Hip new Australopithecus deyiremeda juveniles

November 30, 2025December 1, 2025 / zcofran / Leave a comment

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.

How small apes grow big canine teeth

March 26, 2025December 30, 2025 / zcofran / Leave a comment

Gibbons are sometimes referred to as “lesser apes” since they’re the smaller-bodied cousins of “great apes” like us humans, chimpanzees, gorillas, and orangutans. But what they lack in body mass they make up for in taxonomic diversity, with roughly 20 species distributed across four genus groups (Kim et al., 2011). And while male great apes (except humans) have large canine teeth, both sexes in gibbons have large maxillary canines — flashy weaponry for defending territory.

*Pointy canine teeth peeking out from the upper and lower jaws of an adult female gibbon cared for at the International Primate Protection League (source)*

My research has generally focused on brains and growth throughout human evolution, but I started looking at gibbons a few years ago when the COVID-19 pandemic put research travel on hold. Inspired by Julia Zichello’s 2018 article about gibbon models for understanding hominin evolution and appreciating that “overlooked small apes need more attention,” I had the opportunity to CT scan a unique skeletal collection of white-handed gibbons (Hylobates lar), which was sadly harvested from the forests of Thailand back in the late 1930s. Previous research on skull growth in gibbons has mostly used small samples compiled from different species (and sometimes even different genera). In contrast, this CT dataset includes many individuals at each stage of maturation from late infancy through adulthood, effectively representing a single population at a point in time. So with this larger cross-sectional sample of a single species, we can better understand how gibbon brains and faces grow. And because permanent teeth form in a long, continuous sequence throughout the growth period, an individual’s state of dental development can serve as a marker of where they are along the maturation process.

In a paper hot off the press, Julia Boughner and I analyzed dental development in this unique sample (article here). One of the coolest things we found was that gibbons’ large upper canine teeth are among the first to begin but last to finish tooth formation. In fact, the large canines growing inside relatively small faces may inhibit growth of one of the neighboring incisor teeth until the face has grown to create enough space for it. And while most teeth developing within the jaw begin emerging into the mouth once there’s enough room for them, gibbons’ gargantuan upper canines are forced out of hiding as they outgrow their bony crypts (check out the right-most jaw in the second row below).

Cross-sectional representation of tooth formation in white-handed gibbons, starting with the youngest in the top left and ending with the oldest in the bottom right. The first permanent tooth to form and emerge, M1, is highlighted along with the canine “C.”

In addition to characterizing ‘normal’ dental development, we also observed several developmental anomalies and pathologies in the sample. Our observations corroborate previous research showing that tooth formation generally proceeds ‘as scheduled’ despite various other disturbances to development.

It remains to be seen whether early development of the canine at the cost of delayed incisor formation is a pattern unique among all the apes, since most other studies of ape tooth formation have examined the lower jaw while our study focused on the upper jaws. But the canine-incisor tradeoff that we identified sets the stage for subsequent study of skull growth in this sample, as it highlights the many factors and functions that must be coordinated during growth.

While we have several projects planned with this unique dataset, we have also published the tooth formation data that we analyzed, and the original micro-CT scans themselves will be published to the online repository Morphosource.org soon, once a few more projects are finished.

The hand of Homo naledi points to life before birth

December 5, 2024December 7, 2024 / zcofran / Leave a comment

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.

Did Homo naledi have big babies?

August 8, 2023December 7, 2024 / zcofran / Leave a comment

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

New decade, new syllabi

January 26, 2020 / zcofran / Leave a comment

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.

cropped-screen-shot-2020-01-19-at-1.30.37-pm.png

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

September 3, 2017 / zcofran / Leave a comment

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

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.

#AAPA2017 – Modularity & evolution of the human canine

April 23, 2017April 23, 2017 / zcofran / 1 Comment

I’m recently returned from this year’s AAPA Conference, hosted by Tulane University in New Orleans. What a trip!

Usually my presentations involve fossils and/or growth, but this year I wanted to try a different way of looking at the evolution & development – integration & modularity. In short, biological structures that share a common developmental background and/or function may comprise ‘modules’ that are highly ‘integrated’ with one another, but relatively less integrated with other structures or modules.

I hypothesized that canine reduction in hominins is a result of a shift in modularity of the dentition, such that the canine became more highly integrated with the incisors than with the premolars. I’d thought of this 5 years ago when creating the first rendition of my human evo-devo course (offering again next fall!), but never got to look into it. Interestingly, the results generally supported my predictions, except for one pesky sample…

As my primatologist friends will tell you, male chimps are the worst.

