A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life

Assembling the Tree Of Life (TOL) faces the pressing challenge of incorporating a rapidly growing number of sequenced genomes. This problem is exacerbated by the fact that different sets of genes are informative at different evolutionary scales. Here, we present a novel phylogenetic approach (Nested Phylogenetic Reconstruction) in which each tree node is optimized based on the genes shared at that taxonomic level. We apply such procedure to reconstruct a 216-species eukaryotic TOL and compare it with a standard concatenation-based approach. The resulting topology is highly accurate, and reveals general trends such as the relationship between branch lengths and genome content in eukaryotes. The approach lends itself to continuous update, and we show this by adding 29 and 173 newly-sequenced species in two consecutive steps. The proposed approach, which has been implemented in a fully-automated pipeline, enables the reconstruction and continuous update of highly-resolved phylogenies of sequenced