evolution

Open access opens the skull of Homo naledi

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As I mentioned a few weeks ago, some colleagues and I have recently published an article about brain structure and function of the fossil hominin Homo naledi, based on endocranial evidence. Ben Taub wrote up a nice summary of the paper for IFL Science that lays out some of the main points and bigger picture (here). The article is open access for everyone to read (here), as are the new landmark data and R code (here) that we used to reconstruct and analyze the endocast of the most complete H. naledi skull.

Over the past decade it has become standard practice to publish data and code, to both facilitate transparency and allow others to add to existing datasets. It turns out it’s also important when journals don’t include your high-resolution figures in the final publication and are incapable of replacing the low quality images that made it into print (makes you wonder just what the $5000 article processing charge pays for). So, this is a good opportunity to follow up on the earlier blog post and walk you through the R code that produces the graphs (along with a few other images) that help illustrate the story told by H. naledi endocasts.

Homo naledi is one of the wildest discoveries in human evolution, from its unusual geological contexts to the variability exhibited in the large subfossil sample. The endocasts are tantalizing, since they are as small as those of hominins from over one million years ago, yet they date to only around 300,000 years ago. They buck the general trend of brains getting bigger of the course of human evolution.

Brain size in human evolution. Colored shapes indicate fossils included in the geometric morphometric analyses described below. Data adapted from DeSilva et al. (2021).

Unlike the other small-brained, later Pleistocene hominin Homo floresiensis (a.k.a., “the hobbit”), there is a nice and big sample of H. naledi crania. The floresiensis sample is restricted to a relatively complete skeleton from one individual (“LB1”) and a few other bones from several other individuals. The small brain size of LB1 precipitated a series of studies in the early 2000s, arguing for (or against) various pathological explanations, though I think the consensus today is that H. floresiensis was in fact a small-brained hominin. It probably blew the minds of our human ancestors when they encountered hobbits on Flores 10s of 1000s of years ago. In contrast to the case of H. floresiensis, at least five adult H. naledi crania have been recovered from Rising Star Cave in South Africa, all indicating brain sizes between 460–610 ml.

Homo naledi crania viewed from the left side (top row) with their endocast impressions highlighted in pink (bottom row). Specimens from left to right: LES1, DH1, DH2, DH3, DH4.

Despite having small brains, the impressions from the frontal lobe suggest this part of the brain was organized like that of humans today. This is important in part because this specific region including Brodmann Areas 44-45 (highlighted in blue below) is involved in both spoken language as well as stone tool production. In addition, these naledi endocasts support to the idea, proposed over 100 years ago, that early hominin brains may have been structured like those of modern humans but at smaller sizes.

Inferior frontal lobe morphology viewed from the front-left, in chimpanzee (A) and human (B) brains, and H. naledi endocasts DH3 (C and E) and LES1 (D and F). Brains in A and C are from the National Chimpanzee Brain Resource.

To learn more about the brain of H. naledi, we virtually reconstructed the endocast of the sample’s most complete skull, referred to as “LES1” (the first hominin from the Lesedi Chamber of Rising Star Cave). The R code linked above uses geometric morphometrics to estimate the likely positions of endocranial surfaces that are missing from the actual LES1 fossil. When reconstructing a fossil from fragments, we can rarely know what the original bone truly looked like when it was intact. But with geometric morphometrics, we can estimate missing data based on different references (e.g., a specific Homo erectus fossil or a sample average), allowing us to explore many reasonable alternatives. So, the R code generates 15 reconstructions of the LES1 endocast based on over a dozen fossil hominin references (previously published by Simon Neubauer and colleagues).

Workflow for virtually reconstructing the LES1 endocast. A) Isolate the endocranial surface. B) Duplicate and mirror the endocast, then apply the landmark template to the preserved service (block dots). C) Estimate missing landmarks based on different fossil references (indicated by colored lines and nodes). D) Observe how the reconstructed endocast fits the actual fossil.