Here’s a pdf version of the poster. It was fun to dabble with a new methodology, to see my far-flung friends, and to visit a fun historic place for the AAPA conference. Definitely looking forward to next year in Austin!

Worst year in review

December 31, 2016December 31, 2016 / zcofran / Leave a comment

As we’re wrapping up what may be the worst year in recent global memory, especially geopolitically, let’s take a moment to review some more positive things that came up at Lawnchair in 2016.

Headed home

Alternate subtitle: Go West
This was a quiet year on the blog, with only 18 posts compared with the roughly thirty per year in 2014-2015. The major reason for the silence was that I moved from Kazakhstan back to the US to join the Anthropology Department at Vassar College in New York. With all the movement there was less time to blog. Much of the second half of 2016 was spent setting up the Biological Anthropology Lab at Vassar, which will focus on “virtual” anthropology, including 3D surface scanning…

Cast of early Homo cranium KNM-ER 1470 and 3D surface scan made in the lab using an Artec Spider.

… and 3D printing.

A gibbon endocast, created from a CT scan using Avizo software and printed on a Zortrax M200.

This first semester stateside I reworked my ‘Intro to Bio Anthro’ and ‘Race’ courses, which I think went pretty well being presented to an American audience for the first time. The latter class examines human biological variation, situating empirical observations in modern and historical social contexts. This is an especially important class today as 2016 saw a rise in nationalist and racist movements across the globe. Just yesterday Sarah Zhang published an essay in The Atlantic titled, “Will the Alt-right peddle a new kind of racist genetics?” It’s a great read, and I’m pleased to say that in the Race class this semester, we addressed all of the various social and scientific issues that came up in that piece. Admittedly though, I’m dismayed that this scary question has to be raised at this point in time, but it’s important for scholars to address and publicize given our society’s tragically short and selective memory.

So the first semester went well, and next semester I’ll be teaching a seminar focused on Homo naledi and a mid-level course on the prehistory of Central Asia. The Homo naledi class will be lots of fun, as we’ll used 3D printouts of H. naledi and other hominin species to address questions in human evolution. The Central Asia class will be good prep for when I return to Kazakhstan next summer to continue the hunt for human fossils in the country.

Osteology is still everywhere

A recurring segment over the years has been “Osteology Everywhere,” in which I recount how something I’ve seen out and about reminds me of a certain bone or fossil. Five of the blog 18 posts this year were OAs, and four of these were fossiliferous: I saw …

Anatomy terminology hidden in 3D block letters,

Hominin canines in Kazakhstani baursaki cakes,

The Ardipithecus ramidus ilium in Almaty,

A Homo naledi juvenile femur head in nutmeg,

And a Homo erectus cranium on a Bangkok sidewalk. As I’m teaching a fossil-focused seminar next semester, OA will probably become increasingly about fossils, and I’ll probably get my students involved in the fun as well.

New discoveries and enduring questions

The most-read post on the blog this year was about the recovery of the oldest human Nuclear DNA, from the 450,000 year old Sima de los Huesos fossils. My 2013 prediction that nuclear DNA would conflict with mtDNA by showing these hominins to be closer to Neandertals than Denisovans was shown to be correct.

These results are significant in part because they demonstrate one way that new insights can be gained from fossils that have been known for years. But more intriguingly, the ability of researchers to extract DNA from exceedingly old fossils suggests that this is only the tip of the iceberg.

The other major discoveries I covered this year were the capuchin monkeys who made stone tools and the possibility that living humans and extinct Neandertals share a common pattern of brain development.

An unrelated image from 2016 that makes me laugh.

The comparison between monkey-made and anthropogenic stone tools drives home the now dated fact that humans aren’t the only rock-modifiers. But the significance for the evolution of human tool use is less clear cut – what are the parallels (if any) in the motivation and modification of rocks between hominins and capuchins, who haven’t shared a common ancestor for tens of millions of years? I’m sure we’ll hear more on that in the coming years.

In the case of whether Neandertal brain development is like that of humans, I pointed out that new study’s results differ from previous research probably because of differences samples and methods. The only way to reconcile this issue is for the two teams of researchers, one based in Zurich and the other in Leipzig, to come together or for a third party to try their hand at the analysis. Maybe we’ll see this in 2017, maybe not.

