Fig. 1. Global eukaryotic 18S–28S phylogeny from environmental samples and the distribution of habitats.

a, This tree corresponds to the best maximum-likelihood tree inferred using an alignment with 7,160 sites and the GTRCAT model in RAxML⁹⁹. The tree contains 16,821 OTUs generated from PacBio sequencing of 21 environmental samples (no reference sequences were included). Ring no. 1 around the tree indicates taxonomy of the environmental sequences, with all major eukaryotic lineages considered in this study labelled. Ring no. 2 depicts percentage similarity with the references in the PR² database as calculated using BLAST and was set with a minimum of 70% with the two black lines in the middle indicating 85% and 100% similarity levels. Ring no. 3 depicts the habitat origin of each OTU. b, Hierarchical clustering of the four habitats based on a phylogenetic distance matrix generated using the unweighted UniFrac method (n = 7, n = 5, n = 4 and n = 5 samples for soil, freshwater, marine euphotic and marine aphotic, respectively). All communities were found to differ significantly from each other using Monte Carlo simulations (Bonferroni-adjusted P < 0.001). c, Stacked density plot of branch lengths between taxa pairs from the same or different habitats (n = 14,977,604 taxa pairs with a maximum patristic distance of 1.5 substitutions/site). Note that this plot should be interpreted with caution as taxa pairs do not represent independent datapoints due to phylogenetic relatedness.