Although LES1 is missing nearly all of the bottom of the skull and endocast, all of our reconstructions based on various fossils and an average human are quite similar to one another. In geometric morphometrics, a shape is captured by a configuration of landmarks—in our case, 935 coordinates in 3D space. The Procrustes distance provides a quick summary of the overall shape difference between two individuals (for instance, two different reconstructions of LES1). The R code includes a simple function for calculating pairwise Procrustes distances, and then uses randomization and loops to obtain Procrustes distances between all LES1 reconstructions, between all humans, between all Homo erectus included in the study, and between the average LES1 and all other fossils.

Endocast shape affinities in the full sample. Left: Boxplot of Procrustes distances between all humans, all Homo erectus, and LES1 reconstructions and the fossil sample. Right: Cluster analysis of all Procrustes distances shows that Homo erectus endocasts are most similar to one another, that erectus variation accords with geography, and that LES1 is most similar to the Indonesian H. erectus from Ngandong, Ngawi, and Sambungmacan.

In the left graph above, the pink dots show the shape differences between all LES1 reconstructions: these differences are smaller than all the within-erectus differences and nearly all of the within-human differences. This means that most of the reconstructions are more similar to one another than two different individuals of the same species would be to one another. This in turn means that missing data uncertainty is fairly low for LES1; if we were to run various analyses, the results should be pretty much the same regardless of which LES1 reconstruction we use. Great! (As an aside, we had also estimated the endocranial volumes of each LES1 reconstruction and these ranged from 608–622 ml, a precise span very similar to the first estimate of 610 ml when the fossil was first discovered. But we ended up cutting this from the paper.)

Looking at the same graph, Procrustes distances between LES1 and most of the other fossils are comparable to the within-species variation seen in humans and H. erectus. These distances, along with the cluster analysis in the right side of the image above, show that the LES1 endocast shape is most similar to those of H. erectus from Java (Ngandong, Ngawi, Sambungmacan).

This was an unexpected result. The skull and teeth of H. naledi have been shown to be more similar to earlier members of the genus Homo, but the LES1 endocast doesn’t show this affinity. Plus, these later H. erectus endocasts are almost twice the size of LES1, yet LES1 doesn’t appear to be a simply a H. erectus ‘scaled down’ to a smaller size. The Procrustes distances and cluster analysis highlight overall endocast shape variation in the sample, so the R code then goes on to look at the more detailed differences between LES1 and each fossil reference group. In the next image, the top row compares the scaled and aligned endocasts of LES1 and given reference, while the bottom row color-codes the difference between each 3D coordinate on LES1 and the reference endocast.

Shape differences between H. naledi and each other species ‘type.’ LES1 is depicted in gray in the top and bottom rows. Triangle meshes in the top row show the average endocast shapes, while the spheres on the endocasts below depict differences between the landmark coordinates of LES1 and each reference.

Notice that the inferior frontal lobe appears relatively expanded in LES1 compared to all of the other groups. This corroborates previous research indicating a human-like anatomy in this area that is important for language and tool production. We speculate that the almost-human morphology here (recall the third image in this post) may relate to how different parts of the brain are connected, but much more research is needed to develop this idea.

The last aspect of endocast shape that we examined is the proportional size of the areas surrounding the cerebral cortex versus the cerebellum. The bottom of the cerebellum is cupped by the occipital and temporal bones (dark pink in the image below), while the top and sides of the cerebral cortex are capped by the rest of the endocranial surface (lighter pink below). We can quickly measure the overall sizes of these two brainy coverings based on their 3D landmarks, but we should bear in mind these are only approximations of the cerebrum and cerebellum themselves. The graph below shows how these proxies scale within the sample, with a best-fit line showing the relationship in recent humans. All of the fossil hominins including naledi have relatively smaller cerebella than modern humans, which might suggest a disproportionate expansion of the cerebral cortex later in human evolution.

Size scaling of the bony surfaces covering the cerebral cortex (light pink landmarks) and cerebellum (dark pink landmarks).