There were other cool things in 2016 that I just didn’t get around to writing about, such as the publication of new Laetoli footprints with accompanying free 3D scans, new papers on Homo naledi that are in press in the Journal of Human Evolution, and new analysis of old Lucy (Australopithecus afarensis) fossils suggesting that she spent a lifetime climbing trees but may have sucked at it. But here’s hoping that 2017 tops 2016, on the blog, in the fossil record, and basically on Earth in general.

Did Neandertal brains grow like humans’ or not?

July 26, 2016July 26, 2016 / zcofran / 1 Comment

According to Marcia Ponce de Leon and colleagues, “Brain development is similar in Neandertals and modern humans.” They reached this conclusion after comparing how the shape of the brain case changes across the growth period of humans and Neandertals. This finding differs from earlier studies of Neandertal brain shape growth (Gunz et al. 2010, 2012).

Although Neandertals had similar adult brain sizes as humans do today, the brains are nevertheless slightly different in shape:

Endocranial surfaces of a human (left, blue) and Neandertal (right, red), from Gunz et al. (2012). These surfaces reflect the size and shape of the brain, blood vessels, cerebrospinal fluid, and meninges.

Gunz et al. (2010, 2012) previously showed that endocranial development in humans, but not in Neandertals or chimpanzees, has a “globularization phase” shortly after birth: the endocranial surface becomes overall rounder, largely as a result of the expansion of the cerebellum:

Endocranial (e.g., brain) shape change in humans (blue), Neandertals (red) and chimpanzees (green), Fig. 7 from Gunz et al. (2012). Age groups are indicated by numbers. The human “globularization phase” is represented by the great difference in the y-axis values of groups 1-2 (infants). The Neandertals match the chimpanzee pattern of shape change; Neandertal neonates (LeM2 and M) do not plot as predicted by a human pattern of growth.

Ponce de Leon and colleagues now challenge this result with their own similar analysis, suggesting similar patterns of shape change with Neandertals experiencing this globularization phase as well (note that endocranial shapes are always different, nevertheless):

Endocranial shape change in humans (green) and Neandertals (red), from Ponce de Leon et al. (2016). Note that the human polygons and letters represent age groups, whereas the Neandertal polygons and labels are reconstructions of individual specimens.

The biggest reason for the difference between studies is in the fossil sample. Ponce de Leon et al. have a larger fossil sample, with more non-adults including Dederiyeh 1-2, young infants in the age group where human brains become more globular.

Comparison of fossil samples between the two studies.

But I don’t think this alone accounts for the different findings of the two studies. Overall shape development is depicted in PC 1: in general, older individuals have higher PC1 scores. The globularization detected by Gunz et al. (2010; 2012) is manifest in PC2; the youngest groups overlap entirely on PC1. The biggest difference I see between these studies is where Mezmaiskaya, a neonate, falls on PC2. In the top plot (Gunz et al., 2012), both Mezmaiskaya and the Le Moustier 2 newborn have similar PC2 values as older Neandertals. In the bottom plot (Ponce de Leon et al., 2012), the Mezmaiskaya neonate has lower PC2 scores than the other Neandertals. Note also the great variability in Mezmaiskaya reconstructions of Ponce de Leon et al. compared with Gunz et al.; some of the reconstructions have high PC2 values which would greatly diminish the similarity between samples. It’s also a bit odd that Engis and Roc de Marsal appear “younger” (i.e., lower PC1 score) than the Dederiyeh infants that are actually a little bit older.

Ponce de Leon et al. acknowledge the probable influence of fossil reconstruction methods, and consider other reasons for their novel findings, in the supplementary material. Nevertheless, a great follow-up to this, to settle the issue of Neandertal brain development once and for all, would be for these two research teams to join forces, combining their samples and comparing their reconstructions.

REFERENCES

Gunz P, Neubauer S, Maureille B, & Hublin JJ (2010). Brain development after birth differs between Neanderthals and modern humans. Current Biology : 20 (21) PMID: 21056830

Gunz P, Neubauer S, Golovanova L, Doronichev V, Maureille B, & Hublin JJ (2012). A uniquely modern human pattern of endocranial development. Insights from a new cranial reconstruction of the Neandertal newborn from Mezmaiskaya. Journal of Human Evolution, 62 (2), 300-13 PMID: 22221766

Ponce de León, M., Bienvenu, T., Akazawa, T., & Zollikofer, C. (2016). Brain development is similar in Neanderthals and modern humans Current Biology, 26 (14) DOI: 10.1016/j.cub.2016.06.022

Did GDF6 “gene tweak” allow humans to become upright?

