methods allow researchers to generate multiple, reasonably realistic reconstructions of the same fossil. As Philipp Gunz and colleagues (2009: 61) noted, “While there typically will be shape differences among equally plausible reconstructions, these different estimates might still support a single conclusion. But they need not do so, and all assumptions must be strenuously challenged if one or more reconstructions, or a statistical analysis based on them, are to be treated as arguments for a scientific claim.”

As these paleo pioneers have also acknowledged, making data publicly available will also help assess the extent to which specific reconstructions might affect subsequent interpretations. Both of these research groups have published 3D landmark datasets with some overlapping specimens, allowing us to address this central question. Simon Neubauer and colleagues (2018) published the landmark data used in their reconstruction and analysis of a juvenile Homo erectus cranium (here). A team led by Marcia Ponce de León (2021) and Christophe Zollikofer (2022) have posted comparable data from their endocast reconstructions of Homo erectus from Dmanisi, Georgia (here) and early Homo sapiens from Herto, Ethiopia (here). These great datasets bear on the evolution of brain size and shape—let’s dig in.

Both groups—Neubauer et al. and Ponce de León et al. + Zollikofer et al. (hereafter “PZ”)—include recent modern humans from different skeletal collections and the same nine fossil Homo specimens: KNM-ER 1813 (H. habilis), KNM-ER 1470 (H. rudolfensis), and seven other fossils from Kenya and Indonesia typically attributed to Homo erectus. Most of the fossils required varying extents of reconstruction, from the alignment of separate cranial fragments to the mathematical estimation of endocranial surfaces that aren’t preserved. The two teams measured endocast shape using comparable but slightly different sets of 3D landmark coordinates, so we can’t combine the datasets but we can run the same set of analyses on each sample separately and then compare the results.

Overall size and shape variation in the two datasets. Left: Centroid size of each specimen with the dashed line indicating parity between samples. Center and right: endocast shape variability within the Neubauer (center) and PZ (right) samples; color-coded 3D models beneath each graphs show how endocast shape varies along PC1.

The graphs above show how the nine fossils vary within and between datasets. The 3D landmarks used to measure endocast size and shape return similar overall sizes for each specimen (left graphs). There are differences in the relative positions of a few specimens (ER 3883 vs. WT 15000 and ER 3733 vs. Sambungmacan 3), but these discrepancies are small probably mostly within the range of uncertainty for individual fossil reconstructions.

The effects of different reconstructions on endocranial shape, on the other hand, are a bit more profound. In each dataset, the main dimension of variation (PC1, the horizontal axis in the center and right graphs) captures similar patterns of shape variability. In both samples, fossils with a longer and lower endocast fall on the left side of the graph, while rounder endocasts fall on the right side of the graph. But where individual specimens plot in the graphs (i.e., their overall endocast shape) differs notably between datasets. For example, the “Mojokerto” infant Homo erectus has the roundest shape while WT 15000 has one of the ‘flatter’ shapes in the Neubauer sample, whereas WT 15000 is the ‘roundest’ in the PZ sample.

So, different decisions in the reconstruction process can lead to different overall patterns of shape variation within a sample. This can have important impacts on subsequent analyses. For instance, we often want to assess how similar or different fossil specimens are to one another, looking for clusters of similar shapes that might tell us something meaningful about the biology we’re hoping to capture. The two datasets, however, produce slightly different clusters:

Cluster dendrograms based on shape variation within the two endocast datasets. Fossil specimens are color-coded to highlight difference between the two trees.

Both datasets produce clusters with early H. erectus specimens ER 3733 and ER 3883, and later Indonesian H. erectus fossils Sambungmacan 3 and Solo XI. But the similarities among other fossils differ between the two samples, in ways that could lead to different biological interpretations. One might interpret the Neubauer clustering to mean that the Mojokerto infant differs from the rest since it hadn’t completed brain growth, while the other clusters could potentially reflect evolutionary changes both from early Homo (ER 1813 and 1470) to H. erectus and over time within H. erectus. In contrast, the PZ tree could be interpreted to mean that the adolescent WT 15000 had an ‘underdeveloped’ brain like Mojokerto, while the different clusters of ER 1813 and ER 1470 could reflect a more convoluted pattern of brain evolution from early Homo to H. erectus.

