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Frequently asked questions

A guide to the Current Biology paper:

Neandertal introgression sheds light on modern human endocranial globularity
Philipp Gunz1, Amanda K. Tilot1, Katharina Wittfeld, Alexander Teumer, Chin Yang Shapland, Theo G.M. van Erp, Michael Dannemann, Benjamin Vernot, Simon Neubauer, Tulio Guadalupe, Guillén Fernández, Han G. Brunner, Wolfgang Enard, James Fallon, Norbert Hosten, Uwe Völker, Antonio Profico, Fabio Di Vincenzo, Giorgio Manzi, Janet Kelso, Beate St. Pourcain, Jean-Jacques Hublin, Barbara Franke, Svante Pääbo, Fabio Macciardi, Hans J. Grabe, and Simon E. Fisher.

1 P. Gunz and A.K. Tilot contributed equally.

One of the features that distinguishes modern humans from our extinct relatives and ancestors is the globular shape of the braincase (Figure 1). As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture. However, in the absence of fossil brain tissue the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives, the Neandertals.

Figure 1. Left: Computed tomographic (CT) scan of a Neandertal fossil (La Ferrassie 1). Right: CT scan of a modern human; the cranium was cut open virtually to reveal the inside of the braincase. In a study published in Current Biology Gunz, Tilot and colleagues combine paleoanthropology, archaic genomics, neuroimaging and gene expression to study biological foundations of the characteristic modern human endocranial shape. They find introgressed Neandertal alleles that associate with reduced endocranial globularity and affect expression of genes linked to neurogenesis and myelination.

What motivated your study of endocranial globularity?

Extensive studies of fossils have shown that, in contrast to the elongated endocrania typical of Neandertals and other ancient hominins, a distinctive feature of modern humans is a globular shaped skull and brain. The globular shape of the braincase evolved gradually within our own lineage, independently of brain volume. Even the oldest Homo sapiens fossils from Jebel Irhoud in Morocco, dated to around 300 000 years ago, have endocranial volumes that fall in the range of present-day humans, but their endocranial shapes are elongated. This striking alteration of endocranial shape is likely to reflect evolutionary changes in the organisation of structures of the human brain, perhaps even in the precise ways that different brain areas are connected to each other. However, brain tissue doesn't fossilize, so the underlying biology has remained elusive. Our study addresses this challenging question through a novel interdisciplinary approach that brings together analysis of fossil skulls, ancient genomes, brain imaging and gene expression.

Our aim was to identify potential candidate genes and biological pathways that are related to endocranial globularity. To tightly focus the search, we took advantage of the fact that living humans with European ancestry carry rare fragments of Neandertal DNA buried in their genomes, as a result of interbreeding of different human groups outside of Africa (after Homo sapiens left Africa and encountered Neandertals, e.g., in the Levante and Europe). We reasoned that if we could identify specific Neandertal DNA fragments in a large enough sample of present-day humans, we would be able to test whether any of these fragments push towards a less globular brain shape, allowing us to zoom in on genes that might be important for this trait.

Figure 2. Left: Computed tomographic (CT) scan of a Neandertal fossil (La Ferrassie 1). Right: CT scans of a modern human fetus, a newborn, and an adult (semi-transparent surface). In modern humans the globular endocranial shape emerges soon after birth (just like Neandertal neonates, modern human babies have elongated braincases and endocrania). This suggest developmental differences between modern humans and Neandertals during early brain growth. However, endocranial imprints only capture the outer shape of the brain. They cannot provide direct information about subcortical brain reorganisation.

How much of the Neandertal genome is represented in modern humans?

In present-day people introgressed Neandertal fragments account for ~1-2% of the genomes of non-Africans. As each person carries different Neandertal fragments, collectively ~40% of the Neandertal genome is represented in people living today.

What are the main findings of the new study?

First, we found that the degree of brain globularity varies in different people from the same population, although all living human endocrania are clearly distinct in shape from Neandertals.

Second, we identified Neandertal DNA fragments on chromosomes 1 and 18, carried by living humans, that are correlated with reduced globularity. Like other aspects of brain anatomy, the degree of globularity is likely to be influenced by variation in many different genes, each with a small effect. The effects of each associated Neandertal fragment were subtle, but detectable due to the use of a large sample size in our study (several thousand people).