January 13, 2016January 18, 2016 / zcofran / Leave a comment

The short answer is, “Not really.” But as is often the case, the real story behind so many headlines last week is a bit more complicated.

smh. Links to the first, second, third, and fourth stories.

What are they talking about, Willis?

These headlines, each saying something slightly different, are referring to a study by Indjeian and colleagues published in Cell. Researchers identified a stretch of DNA that is highly conserved across mammals, or in other words, it is very similar between very different organisms. In humans, however, this conserved region is actually missing (“hCONDEL.306”):

Fig. 4A from Indjeian et al. 2016. A stretch of DNA, "hCONDEL.306" is completely missing in humans (as is another stretch, hCONDEL.305) but otherwise very similar between chimpanzees, monkeys and mice.

Fig. 4A from Indjeian et al. 2016. A stretch of DNA on Chromosome 8, “hCONDEL.306,” is very similar between chimpanzees, macaque monkeys, and mice, but is completely missing in humans (as is another stretch, hCONDEL.305).

That a stretch of DNA should be highly conserved across diverse animal groups suggests purifying natural selection has prevented any mutations from occurring here – alterations to this stretch of DNA negatively affected fitness. But that humans should be missing such a highly conserved region suggests that this deletion came under positive natural selection at some point in human evolution. This strategy, of seeking stretches of DNA that are similar between many animals but very different in humans, has led to the identification of hundreds of genetic underpinnings of human uniqueness. Some of these, such as the case in question, involve deleted sequences and have been termed “hCONDELs,” for “regions with high sequence conservation that are surprisingly deleted in humans” (McLean et al., 2011: 216). Others involve the accumulation of mutations where other animals show few or none (e.g., HACNS1; Prabhakar et al. 2008). In many (most?) cases these are “non-coding” sequences of DNA.

How can “non-coding” DNA help make humans upright?

As was predicted 30 years ago (King and Wilson, 1975), what makes humans different from other animals isn’t so much in the protein-coding DNA (the classical understanding of the term, “genes”), but rather in the control of these protein-coding genes. “Non-coding” means that a stretch of DNA may get transcribed into RNA but is not then translated into proteins. But even though these sequences themselves don’t become anything tangible, many are nevertheless critical in regulating gene expression – when, where and how much a gene gets used. It’s wild stuff. Indeed, “Many human accelerated regions are developmental [gene] enhancers” (Capra et al., 2013).

In the present case, hCONDEL.306 refers to the human-specific deletion of a developmental enhancer located near the GDF6 gene, which is a bone morphogenetic protein. The major finding of the paper, as stated succinctly in the Highlights title page, is that “Humans have lost a conserved regulatory element [hCONDEL.306] controlling GDF6 expression…. Mouse phenotypes suggest that [this] deletion is related to digit shortening in human feet.”

How do they link this “gene tweak” to digit shortening?

Since humans have lost this gene enhancer that is highly conserved in other mammals, Indjeian and team reasoned that the chimpanzee DNA sequence associated with this deletion, retaining the enhancer sequence, is likely the ancestral condition from which the human version evolved. They inserted the chimpanzee version into mouse embryos and watched what happened as they developed. The enhancer was only active in the mice’s back legs, specifically in the cartilage that would later become the lateral toe bones and cells that would become a muscle of the big toe (abductor hallucis). These are areas where humans and chimpanzees differ: our lateral toes are shorter than chimps’, and we only have one abductor hallucis muscle whereas chimpanzees have an additional, longer abductor hallucis (Aiello and Dean, 2002). So, we’re on our way to seeing how hCONDEL.306 might relate to our big toe or upright walking, as the headlines say.

But this still doesn’t explain how this deletion affects GDF6 gene expression, and therefore what this does for our feet. Pressing onward, the scientists compared the size of certain bones in mice with a normal Gdf6 gene, and those in which the Gdf6 gene was completely turned off (or “knocked out”). The Gdf6 knock-out mice had shorter lateral toe bones than regular mice, but they also had shorter big toes as well – the previous experiment staining mouse embryos showed the ancestral enhancer was expressed more in the latter toes, not so much the big toe.