Of course, principal components and cluster analyses are statistical approaches for exploring variation within a sample, and they don’t necessarily map onto meaningful phenomena. Biological patterns could ‘override’ variation due to differences in reconstruction. For instance, endocast shape variation due to growth and development could produce marked, characteristic differences between infants and adults. Indeed, if we compare endocast shape of the infant Mojokerto to the average adult H. erectus, both datasets yield fairly similar results:

Endocast shape differences between the Mojokerto infant and adult H. erectus. In both rows, the left side shows Mojokerto (blue/red) aligned to the adult (gray); note that they are scaled to the same size. The center shows where Mojokerto (blue/red) or the adult (yellow) projects more than the other. On the right, lines between points show how corresponding landmarks differ between Mojokerto and the average adult in each sample.

In addition, if groups/species have distinct endocast shapes, such differences could still be captured by studies using different fossil reconstructions. For instance, both studies produce similar results when comparing early Homo specimens ER 1813 and ER 1470, and comparing adult H. erectus and modern humans:

So, getting back to our original question: do different virtual reconstructions produce different results? Yes and no. Yes, there will be observable differences between studies, and these could be subtle (e.g., brain sizes estimates) or more severe (e.g., clustering patterns within a fossil sample). But as Melvin Moss reminded us, we must keep in mind the underlying biological questions when interpreting statistical patterns. Ultimately, fossil preservation is probably the greatest source of variability between different studies. Many researchers will bring similar levels of expertise and similar analytical toolkits to study fossils, but more fragmentary specimens will have greater uncertainty in how to to reconstruct them. In contrast to the different growth patterns identified in the Neandertal studies mentioned at the beginning of this post, the consistent ‘growth’ signal in H. erectus fossils may be due to the fact that the Mojokerto infant is better preserved and required less reconstruction than Neandertal neonates.

As Gunz and colleagues (2009) stressed when they laid out “principles for the virtual reconstruction of hominin crania,” these powerful virtual methods can never produce “the” single correct reconstruction of a fossil. Rather, researchers must acknowledge and remain cognizant of all the decisions and assumptions that go into their reconstructions, and attempt to produce multiple reconstructions reflecting these varied uncertainties. Making data openly available further allows other researchers to assess how conclusions were reached, and to add new fossils to existing datasets.

REFERENCES

Baab, K. L. (2025). A fresh look at an iconic human fossil: Virtual reconstruction of the KNM-WT 15000 cranium. Journal of Human Evolution, 202, 103664. https://doi.org/10.1016/j.jhevol.2025.103664

Gunz, P., Mitteroecker, P., Neubauer, S., Weber, G. W., & Bookstein, F. L. (2009). Principles for the virtual reconstruction of hominin crania. Journal of Human Evolution, 57(1), 48–62. https://doi.org/10.1016/j.jhevol.2009.04.004

Neubauer, S., Gunz, P., Leakey, L., Leakey, M., Hublin, J.-J., & Spoor, F. (2018). Reconstruction, endocranial form and taxonomic affinity of the early Homo calvaria KNM-ER 42700. Journal of Human Evolution, 121, 25–39. https://doi.org/10.1016/j.jhevol.2018.04.005

Ponce De León, M. S., Bienvenu, T., Marom, A., Engel, S., Tafforeau, P., Alatorre Warren, J. L., Lordkipanidze, D., Kurniawan, I., Murti, D. B., Suriyanto, R. A., Koesbardiati, T., & Zollikofer, C. P. E. (2021). The primitive brain of early Homo. Science, 372(6538), 165–171. https://doi.org/10.1126/science.aaz0032

Zollikofer, C. P. E., Bienvenu, T., Beyene, Y., Suwa, G., Asfaw, B., White, T. D., & Ponce De León, M. S. (2022). Endocranial ontogeny and evolution in early Homo sapiens: The evidence from Herto, Ethiopia. Proceedings of the National Academy of Sciences, 119(32), e2123553119. https://doi.org/10.1073/pnas.2123553119

