Understanding how life emerged and evolved on Earth has long been a question that has puzzled humans, and modern scientists have made great strides in finding some answers. Now, our latest research hopes to provide new insights into the origins of life on Earth.

About 375 million years ago, our fish-like ancestors breathed with gills. More than 600 million years ago, the common ancestor of all animals appeared: the microscopic urmanoids. But billions of years before all this happened, all living things must have had a common ancestor, the last universal common ancestor (Luke).

For decades, scientists have tried to identify Luke with different ideas of what he was like. Another area of ​​debate is Luke’s age. The oldest fossils we have are about 3.4 billion years old. Some studies push Luke’s age to 4.5 billion years ago, around the time the Earth was born. Others believe this is impossible because it would take time to create the genetic code and DNA copying machinery.

Luke was not the first life form; he was the organism from which all living organisms descended. However, scientists believe that living organisms may have existed long before Luke. Understanding what Luke was like and when he lived is important in helping us understand how life on Earth evolved.

In our latest study, published in the journal Nature Ecology & Evolution, we used a combination of scientific methods to reconstruct Luca’s genome and show how the genes we found allowed Luca to survive. This project was the culmination of several years of work and an international team of co-authors.

Luke’s character

To reconstruct Luke’s genome, we needed a sample of the genomes (all the genetic information in an organism) of different groups of bacteria and archaea (single-celled organisms other than bacteria) so we could be sure we were sampling modern life. We excluded eukaryotes (plants, animals, and fungi) because scientists believe they arose much later than the archaea and bacteria merged. We had a set of 700 genomes (350 archaea and 350 bacteria) selected from a 2022 study that some of us participated in.

To understand their purpose in modern organisms, we grouped these genes into different families. To do this, we used a database called KEGG, which helps scientists understand the metabolic pathways of organisms (how they support life). We then used these families to create phylogenetic trees (or phylogenies, like a family tree) to understand the relationships between different species and see how they have evolved over time.

“We also created a separate set of 57 genes that are shared by all 700 organisms in our study and are likely present in almost all living organisms. Such genes have not changed much over the past few billion years.”

We used these 57 genes to create a species tree showing the Darwinian relatedness of different organisms. We could then fit our KEGG gene trees onto the species tree and model the rates of gene duplication, transfer, and gene loss. This also allowed us to calculate the probability that Luca had different gene families.

Reconstructing Luke’s genome allowed us to assess his metabolism as if he were alive today. We envision Luca as a highly complex organism with a small genome, like modern bacteria and archaea. However, we found no evidence of photosynthesis (which some bacteria use) or nitrogen fixation, a chemical process that some modern bacteria and archaea use to survive.

How old was Luke?

We also tried a new method to estimate Luke’s age, using genes that we think were copied before Luke and information from the fossil record. Normally, to infer evolutionary timescales, we obtain a phylogeny of the species we are interested in, with homologous genes leading to a common ancestor.

We then find a group of species that are distantly related to the species of interest (an outgroup) to form the root of the phylogeny.

The “branches” that connect species in a phylogeny contain information about the rate at which genetic changes (mutations) occurred and when species diverged. We can use fossil or geological evidence to inform the molecular clock about the potential minimum age at which speciation events occurred.

But we have two problems with Luke. There is no outlier group for the origin of life, and there is little fossil evidence or much geological evidence for the early Earth that we can use to calibrate the molecular clock.

To overcome these limitations, we used parallel genes, which scientists had already tracked in Luca. Paralogous genes are linked together through gene duplication. This can happen when a species splits into two, each with its own copy of the duplicated gene.

By our estimate, Luke roamed the Earth about 4.2 billion years ago. If our estimate of time is close to accurate, things like the genetic code, the transmission of proteins, and life itself must have evolved rapidly soon after the Earth formed.

It won’t be the first time we’ve tried to reconstruct Luka, nor will it be the last. Every year, more organisms are discovered and sequenced, computers get more powerful, and evolutionary models are constantly being improved. As more data and more powerful methods become available, our understanding of Luka may change.

For example, we must take into account that many other organisms were probably alive in Luke’s time that are not represented by any organisms today. If any of Luke’s early descendants did not survive into modern times and their genes were not preserved, we will never be able to trace these gene families back to Luke, meaning that our reconstruction of Luke may be incomplete.

Despite all the technical limitations, our work opens up a new way of understanding Luke, but there is still much work to be done to better understand how life has evolved since the formation of our planet Earth.