The evolutionary relationship between bacteria, archaea and eukaryotes is a hotly debated topic. Much of the ongoing debate is based on assertions that evolutionary relationships and the topology of the tree of life depend on the quality of data generated in genomics studies and the choice of marker genes and taxa that are included in analyses. Williams et al. evaluated the data and analyses that have led to conflicting views in the field and used phylogenomics and the latest supermatrix, supertree and coalescent methods on an expanded dataset to explore the evolutionary relationships between archaea and eukaryotes. The authors interrogated >3,000 gene families in archaea and eukaryotes and confirmed previous studies that eukaryotes originated from within the archaea. They argue that their analyses provide robust support for a two-domain tree of life and for a close relationship between eukaryotes and Asgard archaea, and they suggest that the phylum Heimdallarchaeota is the current best candidate for the closest relatives of eukaryotes. In another study, Zhu et al. investigated the evolutionary proximity between the different domains within the tree of life. The authors constructed a reference phylogeny of 10,575 bacterial and archaeal genomes based on 381 marker genes using a statistical approach that maximized the covered biodiversity. The authors argue that their tree provides a high resolution view of the basal relationships between microbial clades. Remarkably, the tree indicated a closer evolutionary proximity between bacteria and archaea than expected, owing to previous analyses being limited to a few core genes. The authors posit that this observation is supported using multiple tree-building methods and after considering several variables (for example, taxon and site sampling, amino acid substitution heterogeneity and saturation, and non-vertical evolution). Although the debate continues, these studies highlight that new data and tools provide further opportunities to understand the tree of life.