When we imagine the course of human evolution — the roughly three-million-year period from the moment when Lucy began to walk upright through grasses of the Awash River Valley to modern times, it’s hard to determine the moment at which we became human, or at least as human as we might recognize ourselves. After all, there’s only a one percent difference in protein-coding genomes between ourselves and our closest living ancestor, the chimpanzees — even less distinction between our two species than there is between mice and rats. You might be quick to think that the moment we became human was the moment when we grew larger brains that allowed us to explore beyond the trees — endowing us with the ability to create and speak languages that would set us apart from our fellow primates — but how did it happen?
Pursuing an answer to this question, researchers at the SIB Swiss Institute of Bioinformatics collaborated with a team from the University of Lausanne to look for human-specific genetic changes in the brain. Their results, published by Science Advances, offer some new insights into human evolution and developmental biology as well as neuroscience.
Think Expression — Not Sequences
That one percent statistic seems hard for us to process as fact, but it’s not so much about the DNA sequence, or genetic ingredients, as it is the “regulation” of genes that set us apart from our ape relatives — in other words, when, where, and how strongly the genes are expressed in a living organism that play a key role. Although the sequences have been known for some time, specifically, determining and mapping out the regulatory agents that adjust the genes like light switches, has been a difficult task that continues to elude researchers.
Dr. Marc Robinson-Rechavi who served as the group leader at SIB and co-authored the study, suggests that the key is to determine what parts of the genome are influenced by positive selection, the evolutionary mechanism through which favorable traits occur in a population. A classic example proposed by Darwin was the shape of beaks from finches on the Galapagos Island changing in each generation due to the nature of the food supply — a continuity of wet seasons forced the finches to eat larger seeds during the dry season and generations of birds were born with larger beaks equipped for taking on the larger seeds. Surprisingly, with the brain — a great deal of its regulatory elements — those in charge of maintaining the body systems — have been positively selected throughout our history — more so compared to the evolution of critical organs like the human heart or stomach.
Rechavi and his research partner, Dr. Jialin Liu, a researcher who served as the study’s lead author came to their conclusions using a combination of machine learning models and experimental data — creating a model that showed how the proteins used to signal genetic regulation binded in various tissues and then looked at evolutionary differences between humans, chimpanzees, and another fairly close cousin on the family tree: gorillas.
“We now know which are the positively selected regions controlling gene expression in the human brain. And the more we learn about the genes they are controlling, the more complete our understanding of cognition and evolution, and the more scope there will be to act on that understanding,” says Robinson-Rechavi.
Mutations With A Purpose
We tend to think of the word “mutation” in a negative sense — but the reality is that the overwhelming majority of mutations simply happen without us noticing — they take place over a span of time and aren’t necessarily good or bad. They build up at a predictable rate in the amount of time two living species diverge from their common ancestor.
An acceleration, in the rate of mutation however, for a certain part of the genome, can bring with it a positive selection for a mutation that gives one population of species a survival advantage, allowing them to reproduce and pass their mutation on to another generation. The regulatory elements of genes are typically a few nucleotides long, which can make estimating the rate of acceleration exceptionally difficult.
A Matter Of Recognition
The nature of gene expression in the brain and how it impacts social behaviors has been recently studied in other species as well — honey bees were examined in a study reported in the journal eLife this month, where it was shown that just a single error in transcription as mutations occur can affect the way dozens of other genes are expressed — either activating or deactivating an array of them all at once.
“If the queen in a colony dies and the workers fail to rear a replacement queen, some worker bees activate their ovaries and begin to lay eggs,” said Dr. Beryl Jones, a researcher at the University of Illinois Urbana-Champaign who conducted the study alongside her colleague, the entomology professor Dr. Gene Robinson and Dr. Sriram Chandrasekaran, who is a professor of biomedical engineering at the University of Michigan.
“This is an example of ‘behavioral plasticity,’ the ability to change behavior in response to the environment,” Jones said. “We know that behavioral plasticity is influenced by the activity of genes in the brain, but we do not know how genes in the brain work together to regulate these behavioral differences.”
Jones’ study looked at bee colonies run without a queen — and studied the insects’ collective egg-laying and foraging behaviors since they are generally performed for the benefit of the colony, but if done selfishly could become detrimental to that colony. A hive with a queen is maintained as the queen lays eggs and her workers provide food to produce honey — a distinction that comes about because the queens are fed and nurtured apart from the workers as they mature. In a queenless colony, Jones and her colleagues could analyze the worker bees objectively, using bar codes and computer vision. Computer algorithms by the researchers tracked thousands of individual bees and revealed patterns of genetic activity in their brains as it happened from day to day.
A noticeable difference that caught Jones’ eye was the recurring differences between the bees who began foraging in the absence of the queen, compared to their counterparts who began to focus on the task of egg-laying within the hive. The patterns were in fact so consistent that the researchers were able to use the algorithms to accurately predict if one of the tagged bees was a worker or an egg-layer. They also recognized a third group of bees that dabbled in both tasks and also had their own unique gene-expression.
“We identified 15 transcription factors that best explained the behavioral differences in the bees,” says Jones. The findings suggest that changes in the activity of a small number of influential transcription factors can lead to strikingly different behavior.”
“Some of the transcription factors we identified as important for honey bee behavior were previously identified as influencing the evolution of social behavior in other species,” Robinson concluded, indicating that his findings could show how the concept of society with its hierarchies came about in other species — and we may not be far away from knowing the specifics of how shaping each others’ brains became a group effort.
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