Zollikofer, C. P. E., Ponce de León, M. S., Martin, R. D., & Stucki, P. (1995). Neanderthal computer skulls. Nature, 375(6529), 283–285. https://doi.org/10.1038/375283b0

Picking the brain of Homo naledi

/ zcofran / 2 Comments

A question that has come up a lot on the blog is what endocast fossils can tell us about the brains and behaviors of long-extinct animals. This question is especially salient for Homo naledi, an unexpected human cousin that lived in South Africa at the same time as the earliest modern-like humans around 300,000 years ago. Brain size in H. naledi ranged from 460–610 ml, similar to Australopithecus and the earliest Homo over 1.5 million years ago and less than half the size of other, contemporaneous fossil humans. Despite its small brain size, the frontal lobe of H. naledi seems to have been more similar to humans than australopiths, including in the area associated with speech.

To learn more about the brain of Homo naledi, I teamed up with Shawn Hurst and John Hawks to virtually reconstruct the endocast from the most complete skull and skeleton of the species, nicknamed Neo (which means “gift” in the SeSotho language). We have a paper about it coming out soon in the journal Brain Structure and Function, where we show that Neo’s endocast shape is fairly distinct among Pleistocene hominins. We go on to discuss some implications and limitations of our results for understanding the brain and behavior of H. naledi and other hominins. I’ll write more about it when the paper is actually in press, but in the meantime you can get a sneak preview by checking the data and running the analyses for yourself.

The original Neo cranium (left), its preserved endocranial surface (center), and virtually reconstructed endocast shape (right)

I published the landmark data and R code from our study in the open access repository Zenodo (here). I built off the endocast landmark data that Simon Neubauer and colleagues (2018) made available from their study of the KNM-ER 42700 fossil. I created a landmark template from that dataset and applied it to Neo and Australopithecus africanus cranium Sts 5, and then used geometric morphometric methods to reconstruct the missing regions of Neo and compare it to the other hominins. The accompanying R code walks you through inputting these data, estimating missing landmark positions, and comparing endocast shapes of humans and fossil hominins.

Endocast shapes of Neo and a modern human, as viewed from the left, front, and bottom. Endocasts are scaled by size and aligned by the cranial base.

Hopefully these data and code will let others build off our results, add more fossils to the mix, and generate more insights about how the human brain has changed over the past several millions of years.

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

#FossilFriday: Handy habilis’ formidable forearms

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Homo habilis just got some long arms to go along with its dexterous hands. In a recent paper in the journal The Anatomical Record, Fred Grine and colleagues describe and analyze some spectacular fossils recovered near the town of Ileret in Kenya, dating to just over 2 million years ago. There were a few different kinds of human-like species inhabiting the planet around this time, but researchers were able to assign these bones to Homo habilis thanks to some chemical clues connecting them to a nearly complete set of teeth found a few meters away. This partial skeleton of a young adult individual is an incredible discovery, connected by clever scientific sleuthing, and provides important information about an early member of the human lineage.

You can see some great photos of these fossils (as well as a fantastic fossil foot of a different individual) in a 2015 press release from the Turkana Basin Institute. A more recent announcement from the Institut Català Paleontologia includes a photo showing the late great Bill Jungers and fossil maven Meave Leakey with the fossils, which helps show the actual size of the bones.

Ann Gibbons’ article about the discovery has a great quote from paleoanthropologist Stephanie Melillo (who discovered the Burtele foot fossil): “If you dressed up a Homo habilis individual in clothes and you saw her walking in the distance, would you do a double take? This study shows us that the answer is YES!”

Still from a scent of the 1982 movie ET, showing the eponymous ET wearing a wig, dress, bowler hat, shawl, jewelry
Artist’s depiction of Homo habilis dressed up in clothes and you see her walking in the distance (image source)

The reason we might react to seeing Homo habilis like Gertie glimpsing E.T., as this skeleton shows, is that this early human had longer arms (especially forearms) than most of us do today. Thickness of the bones also shows that they were probably quite strong as a result of experiencing lots of force from use during life. Long and strong hominin arms are typically interpreted as evidence that these ancient ancestors spent a good deal of time climbing trees.