In our review of the brain of H. naledi we presented some new data and evidence, and also tried to point toward important areas for future research. These include exploring physical influences on brain/endocast shape—both intrinsically due to connections between different regions of the brain, and extrinsically due to how the eyes, nose, throat, and jaws interact with the brain during growth and development. Bigger samples of both fossils and living apes would also help uncover how the cerebellum has changed over time.

This latter project is ripe for the picking. The shape analyses we presented in the paper basically just entailed creating and applying a 3D landmark template to LES1, and inserting LES1 into an existing dataset. Recall from another recent blog post that second research group, led by Marcia Ponce de León and Christoph Zollikofer, has also published their similar endocast landmark data and provides a much larger fossil and ape sample. It wouldn’t take too much work to create and apply a landmark template from this sample to LES1 and do all the same analyses (and more) that we included in our open access article and code. And because the H. naledi fossils themselves are available for study (originals at the University of the Witwatersrand, and so many 3D models on Morphosource), a more comprehensive analysis of all H. naledi endocasts is well within reach.

So many fossils, so little time!

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

The brain of human animals

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This week I participated in the workshop, “Corpus: The Body in Parts,” organized by Jeremiah Garsha and Jess Beck at University College Dublin (UCD). I joined an interdisciplinary group of researchers from across UCD, as well as keynote speaker Aja Lans (Johns Hopkins University) and artist Liliane Puthod. Our motley crew spent a day discussing different body parts and their intersections across science, society, time, and space. It was fascinating to learn new things about the body and how various parts are viewed in other disciplines, and the discussions have given me a lot to think about for my own research and teaching.

My corporal contribution to the workshop was the brain, so here are some quick notes I put together as I was thinking through what I’d want to talk about that day.

Left side views of five fossil human skulls arranged from left to right. The top row shows the original fossils, while the bottom row shows the same skulls with bone rendered transparent and the brain-covering internal surface highlighted in solid pink.
Fossil crania and the brain endocasts of Homo naledi specimens LES1, DH1, DH2, DH3, and DH4 (reversed).

The brain is central to the human experience, which is what Anthropology is all about. Anthropologists generally align with one of four subfields respectively focusing on culture, language, material expression (archaeology), and biological variation. The brain is the part of the body that enables culture, language, and material expression of the lived experience.

A brain is a like a beautifully congealed soup of fats, sugars, protein, water, salt. This remarkable mixture receives information from the outside world, integrates it along with information about our internal states, and then sends signals to the rest of the body about what to do next. In the context of anthropology, this soup of sentience inside the skull provides each individual human with the ability to cooperate with others to solve novel problems.

Human language is a great example of this universal behavioral flexibility. Language writ large encompasses a set of mostly arbitrary symbols (e.g., sounds, gestures) allowing individuals to express infinite ideas to others. There are literally thousands of languages spoken around the planet today, each using different sounds and rules for how these sounds get constructed to convey meaning. Every person is born capable of learning any of these languages— even several of them—as long as they are immersed in a language from a young age. The network of areas in the brain that enable language are pretty much the same in everyone.

So, the brain contributes to cultural and linguistic variation in humans in that it provides the cognitive scaffolding necessary for cultural expression, but the brain certainly doesn’t ‘determine’ cultural differences across the globe. This is important from a historical perspective because in some of the intellectual precursors to modern anthropology, researchers assumed a strong biological determinism underlying human behavioral variation, leading to scientific racism and eugenics which unfortunately have enduring legacies into the present day. Rather, despite the great cultural diversity among humans today, we are remarkably biologically similar to one another the world over.

