Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Abstract

An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level "supergroups," many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup "Chromalveolata" is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.

FIGURE 1.

Most likely eukaryotic tree of life reconstructed using all 451 taxa and all 16 genes (SSU-rDNA plus 15 protein genes). Major nodes in this topology are robust to analyses of subsets of taxa and genes, which include varying levels of missing data (Table 1). Clades in bold are monophyletic in analyses with 2 or more members except in all:15 in which taxa represented by a single gene were sometimes misplaced. Numbers in boxes represent support at key nodes in analyses with increasing amounts of missing data (10:16, 6:16, 4:16, and all:16 analyses; see Table 1 for more details). Given uncertainties around the root of the eukaryotic tree of life (see text), we have chosen to draw the tree rooted with the well-supported clade Opisthokonta. Dashed line indicates alternate branching pattern seen for Amoebozoa in other analyses. Long branches, indicated by //, have been reduced by half. The 6 lineages labeled by * represent taxa that are misplaced, probably due to LBA, listed from top to bottom with expected clade in parentheses. These are Protoopalina japonica (Stramenopiles), Aggregata octopiana (Apicomplexa), Mikrocytos mackini (Haplosporidia), Centropyxis laevigata (Tubulinea), Marteilioides chungmuensis (unplaced), and Cochliopodium spiniferum (Amoebozoa).

FIGURE 2.

Most likely eukaryotic tree of life reconstructed with 10:16, which includes 88 taxa (each with 10 or more of the genes analyzed in this study) and 16 genes (SSU-rDNA plus 15 protein genes). Thickened lines receive >95% bootstrap support. Other notes as in Methods section and Figure 1.

FIGURE 3.

Maximum likelihood tree of Rhizaria reconstructed with 103 Rhizaria taxa and 16 genes. The SSU-rDNA partition was analyzed with GTR+gamma and proteins with rtREV. Thickened lines receive >80% bootstrap support in all analyses. Node support in boxes from Rhizaria:4-gene, Rhizaria:16-gene, all:16 analyses. Taxa with new data are in bold. Dashed lines indicate nonmonophyly.

FIGURE 4.

Maximum-likelihood tree of Excavata with 75 taxa and 16 genes. The SSU-rDNA partition was analyzed with GTR+gamma and proteins with rtREV. See Figure 3 for other notes.

FIGURE 5.

Summary of major findings—the evolutionary relationships among major lineages of eukaryotes. Clades have been collapsed into those that we view to be strongly supported. The many polytomies represent uncertainties that remain.