These features have previously been documented in some of the few other partial skeletons attributed to Homo habilis, as Grine and colleagues note. Indeed, the new article does a deep dive into what is known (and unknown) about the bones and body of Homo habilis, and it also provides a thoughtful review of recent research cautioning against over-interpreting climbing behaviors from fossil remains.

For more fossil fun, the article’s supporting online material includes “3D manipulative files” of the original specimens, so anyone can have a look at the bones in 3D using Microsoft Word:

Two-panels showing a Microsoft Word window (left panel) with a 3D model of a fossil, beneath which is written "SOM Figure 9. 3D manipulative file of shaft of right acetabulum"; and an internet browser screenshot (right panel) depicting the "Supporting Information" section from this website: https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/ar.70100

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!

The hand of Homo naledi points to life before birth

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Homo naledi is one of my favorite extinct humans, in part because its impressive fossil record provides rare insights into patterns and process of growth and development. When researchers began recovering naledi fossils from Rising Star Cave 10 years ago, one of the coolest finds was this nearly complete hand skeleton. The individual bones were still articulated practically as they were in life so we know which bones belong to which fingers, allowing us grasp how dextrous this ancient human was. And since finger proportions are established before birth during embryonic development, we can see if Homo naledi bodies were assembled in ways more like us or other apes.

The “Hand 1” skeleton of Homo naledi, adapted from a figure by Kivell and colleagues (2015). Left shows the palm-side view while the middle shows the back of the hand. The inset (b) shows many of the palm and finger bones as they were found in situ in Rising Star Cave.

In a paper hot off the press (here), I teamed up with Dr. Tracy Kivell to analyze finger lengths of Homo naledi from the perspective of developmental biology. On the one hand, repeating structures such as teeth or the bones of a finger must be coordinated in their development, and scientists way smarter than me have come up with mathematical models predicting the relative sizes of these structures (for instance, teeth, digits, and more). On the other hand, the relative lengths of the second and fourth digits (pointer and ring fingers, respectively) are influenced by exposure to sex hormones during a narrow window in embryonic development: this ‘digit ratio’ tends to differ between mammalian males and females, and between primate species with different social systems.

So, Tracy and I examined the lengths of the three bones within the second digit (PP2, IP2, DP2) and of the first segment of the second and fourth digits (2P:4P) in Homo naledi, compared to published data for living and fossil primates (here and here). What did we find out?

Summary of our paper showing the finger segments analyzed (left), and graphs of the main results (right). The position of Homo naledi is highlighted by the blue star in each graph.

The first graph above compares the relative length of the first and last segments of the pointer finger across humans, apes, and fossil species. The dashed line shows where the data points are predicted to fall based on a theoretical model of development. There is a general separation between humans and the apes reflecting the fact that humans have a relatively long distal segment, which is important for precise grips when manipulating small objects. Fossil apes from millions of years ago and the 4.4 million year old hominin Ardipithecus are more like apes, while Homo naledi and more recent hominins are more like modern humans. Because both humans and apes fall close to the model predictions, this means the theoretical model does a good job of explaining how fingers develop. Because humans and apes differ from one another, this suggests a subtle ‘tweak’ to embryonic development may underlie the evolution of a precision grip in the human lineage, and that it occurred between the appearance of Ardipithecus and Homo.

The second graph compares the ‘digit ratio’ of the pointer and ring fingers from a handful of fossils with published ratios for humans and the other apes. Importantly, the digit ratio is high in gibbons (Hylobates) which usually form monogamous pair bonds, while the great apes (Pongo, Gorilla, Pan) are characterized by greater aggression and mating competition and have correspondingly lower digit ratios. Ever the bad primates, humans fall in between these two extremes. Most fossil apes and hominins have digit ratios within the range of overlap between the ape and human ratios, but Homo naledi has the highest ratio of all fossil hominins known, just above the human average. It has previously been suggested that humans’ higher ratio compared to earlier hominins may result from natural selection favoring less aggression and more cooperation recently in our evolution. If we can really extrapolate from digit proportions to behavior, this could mean Homo naledi was also less aggressive. This is consistent with the absence of healed skull fractures in the vast cranial sample (such skull injuries are common in much of the rest of the human fossil record).