Third, we found that the associated Neandertal fragments were linked to altered gene activity in tissue from brain structures, including the putamen (in the basal ganglia) and the cerebellum, that might feasibly be relevant to globularity. This work pointed to two genes, each implicated in brain development in prior studies. UBR4 has been shown to be involved in neurogenesis, while PHLPP1 is known to help regulate myelin growth around axons (connections between different neurons).

Figure 3. Schematic of a modern human brain. The left putamen (part of the basal ganglia) is shown in red, the cerebellum is shown in blue.

How are brain shape, endocranial shape, and cognition linked?

Our focus on globularity is not motivated by an idea that brain shape can tell us something simple about our behaviour. In fact, there is no reason to expect any straightforward correlation between overall brain shape and behaviour, and it is unlikely that brain shape has itself been directly subject to evolutionary selection. Braincase shape depends on a complex interplay between cranial bone growth, facial size, and the tempo and mode of neurodevelopment. The motivation behind studying the unique shape of the human braincase is that it represents one of the most well-established and clearly defined anatomical characteristics that distinguishes Homo sapiens from other human species, and one that is tractable to investigate both in fossils and in living humans. Our goal was to use this characteristic observable feature as a window into underlying more elusive aspects of brain biology that are distinctive to modern humans.

How does your method work?

(1) Using computed tomographic (CT) scans of fossil and extant skulls we generated virtual imprints of the interior braincase (endocasts) of modern humans and Neandertals (Figure 4). We then used these distinctive shape differences between modern humans and Neandertals to develop a summary metric for endocranial globularity ("globularity score").

Figure 4. Virtual imprints of the endocranium (endocasts) reveal shape differences between Neandertals (left), and modern humans (right). Left: CT scan of the Neandertal fossil from La Chapelle-aux-Saints with a typical elongated endocranial imprint (red). Right: CT scan of a modern human showing the characteristic globular endocranial shape (blue). Arrows highlight the enlarged posterior cranial fossa (housing the cerebellum) as well as bulging of parietal bones in modern humans compared to Neandertals.

(2) We applied this approach to magnetic resonance imaging (MRI) scans of several thousand human adults to obtain an evolutionarily-derived quantitative index of brain globularity (Figure 5).

(3) Armed with sequence information from archaic hominin genomes, we characterized the DNA of ~4,500 of these adults, using genetic polymorphisms to identify the rare Neandertal fragments that each person carried. We could then test each fragment for association with the degree of brain globularity. Specifically we asked, "Do any of these Neandertal fragments promote a less globular endocranial shape in present-day humans?"

(4) Finally, we studied whether Neandertal fragments associated with endocranial shape had effects on gene activity, in different parts of the brain and in other tissues.

Figure 5. Shown here are the coordinate measurements used to capture endocranial shape from magnetic resonance images of several thousand modern humans.

What are the functions of the two candidate genes?

Like other genes of the genome, these candidate genes have more than one role in the body. Nonetheless, for both candidate genes, there is prior literature establishing that when they are disrupted this has major consequences for brain development, giving clues to their normal functions in the nervous system.

UBR4 affects neurogenesis in the developing neocortex and promotes neuronal migration, among other roles. The function of this gene is well characterized in mice: Loss of the mouse orthologue of UBR4 (called p600) in the developing mouse brain impairs neurogenesis, resulting in microcephaly. In our study we found that in carriers of the relevant Neandertal fragment UBR4 is slightly down-regulated in the putamen (part of the basal ganglia).

PHLPP1 encodes a negative regulator of an important signaling pathway that drives myelination. Differences in myelination pathways suggest differences in the brain's white matter - an intricate network composed of millions of nerve fibers connecting different brain regions into functional circuits (Figure 6). In carriers of the relevant Neandertal fragment, PHLPP1 expression is slightly higher in the cerebellum, which would be predicted to have a dampening effect on cerebellar myelination.

Figure 6. The brain’s white matter is an intricate network composed of millions of nerve fibers connecting different brain regions into functional circuits. These images show the white-matter of a modern human brain as captured by diffusion tensor imaging, seen from the side (left) and from the top (right). The color codes the main fiber-direction. In carriers of the relevant Neandertal fragment, PHLPP1 expression is slightly higher in the cerebellum, which would be predicted to have a dampening effect on cerebellar myelination.

