Every organism alive today traces its lineage back to a single shared ancestor that lived about four billion years ago. Scientists refer to this organism as the “last universal common ancestor,” and it represents the earliest form of life that can currently be examined using established evolutionary methods.

Research on this ancient ancestor shows that many features seen in modern life were already in place at that time. Cells already had membranes, and genetic information was stored in DNA. Because these essential traits were already established, scientists seeking to understand how life first took shape must look even further back in time, to evolutionary events that occurred before this shared ancestor existed.

Studying Life Before the First Common Ancestor

In a study published in the journal Cell Genomics, researchers Aaron Goldman (Oberlin College), Greg Fournier (MIT), and Betül Kaçar (University of Wisconsin-Madison) describe a way to explore that earlier period of evolution. “While the last universal common ancestor is the most ancient organism we can study with evolutionary methods,” said Goldman, “some of the genes in its genome were much older.” The team focuses on a special group of genes called “universal paralogs,” which preserve evidence of biological changes that took place before the last universal common ancestor.

A paralog is a group of related genes that appear multiple times within a single genome. Humans provide a clear example. Our DNA contains eight different hemoglobin genes, all of which produce proteins that carry oxygen through the blood. These genes all originated from a single ancestral globin gene that existed around 800 million years ago. Over long periods of time, repeated copying errors produced extra versions of the gene, and each copy gradually developed its own specialized role.

What Makes Universal Paralogs Unique

Universal paralogs are much rarer. These gene families appear in at least two copies in the genomes of nearly all living organisms. Their widespread presence suggests that the original gene duplication occurred before the last universal common ancestor emerged. Those duplicated genes were then passed down through countless generations and remain present in life today.

Because of this deep evolutionary reach, the authors argue that universal paralogs are a critical yet often overlooked resource for studying the earliest history of life on Earth. This approach is becoming more practical as new AI-based techniques and AI-optimized hardware make it easier to analyze ancient genetic patterns in detail.

“While there are precious few universal paralogs that we know,” says Goldman, “they can give us a lot of information about what life was like before the time of the last universal common ancestor.” Fournier adds, “The history of these universal paralogs is the only information we will ever have about these earliest cellular lineages, and so we need to carefully extract as much knowledge as we can from them.”

Clues to the First Cellular Functions

In their analysis, Goldman, Fournier, and Kaçar reviewed all known universal paralogs. Every one of these genes plays a role in either building proteins or moving molecules across cell membranes. This finding suggests that protein production and membrane transport were among the first biological functions to evolve.

The researchers also emphasize the importance of reconstructing the ancient forms of these genes. In one study from Goldman’s lab at Oberlin, scientists examined a universal paralog family involved in inserting enzymes and other proteins into cell membranes. Using standard methods from evolutionary biology and computational biology, they reconstructed the protein produced by the original ancestral gene.

Their results showed that this simpler, ancient protein could still attach to cell membranes and interact with the machinery that makes proteins. It likely helped early proteins embed themselves into primitive membranes, offering insight into how the earliest cells may have operated

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Source: Scientists find genes that existed before all life on Earth | ScienceDaily