An enduring question is how (and why) our cultural brains evolved in the first place. Answering this question requires a comparative approach, examining how human brains are similar or different to brains of other animals, as well as how brains vary among members of the same species. One of the coolest things to come out of these comparisons is that there isn’t really anything totally ‘new’ about our brains, except for one surprisingly simple thing. The basic components and structures that are found in the human brain are shared among all animals with a backbone, meaning the basic recipe for brain soup is over 500 million years old. The wrinkly outer rind of the brain—the cerebral cortex—is shared across all mammals, meaning it originated over 200 million years ago. Within mammals, humans are a member of a diverse group called primates, and primate brains have some unique characteristics compared to other furry creatures. We’ve known for over 100 years that human brains are much larger than you’d expect for mammals or even primates of our body size; research in the past 20 years or so has shown that ‘under the hood,’ humans have basically just a primate brain scaled up to a large size.

You might be wondering, if our brains aren’t so different from those of other primates, why are we such weird animals capable of behaviors never seen in the hundreds of millions of years that brains have been around? The answer is that, on the one hand, there are emergent properties that arise simply from increasing brain size, and these properties may allow our brains to do things that other animals’ can’t (as far as we know). On the other hand, close study of other animals is showing that they’re actually a lot smarter than we often give them credit for.

Even though we’re seeing ways that humans are like other animals in both the brain and what the brain can do, we are nevertheless unusual in many ways that underscore the human condition, and we still need an explanation for how/why we evolved. Researchers have made many insights into these questions by comparing us with our closest living relatives: chimpanzees and bonobos. You wouldn’t guess it from looking, but these two apes share a more recent common ancestor with us humans than they do with other apes like gorillas and orangutans. This ancestor probably lived some time between 6–8 million years ago, and presumably its brain would have been lot like that of chimps/bonobos. How did we get from that to the big and powerful processor between our ears?

The fossil record provides the only direct evidence (itself rather indirect) of what past brains were like, in the form of endocasts: imprints that the brain makes on the inside of the skull bones during growth. The image I selected for my flash talk (above) shows the endocasts from five fossils of a species called Homo naledi that lived in South Africa around 300,000 years ago. You can see that some are fairly complete (like the one on the left), while others have really prominent impressions created by the outer surface of the brain (like the one second from the right side). All five of these endocasts leave something (or a lot) to be desired. The human fossil record so far provides us with literally hundreds of fossil endocasts at various states of completeness, providing small, blurry windows into brains in the human lineage over the past six million years. Although most are fragmentary, the phantoms of ancient minds, I think they tell a cool story about the human condition, and call for a truly integrative and anthropological approach to studying the brain.

What the fossil evidence seems to show, along with archaeological and modern behavioral research, is that the human brain evolved in order to cooperatively extract and allocate an immense amount of energy from the environment—and a flexibility to do this in almost any environment. Growing a big, human brain requires extensive time and calories; these in turn can only be afforded by cooperative foraging and parenting. So far as we can tell, humans surpass all other animals (or at least primates) in abstract thinking, considering the thoughts and mental states of others, and working with others toward shared goals. The brain as a body part and subject of study is great because we need to draw on diverse types of data and evidence to understand it, an alphabet of disciplines from Anatomy and Anthropology to Physics and Zoology.

Hip new Australopithecus deyiremeda juveniles

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Header: "Australopithecus deyiremeda" but in a gold Harry Potter font, beneath which in the "Chalkduster" font is written, "And the Explosion of non-adult fossils"

Dr. Yohannes Haile-Selassie & colleagues just published some amazing fossils from around 3.4 million years ago, that convincingly link an unusual hominin foot fossil to an ancient human called Australopithecus deyiremeda.

In 2012, Haile-Selassie and team reported a foot fossil from Burtele, Ethiopia, revealing a bipedal creature (like a human) but with some grasping ability in the big toe (like all other primates). Then in 2015, the team presented some jaws and teeth from a nearby geological locality in the Burtele region, around which they designated a new hominin species, Australopithecus deyiremeda. The researchers hesitated to allocate the Burtele foot to this new species since they didn’t have similar fossils for comparison between the different fossil localities. But as the scientists have recently reported, jaws and teeth discovered from the foot site, including an incredible juvenile mandible, match those of Au. deyiremeda from the nearby Burtele sites. Now we can put a foot to the name.

