Phylogenetic Signal in the Eukaryotic Tree of Life

Molecular sequence data have been sampled from 10% of all species known to science. Although it is not yet feasible to assemble these data into a single phylogenetic tree of life, it is possible to quantify how much phylogenetic signal is present. Analysis of 14,289 phylogenies built from 2.6 million sequences in GenBank suggests that signal is strong in vertebrates and specific groups of nonvertebrate model organisms. Across eukaryotes, however, although phylogenetic evidence is very broadly distributed, for the average species in the database it is equivalent to less than one well-supported gene tree. This analysis shows that a stronger sampling effort aimed at genomic depth, in addition to taxonomic breadth, will be required to build high-resolution phylogenetic trees at this scale.