You can see the amazing articulated Homo naledi hand skeleton for yourself on Morphosource. Its completeness reveals how handy Homo naledi was 300,000 years ago, and it can even shed light on the evolution of growth and development (and possibly social behavior) in the human lineage.

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.

Did Homo naledi have big babies?

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I’m working on a project analyzing infant remains of Homo naledi, a species of human that lived in South Africa around 300,000 years ago. In order to paint a full picture of infancy in this species, we need to estimate how big (or small) naledi newborns were. But without fossil neonates that could provide direct evidence of body size at birth, this is a tricky task.

Ideally, we could simply use adult body size estimates for Homo naledi to predict its body size at birth, using the scaling relationship in other primates as a guide. For example, using an average adult body size of 44 kg for Homo naledi (Garvin et al., 2017) yields an estimated newborn size of around 1.5 kg, based on published primate dataset (Barton and Cappellini, 2011). But this approach necessarily overlooks variation within each species, not to mention variation and uncertainty in Homo naledi adult size. In addition, the 95% prediction interval for this estimate ranges from under 1 kg (smaller than an average baboon baby) to almost as large as a human neonate.

Primate body size scaling (Barton & Cappellini, 2011). The black line is the regression for catarrhines (purple squares and blue circles), and the shaded grey area is the 95% prediction interval for newborns at a given adult catarrhine size.

And this gets at the other issue with the regression-based approach to estimating newborn body size in fossil hominins: humans are bad at being primates in some ways, as illustrated here by the fact that we don’t fit the newborn-adult body size relationship that characterizes other catarrhines (apes and monkeys of Africa and Eurasia).

Humans give birth to collosal kids. In contrast, gorillas are the largest living primates as adults, but their newborns are only a little over half the size of human neonates. Why do we have such giant babies? The most proximate reason is that humans are born with adult-ape-sized brains and quite a bit of baby fat as far as mammals go (Kuzawa, 1998). This tells us how babies are big, but it still begs the ultimate question of why—an enduring puzzle that you may have read about in the New York Times last week.

In order to land on a reasonable estimate of newborn body size in extinct humans, we need to figure out when evolution blew up the kid. Unfortunately, the only fossil hominin neonates are two Neandertals from France and Russia dating to under 100,000 years ago­­­—pretty remarkable, but they don’t necessarily tell us about earlier species like Homo naledi.

My colleague Jerry Desilva (2011) worked out a potential solution to this conundrum. He argued that one could work from adult brain size to newborn body size through the following steps. First, in contrast to newborn-adult body size scaling, humans are good catarrhines when it comes to newborn-adult brain size scaling. This means that we can reasonably estimate newborn brain size based on adult brain sizes, which are aplenty in the human fossil record. Second, humans and many other primate newborns have brains roughly 12% of their overall body mass, while the great ape newborns stand out with brains around 10% of their adult size. Putting these two pieces together, one could estimate newborn body size: Adult brain ➡️ newborn brain ➡️ 10–12% newborn body size

DeSilva showed that regardless of whether you use an ape or human model of newborn brain/body size, hominin babies from Australopithecus afarensis 3 million years ago onward were probably large relative to maternal body size, estimated independently using skeletal remains. It’s a bit of a tortuous approach to estimating body size at birth, but the assumptions are reasonable and it’s probably the best way to figure out this important life history variable given the fossil evidence. What does this mean for Homo naledi?

Virtual reconstruction of brain size and shape of the Homo naledi cranium “Neo” (work in progress). At 610 cm3, this is the largest and most complete Homo naledi endocast.