The Burtele fossils help reveal the diversity of early hominins like Australopithecus and the contexts out of which our own genus Homo evolved. What caught my attention hiding among this amazing assemblage was a fossil that only gets a quick mention in the paper—the ischium bone from the hip of a juvenile deyiremeda:

Extended Data Figure 7 from Haile-Selassie et al. (2025). The BRT-VP-2/87 juvenile ischium (from the right side of the body), depicted in side (a), middle (b), and back (c) views.

The fossil, given the catalog number BRT-VP-2/87, represents a different individual from the juvenile jaw mentioned above. It nevertheless provides a great deal of information despite being a small fragment (less than 2 inches long). The authors observe that the body of the ischium that extends beneath the hip joint is quite long, similar to modern apes, fossil Ardipithecus ramidus, and australopiths. This contrasts with the ischium of modern and fossil Homo in which the bone projects less beyond the hip socket:

Right juvenile ischium bones, scaled to similar size and oriented in similar positions. The black line on each depicts the distance from the hip socket margin to the top of the ischial tuberosity (left modified from Scheuer & Black, 2000 Fig. 10.15)

The bottom of the ischium is called the “ischial tuberosity,” and is the attachment surface for the hamstrings muscles. Having a long ischium provides the hamstrings of apes and other arboreal primates with more powerful hip extension—very useful when climbing trees but it also limits how far back the thigh can extend away from the body (Kozma et al., 2018). The shorter ischium of humans, Homo naledi, and other members of our genus may make our hamstrings a little less powerful, but it also helps us fully extend our legs which is crucial to our efficient bipedal walking and running.

Pelvis growth and development in chimpanzees (top row) and humans (bottom row), all scaled to a similar vertical height. Notice the differences in both the relative length of the ischium (blue bracket) and orientation of the ischial tuberosities between chimps and humans, consistent across the growth period. Images modified from Huseynov et al. (2016 and 2017).

Based on studies of modern humans and other primates, we know that this configuration of bones and muscles is established before birth, so we can be confident that adult Au. deyiremeda would have had a similar anatomy to BRT-VP-2/73, albeit at an unknown, larger size. A hip well adapted for climbing is consistent with the Burtele foot with a grasping big toe.

As Haile-Selassie and colleagues note in the online supplementary information accompanying the paper, only immature fossils allow us to reconstruct the evolution of growth and development. But one of the major challenges of studying immature remains is determining their age or state of maturation, which is critical for understanding how much change occurs between, say, infancy and adulthood. The authors of this study note that the qualitative appearance of the BRT-VP-2/73 hip socket surface is like that of modern humans around 6 years of age, yet the fossil is much smaller and more similar in size to 3 year-old humans. My colleagues and I (2022) faced a similar challenge when analyzing a juvenile Homo naledi hip, and we also relied on qualitative comparisons of how the joint “looks” at different stages of development.

But I think we’re at a point now where we can try to quantify some of these tricky developing surfaces to help place immature fossils more precisely along a timeline of development. For example, Peter Stamos & Tim Weaver (2020) adapted a method for quantifying the topography of teeth, to measure the complex curvature of the developing surface of the knee. If these quantitative methods can distinguish different phases of development in large samples of humans and other primates (e.g., Stamos et al., 2025), they could then be extended to the immature hominin fossil record.

Some cool insights could also be gained by applying older and established methods like landmark-based geometric morphometrics, even on quite fragmentary fossils. This approach could capture the development and orientation of the ischial tuberosity relative to the hip socket surface in fragments like BRT-VP-2/73, MLD 8, and Homo naledi fossils (depicted above) and compared with fossil adults. Researchers have also devised robust ways of quantifying size and shape changes during growth based on modern animals, and using these patterns to then ‘grow’ immature fossils to more developed states, for comparison with actual adult fossils (McNulty et al., 2006). Applying this approach to even just the small fossil sample of ischia described here could tell us a lot about how ancient animals moved at different periods in their lives. Someone just needs to park their ischial tuberosities in a chair and do it!