How do these genes influence brain shape?

The effects of carrying these rare Neandertal fragments are subtle, at the gene expression level (small changes in gene activity) and at the phenotypic level (pushing people slightly towards a less globular brain shape). This is only our first glimpse of the genetic underpinnings of the globularity phenotype, which is likely to involve the combined effects of many other genes. Nevertheless, our results provide interesting mechanistic insights, suggesting that the introgressed Neandertal DNA fragments may influence endocranial globularity through effects on neurogenesis and myelination during brain development, in regions of the brain that could plausibly yield alterations in overall shape.

The potential links between evolutionary changes in endocranial globularity and mechanisms affecting the basal ganglia and cerebellum are intriguing, because both brain regions receive direct input from the motor cortex and are involved in the preparation, learning, and sensorimotor coordination of movements. The basal ganglia also contribute to diverse cognitive functions, in memory, attention, planning, skill learning, and potentially speech and language evolution.

Do you expect that other genes also affect endocranial shape?

Yes, most certainly. Globularity is a multifactorial trait, involving combined influences of many different loci, and the effects of individual genetic polymorphisms on overall endocranial shape are small. Moreover, braincase shape depends on a complex interplay between cranial bone growth, facial size, and the tempo and mode of neurodevelopment. It is therefore likely that future genome-wide studies in sufficiently large high-powered samples (tens of thousands of people) will reveal additional relevant genes and associated pathways.

Are you saying that if I carry more Neandertal DNA, then my brain is less globular?

No. Our approach doesn't look for correlations between the total percentage of Neandertal DNA that a person carries and their overall brain shape. Instead, it searches through each Neandertal fragment to find which particular genes have an influence. The problem with examining total amount is that each Neandertal fragment is itself rare and they are scattered through the genome, so that two people who have very similar total amounts of Neandertal DNA (e.g. 1% of their genome) may well carry completely different fragments. And we expect that many of the Neandertal fragments are irrelevant to the globularity phenotype, so by collapsing all of them together as a single sum we would lose the ability to find the real signals. We would also miss the chance to understand which genes are involved and what the biological pathways might be. So, our findings do not suggest that people with the highest percentage of total Neandertal DNA will necessarily have the most elongated brains.

Do your results imply modern humans were smarter than Neandertals?

No. Our results cannot be used to infer what Neandertals could or could not do. This study is about probing evolutionary changes to brain organization and function within the Homo sapiens lineage. Recent archaeological evidence has provided new insights into Neandertal cognition by documenting a suite of sophisticated symbolic behaviors in Neandertals that had previously been attributed exclusively to modern humans, such as the enigmatic structure built deep inside Bruniquel cave, and the Neandertal cave-art from Iberia. We therefore stress that the focus of our paper is brain evolution in modern humans, and not Neandertals.

Did you find evidence for recent selection?

No, even with almost 4,500 individuals, the sample is still too small for this type of analysis to be reliable, so we haven't yet tested it systematically. We are currently working on expanding our sample which should allow questions like this to be addressed in a future study.

What are your future plans?

Our findings suggest developmental mechanisms that might have contributed to the evolution of modern brain shape and function, generating hypotheses that can be tested in the lab, for example using human models of neuronal development.

We are now scaling up our approach, studying larger high-powered samples of tens of thousands of people, such as the UK Biobank. This will enable us to carry out a fully genome-wide screen to reveal additional genes and associated pathways associated with globularity, and will also help reveal how this trait is linked to other aspects of human biology. Overall, the interdisciplinary approach that we developed for this study could be applied more broadly to unresolved questions about human brain evolution.

Is it Neandertal or Neanderthal?

Both versions are correct; “Neandertal” is more common in the USA. The formal species name is Homo neanderthalensis. “Neandertal” means Neander-Valley in German (where two partial skeletons were discovered in a cave). “Thal” is the outdated Old-German spelling, “Tal” the contemporary German spelling. Both versions are pronounced the same (i.e. the “th” is pronounced as a “t”). "

Can everyone use the images for teaching or in publications?

Yes, we are releasing all images under Creative Commons license (CC BY-NC-ND 4.0) for non-commercial use. You can find the high-resolution versions of the illustrations and the figure captions by clicking on this Dropbox-link.