Rooting the tree of life: the phylogenetic jury is still out

Abstract

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.

Keywords: Great Chain of Beings prejudice; model of evolution; simplification; systematic error; tree reconstruction artefact.

Figure 1.

Words shape our minds. In this hypothetical ToL, Archaea and Bacteria form a monophyletic group (Apokaryota), derived from a nucleated ancestor through secondary simplification and concomitant loss of the nucleus. Present-day Eukaryota are named Mitochondriophora after their defining feature, the mitochondrion. Consequently, the last universal common ancestor (LUCA) would have belonged to Karyota (nucleated cells), whereas Prokaryota have probably existed before the advent of the nucleus. Even if apparently unorthodox, such a scenario is currently ruled out only by the power of Aristotle's prejudice and not by hard evidence. On the contrary, the shallow parts of the ToL are replete with secondary simplified lineages (e.g. Microsporidia, apicomplexans, acoelomorph worms, tunicates), which makes a eukaryotic root of the ToL rather more plausible than not. It is also important to note that the vast majority of ancient lineages probably went extinct [79], meaning that our sampling of biodiversity is highly biased. Figure drawn by Rosa Gago.

Figure 2.

Our best substitution models cannot yet address difficult phylogenetic issues, even at shallow depth. We assembled supermatrices by concatenating the translated mitochondrial genomes (12 genes) of nine slow-evolving bivalves (Unionoida), nine fast-evolving bivalves (Pteriomorphia), nine gastropods and nine outgroups. Seven different outgroups were considered, thus resulting in seven different supermatrices, each one containing 36 species and 2016 unambiguously aligned amino acid positions. We then analysed all supermatrices using RAXML [85] and PHYLOBAYES [59] under four different substitution models: LG + Γ, GTR + Γ, CAT + Γ and CATGTR + Γ. Bootstrap proportions (LG and GTR) and posterior probabilities (PPs; CAT and CATGTR) for the monophyly of bivalves (upper tree) and for an alternative (LBA) topology, in which fast-evolving bivalves are attracted by the outgroup (lower tree), were computed from 100 bootstrap pseudo-replicates or from two replicate chains per outgroup/model combination, each one run for 10 000 cycles. The burnin was set to 1000 cycles. In the associated table, outgroups are sorted by descending phylogenetic relatedness to molluscs, not evolutionary distance, to illustrate the fact that the latter parameter is the one that really drives the results. To see this, compare PPs for Hymenoptera versus Maxillopoda, two arthropod clades.

Figure 3.

The amount of model violations in alignments of anciently duplicated genes makes rooting the ToL very difficult. This elongation factor tree was inferred using PHYLOBAYES under the CATGTR + Γ model from an alignment of 211 sequences and 198 unambiguously aligned amino acid positions. Two replicate chains were run for 100 000 cycles and the burnin was set to 50 000 cycles. For clarity, subtrees were collapsed and named after their taxonomic contents. The scale bar corresponds to one substitution per site and the long internal branches discussed in the text are annotated with their length. Bullets indicate branches that are supported by PPs ≥ 0.98. In spite of a general lack of resolution, the EF-Tu and EF-G subtrees hint at two different roots for the ToL and suggest that Archaea are indeed paraphyletic, as repeatedly advocated in the literature.