Tracing ancient life through the genomic record

Since its origins, life has been profoundly interconnected with Earth's history. The genomes that underpin the diversity of modern life forms have thus been shaped by more than three billion years of biological evolution, driven in part by planetary changes that have left lasting traces in their DNA. Together with the geological record, biological molecules offer a comprehensive framework to reveal how life and its environment have co-evolved, the so-called genomic record. Advances in sequencing and computational technologies now allow us to apply genomics to explore the historical traces in the DNA of living organisms to investigate their early evolution and the role of planetary changes in shaping it. In this review, we provide a comprehensive overview of the most widely used genomic approaches-with emphasis on phylogenomic methods-for investigating the nature and evolution of ancient life on Earth. We also examine their pitfalls, limitations, and best practices to minimize biases in interpreting the genomic record. In addition, we highlight advances in two key areas where genomics has revealed insights inaccessible through the fossil record alone: the nature of the Last Universal and Eukaryotic Common Ancestor (LUCA and LECA, respectively) and the origins and evolution of the metabolisms that power life on Earth.