A growing fossil record of immature hominins, alongside technical advances in quantifying and comparing anatomy, mean that we are ready to learn much more about how our extinct ancestors and cousins grew into competent adults.

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.

New decade, new syllabi

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We just kicked off the Spring semester here at Vassar College, and so I’ve got some freshly-updated bio-anthro syllabi hot off the press. This semester, I’m doing my annual introductory class (Anth 120, “Human Origins”), a resurrected seminar (Anth 305: “Human Evo-Devo”), and a second stab at a new methods module (Anth 211: “Virtual Anthropology”).

Anth 120 is similar to previous versions, although this year I’ve taken out a reading/lecture on Paleolithic technology, replaced with articles scrutinizing evolutionary psychology. We’ll see how it goes.

The other two classes are greatly overhauled from previous versions. Anth 211, “Virtual Anthropology,” is my first contribution to a new curricular initiative here at Vassar, which are called “intensives.” Anth 211 is kind of a hybrid between a regular class and an independent study, giving students experience with computer-based, “virtual” methods used in biological anthropology and related fields.  In the first half of the semester, students will get to try out some of these methods and see what kinds of research questions they’re used for. In the 2nd half of the term, students do their own Virtual Anthropology study drawing on the materials in my HEAD Lab, and then present a research poster at the end of the year. I debuted this intensive last Fall, and based on that experience I’m providing a bit more training and have more activities for students this Spring. If last semester’s projects are at all predictive, we should have some fun projects in store this year.

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Anth 305 is a fossil-focused examination of the roles of growth and development in human evolution, and this year’s version is also highly modified from the last time I taught it over two years ago. In that first version, course content was patterned along the skeleton, e.g., one week looked at evolution and development of teeth, next week the spine, etc. Such a bauplan might work for building bodies, but it wasn’t the best for teaching. So this year, we’re spending the first few weeks on the fossil record of human evolution, getting acquainted with the curious characters of our deep past. From there, we go over skeletal / developmental biology, before delving into special evo-devo topics like “morphological integration” and “heterochrony” for the rest of the semester. We’ll also read lots of old, “classic” papers along the way.

Syllabi for these, and other classes, can be found on the teaching page of the site, if you want to learn more.

New anthropology syllabi for 2017

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This Fall I’m teaching three courses at Vassar, two in Anthropology and one in Environmental Studies. Syllabi are posted to my Teaching page in case anyone wants to use them – here are the highlights:

Anth 235: Central Asian Prehistory

Anth 235 site map

I taught this for the first time last Spring, so the Fall syllabus is updated based on how things went in the first go around. This time, students will get more more in depth with the fossil hominins and less on the lithics on the early side. On the more recent end, there are now readings expressly concerned with sites of the Bactrian-Margiana Archaeological Complex, as well as archaeology of both the Tarim and Pazyryk mummies.

Anth 305: Human Evolutionary Developmental Biology

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This is a seminar version of the first class I ever made on my own, previously taught at the University of Michigan and Nazarbayev University. There have been lots of new discoveries and I’ve published more on this topic since the last time I taught the class. I’m  also excited to see how this class goes as a seminar in which students contribute more to discussion, rather than me rambling on about osteoblasts, morphological integration, and the like.

Enst 187: A Prehistoric Perspective on Climate Change

climatesummit

This is a 100% brand spankin new class, that uses the climate-denialist argument, “But climate has always been changing,” as a basis for comparing the past and the present. In this First-year Writing Seminar, we’ll compare arguments for defining the “Anthropocene,” examine how climate change may have impacted human evolution, and study archaeological evidence for how climate change has impacted different prehistoric societies.