Figures 5-6 from Indjeian et al. (2016) sum up the findings. Figure 5 (left) shows that the ancestral version of the GDF6 enhancer (blue staining) is most strongly expressed in the lower half of the body, especially the fifth toe bone. Figure 6 (right) shows that a lack of Gdf6 expression (black bars) results in shorter skull and toe bones. Combining these findings, humans lack a gene enhancer associated with the development of long lateral toes.

hCONDEL.306 doesn’t completely turn off GDF6, so this second experiment doesn’t really tell us exactly what the hCONDEL does. But the results are highly suggestive. Indjeian and team showed that Gdf6 affects toe length, among other skeletal traits, in mice. The ancestral enhancer that humans are missing seems to affect GDF6 activity in the leg/foot only. This illustrates a mechanism of modularity – as the authors state, “Loss of this enhancer would thus preserve normal GDF6 functions in the skull and forelimbs, while confining any … changes to the posterior digits of the hindlimb.” In other words, developmental enhancers allow different parts of the body to evolve independently despite being made by some of the same genes (such as GDF6).

As with any good study, results are intriguing but they raise more questions for future studies. The researchers conducted two experiments to investigate the function of hCONDEL.306: first putting the chimp version in mouse embryos to see where the ancestral enhancer is expressed, and then turning off Gdf6 completely in mice to see what happens. A more direct way to see what hCONDEL.306 does might be to put a longer stretch of the human sequence surrounding GDF6 containing (or rather missing) the ancestral enhancer into mouse embryos. I’m not a molecular biologist so maybe this isn’t possible. But this is important because the ancestral (chimpanzee) enhancer appeared to be most strongly expressed in the little toe, but of course this isn’t our only toe that is short compared to chimps. Similarly, how hCONDEL.306 relates to the abductor hallucis muscle remains in question – does it reduce the size of the intrinsic muscle present in both humans and chimps, or does it prevent development of the longer muscle that chimps have but we lack? We can expect to find hCONDEL.306 in the genomes of Neandertals (and Denisovans?), since they also have short toes, but what would it mean if they retained the ancestral enhancer?

So how does this gene tweak help with upright walking?

This is a really cool paper with important implications for human evolution, but something seems to have been lost in translation between the paper and the headlines (the news pieces themselves are good, though). The upshot of the study is that humans lack a stretch of non-coding DNA, which in chimpanzees (or chimp-ified mice) promotes embryonic development of the lateral toes and a big toe muscle. This may be a genetic basis for at least some aspects of our unique feet that have evolved under natural selection for walking on two legs.

But the headlines misrepresent this result, with words like “led to,” “allowed,” and “caused,” especially when these are followed by “big toe” or “upright walking.” hCONDEL.306 doesn’t really have anything to the big toe bone itself, although it might relate to a muscle affecting our big toe. The only sense in which the “Gene tweak led to humans’ big toe” (first title above) is that hCONDEL.306 might be responsible for our short lateral toes, which make our first toe look big by comparison. The other headlines are misleading since we know from fossil evidence that hominins walked upright long before we have evidence for short toes:

These little piggies get none. Fourth toe bones of living apes and humans (left) and possible hominins from 3-5 million years ago (right).

These little piggies get none. Fourth toe bones of living apes and humans (left) and (probable) hominins from 3-5 million years ago (right). I did my best to get all images to scale.

“Epigenetic,” from the fourth article headline, is simply wrong. Modern day epigenetics is a field concerned with the chemical alterations to the structure of DNA. Even the broad concept of epigenetic as originally devised by Conrad Waddington was about how environments (cellular or outside the body) influence development.

It’s hard to fit all the important and interesting information from scientific papers into news headlines. Still, it would be good if headlines more accurately portrayed scientific findings, especially avoiding such definitive verbs as “caused.” Especially in the realm of biology, people should know that there’s a lot that we still don’t know, that there’s lots more important work left to be done.

References

Aiello and Dean, 2002. Human Evolutionary Anatomy. Academic Press.

Capra et al., 2013. Many human accelerated regions are developmental enhancers. Philosophical Transactions of the Royal Society B 368: 20130025.

Indjeian et al. 2016. Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell http://dx.doi.org/10.1016/j.cell.2015.12.007

King and Wilson, 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116 DOI: 10.1126/science.1090005

McLean et al., 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216-219.

Prabhakar et al., 2008. Human-specific gain of function in a developmental enhancer. Science 321: 1346-1350.

Lawnchair Anthropology

Biological anthropology, paleontology, evolution, and development, by Dr. Zachary Cofran

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