Approximately seven million years ago, humans diverged from our closest animal relatives, chimpanzees, establishing a distinct branch on the evolutionary tree. Over the relatively short timespan since then, our ancestors underwent significant evolutionary changes, acquiring the distinctive traits that define us as humans. Notably, these transformations encompassed the development of a considerably larger brain compared to that of chimpanzees, as well as the adaptation of our bodies for bipedal locomotion. Such physical disparities are rooted in subtle modifications occurring at the level of our DNA. Nonetheless, discerning the precise genetic variations responsible for our evolution can be challenging due to the multitude of minor differences between humans and chimps.
Recently, a group of researchers led by Whitehead Institute Member Jonathan Weissman, in collaboration with Assistant Professor Alex Pollen from the University of California, San Francisco, delved into this intricate question using state-of-the-art tools pioneered in the Weissman lab. By leveraging these cutting-edge techniques, the team managed to narrow down the critical disparities in how humans and chimpanzees depend on specific genes. Their groundbreaking findings, published in the journal Cell on June 20, offer unparalleled insights into the evolutionary paths of humans and chimps, shedding light on the mechanisms that facilitated the development of larger brains in humans.
Studying function rather than genetic code
While humans and chimpanzees share an overwhelmingly similar genetic makeup, only a small fraction of their genes exhibit fundamental differences. The dissimilarities between the two species often lie in the timing and manner in which these shared genes are utilized. However, not all variations in gene usage contribute to significant changes in physical characteristics. To address this challenge, the researchers devised a novel approach to pinpoint the consequential disparities.
The methodology devised by the team involved using stem cells derived from samples of human and chimpanzee skin. They harnessed a tool called CRISPR interference (CRISPRi), which was developed by Weissman’s lab. CRISPRi employs a modified version of the CRISPR/Cas9 gene editing system to effectively silence individual genes. The researchers systematically deactivated each gene in human and chimp stem cells, examining whether the cells continued to proliferate at their normal rate. If the cells exhibited reduced or halted multiplication, it indicated that the deactivated gene was essential—a gene that necessitates activity, specifically producing a protein product, for cell viability. By identifying genes that were essential in one species but not the other, the researchers aimed to uncover fundamental disparities in the fundamental functioning of human and chimp cells.
Rather than focusing on dissimilarities in DNA sequences or gene expression, the approach centered on differences in cellular functionality when specific genes were disabled. This allowed the researchers to disregard differences that did not seem to impact cells significantly. When a variation in gene usage between species exerted a substantial, measurable effect at the cellular level, it likely denoted a meaningful distinction between the species on a broader physical scale. Therefore, the genes identified through this approach were deemed relevant to the distinctive traits that emerged throughout human and chimp evolution.
Weissman, also a biology professor at the Massachusetts Institute of Technology and an Investigator with the Howard Hughes Medical Institute, explained the limitations of other approaches, stating, “The problem with looking at expression changes or changes in DNA sequences is that there are many of them and their functional importance is unclear. This approach looks at changes in how genes interact to perform key biological processes, and what we see by doing that is that, even on the short timescale of human evolution, there has been fundamental rewiring of cells.”
After the completion of the CRISPRi experiments, She compiled a list of genes that appeared to be essential in one species but not the other, subsequently searching for patterns in the data. Many of the 75 genes identified through the experiments formed clusters within the same biological pathways, signifying their involvement in equivalent biological processes. This outcome aligned with the researchers’ expectations since individual minor changes in gene usage may have negligible effects, but when accumulated within the same pathway or process, they can collectively drive substantive changes in a species. The identification of genes clustering in common processes through their approach suggested their success and indicated the likely involvement of those genes in human and chimp evolution.
Pollen emphasized the significance of this approach, stating, “Isolating the genetic changes that made us human has been compared to searching for needles in a haystack because there are millions of genetic differences, and most are likely to have negligible effects on traits. However, we know that there are lots of small effect mutations that in aggregate may account for many species differences. This new approach allows us to study these aggregate effects, enabling us to weigh the impact of the haystack on cellular functions.”
Researchers think bigger brains may rely on genes regulating how quickly cells divide
Among the identified gene clusters, one particular group caught the researchers’ attention: a set of genes essential for chimpanzees but not for humans, involved in regulating the cell cycle. The cell cycle governs the timing and mechanisms by which cells determine when to divide. The regulation of the cell cycle has long been postulated to play a role in the evolution of humans’ large brains. According to the hypothesis, neural progenitors—the cells that eventually develop into neurons and other brain cells—undergo multiple divisions before maturing into fully developed brain cells. The more divisions neural progenitors undergo, the greater the number of cells the brain will contain, ultimately contributing to its larger size.
Scientists speculate that a change occurred during human evolution, allowing neural progenitors to spend less time in a non-dividing phase of the cell cycle and rapidly progress towards division. This seemingly simple alteration would lead to additional divisions, effectively doubling the final count of brain cells.
In line with this widely accepted hypothesis, the researchers discovered that several genes involved in facilitating a quicker transition through the cell cycle were deemed essential in chimpanzee neural progenitor cells but not in human cells.
When these genes were deactivated in chimpanzee neural progenitor cells, the cells lingered in a non-dividing phase. Conversely, when the same genes were deactivated in human cells, the cells continued cycling and dividing. These findings suggest that human neural progenitors may possess enhanced resilience against stressors—such as the loss of cell cycle genes—that could restrict the number of divisions the cells undergo. Consequently, humans are capable of producing a sufficient quantity of cells necessary for constructing a larger brain.
She expressed the significance of their discovery, stating, “This hypothesis has been around for a long time, and I think our study is among the first to show that there is, in fact, a species difference in how the cell cycle is regulated in neural progenitors. We had no idea going in which genes our approach would highlight, and it was really exciting when we saw that one of our strongest findings matched and expanded on this existing hypothesis.”
More subjects lead to more robust results
In contrast to many studies comparing chimpanzees and humans that rely on a limited number of individuals, this research broadened the scope by utilizing samples from six humans and six chimps. This larger sample size ensured that the observed patterns were consistent across multiple individuals within each species, mitigating the risk of mistaking natural genetic variation between individuals as representative of the entire species. Consequently, the researchers could confidently identify the true differences between the two species.
Furthermore, the researchers expanded their analysis by comparing the findings for chimps and humans to orangutans, a species that diverged earlier in the shared evolutionary history. This comparative analysis enabled them to determine the point on the evolutionary tree where changes in gene usage most likely occurred. If a gene was essential in both chimps and orangutans, it was likely vital in their common ancestor. This approach favored the likelihood that a particular difference in gene usage evolved once in a shared ancestor rather than independently multiple times. If a gene was no longer essential in humans, it indicated a shift in its role after the human-chimp split.
Using this framework, the researchers established that changes in cell cycle regulation took place during human evolution, supporting the proposal that these changes contributed to the expansion of the human brain.
Beyond enhancing our understanding of human and chimpanzee evolution, the researchers aim to highlight the efficacy of the CRISPRi approach for studying human evolution and other realms of human biology. Currently, the Weissman and Pollen labs employ this approach to delve into human diseases, seeking subtle variations in gene usage that underlie significant traits such as disease susceptibility or responses to medications.
The researchers anticipate that their approach will facilitate the exploration of numerous minor genetic differences among individuals to identify the impactful ones underlying traits related to health and disease. Much like its effectiveness in identifying the evolutionary changes that shaped us as humans, this approach holds promise for unraveling the genetic foundations of various traits and conditions.