Historical contingency and an herbivorous calamity

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This post was chosen as an Editor's Selection for ResearchBlogging.org

A while ago I asked, “What the hell was Australopithecus boisei doing?” To recap: there’s this weird side branch of human evolution that was dubbed “Australopithecus boisei” and lived in Eastern Africa from around 2.3 – 1.4 million years ago. They lived right alongside our ancestors, early Homo. Humans from around the world today are not as diverse as racists would have you think (really!), so you’d be totally blown away by the diversity of the early Pleistocene. Since 1959 when A. boisei (then Zinjanthropus boisei) was first discovered, people noticed its massive molar and premolar teeth, thick and powerful jaws, and muscle markings indicative of diabolical chewing power. ‘Probably subsisted on a diet of low-quality, hard to chew foods,’ people reasoned.

But a few years ago, this picture changed: evidence from toothwear and the chemical composition of teeth suggested A. boisei was actually eating grass or sedges (see the referred post or a nice recent review by Julia Lee-Thorp for more info). Such a diet is totally at odds with what people had hypothesized based on the size of the chewing muscles and teeth.

Colobus molars, good for shearing apart leaves. (image: http://bit.ly/xefm6t)

I was discussing this last point with a colleague the other day, who could not believe A. boisei ate grasses or the like: Many animals known to eat grass or leaves tend have molars with high crowns with slicing edges for shearing apart a mouthful of vegetation (above), but A. boisei molars are large and low-cusped, becoming fairly flat with wear (below).

Australopithecus boisei specimen KNM-ER 15930 (Leakey & Walker 1988, Figure 8)
But, it occurred to me, maybe high-crowned, shearing molars simply were not an ‘option’ in the evolution of Australopithecus boisei (see note below**). Natural selection is a powerful force of evolution, but it is limited because it can work only with existing variation: it does the best it can with what it’s got. The earliest surefire hominins, Australopithecus anamensis and afarensis, certainly did not have ‘cresty’ molars with pointy cusps, and neither did many late Miocene apes, for that matter. Rather, the ancestors of A. boisei had fairly low bulbous molar cusps, and that’s some serious evolutionary baggage for a hominid hoping to corner the grass and sedge market.
So we can draw up the following hypothesis for the evolution of A. boisei: as the early members of the species moved into a niche of eating grass/sedges, rather than evolve cresty teeth, they increased the size and enamel thickness of their ancestors’ molars to better-withstand their diet. Perhaps this was the ‘easiest’ solution to adapting teeth to a crappy diet (maybe some developmental constraint?). Or perhaps there’s another, yet unidentified food responsible for the species’ curiously high-C4 diet … who knows? Nota bene: this isn’t necessarily what I think happened, it’s just a hypothesis consistent with current evidence about A. boisei‘s anatomy and diet.
If Life on Earth has taught us anything, it’s that there are many ways to do the same thing. What’s more, evolution is highly constrained by pre-existing biology and historical circumstance. Australopithecus boisei may have been ‘a victim of its times,’ forced into an herbivorous niche for which it was ill-equipped.
READ MORE!
Leakey RE, & Walker A (1988). New Australopithecus boisei specimens from east and west Lake Turkana, Kenya. American Journal of Physical Anthropology, 76 (1), 1-24 PMID: 3136654
Lee-Thorp, J. (2011). The demise of “Nutcracker Man” Proceedings of the National Academy of Sciences, 108 (23), 9319-9320 DOI: 10.1073/pnas.1105808108
*Edited 07 Nov 2015
** This blog post was written in 2012. In 2016, Peter Ungar and Leslea Hlusko wrote more on this idea of boisei being constrained in its dental evolution here.

Evolution: What it is and why humans aren’t immune to it

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An alternate title for this post could be “BigThink Too Big For Own Britches.”

Physicist Michio Kaku (via John Hawks via Pharyngula) has re-brought my attention to the fact that a great deal of people (smart people like Kaku included) misunderstand the mechanics of biological evolution. Quite simply, evolution is change in a gene pool over time. This pool could be an entire species or a small population within that species.