There are a few reliable adult brain size estimates for naledi, ranging from 465–610 cm3 (Berger et al., 2015; Garvin et al., 2017; Hawks et al., 2017), which based on catarrhine scaling would predict newborn brain size of around 170–210 cm3 (DeSilva and Lesnik, 2008). These brain sizes would then predict newborn body sizes of around 1.4–2.1 kg: the smol estimate is based on the smallest naledi adult brain size and a human model of newborn brain/body size; the chonk estimate is based on the largest naledi brain size and an ape brain/body model (pinkish stars in the boxplot below, left).

Boxplots of newborn body size in great apes. Gorilla, Chimpanzee, and Bonobo data from the Primate Aging Database (Kemnitz, 2019).

So, did Homo naledi have big babies? On the one hand, no: these 1.4–2.1 kg naledi newborns are outside the human range, and within the range of living great apes.

On the other hand, maybe Homo naledi babies were relatively large, though this depends on the size of Homo naledi adults. Recall from earlier that Garvin and colleagues arrived at an average estimated adult size of 44.2 kg. But this is an average of estimates for 20 separate naledi fossils, and each of these estimates has its own range of uncertainty. Garvin and team reported that the extremes of the prediction intervals for these estimates ranged from 28–62 kg. The second boxplot above shows newborn size relative to the adult average (sexes combined) for each species: for naledi, the six labels compare the smol and large newborn sizes (1.4 and 2.1 kg) with the adult average and extremes (28, 44, and 62 kg). Assuming the ‘true’ naledi sizes are somewhere in the middle of the range of estimates, naledi likely gave birth to babies 3–5% of adult body size, somewhat ‘intermediate’ between chimpanzees and humans (and bonobos…?) and similar to what DeSilva found for other hominins.

This is just a preliminary look at infancy in Homo naledi. There is a lot of uncertainty in these size estimates, but we should still be able to make some interesting inferences about growth and life history in our extinct evolutionary cousin.

REFERENCES

Barton, R. A., & Capellini, I. (2011). Maternal investment, life histories, and the costs of brain growth in mammals. Proceedings of the National Academy of Sciences, 108(15), 6169–6174. https://doi.org/10.1073/pnas.1019140108

Berger, L. R., Hawks, J., de Ruiter, D. J., Churchill, S. E., Schmid, P., Delezene, L. K., … Zipfel, B. (2015). Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. ELife, 4, e09560. https://doi.org/10.7554/eLife.09560

DeSilva, J. M. (2011). A shift toward birthing relatively large infants early in human evolution. Proceedings of the National Academy of Sciences, 108(3), 1022–1027. https://doi.org/10.1073/pnas.1003865108

DeSilva, J. M., & Lesnik, J. J. (2008). Brain size at birth throughout human evolution: A new method for estimating neonatal brain size in hominins. Journal of Human Evolution, 55(6), 1064–1074. https://doi.org/10.1016/j.jhevol.2008.07.008

Garvin, H. M., Elliott, M. C., Delezene, L. K., Hawks, J., Churchill, S. E., Berger, L. R., & Holliday, T. W. (2017). Body size, brain size, and sexual dimorphism in Homo naledi from the Dinaledi Chamber. Journal of Human Evolution, 111, 119–138. https://doi.org/10.1016/j.jhevol.2017.06.010

Hawks, J., Elliott, M., Schmid, P., Churchill, S. E., Ruiter, D. J. de, Roberts, E. M., … Berger, L. R. (2017). New fossil remains of Homo naledi from the Lesedi Chamber, South Africa. ELife, 6, e24232. https://doi.org/10.7554/eLife.24232

Kemnitz, J. W. (2019). Database for indices of aging in nonhuman primates. Innovation in Aging, 3(Suppl 1), S957. https://doi.org/10.1093/geroni/igz038.3472

Kuzawa, C. W. (1998). Adipose tissue in human infancy and childhood: An evolutionary perspective. American Journal of Physical Anthropology, 107(S27), 177–209. https://doi.org/10.1002/(SICI)1096-8644(1998)107:27+<177::AID-AJPA7>3.0.CO;2-B