We may share a connection with our primate cousins thousands of years ago, but a new study shows how humans evolved in ways we never thought possible.
Researchers from the Biomedical Sciences Research Center “Alexander Fleming” (BSRC Flemming) in Greece and Trinity College Dublin, in Ireland, identified 155 genes in our genome that emerged from small, non-coding sections of DNA. Many seem to play a critical role in our biology, showing how completely new species can evolve so quickly that they become essential.
New genes typically arise through known mechanisms such as duplication events, in which our random genetic machinery produces copies of pre-existing genes that can match new functions over time.
But the 155 microgenes in this study appear to have been embedded from scratch, in stretches of DNA that did not previously contain the instructions our bodies use to build molecules.
Since these new genes that encode proteins are thought to be incredibly small, these DNA sequences are difficult to find and difficult to study, and therefore are often overlooked in research.
“This project started in 2017 because I was interested in the development of novel evolutionary genes and how these genes lead to the origin,” says evolutionary geneticist Nikolaos Vakirlis, from BSRC Flemming in Greece.
“It was put on ice for a few years, until another study was published that had very interesting data, allowing us to start this work.”
Another study, published in 2020 by researchers at the University of California San Francisco, cataloged the accumulation of microproteins produced by non-coding regions once described as “junk DNA.”
The team behind this new study then created a genetic ancestral tree to compare those smallest sequences in our genomes against those in 99 other vertebrate species, tracking the evolution of genes over time.
Some of the new “microgenes” identified in this new study can be traced back to the earliest days of mammals, while others are more recent additions. Two genes that stem from a study from which researchers split the human chimpanzee have been discovered.
“To identify and examine the causes in the human race of small proteins that have previously evolved noncoding and acquired function either immediately or shortly after,” writes the team in a public paper.
“This is doubly important: to understand the environment, and the still largely mysterious phenomenon of the rise of a new species, but also to our appreciation of the full functional potential of the human race.”
Microproteins are now known to have a diverse range of functions from helping to regulate the expression of other genes to binding forces to large proteins including our cell membranes. However, while some microproteins perform vital biological functions, some are completely useless.
“When you start with these small sizes of DNA, you’re really on the verge of being interpretable from a genome sequence, and you’re in that zone where it’s hard to know if it’s biologically significant,” explains Trinity College. Dublin geneticist Aoife McLysaght.
The single gene responsible for building the tissue of our heart arose when the common ancestor of humans and chimpanzees branched off from their ancestors. However, if this microgene emerged in the last few million years, it is clearly evident that these evolved parts of our DNA could quickly become essential to the body.
The researchers then explored the functions of the sequences by deleting the genes one by one in lab-grown cells. Forty-four cell cultures came to show a lack of growth, confirming that those now-missing sections of DNA play a critical role in keeping us functioning.
In other comparative analyses, the researchers also identified three new gene variants known to be associated with the disease. The presence of these cases of mutations at a single base position in DNA may suggest some link between dystrophy, retinitis pigmentosa and Alazami syndrome, but further research will be needed to clarify these relationships.
In the light of modern technology and medicine, assessing the scale of biological change humans have experienced as a species at hand can challenge natural selection. However, our fitness has been shaped somewhat by diet and disease pressure over the millennia, and will undoubtedly continue to adapt even within the technologically advanced world.
How the spontaneous creation of new genes occurs within a non-coding region is not yet clear, but with the new ability to study these genes we may be closer to finding out.
“If we’re right in what we’re thinking here, a lot of it has to do with something more functional hidden in the human genome.” he says McLysaght.
The research was published in Cell Reports.
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