There are a number of ways evolution can happen. A mutation is a new genetic variant that arises in an individual, which can then be spread to later generations when that individual reproduces. A single strand of human DNA is like a string of some 3 billion letters. When a person replicates their DNA for it to be passed on to their offspring (meiosis), having to reproduce such a long strand ensures that a mistake is made at least once in a while. Hence mutations increase variation in a gene pool.
But the frequencies of genes in a population can change, that is they may become more or less common within the gene pool. This could happen by genetic drift, which is the random loss of genes. If a gene is neither adaptive nor harmful, it could simply be lost over time due to sheer chance. In contrast to mutation, drift reduces genetic variation.
If genes are adaptive or harmful, their frequency in a gene pool becomes subject to natural selection. If a gene (or set of genes) is adaptive, that means the possessor of those genes will be more likely to survive and reproduce than others, i.e., the individual will be more likely to pass on these genes. Over time, the adaptive genes will increase in frequency in a population. Conversely, genes that lower the likelihood of surviving and reproducing will become less frequent in subsequent generations. Either of these scenarios means selection is reducing genetic variation. But sometimes different forms of a gene can be adaptive in different situations or combinations, so selection will act to maintain both of these in the gene pool. So in contrast to mutation and drift, selection can reduce or maintain genetic variation.
Finally, gene flow refers to genes being introduced into a gene pool from another source. This could occur when someone from one population reproduces with an individual from another population, and so new genes may enter one of the groups. Like mutation, this will increase genetic variation in a gene pool.
Common misconceptions
It may seem counterintuitive, but evolution does not equate with progress. This is a common misconception, probably due to the social ideologies under which evolutionary theory developed. Because of selection, evolution often means that a population becomes better-suited to its environment over time, which seems like progress. But as we’ve seen above, not all evolution is selection; mutation and drift are fairly random processes of evolution that don’t necessarily bear on adaptation. In addition, environments and circumstances change, so that even if something evolved in a place where it was adaptive, it may be harmful in a new context. For example, as the earliest humans lost their body hair, they probably evolved to have darker skin: adaptive in the tropics where humans originated. But later, when early humans moved into more northerly latitudes with less ultraviolet exposure from the sun, the dark skin that was adaptive for a hairless human in a tropical environment came to hinder the body’s vitamin D synthesis: maladaptive!
Also contra popular opinion, individuals do not evolve, populations do. Trojan brand condoms recently had an ad campaign in which they encouraged men to “evolve” by using Trojan condoms when having promiscuous sex. This is in line with the incorrect idea above that ‘evolving’ means ‘becoming better’ or ‘more sophisticated.’ Of course, condoms may actually help a population to evolve: those who use condoms to prevent pregnancy are ensuring they do not pass on their genes. And if there’s any genetic predisposition to make one more likely to use condoms (and there’s not), these genes would certainly become less common in future generations. [I am NOT encouraging people not to use protection, by the way]
So this brings us to a final point: the main misconception expressed in Dr. Kaku’s video is that humans are not evolving. Technology and urbanization, he tells us, have circumvented natural selection on human features (well, the “gross” or visible ones). This is very wrong and shortsighted. In fact, this is one of the bases of the eugenics movement of the early 20th century. Eugenicists thought, ‘Nature is no longer ensuring some people don’t pass on their genes, so we ought to do it ourselves for the good of humankind.’ This first thought, about the insufficiency of Nature, is echoed by Dr. Kaku (though surely he does not think the second).
Simply put, HUMANS ARE STILL EVOLVING. Remember, not all evolution = natural selection. The genetic composition of humankind is still subject to the random forces of mutation and drift. In fact, because the human population size has increased exponentially of late, the fact that there are way more people than ever means that there are more mutations entering the population, and at a faster rate, than ever! But selection is still at work, too. There are still diseases that kill people before they can pass on their genes. There are still environmental situations – even in ‘civilized’ places! – that prevent people from passing on their genes.
We humans are still evolving because we are still subject to the forces of evolution, and we always will be. Now what physicist could’ve told you that?!