The evolutionary history of genomes
Determining the history of species and their evolutionary relationships is often dependent on molecular phylogeny. Analysing hereditary DNA sequences that encode the complex networks of modern life through alignment, provides important information on gene and species evolution. However, genes duplicate, are lost or horizontally transferred, rendering gene tree reconstruction a difficult task. The EU-funded GENESTORY (Assembling genome history from gene stories: Phylogeny aware genome scale inference of ancestral traits and ancient environments) project wished to harness recent advances in genome evolution modelling. They analysed publicly available raw experimental data, and generated novel biological information and large-scale datasets. Alongside these, they combined metabolic networks reconstruction models with models of ancient biodiversity. Scientists performed genome-scale reconstruction of ancestral gene repertoires and aligned the information with system-level models of phenotype, ancient environment and diversity. This approach allowed them to study the evolution of network architecture and understand how specific genes have evolved over time. The Archaea are one of the primary domains of cellular life and play a major role in biogeochemical cycles. Considering their contribution in the origin of eukaryotic cells, it is essential to understand their origin and evolutionary history. To overcome the challenge of time span, GENESTORY researchers employed a new approach that harnesses the information in patterns of gene family evolution to find the root of the archaeal tree and to resolve the metabolism of the earliest archaeal cells. This led to the hypothesis that the first Archaea were anaerobes who utilised carbon dioxide and hydrogen. This approach also quantified the impact of horizontal transfer on archaeal genome evolution. Genome transfer is also evident in several eukaryotic groups, including metazoans, sponges and fungi. Scientists examined thousands of gene families of fungi and cyanobacteria and found compelling evidence that gene transfer plays a significant role in the evolution of fungi comparable to prokaryotes. Taken together, the outcome of the GENESTORY study demonstrated how methods that can deal with genomic data sets can advance our understanding of genomic evolution.
Keywords
Modelling, genome evolution, GENESTORY, Archaea, fungi