Understanding how complex eukaryotic cells—like those that make up animals, plants, and fungi—first evolved from simpler microbes is one of the biggest open questions in biology. Although we tend to think of eukaryotes as large organisms, most of their diversity actually comes from microscopic protists that live in oceans, soils, lakes, and many other environments. Many of these organisms are still poorly understood because they are hard to grow in the lab and have no genomic data available, yet they hold crucial clues about our own deep evolutionary history.
The MacroEpik project set out to explore this hidden microbial world by generating new genomic data from rare or deeply diverging protist lineages. Using techniques such as single-cell sequencing, long- and short-read DNA sequencing, metagenomics, and state-of-the-art evolutionary analyses, the project built a large collection of new genomic resources and used them to tackle major questions about how eukaryotes originated and diversified.
A key accomplishment was greatly expanding genomic sampling for several ancient protist groups—such as mantamonads, CRuMs, ancyromonads, Rhizaria, and Preaxostyla. These new datasets made it possible to produce more reliable evolutionary trees and to better resolve some of the earliest branches in the eukaryotic lineage. They also revealed surprising biological and genetic complexity in organisms that were previously known from only a few fragments of DNA.
MacroEpik also helped clarify how eukaryotes are related to their closest known relatives: the Asgard archaea. By adding new genomes and using improved evolutionary models, the project refined the placement of eukaryotes within this archaeal group and provided a clearer picture of the traits and environments that may have characterised the microbes from which eukaryotes arose. Additional studies showed that extremely salt-loving archaea developed their adaptations independently several times, offering insight into microbial evolution in extreme environments.
Another major focus was understanding how key cellular structures evolved. One striking discovery was a mitochondrial genome that is among the most gene-rich ever found outside a small group of protists, and that still contains an ancient protein-transport system thought to date back to the earliest eukaryotes. The project also traced multiple independent paths of mitochondrial reduction—and even complete loss—in anaerobic microbes, and documented surprising conservation of complex cytoskeletal structures across certain parasitic lineages. In red algae, MacroEpik showed that mitochondrial and plastid genomes have repeatedly expanded through the accumulation of introns.
The project also explored how epigenetic mechanisms—systems that regulate gene activity without changing the DNA sequence—vary across eukaryotes. By generating high-quality genomic and transcriptomic data from many protist groups, MacroEpik showed that epigenetic systems are far more diverse than previously thought. Many protists use unique combinations of chromatin proteins, DNA-methylation pathways, and regulatory machinery, suggesting that epigenetics played an important role in early eukaryotic evolution and adaptation.
All datasets produced by MacroEpik were deposited in public repositories and are already being used by other researchers. The team shared results through publications, invited talks, international workshops, and training opportunities for students and early-career scientists.
Overall, MacroEpik has significantly expanded our understanding of microbial eukaryotes and their evolutionary history. By revealing new lineages and uncovering how fundamental cellular systems evolved, the project provides essential tools and insights for future research on the origins of eukaryotes, the evolution of genomes, and the remarkable diversity of life on Earth.
