Is Human Intelligence Simple? Part 2: Genetics
Did a few genes give us better brains?
Is there a “secret sauce”, a relatively simple physiological mechanism, that enabled human intelligence?
If a few new brain-related mutations arose around the time Homo sapiens evolved or achieved “behavioral modernity”, that would be evidence for the “secret sauce hypothesis.”
So, did this happen?
First of all, one thing that doesn’t qualify as a discrete, sudden “Homo sapiens secret sauce” is brain size. Brain size steadily increased along the evolutionary lineage from apes to humans, a trend that began long before Homo sapiens arose.
Two genes that are associated with brain size, ASPM and MCPH1, were both under positive selection along the whole trajectory from primates to humans.1 In humans, mutations in these genes cause microcephaly, a condition where the brain is abnormally small, causing intellectual disability. It’s a pretty straightforward and consistent picture: these genes really do matter for brain size and cognitive function; skull measurements tell us that brains grew as hominids evolved into humans; and the sequences of these genes varied especially fast along that evolutionary trajectory, indicating positive selection.
A rough estimate that is based on the McDonald–Kreitman test indicates that about 43 advantageous substitutions have taken place in ASPM over the 18–20 million years of evolution from the last common ape ancestors to humans (or ~2 favourable changes per million years). For MCPH1, roughly 45 advantageous changes occurred over 25–30 million years in the lineage from simian ancestors to humans (also ~2 favourable changes per million years).
Zooming in further on brain size, however, there is one allele of the MCPH1 gene that has reached 70% of the current human population and is only about 37,000 years old — around the time that “behaviorally modern” Homo sapiens artifacts appear in Europe, and long after the first arguably “behaviorally modern” artifacts appear in Africa. In fact, patterns in the sequence and inheritance of this allele suggest that it was introduced 37,000 years ago by interbreeding with a different Homo species that separated from modern humans about 1.1 million years ago, which has since gone extinct.2
This is intriguing as a candidate for a “secret sauce” change, but it would still be older than Homo sapiens and still most likely linked to a trait (brain size) that had already been changing gradually for millions of years.
Several other brain-related genes differ between humans and other primates, though in many cases the mutations are shared with Neanderthals, not just Homo sapiens3:
Both humans and Neanderthals have a deletion in the enhancer region of GADD45G, which causes increased nerve cell proliferation.
Humans, Neanderthals, and Denisovans all have three duplications of SRGAP2, a gene involved in brain development that affects brain mass, number of neurons, and synapse formation.
Humans have more copies than any other species of the Olduvai domain in the NBPF genes and the CDKRAP2 gene, which make neurons divide more and take longer to mature. Increasing numbers of Olduvai domain copies correlate with brain size and neuron number, and there has been selection for higher copy number throughout all hominid history.
Humans, Neanderthals, and Denisovans all have the same two amino acid changes from other primates in FOXP2, a gene required for song in birds and speech in humans.
One natural possibility is that “behavioral modernity”, possibly including speech, is actually older than Homo sapiens and was present in other species like Neanderthals.
Most of the above genes that were under active evolutionary selection in hominids and early humans seem to have undergone quantitative changes, like “bigger brains”, “more neurons”, or “more synapses,” rather than a qualitative change. This suggests that human intelligence might be merely a “scaled up” version of earlier hominid or primate intelligence. (Of course, it’s only weak evidence, since we can’t assume that the headline summary of a gene’s function is the only thing it does.)
Looking at differences between human and modern primate brains, we see another qualitative change — delayed peaking of synaptic density. Mammals generally keep growing new synapses through infancy/childhood, then start pruning them in adulthood. Macaques and chimps (green and blue lines, respectively) reach peak synaptic density right after birth, while humans (red line) are still going strong until about age 10.
At the macro-structural level of neural nuclei and fiber systems, human brains are organized identically to other primates’, even including the neural fiber tracts found in human language.4 Any “secret sauce” for human intelligence in the brain has to either be a difference of degree (e.g. brain size, brain region size, synaptic or neuronal density) or a difference at the micro-level, but not a difference in kind at the macro-level.
One thing that does differ between Homo sapiens and our close relatives, Neanderthals and Denisovans, is the roundness of our heads and the flatness of our faces. Anatomically modern humans have more “gracile” or “juvenile” head and face shapes, with less prominent brows and jaws. It turns out that a master regulator of genes related to cranial morphology that differ between us and other archaic hominids is BAZ1B.5 Deletions in this gene cause Williams Syndrome, a neurodevelopmental condition whose symptoms include “elfin” facial features, hypersociability, impaired spatial reasoning, but strong verbal and musical ability. In other words, Williams syndrome (total deletion of the BAZ1B gene) is an extreme version of the ways humans differ from other hominids (more neotenous face shapes and perhaps increased social or verbal abilities, or a “domestication syndrome” similar to the traits found in animals selected for tameness.)
Most of the genetic selection in hominids around brain morphology/function seems to point against the “Homo sapiens secret sauce hypothesis” — the genes are related to metrics like brain size, neuron number, synapse number, and the length of the developmental period for synapse growth, which are mostly “scale”-ish parameters which have been going up in hominids and even older primates for millions of years.
Possible exceptions could still include “language genes”, which might point to a rapid/qualitative (though still pre-Homo sapiens) change that enabled speech, and “domestication genes”, which seem to be truly Homo sapiens specific.
Gilbert, Sandra L., William B. Dobyns, and Bruce T. Lahn. "Genetic links between brain development and brain evolution." Nature Reviews Genetics 6.7 (2005): 581-590.
Evans, Patrick D., et al. "Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage." Proceedings of the National Academy of Sciences 103.48 (2006): 18178-18183.
Somel, Mehmet, Xiling Liu, and Philipp Khaitovich. "Human brain evolution: transcripts, metabolites and their regulators." Nature Reviews Neuroscience 14.2 (2013): 112-127.
Holloway, Ralph L. "The evolution of the hominid brain." Handbook of paleoanthropology 3 (2015).
Zanella, Matteo, et al. "Dosage analysis of the 7q11. 23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication." Science advances 5.12 (2019): eaaw7908.